From d4dd22223ffc90b4028d605c08a797e7ecdf006a Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Tue, 18 Jun 2019 08:14:49 -0700
Subject: [PATCH 001/853] Added trigger to dataset table to update
 history.update_time

---
 .../versions/0155_add_content_update_time.py  | 95 +++++++++++++++++++
 1 file changed, 95 insertions(+)
 create mode 100644 lib/galaxy/model/migrate/versions/0155_add_content_update_time.py

diff --git a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
new file mode 100644
index 000000000000..6bc0a4df21df
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
@@ -0,0 +1,95 @@
+"""
+Adds trigger to dataset table to update history.update_time when 
+contents are changed.
+"""
+
+import logging
+from sqlalchemy import DDL, MetaData
+
+log = logging.getLogger(__name__)
+metadata = MetaData()
+
+
+def upgrade(migrate_engine):
+    print(__doc__)
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    drop_update_trigger(migrate_engine)
+    install_update_trigger(migrate_engine)
+
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    drop_update_trigger(migrate_engine)
+
+
+def not_pg(self, target, bind, state, **kw):
+    return bind.engine.name != 'postgresql'
+
+
+def install_update_trigger(migrate_engine):
+    """Installs trigger on database table to update history table
+    when contents have changed. Installs a function and a trigger
+    for postgres, other sql variants only require the trigger def
+    """
+
+    pg_create_function = DDL("""
+        CREATE FUNCTION update_history_content_update_time()
+            RETURNS trigger
+            LANGUAGE 'plpgsql'
+        AS $BODY$
+        begin 
+            update history h
+            set update_time = current_timestamp
+            from history_dataset_association hda
+            where h.id = hda.history_id
+            and hda.dataset_id = NEW.id;
+            return NEW;
+        end;
+        $BODY$;
+    """).execute_if(dialect='postgresql')
+
+    pg_create_trigger = DDL("""
+        CREATE TRIGGER update_history_update_time
+            BEFORE INSERT OR DELETE OR UPDATE 
+            ON dataset
+            FOR EACH ROW
+            EXECUTE PROCEDURE update_history_content_update_time();
+    """).execute_if(dialect='postgresql')
+
+    trigger = DDL("""
+        CREATE TRIGGER dataset_history_update_time 
+            BEFORE INSERT OR DELETE OR UPDATE 
+            ON dataset
+            FOR EACH ROW
+            BEGIN
+                update history h
+                set update_time = now()
+                from history_dataset_association hda
+                where h.id = hda.history_id
+                and hda.dataset_id = NEW.id;
+            END;
+    """).execute_if(callable_=not_pg)
+
+    pg_create_function.execute(bind=migrate_engine)
+    pg_create_trigger.execute(bind=migrate_engine)
+    trigger.execute(bind=migrate_engine)
+
+
+def drop_update_trigger(migrate_engine):
+    """Drops trigger on dataset table. Also removes associated function
+    for postgres sql variants.
+    """
+
+    pg_drop_trigger = DDL("""
+        DROP TRIGGER IF EXISTS update_history_update_time ON dataset;
+        DROP FUNCTION IF EXISTS update_history_content_update_time();
+    """).execute_if(dialect='postgresql')
+
+    drop_trigger = DDL("""
+        DROP TRIGGER IF EXISTS dataset_history_update_time;
+    """).execute_if(callable_=not_pg)
+
+    pg_drop_trigger.execute(bind=migrate_engine)
+    drop_trigger.execute(bind=migrate_engine)

From 6b925d7a7a230179a516545da50a4a74ba696f4c Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Tue, 18 Jun 2019 16:46:57 -0700
Subject: [PATCH 002/853] Updated sql for finicky sqlite

---
 .../versions/0155_add_content_update_time.py  | 74 +++++++++++--------
 1 file changed, 43 insertions(+), 31 deletions(-)

diff --git a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
index 6bc0a4df21df..2b95c46a94b8 100644
--- a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
@@ -1,9 +1,12 @@
 """
-Adds trigger to dataset table to update history.update_time when 
+Adds trigger to dataset table to update history.update_time when
 contents are changed.
 """
+from __future__ import print_function
 
+import datetime
 import logging
+
 from sqlalchemy import DDL, MetaData
 
 log = logging.getLogger(__name__)
@@ -34,12 +37,12 @@ def install_update_trigger(migrate_engine):
     for postgres, other sql variants only require the trigger def
     """
 
-    pg_create_function = DDL("""
+    pg_create_trigger = DDL("""
         CREATE FUNCTION update_history_content_update_time()
             RETURNS trigger
             LANGUAGE 'plpgsql'
         AS $BODY$
-        begin 
+        begin
             update history h
             set update_time = current_timestamp
             from history_dataset_association hda
@@ -48,48 +51,57 @@ def install_update_trigger(migrate_engine):
             return NEW;
         end;
         $BODY$;
-    """).execute_if(dialect='postgresql')
-
-    pg_create_trigger = DDL("""
         CREATE TRIGGER update_history_update_time
-            BEFORE INSERT OR DELETE OR UPDATE 
+            BEFORE INSERT OR DELETE OR UPDATE
             ON dataset
             FOR EACH ROW
             EXECUTE PROCEDURE update_history_content_update_time();
     """).execute_if(dialect='postgresql')
 
-    trigger = DDL("""
-        CREATE TRIGGER dataset_history_update_time 
-            BEFORE INSERT OR DELETE OR UPDATE 
-            ON dataset
-            FOR EACH ROW
-            BEGIN
-                update history h
-                set update_time = now()
-                from history_dataset_association hda
-                where h.id = hda.history_id
-                and hda.dataset_id = NEW.id;
-            END;
-    """).execute_if(callable_=not_pg)
-
-    pg_create_function.execute(bind=migrate_engine)
     pg_create_trigger.execute(bind=migrate_engine)
-    trigger.execute(bind=migrate_engine)
+
+    # Looks like sqlite doesn't like multiple actions in some
+    # variants, so we build 3 triggers
+    build_trigger('INSERT').execute(bind=migrate_engine)
+    build_trigger('UPDATE').execute(bind=migrate_engine)
+    build_trigger('DELETE').execute(bind=migrate_engine)
 
 
 def drop_update_trigger(migrate_engine):
-    """Drops trigger on dataset table. Also removes associated function
-    for postgres sql variants.
-    """
+    """Drops trigger on dataset table."""
 
     pg_drop_trigger = DDL("""
         DROP TRIGGER IF EXISTS update_history_update_time ON dataset;
         DROP FUNCTION IF EXISTS update_history_content_update_time();
     """).execute_if(dialect='postgresql')
 
-    drop_trigger = DDL("""
-        DROP TRIGGER IF EXISTS dataset_history_update_time;
-    """).execute_if(callable_=not_pg)
-
     pg_drop_trigger.execute(bind=migrate_engine)
-    drop_trigger.execute(bind=migrate_engine)
+    build_drop_trigger("INSERT").execute(bind=migrate_engine)
+    build_drop_trigger("UPDATE").execute(bind=migrate_engine)
+    build_drop_trigger("DELETE").execute(bind=migrate_engine)
+
+
+def build_trigger(op):
+    create_trigger_template = """
+        CREATE TRIGGER BEFORE_{operation}_DATASET
+            BEFORE {operation} ON dataset
+            BEGIN
+                update history
+                set update_time = current_timestamp
+                where id in (
+                    select hda.history_id
+                    from history_dataset_association as hda
+                    where hda.dataset_id = {rowset}.id
+                );
+            END;
+    """
+    rs = 'OLD' if op == 'DELETE' else 'NEW'
+    sql = create_trigger_template.format(operation=op,rowset=rs)
+    return DDL(sql).execute_if(callable_=not_pg)
+
+
+def build_drop_trigger(op):
+    trigger_template = """DROP TRIGGER IF EXISTS BEFORE_{operation}_DATASET;"""
+    sql = trigger_template.format(operation=op)
+    return DDL(sql).execute_if(callable_=not_pg)
+

From 7a52c274e40e7128e9fb6f503e6c162c0c98f600 Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Tue, 18 Jun 2019 16:52:53 -0700
Subject: [PATCH 003/853] Slave to the linting overlords

---
 .../model/migrate/versions/0155_add_content_update_time.py    | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
index 2b95c46a94b8..97a277d7a2f6 100644
--- a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
@@ -4,7 +4,6 @@
 """
 from __future__ import print_function
 
-import datetime
 import logging
 
 from sqlalchemy import DDL, MetaData
@@ -96,7 +95,7 @@ def build_trigger(op):
             END;
     """
     rs = 'OLD' if op == 'DELETE' else 'NEW'
-    sql = create_trigger_template.format(operation=op,rowset=rs)
+    sql = create_trigger_template.format(operation=op, rowset=rs)
     return DDL(sql).execute_if(callable_=not_pg)
 
 
@@ -104,4 +103,3 @@ def build_drop_trigger(op):
     trigger_template = """DROP TRIGGER IF EXISTS BEFORE_{operation}_DATASET;"""
     sql = trigger_template.format(operation=op)
     return DDL(sql).execute_if(callable_=not_pg)
-

From c80ac74de7262558f07226fd38b0428a0f0eb004 Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Tue, 18 Jun 2019 21:29:35 -0700
Subject: [PATCH 004/853] added linting and formatting suggestions to trigger
 generation sql

---
 .../versions/0155_add_content_update_time.py  | 101 +++++++++---------
 1 file changed, 49 insertions(+), 52 deletions(-)

diff --git a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
index 97a277d7a2f6..1f822152b27b 100644
--- a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
@@ -26,80 +26,77 @@ def downgrade(migrate_engine):
     drop_update_trigger(migrate_engine)
 
 
-def not_pg(self, target, bind, state, **kw):
-    return bind.engine.name != 'postgresql'
-
-
 def install_update_trigger(migrate_engine):
     """Installs trigger on database table to update history table
     when contents have changed. Installs a function and a trigger
     for postgres, other sql variants only require the trigger def
     """
 
-    pg_create_trigger = DDL("""
-        CREATE FUNCTION update_history_content_update_time()
-            RETURNS trigger
-            LANGUAGE 'plpgsql'
-        AS $BODY$
-        begin
-            update history h
-            set update_time = current_timestamp
-            from history_dataset_association hda
-            where h.id = hda.history_id
-            and hda.dataset_id = NEW.id;
-            return NEW;
-        end;
-        $BODY$;
-        CREATE TRIGGER update_history_update_time
-            BEFORE INSERT OR DELETE OR UPDATE
-            ON dataset
-            FOR EACH ROW
-            EXECUTE PROCEDURE update_history_content_update_time();
-    """).execute_if(dialect='postgresql')
-
-    pg_create_trigger.execute(bind=migrate_engine)
-
-    # Looks like sqlite doesn't like multiple actions in some
-    # variants, so we build 3 triggers
-    build_trigger('INSERT').execute(bind=migrate_engine)
-    build_trigger('UPDATE').execute(bind=migrate_engine)
-    build_trigger('DELETE').execute(bind=migrate_engine)
+    if migrate_engine.name in ['postgres', 'postgresql']:
+        pg_create_trigger = DDL("""
+            CREATE FUNCTION update_history_content_update_time()
+                RETURNS trigger
+                LANGUAGE 'plpgsql'
+            AS $BODY$
+            BEGIN
+                UPDATE history h
+                SET update_time = current_timestamp
+                FROM history_dataset_association hda
+                WHERE h.id = hda.history_id
+                AND hda.dataset_id = NEW.id;
+                RETURN NEW;
+            END;
+            $BODY$;
+            CREATE TRIGGER update_history_update_time
+                AFTER INSERT OR DELETE OR UPDATE
+                ON dataset
+                FOR EACH ROW
+                EXECUTE PROCEDURE update_history_content_update_time();
+        """)
+        pg_create_trigger.execute(bind=migrate_engine)
+    else:
+        # Looks like sqlite doesn't like multiple actions in some
+        # variants, so we build 3 triggers
+        build_trigger('INSERT').execute(bind=migrate_engine)
+        build_trigger('UPDATE').execute(bind=migrate_engine)
+        build_trigger('DELETE').execute(bind=migrate_engine)
 
 
 def drop_update_trigger(migrate_engine):
     """Drops trigger on dataset table."""
 
-    pg_drop_trigger = DDL("""
-        DROP TRIGGER IF EXISTS update_history_update_time ON dataset;
-        DROP FUNCTION IF EXISTS update_history_content_update_time();
-    """).execute_if(dialect='postgresql')
-
-    pg_drop_trigger.execute(bind=migrate_engine)
-    build_drop_trigger("INSERT").execute(bind=migrate_engine)
-    build_drop_trigger("UPDATE").execute(bind=migrate_engine)
-    build_drop_trigger("DELETE").execute(bind=migrate_engine)
+    if migrate_engine.name in ['postgres', 'postgresql']:
+        pg_drop_trigger = DDL("""
+            DROP TRIGGER IF EXISTS update_history_update_time ON dataset;
+            DROP FUNCTION IF EXISTS update_history_content_update_time;
+        """)
+        pg_drop_trigger.execute(bind=migrate_engine)
+    else:
+        build_drop_trigger('INSERT').execute(bind=migrate_engine)
+        build_drop_trigger('UPDATE').execute(bind=migrate_engine)
+        build_drop_trigger('DELETE').execute(bind=migrate_engine)
 
 
 def build_trigger(op):
     create_trigger_template = """
-        CREATE TRIGGER BEFORE_{operation}_DATASET
-            BEFORE {operation} ON dataset
+        CREATE TRIGGER AFTER_{operation}_DATASET
+            AFTER {operation} ON dataset
             BEGIN
-                update history
-                set update_time = current_timestamp
-                where id in (
-                    select hda.history_id
-                    from history_dataset_association as hda
-                    where hda.dataset_id = {rowset}.id
+                UPDATE history
+                SET update_time = current_timestamp
+                WHERE id IN (
+                    SELECT hda.history_id
+                    FROM history_dataset_association AS hda
+                    WHERE hda.dataset_id = {rowset}.id
                 );
             END;
     """
     rs = 'OLD' if op == 'DELETE' else 'NEW'
     sql = create_trigger_template.format(operation=op, rowset=rs)
-    return DDL(sql).execute_if(callable_=not_pg)
+    return DDL(sql)
 
 
 def build_drop_trigger(op):
-    trigger_template = """DROP TRIGGER IF EXISTS BEFORE_{operation}_DATASET;"""
+    trigger_template = 'DROP TRIGGER IF EXISTS AFTER_{operation}_DATASET;'
     sql = trigger_template.format(operation=op)
-    return DDL(sql).execute_if(callable_=not_pg)
+    return DDL(sql)

From cbcb71fb2f6105522cfd5a9fd15a4d04a5b6d55d Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Tue, 18 Jun 2019 22:19:15 -0700
Subject: [PATCH 005/853] fix sql syntax error in drop statement

---
 .../model/migrate/versions/0155_add_content_update_time.py      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
index 1f822152b27b..3f7b16d025b3 100644
--- a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
@@ -68,7 +68,7 @@ def drop_update_trigger(migrate_engine):
     if migrate_engine.name in ['postgres', 'postgresql']:
         pg_drop_trigger = DDL("""
             DROP TRIGGER IF EXISTS update_history_update_time ON dataset;
-            DROP FUNCTION IF EXISTS update_history_content_update_time;
+            DROP FUNCTION IF EXISTS update_history_content_update_time();
         """)
         pg_drop_trigger.execute(bind=migrate_engine)
     else:

From 7eb3a833ca478901c4a24a4a1c406221901e4255 Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Wed, 19 Jun 2019 08:53:31 -0700
Subject: [PATCH 006/853] Update
 lib/galaxy/model/migrate/versions/0155_add_content_update_time.py

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 .../model/migrate/versions/0155_add_content_update_time.py    | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
index 3f7b16d025b3..f3c876468d42 100644
--- a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
@@ -80,7 +80,9 @@ def drop_update_trigger(migrate_engine):
 def build_trigger(op):
     create_trigger_template = """
         CREATE TRIGGER AFTER_{operation}_DATASET
-            AFTER {operation} ON dataset
+            AFTER {operation}
+            ON dataset
+            FOR EACH ROW
             BEGIN
                 UPDATE history
                 SET update_time = current_timestamp

From 2ca059b9ad14fabc70450ce6723020991552a738 Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Wed, 19 Jun 2019 09:37:21 -0700
Subject: [PATCH 007/853] Modified trigger names to conform to requested format

---
 .../versions/0155_add_content_update_time.py   | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
index f3c876468d42..5c78b30b2c76 100644
--- a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
@@ -34,7 +34,7 @@ def install_update_trigger(migrate_engine):
 
     if migrate_engine.name in ['postgres', 'postgresql']:
         pg_create_trigger = DDL("""
-            CREATE FUNCTION update_history_content_update_time()
+            CREATE FUNCTION update_history_update_time()
                 RETURNS trigger
                 LANGUAGE 'plpgsql'
             AS $BODY$
@@ -47,11 +47,11 @@ def install_update_trigger(migrate_engine):
                 RETURN NEW;
             END;
             $BODY$;
-            CREATE TRIGGER update_history_update_time
+            CREATE TRIGGER trigger_dataset_aidur
                 AFTER INSERT OR DELETE OR UPDATE
                 ON dataset
                 FOR EACH ROW
-                EXECUTE PROCEDURE update_history_content_update_time();
+                EXECUTE PROCEDURE update_history_update_time();
         """)
         pg_create_trigger.execute(bind=migrate_engine)
     else:
@@ -67,8 +67,8 @@ def drop_update_trigger(migrate_engine):
 
     if migrate_engine.name in ['postgres', 'postgresql']:
         pg_drop_trigger = DDL("""
-            DROP TRIGGER IF EXISTS update_history_update_time ON dataset;
-            DROP FUNCTION IF EXISTS update_history_content_update_time();
+            DROP TRIGGER IF EXISTS trigger_dataset_aidur ON dataset;
+            DROP FUNCTION IF EXISTS update_history_update_time();
         """)
         pg_drop_trigger.execute(bind=migrate_engine)
     else:
@@ -79,7 +79,7 @@ def drop_update_trigger(migrate_engine):
 
 def build_trigger(op):
     create_trigger_template = """
-        CREATE TRIGGER AFTER_{operation}_DATASET
+        CREATE TRIGGER trigger_dataset_a{op_initial}r
             AFTER {operation}
             ON dataset
             FOR EACH ROW
@@ -94,11 +94,11 @@ def build_trigger(op):
             END;
     """
     rs = 'OLD' if op == 'DELETE' else 'NEW'
-    sql = create_trigger_template.format(operation=op, rowset=rs)
+    sql = create_trigger_template.format(operation=op, rowset=rs, op_initial=op.lower()[0])
     return DDL(sql)
 
 
 def build_drop_trigger(op):
-    trigger_template = 'DROP TRIGGER IF EXISTS AFTER_{operation}_DATASET;'
-    sql = trigger_template.format(operation=op)
+    drop_template = 'DROP TRIGGER IF EXISTS trigger_dataset_a{op_initial}r;'
+    sql = drop_template.format(op_initial=op.lower()[0])
     return DDL(sql)

From 9400f26eeffb54e25456966fb4d9df5468d89712 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Fri, 6 Sep 2019 22:55:03 +0200
Subject: [PATCH 008/853] move ITs to tools/interactive

(cherry picked from commit 1c5bc4f55a781e48e4fd6017e4e49a52db8c4657)
---
 interactivetool_askomics.xml         |  59 ++++++++++++++++
 interactivetool_bam_iobio.xml        |  44 ++++++++++++
 interactivetool_cellxgene.xml        |  29 ++++++++
 interactivetool_ethercalc.xml        |  63 +++++++++++++++++
 interactivetool_hicbrowser.xml       |  33 +++++++++
 interactivetool_jupyter_notebook.xml | 100 +++++++++++++++++++++++++++
 interactivetool_neo4j.xml            |  41 +++++++++++
 interactivetool_phinch.xml           |  37 ++++++++++
 8 files changed, 406 insertions(+)
 create mode 100644 interactivetool_askomics.xml
 create mode 100644 interactivetool_bam_iobio.xml
 create mode 100644 interactivetool_cellxgene.xml
 create mode 100644 interactivetool_ethercalc.xml
 create mode 100644 interactivetool_hicbrowser.xml
 create mode 100644 interactivetool_jupyter_notebook.xml
 create mode 100644 interactivetool_neo4j.xml
 create mode 100644 interactivetool_phinch.xml

diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml
new file mode 100644
index 000000000000..71c3fe9a437f
--- /dev/null
+++ b/interactivetool_askomics.xml
@@ -0,0 +1,59 @@
+<tool id="interactive_tool_askomics" tool_type="interactive" name="AskOmics" version="0.1">
+    <description>AskOmics, a visual SPARQL query builder</description>
+    <requirements>
+        <container type="docker">quay.io/askomics/askomics-ie:17.12_g19.09</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="AskOmics instance on $infile.display_name" requires_domain="True">
+            <port>6543</port>
+            <url>/login_api_gie?key=abcd</url>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="API_KEY" strip="True">
+            #if $__user__:
+                #for $api_key in $__user__.api_keys:
+                    ${api_key.key}
+                    #break
+                #end for
+            #end if
+        </environment_variable>
+    </environment_variables>
+    <command><![CDATA[
+        #import re
+        ## ToDo: the key could be generated randomly
+        export ASKO_load_url='http://localhost:6543' &&
+        export ASKOMICS_API_KEY='abcd' &&
+        export ASKO_files_dir='/tmp/askomics-ie'  &&
+        export VIRT_Parameters_NumberOfBuffers='10000'  &&
+        export VIRT_Parameters_MaxDirtyBuffers='6000'  &&
+
+        #set link_name = re.sub('[^\w_]', '_', $infile.element_identifier)
+        #if $infile.ext == 'tabular':
+            #set link_name = $link_name + '.tsv'
+        #elif $infile.ext == 'interval':
+            #set link_name = $link_name + '.bed'
+        #else:
+            #set link_name = $link_name + '.' + $infile.ext
+        #end if
+
+        mkdir -p /import &&
+        ln -s '$infile' '/import/$link_name' &&
+
+        bash /start.sh
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="tabular,gff,gff3,bed,interval" label="A datasets with genomic coordinates"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        AskOmics is a visual SPARQL query interface supporting both intuitive data integration and
+        querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL.
+    </help>
+</tool>
diff --git a/interactivetool_bam_iobio.xml b/interactivetool_bam_iobio.xml
new file mode 100644
index 000000000000..2f1c531861ca
--- /dev/null
+++ b/interactivetool_bam_iobio.xml
@@ -0,0 +1,44 @@
+<tool id="interactive_tool_bam_iobio" tool_type="interactive" name="BAM (iobio) Visualisation" version="0.1">
+    <requirements>
+        <container type="docker">qiaoy/iobio-bundle.bam-iobio:1.0-ondemand</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="BAM io.bio visualisation of $infile.display_name" requires_domain="True">
+            <port>80</port>
+            <url><![CDATA[/?bam=http://localhost/tmp/bamfile.bam&region=1]]></url>
+        </entry_point>
+    </entry_points>
+    <command><![CDATA[
+    ## ToDo: websocket could not be found
+    ## WebSocket connection to 'ws://localhost/bamreaddepther/' failed: Error in connection establishment: net::ERR_CONNECTION_REFUSED
+
+    #set $PUB_HOSTNAME = 'localhost'
+    #set $PUB_HTTP_PORT = '80'
+
+    cd /var/www/html &&
+    sed -i "s@\"wss://services.iobio.io/samtools/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samtools/\"@" js/bam.iobio.js/bam.iobio.js &&
+    sed -i "s@\"wss://services.iobio.io/bamreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamreaddepther/\"@" js/bam.iobio.js/bam.iobio.js &&
+    sed -i "s@\"wss://services.iobio.io/bamstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamstatsalive/\"@" js/bam.iobio.js/bam.iobio.js &&
+    sed -i "s@\"wss://services.iobio.io/samheader/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samheader/\"@" js/bam.iobio.js/bam.iobio.js &&
+
+        cp '${infile}' /input/bamfile.bam &&
+        cp '${infile.metadata.bam_index}' /input/bamfile.bam.bai &&
+        mkdir /var/log/supervisor/ &&
+        head -n -2  /etc/supervisor.d/app.conf > /tmp/app.conf &&
+        mv /tmp/app.conf /etc/supervisor.d/app.conf &&
+
+        /usr/bin/supervisord -c /etc/supervisord.conf
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="bam" label="BAM file"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        BAM iobio visualisation.
+    </help>
+</tool>
diff --git a/interactivetool_cellxgene.xml b/interactivetool_cellxgene.xml
new file mode 100644
index 000000000000..546bd7ab58fe
--- /dev/null
+++ b/interactivetool_cellxgene.xml
@@ -0,0 +1,29 @@
+<tool id="interactive_tool_cellxgene" tool_type="interactive" name="Interactive CellXgene Environment" version="0.1">
+    <requirements>
+        <container type="docker">quay.io/galaxy/cellxgene-galaxy-ie:ie2</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Cellxgene Single Cell Visualisation on $infile.display_name" requires_domain="True">
+            <port>80</port>
+        </entry_point>
+    </entry_points>
+    <command><![CDATA[
+        #import re
+        #set $fancy_name = '/tmp/galaxy_cellxgene_' + re.sub('[^\w\-_]', '_', $infile.element_identifier) + '.h5ad'
+        cp '${infile}' '${fancy_name}'
+        &&
+        cellxgene launch --host 0.0.0.0 --port 80 '${fancy_name}'
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="h5ad" label="Concatenate Dataset"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+    Interactive tool for visualising AnnData.
+    </help>
+</tool>
diff --git a/interactivetool_ethercalc.xml b/interactivetool_ethercalc.xml
new file mode 100644
index 000000000000..88676c1e997d
--- /dev/null
+++ b/interactivetool_ethercalc.xml
@@ -0,0 +1,63 @@
+<tool id="interactive_tool_ethercalc" tool_type="interactive" name="EtherCalc" version="0.1">
+    <requirements>
+        <container type="docker">shiltemann/ethercalc-galaxy-ie:17.05</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="EtherCalc instance on $infile.display_name" requires_domain="True">
+            <port>8000</port>
+        </entry_point>
+    </entry_points>
+    <command><![CDATA[
+    
+        forever start `which ethercalc` --cors &
+        bash $wait_script
+        &&
+
+        curl --include --request POST --header "Content-Type: application/json" --data-binary "{ \"room\": \"galaxy\", \"snapshot\": \"...\"}" 'http://localhost:8000/_'
+        &&
+
+        ## put loading message into worksheet in case of large files
+        echo -e "Loading your,dataset\nThis may take, some time for, large files.." > loading.txt
+        &&
+        curl --include --request PUT --header "Content-Type: text/csv" --data-binary @loading.txt http://localhost:8000/_/galaxy
+        &&
+
+        ## remove dump file so this doesnt appear in audit trail
+        rm /dump.json
+        &&
+
+        ## load dataset into worksheet
+        curl --include --request PUT --header "Content-Type: text/csv" --data-binary @$infile http://localhost:8000/_/galaxy
+        &&
+
+        tail -f /etc/hosts
+
+    ]]>
+    </command>
+    <configfiles>
+        <configfile name="wait_script">
+<![CDATA[
+## make sure ethercalc has finished starting up
+STATUS=\$(curl --include 'http://localhost:8000/_/galaxy' 2>&1)
+while [[ \${STATUS} =~ "refused" ]]
+do
+  echo "waiting for ethercalc: \$STATUS \n"
+  STATUS=\$(curl --include 'http://localhost:8000/_/galaxy' 2>&1)
+  sleep 2
+done
+    ]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="infile" type="data" format="tabular,csv,tsv" label="Some tabular dataset"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        EtherCalc is a web spreadsheet.
+        https://ethercalc.net
+    </help>
+</tool>
diff --git a/interactivetool_hicbrowser.xml b/interactivetool_hicbrowser.xml
new file mode 100644
index 000000000000..7aaa8a3e8e7b
--- /dev/null
+++ b/interactivetool_hicbrowser.xml
@@ -0,0 +1,33 @@
+<tool id="interactive_tool_hicbrowser" tool_type="interactive" name="HiCBrowser" version="0.1">
+    <requirements>
+        <container type="docker">bgruening/hicbrowser</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="HiCBrowser on $infile.display_name" requires_domain="True">
+            <port>80</port>
+        </entry_point>
+    </entry_points>
+    <command><![CDATA[
+        #set $PROXY_PREFIX = ""
+        sed -i "s|PROXY_PREFIX|${PROXY_PREFIX}|" /etc/nginx/conf.d/nginx.conf &&
+        rm /data/* -rf &&
+        cp '$infile' /data/data_pack.zip &&
+        cd /data &&
+        unzip data_pack.zip &&
+        supervisord &&
+        tail -f /var/log/supervisor/*
+
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="zip" label="HiCExplorer archive"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        Visualising HiC data with HiCBrowser.
+    </help>
+</tool>
diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml
new file mode 100644
index 000000000000..9dd3e36d3ee4
--- /dev/null
+++ b/interactivetool_jupyter_notebook.xml
@@ -0,0 +1,100 @@
+<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive Jupyter Notebook" version="0.1">
+    <requirements>
+        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:ie2</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Jupyter Interactive Tool" requires_domain="True">
+            <port>8888</port>
+            <url>ipython/tree</url>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($jupyter_notebook.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="API_KEY" strip="True">
+            #if $__user__:
+                #for $api_key in $__user__.api_keys:
+                    ${api_key.key}
+                    #break
+                #end for
+            #end if
+        </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
+    </environment_variables>
+    <command detect_errors="aggressive"><![CDATA[
+        #import re
+        export GALAXY_WORKING_DIR=`pwd` &&
+        mkdir -p ./jupyter/outputs/ &&
+        mkdir -p ./jupyter/data &&
+
+        #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
+        ln -sf '$input' './jupyter/data/${cleaned_name}' &&
+
+        ## change into the directory where the notebooks are located
+        cd ./jupyter/ &&
+        export PATH=/home/jovyan/.local/bin:\$PATH &&
+
+        #if $mode.mode_select == 'scratch':
+            ## copy default notebook
+            cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
+            jupyter trust ./ipython_galaxy_notebook.ipynb &&
+            jupyter lab --no-browser --NotebookApp.shutdown_button=True &&
+            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
+
+        #else:
+            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
+            cp '$mode.ipynb' ./${cleaned_name}.ipynb &&
+            jupyter trust ./${cleaned_name}.ipynb &&
+
+            #if $mode.run_it:
+                jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
+            #else:
+                jupyter lab --no-browser --NotebookApp.shutdown_button=True &&
+            #end if
+            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
+        #end if
+    ]]>
+    </command>
+    <inputs>
+
+        <conditional name="mode">
+            <param name="mode_select" type="select" label="Do you already have a notebook?" help="If not, no problem we will provide you with a default one.">
+                <option value="scratch">Start with a fresh notebook</option>
+                <option value="previous">Load a previous notebook</option>
+            </param>
+            <when value="scratch"/>
+            <when value="previous">
+                <param name="ipynb" type="data" format="ipynb" label="IPython Notebook"/>
+                <param name="run_it" type="boolean" truevalue="true" falsevalue="false" label="Execute notebook and return a new one."
+                    help="This option is useful in workflows when you just want to execute a notebook and not dive into the webfrontend."/>
+            </when>
+        </conditional>
+        <param name="input" type="data" optional="true" label="Include data into the environment"/>
+
+    </inputs>
+    <outputs>
+        <data name="jupyter_notebook" format="ipynb" label="Executed Notebook"></data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="mode" value="previous" />
+            <param name="ipynb" value="test.ipynb" />
+            <param name="run_it" value="true" />
+            <output name="jupyter_notebook" file="test.ipynb" ftype="ipynb"/>
+        </test>
+    </tests>
+    <help>
+    The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations,
+    visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization,
+    machine learning, and much more.
+    
+    Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
+    do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter.
+    
+    You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset.
+    If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history.
+    
+    You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function.
+    </help>
+</tool>
diff --git a/interactivetool_neo4j.xml b/interactivetool_neo4j.xml
new file mode 100644
index 000000000000..0b31a8b303e0
--- /dev/null
+++ b/interactivetool_neo4j.xml
@@ -0,0 +1,41 @@
+<tool id="interactive_tool_neo4j" tool_type="interactive" name="Neo4j (Graph Database)" version="0.1">
+    <requirements>
+        <container type="docker">quay.io/sanbi-sa/neo_ie:3.1.9</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Neo4j on $infile.display_name" requires_domain="True">
+            <port>80</port>
+        </entry_point>
+        <!-- I get some web-socket error that 7687 is not reachable. 
+            but docker does not expose 7687?
+        -->
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="USER_GID">2345</environment_variable>
+        <environment_variable name="USER_UID">2345</environment_variable>
+        <environment_variable name="MONITOR_TRAFFIC">false</environment_variable>
+    </environment_variables>
+    <command><![CDATA[
+        ##export USER_UID=2345 &&
+        ##export USER_GID=2345 &&
+        ##export MONITOR_TRAFFIC=false &&
+        mkdir -p /data/neo4jdb &&
+        unzip '$infile' -d /data/neo4jdb &&
+        ls -l /data/neo4jdb &&
+        sed -i.bak 's@/monitor_traffic.*@@g' /docker-entrypoint.sh &&
+        cd /opt/neo4j &&
+        bash /docker-entrypoint.sh neo4j
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="zip" label="Neo4J data store"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        Neo4j is a highly scalable, robust native graph database.
+    </help>
+</tool>
diff --git a/interactivetool_phinch.xml b/interactivetool_phinch.xml
new file mode 100644
index 000000000000..d77c9274ad35
--- /dev/null
+++ b/interactivetool_phinch.xml
@@ -0,0 +1,37 @@
+<tool id="interactive_tool_pinch" tool_type="interactive" name="Phinch Visualisation" version="0.1">
+    <requirements>
+        <container type="docker">shiltemann/docker-phinch-galaxy:16.04</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Phinch Visualisation of $infile.display_name" requires_domain="True">
+            <port>80</port>
+        </entry_point>
+    </entry_points>
+    <command><![CDATA[
+        ## ToDo nginx, proxy.conf etc can be removed from the container
+
+        #import os
+        #set $name = os.path.splitext(str($infile.display_name))[0]
+        ## in case someone names the data testdata.
+        rm /home/Phinch/data/testdata.biom | true &&
+        ln -s '$infile' /home/Phinch/data/${name}.biom &&
+        cd /home/Phinch/data &&
+        sed -i  "s/'REPLACE_ME'/'${name}.biom'/g" /home/Phinch/scripts/readFile.js &&
+        ## keep it running
+        cd /home/Phinch &&
+        php -S 0.0.0.0:80 2>&1 > /var/log/phinch.log
+
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="biom1" label="Biom1 dataset"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        Interactive tool for visualising Biom data.
+    </help>
+</tool>

From 2f67bb0f4d539b6f768edc635f01c207a5046947 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Fri, 6 Sep 2019 23:05:01 +0200
Subject: [PATCH 009/853] move default notebook as well

(cherry picked from commit 6d8848e399446fdc3cb1e0c81b1e88c80b03c515)
---
 default_notebook.ipynb | 53 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 default_notebook.ipynb

diff --git a/default_notebook.ipynb b/default_notebook.ipynb
new file mode 100644
index 000000000000..e95737524789
--- /dev/null
+++ b/default_notebook.ipynb
@@ -0,0 +1,53 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Welcome to the interactive Galaxy IPython Notebook."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "You can access your data via the dataset number. Using a Python kernel, you can access dataset number 42 with ``handle = open(get(42), 'r')``.\n",
+    "To save data, write your data to a file, and then call ``put('filename.txt')``. The dataset will then be available in your galaxy history.\n<br>",
+    "When using a non-Python kernel, ``get`` and ``put`` are available as command-line tools, which can be accessed using system calls in R, Julia, and Ruby. For example, to read dataset number 42 into R, you can write ```handle <- file(system('get -i 42', intern = TRUE))```.\n",
+    "To save data in R, write the data to a file and then call ``system('put -p filename.txt')``.\n",
+    "Notebooks can be saved to Galaxy by clicking the large green button at the top right of the IPython interface.<br>\n",
+    "More help and informations can be found on the project [website](https://github.com/bgruening/docker-jupyter-notebook)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 2",
+   "language": "python",
+   "name": "python2"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}

From 58a00bef9c035495f46a1a92ac73dbe7fe66751e Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Fri, 6 Sep 2019 23:07:39 +0200
Subject: [PATCH 010/853] improve description of Askomics

(cherry picked from commit 1d4dc27e509a4084857fec63c20698d69979c8eb)
---
 interactivetool_askomics.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml
index 71c3fe9a437f..c1ce9d3bd115 100644
--- a/interactivetool_askomics.xml
+++ b/interactivetool_askomics.xml
@@ -1,5 +1,5 @@
 <tool id="interactive_tool_askomics" tool_type="interactive" name="AskOmics" version="0.1">
-    <description>AskOmics, a visual SPARQL query builder</description>
+    <description>a visual SPARQL query builder</description>
     <requirements>
         <container type="docker">quay.io/askomics/askomics-ie:17.12_g19.09</container>
     </requirements>

From 06bbc492e2faf0d7c7d53d0ac207f34ca3224e21 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Thu, 3 Oct 2019 13:40:33 +0200
Subject: [PATCH 011/853] move to right dir

---
 interactivetool_paraview.xml | 50 ++++++++++++++++++++++++++
 interactivetool_rstudio.xml  | 69 ++++++++++++++++++++++++++++++++++++
 2 files changed, 119 insertions(+)
 create mode 100644 interactivetool_paraview.xml
 create mode 100644 interactivetool_rstudio.xml

diff --git a/interactivetool_paraview.xml b/interactivetool_paraview.xml
new file mode 100644
index 000000000000..c801600ef0e4
--- /dev/null
+++ b/interactivetool_paraview.xml
@@ -0,0 +1,50 @@
+<tool id="interactive_tool_paraview" tool_type="interactive" name="Paraview" version="0.1">
+    <requirements>
+        <!-- kitware/paraviewweb:pvw-v5.6.0-osmesa -->
+        <container type="docker">bmcv/galaxy-paraviewweb:latest</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Paraview based Visualisation of $infile.display_name" requires_domain="True">
+            <port>8777</port>
+            <!--url>apps/Visualizer</url-->
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="SERVER_NAME" strip="True">localhost:8080</environment_variable>
+        <environment_variable name="PROTOCOL">wss</environment_variable>
+        <environment_variable name="EXTRA_PVPYTHON_ARGS">-dr,--mesa-swr</environment_variable>
+    </environment_variables>
+    <command><![CDATA[
+
+service nginx start &&
+
+export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:/usr/local/lib/paraview-\$PV_VERSION_MAJOR/:/usr/local/lib/ &&
+
+mkdir /input/ &&
+
+#if $infile:
+    ln -s '$infile' /input/infile.${infile.ext} &&
+#end if
+
+Visualizer --paraview /usr/local/lib/paraview-\$PV_VERSION_MAJOR/
+    --data /input
+    --port 9777
+    --server-only
+    #if $infile:
+       --load-file infile.${infile.ext}
+    #end if
+
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="png,jpg,tiff" optional="true" label="Optional input dataset"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        ParaView is an open-source, multi-platform application designed to visualize data sets of varying sizes from small to very large.
+    </help>
+</tool>
diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml
new file mode 100644
index 000000000000..30b55db7f118
--- /dev/null
+++ b/interactivetool_rstudio.xml
@@ -0,0 +1,69 @@
+<tool id="interactive_tool_rstudio" tool_type="interactive" name="RStudio" version="0.1">
+    <requirements>
+        <container type="docker">quay.io/erasche/docker-rstudio-notebook:19.05</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="RStudio" requires_domain="True">
+            <port>80</port>
+            <url>rstudio/</url>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($jupyter_notebook.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="API_KEY" strip="True">
+            #if $__user__:
+                #for $api_key in $__user__.api_keys:
+                    ${api_key.key}
+                    #break
+                #end for
+            #end if
+        </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
+    </environment_variables>
+    <command detect_errors="aggressive"><![CDATA[
+        #import re
+        export GALAXY_WORKING_DIR=`pwd` &&
+        mkdir -p ./rstudio/outputs/ &&
+        mkdir -p ./rstudio/data &&
+
+        #if $input:
+            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
+            ln -sf '$input' './rstudio/data/${cleaned_name}' &&
+        #end if
+
+        ## change into the directory where the notebooks are located
+        cd ./rstudio/ &&
+
+        /init
+
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" optional="true" label="Include data into the environment"/>
+    </inputs>
+    <outputs>
+        <data name="jupyter_notebook" format="ipynb" label=""></data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="mode" value="previous" />
+            <param name="ipynb" value="test.ipynb" />
+            <param name="run_it" value="true" />
+            <output name="jupyter_notebook" file="test.ipynb" ftype="ipynb"/>
+        </test>
+    </tests>
+    <help>
+    This familiar R analysis software suite will let you explore your
+    datasets in depth. Comes with ggplot2, RODBC, maps, shinyapps, knitr,
+    LaTeX, bioconductor, cummeRbund, and many more pre-installed packages.
+    
+    Galaxy offers you to use RStudio directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
+    do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in RStudio.
+
+    The convenience functions gx_put() and gx_get() are available to you to interact with your current Galaxy history. You can save your workspace with gx_save(). 
+
+    For example, gx_get(42) will fetch dataset 42 from your history and return the file location 
+    </help>
+</tool>

From 6b0b5edbbfa092e9e51732d8e9ae931b22e197e2 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sat, 5 Oct 2019 23:58:46 +0200
Subject: [PATCH 012/853] add wilson

---
 interactivetool_wilson.xml | 51 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 interactivetool_wilson.xml

diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml
new file mode 100644
index 000000000000..5ce1b73272f3
--- /dev/null
+++ b/interactivetool_wilson.xml
@@ -0,0 +1,51 @@
+<tool id="interactivetool_wilson" tool_type="interactive" name="Wilson" version="0.1">
+    <description>Webbased Interactive Omics visualization</description>
+    <requirements>
+        <container type="docker">loosolab/wilson:2.1.0</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Wilson visualisation of $infile.display_name" requires_domain="True">
+            <port>3838</port>
+        </entry_point>
+    </entry_points>
+    <command><![CDATA[
+        mkdir -p /srv/shiny-server/external_data/ &&
+        ln -s ${infile} /srv/shiny-server/external_data/input.clarion &&
+        export WILSON_LANDING_PAGE='feature_selection' &&
+        exec shiny-server 2>&1
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="tabular,txt" label="Tabular in Clarion format"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+
+`WIlsON: Webbased Interactive Omics visualizatioN <https://github.molgen.mpg.de/loosolab/wilson-apps/wiki>`_
+
+.. class:: infomark
+
+Wilson uses the CLARION file format, which is a generic file format for quantitative comparisons of high throughput screens.
+
+CLARION is a data format specially developed to be used with Wilson, which relies on a tab-delimited table with
+a metadata header to describe the following columns. It is based on the Summarized Experiment format and supports
+all types of data which can be reduced to features and their annotation (e.g. genes, transcripts, proteins, probes)
+with assigned numerical values (e.g. count, score, log2foldchange, z-score, p-value). Most result tables derived from RNA-Seq,
+ChIP/ATAC-Seq, Proteomics, Microarrays, and many other analyses can thus be easily reformatted to become compatible
+without having to modify the code of Wilson for each specific experiment.
+
+Please check the following link for details considering the `CLARION format <https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format>`_.
+
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bty711</citation>
+    </citations>
+</tool>

From 5df22293ef936aabe9d4b4c14e1afb88e2f77662 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sun, 6 Oct 2019 00:01:57 +0200
Subject: [PATCH 013/853] deactivate monitor script

---
 interactivetool_rstudio.xml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml
index 30b55db7f118..7454c973b857 100644
--- a/interactivetool_rstudio.xml
+++ b/interactivetool_rstudio.xml
@@ -36,6 +36,8 @@
         ## change into the directory where the notebooks are located
         cd ./rstudio/ &&
 
+        sed -i 's|/monitor.*||g' /etc/services.d/nginx/run &&
+
         /init
 
     ]]>

From 73dd265703a1fa7b7c65be73aae22138f9fd2512 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sun, 6 Oct 2019 00:48:50 +0200
Subject: [PATCH 014/853] fix tool id

---
 interactivetool_wilson.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml
index 5ce1b73272f3..9d724a0fbe59 100644
--- a/interactivetool_wilson.xml
+++ b/interactivetool_wilson.xml
@@ -1,4 +1,4 @@
-<tool id="interactivetool_wilson" tool_type="interactive" name="Wilson" version="0.1">
+<tool id="interactive_tool_wilson" tool_type="interactive" name="Wilson" version="0.1">
     <description>Webbased Interactive Omics visualization</description>
     <requirements>
         <container type="docker">loosolab/wilson:2.1.0</container>

From c7f5136c8f7942312b2f83075b25e5ff847f9b82 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Tue, 8 Oct 2019 14:51:38 +0200
Subject: [PATCH 015/853] temporarily disable all input data

---
 interactivetool_rstudio.xml | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml
index 7454c973b857..9f39f2273480 100644
--- a/interactivetool_rstudio.xml
+++ b/interactivetool_rstudio.xml
@@ -28,11 +28,6 @@
         mkdir -p ./rstudio/outputs/ &&
         mkdir -p ./rstudio/data &&
 
-        #if $input:
-            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
-            ln -sf '$input' './rstudio/data/${cleaned_name}' &&
-        #end if
-
         ## change into the directory where the notebooks are located
         cd ./rstudio/ &&
 
@@ -43,7 +38,7 @@
     ]]>
     </command>
     <inputs>
-        <param name="input" type="data" optional="true" label="Include data into the environment"/>
+        <!--<param name="input" type="data" optional="true" label="Include data into the environment"/>-->
     </inputs>
     <outputs>
         <data name="jupyter_notebook" format="ipynb" label=""></data>
@@ -60,12 +55,12 @@
     This familiar R analysis software suite will let you explore your
     datasets in depth. Comes with ggplot2, RODBC, maps, shinyapps, knitr,
     LaTeX, bioconductor, cummeRbund, and many more pre-installed packages.
-    
+
     Galaxy offers you to use RStudio directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
     do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in RStudio.
 
-    The convenience functions gx_put() and gx_get() are available to you to interact with your current Galaxy history. You can save your workspace with gx_save(). 
+    The convenience functions gx_put() and gx_get() are available to you to interact with your current Galaxy history. You can save your workspace with gx_save().
 
-    For example, gx_get(42) will fetch dataset 42 from your history and return the file location 
+    For example, gx_get(42) will fetch dataset 42 from your history and return the file location
     </help>
 </tool>

From ae38c98f5adf246d4516ffe9248413099ef893aa Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Tue, 8 Oct 2019 14:52:54 +0200
Subject: [PATCH 016/853] add two more

---
 interactivetool_rstudio.xml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml
index 9f39f2273480..8338497f70c9 100644
--- a/interactivetool_rstudio.xml
+++ b/interactivetool_rstudio.xml
@@ -13,6 +13,8 @@
         <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
         <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
         <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="DEBUG">true</environment_variable>
+        <environment_variable name="DISABLE_AUTH">true</environment_variable>
         <environment_variable name="API_KEY" strip="True">
             #if $__user__:
                 #for $api_key in $__user__.api_keys:

From b92f4720273172cda4b64f96e0ce7e36e797893d Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Tue, 8 Oct 2019 14:53:31 +0200
Subject: [PATCH 017/853] also from prod

---
 interactivetool_jupyter_notebook.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml
index 9dd3e36d3ee4..60cdc00253f5 100644
--- a/interactivetool_jupyter_notebook.xml
+++ b/interactivetool_jupyter_notebook.xml
@@ -39,7 +39,7 @@
             ## copy default notebook
             cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
             jupyter trust ./ipython_galaxy_notebook.ipynb &&
-            jupyter lab --no-browser --NotebookApp.shutdown_button=True &&
+            jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
             cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
 
         #else:
@@ -50,7 +50,7 @@
             #if $mode.run_it:
                 jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
             #else:
-                jupyter lab --no-browser --NotebookApp.shutdown_button=True &&
+                jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
             #end if
             cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
         #end if
@@ -88,13 +88,13 @@
     The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations,
     visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization,
     machine learning, and much more.
-    
+
     Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
     do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter.
-    
+
     You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset.
     If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history.
-    
+
     You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function.
     </help>
 </tool>

From 0bd3376068fe8d9059628b8ac127f4473d16eaf0 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Tue, 8 Oct 2019 14:59:38 +0200
Subject: [PATCH 018/853] switch version

---
 interactivetool_rstudio.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml
index 8338497f70c9..d0b11257a3f3 100644
--- a/interactivetool_rstudio.xml
+++ b/interactivetool_rstudio.xml
@@ -1,6 +1,6 @@
 <tool id="interactive_tool_rstudio" tool_type="interactive" name="RStudio" version="0.1">
     <requirements>
-        <container type="docker">quay.io/erasche/docker-rstudio-notebook:19.05</container>
+        <container type="docker">quay.io/erasche/docker-rstudio-notebook:19.09</container>
     </requirements>
     <entry_points>
         <entry_point name="RStudio" requires_domain="True">

From 8b5d5bf5c5812f101ae00a7e82b9f3c537ae32bf Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Tue, 8 Oct 2019 16:38:15 +0200
Subject: [PATCH 019/853] chown, hacks

---
 interactivetool_rstudio.xml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml
index d0b11257a3f3..8f5d8792bf49 100644
--- a/interactivetool_rstudio.xml
+++ b/interactivetool_rstudio.xml
@@ -35,7 +35,11 @@
 
         sed -i 's|/monitor.*||g' /etc/services.d/nginx/run &&
 
-        /init
+        ##/init
+        rstudio-server start &&
+        /etc/init.d/syslog-ng start &&
+        chmod 777 /tmp -R &&
+        tail -f /var/log/rstudio-server/rserver.log
 
     ]]>
     </command>

From ca0624a341464c4c9b4d9409d509ce3b8cf64ea3 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Tue, 8 Oct 2019 16:48:42 +0200
Subject: [PATCH 020/853] fix pot

---
 interactivetool_rstudio.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml
index 8f5d8792bf49..f15e9047cf40 100644
--- a/interactivetool_rstudio.xml
+++ b/interactivetool_rstudio.xml
@@ -4,7 +4,7 @@
     </requirements>
     <entry_points>
         <entry_point name="RStudio" requires_domain="True">
-            <port>80</port>
+            <port>8787</port>
             <url>rstudio/</url>
         </entry_point>
     </entry_points>

From 48b5cb7bc803031832114c49ab4f2c899fb11c2f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Tue, 8 Oct 2019 20:09:27 +0200
Subject: [PATCH 021/853] latest RStudio changes

---
 interactivetool_rstudio.xml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml
index f15e9047cf40..e6ee98af1544 100644
--- a/interactivetool_rstudio.xml
+++ b/interactivetool_rstudio.xml
@@ -4,7 +4,7 @@
     </requirements>
     <entry_points>
         <entry_point name="RStudio" requires_domain="True">
-            <port>8787</port>
+            <port>80</port>
             <url>rstudio/</url>
         </entry_point>
     </entry_points>
@@ -35,9 +35,10 @@
 
         sed -i 's|/monitor.*||g' /etc/services.d/nginx/run &&
 
-        ##/init
-        rstudio-server start &&
         /etc/init.d/syslog-ng start &&
+        /init &
+        ##rstudio-server start &&
+        sleep 5 &&
         chmod 777 /tmp -R &&
         tail -f /var/log/rstudio-server/rserver.log
 

From d4403bc344cf2d4723bbdf9eefdef115141e56f0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Tue, 8 Oct 2019 20:09:53 +0200
Subject: [PATCH 022/853] use lab entrypoint

---
 interactivetool_jupyter_notebook.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml
index 60cdc00253f5..787d7fa64fa7 100644
--- a/interactivetool_jupyter_notebook.xml
+++ b/interactivetool_jupyter_notebook.xml
@@ -5,7 +5,7 @@
     <entry_points>
         <entry_point name="Jupyter Interactive Tool" requires_domain="True">
             <port>8888</port>
-            <url>ipython/tree</url>
+            <url>ipython/lab</url>
         </entry_point>
     </entry_points>
     <environment_variables>

From 4a558dba1ac0432b57b4bbd62b85adf8c5576a7d Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Tue, 8 Oct 2019 20:32:58 +0200
Subject: [PATCH 023/853] more reverts

---
 interactivetool_rstudio.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml
index e6ee98af1544..63e0eb3adb05 100644
--- a/interactivetool_rstudio.xml
+++ b/interactivetool_rstudio.xml
@@ -39,6 +39,7 @@
         /init &
         ##rstudio-server start &&
         sleep 5 &&
+
         chmod 777 /tmp -R &&
         tail -f /var/log/rstudio-server/rserver.log
 

From b050d84dbdeb31a95a35f0ab1ac84885daeb2718 Mon Sep 17 00:00:00 2001
From: root <root@sn04.bi.uni-freiburg.de>
Date: Wed, 9 Oct 2019 16:02:24 +0200
Subject: [PATCH 024/853] include env

---
 interactivetool_wilson.xml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml
index 9d724a0fbe59..94abe38311df 100644
--- a/interactivetool_wilson.xml
+++ b/interactivetool_wilson.xml
@@ -8,10 +8,12 @@
             <port>3838</port>
         </entry_point>
     </entry_points>
+    <environment_variables>
+        <environment_variable name="WILSON_LANDING_PAGE">feature_selection</environment_variable>
+    </environment_variables>
     <command><![CDATA[
         mkdir -p /srv/shiny-server/external_data/ &&
         ln -s ${infile} /srv/shiny-server/external_data/input.clarion &&
-        export WILSON_LANDING_PAGE='feature_selection' &&
         exec shiny-server 2>&1
     ]]>
     </command>

From 0dbfa7ce3282e003bc3158e622ee8e22815febe6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 9 Oct 2019 23:35:41 +0200
Subject: [PATCH 025/853] use own container

---
 interactivetool_wilson.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml
index 94abe38311df..302ff3b0e4a2 100644
--- a/interactivetool_wilson.xml
+++ b/interactivetool_wilson.xml
@@ -1,7 +1,7 @@
 <tool id="interactive_tool_wilson" tool_type="interactive" name="Wilson" version="0.1">
     <description>Webbased Interactive Omics visualization</description>
     <requirements>
-        <container type="docker">loosolab/wilson:2.1.0</container>
+        <container type="docker">quay.io/bgruening/wilson-app</container>
     </requirements>
     <entry_points>
         <entry_point name="Wilson visualisation of $infile.display_name" requires_domain="True">

From 88e3f31dea523ed69ebfc4fe64a5075dc7096f48 Mon Sep 17 00:00:00 2001
From: root <root@sn04.bi.uni-freiburg.de>
Date: Sat, 12 Oct 2019 00:37:59 +0200
Subject: [PATCH 026/853] fix phinch IE

---
 interactivetool_phinch.xml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/interactivetool_phinch.xml b/interactivetool_phinch.xml
index d77c9274ad35..382cf32f0a9f 100644
--- a/interactivetool_phinch.xml
+++ b/interactivetool_phinch.xml
@@ -1,4 +1,4 @@
-<tool id="interactive_tool_pinch" tool_type="interactive" name="Phinch Visualisation" version="0.1">
+<tool id="interactive_tool_phinch" tool_type="interactive" name="Phinch Visualisation" version="0.1">
     <requirements>
         <container type="docker">shiltemann/docker-phinch-galaxy:16.04</container>
     </requirements>
@@ -11,12 +11,14 @@
         ## ToDo nginx, proxy.conf etc can be removed from the container
 
         #import os
-        #set $name = os.path.splitext(str($infile.display_name))[0]
+        #set $name = os.path.splitext(str($infile.display_name).replace(' ', '_'))[0]
         ## in case someone names the data testdata.
         rm /home/Phinch/data/testdata.biom | true &&
-        ln -s '$infile' /home/Phinch/data/${name}.biom &&
+        ln -s '$infile' '/home/Phinch/data/${name}.biom' &&
         cd /home/Phinch/data &&
         sed -i  "s/'REPLACE_ME'/'${name}.biom'/g" /home/Phinch/scripts/readFile.js &&
+        sed -i  "s/http/https/g" /home/Phinch/scripts/readFile.js &&
+
         ## keep it running
         cd /home/Phinch &&
         php -S 0.0.0.0:80 2>&1 > /var/log/phinch.log

From edd4da31e3a8077424cc3524bc4e988c74a17ddc Mon Sep 17 00:00:00 2001
From: root <root@sn04.bi.uni-freiburg.de>
Date: Sat, 12 Oct 2019 12:16:45 +0200
Subject: [PATCH 027/853] Update Askomics.

---
 interactivetool_askomics.xml | 26 +++++++++++++++++++-------
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml
index c1ce9d3bd115..b4cb6bff0d18 100644
--- a/interactivetool_askomics.xml
+++ b/interactivetool_askomics.xml
@@ -1,17 +1,17 @@
 <tool id="interactive_tool_askomics" tool_type="interactive" name="AskOmics" version="0.1">
-    <description>a visual SPARQL query builder</description>
+    <description>AskOmics, a visual SPARQL query builder</description>
     <requirements>
-        <container type="docker">quay.io/askomics/askomics-ie:17.12_g19.09</container>
+        <container type="docker">askomics/askomics-ie:19.01.3</container>
     </requirements>
     <entry_points>
         <entry_point name="AskOmics instance on $infile.display_name" requires_domain="True">
             <port>6543</port>
-            <url>/login_api_gie?key=abcd</url>
+            <url>/login_api_gie?key=${__user_name__}</url>
         </entry_point>
     </entry_points>
     <environment_variables>
         <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="API_KEY" strip="True">
+        <environment_variable name="GALAXY_API_KEY" strip="True">
             #if $__user__:
                 #for $api_key in $__user__.api_keys:
                     ${api_key.key}
@@ -19,15 +19,26 @@
                 #end for
             #end if
         </environment_variable>
+        <environment_variable name="GALAXY_USER_NAME">${__user_name__}</environment_variable>
+        <environment_variable name="GALAXY_USER_EMAIL">${__user_email__}</environment_variable>
+        <environment_variable name="ASKOMICS_API_KEY">${__user_name__}</environment_variable><!--FIXME: use a random string instead of the username-->
     </environment_variables>
     <command><![CDATA[
         #import re
-        ## ToDo: the key could be generated randomly
+
+        ## AskOmics configuration, don't change anything here
+        export ASKO_files_dir='/tmp/askomics-ie' &&
+        export ASKO_database_path='/tmp/askomics-ie/database.db' &&
         export ASKO_load_url='http://localhost:6543' &&
-        export ASKOMICS_API_KEY='abcd' &&
-        export ASKO_files_dir='/tmp/askomics-ie'  &&
+
+        ## Triplestore configuration. Update VIRT_Parameters_NumberOfBuffers and 
+        ## VIRT_Parameters_MaxDirtyBuffers according to https://github.com/askomics/askomics-docker-compose/tree/master/virtuoso#configuration
+        export SPARQL_UPDATE='true' &&
         export VIRT_Parameters_NumberOfBuffers='10000'  &&
         export VIRT_Parameters_MaxDirtyBuffers='6000'  &&
+        export VIRT_SPARQL_ResultSetMaxRows='100000' &&
+        export VIRT_SPARQL_MaxQueryCostEstimationTime='40000' &&
+        export VIRT_SPARQL_MaxQueryExecutionTime='40000' &&
 
         #set link_name = re.sub('[^\w_]', '_', $infile.element_identifier)
         #if $infile.ext == 'tabular':
@@ -57,3 +68,4 @@
         querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL.
     </help>
 </tool>
+

From 30424102deb606e69b8e29505d722bdee298d821 Mon Sep 17 00:00:00 2001
From: root <root@sn04.bi.uni-freiburg.de>
Date: Sat, 12 Oct 2019 16:35:42 +0200
Subject: [PATCH 028/853] make bam.io.bio work

---
 interactivetool_bam_iobio.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/interactivetool_bam_iobio.xml b/interactivetool_bam_iobio.xml
index 2f1c531861ca..6c78eaa335b6 100644
--- a/interactivetool_bam_iobio.xml
+++ b/interactivetool_bam_iobio.xml
@@ -21,6 +21,9 @@
     sed -i "s@\"wss://services.iobio.io/bamstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamstatsalive/\"@" js/bam.iobio.js/bam.iobio.js &&
     sed -i "s@\"wss://services.iobio.io/samheader/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samheader/\"@" js/bam.iobio.js/bam.iobio.js &&
 
+
+    sed -i 's/deny all;//g' /etc/nginx/nginx.conf &&
+
         cp '${infile}' /input/bamfile.bam &&
         cp '${infile.metadata.bam_index}' /input/bamfile.bam.bai &&
         mkdir /var/log/supervisor/ &&

From fec1801d07540dccb0af8d20c71833f659b97961 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jens=20Preu=C3=9Fner?= <jenzopr@users.noreply.github.com>
Date: Mon, 14 Oct 2019 14:43:40 +0200
Subject: [PATCH 029/853] Handle env vars; updated container to latest tag

---
 interactivetool_wilson.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml
index 302ff3b0e4a2..c362a758c4ea 100644
--- a/interactivetool_wilson.xml
+++ b/interactivetool_wilson.xml
@@ -1,7 +1,7 @@
 <tool id="interactive_tool_wilson" tool_type="interactive" name="Wilson" version="0.1">
     <description>Webbased Interactive Omics visualization</description>
     <requirements>
-        <container type="docker">quay.io/bgruening/wilson-app</container>
+        <container type="docker">loosolab/wilson:2.1.1</container>
     </requirements>
     <entry_points>
         <entry_point name="Wilson visualisation of $infile.display_name" requires_domain="True">
@@ -10,9 +10,12 @@
     </entry_points>
     <environment_variables>
         <environment_variable name="WILSON_LANDING_PAGE">feature_selection</environment_variable>
+        <environment_variable name="WILSON_BLACKLIST_EXAMPLES">true</environment_variable>
     </environment_variables>
     <command><![CDATA[
         mkdir -p /srv/shiny-server/external_data/ &&
+        echo $WILSON_LANDING_PAGE > /home/shiny/.Renviron &&
+        echo $WILSON_BLACKLIST_EXAMPLES >> /home/shiny/.Renviron &&
         ln -s ${infile} /srv/shiny-server/external_data/input.clarion &&
         exec shiny-server 2>&1
     ]]>

From a4f9346b67fbf35fef2c8211d323a5bfb5ba3d3a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jens=20Preu=C3=9Fner?= <jenzopr@users.noreply.github.com>
Date: Wed, 16 Oct 2019 09:39:31 +0200
Subject: [PATCH 030/853] Fixed bug in command for .Renviron construction

---
 interactivetool_wilson.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml
index c362a758c4ea..7f575c43a636 100644
--- a/interactivetool_wilson.xml
+++ b/interactivetool_wilson.xml
@@ -14,8 +14,8 @@
     </environment_variables>
     <command><![CDATA[
         mkdir -p /srv/shiny-server/external_data/ &&
-        echo $WILSON_LANDING_PAGE > /home/shiny/.Renviron &&
-        echo $WILSON_BLACKLIST_EXAMPLES >> /home/shiny/.Renviron &&
+        echo "WILSON_LANDING_PAGE=\$WILSON_LANDING_PAGE" > /home/shiny/.Renviron &&
+        echo "WILSON_BLACKLIST_EXAMPLES=\$WILSON_BLACKLIST_EXAMPLES" >> /home/shiny/.Renviron &&
         ln -s ${infile} /srv/shiny-server/external_data/input.clarion &&
         exec shiny-server 2>&1
     ]]>

From c136c13c5b4bc947ff9dad803c1fd60d818f958f Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Wed, 16 Oct 2019 14:26:04 +0200
Subject: [PATCH 031/853] add wallace IT

---
 interactivetool_wallace.xml | 53 +++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 interactivetool_wallace.xml

diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml
new file mode 100644
index 000000000000..83d70d19f0ca
--- /dev/null
+++ b/interactivetool_wallace.xml
@@ -0,0 +1,53 @@
+<tool id="interactive_tool_wallace" tool_type="interactive" name="Wallace" version="0.1">
+    <description>Webbased Interactive modeling of species niches and distributions</description>
+    <requirements>
+        <container type="docker">quay.io/bgruening/wilson-app</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Wallace visualisation of $infile.display_name" requires_domain="True">
+            <port>3838</port>
+            <url>/sample-apps/SIG/wallace/shiny/</url>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($jupyter_notebook.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="API_KEY" strip="True">
+            #if $__user__:
+                #for $api_key in $__user__.api_keys:
+                    ${api_key.key}
+                    #break
+                #end for
+            #end if
+        </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
+    </environment_variables>
+    <command><![CDATA[
+        ln -s '${infile}' /srv/shiny-server/data/inputdata.txt &&
+        /usr/bin/shiny-server.sh
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="tabular,txt" label="Tabular in Clarion format"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+
+`Wallace <https://github.molgen.mpg.de/loosolab/wilson-apps/wiki>`_ is a modular platform for reproducible modeling of species niches and distributions.
+
+.. class:: infomark
+
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1111/2041-210X.12945</citation>
+    </citations>
+</tool>

From fae69abcf39a1833dfda755114627c35b2d6dffa Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Wed, 16 Oct 2019 14:39:58 +0200
Subject: [PATCH 032/853] some updates

---
 interactivetool_wallace.xml | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml
index 83d70d19f0ca..6a36204caaff 100644
--- a/interactivetool_wallace.xml
+++ b/interactivetool_wallace.xml
@@ -1,7 +1,7 @@
 <tool id="interactive_tool_wallace" tool_type="interactive" name="Wallace" version="0.1">
     <description>Webbased Interactive modeling of species niches and distributions</description>
     <requirements>
-        <container type="docker">quay.io/bgruening/wilson-app</container>
+        <container type="docker">ylebras/wallace-docker</container>
     </requirements>
     <entry_points>
         <entry_point name="Wallace visualisation of $infile.display_name" requires_domain="True">
@@ -32,18 +32,30 @@
         <param name="infile" type="data" format="tabular,txt" label="Tabular in Clarion format"/>
     </inputs>
     <outputs>
-        <data name="outfile" format="txt" />
+        <!--data name="outfile" format="txt" /-->
     </outputs>
     <tests>
     </tests>
     <help>
 <![CDATA[
 
+
+
+
 `Wallace <https://github.molgen.mpg.de/loosolab/wilson-apps/wiki>`_ is a modular platform for reproducible modeling of species niches and distributions.
 
 .. class:: infomark
 
+Example input file (TAB separated)::
 
+  "name"	"longitude"	"latitude"	"countryCode"
+  Accipiter striatus Vieillot, 1808	-60.291838	46.328137	CA
+  Accipiter striatus Vieillot, 1808	-114.58927	35.022485	US
+  Accipiter striatus Vieillot, 1808	-93.37406	30.00586	US
+  Accipiter striatus Vieillot, 1808	-79.336288	43.682218	CA
+  Accipiter striatus Vieillot, 1808	-109.156024	31.904185	US
+  Accipiter striatus Vieillot, 1808	-71.098031	42.297408	US
+  Accipiter striatus Vieillot, 1808	-110.927215	32.18203	US
 
 ]]>
     </help>

From 0d6bc47d2ea2b55eab60f8487978e55635e4f85e Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Wed, 16 Oct 2019 16:34:10 +0200
Subject: [PATCH 033/853] Update interactivetool_wallace.xml

---
 interactivetool_wallace.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml
index 6a36204caaff..66001ee97b9f 100644
--- a/interactivetool_wallace.xml
+++ b/interactivetool_wallace.xml
@@ -29,10 +29,10 @@
     ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="tabular,txt" label="Tabular in Clarion format"/>
+        <param name="infile" type="data" format="tabular,txt,csv,rdata" label="text oriented (tabular or csv) or RData files"/>
     </inputs>
     <outputs>
-        <!--data name="outfile" format="txt" /-->
+        <data name="outfile" format="tabular,txt,csv,rdata" />
     </outputs>
     <tests>
     </tests>
@@ -42,7 +42,7 @@
 
 
 
-`Wallace <https://github.molgen.mpg.de/loosolab/wilson-apps/wiki>`_ is a modular platform for reproducible modeling of species niches and distributions.
+`Wallace <https://wallaceecomod.github.io/>`_ is a flexible platform for reproducible modeling of species niches and distributions.
 
 .. class:: infomark
 

From b6f4fbb1a54657b6d5be4d350f7364652a992c1b Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Wed, 16 Oct 2019 17:05:44 +0200
Subject: [PATCH 034/853] update container input dataset folder

After verification
---
 interactivetool_wallace.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml
index 66001ee97b9f..5dbf29dfd30b 100644
--- a/interactivetool_wallace.xml
+++ b/interactivetool_wallace.xml
@@ -24,7 +24,7 @@
         </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
     </environment_variables>
     <command><![CDATA[
-        ln -s '${infile}' /srv/shiny-server/data/inputdata.txt &&
+        ln -s '${infile}' /import/ &&
         /usr/bin/shiny-server.sh
     ]]>
     </command>

From b831ce30d1753081d0f95b1bea86cabaa6a86038 Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Wed, 16 Oct 2019 17:35:00 +0200
Subject: [PATCH 035/853] only consider csv occurence file as input for now

---
 interactivetool_wallace.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml
index 5dbf29dfd30b..b860dd012679 100644
--- a/interactivetool_wallace.xml
+++ b/interactivetool_wallace.xml
@@ -29,10 +29,10 @@
     ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="tabular,txt,csv,rdata" label="text oriented (tabular or csv) or RData files"/>
+        <param name="infile" type="data" format="csv" label="csv file with for first columns: 'name', 'longitude', 'latitude' informations"/>
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular,txt,csv,rdata" />
+        <data name="outfile" format="rdata" />
     </outputs>
     <tests>
     </tests>

From f91eb0679ffb88bbe448daa6de4ee5c6c63b2a92 Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Wed, 16 Oct 2019 17:46:12 +0200
Subject: [PATCH 036/853] As we will use Galaxy_helper no need to import data
 on the fly

---
 interactivetool_wallace.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml
index b860dd012679..cd958ee3d6cc 100644
--- a/interactivetool_wallace.xml
+++ b/interactivetool_wallace.xml
@@ -24,7 +24,6 @@
         </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
     </environment_variables>
     <command><![CDATA[
-        ln -s '${infile}' /import/ &&
         /usr/bin/shiny-server.sh
     ]]>
     </command>

From 7a75856cd19c83ef5eecf15fce9f7f3af0e5d40c Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Wed, 16 Oct 2019 17:57:14 +0200
Subject: [PATCH 037/853] comment input and output

---
 interactivetool_wallace.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml
index cd958ee3d6cc..14b03ac3d3df 100644
--- a/interactivetool_wallace.xml
+++ b/interactivetool_wallace.xml
@@ -28,10 +28,10 @@
     ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="csv" label="csv file with for first columns: 'name', 'longitude', 'latitude' informations"/>
+        <!--param name="infile" type="data" format="csv" label="csv file with for first columns: 'name', 'longitude', 'latitude' informations"/-->
     </inputs>
     <outputs>
-        <data name="outfile" format="rdata" />
+        <!--data name="outfile" format="rdata" /-->
     </outputs>
     <tests>
     </tests>

From 7bdf4c9c0901924d30effc784c53aa748dd5b78a Mon Sep 17 00:00:00 2001
From: root <root@sn04.bi.uni-freiburg.de>
Date: Wed, 16 Oct 2019 19:29:53 +0200
Subject: [PATCH 038/853] wallace changes

---
 interactivetool_wallace.xml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml
index 14b03ac3d3df..4d8e2c5353b0 100644
--- a/interactivetool_wallace.xml
+++ b/interactivetool_wallace.xml
@@ -4,13 +4,14 @@
         <container type="docker">ylebras/wallace-docker</container>
     </requirements>
     <entry_points>
-        <entry_point name="Wallace visualisation of $infile.display_name" requires_domain="True">
+        <entry_point name="Wallace visualisation" requires_domain="True">
             <port>3838</port>
             <url>/sample-apps/SIG/wallace/shiny/</url>
         </entry_point>
     </entry_points>
     <environment_variables>
-        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($jupyter_notebook.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+
+        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($outfile.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
         <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
         <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
         <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
@@ -24,14 +25,16 @@
         </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
     </environment_variables>
     <command><![CDATA[
+
         /usr/bin/shiny-server.sh
+
     ]]>
     </command>
     <inputs>
         <!--param name="infile" type="data" format="csv" label="csv file with for first columns: 'name', 'longitude', 'latitude' informations"/-->
     </inputs>
     <outputs>
-        <!--data name="outfile" format="rdata" /-->
+        <data name="outfile" format="txt" />
     </outputs>
     <tests>
     </tests>

From 4dd4f0bbe25ac9674e8318f3f5cab7d4e4df7a68 Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Mon, 21 Oct 2019 21:32:14 -0700
Subject: [PATCH 039/853] Added update_time trigger functions and timestamp
 fields

---
 lib/galaxy/model/mapping.py                   |   3 +-
 .../versions/0155_add_content_update_time.py  | 104 ----------
 .../versions/0160_add_content_update_time.py  | 188 ++++++++++++++++++
 3 files changed, 190 insertions(+), 105 deletions(-)
 delete mode 100644 lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
 create mode 100644 lib/galaxy/model/migrate/versions/0160_add_content_update_time.py

diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 4d60b062b6e5..fc7260ddee2a 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -906,7 +906,8 @@
     Column("implicit_output_name", Unicode(255), nullable=True),
     Column("job_id", ForeignKey("job.id"), index=True, nullable=True),
     Column("implicit_collection_jobs_id", ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True),
-)
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now))
 
 model.LibraryDatasetCollectionAssociation.table = Table(
     "library_dataset_collection_association", metadata,
diff --git a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
deleted file mode 100644
index 5c78b30b2c76..000000000000
--- a/lib/galaxy/model/migrate/versions/0155_add_content_update_time.py
+++ /dev/null
@@ -1,104 +0,0 @@
-"""
-Adds trigger to dataset table to update history.update_time when
-contents are changed.
-"""
-from __future__ import print_function
-
-import logging
-
-from sqlalchemy import DDL, MetaData
-
-log = logging.getLogger(__name__)
-metadata = MetaData()
-
-
-def upgrade(migrate_engine):
-    print(__doc__)
-    metadata.bind = migrate_engine
-    metadata.reflect()
-    drop_update_trigger(migrate_engine)
-    install_update_trigger(migrate_engine)
-
-
-def downgrade(migrate_engine):
-    metadata.bind = migrate_engine
-    metadata.reflect()
-    drop_update_trigger(migrate_engine)
-
-
-def install_update_trigger(migrate_engine):
-    """Installs trigger on database table to update history table
-    when contents have changed. Installs a function and a trigger
-    for postgres, other sql variants only require the trigger def
-    """
-
-    if migrate_engine.name in ['postgres', 'postgresql']:
-        pg_create_trigger = DDL("""
-            CREATE FUNCTION update_history_update_time()
-                RETURNS trigger
-                LANGUAGE 'plpgsql'
-            AS $BODY$
-            BEGIN
-                UPDATE history h
-                SET update_time = current_timestamp
-                FROM history_dataset_association hda
-                WHERE h.id = hda.history_id
-                AND hda.dataset_id = NEW.id;
-                RETURN NEW;
-            END;
-            $BODY$;
-            CREATE TRIGGER trigger_dataset_aidur
-                AFTER INSERT OR DELETE OR UPDATE
-                ON dataset
-                FOR EACH ROW
-                EXECUTE PROCEDURE update_history_update_time();
-        """)
-        pg_create_trigger.execute(bind=migrate_engine)
-    else:
-        # Looks like sqlite doesn't like multiple actions in some
-        # variants, so we build 3 triggers
-        build_trigger('INSERT').execute(bind=migrate_engine)
-        build_trigger('UPDATE').execute(bind=migrate_engine)
-        build_trigger('DELETE').execute(bind=migrate_engine)
-
-
-def drop_update_trigger(migrate_engine):
-    """Drops trigger on dataset table."""
-
-    if migrate_engine.name in ['postgres', 'postgresql']:
-        pg_drop_trigger = DDL("""
-            DROP TRIGGER IF EXISTS trigger_dataset_aidur ON dataset;
-            DROP FUNCTION IF EXISTS update_history_update_time();
-        """)
-        pg_drop_trigger.execute(bind=migrate_engine)
-    else:
-        build_drop_trigger('INSERT').execute(bind=migrate_engine)
-        build_drop_trigger('UPDATE').execute(bind=migrate_engine)
-        build_drop_trigger('DELETE').execute(bind=migrate_engine)
-
-
-def build_trigger(op):
-    create_trigger_template = """
-        CREATE TRIGGER trigger_dataset_a{op_initial}r
-            AFTER {operation}
-            ON dataset
-            FOR EACH ROW
-            BEGIN
-                UPDATE history
-                SET update_time = current_timestamp
-                WHERE id IN (
-                    SELECT hda.history_id
-                    FROM history_dataset_association AS hda
-                    WHERE hda.dataset_id = {rowset}.id
-                );
-            END;
-    """
-    rs = 'OLD' if op == 'DELETE' else 'NEW'
-    sql = create_trigger_template.format(operation=op, rowset=rs, op_initial=op.lower()[0])
-    return DDL(sql)
-
-
-def build_drop_trigger(op):
-    drop_template = 'DROP TRIGGER IF EXISTS trigger_dataset_a{op_initial}r;'
-    sql = drop_template.format(op_initial=op.lower()[0])
-    return DDL(sql)
diff --git a/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
new file mode 100644
index 000000000000..72fb1597c3a3
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
@@ -0,0 +1,188 @@
+"""
+Adds timestamps to hdac table. Adds triggers to dataset, hda, hdac tables
+to update history.update_time when contents are changed.
+"""
+from __future__ import print_function
+
+import datetime
+import logging
+
+from sqlalchemy import Column, DateTime, DDL, MetaData, Table
+
+from galaxy.model.migrate.versions.util import add_column, drop_column
+
+log = logging.getLogger(__name__)
+metadata = MetaData()
+
+
+def upgrade(migrate_engine):
+    print(__doc__)
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    create_timestamps(metadata, "history_dataset_collection_association")
+    drop_update_trigger(migrate_engine)
+    install_update_trigger(migrate_engine)
+
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    drop_update_trigger(migrate_engine)
+    drop_timestamps(metadata, "history_dataset_collection_association")
+
+
+def install_update_trigger(migrate_engine):
+    """Installs trigger on dataset table to update history table
+    when contents have changed. Installs a function and a trigger
+    for postgres, other sql variants only require the trigger def
+    """
+
+    if migrate_engine.name in ['postgres', 'postgresql']:
+        pg_create_trigger = DDL("""
+            CREATE FUNCTION update_hda_update_time()
+                RETURNS trigger
+                LANGUAGE 'plpgsql'
+            AS $BODY$
+            BEGIN
+                UPDATE history_dataset_association hda
+                SET update_time = (now() at time zone 'utc')
+                WHERE hda.dataset_id = NEW.id;
+                RETURN NEW;
+            END;
+            $BODY$;
+
+            CREATE FUNCTION update_history_update_time()
+                RETURNS trigger
+                LANGUAGE 'plpgsql'
+            AS $BODY$
+            BEGIN
+                UPDATE history h
+                SET update_time = (now() at time zone 'utc')
+                WHERE h.id = NEW.history_id;
+                RETURN NEW;
+            END;
+            $BODY$;
+
+            CREATE TRIGGER trigger_dataset_aidur
+                AFTER INSERT OR DELETE OR UPDATE
+                ON dataset
+                FOR EACH ROW
+                EXECUTE PROCEDURE update_hda_update_time();
+
+            CREATE TRIGGER trigger_hda_aidur
+                AFTER INSERT OR DELETE OR UPDATE
+                ON history_dataset_association
+                FOR EACH ROW
+                EXECUTE PROCEDURE update_history_update_time();
+
+            CREATE TRIGGER trigger_hdca_aidur
+                AFTER INSERT OR DELETE OR UPDATE
+                ON history_dataset_collection_association
+                FOR EACH ROW
+                EXECUTE PROCEDURE update_history_update_time();
+        """)
+        pg_create_trigger.execute(bind=migrate_engine)
+    else:
+        install_trigger('INSERT', migrate_engine)
+        install_trigger('UPDATE', migrate_engine)
+        install_trigger('DELETE', migrate_engine)
+
+
+def drop_update_trigger(migrate_engine):
+    """Drops trigger on dataset table."""
+
+    if migrate_engine.name in ['postgres', 'postgresql']:
+        drop_trigger_stmt = """
+            DROP TRIGGER IF EXISTS trigger_hdca_aidur ON history_dataset_collection_association;
+            DROP TRIGGER IF EXISTS trigger_hda_aidur ON history_dataset_association;
+            DROP TRIGGER IF EXISTS trigger_dataset_aidur ON dataset;
+            DROP FUNCTION IF EXISTS update_hda_update_time();
+            DROP FUNCTION IF EXISTS update_history_update_time();
+        """
+        pg_drop_trigger = DDL(drop_trigger_stmt)
+        pg_drop_trigger.execute(bind=migrate_engine)
+    else:
+        build_drop_trigger('INSERT', migrate_engine)
+        build_drop_trigger('UPDATE', migrate_engine)
+        build_drop_trigger('DELETE', migrate_engine)
+
+
+def install_trigger(op, migrate_engine):
+    """Installs a single trigger"""
+
+    dataset_trigger = """
+        CREATE TRIGGER trigger_dataset_a{op_initial}r
+            AFTER {operation}
+            ON dataset
+            FOR EACH ROW
+            BEGIN
+                UPDATE history_dataset_association
+                SET update_time = current_timestamp
+                WHERE dataset_id = {rowset}.id;
+            END;
+    """
+
+    hda_trigger = """
+        CREATE TRIGGER trigger_hda_a{op_initial}r
+            AFTER {operation}
+            ON history_dataset_association
+            FOR EACH ROW
+            BEGIN
+                UPDATE history
+                SET update_time = current_timestamp
+                WHERE id = {rowset}.history_id;
+            END;
+    """
+
+    hdca_trigger = """
+        CREATE TRIGGER trigger_hdca_a{op_initial}r
+            AFTER {operation}
+            ON history_dataset_collection_association
+            FOR EACH ROW
+            BEGIN
+                UPDATE history
+                SET update_time = current_timestamp
+                WHERE id = {rowset}.history_id;
+            END;
+    """
+
+    statements = [
+        dataset_trigger,
+        hda_trigger,
+        hdca_trigger
+    ]
+
+    rs = 'OLD' if op == 'DELETE' else 'NEW'
+
+    for statement in statements:
+        sql = statement.format(operation=op, rowset=rs, op_initial=op.lower()[0])
+        create_trigger = DDL(sql)
+        create_trigger.execute(bind=migrate_engine)
+
+
+def build_drop_trigger(op, migrate_engine):
+    statements = [
+        "DROP TRIGGER IF EXISTS trigger_dataset_a{op_initial}r;",
+        "DROP TRIGGER IF EXISTS trigger_hdca_a{op_initial}r;",
+        "DROP TRIGGER IF EXISTS trigger_hda_a{op_initial}r;"
+    ]
+
+    for statement in statements:
+        sql = statement.format(op_initial=op.lower()[0])
+        drop_trigger = DDL(sql)
+        drop_trigger.execute(bind=migrate_engine)
+
+
+def create_timestamps(metadata, table_name):
+    now = datetime.datetime.utcnow
+    create_time_column = Column("create_time", DateTime, default=now)
+    update_time_column = Column("update_time", DateTime, default=now, onupdate=now)
+    target_table = Table(table_name, metadata, autoload=True)
+    add_column(create_time_column, target_table, metadata)
+    add_column(update_time_column, target_table, metadata)
+
+
+def drop_timestamps(metadata, table_name):
+    target_table = Table(table_name, metadata, autoload=True)
+    drop_column("create_time", target_table)
+    drop_column("update_time", target_table)

From cdc31f6ceed82b5db9c69e898e88da010b26b800 Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Mon, 21 Oct 2019 22:55:40 -0700
Subject: [PATCH 040/853] added timestamp filters to api

---
 lib/galaxy/managers/base.py             | 4 ++--
 lib/galaxy/managers/hdas.py             | 8 +++++++-
 lib/galaxy/managers/histories.py        | 5 +++++
 lib/galaxy/managers/history_contents.py | 8 ++++++--
 4 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index 26b0fe2e01bd..fb25e4e1ddaa 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -935,8 +935,8 @@ def _add_parsers(self):
             'encoded_id'    : {'column' : 'id', 'op': ('in'), 'val': self.parse_id_list},
             # dates can be directly passed through the orm into a filter (no need to parse into datetime object)
             'extension'     : {'op': ('eq', 'like', 'in')},
-            'create_time'   : {'op': ('le', 'ge'), 'val': self.parse_date},
-            'update_time'   : {'op': ('le', 'ge'), 'val': self.parse_date},
+            'create_time'   : {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
+            'update_time'   : {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
         })
 
     def parse_filters(self, filter_tuple_list):
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 2673ef53059b..d5c12ec18702 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -293,7 +293,8 @@ def __init__(self, app):
 
             'display_apps',
             'display_types',
-            'visualizations',
+            # 'visualizations',
+            'viz_count',
 
             'validated_state',
             'validated_state_message',
@@ -340,6 +341,7 @@ def add_serializers(self):
             'display_apps'  : self.serialize_display_apps,
             'display_types' : self.serialize_old_display_applications,
             'visualizations': self.serialize_visualization_links,
+            'viz_count'     : self.visualization_links_count,
 
             # 'url'   : url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset" ),
             # TODO: this intermittently causes a routes.GenerationException - temp use the legacy route to prevent this
@@ -417,6 +419,10 @@ def serialize_old_display_applications(self, hda, key, trans=None, **context):
 
         return display_apps
 
+    def visualization_links_count(self, hda, key, trans=None, **context):
+        links = self.serialize_visualization_links(hda, key, trans)
+        return len(links)
+
     def serialize_visualization_links(self, hda, key, trans=None, **context):
         """
         Return a list of dictionaries with links to visualization pages
diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index 31fbaf86c0e0..acbab61c6bd4 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -221,7 +221,9 @@ def __init__(self, app, **kwargs):
         #: ..note: this is a custom view for newer (2016/3) UI and should be considered volatile
         self.add_view('dev-detailed', [
             'contents_url',
+            'empty',
             'size',
+            'nice_size',
             'user_id',
             'create_time',
             'update_time',
@@ -232,6 +234,7 @@ def __init__(self, app, **kwargs):
             # 'contents_states',
             'contents_active',
             'hid_counter',
+            'non_ready_jobs'
         ], include_keys_from='summary')
 
     # assumes: outgoing to json.dumps and sanitized
@@ -393,4 +396,6 @@ def _add_parsers(self):
             # history specific
             'name'          : {'op': ('eq', 'contains', 'like')},
             'genome_build'  : {'op': ('eq', 'contains', 'like')},
+            'create_time'   : {'op': ('le', 'ge', 'gt', 'lt'), 'val': self.parse_date},
+            'update_time'   : {'op': ('le', 'ge', 'gt', 'lt'), 'val': self.parse_date},
         })
diff --git a/lib/galaxy/managers/history_contents.py b/lib/galaxy/managers/history_contents.py
index 2b51ea99647d..3280edcddfe8 100644
--- a/lib/galaxy/managers/history_contents.py
+++ b/lib/galaxy/managers/history_contents.py
@@ -492,6 +492,10 @@ def get_filter(attr, op, val):
                     return sql.column(attr) >= self.parse_date(val)
                 if op == 'le':
                     return sql.column(attr) <= self.parse_date(val)
+                if op == 'gt':
+                    return sql.column(attr) > self.parse_date(val)
+                if op == 'lt':
+                    return sql.column(attr) < self.parse_date(val)
                 self.raise_filter_err(attr, op, val, 'bad op in filter')
 
             if attr == 'state':
@@ -539,6 +543,6 @@ def _add_parsers(self):
             'name'          : {'op': ('eq', 'contains', 'like')},
             'state'         : {'op': ('eq', 'in')},
             'visible'       : {'op': ('eq'), 'val': self.parse_bool},
-            'create_time'   : {'op': ('le', 'ge'), 'val': self.parse_date},
-            'update_time'   : {'op': ('le', 'ge'), 'val': self.parse_date},
+            'create_time'   : {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
+            'update_time'   : {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
         })

From 018e2202c89e96c30161ec4e0d75ef8fbf62b25a Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Tue, 22 Oct 2019 09:08:29 -0700
Subject: [PATCH 041/853] removed features accidentally copied from another
 working branch

---
 lib/galaxy/managers/hdas.py      | 8 +-------
 lib/galaxy/managers/histories.py | 3 ---
 2 files changed, 1 insertion(+), 10 deletions(-)

diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index d5c12ec18702..2673ef53059b 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -293,8 +293,7 @@ def __init__(self, app):
 
             'display_apps',
             'display_types',
-            # 'visualizations',
-            'viz_count',
+            'visualizations',
 
             'validated_state',
             'validated_state_message',
@@ -341,7 +340,6 @@ def add_serializers(self):
             'display_apps'  : self.serialize_display_apps,
             'display_types' : self.serialize_old_display_applications,
             'visualizations': self.serialize_visualization_links,
-            'viz_count'     : self.visualization_links_count,
 
             # 'url'   : url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset" ),
             # TODO: this intermittently causes a routes.GenerationException - temp use the legacy route to prevent this
@@ -419,10 +417,6 @@ def serialize_old_display_applications(self, hda, key, trans=None, **context):
 
         return display_apps
 
-    def visualization_links_count(self, hda, key, trans=None, **context):
-        links = self.serialize_visualization_links(hda, key, trans)
-        return len(links)
-
     def serialize_visualization_links(self, hda, key, trans=None, **context):
         """
         Return a list of dictionaries with links to visualization pages
diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index acbab61c6bd4..7c231537c345 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -221,9 +221,7 @@ def __init__(self, app, **kwargs):
         #: ..note: this is a custom view for newer (2016/3) UI and should be considered volatile
         self.add_view('dev-detailed', [
             'contents_url',
-            'empty',
             'size',
-            'nice_size',
             'user_id',
             'create_time',
             'update_time',
@@ -234,7 +232,6 @@ def __init__(self, app, **kwargs):
             # 'contents_states',
             'contents_active',
             'hid_counter',
-            'non_ready_jobs'
         ], include_keys_from='summary')
 
     # assumes: outgoing to json.dumps and sanitized

From 335499fc5449dfd7ff38104ac84f5e522220425c Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Wed, 23 Oct 2019 10:25:01 -0700
Subject: [PATCH 042/853] changed triggers to before update, added conditional
 column adds

---
 .../versions/0160_add_content_update_time.py  | 80 ++++++++++---------
 1 file changed, 42 insertions(+), 38 deletions(-)

diff --git a/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
index 72fb1597c3a3..02f2291f89b9 100644
--- a/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
@@ -28,7 +28,7 @@ def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
     drop_update_trigger(migrate_engine)
-    drop_timestamps(metadata, "history_dataset_collection_association")
+    # drop_timestamps(metadata, "history_dataset_collection_association")
 
 
 def install_update_trigger(migrate_engine):
@@ -39,44 +39,46 @@ def install_update_trigger(migrate_engine):
 
     if migrate_engine.name in ['postgres', 'postgresql']:
         pg_create_trigger = DDL("""
-            CREATE FUNCTION update_hda_update_time()
+            CREATE OR REPLACE FUNCTION update_hda_update_time()
                 RETURNS trigger
                 LANGUAGE 'plpgsql'
             AS $BODY$
             BEGIN
                 UPDATE history_dataset_association hda
                 SET update_time = (now() at time zone 'utc')
-                WHERE hda.dataset_id = NEW.id;
+                WHERE hda.dataset_id = NEW.id
+                AND hda.update_time < (now() at time zone 'utc');
                 RETURN NEW;
             END;
             $BODY$;
 
-            CREATE FUNCTION update_history_update_time()
+            CREATE OR REPLACE FUNCTION update_history_update_time()
                 RETURNS trigger
                 LANGUAGE 'plpgsql'
             AS $BODY$
             BEGIN
                 UPDATE history h
                 SET update_time = (now() at time zone 'utc')
-                WHERE h.id = NEW.history_id;
+                WHERE h.id = NEW.history_id
+                AND h.update_time < (now() at time zone 'utc');
                 RETURN NEW;
             END;
             $BODY$;
 
-            CREATE TRIGGER trigger_dataset_aidur
-                AFTER INSERT OR DELETE OR UPDATE
+            CREATE TRIGGER trigger_dataset_bidur
+                BEFORE INSERT OR DELETE OR UPDATE
                 ON dataset
                 FOR EACH ROW
                 EXECUTE PROCEDURE update_hda_update_time();
 
-            CREATE TRIGGER trigger_hda_aidur
-                AFTER INSERT OR DELETE OR UPDATE
+            CREATE TRIGGER trigger_hda_bidur
+                BEFORE INSERT OR DELETE OR UPDATE
                 ON history_dataset_association
                 FOR EACH ROW
                 EXECUTE PROCEDURE update_history_update_time();
 
-            CREATE TRIGGER trigger_hdca_aidur
-                AFTER INSERT OR DELETE OR UPDATE
+            CREATE TRIGGER trigger_hdca_bidur
+                BEFORE INSERT OR DELETE OR UPDATE
                 ON history_dataset_collection_association
                 FOR EACH ROW
                 EXECUTE PROCEDURE update_history_update_time();
@@ -93,11 +95,8 @@ def drop_update_trigger(migrate_engine):
 
     if migrate_engine.name in ['postgres', 'postgresql']:
         drop_trigger_stmt = """
-            DROP TRIGGER IF EXISTS trigger_hdca_aidur ON history_dataset_collection_association;
-            DROP TRIGGER IF EXISTS trigger_hda_aidur ON history_dataset_association;
-            DROP TRIGGER IF EXISTS trigger_dataset_aidur ON dataset;
-            DROP FUNCTION IF EXISTS update_hda_update_time();
-            DROP FUNCTION IF EXISTS update_history_update_time();
+            DROP FUNCTION IF EXISTS update_hda_update_time() CASCADE;
+            DROP FUNCTION IF EXISTS update_history_update_time() CASCADE;
         """
         pg_drop_trigger = DDL(drop_trigger_stmt)
         pg_drop_trigger.execute(bind=migrate_engine)
@@ -111,38 +110,41 @@ def install_trigger(op, migrate_engine):
     """Installs a single trigger"""
 
     dataset_trigger = """
-        CREATE TRIGGER trigger_dataset_a{op_initial}r
-            AFTER {operation}
+        CREATE TRIGGER trigger_dataset_b{op_initial}r
+            BEFORE {operation}
             ON dataset
             FOR EACH ROW
             BEGIN
                 UPDATE history_dataset_association
                 SET update_time = current_timestamp
-                WHERE dataset_id = {rowset}.id;
+                WHERE dataset_id = {rowset}.id
+                AND update_time < current_timestamp;
             END;
     """
 
     hda_trigger = """
-        CREATE TRIGGER trigger_hda_a{op_initial}r
-            AFTER {operation}
+        CREATE TRIGGER trigger_hda_b{op_initial}r
+            BEFORE {operation}
             ON history_dataset_association
             FOR EACH ROW
             BEGIN
                 UPDATE history
                 SET update_time = current_timestamp
-                WHERE id = {rowset}.history_id;
+                WHERE id = {rowset}.history_id
+                AND update_time < current_timestamp;
             END;
     """
 
     hdca_trigger = """
-        CREATE TRIGGER trigger_hdca_a{op_initial}r
-            AFTER {operation}
+        CREATE TRIGGER trigger_hdca_b{op_initial}r
+            BEFORE {operation}
             ON history_dataset_collection_association
             FOR EACH ROW
             BEGIN
                 UPDATE history
                 SET update_time = current_timestamp
-                WHERE id = {rowset}.history_id;
+                WHERE id = {rowset}.history_id
+                AND update_time < current_timestamp;
             END;
     """
 
@@ -162,9 +164,9 @@ def install_trigger(op, migrate_engine):
 
 def build_drop_trigger(op, migrate_engine):
     statements = [
-        "DROP TRIGGER IF EXISTS trigger_dataset_a{op_initial}r;",
-        "DROP TRIGGER IF EXISTS trigger_hdca_a{op_initial}r;",
-        "DROP TRIGGER IF EXISTS trigger_hda_a{op_initial}r;"
+        "DROP TRIGGER IF EXISTS trigger_dataset_b{op_initial}r;",
+        "DROP TRIGGER IF EXISTS trigger_hdca_b{op_initial}r;",
+        "DROP TRIGGER IF EXISTS trigger_hda_b{op_initial}r;"
     ]
 
     for statement in statements:
@@ -175,14 +177,16 @@ def build_drop_trigger(op, migrate_engine):
 
 def create_timestamps(metadata, table_name):
     now = datetime.datetime.utcnow
-    create_time_column = Column("create_time", DateTime, default=now)
-    update_time_column = Column("update_time", DateTime, default=now, onupdate=now)
     target_table = Table(table_name, metadata, autoload=True)
-    add_column(create_time_column, target_table, metadata)
-    add_column(update_time_column, target_table, metadata)
-
-
-def drop_timestamps(metadata, table_name):
-    target_table = Table(table_name, metadata, autoload=True)
-    drop_column("create_time", target_table)
-    drop_column("update_time", target_table)
+    if 'create_time' not in target_table.c:
+        create_time_column = Column("create_time", DateTime, default=now)
+        add_column(create_time_column, target_table, metadata)
+    if 'update_time' not in target_table.c:
+        update_time_column = Column("update_time", DateTime, default=now, onupdate=now)
+        add_column(update_time_column, target_table, metadata)
+
+
+# def drop_timestamps(metadata, table_name):
+#     target_table = Table(table_name, metadata, autoload=True)
+#     drop_column("create_time", target_table)
+#     drop_column("update_time", target_table)

From 4599cabec1100eab48286e6caa66d065061d9572 Mon Sep 17 00:00:00 2001
From: root <root@sn04.bi.uni-freiburg.de>
Date: Wed, 23 Oct 2019 19:43:04 +0200
Subject: [PATCH 043/853] update askomics to version 1.0

---
 interactivetool_askomics.xml | 56 ++++++++++++++++++++----------------
 1 file changed, 32 insertions(+), 24 deletions(-)

diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml
index b4cb6bff0d18..2dd06fe28ba2 100644
--- a/interactivetool_askomics.xml
+++ b/interactivetool_askomics.xml
@@ -1,16 +1,25 @@
-<tool id="interactive_tool_askomics" tool_type="interactive" name="AskOmics" version="0.1">
-    <description>AskOmics, a visual SPARQL query builder</description>
+<tool id="interactive_tool_askomics" tool_type="interactive" name="AskOmics" version="1.0">
+    <description>a visual SPARQL query builder</description>
     <requirements>
-        <container type="docker">askomics/askomics-ie:19.01.3</container>
+        <container type="docker">askomics/flaskomics-with-dependencies:3.1.1</container>
     </requirements>
     <entry_points>
         <entry_point name="AskOmics instance on $infile.display_name" requires_domain="True">
-            <port>6543</port>
-            <url>/login_api_gie?key=${__user_name__}</url>
+            <port>5000</port>
+            <url>/loginapikey/${__user_name__}</url>
         </entry_point>
     </entry_points>
     <environment_variables>
+        <!-- AskOmics user -->
+        <environment_variable name="CREATE_USER">true</environment_variable>
+        <environment_variable name="USER_FIRST_NAME">${__user_name__}</environment_variable>
+        <environment_variable name="USER_LAST_NAME">Galaxy</environment_variable>
+        <environment_variable name="USER_USERNAME">${__user_name__}</environment_variable>
+        <environment_variable name="USER_EMAIL">${__user_email__}</environment_variable>
+        <environment_variable name="USER_APIKEY">${__user_name__}</environment_variable>
+        <!-- Galaxy info -->
         <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+
         <environment_variable name="GALAXY_API_KEY" strip="True">
             #if $__user__:
                 #for $api_key in $__user__.api_keys:
@@ -19,27 +28,26 @@
                 #end for
             #end if
         </environment_variable>
-        <environment_variable name="GALAXY_USER_NAME">${__user_name__}</environment_variable>
-        <environment_variable name="GALAXY_USER_EMAIL">${__user_email__}</environment_variable>
-        <environment_variable name="ASKOMICS_API_KEY">${__user_name__}</environment_variable><!--FIXME: use a random string instead of the username-->
+        <!-- AskOmics config -->
+        <environment_variable name="DEPMODE">prod</environment_variable>
+        <environment_variable name="MAX_CELERY_QUEUE">1</environment_variable>
+        <environment_variable name="ASKO_askomics_subtitle">Galaxy</environment_variable>
+        <environment_variable name="ASKO_askomics_footer_message">AskOmics Interactive Tool for Galaxy</environment_variable>
+        <environment_variable name="ASKO_askomics_data_directory">/tmp/askomics-it</environment_variable>
+        <environment_variable name="ASKO_askomics_database_path">/tmp/askomics-it/database.db</environment_variable>
+        <environment_variable name="ASKO_triplestore_load_url">http://localhost:5000</environment_variable>
+        <!-- Virtuoso config -->
+        <environment_variable name="SPARQL_UPDATE">true</environment_variable>
+        <!-- 
+        Update the following environment variables according to how much memory you want to allow to virtuoso
+        see https://github.com/askomics/flaskomics-docker-compose#configure-virtuoso for help
+         -->
+        <environment_variable name="VIRT_Parameters_NumberOfBuffers">85000</environment_variable>
+        <environment_variable name="VIRT_Parameters_MaxDirtyBuffers">65000</environment_variable>
     </environment_variables>
     <command><![CDATA[
         #import re
 
-        ## AskOmics configuration, don't change anything here
-        export ASKO_files_dir='/tmp/askomics-ie' &&
-        export ASKO_database_path='/tmp/askomics-ie/database.db' &&
-        export ASKO_load_url='http://localhost:6543' &&
-
-        ## Triplestore configuration. Update VIRT_Parameters_NumberOfBuffers and 
-        ## VIRT_Parameters_MaxDirtyBuffers according to https://github.com/askomics/askomics-docker-compose/tree/master/virtuoso#configuration
-        export SPARQL_UPDATE='true' &&
-        export VIRT_Parameters_NumberOfBuffers='10000'  &&
-        export VIRT_Parameters_MaxDirtyBuffers='6000'  &&
-        export VIRT_SPARQL_ResultSetMaxRows='100000' &&
-        export VIRT_SPARQL_MaxQueryCostEstimationTime='40000' &&
-        export VIRT_SPARQL_MaxQueryExecutionTime='40000' &&
-
         #set link_name = re.sub('[^\w_]', '_', $infile.element_identifier)
         #if $infile.ext == 'tabular':
             #set link_name = $link_name + '.tsv'
@@ -52,11 +60,11 @@
         mkdir -p /import &&
         ln -s '$infile' '/import/$link_name' &&
 
-        bash /start.sh
+        /askomics/start_all.sh
     ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="tabular,gff,gff3,bed,interval" label="A datasets with genomic coordinates"/>
+        <param name="infile" type="data" optional="true" format="tabular,gff,gff3,interval" label="A dataset to load into AskOmics"/>
     </inputs>
     <outputs>
         <data name="outfile" format="txt" />

From 691b7f039781a3052706b5eb82ae1a53b5984d8b Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Wed, 23 Oct 2019 10:48:33 -0700
Subject: [PATCH 044/853] removed drop column because it was requested that
 update_time go in the initial db mappings

---
 .../model/migrate/versions/0160_add_content_update_time.py      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
index 02f2291f89b9..512c97c13cba 100644
--- a/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
@@ -9,7 +9,7 @@
 
 from sqlalchemy import Column, DateTime, DDL, MetaData, Table
 
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import add_column
 
 log = logging.getLogger(__name__)
 metadata = MetaData()

From 2ffb21c87b5e1da4315df67368755dc64a6127a0 Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Wed, 23 Oct 2019 11:58:18 -0700
Subject: [PATCH 045/853] restored drop-timestamps because this migration only
 operates on existing databases

---
 .../migrate/versions/0160_add_content_update_time.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
index 512c97c13cba..dbf8c84598ce 100644
--- a/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
@@ -9,7 +9,7 @@
 
 from sqlalchemy import Column, DateTime, DDL, MetaData, Table
 
-from galaxy.model.migrate.versions.util import add_column
+from galaxy.model.migrate.versions.util import add_column, drop_column
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -28,7 +28,7 @@ def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
     drop_update_trigger(migrate_engine)
-    # drop_timestamps(metadata, "history_dataset_collection_association")
+    drop_timestamps(metadata, "history_dataset_collection_association")
 
 
 def install_update_trigger(migrate_engine):
@@ -186,7 +186,7 @@ def create_timestamps(metadata, table_name):
         add_column(update_time_column, target_table, metadata)
 
 
-# def drop_timestamps(metadata, table_name):
-#     target_table = Table(table_name, metadata, autoload=True)
-#     drop_column("create_time", target_table)
-#     drop_column("update_time", target_table)
+def drop_timestamps(metadata, table_name):
+    target_table = Table(table_name, metadata, autoload=True)
+    drop_column("create_time", target_table)
+    drop_column("update_time", target_table)

From 954e54170f3fe416536de2eb5a1ecb5fcd48ace1 Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Thu, 24 Oct 2019 01:38:40 -0700
Subject: [PATCH 046/853] Referenced galaxy aliased orm.now

---
 .../model/migrate/versions/0160_add_content_update_time.py    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
index dbf8c84598ce..41efe6cbc670 100644
--- a/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
@@ -4,13 +4,14 @@
 """
 from __future__ import print_function
 
-import datetime
 import logging
 
 from sqlalchemy import Column, DateTime, DDL, MetaData, Table
 
 from galaxy.model.migrate.versions.util import add_column, drop_column
 
+from galaxy.model.orm.now import now
+
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
@@ -176,7 +177,6 @@ def build_drop_trigger(op, migrate_engine):
 
 
 def create_timestamps(metadata, table_name):
-    now = datetime.datetime.utcnow
     target_table = Table(table_name, metadata, autoload=True)
     if 'create_time' not in target_table.c:
         create_time_column = Column("create_time", DateTime, default=now)

From 8bbc6f69feda269e8b04208cf9577c4381721954 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 24 Oct 2019 17:12:21 -0400
Subject: [PATCH 047/853] Galaxy InteractiveTools cluster fixes from EU

---
 interactivetool_jupyter_notebook.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml
index 9dd3e36d3ee4..60cdc00253f5 100644
--- a/interactivetool_jupyter_notebook.xml
+++ b/interactivetool_jupyter_notebook.xml
@@ -39,7 +39,7 @@
             ## copy default notebook
             cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
             jupyter trust ./ipython_galaxy_notebook.ipynb &&
-            jupyter lab --no-browser --NotebookApp.shutdown_button=True &&
+            jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
             cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
 
         #else:
@@ -50,7 +50,7 @@
             #if $mode.run_it:
                 jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
             #else:
-                jupyter lab --no-browser --NotebookApp.shutdown_button=True &&
+                jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
             #end if
             cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
         #end if
@@ -88,13 +88,13 @@
     The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations,
     visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization,
     machine learning, and much more.
-    
+
     Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
     do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter.
-    
+
     You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset.
     If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history.
-    
+
     You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function.
     </help>
 </tool>

From a408f3e479f4a17cf53756ddf106fbde009791ad Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 28 Oct 2019 15:58:40 -0400
Subject: [PATCH 048/853] Structured access to Galaxy internals for ITs.

---
 interactivetool_askomics.xml         | 11 ++---------
 interactivetool_jupyter_notebook.xml | 15 ++++-----------
 2 files changed, 6 insertions(+), 20 deletions(-)

diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml
index c1ce9d3bd115..7f997b54e632 100644
--- a/interactivetool_askomics.xml
+++ b/interactivetool_askomics.xml
@@ -10,15 +10,8 @@
         </entry_point>
     </entry_points>
     <environment_variables>
-        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="API_KEY" strip="True">
-            #if $__user__:
-                #for $api_key in $__user__.api_keys:
-                    ${api_key.key}
-                    #break
-                #end for
-            #end if
-        </environment_variable>
+        <environment_variable name="GALAXY_URL">$__galaxy_url</environment_variable>
+        <environment_variable name="API_KEY" inject="api_key" />
     </environment_variables>
     <command><![CDATA[
         #import re
diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml
index 60cdc00253f5..44c972c2eb5b 100644
--- a/interactivetool_jupyter_notebook.xml
+++ b/interactivetool_jupyter_notebook.xml
@@ -9,18 +9,11 @@
         </entry_point>
     </entry_points>
     <environment_variables>
-        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($jupyter_notebook.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="HISTORY_ID">$__history_id</environment_variable>
+        <environment_variable name="REMOTE_HOST">$__galaxy_url</environment_variable>
         <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
-        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="API_KEY" strip="True">
-            #if $__user__:
-                #for $api_key in $__user__.api_keys:
-                    ${api_key.key}
-                    #break
-                #end for
-            #end if
-        </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
+        <environment_variable name="GALAXY_URL">$__galaxy_url</environment_variable>
+        <environment_variable name="API_KEY" inject="api_key" />
     </environment_variables>
     <command detect_errors="aggressive"><![CDATA[
         #import re

From ee5effc81025d31abe7c28aa5595e82d0cb82169 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 29 Oct 2019 08:29:02 -0400
Subject: [PATCH 049/853] Cleanup structured IT internals access commit.

- Unit test fixes and added tests.
- Change __history_id to __history_id__ per comment from @bgruening
---
 interactivetool_askomics.xml         | 2 +-
 interactivetool_jupyter_notebook.xml | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml
index 7f997b54e632..b5f0b4d56a4a 100644
--- a/interactivetool_askomics.xml
+++ b/interactivetool_askomics.xml
@@ -10,7 +10,7 @@
         </entry_point>
     </entry_points>
     <environment_variables>
-        <environment_variable name="GALAXY_URL">$__galaxy_url</environment_variable>
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
         <environment_variable name="API_KEY" inject="api_key" />
     </environment_variables>
     <command><![CDATA[
diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml
index 44c972c2eb5b..914a50a0ec8a 100644
--- a/interactivetool_jupyter_notebook.xml
+++ b/interactivetool_jupyter_notebook.xml
@@ -9,10 +9,10 @@
         </entry_point>
     </entry_points>
     <environment_variables>
-        <environment_variable name="HISTORY_ID">$__history_id</environment_variable>
-        <environment_variable name="REMOTE_HOST">$__galaxy_url</environment_variable>
+        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
+        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
         <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
-        <environment_variable name="GALAXY_URL">$__galaxy_url</environment_variable>
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
         <environment_variable name="API_KEY" inject="api_key" />
     </environment_variables>
     <command detect_errors="aggressive"><![CDATA[

From 7b3a98cea39163f3c2357b47a093f847d036eefd Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Tue, 12 Nov 2019 00:59:32 +0100
Subject: [PATCH 050/853] add pyiron tool

---
 interactivetool_pyiron.xml | 96 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 96 insertions(+)
 create mode 100644 interactivetool_pyiron.xml

diff --git a/interactivetool_pyiron.xml b/interactivetool_pyiron.xml
new file mode 100644
index 000000000000..d56abbb3b666
--- /dev/null
+++ b/interactivetool_pyiron.xml
@@ -0,0 +1,96 @@
+<tool id="interactive_tool_pyiron" tool_type="interactive" name="PyIron Interactive Jupyter Notebook" version="0.1">
+    <requirements>
+        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:pyiron</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="PyIron" requires_domain="True">
+            <port>8888</port>
+            <url>ipython/lab</url>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
+        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
+        <environment_variable name="API_KEY" inject="api_key" />
+    </environment_variables>
+    <command detect_errors="aggressive"><![CDATA[
+        #import re
+        export GALAXY_WORKING_DIR=`pwd` &&
+        mkdir -p ./jupyter/outputs/ &&
+        mkdir -p ./jupyter/data &&
+
+        #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
+        ln -sf '$input' './jupyter/data/${cleaned_name}' &&
+
+        ## change into the directory where the notebooks are located
+        cd ./jupyter/ &&
+        export PATH=/home/jovyan/.local/bin:\$PATH &&
+
+        #if $mode.mode_select == 'scratch':
+            ## copy default notebook
+            cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
+            jupyter trust ./ipython_galaxy_notebook.ipynb &&
+            jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
+
+        #else:
+            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
+            cp '$mode.ipynb' ./${cleaned_name}.ipynb &&
+            jupyter trust ./${cleaned_name}.ipynb &&
+
+            #if $mode.run_it:
+                jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
+            #else:
+                jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+            #end if
+            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
+        #end if
+    ]]>
+    </command>
+    <inputs>
+
+        <conditional name="mode">
+            <param name="mode_select" type="select" label="Do you already have a notebook?" help="If not, no problem we will provide you with a default one.">
+                <option value="scratch">Start with a fresh notebook</option>
+                <option value="previous">Load a previous notebook</option>
+            </param>
+            <when value="scratch"/>
+            <when value="previous">
+                <param name="ipynb" type="data" format="ipynb" label="IPython Notebook"/>
+                <param name="run_it" type="boolean" truevalue="true" falsevalue="false" label="Execute notebook and return a new one."
+                    help="This option is useful in workflows when you just want to execute a notebook and not dive into the webfrontend."/>
+            </when>
+        </conditional>
+        <param name="input" type="data" optional="true" label="Include data into the environment"/>
+
+    </inputs>
+    <outputs>
+        <data name="jupyter_notebook" format="ipynb" label="Executed Notebook"></data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="mode" value="previous" />
+            <param name="ipynb" value="test.ipynb" />
+            <param name="run_it" value="true" />
+            <output name="jupyter_notebook" file="test.ipynb" ftype="ipynb"/>
+        </test>
+    </tests>
+    <help>
+
+    pyiron - an integrated development environment (IDE) for computational materials science. It combines several tools in a common platform:
+
+    The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations,
+    visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization,
+    machine learning, and much more.
+
+    Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
+    do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter.
+
+    You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset.
+    If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history.
+
+    You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function.
+    </help>
+</tool>

From 9eabec14dffb25a8a69bf8d186d26f710fd7db76 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Tue, 12 Nov 2019 09:37:05 +0100
Subject: [PATCH 051/853] add new envs to pyiron

---
 interactivetool_pyiron.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/interactivetool_pyiron.xml b/interactivetool_pyiron.xml
index d56abbb3b666..0f5ac65a00f1 100644
--- a/interactivetool_pyiron.xml
+++ b/interactivetool_pyiron.xml
@@ -14,10 +14,13 @@
         <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
         <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
         <environment_variable name="API_KEY" inject="api_key" />
+        <environment_variable name="PYIRONRESOURCEPATHS">/home/jovyan/resources</environment_variable>
     </environment_variables>
     <command detect_errors="aggressive"><![CDATA[
         #import re
         export GALAXY_WORKING_DIR=`pwd` &&
+        export PYIRONPROJECTPATHS = ${PWD} &&
+
         mkdir -p ./jupyter/outputs/ &&
         mkdir -p ./jupyter/data &&
 

From 30166c777dc5f91534760c3447dee7bac2ce3a4e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Tue, 12 Nov 2019 10:48:13 +0100
Subject: [PATCH 052/853] small edits to pyiron

---
 interactivetool_pyiron.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/interactivetool_pyiron.xml b/interactivetool_pyiron.xml
index 0f5ac65a00f1..9657bc87c3bd 100644
--- a/interactivetool_pyiron.xml
+++ b/interactivetool_pyiron.xml
@@ -3,7 +3,7 @@
         <container type="docker">quay.io/bgruening/docker-jupyter-notebook:pyiron</container>
     </requirements>
     <entry_points>
-        <entry_point name="PyIron" requires_domain="True">
+        <entry_point name="PyIron Workbench" requires_domain="True">
             <port>8888</port>
             <url>ipython/lab</url>
         </entry_point>
@@ -70,7 +70,7 @@
 
     </inputs>
     <outputs>
-        <data name="jupyter_notebook" format="ipynb" label="Executed Notebook"></data>
+        <data name="jupyter_notebook" format="ipynb" label="PyIron Workbench"></data>
     </outputs>
     <tests>
         <test expect_num_outputs="1">

From 8c752d470358d1fc561764299aa7a40092ba2ca9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Tue, 12 Nov 2019 10:55:57 +0100
Subject: [PATCH 053/853] use proper PWD

---
 interactivetool_pyiron.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/interactivetool_pyiron.xml b/interactivetool_pyiron.xml
index 9657bc87c3bd..68d590407278 100644
--- a/interactivetool_pyiron.xml
+++ b/interactivetool_pyiron.xml
@@ -18,8 +18,8 @@
     </environment_variables>
     <command detect_errors="aggressive"><![CDATA[
         #import re
-        export GALAXY_WORKING_DIR=`pwd` &&
-        export PYIRONPROJECTPATHS = ${PWD} &&
+        export GALAXY_WORKING_DIR=\${PWD} &&
+        export PYIRONPROJECTPATHS=\${PWD} &&
 
         mkdir -p ./jupyter/outputs/ &&
         mkdir -p ./jupyter/data &&

From 94b3109129a996d07d58d9ef850c23f256972a18 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Tue, 12 Nov 2019 13:54:09 +0100
Subject: [PATCH 054/853] Update interactivetool_pyiron.xml

---
 interactivetool_pyiron.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/interactivetool_pyiron.xml b/interactivetool_pyiron.xml
index 68d590407278..69caecdf71b7 100644
--- a/interactivetool_pyiron.xml
+++ b/interactivetool_pyiron.xml
@@ -29,6 +29,7 @@
 
         ## change into the directory where the notebooks are located
         cd ./jupyter/ &&
+        cp \${HOME}/examples/* ./ &&
         export PATH=/home/jovyan/.local/bin:\$PATH &&
 
         #if $mode.mode_select == 'scratch':

From f953b39beacb6f628a08a6c5fba236891e0c214f Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Wed, 13 Nov 2019 16:29:48 +0100
Subject: [PATCH 055/853] add guacamole_desktop

---
 interactivetool_guacamole_desktop.xml | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 interactivetool_guacamole_desktop.xml

diff --git a/interactivetool_guacamole_desktop.xml b/interactivetool_guacamole_desktop.xml
new file mode 100644
index 000000000000..a63ce1089911
--- /dev/null
+++ b/interactivetool_guacamole_desktop.xml
@@ -0,0 +1,26 @@
+<tool id="interactive_tool_guacamole_desktop" tool_type="interactive" name="Ubuntu XFCE Desktop" version="0.1">
+    <requirements>
+        <container type="docker">cyverse/ubuntu18-xfce-desktop</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Remote Desktop" requires_domain="True">
+            <port>8000</port>
+        </entry_point>
+    </entry_points>
+    <command><![CDATA[
+        sudo -E /startup.sh
+    ]]>
+    </command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        Simple Ubuntu XFCE all-in-one desktop.
+        Username: "user"
+        Password: "password"
+    </help>
+</tool>

From cbf5cd49c42164b7d1643029affe5145d159b543 Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Wed, 13 Nov 2019 15:13:17 -0800
Subject: [PATCH 056/853] Moved triggers into main model init re:8300

---
 lib/galaxy/model/mapping.py                   |   2 +
 .../versions/0160_add_content_update_time.py  | 192 ------------------
 .../versions/0161_add_content_update_time.py  |  47 +++++
 lib/galaxy/model/triggers.py                  | 155 ++++++++++++++
 4 files changed, 204 insertions(+), 192 deletions(-)
 delete mode 100644 lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
 create mode 100644 lib/galaxy/model/migrate/versions/0161_add_content_update_time.py
 create mode 100644 lib/galaxy/model/triggers.py

diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index fb4b4a53a4b5..85b57324a65a 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -42,6 +42,7 @@
 from galaxy.model.orm.engine_factory import build_engine
 from galaxy.model.orm.now import now
 from galaxy.model.security import GalaxyRBACAgent
+from galaxy.model.triggers import install_timestamp_triggers
 
 log = logging.getLogger(__name__)
 
@@ -2855,6 +2856,7 @@ def init(file_path, url, engine_options=None, create_tables=False, map_install_m
     # Create tables if needed
     if create_tables:
         metadata.create_all()
+        install_timestamp_triggers(engine)
         # metadata.engine.commit()
 
     result.create_tables = create_tables
diff --git a/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
deleted file mode 100644
index 41efe6cbc670..000000000000
--- a/lib/galaxy/model/migrate/versions/0160_add_content_update_time.py
+++ /dev/null
@@ -1,192 +0,0 @@
-"""
-Adds timestamps to hdac table. Adds triggers to dataset, hda, hdac tables
-to update history.update_time when contents are changed.
-"""
-from __future__ import print_function
-
-import logging
-
-from sqlalchemy import Column, DateTime, DDL, MetaData, Table
-
-from galaxy.model.migrate.versions.util import add_column, drop_column
-
-from galaxy.model.orm.now import now
-
-log = logging.getLogger(__name__)
-metadata = MetaData()
-
-
-def upgrade(migrate_engine):
-    print(__doc__)
-    metadata.bind = migrate_engine
-    metadata.reflect()
-    create_timestamps(metadata, "history_dataset_collection_association")
-    drop_update_trigger(migrate_engine)
-    install_update_trigger(migrate_engine)
-
-
-def downgrade(migrate_engine):
-    metadata.bind = migrate_engine
-    metadata.reflect()
-    drop_update_trigger(migrate_engine)
-    drop_timestamps(metadata, "history_dataset_collection_association")
-
-
-def install_update_trigger(migrate_engine):
-    """Installs trigger on dataset table to update history table
-    when contents have changed. Installs a function and a trigger
-    for postgres, other sql variants only require the trigger def
-    """
-
-    if migrate_engine.name in ['postgres', 'postgresql']:
-        pg_create_trigger = DDL("""
-            CREATE OR REPLACE FUNCTION update_hda_update_time()
-                RETURNS trigger
-                LANGUAGE 'plpgsql'
-            AS $BODY$
-            BEGIN
-                UPDATE history_dataset_association hda
-                SET update_time = (now() at time zone 'utc')
-                WHERE hda.dataset_id = NEW.id
-                AND hda.update_time < (now() at time zone 'utc');
-                RETURN NEW;
-            END;
-            $BODY$;
-
-            CREATE OR REPLACE FUNCTION update_history_update_time()
-                RETURNS trigger
-                LANGUAGE 'plpgsql'
-            AS $BODY$
-            BEGIN
-                UPDATE history h
-                SET update_time = (now() at time zone 'utc')
-                WHERE h.id = NEW.history_id
-                AND h.update_time < (now() at time zone 'utc');
-                RETURN NEW;
-            END;
-            $BODY$;
-
-            CREATE TRIGGER trigger_dataset_bidur
-                BEFORE INSERT OR DELETE OR UPDATE
-                ON dataset
-                FOR EACH ROW
-                EXECUTE PROCEDURE update_hda_update_time();
-
-            CREATE TRIGGER trigger_hda_bidur
-                BEFORE INSERT OR DELETE OR UPDATE
-                ON history_dataset_association
-                FOR EACH ROW
-                EXECUTE PROCEDURE update_history_update_time();
-
-            CREATE TRIGGER trigger_hdca_bidur
-                BEFORE INSERT OR DELETE OR UPDATE
-                ON history_dataset_collection_association
-                FOR EACH ROW
-                EXECUTE PROCEDURE update_history_update_time();
-        """)
-        pg_create_trigger.execute(bind=migrate_engine)
-    else:
-        install_trigger('INSERT', migrate_engine)
-        install_trigger('UPDATE', migrate_engine)
-        install_trigger('DELETE', migrate_engine)
-
-
-def drop_update_trigger(migrate_engine):
-    """Drops trigger on dataset table."""
-
-    if migrate_engine.name in ['postgres', 'postgresql']:
-        drop_trigger_stmt = """
-            DROP FUNCTION IF EXISTS update_hda_update_time() CASCADE;
-            DROP FUNCTION IF EXISTS update_history_update_time() CASCADE;
-        """
-        pg_drop_trigger = DDL(drop_trigger_stmt)
-        pg_drop_trigger.execute(bind=migrate_engine)
-    else:
-        build_drop_trigger('INSERT', migrate_engine)
-        build_drop_trigger('UPDATE', migrate_engine)
-        build_drop_trigger('DELETE', migrate_engine)
-
-
-def install_trigger(op, migrate_engine):
-    """Installs a single trigger"""
-
-    dataset_trigger = """
-        CREATE TRIGGER trigger_dataset_b{op_initial}r
-            BEFORE {operation}
-            ON dataset
-            FOR EACH ROW
-            BEGIN
-                UPDATE history_dataset_association
-                SET update_time = current_timestamp
-                WHERE dataset_id = {rowset}.id
-                AND update_time < current_timestamp;
-            END;
-    """
-
-    hda_trigger = """
-        CREATE TRIGGER trigger_hda_b{op_initial}r
-            BEFORE {operation}
-            ON history_dataset_association
-            FOR EACH ROW
-            BEGIN
-                UPDATE history
-                SET update_time = current_timestamp
-                WHERE id = {rowset}.history_id
-                AND update_time < current_timestamp;
-            END;
-    """
-
-    hdca_trigger = """
-        CREATE TRIGGER trigger_hdca_b{op_initial}r
-            BEFORE {operation}
-            ON history_dataset_collection_association
-            FOR EACH ROW
-            BEGIN
-                UPDATE history
-                SET update_time = current_timestamp
-                WHERE id = {rowset}.history_id
-                AND update_time < current_timestamp;
-            END;
-    """
-
-    statements = [
-        dataset_trigger,
-        hda_trigger,
-        hdca_trigger
-    ]
-
-    rs = 'OLD' if op == 'DELETE' else 'NEW'
-
-    for statement in statements:
-        sql = statement.format(operation=op, rowset=rs, op_initial=op.lower()[0])
-        create_trigger = DDL(sql)
-        create_trigger.execute(bind=migrate_engine)
-
-
-def build_drop_trigger(op, migrate_engine):
-    statements = [
-        "DROP TRIGGER IF EXISTS trigger_dataset_b{op_initial}r;",
-        "DROP TRIGGER IF EXISTS trigger_hdca_b{op_initial}r;",
-        "DROP TRIGGER IF EXISTS trigger_hda_b{op_initial}r;"
-    ]
-
-    for statement in statements:
-        sql = statement.format(op_initial=op.lower()[0])
-        drop_trigger = DDL(sql)
-        drop_trigger.execute(bind=migrate_engine)
-
-
-def create_timestamps(metadata, table_name):
-    target_table = Table(table_name, metadata, autoload=True)
-    if 'create_time' not in target_table.c:
-        create_time_column = Column("create_time", DateTime, default=now)
-        add_column(create_time_column, target_table, metadata)
-    if 'update_time' not in target_table.c:
-        update_time_column = Column("update_time", DateTime, default=now, onupdate=now)
-        add_column(update_time_column, target_table, metadata)
-
-
-def drop_timestamps(metadata, table_name):
-    target_table = Table(table_name, metadata, autoload=True)
-    drop_column("create_time", target_table)
-    drop_column("update_time", target_table)
diff --git a/lib/galaxy/model/migrate/versions/0161_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0161_add_content_update_time.py
new file mode 100644
index 000000000000..7b85a4f68867
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0161_add_content_update_time.py
@@ -0,0 +1,47 @@
+"""
+Adds timestamps to hdac table. Adds triggers to dataset, hda, hdac tables
+to update history.update_time when contents are changed.
+"""
+from __future__ import print_function
+
+import logging
+
+from sqlalchemy import Column, DateTime, MetaData, Table
+
+from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.orm.now import now
+from galaxy.model.triggers import drop_timestamp_triggers, install_timestamp_triggers
+
+log = logging.getLogger(__name__)
+metadata = MetaData()
+
+
+def upgrade(migrate_engine):
+    print(__doc__)
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    create_timestamps(metadata, "history_dataset_collection_association")
+    install_timestamp_triggers(migrate_engine)
+
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+    drop_timestamp_triggers(migrate_engine)
+    drop_timestamps(metadata, "history_dataset_collection_association")
+
+
+def create_timestamps(metadata, table_name):
+    target_table = Table(table_name, metadata, autoload=True)
+    if 'create_time' not in target_table.c:
+        create_time_column = Column("create_time", DateTime, default=now)
+        add_column(create_time_column, target_table, metadata)
+    if 'update_time' not in target_table.c:
+        update_time_column = Column("update_time", DateTime, default=now, onupdate=now)
+        add_column(update_time_column, target_table, metadata)
+
+
+def drop_timestamps(metadata, table_name):
+    target_table = Table(table_name, metadata, autoload=True)
+    drop_column("create_time", target_table)
+    drop_column("update_time", target_table)
diff --git a/lib/galaxy/model/triggers.py b/lib/galaxy/model/triggers.py
new file mode 100644
index 000000000000..c855f5bbc823
--- /dev/null
+++ b/lib/galaxy/model/triggers.py
@@ -0,0 +1,155 @@
+"""
+Database trigger installation and removal
+"""
+
+from sqlalchemy import DDL
+
+
+def install_timestamp_triggers(engine):
+    """Install update_time propagation triggers for history data tables"""
+    sql = get_install_trigger_sql(engine.name)
+    execute_statements(engine, sql)
+
+
+def drop_timestamp_triggers(engine):
+    """Remove update_time propagation triggers for historydata tables"""
+    sql = get_drop_trigger_sql(engine.name)
+    execute_statements(engine, sql)
+
+
+def execute_statements(engine, statements):
+    for statement in statements:
+        cmd = DDL(statement)
+        cmd.execute(bind=engine)
+
+
+def get_install_trigger_sql(variant):
+    """Build statements to install timestamp triggers"""
+
+    sql = []
+
+    if variant in ['postgres', 'postgresql']:
+        """Postgres has a separate function definition and a trigger
+        assignment. The first two statements the functions, and
+        the later assign those functions to triggers on tables"""
+
+        # function: history trigger function
+        sql.append(build_pg_timestamp_func('update_history_update_time', 'history', new_key='history_id'))
+
+        # function: hda trigger function
+        sql.append(build_pg_timestamp_func('update_hda_update_time', 'history_dataset_association', local_key='dataset_id'))
+
+        # trigger: changes to datasets -> update hda
+        sql.append(build_pg_trigger('trigger_dataset_bidur', 'dataset', 'update_hda_update_time'))
+
+        # trigger: changes to hda -> update history
+        sql.append(build_pg_trigger('trigger_hda_bidur', 'history_dataset_association', 'update_history_update_time'))
+
+        # trigger: change hdca -> update history
+        sql.append(build_pg_trigger('trigger_hdca_bidur', 'history_dataset_collection_association', 'update_history_update_time'))
+
+    else:
+        """Other database variants are more granular. Requiring separate
+        statements for INSERT/UPDATE/DELETE, and the body of the trigger
+        is not necessarily reusable with a function"""
+
+        for operation in ['INSERT', 'UPDATE', 'DELETE']:
+
+            # change dataset -> update hda
+            sql.append(build_timestamp_trigger(
+                operation, 'dataset', 'history_dataset_association',
+                target_key='dataset_id'))
+
+            # change hda -> update history
+            sql.append(build_timestamp_trigger(
+                operation, 'history_dataset_association', 'history',
+                source_key='history_id'))
+
+            # change hdca -> update history
+            sql.append(build_timestamp_trigger(
+                operation, 'history_dataset_collection_association', 'history',
+                source_key='history_id'))
+
+    return sql
+
+
+def build_pg_timestamp_func(fn_name, table_name, local_key='id', new_key='id', stamp='update_time'):
+    """creates a postgres timestamp trigger function"""
+
+    tmpl = """
+        CREATE OR REPLACE FUNCTION {fn_name}()
+            RETURNS trigger
+            LANGUAGE 'plpgsql'
+        AS $BODY$
+            BEGIN
+                UPDATE {table_name}
+                SET {stamp} = (now() at time zone 'utc')
+                WHERE {local_key} = NEW.{new_key}
+                AND {stamp} < (now() at time zone 'utc');
+                RETURN NEW;
+            END;
+        $BODY$;
+    """
+
+    return tmpl.format(**locals())
+
+
+def build_pg_trigger(trigger_name, table_name, fn_name, when='BEFORE'):
+    """creates a postgres trigger"""
+
+    tmpl = """
+        CREATE TRIGGER {trigger_name}
+            {when} INSERT OR DELETE OR UPDATE
+            ON {table_name}
+            FOR EACH ROW
+            EXECUTE PROCEDURE {fn_name}();
+    """
+
+    return tmpl.format(**locals())
+
+
+def build_timestamp_trigger(operation, source_table, target_table, source_key='id', target_key='id', when='BEFORE'):
+    """creates a non-postgres update_time trigger"""
+
+    op_initial = operation.lower()[0]
+    when_initial = when.lower()[0]
+    rowset = 'OLD' if operation == 'DELETE' else 'NEW'
+
+    tmpl = """
+        CREATE TRIGGER trigger_{source_table}_{when_initial}{op_initial}r
+            {when} {operation}
+            ON {source_table}
+            FOR EACH ROW
+            BEGIN
+                UPDATE {target_table}
+                SET update_time = current_timestamp
+                WHERE {target_key} = {rowset}.{source_key};
+            END;
+    """
+
+    return tmpl.format(**locals())
+
+
+def get_drop_trigger_sql(variant):
+    """For use in migrations, creates drop statements when uninstalling triggers"""
+
+    sql = []
+
+    if variant in ['postgres', 'postgresql']:
+        sql.append("DROP FUNCTION IF EXISTS update_hda_update_time() CASCADE;")
+        sql.append("DROP FUNCTION IF EXISTS update_history_update_time() CASCADE;")
+    else:
+        for operation in ['INSERT', 'UPDATE', 'DELETE']:
+            sql.append(build_drop_trigger(operation, "dataset"))
+            sql.append(build_drop_trigger(operation, "history_dataset_association"))
+            sql.append(build_drop_trigger(operation, "history_dataset_collection_association"))
+
+    return sql
+
+
+def build_drop_trigger(operation, source_table, when='BEFORE'):
+    """drops a non-postgres trigger by name"""
+    op_initial = operation.lower()[0]
+    when_initial = when.lower()[0]
+    tmpl = "DROP TRIGGER IF EXISTS trigger_{source_table}_{when_initial}{op_initial}r"
+    return tmpl.format(**locals())

From 99da6e95b01f1051f5393bbb14fc5bb383183a8f Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Thu, 14 Nov 2019 02:16:18 +0100
Subject: [PATCH 057/853] several enhancements and fixes

---
 interactivetool_guacamole_desktop.xml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/interactivetool_guacamole_desktop.xml b/interactivetool_guacamole_desktop.xml
index a63ce1089911..665f4d33eb81 100644
--- a/interactivetool_guacamole_desktop.xml
+++ b/interactivetool_guacamole_desktop.xml
@@ -1,13 +1,15 @@
 <tool id="interactive_tool_guacamole_desktop" tool_type="interactive" name="Ubuntu XFCE Desktop" version="0.1">
     <requirements>
-        <container type="docker">cyverse/ubuntu18-xfce-desktop</container>
+        <container type="docker">quay.io/bgruening/guacamole-desktop</container>
     </requirements>
     <entry_points>
         <entry_point name="Remote Desktop" requires_domain="True">
-            <port>8000</port>
+            <port>8080</port>
+            <url><![CDATA[?username=user&password=password]]></url>
         </entry_point>
     </entry_points>
-    <command><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
+        sudo chmod 667 /tmp/ -R &&
         sudo -E /startup.sh
     ]]>
     </command>
@@ -19,8 +21,7 @@
     <tests>
     </tests>
     <help>
-        Simple Ubuntu XFCE all-in-one desktop.
-        Username: "user"
-        Password: "password"
+        Simple Ubuntu XFCE all-in-one desktop. The Username is "user" and the Password is "password".
+        This image is based on the awesome work from CyVerse.
     </help>
 </tool>

From 8cc60b2fedbec558f454ea23fabd427d3889f8ba Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Thu, 14 Nov 2019 08:01:32 -0800
Subject: [PATCH 058/853] removed unnecessary criteria in updatetime trigger

---
 .../model/migrate/versions/0161_add_content_update_time.py  | 1 +
 lib/galaxy/model/triggers.py                                | 6 +++---
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/model/migrate/versions/0161_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0161_add_content_update_time.py
index 7b85a4f68867..a9879b23f723 100644
--- a/lib/galaxy/model/migrate/versions/0161_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0161_add_content_update_time.py
@@ -21,6 +21,7 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
     create_timestamps(metadata, "history_dataset_collection_association")
+    drop_timestamp_triggers(migrate_engine)
     install_timestamp_triggers(migrate_engine)
 
 
diff --git a/lib/galaxy/model/triggers.py b/lib/galaxy/model/triggers.py
index c855f5bbc823..a4afa91c20d2 100644
--- a/lib/galaxy/model/triggers.py
+++ b/lib/galaxy/model/triggers.py
@@ -73,7 +73,7 @@ def get_install_trigger_sql(variant):
     return sql
 
 
-def build_pg_timestamp_func(fn_name, table_name, local_key='id', new_key='id', stamp='update_time'):
+def build_pg_timestamp_func(fn_name, table_name, local_key='id', new_key='id'):
     """creates a postgres timestamp trigger function"""
 
     tmpl = """
@@ -83,9 +83,9 @@ def build_pg_timestamp_func(fn_name, table_name, local_key='id', new_key='id', s
         AS $BODY$
             BEGIN
                 UPDATE {table_name}
-                SET {stamp} = (now() at time zone 'utc')
+                SET update_time = (now() at time zone 'utc')
                 WHERE {local_key} = NEW.{new_key}
-                AND {stamp} < (now() at time zone 'utc');
+                AND update_time < (now() at time zone 'utc');
                 RETURN NEW;
             END;
         $BODY$;

From 1b16e10c4f0e52bbb108504c8f6536dd3838ce45 Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Thu, 14 Nov 2019 10:00:36 -0800
Subject: [PATCH 059/853] added check to drop existing triggers upon
 installation, appears to affect unit tests

---
 .../model/migrate/versions/0161_add_content_update_time.py       | 1 -
 lib/galaxy/model/triggers.py                                     | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/migrate/versions/0161_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0161_add_content_update_time.py
index a9879b23f723..7b85a4f68867 100644
--- a/lib/galaxy/model/migrate/versions/0161_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0161_add_content_update_time.py
@@ -21,7 +21,6 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
     create_timestamps(metadata, "history_dataset_collection_association")
-    drop_timestamp_triggers(migrate_engine)
     install_timestamp_triggers(migrate_engine)
 
 
diff --git a/lib/galaxy/model/triggers.py b/lib/galaxy/model/triggers.py
index a4afa91c20d2..415d66f43245 100644
--- a/lib/galaxy/model/triggers.py
+++ b/lib/galaxy/model/triggers.py
@@ -8,6 +8,7 @@
 def install_timestamp_triggers(engine):
     """Install update_time propagation triggers for history data tables"""
     sql = get_install_trigger_sql(engine.name)
+    drop_timestamp_triggers(engine)
     execute_statements(engine, sql)
 
 

From c2a0fe3a552dd8033a0d2dcf61c36a736e13b689 Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Fri, 15 Nov 2019 12:11:12 -0800
Subject: [PATCH 060/853] fixed trigger return values, simplified pg triggers

---
 lib/galaxy/model/triggers.py | 155 ++++++++++++++++++-----------------
 1 file changed, 80 insertions(+), 75 deletions(-)

diff --git a/lib/galaxy/model/triggers.py b/lib/galaxy/model/triggers.py
index 415d66f43245..526922aa3d7a 100644
--- a/lib/galaxy/model/triggers.py
+++ b/lib/galaxy/model/triggers.py
@@ -7,60 +7,44 @@
 
 def install_timestamp_triggers(engine):
     """Install update_time propagation triggers for history data tables"""
-    sql = get_install_trigger_sql(engine.name)
-    drop_timestamp_triggers(engine)
-    execute_statements(engine, sql)
+    statements = get_timestamp_install_sql(engine.name)
+    execute_statements(engine, statements)
 
 
 def drop_timestamp_triggers(engine):
     """Remove update_time propagation triggers for historydata tables"""
-    sql = get_drop_trigger_sql(engine.name)
-    execute_statements(engine, sql)
+    statements = get_timestamp_drop_sql(engine.name)
+    execute_statements(engine, statements)
 
 
 def execute_statements(engine, statements):
-    for statement in statements:
-        cmd = DDL(statement)
+    for sql in statements:
+        cmd = DDL(sql)
         cmd.execute(bind=engine)
 
 
-def get_install_trigger_sql(variant):
-    """Build statements to install timestamp triggers"""
+def get_timestamp_install_sql(variant):
+    """Generate a list of sql statements for insalllation of timetamp triggers"""
 
-    sql = []
-
-    if variant in ['postgres', 'postgresql']:
-        """Postgres has a separate function definition and a trigger
-        assignment. The first two statements the functions, and
-        the later assign those functions to triggers on tables"""
-
-        # function: history trigger function
-        sql.append(build_pg_timestamp_func('update_history_update_time', 'history', new_key='history_id'))
-
-        # function: hda trigger function
-        sql.append(build_pg_timestamp_func('update_hda_update_time', 'history_dataset_association', local_key='dataset_id'))
-
-        # trigger: changes to datasets -> update hda
-        sql.append(build_pg_trigger('trigger_dataset_bidur', 'dataset', 'update_hda_update_time'))
+    sql = get_timestamp_drop_sql(variant)
 
-        # trigger: changes to hda -> update history
-        sql.append(build_pg_trigger('trigger_hda_bidur', 'history_dataset_association', 'update_history_update_time'))
+    if 'postgres' in variant:
+        # Postgres has a separate function definition and a trigger
+        # assignment. The first two statements the functions, and
+        # the later assign those functions to triggers on tables
 
-        # trigger: change hdca -> update history
-        sql.append(build_pg_trigger('trigger_hdca_bidur', 'history_dataset_collection_association', 'update_history_update_time'))
+        fn_name = 'update_history_update_time'
+        sql.append(build_pg_timestamp_fn(fn_name, 'history', source_key='history_id'))
+        sql.append(build_pg_trigger('history_dataset_association', fn_name))
+        sql.append(build_pg_trigger('history_dataset_collection_association', fn_name))
 
     else:
-        """Other database variants are more granular. Requiring separate
-        statements for INSERT/UPDATE/DELETE, and the body of the trigger
-        is not necessarily reusable with a function"""
+        # Other database variants are more granular. Requiring separate
+        # statements for INSERT/UPDATE/DELETE, and the body of the trigger
+        # is not necessarily reusable with a function
 
         for operation in ['INSERT', 'UPDATE', 'DELETE']:
 
-            # change dataset -> update hda
-            sql.append(build_timestamp_trigger(
-                operation, 'dataset', 'history_dataset_association',
-                target_key='dataset_id'))
-
             # change hda -> update history
             sql.append(build_timestamp_trigger(
                 operation, 'history_dataset_association', 'history',
@@ -74,83 +58,104 @@ def get_install_trigger_sql(variant):
     return sql
 
 
-def build_pg_timestamp_func(fn_name, table_name, local_key='id', new_key='id'):
-    """creates a postgres timestamp trigger function"""
+def get_timestamp_drop_sql(variant):
+    """generate a list of statements to drop the timestammp update triggers"""
 
-    tmpl = """
+    sql = []
+
+    if 'postgres' in variant:
+        sql.append("DROP FUNCTION IF EXISTS update_history_update_time() CASCADE;")
+    else:
+        for operation in ['INSERT', 'UPDATE', 'DELETE']:
+            sql.append(build_drop_trigger(operation, 'history_dataset_association'))
+            sql.append(build_drop_trigger(operation, 'history_dataset_collection_association'))
+
+    return sql
+
+
+def build_pg_timestamp_fn(fn_name, table_name, local_key='id', source_key='id', stamp_column='update_time'):
+    """Generates a postgres history update timestamp function"""
+
+    sql = """
         CREATE OR REPLACE FUNCTION {fn_name}()
             RETURNS trigger
             LANGUAGE 'plpgsql'
         AS $BODY$
             BEGIN
-                UPDATE {table_name}
-                SET update_time = (now() at time zone 'utc')
-                WHERE {local_key} = NEW.{new_key}
-                AND update_time < (now() at time zone 'utc');
-                RETURN NEW;
+                IF (TG_OP = 'DELETE') THEN
+                    UPDATE {table_name}
+                    SET {stamp_column} = (now() at time zone 'utc')
+                    WHERE {local_key} = OLD.{source_key};
+                    RETURN OLD;
+                ELSEIF (TG_OP = 'UPDATE') THEN
+                    UPDATE {table_name}
+                    SET {stamp_column} = (now() at time zone 'utc')
+                    WHERE {local_key} = NEW.{source_key} OR {local_key} = OLD.{source_key};
+                    RETURN NEW;
+                ELSIF (TG_OP = 'INSERT') THEN
+                    UPDATE {table_name}
+                    SET {stamp_column} = (now() at time zone 'utc')
+                    WHERE {local_key} = NEW.{source_key};
+                    RETURN NEW;
+                END IF;
             END;
         $BODY$;
     """
-
-    return tmpl.format(**locals())
+    return sql.format(**locals())
 
 
-def build_pg_trigger(trigger_name, table_name, fn_name, when='BEFORE'):
-    """creates a postgres trigger"""
+def build_pg_trigger(table_name, fn_name):
+    """assigns a postgres trigger to indicated table, calling user-defined function"""
 
+    trigger_name = "trigger_{table_name}_biudr".format(**locals())
     tmpl = """
         CREATE TRIGGER {trigger_name}
-            {when} INSERT OR DELETE OR UPDATE
+            BEFORE INSERT OR DELETE OR UPDATE
             ON {table_name}
             FOR EACH ROW
             EXECUTE PROCEDURE {fn_name}();
     """
-
     return tmpl.format(**locals())
 
 
 def build_timestamp_trigger(operation, source_table, target_table, source_key='id', target_key='id', when='BEFORE'):
     """creates a non-postgres update_time trigger"""
 
-    op_initial = operation.lower()[0]
-    when_initial = when.lower()[0]
-    rowset = 'OLD' if operation == 'DELETE' else 'NEW'
+    trigger_name = get_trigger_name(operation, source_table, when)
+
+    # three different update clauses depending on update/insert/delete
+    clause = ""
+    if operation == "DELETE":
+        clause = "{target_key} = OLD.{source_key}"
+    elif operation == "UPDATE":
+        clause = "{target_key} = NEW.{source_key} OR {target_key} = OLD.{source_key}"
+    else:
+        clause = "{target_key} = NEW.{source_key}"
+    clause = clause.format(**locals())
 
     tmpl = """
-        CREATE TRIGGER trigger_{source_table}_{when_initial}{op_initial}r
+        CREATE TRIGGER {trigger_name}
             {when} {operation}
             ON {source_table}
             FOR EACH ROW
             BEGIN
                 UPDATE {target_table}
                 SET update_time = current_timestamp
-                WHERE {target_key} = {rowset}.{source_key};
+                WHERE {clause};
             END;
     """
-
     return tmpl.format(**locals())
 
 
-def get_drop_trigger_sql(variant):
-    """For use in migrations, creates drop statements when uninstalling triggers"""
-
-    sql = []
-
-    if variant in ['postgres', 'postgresql']:
-        sql.append("DROP FUNCTION IF EXISTS update_hda_update_time() CASCADE;")
-        sql.append("DROP FUNCTION IF EXISTS update_history_update_time() CASCADE;")
-    else:
-        for operation in ['INSERT', 'UPDATE', 'DELETE']:
-            sql.append(build_drop_trigger(operation, "dataset"))
-            sql.append(build_drop_trigger(operation, "history_dataset_association"))
-            sql.append(build_drop_trigger(operation, "history_dataset_collection_association"))
-
-    return sql
-
-
 def build_drop_trigger(operation, source_table, when='BEFORE'):
     """drops a non-postgres trigger by name"""
+    trigger_name = get_trigger_name(operation, source_table, when)
+    return "DROP TRIGGER IF EXISTS {trigger_name}".format(**locals())
+
+
+def get_trigger_name(operation, source_table, when='BEFORE'):
+    """non-postgres trigger name"""
     op_initial = operation.lower()[0]
     when_initial = when.lower()[0]
-    tmpl = "DROP TRIGGER IF EXISTS trigger_{source_table}_{when_initial}{op_initial}r"
-    return tmpl.format(**locals())
+    trigger_name = "trigger_{source_table}_{when_initial}{op_initial}r".format(**locals())
+    return trigger_name

From ac05f6a880be57a371f6d06a642db8536c792865 Mon Sep 17 00:00:00 2001
From: Mason <nerdinacan@gmail.com>
Date: Wed, 20 Nov 2019 10:24:33 -0800
Subject: [PATCH 061/853] update_time migration version number bump to fit dev

---
 ...add_content_update_time.py => 0162_add_content_update_time.py} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename lib/galaxy/model/migrate/versions/{0161_add_content_update_time.py => 0162_add_content_update_time.py} (100%)

diff --git a/lib/galaxy/model/migrate/versions/0161_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0162_add_content_update_time.py
similarity index 100%
rename from lib/galaxy/model/migrate/versions/0161_add_content_update_time.py
rename to lib/galaxy/model/migrate/versions/0162_add_content_update_time.py

From ce872ac1ae789a8770ddf037fc75170a73e35816 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Mon, 25 Nov 2019 22:16:04 +0100
Subject: [PATCH 062/853] add new interactive VCF tool

---
 interactivetool_vcf_iobio.xml | 54 +++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 interactivetool_vcf_iobio.xml

diff --git a/interactivetool_vcf_iobio.xml b/interactivetool_vcf_iobio.xml
new file mode 100644
index 000000000000..898a34f74442
--- /dev/null
+++ b/interactivetool_vcf_iobio.xml
@@ -0,0 +1,54 @@
+<tool id="interactive_tool_vcf_iobio" tool_type="interactive" name="VCF (iobio) Visualisation" version="0.1">
+    <requirements>
+        <container type="docker">qiaoy/iobio-bundle.vcf-iobio:dev-ondemand</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="VCF io.bio visualisation of $infile.display_name" requires_domain="True">
+            <port>80</port>
+            <url><![CDATA[/?bam=http://localhost/tmp/bamfile.bam&region=1]]></url>
+        </entry_point>
+    </entry_points>
+    <command><![CDATA[
+    ## ToDo: websocket could not be found
+    ## WebSocket connection to 'ws://localhost/bamreaddepther/' failed: Error in connection establishment: net::ERR_CONNECTION_REFUSED
+
+    #set $PUB_HOSTNAME = 'localhost'
+    #set $PUB_HTTP_PORT = '80'
+
+    cd /var/www/html &&
+    ##sed -i "s@\"wss://services.iobio.io/samtools/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samtools/\"@" js/bam.iobio.js/bam.iobio.js &&
+    ##sed -i "s@\"wss://services.iobio.io/bamreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamreaddepther/\"@" js/bam.iobio.js/bam.iobio.js &&
+    sed -i "s@\"wss://services.iobio.io/vcfreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfreaddepther/\"@" js/vcf.iobio.js/vcf.iobio.js &&
+    sed -i "s@\"wss://services.iobio.io/vcfstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfstatsalive/\"@" js/vcf.iobio.js/vcf.iobio.js &&
+    ##sed -i "s@\"wss://services.iobio.io/bamstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamstatsalive/\"@" js/bam.iobio.js/bam.iobio.js &&
+    sed -i "s@\"wss://services.iobio.io/tabix/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/tabix/\"@" js/vcf.iobio.js/vcf.iobio.js &&
+
+
+##s@ws://tabix.iobio.io@ws://" + window.location.hostname + ":8000@
+##s@ws://vcfreaddepther.iobio.io@ws://" + window.location.hostname + ":8001@
+##s@ws://vcfstatsalive.iobio.io@ws://" + window.location.hostname + ":8002@
+
+
+        sed -i 's/deny all;//g' /etc/nginx/nginx.conf &&
+
+        cp '${infile}' /input/vcffile.vcf &&
+        ##cp '${infile.metadata.bam_index}' /input/vcffile.bam.bai &&
+        mkdir /var/log/supervisor/ &&
+        head -n -2  /etc/supervisor.d/app.conf > /tmp/app.conf &&
+        mv /tmp/app.conf /etc/supervisor.d/app.conf &&
+
+        /usr/bin/supervisord -c /etc/supervisord.conf
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="vcf" label="VCF file"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        VCF iobio visualisation.
+    </help>
+</tool>

From 5ff93313a59871f6cb620924403caae8e6e0afba Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Tue, 26 Nov 2019 09:27:22 +0100
Subject: [PATCH 063/853] add climate notebook

---
 interactivetool_climate_notebook.xml | 95 ++++++++++++++++++++++++++++
 1 file changed, 95 insertions(+)
 create mode 100644 interactivetool_climate_notebook.xml

diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml
new file mode 100644
index 000000000000..1d12e46316e4
--- /dev/null
+++ b/interactivetool_climate_notebook.xml
@@ -0,0 +1,95 @@
+<tool id="interactive_tool_climate_notebook" tool_type="interactive" name="Interactive Climate Notebook" version="0.1">
+    <requirements>
+        <container type="docker">nordicesmhub/docker-climate-notebook:1.0</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Climate Interactive Tool" requires_domain="True">
+            <port>8888</port>
+            <url>ipython/lab</url>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
+        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
+        <environment_variable name="API_KEY" inject="api_key" />
+    </environment_variables>
+    <command detect_errors="aggressive"><![CDATA[
+        #import re
+        export GALAXY_WORKING_DIR=`pwd` &&
+        mkdir -p ./jupyter/outputs/ &&
+        mkdir -p ./jupyter/data &&
+
+        #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
+        ln -sf '$input' './jupyter/data/${cleaned_name}' &&
+
+        ## change into the directory where the notebooks are located
+        cd ./jupyter/ &&
+        export PATH=/home/jovyan/.local/bin:\$PATH &&
+
+        #if $mode.mode_select == 'scratch':
+            ## copy default notebook
+            cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
+            jupyter trust ./ipython_galaxy_notebook.ipynb &&
+            jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
+
+        #else:
+            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
+            cp '$mode.ipynb' ./${cleaned_name}.ipynb &&
+            jupyter trust ./${cleaned_name}.ipynb &&
+
+            #if $mode.run_it:
+                jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
+            #else:
+                jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+            #end if
+            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
+        #end if
+    ]]>
+    </command>
+    <inputs>
+
+        <conditional name="mode">
+            <param name="mode_select" type="select" label="Do you already have a notebook?" help="If not, no problem we will provide you with a default one.">
+                <option value="scratch">Start with a fresh notebook</option>
+                <option value="previous">Load a previous notebook</option>
+            </param>
+            <when value="scratch"/>
+            <when value="previous">
+                <param name="ipynb" type="data" format="ipynb" label="IPython Notebook"/>
+                <param name="run_it" type="boolean" truevalue="true" falsevalue="false" label="Execute notebook and return a new one."
+                    help="This option is useful in workflows when you just want to execute a notebook and not dive into the webfrontend."/>
+            </when>
+        </conditional>
+        <param name="input" type="data" optional="true" label="Include data into the environment"/>
+
+    </inputs>
+    <outputs>
+        <data name="jupyter_notebook" format="ipynb" label="Executed Climate Notebook"></data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="mode" value="previous" />
+            <param name="ipynb" value="test.ipynb" />
+            <param name="run_it" value="true" />
+            <output name="jupyter_notebook" file="test.ipynb" ftype="ipynb"/>
+        </test>
+    </tests>
+    <help>
+    The Climate Notebook is based on Jupyter an open-source web application that allows you to create and share documents that contain live code, equations,
+    visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization,
+    machine learning, and much more.
+
+    Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
+    do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter.
+
+    You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset.
+    If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history.
+
+    You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function.
+
+    The Climate version of the Jupyter Notebook offers a lot of preinstalled tools for climate science.
+    </help>
+</tool>

From 03dc5828f9a402ce23675a9de841d921b147afe5 Mon Sep 17 00:00:00 2001
From: Anne Fouilloux <annefou@geo.uio.no>
Date: Tue, 26 Nov 2019 13:30:13 +0100
Subject: [PATCH 064/853] complement help for interactive climate notebook by
 adding the list of available packages and a link to pangeo

---
 interactivetool_climate_notebook.xml | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml
index 1d12e46316e4..aa1692ada80c 100644
--- a/interactivetool_climate_notebook.xml
+++ b/interactivetool_climate_notebook.xml
@@ -90,6 +90,22 @@
 
     You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function.
 
-    The Climate version of the Jupyter Notebook offers a lot of preinstalled tools for climate science.
+    The Climate version of the Jupyter Notebook offers a lot of preinstalled tools for climate science. The list of packages is based on what is available 
+	on the [Pangeo](http://pangeo.io/) platform and [Pangeo stacks](https://pangeo-data.github.io/pangeo-stacks/).
+
+    - **Core scipy packages**: numpy, scipy, matplotlib, pandas, xarray, sparse and sympy
+    - **Data science**: scikit-image, scikit-learn, dask-ml, tensorflow, keras, pytorch-cpu, dask_labextension
+    - **Visualization**: holoviews, panel, geoviews, hvplot, geoviews, datashader, seaborn, altair, descartes, folium, vega, 
+	                     vega_datasets, palettable, cmocean,plotly, psy-maps, psy-reg, psyplot, psyplot-gui, psy-maps, psy-reg,
+						 geopy, branca
+	- **Geospatial**: iris, cartopy, basemap, basemap-data-hires, geopandas, rasterio, netcdf4, erddapy, pydap, h5py, h5netcdf, regionmask and rio-cogeo
+    - **Geoscience related**: climlab, metpy, satpy, gsw, eofs, esmpy, xesmf, windspharm, rasterstats, geojsoncontour
+	- **Climate related**: pyaerocom, cdo, cdsapi, cfgrib, cis. esmvaltool, nc-time-axis, nco
+	- **Intake related**: intake, intake-xarray, intake-esm, fsspec and intake-stac
+    - **zarr related**: zarr, numcodecs, python-blosc, lz4, gcsfs, s3fs, tiledb-py
+    - **jupyter related**: ipyleaflet, papermill, jupytext, ipydatawidgets, sidecar
+    - **xarray related**: xgcm, xrft, xhistogram, xlrd, xrviz, climpred, pytide, pyinterp
+    - **misc**: python-wget, prefect, requests, pillow, pip, nbgitpuller, pysplit, biopython, bioblend and galaxy-ie-helpers
+
     </help>
 </tool>

From 91d2eea4ae54ef5f3f03000757dddef135d76290 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Tue, 26 Nov 2019 17:13:14 +0100
Subject: [PATCH 065/853] add some VCF fixes

---
 interactivetool_vcf_iobio.xml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/interactivetool_vcf_iobio.xml b/interactivetool_vcf_iobio.xml
index 898a34f74442..4bb1d4eeec9d 100644
--- a/interactivetool_vcf_iobio.xml
+++ b/interactivetool_vcf_iobio.xml
@@ -16,12 +16,12 @@
     #set $PUB_HTTP_PORT = '80'
 
     cd /var/www/html &&
-    ##sed -i "s@\"wss://services.iobio.io/samtools/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samtools/\"@" js/bam.iobio.js/bam.iobio.js &&
-    ##sed -i "s@\"wss://services.iobio.io/bamreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamreaddepther/\"@" js/bam.iobio.js/bam.iobio.js &&
-    sed -i "s@\"wss://services.iobio.io/vcfreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfreaddepther/\"@" js/vcf.iobio.js/vcf.iobio.js &&
-    sed -i "s@\"wss://services.iobio.io/vcfstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfstatsalive/\"@" js/vcf.iobio.js/vcf.iobio.js &&
-    ##sed -i "s@\"wss://services.iobio.io/bamstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamstatsalive/\"@" js/bam.iobio.js/bam.iobio.js &&
-    sed -i "s@\"wss://services.iobio.io/tabix/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/tabix/\"@" js/vcf.iobio.js/vcf.iobio.js &&
+    ##sed -i "s@\"wss://services.iobio.io/samtools/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samtools/\"@" app/bam.iobio.js &&
+    ##sed -i "s@\"wss://services.iobio.io/bamreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamreaddepther/\"@" app/bam.iobio.js &&
+    sed -i "s@\"wss://services.iobio.io/vcfdepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfdepther/\"@" app/vcf.iobio.js &&
+    sed -i "s@\"wss://services.iobio.io/vcfstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfstatsalive/\"@" app/vcf.iobio.js &&
+    ##sed -i "s@\"wss://services.iobio.io/bamstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamstatsalive/\"@" app/bam.iobio.js &&
+    sed -i "s@\"wss://services.iobio.io/tabix/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/tabix/\"@" app/vcf.iobio.js &&
 
 
 ##s@ws://tabix.iobio.io@ws://" + window.location.hostname + ":8000@

From da4d1a043c47f38c4228e397b9847c55c62fb20c Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Tue, 26 Nov 2019 19:58:33 +0100
Subject: [PATCH 066/853] update vcf IE

---
 interactivetool_vcf_iobio.xml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/interactivetool_vcf_iobio.xml b/interactivetool_vcf_iobio.xml
index 4bb1d4eeec9d..dc585d8818c6 100644
--- a/interactivetool_vcf_iobio.xml
+++ b/interactivetool_vcf_iobio.xml
@@ -5,7 +5,7 @@
     <entry_points>
         <entry_point name="VCF io.bio visualisation of $infile.display_name" requires_domain="True">
             <port>80</port>
-            <url><![CDATA[/?bam=http://localhost/tmp/bamfile.bam&region=1]]></url>
+            <url><![CDATA[/?vcf=http://localhost/tmp/vcffile.vcf&region=1]]></url>
         </entry_point>
     </entry_points>
     <command><![CDATA[
@@ -33,7 +33,6 @@
 
         cp '${infile}' /input/vcffile.vcf &&
         ##cp '${infile.metadata.bam_index}' /input/vcffile.bam.bai &&
-        mkdir /var/log/supervisor/ &&
         head -n -2  /etc/supervisor.d/app.conf > /tmp/app.conf &&
         mv /tmp/app.conf /etc/supervisor.d/app.conf &&
 

From eb84e6743d81ad1fc602085f5c10b8500ad82486 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Wed, 27 Nov 2019 13:14:19 +0100
Subject: [PATCH 067/853] add latest VCF changes

---
 interactivetool_vcf_iobio.xml | 39 ++++++++++++++++-------------------
 1 file changed, 18 insertions(+), 21 deletions(-)

diff --git a/interactivetool_vcf_iobio.xml b/interactivetool_vcf_iobio.xml
index dc585d8818c6..3be0266c5931 100644
--- a/interactivetool_vcf_iobio.xml
+++ b/interactivetool_vcf_iobio.xml
@@ -5,49 +5,46 @@
     <entry_points>
         <entry_point name="VCF io.bio visualisation of $infile.display_name" requires_domain="True">
             <port>80</port>
-            <url><![CDATA[/?vcf=http://localhost/tmp/vcffile.vcf&region=1]]></url>
+            <url><![CDATA[/?vcf=http://localhost/tmp/vcffile.vcf.gz]]></url>
         </entry_point>
     </entry_points>
     <command><![CDATA[
-    ## ToDo: websocket could not be found
-    ## WebSocket connection to 'ws://localhost/bamreaddepther/' failed: Error in connection establishment: net::ERR_CONNECTION_REFUSED
-
     #set $PUB_HOSTNAME = 'localhost'
     #set $PUB_HTTP_PORT = '80'
 
     cd /var/www/html &&
-    ##sed -i "s@\"wss://services.iobio.io/samtools/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samtools/\"@" app/bam.iobio.js &&
-    ##sed -i "s@\"wss://services.iobio.io/bamreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamreaddepther/\"@" app/bam.iobio.js &&
     sed -i "s@\"wss://services.iobio.io/vcfdepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfdepther/\"@" app/vcf.iobio.js &&
     sed -i "s@\"wss://services.iobio.io/vcfstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfstatsalive/\"@" app/vcf.iobio.js &&
-    ##sed -i "s@\"wss://services.iobio.io/bamstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamstatsalive/\"@" app/bam.iobio.js &&
     sed -i "s@\"wss://services.iobio.io/tabix/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/tabix/\"@" app/vcf.iobio.js &&
 
+    sed -i 's/deny all;//g' /etc/nginx/nginx.conf &&
 
-##s@ws://tabix.iobio.io@ws://" + window.location.hostname + ":8000@
-##s@ws://vcfreaddepther.iobio.io@ws://" + window.location.hostname + ":8001@
-##s@ws://vcfstatsalive.iobio.io@ws://" + window.location.hostname + ":8002@
-
+    ln -s '$infile' /input/vcffile.vcf.gz &&
+    #if $infile.metadata.tabix_index:
+        ln -s '${infile.metadata.tabix_index}' /input/vcffile.vcf.gz.tbi &&
+    #end if
 
-        sed -i 's/deny all;//g' /etc/nginx/nginx.conf &&
+    head -n -2  /etc/supervisor.d/app.conf > /tmp/app.conf &&
+    mv /tmp/app.conf /etc/supervisor.d/app.conf &&
+    /usr/bin/supervisord -c /etc/supervisord.conf
 
-        cp '${infile}' /input/vcffile.vcf &&
-        ##cp '${infile.metadata.bam_index}' /input/vcffile.bam.bai &&
-        head -n -2  /etc/supervisor.d/app.conf > /tmp/app.conf &&
-        mv /tmp/app.conf /etc/supervisor.d/app.conf &&
-
-        /usr/bin/supervisord -c /etc/supervisord.conf
     ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="vcf" label="VCF file"/>
+        <param name="infile" type="data" format="vcf_bgzip" label="Compressed VCF file"/>
     </inputs>
     <outputs>
         <data name="outfile" format="txt" />
     </outputs>
     <tests>
     </tests>
-    <help>
-        VCF iobio visualisation.
+    <help><![CDATA[
+Examine your variant file in seconds with the VCF `iobio visualisation <https://vcf.iobio.io>`_.
+
+This visualization is using Galaxy Interactive Tool and utilizes an all-in-one Docker container from http://iobio.io.
+
+Make sure your VCF file is compressed to the vcf_bgzip datatype to load it into the Visualization.
+    ]]>
     </help>
 </tool>
+

From a6ed2d61ba622850748963327b6f63c4ffbfa72a Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Sat, 30 Nov 2019 22:46:10 +0100
Subject: [PATCH 068/853] A first try of openrefine GIE -> interactivetool

---
 interactivetool_openrefine.xml | 64 ++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 interactivetool_openrefine.xml

diff --git a/interactivetool_openrefine.xml b/interactivetool_openrefine.xml
new file mode 100644
index 000000000000..17680fb6d0ee
--- /dev/null
+++ b/interactivetool_openrefine.xml
@@ -0,0 +1,64 @@
+<tool id="interactive_tool_openrefine" tool_type="interactive" name="openrefine" version="0.1">
+    <description>Working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data.</description>
+    <requirements>
+        <container type="docker">ylebras/openrefine-docker</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Openrefine visualisation" requires_domain="True">
+            <port>80</port>
+            <url></url>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+
+        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($outfile.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="API_KEY" strip="True">
+            #if $__user__:
+                #for $api_key in $__user__.api_keys:
+                    ${api_key.key}
+                    #break
+                #end for
+            #end if
+        </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
+    </environment_variables>
+    <command><![CDATA[
+
+        /startup.sh
+
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="tabular" label="tabular file"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+
+
+
+
+`Openrefine <https://openrefine.org/>`_ (previously Google Refine) is a powerful tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data.
+
+.. class:: infomark
+
+Example input file (TAB separated)::
+
+  "name"	"longitude"	"latitude"	"countryCode"
+  Accipiter striatus Vieillot, 1808	-60.291838	46.328137	CA
+  Accipiter striatus Vieillot, 1808	-114.58927	35.022485	US
+  Accipiter striatus Vieillot, 1808	-93.37406	30.00586	US
+  Accipiter striatus Vieillot, 1808	-79.336288	43.682218	CA
+  Accipiter striatus Vieillot, 1808	-109.156024	31.904185	US
+  Accipiter striatus Vieillot, 1808	-71.098031	42.297408	US
+  Accipiter striatus Vieillot, 1808	-110.927215	32.18203	US
+
+]]>
+    </help>
+</tool>

From a97099d7cced23d10f4833a2c2f9ff7ce331924f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sun, 1 Dec 2019 14:17:01 +0100
Subject: [PATCH 069/853] so this should work, I hope

---
 interactivetool_openrefine.xml | 63 ++++++++++++++++++++--------------
 1 file changed, 38 insertions(+), 25 deletions(-)

diff --git a/interactivetool_openrefine.xml b/interactivetool_openrefine.xml
index 17680fb6d0ee..956073db48a3 100644
--- a/interactivetool_openrefine.xml
+++ b/interactivetool_openrefine.xml
@@ -1,32 +1,46 @@
-<tool id="interactive_tool_openrefine" tool_type="interactive" name="openrefine" version="0.1">
-    <description>Working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data.</description>
+<tool id="interactive_tool_openrefine" tool_type="interactive" name="OpenRefine" version="0.1">
+    <description>Working with messy data</description>
     <requirements>
         <container type="docker">ylebras/openrefine-docker</container>
     </requirements>
     <entry_points>
         <entry_point name="Openrefine visualisation" requires_domain="True">
-            <port>80</port>
-            <url></url>
+            <port>3333</port>
         </entry_point>
     </entry_points>
     <environment_variables>
-
-        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($outfile.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
+        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
         <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
-        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="API_KEY" strip="True">
-            #if $__user__:
-                #for $api_key in $__user__.api_keys:
-                    ${api_key.key}
-                    #break
-                #end for
-            #end if
-        </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
+        <environment_variable name="API_KEY" inject="api_key" />
     </environment_variables>
-    <command><![CDATA[
+    <configfiles>
+        <configfile name="start_openrefine"><![CDATA[
+exec /OpenRefine/refine -i 0.0.0.0 -m \$GALAXY_MEMORY_MB &
+
+##Check if openrefine is up to work
+STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>\&1)
+while [[ \${STATUS} =~ "refused" ]]
+do
+  echo "Waiting for openrefine: \$STATUS \n"
+  STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>\&1)
+  sleep 4
+done
+]]>
+        </configfile>
+    </configfiles>
+    <command detect_errors="aggressive"><![CDATA[
+
+cp '$infile' /import/input.tabular &&
+cat '$start_openrefine' &&
+bash '$start_openrefine' &&
 
-        /startup.sh
+## Createnew project with the dataset
+cd /refine-python &&
+python openrefine_create_project_API.py '/import/input.tabular' &&
+
+tail -f /dev/null
 
     ]]>
     </command>
@@ -34,17 +48,16 @@
         <param name="infile" type="data" format="tabular" label="tabular file"/>
     </inputs>
     <outputs>
-        <data name="outfile" format="txt" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
+        <test expect_num_outputs="1">
+        </test>
     </tests>
-    <help>
-<![CDATA[
-
-
-
+    <help><![CDATA[
 
-`Openrefine <https://openrefine.org/>`_ (previously Google Refine) is a powerful tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data.
+`Openrefine <https://openrefine.org/>`_ (previously Google Refine) is a powerful tool for working with messy data:
+cleaning it; transforming it from one format into another; and extending it with web services and external data.
 
 .. class:: infomark
 

From 466d8d38ab48a829205e17a37d38f581aa90db6e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sun, 1 Dec 2019 14:34:43 +0100
Subject: [PATCH 070/853] small fix

---
 interactivetool_openrefine.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/interactivetool_openrefine.xml b/interactivetool_openrefine.xml
index 956073db48a3..11a0b01ffc3c 100644
--- a/interactivetool_openrefine.xml
+++ b/interactivetool_openrefine.xml
@@ -20,11 +20,11 @@
 exec /OpenRefine/refine -i 0.0.0.0 -m \$GALAXY_MEMORY_MB &
 
 ##Check if openrefine is up to work
-STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>\&1)
+STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>&1)
 while [[ \${STATUS} =~ "refused" ]]
 do
   echo "Waiting for openrefine: \$STATUS \n"
-  STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>\&1)
+  STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>&1)
   sleep 4
 done
 ]]>

From 7fcbf9c6dd142d91c6f5cabd6d067f3be4e81c76 Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Mon, 2 Dec 2019 11:34:43 +0100
Subject: [PATCH 071/853] Create interactivetool_radiant.xml

First try
---
 interactivetool_radiant.xml | 75 +++++++++++++++++++++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100644 interactivetool_radiant.xml

diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml
new file mode 100644
index 000000000000..d48cd9cf1260
--- /dev/null
+++ b/interactivetool_radiant.xml
@@ -0,0 +1,75 @@
+<tool id="interactive_tool_radiant" tool_type="interactive" name="radiant" version="0.1">
+    <description>Data analytics using Radiant R Shiny app</description>
+    <requirements>
+        <container type="docker">ylebras/radiant-docker</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="radiant visualisation" requires_domain="True">
+            <port>3838</port>
+            <url>/sample-apps/STAT/</url>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+
+        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($outfile.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="API_KEY" strip="True">
+            #if $__user__:
+                #for $api_key in $__user__.api_keys:
+                    ${api_key.key}
+                    #break
+                #end for
+            #end if
+        </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
+    </environment_variables>
+    <command><![CDATA[
+
+        /usr/bin/shiny-server.sh
+
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="tabular,csv" label="tabular or csv file"/>
+    </inputs>
+    <outputs>
+        <!--data name="outfile" format="txt" /-->
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+
+
+
+
+`Radiant <https://radiant-rstats.github.io/docs/>`_ is an open-source platform-independent browser-based interface for business analytics in R. The application is based on the Shiny package and can be run locally or on a server. Radiant was developed by Vincent Nijs. Please use the issue tracker on GitHub to suggest enhancements or report problems: https://github.com/radiant-rstats/radiant/issues. For other questions and comments please use radiant@rady.ucsd.edu.
+Key features
+
+- Explore: Quickly and easily summarize, visualize, and analyze your data
+- Cross-platform: It runs in a browser on Windows, Mac, and Linux
+- Reproducible: Recreate results and share work with others as a state file or an Rmarkdown report
+- Programming: Integrate Radiant’s analysis functions with your own R-code
+- Context: Data and examples focus on business applications
+
+
+.. class:: infomark
+
+Example input file (TAB separated)::
+
+  "name"	"longitude"	"latitude"	"countryCode"
+  Accipiter striatus Vieillot, 1808	-60.291838	46.328137	CA
+  Accipiter striatus Vieillot, 1808	-114.58927	35.022485	US
+  Accipiter striatus Vieillot, 1808	-93.37406	30.00586	US
+  Accipiter striatus Vieillot, 1808	-79.336288	43.682218	CA
+  Accipiter striatus Vieillot, 1808	-109.156024	31.904185	US
+  Accipiter striatus Vieillot, 1808	-71.098031	42.297408	US
+  Accipiter striatus Vieillot, 1808	-110.927215	32.18203	US
+
+]]>
+    </help>
+    <citations>
+        <!--citation type="doi">10.1111/2041-210X.12945</citation-->
+    </citations>
+</tool>

From b9df1d6eb01024381abbf0d5f7b87646829e1bca Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Mon, 2 Dec 2019 11:47:00 +0100
Subject: [PATCH 072/853] Create interactivetool_geoexplorer.xml

---
 interactivetool_geoexplorer.xml | 69 +++++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 interactivetool_geoexplorer.xml

diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml
new file mode 100644
index 000000000000..ba51c7c70edd
--- /dev/null
+++ b/interactivetool_geoexplorer.xml
@@ -0,0 +1,69 @@
+<tool id="interactive_tool_geoexplorer" tool_type="interactive" name="geoexplorer" version="0.1">
+    <description>An interactive spatial analysis platform using ggvis and Leaflet</description>
+    <requirements>
+        <container type="docker">ylebras/geoexplorer-docker</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="geoexplorer visualisation" requires_domain="True">
+            <port>3838</port>
+            <url>/sample-apps/SIG/</url>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+
+        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($outfile.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="API_KEY" strip="True">
+            #if $__user__:
+                #for $api_key in $__user__.api_keys:
+                    ${api_key.key}
+                    #break
+                #end for
+            #end if
+        </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
+    </environment_variables>
+    <command><![CDATA[
+
+        /usr/bin/shiny-server.sh
+
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="csv" label="csv file"/>
+    </inputs>
+    <outputs>
+        <!--data name="outfile" format="txt" /-->
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+
+
+`GeoExplorer <https://radiant-rstats.github.io/docs/>`_ is An interactive spatial analysis platform using ggvis and Leaflet.
+
+Author: David Stephens
+
+App: http://www.davesteps.com/geoExploreR/
+
+.. class:: infomark
+
+Example input file (TAB separated)::
+
+  "name"	"longitude"	"latitude"	"countryCode"
+  Accipiter striatus Vieillot, 1808	-60.291838	46.328137	CA
+  Accipiter striatus Vieillot, 1808	-114.58927	35.022485	US
+  Accipiter striatus Vieillot, 1808	-93.37406	30.00586	US
+  Accipiter striatus Vieillot, 1808	-79.336288	43.682218	CA
+  Accipiter striatus Vieillot, 1808	-109.156024	31.904185	US
+  Accipiter striatus Vieillot, 1808	-71.098031	42.297408	US
+  Accipiter striatus Vieillot, 1808	-110.927215	32.18203	US
+
+]]>
+    </help>
+    <citations>
+        <!--citation type="doi">10.1111/2041-210X.12945</citation-->
+    </citations>
+</tool>

From ea43b3c5b5a5b62a12b820d50712a93006231df5 Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Mon, 2 Dec 2019 13:56:23 +0100
Subject: [PATCH 073/853] correct Galaxy environment variables

---
 interactivetool_geoexplorer.xml | 17 +++++------------
 1 file changed, 5 insertions(+), 12 deletions(-)

diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml
index ba51c7c70edd..0667c42d5d7f 100644
--- a/interactivetool_geoexplorer.xml
+++ b/interactivetool_geoexplorer.xml
@@ -10,19 +10,12 @@
         </entry_point>
     </entry_points>
     <environment_variables>
-
-        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($outfile.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
+        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
         <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
-        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="API_KEY" strip="True">
-            #if $__user__:
-                #for $api_key in $__user__.api_keys:
-                    ${api_key.key}
-                    #break
-                #end for
-            #end if
-        </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
+        <environment_variable name="API_KEY" inject="api_key" />
+        </environment_variable>
     </environment_variables>
     <command><![CDATA[
 

From 3c0943ad8d4ee0b3c84040cf504abbaa49068f5e Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Mon, 2 Dec 2019 13:57:32 +0100
Subject: [PATCH 074/853] correct env variables

---
 interactivetool_radiant.xml | 17 +++++------------
 1 file changed, 5 insertions(+), 12 deletions(-)

diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml
index d48cd9cf1260..7b87bfe3eade 100644
--- a/interactivetool_radiant.xml
+++ b/interactivetool_radiant.xml
@@ -10,19 +10,12 @@
         </entry_point>
     </entry_points>
     <environment_variables>
-
-        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($outfile.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
+        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
         <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
-        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="API_KEY" strip="True">
-            #if $__user__:
-                #for $api_key in $__user__.api_keys:
-                    ${api_key.key}
-                    #break
-                #end for
-            #end if
-        </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
+        <environment_variable name="API_KEY" inject="api_key" />
+        </environment_variable>
     </environment_variables>
     <command><![CDATA[
 

From a09a0378806a61697f1f0b39d0969cbcf7ff4788 Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Mon, 2 Dec 2019 14:10:39 +0100
Subject: [PATCH 075/853] update citation

---
 interactivetool_geoexplorer.xml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml
index 0667c42d5d7f..894dd590c23c 100644
--- a/interactivetool_geoexplorer.xml
+++ b/interactivetool_geoexplorer.xml
@@ -57,6 +57,12 @@ Example input file (TAB separated)::
 ]]>
     </help>
     <citations>
-        <!--citation type="doi">10.1111/2041-210X.12945</citation-->
+           <citation type="bibtex">@misc{githubsurvey2018,
+           author       = {davesteps},
+           title        = {{dashboard to visualise geographic data}},
+           publisher    = {Github},
+           url          = {https://github.com/davesteps/geoExploreR}
+           }
+          }</citation>
     </citations>
 </tool>

From 980b7344a1d3019e22ff64b438383da654dab4fd Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Mon, 2 Dec 2019 14:12:40 +0100
Subject: [PATCH 076/853] update citation

---
 interactivetool_radiant.xml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml
index 7b87bfe3eade..ef7165b9897b 100644
--- a/interactivetool_radiant.xml
+++ b/interactivetool_radiant.xml
@@ -63,6 +63,12 @@ Example input file (TAB separated)::
 ]]>
     </help>
     <citations>
-        <!--citation type="doi">10.1111/2041-210X.12945</citation-->
+           <citation type="bibtex">@misc{githubsurvey2018,
+           author       = {vnijs},
+           title        = {{Radiant - Business analytics using R and Shiny}},
+           publisher    = {Github},
+           url          = {https://github.com/vnijs/radiant}
+           }
+          }</citation>
     </citations>
 </tool>

From c4b5f3ff41e958b3f06897dd4e4c22897b8b7d6a Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Mon, 2 Dec 2019 14:15:14 +0100
Subject: [PATCH 077/853] remove empty lines

---
 interactivetool_radiant.xml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml
index ef7165b9897b..40615e71a0af 100644
--- a/interactivetool_radiant.xml
+++ b/interactivetool_radiant.xml
@@ -18,9 +18,7 @@
         </environment_variable>
     </environment_variables>
     <command><![CDATA[
-
         /usr/bin/shiny-server.sh
-
     ]]>
     </command>
     <inputs>
@@ -33,10 +31,6 @@
     </tests>
     <help>
 <![CDATA[
-
-
-
-
 `Radiant <https://radiant-rstats.github.io/docs/>`_ is an open-source platform-independent browser-based interface for business analytics in R. The application is based on the Shiny package and can be run locally or on a server. Radiant was developed by Vincent Nijs. Please use the issue tracker on GitHub to suggest enhancements or report problems: https://github.com/radiant-rstats/radiant/issues. For other questions and comments please use radiant@rady.ucsd.edu.
 Key features
 
@@ -46,7 +40,6 @@ Key features
 - Programming: Integrate Radiant’s analysis functions with your own R-code
 - Context: Data and examples focus on business applications
 
-
 .. class:: infomark
 
 Example input file (TAB separated)::

From b4bc34122677563dcd6f8c328b584fef3890ec27 Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Mon, 2 Dec 2019 17:30:55 +0100
Subject: [PATCH 078/853] modify url

---
 interactivetool_radiant.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml
index 40615e71a0af..691a6ec1ae93 100644
--- a/interactivetool_radiant.xml
+++ b/interactivetool_radiant.xml
@@ -6,7 +6,7 @@
     <entry_points>
         <entry_point name="radiant visualisation" requires_domain="True">
             <port>3838</port>
-            <url>/sample-apps/STAT/</url>
+            <url>/sample-apps/STAT/inst/app</url>
         </entry_point>
     </entry_points>
     <environment_variables>

From b5bcaead979c8cc04d24bb77a95cc30c1bb19597 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Mon, 2 Dec 2019 20:15:58 +0100
Subject: [PATCH 079/853] small changes to new ITs

---
 interactivetool_geoexplorer.xml | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml
index 894dd590c23c..d709f0c0360f 100644
--- a/interactivetool_geoexplorer.xml
+++ b/interactivetool_geoexplorer.xml
@@ -15,19 +15,23 @@
         <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
         <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
         <environment_variable name="API_KEY" inject="api_key" />
-        </environment_variable>
     </environment_variables>
     <command><![CDATA[
 
-        /usr/bin/shiny-server.sh
+        mkdir -p /srv/shiny-server/data/ &&
+        ln -s '$infile' /srv/shiny-server/data/inputdata.txt &&
+        mkdir -p /var/log/shiny-server &&
+        chown shiny.shiny /var/log/shiny-server &&
+
+        exec shiny-server >> /var/log/shiny-server.log 2>&1 
 
     ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="csv" label="csv file"/>
+        <param name="infile" type="data" format="tabular,csv" label="csv file"/>
     </inputs>
     <outputs>
-        <!--data name="outfile" format="txt" /-->
+        <data name="outfile" format="txt" />
     </outputs>
     <tests>
     </tests>

From 53bc67882fef3797bfacc9608d6a953098fe98ad Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Mon, 2 Dec 2019 20:16:03 +0100
Subject: [PATCH 080/853] small changes to new ITs

---
 interactivetool_radiant.xml | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml
index 40615e71a0af..ba84b9f43722 100644
--- a/interactivetool_radiant.xml
+++ b/interactivetool_radiant.xml
@@ -15,17 +15,21 @@
         <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
         <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
         <environment_variable name="API_KEY" inject="api_key" />
-        </environment_variable>
     </environment_variables>
     <command><![CDATA[
-        /usr/bin/shiny-server.sh
+        mkdir -p /var/log/shiny-server &&
+        chown shiny.shiny /var/log/shiny-server &&
+
+        chown shiny.shiny /home/shiny/.Rprofile &&
+
+        exec shiny-server >> /var/log/shiny-server.log 2>&1
     ]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="tabular,csv" label="tabular or csv file"/>
     </inputs>
     <outputs>
-        <!--data name="outfile" format="txt" /-->
+        <data name="outfile" format="txt" />
     </outputs>
     <tests>
     </tests>

From 70d84c7d933a062ea0049394b24cf40b54315806 Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Tue, 3 Dec 2019 09:09:42 +0100
Subject: [PATCH 081/853] add input file mandatory format

---
 interactivetool_geoexplorer.xml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml
index 894dd590c23c..c5420332887a 100644
--- a/interactivetool_geoexplorer.xml
+++ b/interactivetool_geoexplorer.xml
@@ -43,9 +43,11 @@ App: http://www.davesteps.com/geoExploreR/
 
 .. class:: infomark
 
+**Input data file MUST have as longitude column clomun 2, and as latitude column, column 3**
+
 Example input file (TAB separated)::
 
-  "name"	"longitude"	"latitude"	"countryCode"
+  "name"	"x"	"y"	"countryCode"
   Accipiter striatus Vieillot, 1808	-60.291838	46.328137	CA
   Accipiter striatus Vieillot, 1808	-114.58927	35.022485	US
   Accipiter striatus Vieillot, 1808	-93.37406	30.00586	US

From 63c7d543b0c9cc187dc9bfde09172c8fa8e474fb Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@irisa.fr>
Date: Fri, 13 Dec 2019 09:49:19 +0100
Subject: [PATCH 082/853] Fix env var name + update

---
 interactivetool_askomics.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml
index 095d27f9f2b6..94cf111a2f35 100644
--- a/interactivetool_askomics.xml
+++ b/interactivetool_askomics.xml
@@ -1,7 +1,7 @@
 <tool id="interactive_tool_askomics" tool_type="interactive" name="AskOmics" version="1.0">
     <description>a visual SPARQL query builder</description>
     <requirements>
-        <container type="docker">askomics/flaskomics-with-dependencies:3.1.1</container>
+        <container type="docker">askomics/flaskomics-with-dependencies:3.2.0</container>
     </requirements>
     <entry_points>
         <entry_point name="AskOmics instance on $infile.display_name" requires_domain="True">
@@ -19,7 +19,7 @@
         <environment_variable name="USER_APIKEY">${__user_name__}</environment_variable>
         <!-- Galaxy info -->
         <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
-        <environment_variable name="API_KEY" inject="api_key" />
+        <environment_variable name="GALAXY_API_KEY" inject="api_key" />
         <!-- AskOmics config -->
         <environment_variable name="DEPMODE">prod</environment_variable>
         <environment_variable name="MAX_CELERY_QUEUE">1</environment_variable>

From 1d78a090d8ea0ca2ecbd94f759534698b9c83cdf Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Fri, 13 Dec 2019 17:39:57 +0100
Subject: [PATCH 083/853] add data import (#43)

I was frogetting the data import part apparently :)
---
 interactivetool_radiant.xml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml
index 769dc90f5cc9..67c0205cc0e0 100644
--- a/interactivetool_radiant.xml
+++ b/interactivetool_radiant.xml
@@ -17,6 +17,10 @@
         <environment_variable name="API_KEY" inject="api_key" />
     </environment_variables>
     <command><![CDATA[
+        
+        mkdir -p /srv/shiny-server/data/ &&
+        ln -s '$infile' /srv/shiny-server/data/inputdata.txt &&
+
         mkdir -p /var/log/shiny-server &&
         chown shiny.shiny /var/log/shiny-server &&
 

From 0c3ce1a905e22494211b962229eb641d305f7464 Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Fri, 13 Dec 2019 19:14:33 +0100
Subject: [PATCH 084/853] Copy inputdata instead of ln -s + help section update
 (#44)

* Copy inputdata instead of ln -s

* Copy inputdata instead of ln -s

* Modify input datatype in help
---
 interactivetool_geoexplorer.xml | 18 +++++++++---------
 interactivetool_radiant.xml     |  2 +-
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml
index 77375fd5725a..7256cb402c28 100644
--- a/interactivetool_geoexplorer.xml
+++ b/interactivetool_geoexplorer.xml
@@ -19,7 +19,7 @@
     <command><![CDATA[
 
         mkdir -p /srv/shiny-server/data/ &&
-        ln -s '$infile' /srv/shiny-server/data/inputdata.txt &&
+        cp '$infile' /srv/shiny-server/data/inputdata.txt &&
         mkdir -p /var/log/shiny-server &&
         chown shiny.shiny /var/log/shiny-server &&
 
@@ -49,16 +49,16 @@ App: http://www.davesteps.com/geoExploreR/
 
 **Input data file MUST have as longitude column clomun 2, and as latitude column, column 3**
 
-Example input file (TAB separated)::
+Example input file (csv)::
 
   "name"	"x"	"y"	"countryCode"
-  Accipiter striatus Vieillot, 1808	-60.291838	46.328137	CA
-  Accipiter striatus Vieillot, 1808	-114.58927	35.022485	US
-  Accipiter striatus Vieillot, 1808	-93.37406	30.00586	US
-  Accipiter striatus Vieillot, 1808	-79.336288	43.682218	CA
-  Accipiter striatus Vieillot, 1808	-109.156024	31.904185	US
-  Accipiter striatus Vieillot, 1808	-71.098031	42.297408	US
-  Accipiter striatus Vieillot, 1808	-110.927215	32.18203	US
+  "Accipiter striatus Vieillot, 1808"	-60.291838	46.328137	CA
+  "Accipiter striatus Vieillot, 1808"	-114.58927	35.022485	US
+  "Accipiter striatus Vieillot, 1808"	-93.37406	30.00586	US
+  "Accipiter striatus Vieillot, 1808"	-79.336288	43.682218	CA
+  "Accipiter striatus Vieillot, 1808"	-109.156024	31.904185	US
+  "Accipiter striatus Vieillot, 1808"	-71.098031	42.297408	US
+  "Accipiter striatus Vieillot, 1808"	-110.927215	32.18203	US
 
 ]]>
     </help>
diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml
index 67c0205cc0e0..05b623d0ffc3 100644
--- a/interactivetool_radiant.xml
+++ b/interactivetool_radiant.xml
@@ -19,7 +19,7 @@
     <command><![CDATA[
         
         mkdir -p /srv/shiny-server/data/ &&
-        ln -s '$infile' /srv/shiny-server/data/inputdata.txt &&
+        cp '$infile' /srv/shiny-server/data/inputdata.txt &&
 
         mkdir -p /var/log/shiny-server &&
         chown shiny.shiny /var/log/shiny-server &&

From 0acfbe350c2edf30f66795dcdde45658f850ab47 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Tue, 17 Dec 2019 00:01:25 +0100
Subject: [PATCH 085/853] Update interactivetool_jupyter_notebook.xml

---
 interactivetool_jupyter_notebook.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml
index 4665d48a3c3a..8ecafd6f75a6 100644
--- a/interactivetool_jupyter_notebook.xml
+++ b/interactivetool_jupyter_notebook.xml
@@ -22,7 +22,7 @@
         mkdir -p ./jupyter/data &&
 
         #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
-        ln -sf '$input' './jupyter/data/${cleaned_name}' &&
+        cp '$input' './jupyter/data/${cleaned_name}' &&
 
         ## change into the directory where the notebooks are located
         cd ./jupyter/ &&

From bcf600696722b41a79db12cd9aed8edbffdc036a Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Fri, 20 Dec 2019 19:38:16 +0100
Subject: [PATCH 086/853] Update help and input data file type (#45)

---
 interactivetool_geoexplorer.xml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml
index 7256cb402c28..3c8e1f5a5367 100644
--- a/interactivetool_geoexplorer.xml
+++ b/interactivetool_geoexplorer.xml
@@ -47,18 +47,18 @@ App: http://www.davesteps.com/geoExploreR/
 
 .. class:: infomark
 
-**Input data file MUST have as longitude column clomun 2, and as latitude column, column 3**
+**Input data file MUST have as a uniq ID per row on first column, longitude column on column 2, latitude column on column 3 and quantitative values on 4th column **
 
 Example input file (csv)::
 
-  "name"	"x"	"y"	"countryCode"
-  "Accipiter striatus Vieillot, 1808"	-60.291838	46.328137	CA
-  "Accipiter striatus Vieillot, 1808"	-114.58927	35.022485	US
-  "Accipiter striatus Vieillot, 1808"	-93.37406	30.00586	US
-  "Accipiter striatus Vieillot, 1808"	-79.336288	43.682218	CA
-  "Accipiter striatus Vieillot, 1808"	-109.156024	31.904185	US
-  "Accipiter striatus Vieillot, 1808"	-71.098031	42.297408	US
-  "Accipiter striatus Vieillot, 1808"	-110.927215	32.18203	US
+"ID"	"x"	"y"	"test"
+01	-60.291838	46.328137	2
+02	-114.58927	35.022485	3
+03	-93.37406	30.00586	4
+04	-79.336288	43.682218	5
+05	-109.156024	31.904185	2
+06	-71.098031	42.297408	9
+07	-110.927215	32.18203	12
 
 ]]>
     </help>

From 4d461a5e91d24bf8d4c28aeaa95a166d765138d2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 16 Jan 2020 19:28:56 +0100
Subject: [PATCH 087/853] fix jupyter

---
 interactivetool_jupyter_notebook.xml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml
index 8ecafd6f75a6..c86717460df0 100644
--- a/interactivetool_jupyter_notebook.xml
+++ b/interactivetool_jupyter_notebook.xml
@@ -21,9 +21,10 @@
         mkdir -p ./jupyter/outputs/ &&
         mkdir -p ./jupyter/data &&
 
-        #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
-        cp '$input' './jupyter/data/${cleaned_name}' &&
-
+        #if $input:
+            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
+            cp '$input' './jupyter/data/${cleaned_name}' &&
+        #end if
         ## change into the directory where the notebooks are located
         cd ./jupyter/ &&
         export PATH=/home/jovyan/.local/bin:\$PATH &&

From 944ee259d07b060513928c131d6f94481e44cbc4 Mon Sep 17 00:00:00 2001
From: Joachim Wolff <wolffj@informatik.uni-freiburg.de>
Date: Thu, 16 Jan 2020 20:58:36 +0100
Subject: [PATCH 088/853] Release 19.09 europe (#47)

* Interactive tool for higlass

* Changes as requested
---
 interactivetool_higlass.xml | 38 +++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 interactivetool_higlass.xml

diff --git a/interactivetool_higlass.xml b/interactivetool_higlass.xml
new file mode 100644
index 000000000000..8f3231e28c41
--- /dev/null
+++ b/interactivetool_higlass.xml
@@ -0,0 +1,38 @@
+<tool id="interactive_tool_higlass" tool_type="interactive" name="HiGlass" version="1.8.0">
+    <description>an interactive Hi-C data visualizer</description>
+    <requirements>
+        <container type="docker">higlass/higlass-docker</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="HiGlass Visualisation on $matrix.display_name" requires_domain="True">
+            <port>80</port>
+        </entry_point>
+    </entry_points>
+    <command><![CDATA[
+        mkdir higlass-local-data
+        && mkdir higlass-local-tmp
+        
+        && ln -s '$matrix' 'higlass-local-tmp/matrix_name.$matrix.ext'
+         
+        && python higlass-server/manage.py ingest_tileset --filename '/tmp/matrix_name.$matrix.ext' --filetype cooler --datatype matrix
+        
+    ]]>
+    </command>
+    <inputs>
+        <param name="matrix" type="data" format="cool" label="Cool file with multiple resolutions"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+    Interactive tool for visualising Hi-C data, works only for multi-cooler files which store multiple resolutions.
+    For a detailed documentaition please visit https://docs.higlass.io/.
+    </help>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/s13059-018-1486-1</citation>
+        </citations>
+    </xml>
+</tool>

From 40640440185384998a915b7059059f3b3779ada6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 16 Jan 2020 21:44:08 +0100
Subject: [PATCH 089/853] restrict tool to mcool file

---
 interactivetool_higlass.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interactivetool_higlass.xml b/interactivetool_higlass.xml
index 8f3231e28c41..1571b811a3a1 100644
--- a/interactivetool_higlass.xml
+++ b/interactivetool_higlass.xml
@@ -19,7 +19,7 @@
     ]]>
     </command>
     <inputs>
-        <param name="matrix" type="data" format="cool" label="Cool file with multiple resolutions"/>
+        <param name="matrix" type="data" format="mcool" label="Cool file with multiple resolutions"/>
     </inputs>
     <outputs>
         <data name="outfile" format="txt" />

From 4229b1783ebee7d2228770edd30ba0d131dab0bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 22 Jan 2020 09:22:08 +0100
Subject: [PATCH 090/853] Update interactivetool_cellxgene.xml

---
 interactivetool_cellxgene.xml | 95 +++++++++++++++++++++++++++++++++--
 1 file changed, 90 insertions(+), 5 deletions(-)

diff --git a/interactivetool_cellxgene.xml b/interactivetool_cellxgene.xml
index 546bd7ab58fe..3c99f3a393b5 100644
--- a/interactivetool_cellxgene.xml
+++ b/interactivetool_cellxgene.xml
@@ -3,27 +3,112 @@
         <container type="docker">quay.io/galaxy/cellxgene-galaxy-ie:ie2</container>
     </requirements>
     <entry_points>
-        <entry_point name="Cellxgene Single Cell Visualisation on $infile.display_name" requires_domain="True">
+        <entry_point name="Cellxgene Single Cell Visualization on $infile.display_name" requires_domain="True">
             <port>80</port>
         </entry_point>
     </entry_points>
-    <command><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
         #import re
         #set $fancy_name = '/tmp/galaxy_cellxgene_' + re.sub('[^\w\-_]', '_', $infile.element_identifier) + '.h5ad'
         cp '${infile}' '${fancy_name}'
         &&
-        cellxgene launch --host 0.0.0.0 --port 80 '${fancy_name}'
+        #set $experimental_annotations_file_tmp = '/tmp/galaxy_cellxgene_experimental_annotations.csv'
+        #if $experimental_annotations.experimental_annotations_select == 'enable':
+            #if $experimental_annotations.experimental_annotations_file:
+                cp '${experimental_annotations.experimental_annotations_file}' '${experimental_annotations_file_tmp}'
+            #else:
+                touch '${experimental_annotations_file_tmp}'
+            #end if
+            &&
+        #end if
+
+        cellxgene launch --host '0.0.0.0' --port 80 '${fancy_name}'
+
+        #if $diffexp.diffexp_select == 'enable'
+            --diffexp-lfc-cutoff '${diffexp.diffexp_lfc_cutoff}'
+        #else:
+            --disable-diffexp
+        #end if
+
+        #for $embedding in $embeddings:
+           --embedding '${embedding.embedding}'
+        #end for
+
+        #if $experimental_annotations.experimental_annotations_select == 'enable':
+            --experimental-annotations
+            --experimental-annotations-file '${experimental_annotations_file_tmp}'
+        #end if
+
+        --max-category-items '${max_category_items}'
+
+        #if str($title):
+            --title '${title}'
+        #end if
+
+        #if str($obs_names):
+            --obs-names '${obs_names}'
+        #end if
+
+        #if str($var_names):
+            --var-names '${var_names}'
+        #end if
+
+        ${backed}
+
+        #if $experimental_annotations.experimental_annotations_select == 'enable':
+            &&
+            cp '${experimental_annotations_file_tmp}' '${experimental_annotations_output}'
+        #end if
     ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="h5ad" label="Concatenate Dataset"/>
+        <param name="infile" type="data" format="h5ad" label="AnnData Dataset" help="Requires layout"/>
+        <conditional name="diffexp">
+            <param name="diffexp_select" type="select" label="On demand differential expression">
+                <option value="enable" selected="True">Enable</option>
+                <option value="disable">Disable</option>
+            </param>
+            <when value="disable"/>
+            <when value="enable">
+                <param name="diffexp_lfc_cutoff" type="float" value="0.01" label="threshold for log fold change" help="Genes are only returned in differential expression if the effect size is above the specified threshold for log fold change. Defaults to 0.01" argument="--diffexp-lfc-cutoff"/>
+            </when>
+        </conditional>
+        <repeat name="embeddings" title="Embeddings">
+            <param name="embedding" type="text" value="" optional="false" label="Embedding name" help="eg, 'umap'; Defaults to all." argument="--embedding"/>
+        </repeat>
+        <conditional name="experimental_annotations">
+            <param name="experimental_annotations_select" type="select" label="Enable user annotation of data (experimental)">
+                <option value="enable">Enable</option>
+                <option value="disable" selected="True">Disable</option>
+            </param>
+            <when value="disable"/>
+            <when value="enable">
+                <param name="experimental_annotations_file" type="data" format="csv" optional="true" label="Annotations file" help="CSV file to initialize editing of existing annotations;" argument="--experimental-annotations-file"/>
+            </when>
+        </conditional>
+        <param name="max_category_items" type="integer" value="1000" label="Do not display categories with more distinct values than specified." help="Defaults to 1000" argument="--max-category-items"/>
+        <param name="title" type="text" value="" label="Title to display" help="If omitted will use file name." argument="--title"/>
+        <param name="obs_names" type="text" value="" label="Name of annotation field to use for observations" help="Leave empty to default to obs index" argument="--obs-names"/>
+        <param name="var_names" type="text" value="" label="Name of annotation to use for variables" help="Leave empty to default to var index" argument="--var-names"/>
+        <param name="backed" type="boolean" truevalue="--backed" falsevalue ="" checked="false" label="Load data in file-backed mode" help="This may save memory, but may result in slower overall performance." argument="--backed"/>
     </inputs>
     <outputs>
         <data name="out_file1" format="txt" />
+        <data name="experimental_annotations_output" format="csv">
+            <filter>experimental_annotations['experimental_annotations_select'] == 'enable'</filter>
+        </data>
     </outputs>
     <tests>
     </tests>
     <help>
-    Interactive tool for visualising AnnData.
+    An interactive explorer for single-cell transcriptomics (AnnData formatted) data
+
+    cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas. Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data.
+
+    Whether you need to visualize one thousand cells or one million, cellxgene helps you gain insight into your single-cell data.
+    https://github.com/chanzuckerberg/cellxgene
     </help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.3554576</citation>
+    </citations>
 </tool>

From 7dc87aed78de749e2226049a503627c36d644d7c Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 31 Jan 2020 13:38:36 +0100
Subject: [PATCH 091/853] data_column use_header_names test and docs

- add a test (also as example)
- clarify in the docs
---
 lib/galaxy/tool_util/xsd/galaxy.xsd    |  8 +++++---
 test/functional/tools/column_param.xml | 10 ++++++++--
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index 6ae0e3e102cd..f994bc85272e 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -2563,8 +2563,10 @@ Set to ``false`` to not force user to select an option in the list.</xs:document
             <xs:documentation xml:lang="en">Used only if the ``type`` attribute
 value is ``data_column``, if ``true`` Galaxy assumes first row of ``data_ref``
 is a header and builds the select list with these values rather than the more
-generic ``c1`` ... ``cN``.
-</xs:documentation>
+generic ``c1`` ... ``cN`` (i.e. it will be ``c1: head1`` ... ``cN: headN``).
+Note that the content of the Cheetah variable is still
+the column index.
+            </xs:documentation>
           </xs:annotation>
         </xs:attribute>
         <xs:attribute name="display" type="DisplayType">
@@ -4830,7 +4832,7 @@ write out a JSON representation of the tool parameters.
 
 *Example*
 
-The following will create a cheetah variable that can be evaluated as ``$inputs`` that
+The following will create a Cheetah variable that can be evaluated as ``$inputs`` that
 will contain the tool parameter inputs.
 
 ```xml
diff --git a/test/functional/tools/column_param.xml b/test/functional/tools/column_param.xml
index 92b979210e7a..f89979179dfc 100644
--- a/test/functional/tools/column_param.xml
+++ b/test/functional/tools/column_param.xml
@@ -1,10 +1,13 @@
 <tool id="column_param" name="Column Param">
-  <command>
+  <command><![CDATA[
+    echo "col $col" &&
+    echo "col_names $col_names" &&
     cut -f '$col' '$input1' > '$output1'
-  </command>
+  ]]></command>
   <inputs>
     <param type="data" format="tabular" name="input1" label="Input 1" />
     <param name="col" type="data_column" data_ref="input1" label="Column to Use" />
+    <param name="col_names" type="data_column" data_ref="input1" use_header_names="true" label="Column to Use" />
   </inputs>
   <outputs>
     <data name="output1" format="tabular" />
@@ -13,8 +16,11 @@
     <test>
       <param name="input1" value="2.tabular" />
       <param name="col" value="2" />
+      <param name="col_names" value="2" />
       <output name="output1">
         <assert_contents>
+          <has_line line="col 2" />
+          <has_line line="col_names 2" />
           <has_line line="68" />
         </assert_contents>
       </output>

From b5b4f0955627408205509eeded6ff818f1db602b Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 31 Jan 2020 13:41:49 +0100
Subject: [PATCH 092/853] fix potential bug

empty columns must not be stripped
---
 lib/galaxy/tools/parameters/basic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 5fc67474e97d..b6cecb959f55 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1271,7 +1271,7 @@ def get_options(self, trans, other_values):
             try:
                 with open(dataset.get_file_name(), 'r') as f:
                     head = f.readline()
-                cnames = head.rstrip().split('\t')
+                cnames = head.rstrip("\n\r ").split('\t')
                 column_list = [('%d' % (i + 1), 'c%d: %s' % (i + 1, x)) for i, x in enumerate(cnames)]
                 if self.numerical:  # If numerical was requested, filter columns based on metadata
                     if hasattr(dataset, 'metadata') and hasattr(dataset.metadata, 'column_types'):

From 61e227dd855db95cee23d4e15015a91b606dee2e Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 31 Jan 2020 15:53:32 +0100
Subject: [PATCH 093/853] add missing tool output

---
 test/functional/tools/column_param.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/functional/tools/column_param.xml b/test/functional/tools/column_param.xml
index f89979179dfc..dad77b65b6bd 100644
--- a/test/functional/tools/column_param.xml
+++ b/test/functional/tools/column_param.xml
@@ -1,8 +1,8 @@
 <tool id="column_param" name="Column Param">
   <command><![CDATA[
-    echo "col $col" &&
-    echo "col_names $col_names" &&
-    cut -f '$col' '$input1' > '$output1'
+    echo "col $col" >> '$output1' &&
+    echo "col_names $col_names" >> '$output1' &&
+	cut -f '$col' '$input1' >> '$output1'
   ]]></command>
   <inputs>
     <param type="data" format="tabular" name="input1" label="Input 1" />

From a93a69dc5932f6686248d24e70334ad38b073ec5 Mon Sep 17 00:00:00 2001
From: Anne Fouilloux <annefou@geo.uio.no>
Date: Sun, 2 Feb 2020 13:44:05 +0100
Subject: [PATCH 094/853] add panoply as new interative tool (#50)

---
 interactivetool_panoply.xml | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 interactivetool_panoply.xml

diff --git a/interactivetool_panoply.xml b/interactivetool_panoply.xml
new file mode 100644
index 000000000000..6abb7b8e2c98
--- /dev/null
+++ b/interactivetool_panoply.xml
@@ -0,0 +1,28 @@
+<tool id="interactive_tool_panoply" tool_type="interactive" name="panoply" version="0.1">
+    <requirements>
+        <container type="docker">quay.io/nordicesmhub/docker-panoply</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Panoply on $infile.display_name" requires_domain="True">
+            <port>5800</port>
+        </entry_point>
+    </entry_points>
+    <command><![CDATA[
+        rm /opt/data/* -rf &&
+        cp '$infile' /opt/data/'$infile.display_name' &&
+        cd /opt/data &&
+        /opt/PanoplyJ/panoply.sh
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="netcdf,h5" label="netcdf"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="png" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        `Panoply <https://www.giss.nasa.gov/tools/panoply/>`_ plots geo-referenced and other arrays from netCDF, HDF, GRIB, and other datasets.
+    </help>
+</tool>

From 081dd5ec7307fec1bb1805ad3b77eee634415bb5 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sun, 2 Feb 2020 23:24:45 +0100
Subject: [PATCH 095/853] fix panoply IT

---
 interactivetool_panoply.xml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/interactivetool_panoply.xml b/interactivetool_panoply.xml
index 6abb7b8e2c98..66c18d5139f2 100644
--- a/interactivetool_panoply.xml
+++ b/interactivetool_panoply.xml
@@ -1,4 +1,5 @@
-<tool id="interactive_tool_panoply" tool_type="interactive" name="panoply" version="0.1">
+<tool id="interactive_tool_panoply" tool_type="interactive" name="Panoply" version="0.1">
+    <description>interative plotting tool for geo-referenced data</description>
     <requirements>
         <container type="docker">quay.io/nordicesmhub/docker-panoply</container>
     </requirements>
@@ -9,9 +10,9 @@
     </entry_points>
     <command><![CDATA[
         rm /opt/data/* -rf &&
-        cp '$infile' /opt/data/'$infile.display_name' &&
+        cp '$infile' '/opt/data/$infile.display_name' &&
         cd /opt/data &&
-        /opt/PanoplyJ/panoply.sh
+        /init
     ]]>
     </command>
     <inputs>
@@ -22,7 +23,8 @@
     </outputs>
     <tests>
     </tests>
-    <help>
+    <help><![CDATA[
         `Panoply <https://www.giss.nasa.gov/tools/panoply/>`_ plots geo-referenced and other arrays from netCDF, HDF, GRIB, and other datasets.
+    ]]>
     </help>
 </tool>

From f04a60a9b46055894b30a21212220f61dcca436c Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Mon, 3 Feb 2020 08:00:16 +0100
Subject: [PATCH 096/853] higlass changes

---
 interactivetool_higlass.xml | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/interactivetool_higlass.xml b/interactivetool_higlass.xml
index 1571b811a3a1..20ffda8df0bd 100644
--- a/interactivetool_higlass.xml
+++ b/interactivetool_higlass.xml
@@ -1,7 +1,7 @@
 <tool id="interactive_tool_higlass" tool_type="interactive" name="HiGlass" version="1.8.0">
     <description>an interactive Hi-C data visualizer</description>
     <requirements>
-        <container type="docker">higlass/higlass-docker</container>
+        <container type="docker">image-default</container>
     </requirements>
     <entry_points>
         <entry_point name="HiGlass Visualisation on $matrix.display_name" requires_domain="True">
@@ -9,13 +9,12 @@
         </entry_point>
     </entry_points>
     <command><![CDATA[
-        mkdir higlass-local-data
-        && mkdir higlass-local-tmp
-        
-        && ln -s '$matrix' 'higlass-local-tmp/matrix_name.$matrix.ext'
-         
-        && python higlass-server/manage.py ingest_tileset --filename '/tmp/matrix_name.$matrix.ext' --filetype cooler --datatype matrix
-        
+
+        ln -s '$matrix' /tmp/matrix.cool
+        && supervisord
+        && sleep 10
+        && python higlass-server/manage.py ingest_tileset --filename /tmp/matrix.cool --filetype cooler --datatype matrix
+        && tail -f /etc/hosts
     ]]>
     </command>
     <inputs>

From 85a441148f606c30242d9a614f63cf4a1ac20c78 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Mon, 3 Feb 2020 23:30:14 +0100
Subject: [PATCH 097/853] Update interactivetool_higlass.xml

---
 interactivetool_higlass.xml | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/interactivetool_higlass.xml b/interactivetool_higlass.xml
index 20ffda8df0bd..6d0510925da3 100644
--- a/interactivetool_higlass.xml
+++ b/interactivetool_higlass.xml
@@ -1,7 +1,7 @@
 <tool id="interactive_tool_higlass" tool_type="interactive" name="HiGlass" version="1.8.0">
     <description>an interactive Hi-C data visualizer</description>
     <requirements>
-        <container type="docker">image-default</container>
+        <container type="docker">quay.io/bgruening/galaxy-higlass</container>
     </requirements>
     <entry_points>
         <entry_point name="HiGlass Visualisation on $matrix.display_name" requires_domain="True">
@@ -9,19 +9,20 @@
         </entry_point>
     </entry_points>
     <command><![CDATA[
-
-        ln -s '$matrix' /tmp/matrix.cool
-        && supervisord
-        && sleep 10
-        && python higlass-server/manage.py ingest_tileset --filename /tmp/matrix.cool --filetype cooler --datatype matrix
-        && tail -f /etc/hosts
+        cp '$matrix' /tmp/matrix.cool &&
+        cd /home/higlass/projects &&
+        mkdir -p data/log/ &&
+        supervisord &&
+       	sleep 5 &&
+        python higlass-server/manage.py ingest_tileset --filename /tmp/matrix.cool --filetype cooler --datatype matrix &&
+        tail -f /var/log/supervisor/*
     ]]>
     </command>
     <inputs>
-        <param name="matrix" type="data" format="mcool" label="Cool file with multiple resolutions"/>
+	<param name="matrix" type="data" format="mcool" label="Cool file with multiple resolutions"/>
     </inputs>
     <outputs>
-        <data name="outfile" format="txt" />
+	<data name="outfile" format="txt" />
     </outputs>
     <tests>
     </tests>
@@ -35,3 +36,4 @@
         </citations>
     </xml>
 </tool>
+

From 49699aecc341066e2004e9f329c4413e03a93590 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 6 Feb 2020 12:48:49 -0500
Subject: [PATCH 098/853] Added integration test that spins up a Dockerized
 iRODS server, and runs a few tests agianst it.

---
 .../default/pinned-dev-requirements.txt       |   1 +
 lib/galaxy_test/driver/integration_util.py    |   2 +-
 .../irods_beginner_training_2016.pdf          | Bin 0 -> 497249 bytes
 test/integration/objectstore/test_irods.py    | 177 ++++++++++++++++++
 4 files changed, 179 insertions(+), 1 deletion(-)
 create mode 100644 test/integration/objectstore/irods_beginner_training_2016.pdf
 create mode 100644 test/integration/objectstore/test_irods.py

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index 916d6375727b..facffd36b33a 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -43,6 +43,7 @@ pytest-metadata==1.8.0
 pytest-postgresql==1.4.1
 pytest-pythonpath==0.7.3
 pytest==4.6.9
+python-irodsclient==0.8.2
 pytz==2019.3
 pyyaml==5.3
 recommonmark==0.6.0
diff --git a/lib/galaxy_test/driver/integration_util.py b/lib/galaxy_test/driver/integration_util.py
index 59e3ef17b860..2e402984cc0b 100644
--- a/lib/galaxy_test/driver/integration_util.py
+++ b/lib/galaxy_test/driver/integration_util.py
@@ -2,7 +2,7 @@
 
 Tests that start an actual Galaxy server with a particular configuration in
 order to test something that cannot be tested with the default functional/api
-tessting configuration.
+testing configuration.
 """
 import os
 from unittest import skip, SkipTest, TestCase
diff --git a/test/integration/objectstore/irods_beginner_training_2016.pdf b/test/integration/objectstore/irods_beginner_training_2016.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..2344e41888a526cb3697b1c1b6c241a7cd974069
GIT binary patch
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diff --git a/test/integration/objectstore/test_irods.py b/test/integration/objectstore/test_irods.py
new file mode 100644
index 000000000000..636b73ee7ed6
--- /dev/null
+++ b/test/integration/objectstore/test_irods.py
@@ -0,0 +1,177 @@
+import os
+import pytest
+import shutil
+import ssl
+import subprocess
+import time
+
+from irods.exception import CollectionDoesNotExist
+from irods.exception import DataObjectDoesNotExist
+from irods.session import iRODSSession
+
+from galaxy_test.driver import integration_util
+
+SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
+
+class IrodsObjectStoreIntegrationTestCase(integration_util.IntegrationTestCase):
+
+    container_name = "irods_server"
+
+    @classmethod
+    def setUpClass(cls):
+        print('Starting setUpClass')
+        super(IrodsObjectStoreIntegrationTestCase, cls).setUpClass()
+        IrodsObjectStoreIntegrationTestCase.start_irods_server(container_name=IrodsObjectStoreIntegrationTestCase.container_name)
+
+        # Let the server start before running the test
+        time.sleep(10)
+        print('Finishing setUpClass')
+
+    @classmethod
+    def tearDownClass(cls): 
+        print('Starting tearDownClass')
+        super(IrodsObjectStoreIntegrationTestCase, cls).tearDownClass()
+        IrodsObjectStoreIntegrationTestCase.stop_irods_server(container_name=IrodsObjectStoreIntegrationTestCase.container_name)       
+        print('Finishing tearDownClass')
+
+    @classmethod
+    def start_irods_server(cls, container_name, postgres_port=5432, irods_port=1247, docker_image='kxk302/irods-server:0.1'):
+        start_server = ['docker', 'run', '-h', 'localhost', '-p', '{port}:5432'.format(port=postgres_port), '-p', '{port}:1247'.format(port=irods_port), '-d', '--name', container_name, docker_image]
+        subprocess.check_call(start_server) 
+        
+    @classmethod
+    def stop_irods_server(cls, container_name):
+        subprocess.check_call(['docker', 'rm', '-f', container_name])
+
+    def test_get_existing_collection(self):
+        with iRODSSession(host='localhost', 
+            port='1247', 
+            user='rods',  
+            password='rods', 
+            zone='tempZone') as session:
+
+            zone='tempZone'
+            user='rods'
+        
+            aCollection = "/" + zone + "/home/" + user
+
+            coll = session.collections.get(aCollection)
+            assert coll.path == aCollection, "Error! Got wrong collection path"
+            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
+            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!"
+
+    def test_create_delete_new_collection(self):
+        with iRODSSession(host='localhost', 
+            port='1247', 
+            user='rods',  
+            password='rods', 
+            zone='tempZone') as session:
+
+            zone='tempZone'
+            user='rods'
+
+            newCollection = "/" + zone + "/home/" + user + "/testdir"
+    
+            coll = session.collections.create(newCollection)
+            assert coll.path == newCollection, "Error! Got wrong collection path"
+            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
+            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!" 
+
+            coll.remove(recurse=True, force=True)
+
+            with pytest.raises(CollectionDoesNotExist):
+                coll = session.collections.get(newCollection)
+
+    def test_create_delete_new_data_object(self):
+        with iRODSSession(host='localhost', 
+            port='1247', 
+            user='rods',  
+            password='rods', 
+            zone='tempZone') as session:
+
+            zone='tempZone'
+            user='rods'
+     
+            newCollection = "/" + zone + "/home/" + user + "/testdir"
+            newDataObject = newCollection + "/testDataObject"
+
+            # Create new collection
+            coll = session.collections.create(newCollection)
+            assert coll.path == newCollection, "Error! Got wrong collection path"
+            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
+            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!"
+
+            # Create data object
+            obj = session.data_objects.create(newDataObject)
+            assert obj.name == "testDataObject", "Error! Got wrong data object"
+
+            # Delete data object
+            obj.unlink(force=True)
+
+            # Get data object
+            with pytest.raises(DataObjectDoesNotExist):
+                obj = session.data_objects.get(newDataObject)
+
+            # Delete collection
+            coll.remove(recurse=True, force=True)
+
+            with pytest.raises(CollectionDoesNotExist):
+                coll = session.collections.get(newCollection)
+
+    def test_populate_fetch_new_data_object(self):
+        with iRODSSession(host='localhost', 
+            port='1247', 
+            user='rods',  
+            password='rods', 
+            zone='tempZone') as session:
+
+            zone='tempZone'
+            user='rods'
+
+            newCollection = "/" + zone + "/home/" + user + "/testdir"
+            fileName = "irods_beginner_training_2016.pdf"
+            fileNamePath = os.path.join(SCRIPT_DIRECTORY, fileName)
+            backupFileName = "irods_beginner_training_2016_backup.pdf"
+            backupFileNamePath = os.path.join(SCRIPT_DIRECTORY, backupFileName)
+ 
+            # Copy file from backup
+            shutil.copyfile(fileNamePath, backupFileNamePath)
+
+            # Create new collection 
+            coll = session.collections.create(newCollection)
+            assert coll.path == newCollection, "Error! Got wrong collection path"
+            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
+            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!" 
+
+            # Create new data object
+            session.data_objects.put(backupFileNamePath, newCollection + "/" + backupFileName)
+    
+            # Delete local file
+            os.remove(backupFileNamePath)         
+    
+            # Get the data object back
+            obj = session.data_objects.get(newCollection + "/" + backupFileName)
+    
+            # Write the data object to the file system
+            with obj.open("r") as f_in, open(backupFileNamePath, "wb") as f_out:
+                f_out.write(f_in.read())
+    
+            # Assert the size of file fetched from iRODS matches the local backup copy
+            assert os.path.getsize(fileNamePath) == os.path.getsize(backupFileNamePath), "Error! Size of file fetched from iRODS does not match the size of the original file" 
+    
+            # Delete local file
+            os.remove(backupFileNamePath)         
+    
+            # Delete data object
+            obj.unlink(force=True)
+    
+            # Get data object
+            with pytest.raises(DataObjectDoesNotExist):
+                obj = session.data_objects.get(newCollection + "/" + backupFileName)
+    
+            # Delete collection
+            coll.remove(recurse=True, force=True)
+    
+            # Get collection
+            with pytest.raises(CollectionDoesNotExist):
+                coll = session.collections.get(newCollection)

From 4c7c2da3bd7aa6d5c38c8cb70beea90a302db4ca Mon Sep 17 00:00:00 2001
From: Anne Fouilloux <annefou@geo.uio.no>
Date: Sat, 8 Feb 2020 20:26:29 +0100
Subject: [PATCH 099/853] try to fix panoply interactive tool (#51)

* try to fix panoply interactive tool

* add colorbars for panoply

* remove colorbars
moved colorbars to dockerfile. Untar colorbars.tar in the user home
---
 interactivetool_panoply.xml | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/interactivetool_panoply.xml b/interactivetool_panoply.xml
index 66c18d5139f2..2323bcae5c35 100644
--- a/interactivetool_panoply.xml
+++ b/interactivetool_panoply.xml
@@ -9,17 +9,26 @@
         </entry_point>
     </entry_points>
     <command><![CDATA[
-        rm /opt/data/* -rf &&
-        cp '$infile' '/opt/data/$infile.display_name' &&
-        cd /opt/data &&
-        /init
+        current_pwd=`pwd` &&
+        ln -s $current_pwd /config &&
+	mkdir /config/home  &&
+	mkdir /config/home/output &&
+	export HOME=/config/home &&
+	ln -s '$infile' '/config/home/$infile.display_name' &&
+	mkdir /config/home/.gissjava &&
+	cd /config/home/.gissjava    &&
+	tar xvf /opt/PanoplyJ/colorbars.tar &&
+	cd /config/home &&
+	/init
     ]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="netcdf,h5" label="netcdf"/>
     </inputs>
     <outputs>
-        <data name="outfile" format="png" />
+        <data name="outfile" format="png">
+	   <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true"/>
+	</data>
     </outputs>
     <tests>
     </tests>

From 55dc0e6a2f361dbcbeda6fec22be38da27e17fd2 Mon Sep 17 00:00:00 2001
From: Gianmauro Cuccuru <gmauro@gmail.com>
Date: Tue, 11 Feb 2020 11:16:37 +0100
Subject: [PATCH 100/853] add a new function to get the local ip address

---
 lib/galaxy_ext/container_monitor/monitor.py | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy_ext/container_monitor/monitor.py b/lib/galaxy_ext/container_monitor/monitor.py
index 86987b81e2da..35e3c58d6fdb 100644
--- a/lib/galaxy_ext/container_monitor/monitor.py
+++ b/lib/galaxy_ext/container_monitor/monitor.py
@@ -12,6 +12,19 @@
 from galaxy.tool_util.deps import docker_util
 
 
+def get_ip():
+    s = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
+    try:
+        # doesn't even have to be reachable
+        s.connect(('10.255.255.255', 1))
+        ip = s.getsockname()[0]
+    except Exception:
+        ip = None
+    finally:
+        s.close()
+    return ip
+
+
 def parse_ports(container_name, connection_configuration):
     while True:
         ports_command = docker_util.build_docker_simple_command("port", container_name=container_name, **connection_configuration)
@@ -41,11 +54,7 @@ def main():
         try:
             ports_raw = parse_ports(container_name, connection_configuration)
             if ports_raw is not None:
-                try:
-                    host_ip = socket.gethostbyname(socket.gethostname())
-                except Exception:
-                    # doesn't work on OS X
-                    host_ip = None
+                host_ip = get_ip()
                 with open("container_runtime.json", "w") as f:
                     ports = docker_util.parse_port_text(ports_raw)
                     if host_ip is not None:

From e5d1a7f1670c48e2077c9a2abc15eabdf352007e Mon Sep 17 00:00:00 2001
From: Gianmauro Cuccuru <gmauro@gmail.com>
Date: Tue, 11 Feb 2020 15:07:07 +0100
Subject: [PATCH 101/853] move the function into a different path

---
 lib/galaxy/util/sockets.py                  | 13 +++++++++++++
 lib/galaxy_ext/container_monitor/monitor.py | 15 +--------------
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/lib/galaxy/util/sockets.py b/lib/galaxy/util/sockets.py
index ffc246627e1d..826e69c1a23c 100644
--- a/lib/galaxy/util/sockets.py
+++ b/lib/galaxy/util/sockets.py
@@ -4,6 +4,19 @@
 import subprocess
 
 
+def get_ip():
+    s = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
+    try:
+        # doesn't even have to be reachable
+        s.connect(('10.255.255.255', 1))
+        ip = s.getsockname()[0]
+    except Exception:
+        ip = None
+    finally:
+        s.close()
+    return ip
+
+
 def unused_port(range=None):
     if range:
         return __unused_port_on_range(range)
diff --git a/lib/galaxy_ext/container_monitor/monitor.py b/lib/galaxy_ext/container_monitor/monitor.py
index 35e3c58d6fdb..e3254f2cc70f 100644
--- a/lib/galaxy_ext/container_monitor/monitor.py
+++ b/lib/galaxy_ext/container_monitor/monitor.py
@@ -1,6 +1,5 @@
 import json
 import os
-import socket
 import subprocess
 import sys
 import tempfile
@@ -10,19 +9,7 @@
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir)))
 
 from galaxy.tool_util.deps import docker_util
-
-
-def get_ip():
-    s = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
-    try:
-        # doesn't even have to be reachable
-        s.connect(('10.255.255.255', 1))
-        ip = s.getsockname()[0]
-    except Exception:
-        ip = None
-    finally:
-        s.close()
-    return ip
+from galaxy.util.sockets import get_ip
 
 
 def parse_ports(container_name, connection_configuration):

From bda4454671564810febbe4491a923e95d47c6344 Mon Sep 17 00:00:00 2001
From: Anne Fouilloux <annefou@geo.uio.no>
Date: Sat, 15 Feb 2020 12:22:19 +0100
Subject: [PATCH 102/853] update docker for interactive climate (#53)

* update docker for interactive climate

* test if data or not before copy
---
 interactivetool_climate_notebook.xml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml
index aa1692ada80c..0ddca7eacb83 100644
--- a/interactivetool_climate_notebook.xml
+++ b/interactivetool_climate_notebook.xml
@@ -1,6 +1,6 @@
-<tool id="interactive_tool_climate_notebook" tool_type="interactive" name="Interactive Climate Notebook" version="0.1">
+<tool id="interactive_tool_climate_notebook" tool_type="interactive" name="Interactive Climate Notebook" version="0.2">
     <requirements>
-        <container type="docker">nordicesmhub/docker-climate-notebook:1.0</container>
+        <container type="docker">nordicesmhub/docker-climate-notebook:1.2</container>
     </requirements>
     <entry_points>
         <entry_point name="Climate Interactive Tool" requires_domain="True">
@@ -21,8 +21,10 @@
         mkdir -p ./jupyter/outputs/ &&
         mkdir -p ./jupyter/data &&
 
-        #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
-        ln -sf '$input' './jupyter/data/${cleaned_name}' &&
+        #if $input:
+            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
+            cp '$input' './jupyter/data/${cleaned_name}' &&
+        #end if
 
         ## change into the directory where the notebooks are located
         cd ./jupyter/ &&

From 79d63abf72566c85dfdd486e587005796e78f42f Mon Sep 17 00:00:00 2001
From: Anne Fouilloux <annefou@geo.uio.no>
Date: Sat, 15 Feb 2020 15:01:26 +0100
Subject: [PATCH 103/853] Try to follow panoply developer recommendations (#52)

* Try to follow panoply developer recommendations
to fix errors

* bug fix: do not fail if no png
If users do not create any png files, it should not fail
---
 interactivetool_panoply.xml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/interactivetool_panoply.xml b/interactivetool_panoply.xml
index 2323bcae5c35..5e84abffe8ac 100644
--- a/interactivetool_panoply.xml
+++ b/interactivetool_panoply.xml
@@ -9,17 +9,17 @@
         </entry_point>
     </entry_points>
     <command><![CDATA[
-        current_pwd=`pwd` &&
-        ln -s $current_pwd /config &&
-	mkdir /config/home  &&
+        mkdir output &&
+        mkdir /config/home  &&
 	mkdir /config/home/output &&
 	export HOME=/config/home &&
-	ln -s '$infile' '/config/home/$infile.display_name' &&
+	cp '$infile' '/config/home/$infile.display_name' &&
 	mkdir /config/home/.gissjava &&
 	cd /config/home/.gissjava    &&
 	tar xvf /opt/PanoplyJ/colorbars.tar &&
-	cd /config/home &&
-	/init
+	cd - &&
+	/init &&
+	cp /config/home/output/*.png output/. | true
     ]]>
     </command>
     <inputs>

From 057dc3a9cc47a31c54d45ac47b81e92528237af7 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Wed, 19 Feb 2020 13:53:17 -0500
Subject: [PATCH 104/853] Revised parts of rods.py to use the new iRods Python
 client code. test_datatype_upload.py passes now with iRods as the object
 store.

---
 lib/galaxy/objectstore/rods.py | 985 ++++++++++++++++++++++++---------
 lib/galaxy/objectstore/s3.py   |   4 +-
 2 files changed, 713 insertions(+), 276 deletions(-)

diff --git a/lib/galaxy/objectstore/rods.py b/lib/galaxy/objectstore/rods.py
index 65114037c16b..872354330f85 100644
--- a/lib/galaxy/objectstore/rods.py
+++ b/lib/galaxy/objectstore/rods.py
@@ -1,20 +1,27 @@
 """
 Object Store plugin for the Integrated Rule-Oriented Data Store (iRODS)
-
-The module is named rods to avoid conflicting with the PyRods module, irods
 """
-
 import logging
+import multiprocessing
 import os
+from pathlib import Path
+import shutil
+import subprocess
+import threading
 import time
+from datetime import datetime
+
 from posixpath import (
     basename as path_basename,
     dirname as path_dirname,
     join as path_join
 )
-
 try:
     import irods
+    import irods.keywords as kw
+    from irods.exception import CollectionDoesNotExist
+    from irods.exception import DataObjectDoesNotExist
+    from irods.session import iRODSSession
 except ImportError:
     irods = None
 
@@ -22,59 +29,275 @@
     ObjectInvalid,
     ObjectNotFound
 )
+from galaxy.util import (
+    directory_hash_id,
+    string_as_bool,
+    umask_fix_perms,
+    which,
+)
 from galaxy.util.path import safe_relpath
+from galaxy.util.sleeper import Sleeper
+from .s3_multipart_upload import multipart_upload
 from ..objectstore import (
     DiskObjectStore,
-    local_extra_dirs
+    local_extra_dirs,
+    convert_bytes
 )
 
-IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this '
-                        'feature, please install it')
+IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this feature, please install it')
 
 log = logging.getLogger(__name__)
 
+def parse_config_xml(config_xml):
+    print('IRODS2: inside parse_config_xml')
+    try:
+        a_xml = config_xml.findall('auth')[0]
+        username = a_xml.get('username')
+        password = a_xml.get('password')
 
-class IRODSObjectStore(DiskObjectStore):
-    """
-    Galaxy object store based on iRODS
-    """
+        b_xml = config_xml.findall('resource')[0]
+        resource_name = b_xml.get('name')
 
-    def __init__(self, config, file_path=None, extra_dirs=None):
-        super(IRODSObjectStore, self).__init__(config, file_path=file_path, extra_dirs=extra_dirs)
-        assert irods is not None, IRODS_IMPORT_MESSAGE
-        self.cache_path = config.object_store_cache_path
-        self.default_resource = config.irods_default_resource or None
+        b_xml = config_xml.findall('zone')[0]
+        zone_name = b_xml.get('name')
 
-        # Connect to iRODS (AssertionErrors will be raised if anything goes wrong)
-        self.rods_env, self.rods_conn = rods_connect()
-
-        # if the root collection path in the config is unset or relative, try to use a sensible default
-        if config.irods_root_collection_path is None or (config.irods_root_collection_path is not None and not config.irods_root_collection_path.startswith('/')):
-            rods_home = self.rods_env.rodsHome
-            assert rods_home != '', "Unable to initialize iRODS Object Store: rodsHome cannot be determined and irods_root_collection_path in Galaxy config is unset or not absolute."
-            if config.irods_root_collection_path is None:
-                self.root_collection_path = path_join(rods_home, 'galaxy_data')
-            else:
-                self.root_collection_path = path_join(rods_home, config.irods_root_collection_path)
+        cn_xml = config_xml.findall('connection')
+        if not cn_xml:
+            cn_xml = {}
         else:
-            self.root_collection_path = config.irods_root_collection_path
-
-        # will return a collection object regardless of whether it exists
-        self.root_collection = irods.irodsCollection(self.rods_conn, self.root_collection_path)
-
-        if self.root_collection.getId() == -1:
-            log.warning("iRODS root collection does not exist, will attempt to create: %s", self.root_collection_path)
-            self.root_collection.upCollection()
-            assert self.root_collection.createCollection(os.path.basename(self.root_collection_path)) == 0, "iRODS root collection creation failed: %s" % self.root_collection_path
-            self.root_collection = irods.irodsCollection(self.rods_conn, self.root_collection_path)
-            assert self.root_collection.getId() != -1, "iRODS root collection creation claimed success but still does not exist"
-
-        if self.default_resource is None:
-            self.default_resource = self.rods_env.rodsDefResource
-
-        log.info("iRODS data for this instance will be stored in collection: %s, resource: %s", self.root_collection_path, self.default_resource)
-
-    def __get_rods_path(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, strip_dat=True, **kwargs):
+            cn_xml = cn_xml[0]
+
+        host = cn_xml.get('host', None)
+        port = int(cn_xml.get('port', 0))
+
+        c_xml = config_xml.findall('cache')[0]
+        cache_size = float(c_xml.get('size', -1))
+        staging_path = c_xml.get('path', None)
+
+        tag, attrs = 'extra_dir', ('type', 'path')
+        extra_dirs = config_xml.findall(tag)
+        if not extra_dirs:
+            msg = 'No {tag} element in XML tree'.format(tag=tag)
+            log.error(msg)
+            raise Exception(msg)
+        extra_dirs = [dict(((k, e.get(k)) for k in attrs)) for e in extra_dirs]
+
+        return {
+            'auth': {
+                'username': username,
+                'password': password,
+            },
+            'resource': {
+                'name': resource_name,
+            },
+            'zone': {
+                'name': zone_name,
+            },
+            'connection': {
+                'host': host,
+                'port': port,
+            },
+            'cache': {
+                'size': cache_size,
+                'path': staging_path,
+            },
+            'extra_dirs': extra_dirs,
+        }
+    except Exception:
+        # Toss it back up after logging, we can't continue loading at this point.
+        log.exception("Malformed iRODS ObjectStore Configuration XML -- unable to continue")
+        raise
+
+class CloudConfigMixin(object):
+
+    def _config_to_dict(self):
+        print('IRODS2: inside _config_to_dict')
+        return {
+            'auth': {
+                'username': self.username,
+                'password': self.password,
+            },
+            'resource': {
+                'name': self.resource,
+            },
+            'zone': {
+                'name': self.zone,
+            },
+            'connection': {
+                'host': self.host,
+                'port': self.port,
+            },
+            'cache': {
+                'size': self.cache_size,
+                'path': self.staging_path,
+            }
+        }
+
+class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
+    """
+    Object store that stores objects as data objects in an iRODS collection. A local cache 
+    exists that is used as an intermediate location for files between Galaxy and iRODS.
+    """
+    
+    store_type = 'irods'
+    
+    #def _get_bucket(self, bucket_name):
+    #def _get_size_in_s3(self, rel_path):
+    #def _key_exists(self, rel_path):
+
+    def __init__(self, config, config_dict):
+        super(IRODSObjectStore, self).__init__(config, config_dict)
+        print('IRODS2: inside __init__')
+
+        auth_dict = config_dict['auth']
+        self.username = auth_dict.get('username')
+        self.password = auth_dict.get('password')
+
+        resource_dict = config_dict['resource']
+        self.resource = resource_dict.get('name')
+
+        zone_dict = config_dict['zone']
+        self.zone = zone_dict.get('name')
+
+        connection_dict = config_dict['connection']
+        self.host = connection_dict.get('host')
+        self.port = connection_dict.get('port')
+
+        cache_dict = config_dict['cache']
+        self.cache_size = cache_dict.get('size', -1)
+        self.staging_path = cache_dict.get('path') or self.config.object_store_cache_path
+
+        extra_dirs = dict((e['type'], e['path']) for e in config_dict.get('extra_dirs', []))
+        self.extra_dirs.update(extra_dirs)
+
+        log.debug("Object cache dir: %s", self.staging_path)
+        log.debug("Job work dir: %s", self.extra_dirs['job_work'])
+
+        self._initialize()
+        
+    def __del__(self):
+        print('IRODS2: inside __del__')
+        self.session.cleanup()
+
+    def _initialize(self):
+        if irods is None:
+            raise Exception(IRODS_IMPORT_MESSAGE)
+
+        self.home =  "/" + self.zone + "/home/" + self.username
+
+        self.session = self._configure_connection()
+        #self.bucket = self._get_bucket(self.bucket)
+        # Clean cache only if value is set in galaxy.ini
+        if self.cache_size != -1:
+            # Convert GBs to bytes for comparison
+            self.cache_size = self.cache_size * 1073741824
+            # Helper for interruptable sleep
+            self.sleeper = Sleeper()
+            self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
+            self.cache_monitor_thread.start()
+            log.info("Cache cleaner manager started")
+        # Test if 'axel' is available for parallel download and pull the key into cache
+        if which('axel'):
+            self.use_axel = True
+        else:
+            self.use_axel = False
+
+    def _configure_connection(self, host='localhost', port='1247', user='rods', password='rods', zone='tempZone'):
+         with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
+            ###assert session.pool.get_connection() == 1, 'Failed to establish iRODS session'
+            print('IRODS2: inside iRODSSession')
+            return session
+
+    @classmethod
+    def parse_xml(cls, config_xml):
+        print('IRODS2: inside parse_xml')
+        return parse_config_xml(config_xml)
+
+    def to_dict(self):
+        print('IRODS: inside to_dict') 
+        as_dict = super(IRODSObjectStore, self).to_dict()
+        as_dict.update(self._config_to_dict())
+        return as_dict
+
+    def __cache_monitor(self):
+        time.sleep(2)  # Wait for things to load before starting the monitor
+        while self.running:
+            total_size = 0
+            # Is this going to be too expensive of an operation to be done frequently?
+            file_list = []
+            for dirpath, _, filenames in os.walk(self.staging_path):
+                for filename in filenames:
+                    filepath = os.path.join(dirpath, filename)
+                    file_size = os.path.getsize(filepath)
+                    total_size += file_size
+                    # Get the time given file was last accessed
+                    last_access_time = time.localtime(os.stat(filepath)[7])
+                    # Compose a tuple of the access time and the file path
+                    file_tuple = last_access_time, filepath, file_size
+                    file_list.append(file_tuple)
+            # Sort the file list (based on access time)
+            file_list.sort()
+            # Initiate cleaning once within 10% of the defined cache size?
+            cache_limit = self.cache_size * 0.9
+            if total_size > cache_limit:
+                log.info("Initiating cache cleaning: current cache size: %s; clean until smaller than: %s",
+                         convert_bytes(total_size), convert_bytes(cache_limit))
+                # How much to delete? If simply deleting up to the cache-10% limit,
+                # is likely to be deleting frequently and may run the risk of hitting
+                # the limit - maybe delete additional #%?
+                # For now, delete enough to leave at least 10% of the total cache free
+                delete_this_much = total_size - cache_limit
+                self.__clean_cache(file_list, delete_this_much)
+            self.sleeper.sleep(30)  # Test cache size every 30 seconds?
+
+    def __clean_cache(self, file_list, delete_this_much):
+        """ Keep deleting files from the file_list until the size of the deleted
+        files is greater than the value in delete_this_much parameter.
+
+        :type file_list: list
+        :param file_list: List of candidate files that can be deleted. This method
+            will start deleting files from the beginning of the list so the list
+            should be sorted accordingly. The list must contains 3-element tuples,
+            positioned as follows: position 0 holds file last accessed timestamp
+            (as time.struct_time), position 1 holds file path, and position 2 has
+            file size (e.g., (<access time>, /mnt/data/dataset_1.dat), 472394)
+
+        :type delete_this_much: int
+        :param delete_this_much: Total size of files, in bytes, that should be deleted.
+        """
+        # Keep deleting datasets from file_list until deleted_amount does not
+        # exceed delete_this_much; start deleting from the front of the file list,
+        # which assumes the oldest files come first on the list.
+        deleted_amount = 0
+        for entry in file_list:
+            if deleted_amount < delete_this_much:
+                deleted_amount += entry[2]
+                os.remove(entry[1])
+                # Debugging code for printing deleted files' stats
+                # folder, file_name = os.path.split(f[1])
+                # file_date = time.strftime("%m/%d/%y %H:%M:%S", f[0])
+                # log.debug("%s. %-25s %s, size %s (deleted %s/%s)" \
+                #     % (i, file_name, convert_bytes(f[2]), file_date, \
+                #     convert_bytes(deleted_amount), convert_bytes(delete_this_much)))
+            else:
+                log.debug("Cache cleaning done. Total space freed: %s", convert_bytes(deleted_amount))
+                return
+
+   # def _get_bucket(self, bucket_name):
+
+    def _fix_permissions(self, rel_path):
+        """ Set permissions on rel_path"""
+        for basedir, _, files in os.walk(rel_path):
+            umask_fix_perms(basedir, self.config.umask, 0o777, self.config.gid)
+            for filename in files:
+                path = os.path.join(basedir, filename)
+                # Ignore symlinks
+                if os.path.islink(path):
+                    continue
+                umask_fix_perms(path, self.config.umask, 0o666, self.config.gid)
+
+    def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs):
+        print('************* Entering _construct_path **************')
         # extra_dir should never be constructed from provided data but just
         # make sure there are no shenannigans afoot
         if extra_dir and extra_dir != os.path.normpath(extra_dir):
@@ -86,270 +309,484 @@ def __get_rods_path(self, obj, base_dir=None, dir_only=False, extra_dir=None, ex
             if not safe_relpath(alt_name):
                 log.warning('alt_name would locate path outside dir: %s', alt_name)
                 raise ObjectInvalid("The requested object is invalid")
-            # alt_name can contain parent directory references, but iRODS will
-            # not follow them, so if they are valid we normalize them out
+            # alt_name can contain parent directory references, but S3 will not
+            # follow them, so if they are valid we normalize them out
             alt_name = os.path.normpath(alt_name)
-        path = ""
+        rel_path = os.path.join(*directory_hash_id(obj.id))
+        print('obj.id: ', obj.id)
+        print('rel_path: ', rel_path)
         if extra_dir is not None:
-            path = extra_dir
+            if extra_dir_at_root:
+                rel_path = os.path.join(extra_dir, rel_path)
+                print('rel_path: ', rel_path)
+            else:
+                rel_path = os.path.join(rel_path, extra_dir)
+                print('rel_path: ', rel_path)
 
-        # extra_dir_at_root is ignored - since the iRODS plugin does not use
-        # the directory hash, there is only one level of subdirectory.
+        # for JOB_WORK directory
+        if obj_dir:
+            rel_path = os.path.join(rel_path, str(obj.id))
+        if base_dir:
+            base = self.extra_dirs.get(base_dir)
+            print('************* Exiting 1 _construct_path **************')
+            return os.path.join(base, rel_path)
+
+        # S3 folders are marked by having trailing '/' so add it now
+        ###rel_path = '%s/' % rel_path
 
         if not dir_only:
-            # the .dat extension is stripped when stored in iRODS
-            # TODO: is the strip_dat kwarg the best way to implement this?
-            if strip_dat and alt_name and alt_name.endswith('.dat'):
-                alt_name = os.path.splitext(alt_name)[0]
-            default_name = 'dataset_%s' % obj.id
-            if not strip_dat:
-                default_name += '.dat'
-            path = path_join(path, alt_name if alt_name else default_name)
-
-        path = path_join(self.root_collection_path, path)
-        return path
-
-    def __get_cache_path(self, obj, **kwargs):
-        # FIXME: does not handle collections
-        # FIXME: collisions could occur here
-        return os.path.join(self.cache_path, path_basename(self.__get_rods_path(obj, strip_dat=False, **kwargs)))
-
-    def __clean_cache_entry(self, obj, **kwargs):
-        # FIXME: does not handle collections
+            rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
+        print('************* Exiting 2 _construct_path **************')
+        return rel_path
+
+    def _get_cache_path(self, rel_path):
+        return os.path.abspath(os.path.join(self.staging_path, rel_path))
+
+    #def _get_transfer_progress(self):
+    #    return self.transfer_progress
+
+    #def _get_size_in_s3(self, rel_path):
+
+    def _get_size_in_irods(self, rel_path):
+        '''
         try:
-            os.unlink(self.__get_cache_path(obj, **kwargs))
-        except OSError:
-            # it is expected that we'll call this method a lot regardless of
-            # whether we think the cached file exists
-            pass
+            key = self.bucket.get_key(rel_path)
+            if key:
+                return key.size
+        except S3ResponseError:
+            log.exception("Could not get size of key '%s' from S3", rel_path)
+            return -1
+        '''
+
+    def _data_object_exists(self, rel_path):
+        exists = False
+        try:
+            # A hackish way of testing if the rel_path is a folder vs a file
+            is_dir = rel_path[-1] == '/'
+            if is_dir:
+                keyresult = self.bucket.get_all_keys(prefix=rel_path)
+                if len(keyresult) > 0:
+                    exists = True
+                else:
+                    exists = False
+            else:
+                key = Key(self.bucket, rel_path)
+                exists = key.exists()
+        except S3ResponseError:
+            log.exception("Trouble checking existence of S3 key '%s'", rel_path)
+            return False
+        if rel_path[0] == '/':
+            raise
+        return exists
+
+    def _in_cache(self, rel_path):
+        """ Check if the given dataset is in the local cache and return True if so. """
+        # log.debug("------ Checking cache for rel_path %s" % rel_path)
+        print('*************** Entering _in_cache() *****************')
+        cache_path = self._get_cache_path(rel_path)
+        print('cache_path: ', cache_path)
+        print('os.path.exists: ', os.path.exists(cache_path))
+        print('*************** Exiting _in_cache() *****************')
+        return os.path.exists(cache_path)
+        # TODO: Part of checking if a file is in cache should be to ensure the
+        # size of the cached file matches that on S3. Once the upload tool explicitly
+        # creates, this check sould be implemented- in the mean time, it's not
+        # looking likely to be implementable reliably.
+        # if os.path.exists(cache_path):
+        #     # print("***1 %s exists" % cache_path)
+        #     if self._key_exists(rel_path):
+        #         # print("***2 %s exists in S3" % rel_path)
+        #         # Make sure the size in cache is available in its entirety
+        #         # print("File '%s' cache size: %s, S3 size: %s" % (cache_path, os.path.getsize(cache_path), self._get_size_in_s3(rel_path)))
+        #         if os.path.getsize(cache_path) == self._get_size_in_s3(rel_path):
+        #             # print("***2.1 %s exists in S3 and the size is the same as in cache (in_cache=True)" % rel_path)
+        #             exists = True
+        #         else:
+        #             # print("***2.2 %s exists but differs in size from cache (in_cache=False)" % cache_path)
+        #             exists = False
+        #     else:
+        #         # Although not perfect decision making, this most likely means
+        #         # that the file is currently being uploaded
+        #         # print("***3 %s found in cache but not in S3 (in_cache=True)" % cache_path)
+        #         exists = True
+        # else:
+
+    def _pull_into_cache(self, rel_path):
+        # Ensure the cache directory structure exists (e.g., dataset_#_files/)
+        rel_path_dir = os.path.dirname(rel_path)
+        if not os.path.exists(self._get_cache_path(rel_path_dir)):
+            os.makedirs(self._get_cache_path(rel_path_dir))
+        # Now pull in the file
+        file_ok = self._download(rel_path)
+        self._fix_permissions(self._get_cache_path(rel_path_dir))
+        return file_ok
+
+    #def _transfer_cb(self, complete, total):
+    #    self.transfer_progress += 10
+
+    def _download(self, rel_path):
+        try:
+            log.debug("Pulling key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
+            key = self.bucket.get_key(rel_path)
+            # Test if cache is large enough to hold the new file
+            if self.cache_size > 0 and key.size > self.cache_size:
+                log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
+                             rel_path, key.size, self.cache_size)
+                return False
+            if self.use_axel:
+                log.debug("Parallel pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
+                ncores = multiprocessing.cpu_count()
+                url = key.generate_url(7200)
+                ret_code = subprocess.call(['axel', '-a', '-n', ncores, url])
+                if ret_code == 0:
+                    return True
+            else:
+                log.debug("Pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
+                self.transfer_progress = 0  # Reset transfer progress counter
+                key.get_contents_to_filename(self._get_cache_path(rel_path), cb=self._transfer_cb, num_cb=10)
+                return True
+        except S3ResponseError:
+            log.exception("Problem downloading key '%s' from S3 bucket '%s'", rel_path, self.bucket.name)
+        return False
 
-    def __get_rods_handle(self, obj, mode='r', **kwargs):
-        if kwargs.get('dir_only', False):
-            return irods.irodsCollection(self.rods_conn, self.__get_rods_path(obj, **kwargs))
+    def _push_to_os(self, rel_path, source_file=None, from_string=None):
+        """
+        Push the file pointed to by ``rel_path`` to the iRODS. Extract folder name 
+        from rel_path as iRODS collection name, and extract file name from rel_path
+        as iRODS data object name.
+        If ``source_file`` is provided, push that file instead while
+        still using ``rel_path`` for collection and object tore names.
+        If ``from_string`` is provided, set contents of the file to the value of
+        the string.
+        """
+        print('**** Entering _push_to_os ****')
+        print('IRODS: rel_path: ', rel_path)
+        p = Path(rel_path)
+        print('p: ', p)
+        print('p.parent: ', p.parent)
+        print('p.stem: ', p.stem)
+        print('p.suffix: ', p.suffix)
+
+        data_object =  p.stem + p.suffix
+        subcollection = p.parent
+        print('data_object: ', data_object)
+        print('subcollection: ', subcollection)
+
+        source_file = source_file if source_file else self._get_cache_path(rel_path)
+        print('IRODS: source_file: ', source_file)
+
+        options = {kw.FORCE_FLAG_KW: ''}
+
+        if os.path.exists(source_file):
+            # Check if the data object exists in iRODS
+            subcollection_path = self.home + "/" + str(subcollection)
+            full_irods_path = subcollection_path + "/" + str(data_object) 
+            print('full_irods_path: ', full_irods_path)
+            exists = self.session.data_objects.exists(full_irods_path)
+            if os.path.getsize(source_file) == 0 and exists:
+                log.debug("Wanted to push file '%s' to iRODS collection '%s' but its size is 0; skipping.", source_file, rel_path)
+                print('**** Exiting 1 _push_to_os ****')
+                return True
+            if from_string:
+                data_obj = self.session.data_objects.create(full_irods_path, recurse=True, **options)
+                with data_obj.open('w') as data_obj_fp:
+                    data_obj_fp.write(from_string)
+                log.debug("Pushed data from string '%s' to collection '%s'", from_string, full_irods_path)
+            else:
+                start_time = datetime.now()
+                log.debug("Pushing cache file '%s' of size %s bytes to collection '%s'", source_file, os.path.getsize(source_file), rel_path)
+                
+                # Create sub-collection first
+                self.session.collections.create(subcollection_path)
+
+                file_content = None
+                with open(source_file, 'rb') as content_file:
+                    file_content = content_file.read()
+                
+                # Write to file in subcollection created above
+                data_obj = self.session.data_objects.create(full_irods_path, recurse=True, **options)
+                with data_obj.open('w') as data_obj_fp:
+                    data_obj_fp.write(file_content)
+
+                end_time = datetime.now()
+                log.debug("Pushed cache file '%s' to collection '%s' (%s bytes transfered in %s sec)",
+                          source_file, rel_path, os.path.getsize(source_file), end_time - start_time)
+            print('**** Exiting 2 _push_to_os ****')
+            return True
         else:
-            return irods.irodsOpen(self.rods_conn, self.__get_rods_path(obj, **kwargs), mode)
+            log.error("Tried updating key '%s' from source file '%s', but source file does not exist.",
+                      rel_path, source_file)
+
+        print('**** Exiting 3 _push_to_os ****')
+        return False
 
-    def __mkcolls(self, rods_path):
+    def file_ready(self, obj, **kwargs):
         """
-        An os.makedirs() for iRODS collections.  `rods_path` is the desired collection to create.
+        A helper method that checks if a file corresponding to a dataset is
+        ready and available to be used. Return ``True`` if so, ``False`` otherwise.
         """
-        assert rods_path.startswith(self.root_collection_path + '/'), '__mkcolls(): Creating collections outside the root collection is not allowed (requested path was: %s)' % rods_path
-        mkcolls = []
-        c = irods.irodsCollection(self.rods_conn, rods_path)
-        while c.getId() == -1:
-            assert c.getCollName().startswith(self.root_collection_path + '/'), '__mkcolls(): Attempted to move above the root collection: %s' % c.getCollName()
-            mkcolls.append(c.getCollName())
-            c.upCollection()
-        for collname in reversed(mkcolls):
-            log.debug('Creating collection %s' % collname)
-            ci = irods.collInp_t()
-            ci.collName = collname
-            status = irods.rcCollCreate(self.rods_conn, ci)
-            assert status == 0, '__mkcolls(): Failed to create collection: %s' % collname
-
-    @local_extra_dirs
+        rel_path = self._construct_path(obj, **kwargs)
+        # Make sure the size in cache is available in its entirety
+        if self._in_cache(rel_path):
+            if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_s3(rel_path):
+                return True
+            log.debug("Waiting for dataset %s to transfer from OS: %s/%s", rel_path,
+                      os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_s3(rel_path))
+        return False
+
     def exists(self, obj, **kwargs):
-        doi = irods.dataObjInp_t()
-        doi.objPath = self.__get_rods_path(obj, **kwargs)
-        log.debug('exists(): checking: %s', doi.objPath)
-        return irods.rcObjStat(self.rods_conn, doi) is not None
+        print('*************Entering exists()*************')
+        in_cache = in_irods = False
+        for key, value in kwargs.items():
+            print("The value of {} is {}".format(key, value))
+        rel_path = self._construct_path(obj, **kwargs)
+        print('rel_path: ', rel_path)
+
+        # Check cache
+        if self._in_cache(rel_path):
+            in_cache = True
+        # Check iRODS 
+        ###in_irods = self._data_object_exists(rel_path)
+
+        # dir_only does not get synced so shortcut the decision
+        dir_only = kwargs.get('dir_only', False)
+        base_dir = kwargs.get('base_dir', None)
+        if dir_only:
+            if in_cache or in_irods:
+                print('*************Exiting  1 exists()*************')
+                return True
+            # for JOB_WORK directory
+            elif base_dir:
+                if not os.path.exists(rel_path):
+                    os.makedirs(rel_path)
+                print('*************Exiting  2 exists()*************')
+                return True
+            else:
+                print('*************Exiting  3 exists()*************')
+                return False
+
+        # TODO: Sync should probably not be done here. Add this to an async upload stack?
+        if in_cache and not in_irods:
+            self._push_to_os(rel_path, source_file=self._get_cache_path(rel_path))
+            print('*************Exiting  4 exists()*************')
+            return True
+        elif in_irods:
+            print('*************Exiting  5 exists()*************')
+            return True
+        else:
+            print('*************Exiting  6 exists()*************')
+            return False
 
-    @local_extra_dirs
     def create(self, obj, **kwargs):
         if not self.exists(obj, **kwargs):
-            rods_path = self.__get_rods_path(obj, **kwargs)
-            log.debug('create(): %s', rods_path)
+
+            # Pull out locally used fields
+            extra_dir = kwargs.get('extra_dir', None)
+            extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
             dir_only = kwargs.get('dir_only', False)
-            # short circuit collection creation since most of the time it will
-            # be the root collection which already exists
-            collection_path = rods_path if dir_only else path_dirname(rods_path)
-            if collection_path != self.root_collection_path:
-                self.__mkcolls(collection_path)
+            alt_name = kwargs.get('alt_name', None)
+
+            # Construct hashed path
+            rel_path = os.path.join(*directory_hash_id(obj.id))
+
+            # Optionally append extra_dir
+            if extra_dir is not None:
+                if extra_dir_at_root:
+                    rel_path = os.path.join(extra_dir, rel_path)
+                else:
+                    rel_path = os.path.join(rel_path, extra_dir)
+
+            # Create given directory in cache
+            cache_dir = os.path.join(self.staging_path, rel_path)
+            if not os.path.exists(cache_dir):
+                os.makedirs(cache_dir)
+
+            # Although not really necessary to create S3 folders (because S3 has
+            # flat namespace), do so for consistency with the regular file system
+            # S3 folders are marked by having trailing '/' so add it now
+            # s3_dir = '%s/' % rel_path
+            # self._push_to_os(s3_dir, from_string='')
+            # If instructed, create the dataset in cache & in S3
             if not dir_only:
-                # rcDataObjCreate is used instead of the irodsOpen wrapper so
-                # that we can prevent overwriting
-                doi = irods.dataObjInp_t()
-                doi.objPath = rods_path
-                doi.createMode = 0o640
-                doi.dataSize = 0  # 0 actually means "unknown", although literally 0 would be preferable
-                irods.addKeyVal(doi.condInput, irods.DEST_RESC_NAME_KW, self.default_resource)
-                status = irods.rcDataObjCreate(self.rods_conn, doi)
-                assert status >= 0, 'create(): rcDataObjCreate() failed: %s: %s: %s' % (rods_path, status, irods.strerror(status))
-
-    @local_extra_dirs
+                rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
+                open(os.path.join(self.staging_path, rel_path), 'w').close()
+                self._push_to_os(rel_path, from_string='')
+
     def empty(self, obj, **kwargs):
-        assert 'dir_only' not in kwargs, 'empty(): `dir_only` parameter is invalid here'
-        h = self.__get_rods_handle(obj, **kwargs)
-        try:
-            return h.getSize() == 0
-        except AttributeError:
-            # h is None
-            raise ObjectNotFound()
+        if self.exists(obj, **kwargs):
+            return bool(self.size(obj, **kwargs) > 0)
+        else:
+            raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
+                                 % (str(obj), str(kwargs)))
 
     def size(self, obj, **kwargs):
-        assert 'dir_only' not in kwargs, 'size(): `dir_only` parameter is invalid here'
-        h = self.__get_rods_handle(obj, **kwargs)
-        try:
-            return h.getSize()
-        except AttributeError:
-            # h is None
-            return 0
+        print('*************** Entering size ****************')
+        rel_path = self._construct_path(obj, **kwargs)
+        if self._in_cache(rel_path):
+            try:
+                print('*************** Exiting 1 size ****************')
+                return os.path.getsize(self._get_cache_path(rel_path))
+            except OSError as ex:
+                log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s", rel_path, ex)
+        elif self.exists(obj, **kwargs):
+            print('*************** Exiting 2 size ****************')
+            ## 
+            ## TODO
+            ## 
+            return self._get_size_in_s3(rel_path)
+        log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
+        print('*************** Exiting 3 size ****************')
+        return 0
 
-    @local_extra_dirs
     def delete(self, obj, entire_dir=False, **kwargs):
-        assert 'dir_only' not in kwargs, 'delete(): `dir_only` parameter is invalid here'
-        rods_path = self.__get_rods_path(obj, **kwargs)
-        # __get_rods_path prepends self.root_collection_path but we are going
-        # to ensure that it's valid anyway for safety's sake
-        assert rods_path.startswith(self.root_collection_path + '/'), 'ERROR: attempt to delete object outside root collection (path was: %s)' % rods_path
-        if entire_dir:
-            # TODO
-            raise NotImplementedError()
-        h = self.__get_rods_handle(obj, **kwargs)
+        rel_path = self._construct_path(obj, **kwargs)
+        extra_dir = kwargs.get('extra_dir', None)
+        base_dir = kwargs.get('base_dir', None)
+        dir_only = kwargs.get('dir_only', False)
+        obj_dir = kwargs.get('obj_dir', False)
         try:
-            # note: PyRods' irodsFile.delete() does not set force
-            status = h.delete()
-            assert status == 0, '%d: %s' % (status, irods.strerror(status))
-            return True
-        except AttributeError:
-            log.warning('delete(): operation failed: object does not exist: %s', rods_path)
-        except AssertionError as e:
-            # delete() does not raise on deletion failure
-            log.error('delete(): operation failed: %s', e)
-        finally:
-            # remove the cached entry (finally is executed even when the try
-            # contains a return)
-            self.__clean_cache_entry(self, obj, **kwargs)
+            # Remove temparory data in JOB_WORK directory
+            if base_dir and dir_only and obj_dir:
+                shutil.rmtree(os.path.abspath(rel_path))
+                return True
+
+            # For the case of extra_files, because we don't have a reference to
+            # individual files/keys we need to remove the entire directory structure
+            # with all the files in it. This is easy for the local file system,
+            # but requires iterating through each individual key in S3 and deleing it.
+            if entire_dir and extra_dir:
+                shutil.rmtree(self._get_cache_path(rel_path))
+                results = self.bucket.get_all_keys(prefix=rel_path)
+                for key in results:
+                    log.debug("Deleting key %s", key.name)
+                    key.delete()
+                return True
+            else:
+                # Delete from cache first
+                os.unlink(self._get_cache_path(rel_path))
+                # Delete from S3 as well
+                if self._key_exists(rel_path):
+                    key = Key(self.bucket, rel_path)
+                    log.debug("Deleting key %s", key.name)
+                    key.delete()
+                    return True
+        except S3ResponseError:
+            log.exception("Could not delete key '%s' from S3", rel_path)
+        except OSError:
+            log.exception('%s delete error', self.get_filename(obj, **kwargs))
         return False
 
-    @local_extra_dirs
     def get_data(self, obj, start=0, count=-1, **kwargs):
-        log.debug('get_data(): %s')
-        h = self.__get_rods_handle(obj, **kwargs)
-        try:
-            h.seek(start)
-        except AttributeError:
-            raise ObjectNotFound()
-        if count == -1:
-            return h.read()
-        else:
-            return h.read(count)
-        # TODO: make sure implicit close is okay, DiskObjectStore actually
-        # reads data into a var, closes, and returns the var
+        rel_path = self._construct_path(obj, **kwargs)
+        # Check cache first and get file if not there
+        if not self._in_cache(rel_path):
+            self._pull_into_cache(rel_path)
+        # Read the file content from cache
+        data_file = open(self._get_cache_path(rel_path), 'r')
+        data_file.seek(start)
+        content = data_file.read(count)
+        data_file.close()
+        return content
 
-    @local_extra_dirs
     def get_filename(self, obj, **kwargs):
-        log.debug("get_filename(): called on %s %s. For better performance, avoid this method and use get_data() instead.", obj.__class__.__name__, obj.id)
-        cached_path = self.__get_cache_path(obj, **kwargs)
+        base_dir = kwargs.get('base_dir', None)
+        dir_only = kwargs.get('dir_only', False)
+        obj_dir = kwargs.get('obj_dir', False)
+        rel_path = self._construct_path(obj, **kwargs)
+
+        # for JOB_WORK directory
+        if base_dir and dir_only and obj_dir:
+            return os.path.abspath(rel_path)
+
+        cache_path = self._get_cache_path(rel_path)
+        # S3 does not recognize directories as files so cannot check if those exist.
+        # So, if checking dir only, ensure given dir exists in cache and return
+        # the expected cache path.
+        # dir_only = kwargs.get('dir_only', False)
+        # if dir_only:
+        #     if not os.path.exists(cache_path):
+        #         os.makedirs(cache_path)
+        #     return cache_path
+        # Check if the file exists in the cache first
+        if self._in_cache(rel_path):
+            return cache_path
+        # Check if the file exists in persistent storage and, if it does, pull it into cache
+        elif self.exists(obj, **kwargs):
+            if dir_only:  # Directories do not get pulled into cache
+                return cache_path
+            else:
+                if self._pull_into_cache(rel_path):
+                    return cache_path
+        # For the case of retrieving a directory only, return the expected path
+        # even if it does not exist.
+        # if dir_only:
+        #     return cache_path
+        raise ObjectNotFound('objectstore.get_filename, no cache_path: %s, kwargs: %s'
+                             % (str(obj), str(kwargs)))
+        # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
-        if not self.exists(obj, **kwargs):
-            raise ObjectNotFound()
-
-        # TODO: implement or define whether dir_only is valid
-        if 'dir_only' in kwargs:
-            raise NotImplementedError()
-
-        # cache hit
-        if os.path.exists(cached_path):
-            return os.path.abspath(cached_path)
-
-        # cache miss
-        # TODO: thread this
-        incoming_path = os.path.join(os.path.dirname(cached_path), "__incoming_%s" % os.path.basename(cached_path))
-        doi = irods.dataObjInp_t()
-        doi.objPath = self.__get_rods_path(obj, **kwargs)
-        doi.dataSize = 0  # TODO: does this affect performance? should we get size?
-        doi.numThreads = 0
-        # TODO: might want to VERIFY_CHKSUM_KW
-        log.debug('get_filename(): caching %s to %s', doi.objPath, incoming_path)
-
-        # do the iget
-        status = irods.rcDataObjGet(self.rods_conn, doi, incoming_path)
-
-        # if incoming already exists, we'll wait for another process or thread
-        # to finish caching
-        if status != irods.OVERWRITE_WITHOUT_FORCE_FLAG:
-            assert status == 0, 'get_filename(): iget %s failed (%s): %s' % (doi.objPath, status, irods.strerror(status))
-            # POSIX rename is atomic
-            # TODO: rename without clobbering
-            os.rename(incoming_path, cached_path)
-            log.debug('get_filename(): cached %s to %s', doi.objPath, cached_path)
-
-        # another process or thread is caching, wait for it
-        while not os.path.exists(cached_path):
-            # TODO: force restart after mod time > some configurable, or
-            # otherwise deal with this potential deadlock and interrupted
-            # transfers
-            time.sleep(5)
-            log.debug("get_filename(): waiting on incoming '%s' for %s %s", incoming_path, obj.__class__.__name__, obj.id)
-
-        return os.path.abspath(cached_path)
-
-    @local_extra_dirs
     def update_from_file(self, obj, file_name=None, create=False, **kwargs):
-        assert 'dir_only' not in kwargs, 'update_from_file(): `dir_only` parameter is invalid here'
-
-        # do not create if not requested
-        if create and not self.exists(obj, **kwargs):
-            raise ObjectNotFound()
-
-        if file_name is None:
-            file_name = self.__get_cache_path(obj, **kwargs)
-
-        # put will create if necessary
-        doi = irods.dataObjInp_t()
-        doi.objPath = self.__get_rods_path(obj, **kwargs)
-        doi.createMode = 0o640
-        doi.dataSize = os.stat(file_name).st_size
-        doi.numThreads = 0
-        irods.addKeyVal(doi.condInput, irods.DEST_RESC_NAME_KW, self.default_resource)
-        irods.addKeyVal(doi.condInput, irods.FORCE_FLAG_KW, '')
-        # TODO: might want to VERIFY_CHKSUM_KW
-        log.debug('update_from_file(): updating %s to %s', file_name, doi.objPath)
-
-        # do the iput
-        status = irods.rcDataObjPut(self.rods_conn, doi, file_name)
-        assert status == 0, 'update_from_file(): iput %s failed (%s): %s' % (doi.objPath, status, irods.strerror(status))
+        if create:
+            self.create(obj, **kwargs)
+        if self.exists(obj, **kwargs):
+            rel_path = self._construct_path(obj, **kwargs)
+            # Chose whether to use the dataset file itself or an alternate file
+            if file_name:
+                source_file = os.path.abspath(file_name)
+                # Copy into cache
+                cache_file = self._get_cache_path(rel_path)
+                try:
+                    if source_file != cache_file:
+                        # FIXME? Should this be a `move`?
+                        shutil.copy2(source_file, cache_file)
+                    self._fix_permissions(cache_file)
+                except OSError:
+                    log.exception("Trouble copying source file '%s' to cache '%s'", source_file, cache_file)
+            else:
+                source_file = self._get_cache_path(rel_path)
+            # Update the file on S3
+            self._push_to_os(rel_path, source_file)
+        else:
+            raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
+                                 % (str(obj), str(kwargs)))
 
     def get_object_url(self, obj, **kwargs):
+        if self.exists(obj, **kwargs):
+            rel_path = self._construct_path(obj, **kwargs)
+            try:
+                key = Key(self.bucket, rel_path)
+                return key.generate_url(expires_in=86400)  # 24hrs
+            except S3ResponseError:
+                log.exception("Trouble generating URL for dataset '%s'", rel_path)
         return None
 
     def get_store_usage_percent(self):
         return 0.0
 
+'''
+        ###########################################################        
+        ## These should be read from env variables or a config file
+        ###########################################################        
+        # host='localhost' 
+        host='127.0.0.1' 
+        port='1247' 
+        user='rods'  
+        password='rods' 
+        zone='tempZone'
+        ###defaultResource = 'demoResc'
 
-# monkeypatch an strerror method into the irods module
-def _rods_strerror(errno):
-    """
-    The missing `strerror` for iRODS error codes
-    """
-    if not hasattr(irods, '__rods_strerror_map'):
-        irods.__rods_strerror_map = {}
-        for name in dir(irods):
-            v = getattr(irods, name)
-            if type(v) == int and v < 0:
-                irods.__rods_strerror_map[v] = name
-    return irods.__rods_strerror_map.get(errno, 'GALAXY_NO_ERRNO_MAPPING_FOUND')
-
-
-if irods is not None:
-    irods.strerror = _rods_strerror
-
-
-def rods_connect():
-    """
-    A basic iRODS connection mechanism that connects using the current iRODS
-    environment
-    """
-    status, env = irods.getRodsEnv()
-    assert status == 0, 'connect(): getRodsEnv() failed (%s): %s' % (status, irods.strerror(status))
-    conn, err = irods.rcConnect(env.rodsHost,
-                                env.rodsPort,
-                                env.rodsUserName,
-                                env.rodsZone)
-    assert err.status == 0, 'connect(): rcConnect() failed (%s): %s' % (err.status, err.msg)
-    status, pw = irods.obfGetPw()
-    assert status == 0, 'connect(): getting password with obfGetPw() failed (%s): %s' % (status, irods.strerror(status))
-    status = irods.clientLoginWithObfPassword(conn, pw)
-    assert status == 0, 'connect(): logging in with clientLoginWithObfPassword() failed (%s): %s' % (status, irods.strerror(status))
-    return env, conn
+        # Connect to iRODS (AssertionErrors will be raised if anything goes wrong)
+        self.session = irods_connect(host, port, user, password, zone)
+
+        # Set iRODS home path
+        ###self.home_path = "/" + zone + "/home/" + user + '/galaxy_data'
+        self.home_path = "/" + zone + "/home/" + user
+        assert self.home_path != '', "Unable to initialize iRODS Object Store: irods_home cannot be determined."
+
+        # Will return a collection object regardless of whether it exists
+        self.root_collection = self.session.collections.get(self.home_path)
+        if self.root_collection.path != self.home_path:
+            log.warning("iRODS root collection does not exist, will attempt to create: %s", self.home_path)
+            self.root_collection = self.session.collections.create(self.home_path)
+            assert self.root_collection.path == self.home_path, "iRODS root collection creation failed: %s" % self.home_path
+'''
\ No newline at end of file
diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index 0ecd8891447e..0c2ea1281329 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -167,8 +167,8 @@ def __init__(self, config, config_dict):
             (e['type'], e['path']) for e in config_dict.get('extra_dirs', []))
         self.extra_dirs.update(extra_dirs)
 
-        log.debug("Object cache dir:    %s", self.staging_path)
-        log.debug("       job work dir: %s", self.extra_dirs['job_work'])
+        log.debug("Object cache dir: %s", self.staging_path)
+        log.debug("Job work dir: %s", self.extra_dirs['job_work'])
 
         self._initialize()
 

From cc0a71bc14ec7cef0e85c82b607769547b36ea8d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 20 Feb 2020 13:22:14 +0100
Subject: [PATCH 105/853] Make dataset discovery respect final_job_state

Fixes https://github.com/galaxyproject/galaxy/issues/9394
---
 lib/galaxy/job_execution/output_collect.py    |  9 +++--
 lib/galaxy/jobs/__init__.py                   |  5 ++-
 lib/galaxy/metadata/set_metadata.py           | 10 ++++-
 lib/galaxy/model/store/discover.py            | 38 +++++++++++--------
 lib/galaxy/tools/__init__.py                  |  5 ++-
 lib/galaxy_test/api/test_tools.py             | 16 ++++++++
 .../collection_creates_dynamic_nested.xml     |  6 ++-
 7 files changed, 64 insertions(+), 25 deletions(-)

diff --git a/lib/galaxy/job_execution/output_collect.py b/lib/galaxy/job_execution/output_collect.py
index 68602df59bcf..713c657e33c1 100644
--- a/lib/galaxy/job_execution/output_collect.py
+++ b/lib/galaxy/job_execution/output_collect.py
@@ -121,7 +121,7 @@ def collect_dynamic_outputs(
                 hdca = job_context.create_hdca(name, structure)
             persist_elements_to_hdca(job_context, elements, hdca, collector=DEFAULT_DATASET_COLLECTOR)
         elif destination_type == "hdas":
-            persist_hdas(elements, job_context)
+            persist_hdas(elements, job_context, final_job_state=job_context.final_job_state)
 
     for name, has_collection in output_collections.items():
         output_collection_def = job_context.output_collection_def(name)
@@ -152,6 +152,7 @@ def collect_dynamic_outputs(
                 filenames,
                 name=output_collection_def.name,
                 metadata_source_name=output_collection_def.metadata_source,
+                final_job_state=job_context.final_job_state,
             )
             collection_builder.populate()
         except Exception:
@@ -175,7 +176,7 @@ def find_files(self, output_name, collection, dataset_collectors):
 
 class JobContext(ModelPersistenceContext, BaseJobContext):
 
-    def __init__(self, tool, tool_provided_metadata, job, job_working_directory, permission_provider, metadata_source_provider, input_dbkey, object_store):
+    def __init__(self, tool, tool_provided_metadata, job, job_working_directory, permission_provider, metadata_source_provider, input_dbkey, object_store, final_job_state):
         self.tool = tool
         self.metadata_source_provider = metadata_source_provider
         self.permission_provider = permission_provider
@@ -186,6 +187,7 @@ def __init__(self, tool, tool_provided_metadata, job, job_working_directory, per
         self.job_working_directory = job_working_directory
         self.tool_provided_metadata = tool_provided_metadata
         self.object_store = object_store
+        self.final_job_state = final_job_state
 
     @property
     def work_context(self):
@@ -296,7 +298,7 @@ def job_id(self):
 
 class SessionlessJobContext(SessionlessModelPersistenceContext, BaseJobContext):
 
-    def __init__(self, metadata_params, tool_provided_metadata, object_store, export_store, import_store, working_directory):
+    def __init__(self, metadata_params, tool_provided_metadata, object_store, export_store, import_store, working_directory, final_job_state):
         # TODO: use a metadata source provider... (pop from inputs and add parameter)
         # TODO: handle input_dbkey...
         input_dbkey = "?"
@@ -305,6 +307,7 @@ def __init__(self, metadata_params, tool_provided_metadata, object_store, export
         self.tool_provided_metadata = tool_provided_metadata
         self.import_store = import_store
         self.input_dbkey = input_dbkey
+        self.final_job_state = final_job_state
 
     def output_collection_def(self, name):
         tool_as_dict = self.metadata_params["tool"]
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 04e036d09b5b..f9cce38d98db 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1684,7 +1684,7 @@ def fail():
         if not extended_metadata:
             # importing metadata will discover outputs if extended metadata
             # is enabled.
-            self.discover_outputs(job, inp_data, out_data, out_collections)
+            self.discover_outputs(job, inp_data, out_data, out_collections, final_job_state=final_job_state)
 
         # Certain tools require tasks to be completed after job execution
         # ( this used to be performed in the "exec_after_process" hook, but hooks are deprecated ).
@@ -1732,7 +1732,7 @@ def fail():
         self.cleanup(delete_files=delete_files)
         log.debug(finish_timer.to_str(job_id=self.job_id, tool_id=job.tool_id))
 
-    def discover_outputs(self, job, inp_data, out_data, out_collections):
+    def discover_outputs(self, job, inp_data, out_data, out_collections, final_job_state):
         # Try to just recover input_ext and dbkey from job parameters (used and set in
         # galaxy.tools.actions). Old jobs may have not set these in the job parameters
         # before persisting them.
@@ -1765,6 +1765,7 @@ def discover_outputs(self, job, inp_data, out_data, out_collections):
             inp_data=inp_data,
             input_ext=input_ext,
             input_dbkey=input_dbkey,
+            final_job_state=final_job_state,
         )
 
     def check_tool_output(self, tool_stdout, tool_stderr, tool_exit_code, job, job_stdout=None, job_stderr=None):
diff --git a/lib/galaxy/metadata/set_metadata.py b/lib/galaxy/metadata/set_metadata.py
index 4d0c050ca362..db50f6c38e29 100644
--- a/lib/galaxy/metadata/set_metadata.py
+++ b/lib/galaxy/metadata/set_metadata.py
@@ -279,7 +279,15 @@ def set_meta(new_dataset_instance, file_dict):
         # discover extra outputs...
         from galaxy.job_execution.output_collect import collect_dynamic_outputs, collect_primary_datasets, SessionlessJobContext
 
-        job_context = SessionlessJobContext(metadata_params, tool_provided_metadata, object_store, export_store, import_model_store, os.path.join(tool_job_working_directory, "working"))
+        job_context = SessionlessJobContext(
+            metadata_params,
+            tool_provided_metadata,
+            object_store,
+            export_store,
+            import_model_store,
+            os.path.join(tool_job_working_directory, "working"),
+            final_job_state=final_job_state,
+        )
 
         output_collections = {}
         for name, output_collection in metadata_params["output_collections"].items():
diff --git a/lib/galaxy/model/store/discover.py b/lib/galaxy/model/store/discover.py
index 0d668ff93bb1..0470cdd158f5 100644
--- a/lib/galaxy/model/store/discover.py
+++ b/lib/galaxy/model/store/discover.py
@@ -58,6 +58,7 @@ def create_dataset(
         sources=[],
         hashes=[],
         created_from_basename=None,
+        final_job_state='ok',
     ):
         sa_session = self.sa_session
 
@@ -103,10 +104,10 @@ def create_dataset(
                                                                      flush=False,
                                                                      sa_session=sa_session)
                 ld.library_dataset_dataset_association = ldda
-                ldda.raw_set_dataset_state(ldda.states.OK)
 
                 self.add_library_dataset_to_folder(library_folder, ld)
                 primary_data = ldda
+        primary_data.raw_set_dataset_state(final_job_state)
 
         for source_dict in sources:
             source = galaxy.model.DatasetSource()
@@ -165,20 +166,28 @@ def create_dataset(
                 dataset_att_name = dataset_att_by_name.get(att_set, att_set)
                 setattr(primary_data, dataset_att_name, dataset_attributes.get(att_set, getattr(primary_data, dataset_att_name)))
 
-        metadata_dict = dataset_attributes.get('metadata', None)
-        if metadata_dict:
-            if "dbkey" in dataset_attributes:
-                metadata_dict["dbkey"] = dataset_attributes["dbkey"]
-            # branch tested with tool_provided_metadata_3 / tool_provided_metadata_10
-            primary_data.metadata.from_JSON_dict(json_dict=metadata_dict)
-        else:
-            primary_data.set_meta()
+        try:
+            metadata_dict = dataset_attributes.get('metadata', None)
+            if metadata_dict:
+                if "dbkey" in dataset_attributes:
+                    metadata_dict["dbkey"] = dataset_attributes["dbkey"]
+                # branch tested with tool_provided_metadata_3 / tool_provided_metadata_10
+                primary_data.metadata.from_JSON_dict(json_dict=metadata_dict)
+            else:
+                primary_data.set_meta()
+        except Exception:
+            if primary_data.state == galaxy.model.HistoryDatasetAssociation.states.OK:
+                primary_data.state = galaxy.model.HistoryDatasetAssociation.states.FAILED_METADATA
+            log.exception("Exception occured while setting metdata")
 
-        primary_data.set_peek()
+        try:
+            primary_data.set_peek()
+        except Exception:
+            log.exception("Exception occured while setting dataset peek")
 
         return primary_data
 
-    def populate_collection_elements(self, collection, root_collection_builder, filenames, name=None, metadata_source_name=None):
+    def populate_collection_elements(self, collection, root_collection_builder, filenames, name=None, metadata_source_name=None, final_job_state='ok'):
         # TODO: allow configurable sorting.
         #    <sort by="lexical" /> <!-- default -->
         #    <sort by="reverse_lexical" />
@@ -225,6 +234,7 @@ def populate_collection_elements(self, collection, root_collection_builder, file
                 sources=sources,
                 hashes=hashes,
                 created_from_basename=created_from_basename,
+                final_job_state=final_job_state,
             )
             log.debug(
                 "(%s) Created dynamic collection dataset for path [%s] with element identifier [%s] for output [%s] %s",
@@ -256,8 +266,6 @@ def populate_collection_elements(self, collection, root_collection_builder, file
             association_name = '__new_primary_file_%s|%s__' % (name, element_identifier_str)
             self.add_output_dataset_association(association_name, dataset)
 
-            dataset.raw_set_dataset_state('ok')
-
         self.flush()
 
     @abc.abstractproperty
@@ -511,7 +519,7 @@ def persist_elements_to_folder(model_persistence_context, elements, library_fold
             )
 
 
-def persist_hdas(elements, model_persistence_context):
+def persist_hdas(elements, model_persistence_context, final_job_state='ok'):
     # discover files as individual datasets for the target history
     datasets = []
 
@@ -553,8 +561,8 @@ def collect_elements_for_history(elements):
                     sources=sources,
                     hashes=hashes,
                     created_from_basename=created_from_basename,
+                    final_job_state=final_job_state,
                 )
-                dataset.raw_set_dataset_state('ok')
                 if not hda_id:
                     datasets.append(dataset)
 
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 3a01212badc7..a6564a5543cb 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1783,7 +1783,7 @@ def job_failed(self, job_wrapper, message, exception=False):
         """
         pass
 
-    def discover_outputs(self, out_data, out_collections, tool_provided_metadata, tool_working_directory, job, input_ext, input_dbkey, inp_data=None):
+    def discover_outputs(self, out_data, out_collections, tool_provided_metadata, tool_working_directory, job, input_ext, input_dbkey, inp_data=None, final_job_state='ok'):
         """
         Find any additional datasets generated by a tool and attach (for
         cases where number of outputs is not known in advance).
@@ -1802,6 +1802,7 @@ def discover_outputs(self, out_data, out_collections, tool_provided_metadata, to
             metadata_source_provider,
             input_dbkey,
             object_store=tool.app.object_store,
+            final_job_state=final_job_state,
         )
         collected = output_collect.collect_primary_datasets(
             job_context,
@@ -2480,7 +2481,7 @@ def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kw
             try:
                 dataset.set_peek()
             except Exception:
-                log.exception()
+                log.exception("Exception occured while setting dataset peek")
             self.sa_session.add(dataset)
             self.sa_session.flush()
 
diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index b29404c3751f..c14ab404ffb3 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -917,6 +917,22 @@ def test_dynamic_list_output(self, history_id):
         output_element_hda_0 = output_element_0["object"]
         assert output_element_hda_0["metadata_column_types"] is not None
 
+    @skip_without_tool("collection_creates_dynamic_nested")
+    @uses_test_history(require_new=False)
+    def test_dynamic_list_output_datasets_in_failed_state(self, history_id):
+        inputs = {
+            'fail_bool': True
+        }
+        create = self._run("collection_creates_dynamic_nested", history_id, inputs, assert_ok=False, wait_for_job=True)
+        self._assert_status_code_is(create, 200)
+        collection = self._get("dataset_collections/%s" % create.json()["output_collections"][0]["id"], data={"instance_type": "history"}).json()
+        assert collection['element_count'] == 3
+        for nested_collection in collection['elements']:
+            nested_collection = nested_collection['object']
+            assert nested_collection['element_count'] == 2
+            for element in nested_collection['elements']:
+                assert element['object']['state'] == 'error'
+
     def test_nonadmin_users_cannot_create_tools(self):
         payload = dict(
             representation=json.dumps(MINIMAL_TOOL),
diff --git a/test/functional/tools/collection_creates_dynamic_nested.xml b/test/functional/tools/collection_creates_dynamic_nested.xml
index 40a3f50247c3..0e4c122d5e39 100644
--- a/test/functional/tools/collection_creates_dynamic_nested.xml
+++ b/test/functional/tools/collection_creates_dynamic_nested.xml
@@ -1,4 +1,4 @@
-<tool id="collection_creates_dynamic_nested" name="collection_creates_dynamic_nested" version="0.1.0">
+<tool id="collection_creates_dynamic_nested" name="collection_creates_dynamic_nested" version="0.1.0" profile="16.04">
   <command><![CDATA[
     echo "A" > oe1_ie1.fq ;
     echo "B" > oe1_ie2.fq ;
@@ -6,11 +6,13 @@
     echo "D" > oe2_ie2.fq ;
     echo "E" > oe3_ie1.fq ;
     echo "F" > oe3_ie2.fq ;
-    sleep '$sleep_time';    
+    sleep '$sleep_time';
+    exit $fail_bool
   ]]></command>
   <inputs>
     <param name="foo" type="text" label="Dummy Parameter" />
     <param name="sleep_time" type="integer" label="Sleep Time" value="0" />
+    <param name="fail_bool" type="boolean" label="Fail tool run?" truevalue="1" falsevalue="0"/>
   </inputs>
   <outputs>
     <collection name="list_output" type="list:list" label="Duplicate List">

From bc1013c001e1207bbf1b24334db97d350b1c1d07 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 22 Dec 2019 11:03:55 +0100
Subject: [PATCH 106/853] Add more repository installation test cases

These were supposed to not pass without
https://github.com/galaxyproject/galaxy/pull/9159, but they do.
I don't think this increases test coverage but it might be handy
to have this as integration test cases when we rip out the toolshed
from the Galaxy code base ?
---
 test/integration/test_repository_operations.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/test/integration/test_repository_operations.py b/test/integration/test_repository_operations.py
index ea41c27ae224..13a8c010372e 100644
--- a/test/integration/test_repository_operations.py
+++ b/test/integration/test_repository_operations.py
@@ -41,6 +41,21 @@ def test_repository_uninstall(self):
         self._install_repository()
         self._uninstall_repository()
 
+    def test_datatype_uninstall(self):
+        repo = ('devteam', 'blast_datatypes', '01b38f20197e')
+        self.install_repository(*repo)
+        self.uninstall_repository(*repo)
+
+    def test_package_uninstall(self):
+        repo = ('iuc', 'package_fastqc_0_11_4', 'a8f485b2efd9')
+        self.install_repository(*repo)
+        self.uninstall_repository(*repo)
+
+    def test_tool_with_package_dependency_uninstall(self):
+        repo = ('iuc', 'fastqc', 'e7b2202befea')
+        self.install_repository(*repo)
+        self.uninstall_repository(*repo)
+
     def test_repository_update(self):
         response = self._install_repository(revision=REVISION_4, version="0.0.3")[0]
         assert response['ctx_rev'] == '4'

From 8682677f8f90e84e66a30e944b750d91751c21b8 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 20 Feb 2020 14:00:18 -0500
Subject: [PATCH 107/853] Parse highlight property in default uploader
 component

---
 client/galaxy/scripts/components/Upload/Default.vue | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/Upload/Default.vue b/client/galaxy/scripts/components/Upload/Default.vue
index 064918b16fb7..0e257cc18c46 100644
--- a/client/galaxy/scripts/components/Upload/Default.vue
+++ b/client/galaxy/scripts/components/Upload/Default.vue
@@ -1,5 +1,5 @@
 <template>
-    <upload-wrapper ref="wrapper" :top-info="topInfo">
+    <upload-wrapper ref="wrapper" :top-info="topInfo" :hightlight-box="hightlightBox">
         <div class="upload-helper" v-show="showHelper"><i class="fa fa-files-o" />Drop files here</div>
         <table class="upload-table ui-table-striped" v-show="!showHelper" ref="uploadTable">
             <thead>
@@ -114,6 +114,7 @@ export default {
     data() {
         return {
             topInfo: "",
+            hightlightBox: false,
             showHelper: true,
             extension: this.app.defaultExtension,
             genome: this.app.defaultGenome,

From e84784d9a7852de36abb12397734e4754b2d25c2 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 20 Feb 2020 14:50:03 -0500
Subject: [PATCH 108/853] Disable the admin_toolshed controller (except for
 tests).

---
 .../galaxy/controllers/admin_toolshed.py      | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index eb0126d8b7a3..3c5824172b73 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1,12 +1,14 @@
 import json
 import logging
 import os
+from functools import wraps
 
 from six import string_types
 from sqlalchemy import or_
 
 import tool_shed.repository_types.util as rt_util
 from galaxy import util, web
+from galaxy.exceptions import ConfigDoesNotAllowException
 from galaxy.tool_shed.galaxy_install import install_manager
 from galaxy.tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
 from galaxy.tool_shed.galaxy_install.tools import tool_panel_manager
@@ -31,12 +33,24 @@
 log = logging.getLogger(__name__)
 
 
+def legacy_tool_shed_endpoint(func):
+    # admin only and only available if running test cases.
+    @wraps(func)
+    def wrapper(trans, *args, **kwargs):
+        if not trans.app.config.config_dict.get("running_functional_tests", False):
+            raise ConfigDoesNotAllowException("Legacy tool shed endpoint only available during testing.")
+        return func(trans, *args, **kwargs)
+
+    return wrapper
+
+
 class AdminToolshed(AdminGalaxy):
 
     installed_repository_grid = admin_toolshed_grids.InstalledRepositoryGrid()
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def activate_repository(self, trans, **kwd):
         """Activate a repository that was deactivated but not uninstalled."""
         repository_id = kwd['id']
@@ -59,6 +73,7 @@ def activate_repository(self, trans, **kwd):
 
     @web.legacy_expose_api
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def browse_repositories(self, trans, **kwd):
         message = kwd.get('message', '')
         status = kwd.get('status', '')
@@ -73,6 +88,7 @@ def browse_repositories(self, trans, **kwd):
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def restore_repository(self, trans, **kwd):
         repository_id = kwd['id']
         repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
@@ -157,6 +173,7 @@ def display_image_in_repository(self, trans, **kwd):
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def view_tool_metadata(self, trans, repository_id, tool_id, **kwd):
         message = escape(kwd.get('message', ''))
         status = kwd.get('status', 'done')
@@ -193,11 +210,13 @@ def view_tool_metadata(self, trans, repository_id, tool_id, **kwd):
     @web.json
     @web.require_admin
     @web.do_not_cache
+    @legacy_tool_shed_endpoint
     def get_file_contents(self, trans, file_path, repository_id):
         return suc.get_repository_file_contents(trans.app, file_path, repository_id, is_admin=True)
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def get_tool_dependencies(self, trans, repository_id, repository_name, repository_owner, changeset_revision):
         """
         Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for
@@ -224,6 +243,7 @@ def get_tool_dependencies(self, trans, repository_id, repository_name, repositor
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def get_updated_repository_information(self, trans, repository_id, repository_name, repository_owner, changeset_revision):
         """
         Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall
@@ -246,6 +266,7 @@ def get_updated_repository_information(self, trans, repository_id, repository_na
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def initiate_tool_dependency_installation(self, trans, tool_dependencies, **kwd):
         """
         Install specified dependencies for repository tools.  The received list of tool_dependencies
@@ -285,6 +306,7 @@ def initiate_tool_dependency_installation(self, trans, tool_dependencies, **kwd)
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def install_latest_repository_revision(self, trans, **kwd):
         """Install the latest installable revision of a repository that has been previously installed."""
         repository_id = kwd.get('id', None)
@@ -336,6 +358,7 @@ def install_latest_repository_revision(self, trans, **kwd):
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def install_tool_dependencies_with_update(self, trans, **kwd):
         """
         Updating an installed tool shed repository where new tool dependencies but no new repository
@@ -411,6 +434,7 @@ def install_tool_dependencies_with_update(self, trans, **kwd):
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def install_repositories(self, trans, **kwd):
         reinstalling = util.string_as_bool(kwd.get('reinstalling', False))
         encoded_kwd = kwd.get('encoded_kwd')
@@ -436,6 +460,7 @@ def install_repositories(self, trans, **kwd):
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def manage_repository(self, trans, **kwd):
         message = escape(kwd.get('message', ''))
         status = kwd.get('status', 'done')
@@ -509,6 +534,7 @@ def manage_repository(self, trans, **kwd):
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def monitor_repository_installation(self, trans, **kwd):
         tsr_ids = common_util.get_tool_shed_repository_ids(**kwd)
         if not tsr_ids:
@@ -530,6 +556,7 @@ def monitor_repository_installation(self, trans, **kwd):
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def prepare_for_install(self, trans, **kwd):
         if not suc.have_shed_tool_conf_for_install(trans.app):
             message = 'The <b>tool_config_file</b> setting in <b>galaxy.ini</b> must include at least one '
@@ -810,6 +837,7 @@ def prepare_for_install(self, trans, **kwd):
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def reinstall_repository(self, trans, **kwd):
         """
         Reinstall a tool shed repository that has been previously uninstalled, making sure to handle all repository
@@ -981,6 +1009,7 @@ def repository_installation_status_updates(self, trans, ids=None, status_list=No
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def reselect_tool_panel_section(self, trans, **kwd):
         """
         Select or change the tool panel section to contain the tools included in the tool shed repository
@@ -1151,6 +1180,7 @@ def reselect_tool_panel_section(self, trans, **kwd):
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def uninstall_tool_dependencies(self, trans, **kwd):
         message = escape(kwd.get('message', ''))
         status = kwd.get('status', 'done')
@@ -1195,6 +1225,7 @@ def uninstall_tool_dependencies(self, trans, **kwd):
 
     @web.expose
     @web.require_admin
+    @legacy_tool_shed_endpoint
     def update_to_changeset_revision(self, trans, **kwd):
         """Update a cloned repository to the latest revision possible."""
         message = escape(kwd.get('message', ''))

From 07576c6bef610f56fc494d145cf09d1b1c048155 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 20 Feb 2020 16:33:39 -0500
Subject: [PATCH 109/853] More revision to rods.py

---
 lib/galaxy/objectstore/rods.py | 305 ++++++++++++---------------------
 1 file changed, 105 insertions(+), 200 deletions(-)

diff --git a/lib/galaxy/objectstore/rods.py b/lib/galaxy/objectstore/rods.py
index 872354330f85..2ec313d86c36 100644
--- a/lib/galaxy/objectstore/rods.py
+++ b/lib/galaxy/objectstore/rods.py
@@ -1,26 +1,20 @@
 """
 Object Store plugin for the Integrated Rule-Oriented Data Store (iRODS)
 """
+from datetime import datetime
 import logging
-import multiprocessing
 import os
 from pathlib import Path
 import shutil
-import subprocess
 import threading
 import time
-from datetime import datetime
 
-from posixpath import (
-    basename as path_basename,
-    dirname as path_dirname,
-    join as path_join
-)
 try:
     import irods
     import irods.keywords as kw
     from irods.exception import CollectionDoesNotExist
     from irods.exception import DataObjectDoesNotExist
+    from irods.exception import NetworkException
     from irods.session import iRODSSession
 except ImportError:
     irods = None
@@ -31,13 +25,10 @@
 )
 from galaxy.util import (
     directory_hash_id,
-    string_as_bool,
     umask_fix_perms,
-    which,
 )
 from galaxy.util.path import safe_relpath
 from galaxy.util.sleeper import Sleeper
-from .s3_multipart_upload import multipart_upload
 from ..objectstore import (
     DiskObjectStore,
     local_extra_dirs,
@@ -49,7 +40,6 @@
 log = logging.getLogger(__name__)
 
 def parse_config_xml(config_xml):
-    print('IRODS2: inside parse_config_xml')
     try:
         a_xml = config_xml.findall('auth')[0]
         username = a_xml.get('username')
@@ -111,7 +101,6 @@ def parse_config_xml(config_xml):
 class CloudConfigMixin(object):
 
     def _config_to_dict(self):
-        print('IRODS2: inside _config_to_dict')
         return {
             'auth': {
                 'username': self.username,
@@ -135,19 +124,17 @@ def _config_to_dict(self):
 
 class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
     """
-    Object store that stores objects as data objects in an iRODS collection. A local cache 
+    Object store that stores objects as data objects in an iRODS collections. A local cache 
     exists that is used as an intermediate location for files between Galaxy and iRODS.
     """
     
     store_type = 'irods'
     
     #def _get_bucket(self, bucket_name):
-    #def _get_size_in_s3(self, rel_path):
     #def _key_exists(self, rel_path):
 
     def __init__(self, config, config_dict):
         super(IRODSObjectStore, self).__init__(config, config_dict)
-        print('IRODS2: inside __init__')
 
         auth_dict = config_dict['auth']
         self.username = auth_dict.get('username')
@@ -176,7 +163,6 @@ def __init__(self, config, config_dict):
         self._initialize()
         
     def __del__(self):
-        print('IRODS2: inside __del__')
         self.session.cleanup()
 
     def _initialize(self):
@@ -185,8 +171,7 @@ def _initialize(self):
 
         self.home =  "/" + self.zone + "/home/" + self.username
 
-        self.session = self._configure_connection()
-        #self.bucket = self._get_bucket(self.bucket)
+        self.session = self._configure_connection(host=self.host, port=self.port, user=self.username, password=self.password, zone=self.zone)
         # Clean cache only if value is set in galaxy.ini
         if self.cache_size != -1:
             # Convert GBs to bytes for comparison
@@ -196,25 +181,18 @@ def _initialize(self):
             self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
             self.cache_monitor_thread.start()
             log.info("Cache cleaner manager started")
-        # Test if 'axel' is available for parallel download and pull the key into cache
-        if which('axel'):
-            self.use_axel = True
-        else:
-            self.use_axel = False
 
     def _configure_connection(self, host='localhost', port='1247', user='rods', password='rods', zone='tempZone'):
-         with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
-            ###assert session.pool.get_connection() == 1, 'Failed to establish iRODS session'
-            print('IRODS2: inside iRODSSession')
+        with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
+            # Throws NetworkException if connection fails  
+            session.pool.get_connection()
             return session
 
     @classmethod
     def parse_xml(cls, config_xml):
-        print('IRODS2: inside parse_xml')
         return parse_config_xml(config_xml)
 
     def to_dict(self):
-        print('IRODS: inside to_dict') 
         as_dict = super(IRODSObjectStore, self).to_dict()
         as_dict.update(self._config_to_dict())
         return as_dict
@@ -283,8 +261,6 @@ def __clean_cache(self, file_list, delete_this_much):
                 log.debug("Cache cleaning done. Total space freed: %s", convert_bytes(deleted_amount))
                 return
 
-   # def _get_bucket(self, bucket_name):
-
     def _fix_permissions(self, rel_path):
         """ Set permissions on rel_path"""
         for basedir, _, files in os.walk(rel_path):
@@ -297,7 +273,6 @@ def _fix_permissions(self, rel_path):
                 umask_fix_perms(path, self.config.umask, 0o666, self.config.gid)
 
     def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs):
-        print('************* Entering _construct_path **************')
         # extra_dir should never be constructed from provided data but just
         # make sure there are no shenannigans afoot
         if extra_dir and extra_dir != os.path.normpath(extra_dir):
@@ -313,80 +288,61 @@ def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, ext
             # follow them, so if they are valid we normalize them out
             alt_name = os.path.normpath(alt_name)
         rel_path = os.path.join(*directory_hash_id(obj.id))
-        print('obj.id: ', obj.id)
-        print('rel_path: ', rel_path)
         if extra_dir is not None:
             if extra_dir_at_root:
                 rel_path = os.path.join(extra_dir, rel_path)
-                print('rel_path: ', rel_path)
             else:
                 rel_path = os.path.join(rel_path, extra_dir)
-                print('rel_path: ', rel_path)
 
         # for JOB_WORK directory
         if obj_dir:
             rel_path = os.path.join(rel_path, str(obj.id))
         if base_dir:
             base = self.extra_dirs.get(base_dir)
-            print('************* Exiting 1 _construct_path **************')
             return os.path.join(base, rel_path)
 
-        # S3 folders are marked by having trailing '/' so add it now
-        ###rel_path = '%s/' % rel_path
-
         if not dir_only:
             rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
-        print('************* Exiting 2 _construct_path **************')
         return rel_path
 
     def _get_cache_path(self, rel_path):
         return os.path.abspath(os.path.join(self.staging_path, rel_path))
 
-    #def _get_transfer_progress(self):
-    #    return self.transfer_progress
+    # rel_path is file or folder?
+    def _get_size_in_irods(self, rel_path):
+        p = Path(rel_path)
+        data_object_name =  p.stem + p.suffix
+        subcollection_name = p.parent
 
-    #def _get_size_in_s3(self, rel_path):
+        collection_path = self.home + "/" + str(subcollection_name)
+        data_object_path = collection_path + "/" + str(data_object_name) 
 
-    def _get_size_in_irods(self, rel_path):
-        '''
         try:
-            key = self.bucket.get_key(rel_path)
-            if key:
-                return key.size
-        except S3ResponseError:
-            log.exception("Could not get size of key '%s' from S3", rel_path)
+            data_obj = self.session.data_objects.get(data_object_path)
+            return data_obj.__sizeof__()
+        except (DataObjectDoesNotExist, CollectionDoesNotExist):
+            log.warn("Collection or data object (%s) does not exist", data_object_path)
             return -1
-        '''
 
+    # rel_path is file or folder?
     def _data_object_exists(self, rel_path):
-        exists = False
+        p = Path(rel_path)
+        data_object_name =  p.stem + p.suffix
+        subcollection_name = p.parent
+
+        collection_path = self.home + "/" + str(subcollection_name)
+        data_object_path = collection_path + "/" + str(data_object_name) 
+
         try:
-            # A hackish way of testing if the rel_path is a folder vs a file
-            is_dir = rel_path[-1] == '/'
-            if is_dir:
-                keyresult = self.bucket.get_all_keys(prefix=rel_path)
-                if len(keyresult) > 0:
-                    exists = True
-                else:
-                    exists = False
-            else:
-                key = Key(self.bucket, rel_path)
-                exists = key.exists()
-        except S3ResponseError:
-            log.exception("Trouble checking existence of S3 key '%s'", rel_path)
-            return False
-        if rel_path[0] == '/':
-            raise
-        return exists
+            self.session.data_objects.get(data_object_path)
+            return True 
+        except (DataObjectDoesNotExist, CollectionDoesNotExist):
+            log.warn("Collection or data object (%s) does not exist", data_object_path)
+            return False 
 
     def _in_cache(self, rel_path):
         """ Check if the given dataset is in the local cache and return True if so. """
-        # log.debug("------ Checking cache for rel_path %s" % rel_path)
-        print('*************** Entering _in_cache() *****************')
         cache_path = self._get_cache_path(rel_path)
-        print('cache_path: ', cache_path)
-        print('os.path.exists: ', os.path.exists(cache_path))
-        print('*************** Exiting _in_cache() *****************')
         return os.path.exists(cache_path)
         # TODO: Part of checking if a file is in cache should be to ensure the
         # size of the cached file matches that on S3. Once the upload tool explicitly
@@ -421,33 +377,34 @@ def _pull_into_cache(self, rel_path):
         self._fix_permissions(self._get_cache_path(rel_path_dir))
         return file_ok
 
-    #def _transfer_cb(self, complete, total):
-    #    self.transfer_progress += 10
-
     def _download(self, rel_path):
+        log.debug("Pulling data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
+
+        p = Path(rel_path)
+        data_object_name =  p.stem + p.suffix
+        subcollection_name = p.parent
+
+        collection_path = self.home + "/" + str(subcollection_name)
+        data_object_path = collection_path + "/" + str(data_object_name) 
+        data_obj = None
+
         try:
-            log.debug("Pulling key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
-            key = self.bucket.get_key(rel_path)
-            # Test if cache is large enough to hold the new file
-            if self.cache_size > 0 and key.size > self.cache_size:
-                log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
-                             rel_path, key.size, self.cache_size)
-                return False
-            if self.use_axel:
-                log.debug("Parallel pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
-                ncores = multiprocessing.cpu_count()
-                url = key.generate_url(7200)
-                ret_code = subprocess.call(['axel', '-a', '-n', ncores, url])
-                if ret_code == 0:
-                    return True
-            else:
-                log.debug("Pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
-                self.transfer_progress = 0  # Reset transfer progress counter
-                key.get_contents_to_filename(self._get_cache_path(rel_path), cb=self._transfer_cb, num_cb=10)
-                return True
-        except S3ResponseError:
-            log.exception("Problem downloading key '%s' from S3 bucket '%s'", rel_path, self.bucket.name)
-        return False
+            data_obj = self.session.data_objects.get(data_object_path)
+        except (DataObjectDoesNotExist, CollectionDoesNotExist):
+            log.warn("Collection or data object (%s) does not exist", data_object_path)
+            return False 
+
+        if self.cache_size > 0 and data_obj.__sizeof__() > self.cache_size:
+            log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
+                         rel_path, data_obj.__sizeof__(), self.cache_size)
+            return False
+
+        log.debug("Pulled data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
+        
+        with data_obj.open('rb') as data_obj_fp, open(self._get_cache_path(rel_path), "wb") as cache_fp:
+            content = data_obj_fp.read()
+            cache_fp.write(content)
+        return True
 
     def _push_to_os(self, rel_path, source_file=None, from_string=None):
         """
@@ -455,69 +412,52 @@ def _push_to_os(self, rel_path, source_file=None, from_string=None):
         from rel_path as iRODS collection name, and extract file name from rel_path
         as iRODS data object name.
         If ``source_file`` is provided, push that file instead while
-        still using ``rel_path`` for collection and object tore names.
-        If ``from_string`` is provided, set contents of the file to the value of
-        the string.
+        still using ``rel_path`` for collection and object store names.
+        If ``from_string`` is provided, set contents of the file to the value of the string.
         """
-        print('**** Entering _push_to_os ****')
-        print('IRODS: rel_path: ', rel_path)
         p = Path(rel_path)
-        print('p: ', p)
-        print('p.parent: ', p.parent)
-        print('p.stem: ', p.stem)
-        print('p.suffix: ', p.suffix)
-
-        data_object =  p.stem + p.suffix
-        subcollection = p.parent
-        print('data_object: ', data_object)
-        print('subcollection: ', subcollection)
+        data_object_name =  p.stem + p.suffix
+        subcollection_name = p.parent
 
         source_file = source_file if source_file else self._get_cache_path(rel_path)
-        print('IRODS: source_file: ', source_file)
-
         options = {kw.FORCE_FLAG_KW: ''}
 
         if os.path.exists(source_file):
             # Check if the data object exists in iRODS
-            subcollection_path = self.home + "/" + str(subcollection)
-            full_irods_path = subcollection_path + "/" + str(data_object) 
-            print('full_irods_path: ', full_irods_path)
-            exists = self.session.data_objects.exists(full_irods_path)
+            collection_path = self.home + "/" + str(subcollection_name)
+            data_object_path = collection_path + "/" + str(data_object_name) 
+            exists = self.session.data_objects.exists(data_object_path)
             if os.path.getsize(source_file) == 0 and exists:
                 log.debug("Wanted to push file '%s' to iRODS collection '%s' but its size is 0; skipping.", source_file, rel_path)
-                print('**** Exiting 1 _push_to_os ****')
                 return True
             if from_string:
-                data_obj = self.session.data_objects.create(full_irods_path, recurse=True, **options)
+                data_obj = self.session.data_objects.create(data_object_path, recurse=True, **options)
                 with data_obj.open('w') as data_obj_fp:
                     data_obj_fp.write(from_string)
-                log.debug("Pushed data from string '%s' to collection '%s'", from_string, full_irods_path)
+                log.debug("Pushed data from string '%s' to collection '%s'", from_string, data_object_path)
             else:
                 start_time = datetime.now()
                 log.debug("Pushing cache file '%s' of size %s bytes to collection '%s'", source_file, os.path.getsize(source_file), rel_path)
                 
                 # Create sub-collection first
-                self.session.collections.create(subcollection_path)
+                self.session.collections.create(collection_path, recurse=True)
 
                 file_content = None
                 with open(source_file, 'rb') as content_file:
                     file_content = content_file.read()
                 
                 # Write to file in subcollection created above
-                data_obj = self.session.data_objects.create(full_irods_path, recurse=True, **options)
+                data_obj = self.session.data_objects.create(data_object_path, recurse=True, **options)
                 with data_obj.open('w') as data_obj_fp:
                     data_obj_fp.write(file_content)
 
                 end_time = datetime.now()
                 log.debug("Pushed cache file '%s' to collection '%s' (%s bytes transfered in %s sec)",
                           source_file, rel_path, os.path.getsize(source_file), end_time - start_time)
-            print('**** Exiting 2 _push_to_os ****')
             return True
         else:
             log.error("Tried updating key '%s' from source file '%s', but source file does not exist.",
                       rel_path, source_file)
-
-        print('**** Exiting 3 _push_to_os ****')
         return False
 
     def file_ready(self, obj, **kwargs):
@@ -528,53 +468,43 @@ def file_ready(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         # Make sure the size in cache is available in its entirety
         if self._in_cache(rel_path):
-            if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_s3(rel_path):
+            if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_irods(rel_path):
                 return True
             log.debug("Waiting for dataset %s to transfer from OS: %s/%s", rel_path,
-                      os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_s3(rel_path))
+                      os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_irods(rel_path))
         return False
 
     def exists(self, obj, **kwargs):
-        print('*************Entering exists()*************')
         in_cache = in_irods = False
-        for key, value in kwargs.items():
-            print("The value of {} is {}".format(key, value))
         rel_path = self._construct_path(obj, **kwargs)
-        print('rel_path: ', rel_path)
 
         # Check cache
         if self._in_cache(rel_path):
             in_cache = True
         # Check iRODS 
-        ###in_irods = self._data_object_exists(rel_path)
+        in_irods = self._data_object_exists(rel_path)
 
         # dir_only does not get synced so shortcut the decision
         dir_only = kwargs.get('dir_only', False)
         base_dir = kwargs.get('base_dir', None)
         if dir_only:
             if in_cache or in_irods:
-                print('*************Exiting  1 exists()*************')
                 return True
             # for JOB_WORK directory
             elif base_dir:
                 if not os.path.exists(rel_path):
                     os.makedirs(rel_path)
-                print('*************Exiting  2 exists()*************')
                 return True
             else:
-                print('*************Exiting  3 exists()*************')
                 return False
 
         # TODO: Sync should probably not be done here. Add this to an async upload stack?
         if in_cache and not in_irods:
             self._push_to_os(rel_path, source_file=self._get_cache_path(rel_path))
-            print('*************Exiting  4 exists()*************')
             return True
         elif in_irods:
-            print('*************Exiting  5 exists()*************')
             return True
         else:
-            print('*************Exiting  6 exists()*************')
             return False
 
     def create(self, obj, **kwargs):
@@ -601,12 +531,6 @@ def create(self, obj, **kwargs):
             if not os.path.exists(cache_dir):
                 os.makedirs(cache_dir)
 
-            # Although not really necessary to create S3 folders (because S3 has
-            # flat namespace), do so for consistency with the regular file system
-            # S3 folders are marked by having trailing '/' so add it now
-            # s3_dir = '%s/' % rel_path
-            # self._push_to_os(s3_dir, from_string='')
-            # If instructed, create the dataset in cache & in S3
             if not dir_only:
                 rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
@@ -620,22 +544,15 @@ def empty(self, obj, **kwargs):
                                  % (str(obj), str(kwargs)))
 
     def size(self, obj, **kwargs):
-        print('*************** Entering size ****************')
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
-                print('*************** Exiting 1 size ****************')
                 return os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s", rel_path, ex)
         elif self.exists(obj, **kwargs):
-            print('*************** Exiting 2 size ****************')
-            ## 
-            ## TODO
-            ## 
-            return self._get_size_in_s3(rel_path)
+            return self._get_size_in_irods(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
-        print('*************** Exiting 3 size ****************')
         return 0
 
     def delete(self, obj, entire_dir=False, **kwargs):
@@ -651,9 +568,12 @@ def delete(self, obj, entire_dir=False, **kwargs):
                 return True
 
             # For the case of extra_files, because we don't have a reference to
-            # individual files/keys we need to remove the entire directory structure
+            # individual files we need to remove the entire directory structure
             # with all the files in it. This is easy for the local file system,
-            # but requires iterating through each individual key in S3 and deleing it.
+            # but requires iterating through each individual key in irods and deleing it.
+            #
+            # TODO!!!
+            #
             if entire_dir and extra_dir:
                 shutil.rmtree(self._get_cache_path(rel_path))
                 results = self.bucket.get_all_keys(prefix=rel_path)
@@ -664,14 +584,23 @@ def delete(self, obj, entire_dir=False, **kwargs):
             else:
                 # Delete from cache first
                 os.unlink(self._get_cache_path(rel_path))
-                # Delete from S3 as well
-                if self._key_exists(rel_path):
-                    key = Key(self.bucket, rel_path)
-                    log.debug("Deleting key %s", key.name)
-                    key.delete()
+                # Delete from irods as well
+                p = Path(rel_path)
+                data_object_name =  p.stem + p.suffix
+                subcollection_name = p.parent
+
+                collection_path = self.home + "/" + str(subcollection_name)
+                data_object_path = collection_path + "/" + str(data_object_name) 
+
+                try:
+                    data_obj = self.session.data_objects.get(data_object_path)
+                    # remove object
+                    data_obj.unlink(force=True)
                     return True
-        except S3ResponseError:
-            log.exception("Could not delete key '%s' from S3", rel_path)
+                except (DataObjectDoesNotExist, CollectionDoesNotExist):
+                    log.info("Collection or data object (%s) does not exist", data_object_path)
+                    return True 
+
         except OSError:
             log.exception('%s delete error', self.get_filename(obj, **kwargs))
         return False
@@ -699,7 +628,7 @@ def get_filename(self, obj, **kwargs):
             return os.path.abspath(rel_path)
 
         cache_path = self._get_cache_path(rel_path)
-        # S3 does not recognize directories as files so cannot check if those exist.
+        # iRODS does not recognize directories as files so cannot check if those exist.
         # So, if checking dir only, ensure given dir exists in cache and return
         # the expected cache path.
         # dir_only = kwargs.get('dir_only', False)
@@ -750,43 +679,19 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
+    # Unlike S3, url is not really applicable to iRODS
     def get_object_url(self, obj, **kwargs):
         if self.exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
-            try:
-                key = Key(self.bucket, rel_path)
-                return key.generate_url(expires_in=86400)  # 24hrs
-            except S3ResponseError:
-                log.exception("Trouble generating URL for dataset '%s'", rel_path)
-        return None
+
+            p = Path(rel_path)
+            data_object_name =  p.stem + p.suffix
+            subcollection_name = p.parent
+
+            collection_path = self.home + "/" + str(subcollection_name)
+            data_object_path = collection_path + "/" + str(data_object_name)
+            
+            return data_object_path
 
     def get_store_usage_percent(self):
-        return 0.0
-
-'''
-        ###########################################################        
-        ## These should be read from env variables or a config file
-        ###########################################################        
-        # host='localhost' 
-        host='127.0.0.1' 
-        port='1247' 
-        user='rods'  
-        password='rods' 
-        zone='tempZone'
-        ###defaultResource = 'demoResc'
-
-        # Connect to iRODS (AssertionErrors will be raised if anything goes wrong)
-        self.session = irods_connect(host, port, user, password, zone)
-
-        # Set iRODS home path
-        ###self.home_path = "/" + zone + "/home/" + user + '/galaxy_data'
-        self.home_path = "/" + zone + "/home/" + user
-        assert self.home_path != '', "Unable to initialize iRODS Object Store: irods_home cannot be determined."
-
-        # Will return a collection object regardless of whether it exists
-        self.root_collection = self.session.collections.get(self.home_path)
-        if self.root_collection.path != self.home_path:
-            log.warning("iRODS root collection does not exist, will attempt to create: %s", self.home_path)
-            self.root_collection = self.session.collections.create(self.home_path)
-            assert self.root_collection.path == self.home_path, "iRODS root collection creation failed: %s" % self.home_path
-'''
\ No newline at end of file
+        return 0.0
\ No newline at end of file

From efad255bd72b151c4773461d0e12291f4af17666 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 20 Feb 2020 16:40:29 -0500
Subject: [PATCH 110/853] Renamed file to irods

---
 lib/galaxy/objectstore/__init__.py           | 2 +-
 lib/galaxy/objectstore/{rods.py => irods.py} | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename lib/galaxy/objectstore/{rods.py => irods.py} (100%)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index 82d4878eb142..68173f3a478a 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -911,7 +911,7 @@ def type_to_object_store_class(store, fsmon=False):
         objectstore_class = HierarchicalObjectStore
         objectstore_constructor_kwds["fsmon"] = fsmon
     elif store == 'irods':
-        from .rods import IRODSObjectStore
+        from .irods import IRODSObjectStore
         objectstore_class = IRODSObjectStore
     elif store == 'azure_blob':
         from .azure_blob import AzureBlobObjectStore
diff --git a/lib/galaxy/objectstore/rods.py b/lib/galaxy/objectstore/irods.py
similarity index 100%
rename from lib/galaxy/objectstore/rods.py
rename to lib/galaxy/objectstore/irods.py

From b43236d70b74d854a2317c23552d5fc856658b8c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 20 Feb 2020 16:44:37 -0500
Subject: [PATCH 111/853] Fix shed image resolution to actually test base-path
 images as intended (and then fail through to static/images)

---
 .../galaxy/controllers/shed_tool_static.py    | 40 +++++++++++++------
 1 file changed, 27 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py b/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py
index d938f86c958b..bcc722f81dbd 100644
--- a/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py
+++ b/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py
@@ -9,6 +9,12 @@
 log = logging.getLogger(__name__)
 
 
+def _asset_exists_and_is_safe(repo_path, asset_path):
+    if not safe_contains(repo_path, asset_path):
+        raise RequestParameterInvalidException()
+    return os.path.exists(asset_path)
+
+
 class ShedToolStatic(BaseUIController):
 
     @web.expose
@@ -26,17 +32,25 @@ def index(self, trans, shed, owner, repo, tool, version, image_file):
         """
         guid = '/'.join([shed, 'repos', owner, repo, tool, version])
         tool = trans.app.toolbox.get_tool(guid)
-        repo_path = tool._repository_dir
-        if 'static/images' not in image_file:
-            path = join(repo_path, 'static', 'images', image_file)
+        repo_path = os.path.abspath(tool._repository_dir)
+        asset_path = os.path.abspath(join(repo_path, image_file))
+
+        # test specified image_file path exactly first, then fail through to
+        # other locations.
+        # Might want to swap this around and check for static/images first if
+        # that's the new(?) standard.
+        if not _asset_exists_and_is_safe(repo_path, asset_path):
+            if 'static/images' not in image_file:
+                asset_path = join(repo_path, 'static', 'images', image_file)
+                if not _asset_exists_and_is_safe(repo_path, asset_path):
+                    asset_path = None
+
+        if asset_path:
+            ext = os.path.splitext(image_file)[-1].lstrip('.')
+            if ext:
+                mime = trans.app.datatypes_registry.get_mimetype_by_extension(ext)
+                if mime:
+                    trans.response.set_content_type(mime)
+            return open(asset_path, 'rb')
         else:
-            path = join(repo_path, image_file)
-        if not safe_contains(os.path.abspath(repo_path), os.path.abspath(path)):
-            raise RequestParameterInvalidException()
-        ext = os.path.splitext(image_file)[-1].lstrip('.')
-        if ext:
-            mime = trans.app.datatypes_registry.get_mimetype_by_extension(ext)
-            if mime:
-                trans.response.set_content_type(mime)
-        if os.path.exists(path):
-            return open(path, 'rb')
+            return None

From b735f2c5abf95470a3d5599a260829677eab3163 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 20 Feb 2020 17:03:30 -0500
Subject: [PATCH 112/853] Was trying to figure out what this does to review it
 and realized there was a mismatch here.  hightlight->highlight

---
 client/galaxy/scripts/components/Upload/Collection.vue    | 8 ++++----
 client/galaxy/scripts/components/Upload/Default.vue       | 8 ++++----
 client/galaxy/scripts/components/Upload/UploadWrapper.vue | 4 ++--
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/client/galaxy/scripts/components/Upload/Collection.vue b/client/galaxy/scripts/components/Upload/Collection.vue
index 57e0a42bdc26..d120e81f1cbf 100644
--- a/client/galaxy/scripts/components/Upload/Collection.vue
+++ b/client/galaxy/scripts/components/Upload/Collection.vue
@@ -1,5 +1,5 @@
 <template>
-    <upload-wrapper ref="wrapper" :top-info="topInfo" :hightlight-box="hightlightBox">
+    <upload-wrapper ref="wrapper" :top-info="topInfo" :highlight-box="highlightBox">
         <div class="upload-helper" v-show="showHelper"><i class="fa fa-files-o" />Drop files here</div>
         <table class="upload-table ui-table-striped" v-show="!showHelper" ref="uploadTable">
             <thead>
@@ -149,7 +149,7 @@ export default {
             enableStart: false,
             enableSources: false,
             enableBuild: false,
-            hightlightBox: false,
+            highlightBox: false,
             rowUploadModel: UploadRow,
             btnLocalTitle: _l("Choose local files"),
             btnCreateTitle: _l("Paste/Fetch data"),
@@ -193,10 +193,10 @@ export default {
                 this._eventComplete();
             },
             ondragover: () => {
-                this.hightlightBox = true;
+                this.highlightBox = true;
             },
             ondragleave: () => {
-                this.hightlightBox = false;
+                this.highlightBox = false;
             }
         });
         this.collection.on("remove", model => {
diff --git a/client/galaxy/scripts/components/Upload/Default.vue b/client/galaxy/scripts/components/Upload/Default.vue
index 0e257cc18c46..fcfee878da40 100644
--- a/client/galaxy/scripts/components/Upload/Default.vue
+++ b/client/galaxy/scripts/components/Upload/Default.vue
@@ -1,5 +1,5 @@
 <template>
-    <upload-wrapper ref="wrapper" :top-info="topInfo" :hightlight-box="hightlightBox">
+    <upload-wrapper ref="wrapper" :top-info="topInfo" :highlight-box="highlightBox">
         <div class="upload-helper" v-show="showHelper"><i class="fa fa-files-o" />Drop files here</div>
         <table class="upload-table ui-table-striped" v-show="!showHelper" ref="uploadTable">
             <thead>
@@ -114,7 +114,7 @@ export default {
     data() {
         return {
             topInfo: "",
-            hightlightBox: false,
+            highlightBox: false,
             showHelper: true,
             extension: this.app.defaultExtension,
             genome: this.app.defaultGenome,
@@ -172,10 +172,10 @@ export default {
                 this._eventComplete();
             },
             ondragover: () => {
-                this.hightlightBox = true;
+                this.highlightBox = true;
             },
             ondragleave: () => {
-                this.hightlightBox = false;
+                this.highlightBox = false;
             }
         });
         this.collection.on("remove", model => {
diff --git a/client/galaxy/scripts/components/Upload/UploadWrapper.vue b/client/galaxy/scripts/components/Upload/UploadWrapper.vue
index c62a4d271499..8666b30be05e 100644
--- a/client/galaxy/scripts/components/Upload/UploadWrapper.vue
+++ b/client/galaxy/scripts/components/Upload/UploadWrapper.vue
@@ -4,7 +4,7 @@
         <div class="upload-top">
             <div class="upload-top-info" v-html="topInfo"></div>
         </div>
-        <div class="upload-box" ref="uploadBox" :style="boxStyle" :class="{ highlight: hightlightBox }">
+        <div class="upload-box" ref="uploadBox" :style="boxStyle" :class="{ highlight: highlightBox }">
             <slot />
         </div>
         <div class="upload-footer" v-if="hasFooter">
@@ -28,7 +28,7 @@ export default {
             type: String,
             default: "upload-view-default"
         },
-        hightlightBox: {
+        highlightBox: {
             type: Boolean,
             default: false
         }

From 6ed152d9763a076fb87e3e36df0a19d95cfd0f79 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 20 Feb 2020 17:50:46 -0500
Subject: [PATCH 113/853] Throw exception for invalid requested image instead
 of just returning nothing, so we can catch these in sentry.

---
 lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py b/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py
index bcc722f81dbd..042e8184f9cd 100644
--- a/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py
+++ b/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py
@@ -53,4 +53,4 @@ def index(self, trans, shed, owner, repo, tool, version, image_file):
                     trans.response.set_content_type(mime)
             return open(asset_path, 'rb')
         else:
-            return None
+            raise RequestParameterInvalidException()

From ac6913e500baf2ab1cbc809e35a254e8b1a3a6df Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 20 Feb 2020 17:55:43 -0500
Subject: [PATCH 114/853] Use ES6 function declaration to handle error response
 in workflow run form

---
 client/galaxy/scripts/mvc/tool/tool-form-composite.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
index d34cfd9418af..ce80873c1235 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
@@ -556,7 +556,7 @@ var View = Backbone.View.extend({
                         this.submissionErrorModal(job_def, response);
                     }
                 },
-                error: function(response) {
+                error: response => {
                     Galaxy.emit.debug("tool-form-composite::submit", "Submission failed.", response);
                     var input_found = false;
                     if (response && response.err_data) {

From ef5e04d525926a776c0d6b2824873d5edeefd954 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Thu, 20 Feb 2020 20:23:55 -0500
Subject: [PATCH 115/853] quote plus dbkeys in igv GEDAs

---
 display_applications/igv/bam.xml             | 6 +++---
 display_applications/igv/gff.xml             | 6 +++---
 display_applications/igv/interval_as_bed.xml | 6 +++---
 display_applications/igv/vcf.xml             | 6 +++---
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/display_applications/igv/bam.xml b/display_applications/igv/bam.xml
index 82a514aae841..8311ddf1bf96 100644
--- a/display_applications/igv/bam.xml
+++ b/display_applications/igv/bam.xml
@@ -74,9 +74,9 @@
         </param>
         <param type="template" name="redirect_url" strip="True" >
             #if $site_id.startswith( 'local_' )
-                ${site_link}?file=${bam_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?file=${bam_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #elif $site_id.startswith( 'web_link_' ):
-                ${site_link}?sessionURL=${bam_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?sessionURL=${bam_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #else:
                 ${jnlp.url}
             #end if
@@ -86,7 +86,7 @@
         <!-- Our input data table is one line per dbkey -->
         <filter>${ $dataset.dbkey == $value }</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
-        <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bam_file.qp}&amp;genome=${bam_file.dbkey}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
+        <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bam_file.qp}&amp;genome=${qp($bam_file.dbkey)}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
         <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
         <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" />
     </dynamic_links>
diff --git a/display_applications/igv/gff.xml b/display_applications/igv/gff.xml
index 78b6e6a357fa..6dfaab812220 100644
--- a/display_applications/igv/gff.xml
+++ b/display_applications/igv/gff.xml
@@ -73,9 +73,9 @@
         </param>
         <param type="template" name="redirect_url" strip="True" >
             #if $site_id.startswith( 'local_' )
-                ${site_link}?file=${gff_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?file=${gff_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #elif $site_id.startswith( 'web_link_' ):
-                ${site_link}?sessionURL=${gff_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?sessionURL=${gff_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #else:
                 ${jnlp.url}
             #end if
@@ -85,7 +85,7 @@
         <!-- Our input data table is one line per dbkey -->
         <filter>${ $dataset.dbkey == $value }</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
-        <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${gff_file.qp}&amp;genome=${gff_file.dbkey}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
+        <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${gff_file.qp}&amp;genome=${qp($gff_file.dbkey)}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
         <param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" />
     </dynamic_links>
 </display>
diff --git a/display_applications/igv/interval_as_bed.xml b/display_applications/igv/interval_as_bed.xml
index aee3acc5bdf5..f0c767328f04 100644
--- a/display_applications/igv/interval_as_bed.xml
+++ b/display_applications/igv/interval_as_bed.xml
@@ -73,9 +73,9 @@
         </param>
         <param type="template" name="redirect_url" strip="True" >
             #if $site_id.startswith( 'local_' )
-                ${site_link}?file=${bed_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?file=${bed_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #elif $site_id.startswith( 'web_link_' ):
-                ${site_link}?sessionURL=${bed_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?sessionURL=${bed_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #else:
                 ${jnlp.url}
             #end if
@@ -85,7 +85,7 @@
         <!-- Our input data table is one line per dbkey -->
         <filter>${ $dataset.dbkey == $value }</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
-        <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bed_file.qp}&amp;genome=${bed_file.dbkey}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
+        <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bed_file.qp}&amp;genome=${qp($bed_file.dbkey)}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
         <param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict" />
     </dynamic_links>
 </display>
diff --git a/display_applications/igv/vcf.xml b/display_applications/igv/vcf.xml
index 8a0f3191b098..116958ac99a7 100644
--- a/display_applications/igv/vcf.xml
+++ b/display_applications/igv/vcf.xml
@@ -74,9 +74,9 @@
         </param>
         <param type="template" name="redirect_url" strip="True" >
             #if $site_id.startswith( 'local_' )
-                ${site_link}?file=${bgzip_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?file=${bgzip_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #elif $site_id.startswith( 'web_link_' ):
-                ${site_link}?sessionURL=${bgzip_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?sessionURL=${bgzip_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #else:
                 ${jnlp.url}
             #end if
@@ -86,7 +86,7 @@
         <!-- Our input data table is one line per dbkey -->
         <filter>${ $dataset.dbkey == $value }</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
-        <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bgzip_file.qp}&amp;genome=$bgzip_file.dbkey&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
+        <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bgzip_file.qp}&amp;genome=${qp($bgzip_file.dbkey)}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
         <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
         <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
     </dynamic_links>

From 4d27d834e940e378061c1f00a1e0fdeb287229dd Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Thu, 20 Feb 2020 20:25:34 -0500
Subject: [PATCH 116/853] add igv genbank GEDA

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 75bff7943264..b52c4276610e 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -521,7 +521,9 @@
     <datatype extension="embl" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
     <datatype extension="fitch" type="galaxy.datatypes.data:Text" subclass="true"/>
     <datatype extension="gcg" type="galaxy.datatypes.data:Text" subclass="true"/>
-    <datatype extension="genbank" auto_compressed_types="gz" sniff_compressed_types="true" type="galaxy.datatypes.sequence:Genbank" display_in_upload="True"/>
+    <datatype extension="genbank" auto_compressed_types="gz" sniff_compressed_types="true" type="galaxy.datatypes.sequence:Genbank" display_in_upload="True">
+      <display file="igv/genbank.xml"/>
+    </datatype>
     <datatype extension="hennig86" type="galaxy.datatypes.data:Text" subclass="true"/>
     <datatype extension="ig" type="galaxy.datatypes.data:Text" subclass="true"/>
     <datatype extension="jackknifer" type="galaxy.datatypes.data:Text" subclass="true"/>

From f012b3055b2f38a60c8518a7ad4ae514212e0200 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Thu, 20 Feb 2020 20:49:55 -0500
Subject: [PATCH 117/853] IGV GEDAs only set genome if dbkey is set

---
 display_applications/igv/bam.xml             | 11 +++++++++--
 display_applications/igv/gff.xml             | 11 +++++++++--
 display_applications/igv/interval_as_bed.xml | 11 +++++++++--
 display_applications/igv/vcf.xml             | 11 +++++++++--
 4 files changed, 36 insertions(+), 8 deletions(-)

diff --git a/display_applications/igv/bam.xml b/display_applications/igv/bam.xml
index 8311ddf1bf96..2d273bda8a1b 100644
--- a/display_applications/igv/bam.xml
+++ b/display_applications/igv/bam.xml
@@ -21,6 +21,11 @@
                 $bam_file.dbkey
             #end if
         </param>
+        <param type="template" name="site_organism_query_param" strip="True">
+            #if str($site_organism) not in ['','?']:
+                &amp;genome=${qp($site_organism)}
+            #end if
+        </param>
         <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><![CDATA[
 <?xml version="1.0" encoding="utf-8"?>
 <jnlp
@@ -65,8 +70,10 @@
         <nativelib href="hdfnative-linux64.jar"/>
     </resources>
   <application-desc main-class="org.broad.igv.ui.IGVMainFrame">
+     #if str($site_organism) not in ['?','']:
      <argument>-g</argument>
      <argument>${site_organism}</argument>
+     #end if
      <argument>${bam_file.url}</argument>
   </application-desc>
 </jnlp>
@@ -74,9 +81,9 @@
         </param>
         <param type="template" name="redirect_url" strip="True" >
             #if $site_id.startswith( 'local_' )
-                ${site_link}?file=${bam_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?file=${bam_file.qp}${site_organism_query_param}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #elif $site_id.startswith( 'web_link_' ):
-                ${site_link}?sessionURL=${bam_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?sessionURL=${bam_file.qp}${site_organism_query_param}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #else:
                 ${jnlp.url}
             #end if
diff --git a/display_applications/igv/gff.xml b/display_applications/igv/gff.xml
index 6dfaab812220..d36b8c368c6d 100644
--- a/display_applications/igv/gff.xml
+++ b/display_applications/igv/gff.xml
@@ -20,6 +20,11 @@
                 $gff_file.dbkey
             #end if
         </param>
+        <param type="template" name="site_organism_query_param" strip="True">
+            #if str($site_organism) not in ['','?']:
+                &amp;genome=${qp($site_organism)}
+            #end if
+        </param>
         <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><![CDATA[
 <?xml version="1.0" encoding="utf-8"?>
 <jnlp
@@ -64,8 +69,10 @@
         <nativelib href="hdfnative-linux64.jar"/>
     </resources>
   <application-desc main-class="org.broad.igv.ui.IGVMainFrame">
+     #if str($site_organism) not in ['?','']:
      <argument>-g</argument>
      <argument>${site_organism}</argument>
+     #end if
      <argument>${gff_file.url}</argument>
   </application-desc>
 </jnlp>
@@ -73,9 +80,9 @@
         </param>
         <param type="template" name="redirect_url" strip="True" >
             #if $site_id.startswith( 'local_' )
-                ${site_link}?file=${gff_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?file=${gff_file.qp}${site_organism_query_param}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #elif $site_id.startswith( 'web_link_' ):
-                ${site_link}?sessionURL=${gff_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?sessionURL=${gff_file.qp}${site_organism_query_param}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #else:
                 ${jnlp.url}
             #end if
diff --git a/display_applications/igv/interval_as_bed.xml b/display_applications/igv/interval_as_bed.xml
index f0c767328f04..61ea274d22a0 100644
--- a/display_applications/igv/interval_as_bed.xml
+++ b/display_applications/igv/interval_as_bed.xml
@@ -20,6 +20,11 @@
                 $bed_file.dbkey
             #end if
         </param>
+        <param type="template" name="site_organism_query_param" strip="True">
+            #if str($site_organism) not in ['','?']:
+                &amp;genome=${qp($site_organism)}
+            #end if
+        </param>
         <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><![CDATA[
 <?xml version="1.0" encoding="utf-8"?>
 <jnlp
@@ -64,8 +69,10 @@
         <nativelib href="hdfnative-linux64.jar"/>
     </resources>
   <application-desc main-class="org.broad.igv.ui.IGVMainFrame">
+     #if str($site_organism) not in ['?','']:
      <argument>-g</argument>
      <argument>${site_organism}</argument>
+     #end if
      <argument>${bed_file.url}</argument>
   </application-desc>
 </jnlp>
@@ -73,9 +80,9 @@
         </param>
         <param type="template" name="redirect_url" strip="True" >
             #if $site_id.startswith( 'local_' )
-                ${site_link}?file=${bed_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?file=${bed_file.qp}${site_organism_query_param}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #elif $site_id.startswith( 'web_link_' ):
-                ${site_link}?sessionURL=${bed_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?sessionURL=${bed_file.qp}${site_organism_query_param}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #else:
                 ${jnlp.url}
             #end if
diff --git a/display_applications/igv/vcf.xml b/display_applications/igv/vcf.xml
index 116958ac99a7..f2c1e07966af 100644
--- a/display_applications/igv/vcf.xml
+++ b/display_applications/igv/vcf.xml
@@ -21,6 +21,11 @@
                 $bgzip_file.dbkey
             #end if
         </param>
+        <param type="template" name="site_organism_query_param" strip="True">
+            #if str($site_organism) not in ['','?']:
+                &amp;genome=${qp($site_organism)}
+            #end if
+        </param>
         <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><![CDATA[
 <?xml version="1.0" encoding="utf-8"?>
 <jnlp
@@ -65,8 +70,10 @@
         <nativelib href="hdfnative-linux64.jar"/>
     </resources>
   <application-desc main-class="org.broad.igv.ui.IGVMainFrame">
+     #if str($site_organism) not in ['?','']:
      <argument>-g</argument>
      <argument>${site_organism}</argument>
+     #end if
      <argument>${bgzip_file.url}</argument>
   </application-desc>
 </jnlp>
@@ -74,9 +81,9 @@
         </param>
         <param type="template" name="redirect_url" strip="True" >
             #if $site_id.startswith( 'local_' )
-                ${site_link}?file=${bgzip_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?file=${bgzip_file.qp}${site_organism_query_param}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #elif $site_id.startswith( 'web_link_' ):
-                ${site_link}?sessionURL=${bgzip_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?sessionURL=${bgzip_file.qp}${site_organism_query_param}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #else:
                 ${jnlp.url}
             #end if

From 66856d25a114e15a1acf6206262f8e0f6c82190a Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Thu, 20 Feb 2020 20:53:45 -0500
Subject: [PATCH 118/853] missing igv genbank geda

---
 display_applications/igv/genbank.xml | 99 ++++++++++++++++++++++++++++
 1 file changed, 99 insertions(+)
 create mode 100644 display_applications/igv/genbank.xml

diff --git a/display_applications/igv/genbank.xml b/display_applications/igv/genbank.xml
new file mode 100644
index 000000000000..0fb20987bfaf
--- /dev/null
+++ b/display_applications/igv/genbank.xml
@@ -0,0 +1,99 @@
+<?xml version="1.0"?>
+<display id="igv_genbank" version="1.0.0" name="display with IGV">
+    <!-- Load links from file: one line to one link -->
+    <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1">
+        <!-- Define parameters by column from file, allow splitting on builds -->
+        <dynamic_param name="site_id" value="0"/>
+        <dynamic_param name="site_name" value="1"/>
+        <dynamic_param name="site_link" value="2"/>
+        <dynamic_param name="site_dbkeys" value="3" split="True" separator="," />
+        <dynamic_param name="site_organisms" value="4" split="True" separator="," />
+        <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
+        <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter>
+        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+        <url>${redirect_url}</url>
+        <param type="data" name="genbank_file" url="galaxy_${DATASET_HASH}.gb" format="genbank" />
+        <param type="template" name="site_organism" strip="True" >
+            #if ($dataset.dbkey in $site_dbkeys)
+                $site_organisms[ $site_dbkeys.index( $genbank_file.dbkey ) ]
+            #else:
+                $genbank_file.dbkey
+            #end if
+        </param>
+        <param type="template" name="site_organism_query_param" strip="True">
+            #if str($site_organism) not in ['','?']:
+                &amp;genome=${qp($site_organism)}
+            #end if
+        </param>
+        <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><![CDATA[
+<?xml version="1.0" encoding="utf-8"?>
+<jnlp
+  spec="1.0+"
+  codebase="${site_link}">
+  <information>
+    <title>IGV 1.5</title>
+    <vendor>The Broad Institute</vendor>
+    <homepage href="http://www.broadinstitute.org/igv"/>
+    <description>IGV Software</description>
+    <description kind="short">IGV</description>
+  </information>
+  <security>
+      <all-permissions/>
+  </security>
+  <resources>
+<j2se version="1.5+" initial-heap-size="256m" max-heap-size="1100m"/>
+    <jar href="igv.jar" download="eager" main="true"/>
+    <jar href="batik-codec.jar" download="eager"/>
+    <property name="apple.laf.useScreenMenuBar" value="true"/>
+    <property name="com.apple.mrj.application.growbox.intrudes" value="false"/>
+    <property name="com.apple.mrj.application.live-resize" value="true"/>
+    <property name="com.apple.macos.smallTabs" value="true"/>
+  </resources>
+    <resources os="Mac" arch="i386">
+        <property name="apple.awt.graphics.UseQuartz" value="false"/>
+        <nativelib href="hdfnative-macintel.jar"/>
+    </resources>
+    <resources os="Mac" arch="ppc">
+        <property name="apple.awt.graphics.UseQuartz" value="false"/>
+        <nativelib href="hdfnative-macppc.jar"/>
+    </resources>
+    <resources os="Mac" arch="PowerPC">
+        <property name="apple.awt.graphics.UseQuartz" value="false"/>
+        <nativelib href="hdfnative-macppc.jar"/>
+    </resources>
+    <resources os="Windows">
+        <property name="sun.java2d.noddraw" value="true"/>
+        <nativelib href="hdfnative-win.jar"/>
+    </resources>
+    <resources os="Linux">
+        <nativelib href="hdfnative-linux64.jar"/>
+    </resources>
+  <application-desc main-class="org.broad.igv.ui.IGVMainFrame">
+     #if str($site_organism) not in ['?','']:
+     <argument>-g</argument>
+     <argument>${site_organism}</argument>
+     #end if
+     <argument>${genbank_file.url}</argument>
+  </application-desc>
+</jnlp>
+]]>
+        </param>
+        <param type="template" name="redirect_url" strip="True" >
+            #if $site_id.startswith( 'local_' )
+                ${site_link}?file=${genbank_file.qp}${site_organism_query_param}&amp;merge=true&amp;name=${qp( ( $genbank_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+            #elif $site_id.startswith( 'web_link_' ):
+                ${site_link}?sessionURL=${genbank_file.qp}${site_organism_query_param}&amp;merge=true&amp;name=${qp( ( $genbank_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+            #else:
+                ${jnlp.url}
+            #end if
+        </param>
+    </dynamic_links>
+    <dynamic_links from_data_table="igv_broad_genomes" skip_startswith="#" id="value" name="name">
+        <!-- Our input data table is one line per dbkey -->
+        <filter>${ $dataset.dbkey == $value }</filter>
+        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+        <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${genbank_file.qp}&amp;genome=${qp($genbank_file.dbkey)}&amp;merge=true&amp;name=${qp( ( $genbank_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
+        <param type="data" name="genbank_file" url="galaxy_${DATASET_HASH}.gb" format="genbank" />
+    </dynamic_links>
+</display>
+<!-- Dan Blankenberg -->

From e8c5c05a509022c380724995a1187acff58a641a Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 15 Nov 2019 15:06:16 +0100
Subject: [PATCH 119/853] datatypes: new data types for OpenMS

- added MascotXML (datatype and sniffer)
- added ConsensusXML, IdXML, FeatureXML, Ms2, Wiff
- sorted the sniffers alphabetically to simplify maintenance

needed here galaxyproteomics/tools-galaxyp#266
---
 .../config/sample/datatypes_conf.xml.sample   | 25 ++++++++++++-------
 lib/galaxy/datatypes/proteomics.py            |  7 ++++++
 2 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index f2aacad6d03c..a5727cf47291 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -248,6 +248,7 @@
     <datatype extension="agilentmasshunter.d.tar" type="galaxy.datatypes.binary:MassHunterTar" display_in_upload="true"/>
     <datatype extension="watersmasslynx.raw.tar" type="galaxy.datatypes.binary:MassLynxTar" display_in_upload="true"/>
     <datatype extension="wiff.tar" type="galaxy.datatypes.binary:WiffTar" display_in_upload="true"/>
+    <datatype extension="mascotxml" type="galaxy.datatypes.proteomics:MascotXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="nmrml" type="galaxy.datatypes.proteomics:NmrML" mimetype="application/xml" display_in_upload="true" description="nmrML is an open mark-up language for NMR data." description_url="http://nmrml.org/schema/"/>
     <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf" display_in_upload="true"/>
@@ -835,21 +836,27 @@
     <sniffer type="galaxy.datatypes.xml:Phyloxml"/>
     <sniffer type="galaxy.datatypes.xml:Owl"/>
     <sniffer type="galaxy.datatypes.xml:Sbml"/>
-    <sniffer type="galaxy.datatypes.proteomics:MzML"/>
-    <sniffer type="galaxy.datatypes.proteomics:NmrML"/>
-    <sniffer type="galaxy.datatypes.proteomics:TandemXML"/>
-    <sniffer type="galaxy.datatypes.proteomics:PepXml"/>
+    <sniffer type="galaxy.datatypes.proteomics:ConsensusXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:IdXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:FeatureXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:MascotXML"/>
     <sniffer type="galaxy.datatypes.proteomics:Mgf"/>
-    <sniffer type="galaxy.datatypes.proteomics:ProtXML"/>
-    <sniffer type="galaxy.datatypes.proteomics:MzXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:Ms2"/>
+    <sniffer type="galaxy.datatypes.proteomics:Msp"/>
     <sniffer type="galaxy.datatypes.proteomics:MzData"/>
-    <sniffer type="galaxy.datatypes.proteomics:TraML"/>
     <sniffer type="galaxy.datatypes.proteomics:MzIdentML"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzML"/>
     <sniffer type="galaxy.datatypes.proteomics:MzQuantML"/>
-    <sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
-    <sniffer type="galaxy.datatypes.proteomics:Msp"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:NmrML"/>
+    <sniffer type="galaxy.datatypes.proteomics:PepXml"/>
+    <sniffer type="galaxy.datatypes.proteomics:ProtXML"/>
     <sniffer type="galaxy.datatypes.proteomics:SPLib"/>
+    <sniffer type="galaxy.datatypes.proteomics:TandemXML"/>
     <sniffer type="galaxy.datatypes.proteomics:ThermoRAW"/>
+    <sniffer type="galaxy.datatypes.proteomics:TraML"/>
+    <sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:Wiff"/>
     <sniffer type="galaxy.datatypes.molecules:CML"/>
     <sniffer type="galaxy.datatypes.xml:GenericXml"/>
     <sniffer type="galaxy.datatypes.triples:HDT"/>
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index ee6c4bc8d7be..c651e8161fb6 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -127,6 +127,13 @@ class PepXml(ProteomicsXml):
     root = "msms_pipeline_analysis"
 
 
+class MascotXML(ProteomicsXml):
+    """mzXML data"""
+    file_ext = "mascotxml"
+    blurb = "mascot Mass Spectrometry data"
+    root = "mascot_search_results"
+
+
 class MzML(ProteomicsXml):
     """mzML data"""
     edam_format = "format_3244"

From d9613233147759ca50f1db59825df4c19783f49e Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 18 Nov 2019 23:39:24 +0100
Subject: [PATCH 120/853] add XQuest XML data type

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 2 ++
 lib/galaxy/datatypes/proteomics.py                 | 6 ++++++
 2 files changed, 8 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index a5727cf47291..a16417890864 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -262,6 +262,7 @@
     <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="uniprotxml" type="galaxy.datatypes.proteomics:UniProtXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="xquest.xml" type="galaxy.datatypes.proteomics:XquestXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp" display_in_upload="true"/>
     <datatype extension="splib_noindex" type="galaxy.datatypes.proteomics:SPLibNoIndex" display_in_upload="true"/>
     <datatype extension="splib" type="galaxy.datatypes.proteomics:SPLib" display_in_upload="true"/>
@@ -856,6 +857,7 @@
     <sniffer type="galaxy.datatypes.proteomics:ThermoRAW"/>
     <sniffer type="galaxy.datatypes.proteomics:TraML"/>
     <sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:XquestXML"/>
     <sniffer type="galaxy.datatypes.proteomics:Wiff"/>
     <sniffer type="galaxy.datatypes.molecules:CML"/>
     <sniffer type="galaxy.datatypes.xml:GenericXml"/>
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index c651e8161fb6..6d36c6456fbd 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -225,6 +225,12 @@ class UniProtXML(ProteomicsXml):
     root = "uniprot"
 
 
+class XquestXML(ProteomicsXml):
+    file_ext = "xquest.xml"
+    blurb = "XQuest XML file"
+    root = "xquest_results"
+
+
 class Mgf(Text):
     """Mascot Generic Format data"""
     edam_data = "data_2536"

From 43c8281d95a7203846edd4eaaefec5c3ed9a612d Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 19 Nov 2019 12:20:39 +0100
Subject: [PATCH 121/853] add pqp file format

subject to https://github.com/OpenMS/OpenMS/issues/4365
---
 .../config/sample/datatypes_conf.xml.sample   |  2 ++
 lib/galaxy/datatypes/binary.py                | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index a16417890864..ad5745085cea 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -258,6 +258,7 @@
     <datatype extension="ms2" type="galaxy.datatypes.proteomics:Ms2" display_in_upload="true"/>
     <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="mz.sqlite" type="galaxy.datatypes.binary:MzSQlite" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="pqp" type="galaxy.datatypes.binary:PQP" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml" display_in_upload="true"/>
@@ -790,6 +791,7 @@
     <sniffer type="galaxy.datatypes.binary:TwoBit"/>
     <sniffer type="galaxy.datatypes.binary:GeminiSQLite"/>
     <sniffer type="galaxy.datatypes.binary:MzSQlite"/>
+    <sniffer type="galaxy.datatypes.binary:PQP"/>
     <sniffer type="galaxy.datatypes.binary:IdpDB"/>
     <sniffer type="galaxy.datatypes.binary:ElibSQlite"/>
     <sniffer type="galaxy.datatypes.binary:DlibSQlite"/>
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 36b655d30c38..cbfef66ee19e 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -1570,6 +1570,25 @@ def sniff(self, filename):
         return False
 
 
+class PQP(SQlite):
+    """Class describing a Peptide query parameters file"""
+    file_ext = "pqp"
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        super(PQP, self).set_meta(dataset, overwrite=overwrite, **kwd)
+
+    def sniff(self, filename):
+        """
+        table definition according to https://github.com/grosenberger/OpenMS/blob/develop/src/openms/source/ANALYSIS/OPENSWATH/TransitionPQPFile.cpp#L264
+        for now VERSION GENE PEPTIDE_GENE_MAPPING are excluded, since
+        there is test data wo these tables, see also here https://github.com/OpenMS/OpenMS/issues/4365
+        """
+        table_names = ['COMPOUND', 'PEPTIDE', 'PEPTIDE_PROTEIN_MAPPING', 'PRECURSOR',
+                       'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
+                       'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING']
+        return super(PQP, self).sniff(filename) and self.sniff_table_names(filename, table_names)
+
+
 class BlibSQlite(SQlite):
     """Class describing a Proteomics Spectral Library Sqlite database """
     MetadataElement(name="blib_version", default='1.8', param=MetadataParameter, desc="Blib Version",

From 32dc2050007fcf453c114c0193dcf6f2d2ed214b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 21 Feb 2020 13:19:35 +0100
Subject: [PATCH 122/853] Fix get_keys_from_dict

---
 lib/galaxy/jobs/dynamic_tool_destination.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/jobs/dynamic_tool_destination.py b/lib/galaxy/jobs/dynamic_tool_destination.py
index e2bebc4e3bcb..809e3eec9624 100755
--- a/lib/galaxy/jobs/dynamic_tool_destination.py
+++ b/lib/galaxy/jobs/dynamic_tool_destination.py
@@ -66,11 +66,12 @@ def get_keys_from_dict(dl, keys_list):
     """
     This function builds a list using the keys from nest dictionaries
     """
+    assert isinstance(keys_list, list)
     if isinstance(dl, dict):
-        keys_list += dl.keys()
-        map(lambda x: get_keys_from_dict(x, keys_list), dl.values())
+        keys_list += list(dl.keys())
+        list(map(lambda x: get_keys_from_dict(x, keys_list), dl.values()))
     elif isinstance(dl, list):
-        map(lambda x: get_keys_from_dict(x, keys_list), dl)
+        list(map(lambda x: get_keys_from_dict(x, keys_list), dl))
 
 
 class RuleValidator(object):

From 35b5a27c71431b7495cab41b53e1d462d311ee81 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 21 Feb 2020 13:46:04 +0100
Subject: [PATCH 123/853] Fix many places where map use is wrong on python 3

---
 lib/galaxy/managers/sharable.py                     | 4 ++--
 lib/galaxy/tool_util/deps/dependencies.py           | 2 +-
 lib/galaxy/tool_util/deps/resolvers/__init__.py     | 2 +-
 lib/galaxy/tool_util/parser/cwl.py                  | 2 +-
 lib/galaxy/tool_util/parser/interface.py            | 2 +-
 lib/galaxy/tool_util/verify/interactor.py           | 2 +-
 lib/galaxy/tools/__init__.py                        | 2 +-
 lib/galaxy/tools/parameters/basic.py                | 2 +-
 lib/galaxy/util/object_wrapper.py                   | 2 +-
 lib/galaxy/webapps/reports/controllers/jobs.py      | 8 ++++----
 lib/galaxy/webapps/reports/controllers/users.py     | 4 ++--
 lib/galaxy/webapps/reports/controllers/workflows.py | 4 ++--
 12 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index f6569ac374b1..2bac58cd9e54 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -152,7 +152,7 @@ def share_with(self, item, user, flush=True):
         # precondition: user has been validated
         # allow user to be a list and call recursivly
         if isinstance(user, list):
-            return map(lambda user: self.share_with(item, user, flush=False), user)
+            return list(map(lambda user: self.share_with(item, user, flush=False), user))
         # get or create
         existing = self.get_share_assocs(item, user=user)
         if existing:
@@ -181,7 +181,7 @@ def unshare_with(self, item, user, flush=True):
         Delete a user share (or list of shares) from the database.
         """
         if isinstance(user, list):
-            return map(lambda user: self.unshare_with(item, user, flush=False), user)
+            return list(map(lambda user: self.unshare_with(item, user, flush=False), user))
         # Look for and delete sharing relation for user.
         user_share_assoc = self.get_share_assocs(item, user=user)[0]
         self.session().delete(user_share_assoc)
diff --git a/lib/galaxy/tool_util/deps/dependencies.py b/lib/galaxy/tool_util/deps/dependencies.py
index 3d67c91059cd..b53774551ec9 100644
--- a/lib/galaxy/tool_util/deps/dependencies.py
+++ b/lib/galaxy/tool_util/deps/dependencies.py
@@ -99,7 +99,7 @@ def from_dict(as_dict):
         requirements_dicts = as_dict.get('requirements', [])
         requirements = ToolRequirements.from_list(requirements_dicts)
         installed_tool_dependencies_dicts = as_dict.get('installed_tool_dependencies', [])
-        installed_tool_dependencies = map(DependenciesDescription._toolshed_install_dependency_from_dict, installed_tool_dependencies_dicts)
+        installed_tool_dependencies = list(map(DependenciesDescription._toolshed_install_dependency_from_dict, installed_tool_dependencies_dicts))
         return DependenciesDescription(
             requirements=requirements,
             installed_tool_dependencies=installed_tool_dependencies
diff --git a/lib/galaxy/tool_util/deps/resolvers/__init__.py b/lib/galaxy/tool_util/deps/resolvers/__init__.py
index 99cd83ae1db2..14e1108e82f0 100644
--- a/lib/galaxy/tool_util/deps/resolvers/__init__.py
+++ b/lib/galaxy/tool_util/deps/resolvers/__init__.py
@@ -103,7 +103,7 @@ def _mapping_file_to_list(mapping_file):
         except (OSError, IOError) as exc:
             if exc.errno != errno.ENOENT:
                 raise
-        return map(RequirementMapping.from_dict, raw_mapping)
+        return list(map(RequirementMapping.from_dict, raw_mapping))
 
     def _expand_mappings(self, requirement):
         for mapping in self._mappings:
diff --git a/lib/galaxy/tool_util/parser/cwl.py b/lib/galaxy/tool_util/parser/cwl.py
index 5715d165b8d0..107a2b5bd5e1 100644
--- a/lib/galaxy/tool_util/parser/cwl.py
+++ b/lib/galaxy/tool_util/parser/cwl.py
@@ -163,7 +163,7 @@ class CwlPageSource(PageSource):
 
     def __init__(self, tool_proxy):
         cwl_instances = tool_proxy.input_instances()
-        self._input_list = map(self._to_input_source, cwl_instances)
+        self._input_list = list(map(self._to_input_source, cwl_instances))
 
     def _to_input_source(self, input_instance):
         as_dict = input_instance.to_dict()
diff --git a/lib/galaxy/tool_util/parser/interface.py b/lib/galaxy/tool_util/parser/interface.py
index 195a70ffbd6d..79f438bc5dd0 100644
--- a/lib/galaxy/tool_util/parser/interface.py
+++ b/lib/galaxy/tool_util/parser/interface.py
@@ -399,7 +399,7 @@ def element_to_dict(element_dict):
             "model_class": "TestCollectionDef",
             "attributes": self.attrib,
             "collection_type": self.collection_type,
-            "elements": map(element_to_dict, self.elements or []),
+            "elements": list(map(element_to_dict, self.elements or [])),
             "name": self.name,
         }
 
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index cac93ddd30d2..c5d2fbd78085 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -1088,7 +1088,7 @@ def to_dict(self):
         return {
             "inputs": inputs_dict,
             "outputs": self.outputs,
-            "output_collections": map(lambda o: o.to_dict(), self.output_collections),
+            "output_collections": list(map(lambda o: o.to_dict(), self.output_collections)),
             "num_outputs": self.num_outputs,
             "command_line": self.command_line,
             "command_version": self.command_version,
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 3a01212badc7..af162bc5f79e 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2636,7 +2636,7 @@ def check_dataset_instance(input_dataset):
                 if not input_dataset_collection.collection.populated:
                     raise ToolInputsNotReadyException("An input collection is not populated.")
 
-            map(check_dataset_instance, input_dataset_collection.dataset_instances)
+            list(map(check_dataset_instance, input_dataset_collection.dataset_instances))
 
     def _add_datasets_to_history(self, history, elements, datasets_visible=False):
         datasets = []
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index b92c21b60d63..fabcf83f53e1 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -936,7 +936,7 @@ def to_text(self, value):
         # FIXME: Currently only translating values back to labels if they
         #        are not dynamic
         if self.is_dynamic:
-            rval = map(str, value)
+            rval = [str(_) for _ in value]
         else:
             options = list(self.static_options)
             rval = []
diff --git a/lib/galaxy/util/object_wrapper.py b/lib/galaxy/util/object_wrapper.py
index 8a1b08268711..8fcd472eb596 100644
--- a/lib/galaxy/util/object_wrapper.py
+++ b/lib/galaxy/util/object_wrapper.py
@@ -144,7 +144,7 @@ def __do_wrap(value):
             return safe_class(value, safe_string_wrapper_function=__do_wrap)
         for this_type in __WRAP_SEQUENCES__ + __WRAP_SETS__:
             if isinstance(value, this_type):
-                return this_type(map(__do_wrap, value))
+                return this_type(list(map(__do_wrap, value)))
         for this_type in __WRAP_MAPPINGS__:
             if isinstance(value, this_type):
                 # Wrap both key and value
diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py
index 2c8c2a5a7739..bf346dc18ecd 100644
--- a/lib/galaxy/webapps/reports/controllers/jobs.py
+++ b/lib/galaxy/webapps/reports/controllers/jobs.py
@@ -164,11 +164,11 @@ def filter(self, trans, user, query, column_filter):
             # We are either filtering on a date like YYYY-MM-DD or on a month like YYYY-MM,
             # so we need to figure out which type of date we have
             if column_filter.count('-') == 2:  # We are filtering on a date like YYYY-MM-DD
-                year, month, day = map(int, column_filter.split("-"))
+                year, month, day = list(map(int, column_filter.split("-")))
                 start_date = date(year, month, day)
                 end_date = start_date + timedelta(days=1)
             if column_filter.count('-') == 1:  # We are filtering on a month like YYYY-MM
-                year, month = map(int, column_filter.split("-"))
+                year, month = list(map(int, column_filter.split("-")))
                 start_date = date(year, month, 1)
                 end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
 
@@ -371,7 +371,7 @@ def specified_month_all(self, trans, **kwd):
         specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
         specified_month = specified_date[:7]
 
-        year, month = map(int, specified_month.split("-"))
+        year, month = list(map(int, specified_month.split("-")))
         start_date = date(year, month, 1)
         end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
         month_label = start_date.strftime("%B")
@@ -472,7 +472,7 @@ def specified_month_in_error(self, trans, **kwd):
         # If specified_date is not received, we'll default to the current month
         specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
         specified_month = specified_date[:7]
-        year, month = map(int, specified_month.split("-"))
+        year, month = list(map(int, specified_month.split("-")))
         start_date = date(year, month, 1)
         end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
         month_label = start_date.strftime("%B")
diff --git a/lib/galaxy/webapps/reports/controllers/users.py b/lib/galaxy/webapps/reports/controllers/users.py
index e8bfcfd15766..e19351e3f8c9 100644
--- a/lib/galaxy/webapps/reports/controllers/users.py
+++ b/lib/galaxy/webapps/reports/controllers/users.py
@@ -61,7 +61,7 @@ def specified_month(self, trans, **kwd):
         # If specified_date is not received, we'll default to the current month
         specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
         specified_month = specified_date[:7]
-        year, month = map(int, specified_month.split("-"))
+        year, month = list(map(int, specified_month.split("-")))
         start_date = date(year, month, 1)
         end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
         month_label = start_date.strftime("%B")
@@ -91,7 +91,7 @@ def specified_date(self, trans, **kwd):
         message = escape(util.restore_text(kwd.get('message', '')))
         # If specified_date is not received, we'll default to the current month
         specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
-        year, month, day = map(int, specified_date.split("-"))
+        year, month, day = list(map(int, specified_date.split("-")))
         start_date = date(year, month, day)
         end_date = start_date + timedelta(days=1)
         day_of_month = start_date.strftime("%d")
diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py
index a61992333f6d..51a34ce3b7ea 100644
--- a/lib/galaxy/webapps/reports/controllers/workflows.py
+++ b/lib/galaxy/webapps/reports/controllers/workflows.py
@@ -64,14 +64,14 @@ def filter(self, trans, user, query, column_filter):
             # so we need to figure out which type of date we have
             if column_filter.count('-') == 2:
                 # We are filtering on a date like YYYY-MM-DD
-                year, month, day = map(int, column_filter.split("-"))
+                year, month, day = list(map(int, column_filter.split("-")))
                 start_date = date(year, month, day)
                 end_date = start_date + timedelta(days=1)
                 return query.filter(and_(self.model_class.table.c.create_time >= start_date,
                                          self.model_class.table.c.create_time < end_date))
             if column_filter.count('-') == 1:
                 # We are filtering on a month like YYYY-MM
-                year, month = map(int, column_filter.split("-"))
+                year, month = list(map(int, column_filter.split("-")))
                 start_date = date(year, month, 1)
                 end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
                 return query.filter(and_(self.model_class.table.c.create_time >= start_date,

From 1c7f84b044c7efeb4565aff2788ac80a942e96e6 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 21 Feb 2020 12:00:43 -0500
Subject: [PATCH 124/853] Remove workflow node style dependencies to base.css

---
 .../components/Workflow/Editor/Node.vue       | 11 ++++----
 .../scripts/mvc/workflow/workflow-manager.js  |  2 +-
 .../scripts/mvc/workflow/workflow-node.js     |  6 ++---
 .../mvc/workflow/workflow-view-node.js        |  4 +--
 client/galaxy/style/scss/workflow.scss        | 27 ++++++++++---------
 5 files changed, 27 insertions(+), 23 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 444443f16c23..5de4895e8177 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -1,9 +1,10 @@
 <template>
     <div>
-        <div class="toolFormTitle unselectable clearfix">
-            <i :class="iconClass" />
-            <span class="node-title">{{ title }}</span>
-            <span class="sr-only">&nbsp;Node</span>
+        <div class="node-header unselectable clearfix">
+            <div class="header float-left">
+                <i :class="iconClass" />
+                <span class="node-title">{{ title }}</span>
+            </div>
             <div class="buttons float-right">
                 <a
                     v-if="canClone"
@@ -22,7 +23,7 @@
                 />
             </div>
         </div>
-        <div class="toolFormBody">
+        <div class="node-body">
             <div>
                 <loading-span message="Loading details" />
             </div>
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index 16ffd2c71567..cc8f7cf83ac6 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -134,7 +134,7 @@ class Workflow extends EventEmitter {
 
         // Create node wrapper
         const container = document.createElement("div");
-        container.className = "toolForm toolFormInCanvas";
+        container.className = "workflow-node";
         document.getElementById("canvas-container").appendChild(container);
         var $f = $(container);
 
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js
index 2952b9b04be6..72ca51e2754b 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js
@@ -191,7 +191,7 @@ export class Node {
         $(this.element).remove();
     }
     make_active() {
-        $(this.element).addClass("toolForm-active");
+        $(this.element).addClass("node-active");
     }
     make_inactive() {
         // Keep inactive nodes stacked from most to least recently active
@@ -202,7 +202,7 @@ export class Node {
             p.appendChild(element);
         })(element.parentNode);
         // Remove active class
-        $(element).removeClass("toolForm-active");
+        $(element).removeClass("node-active");
     }
     set_tool_version() {
         if (this.type === "tool" && this.config_form) {
@@ -341,7 +341,7 @@ export class Node {
         this.redraw();
     }
     error(text) {
-        var b = $(this.element).find(".toolFormBody");
+        var b = $(this.element).find(".node-body");
         b.find("div").remove();
         var tmp = `<div style='color: red; text-style: italic;'>${text}</div>`;
         this.config_form = tmp;
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
index c18207dd113a..2b16458a0ff7 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
@@ -9,7 +9,7 @@ export class NodeView {
         this.$el = options.$el;
         this.node = options.node;
         this.output_width = Math.max(150, this.$el.width());
-        this.tool_body = this.$el.find(".toolFormBody");
+        this.tool_body = this.$el.find(".node-body");
         this.tool_body.find("div").remove();
         this.newInputsDiv().appendTo(this.tool_body);
         this.terminalViews = {};
@@ -28,7 +28,7 @@ export class NodeView {
     }
 
     renderToolErrors() {
-        this.node.errors ? this.$el.addClass("tool-node-error") : this.$el.removeClass("tool-node-error");
+        this.node.errors ? this.$el.addClass("node-error") : this.$el.removeClass("node-error");
     }
 
     newInputsDiv() {
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 30e5e950d056..5061dc8b904e 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -7,40 +7,43 @@
         display: flex;
         flex-direction: column;
         flex-grow: 1;
-        .toolForm.toolFormInCanvas {
+        .workflow-node {
             @extend .card;
+            @extend .position-absolute;
             z-index: 100;
             width: $worfklow-node-width;
-            position: absolute;
-            border-color: $brand-primary;
-            &.toolForm-active {
+            border: solid $brand-primary 1px;
+            &.node-active {
                 z-index: 1001;
                 box-shadow: 0 0 0 2px $brand-primary;
             }
-            .toolFormTitle {
+            .node-header {
                 @extend .card-header;
                 @extend .py-1;
                 @extend .px-2;
                 cursor: move;
                 background: $brand-secondary;
+                .header {
+                    width: 7rem;
+                }
             }
-            .toolFormBody {
+            .node-body {
                 @extend .card-body;
                 @extend .p-0;
                 @extend .mx-2;
                 .rule {
                     height: 0;
                     border: none;
-                    border-bottom: dotted black 1px;
+                    border-bottom: dotted $brand-primary 1px;
                     margin: 0 5px;
                 }
             }
         }
-        .toolForm.toolFormInCanvas.tool-node-error {
-            border-color: $state-danger-border;
-            .toolFormTitle {
-                background: $state-danger-bg;
-                border-color: $state-danger-border;
+        .workflow-node.node-error {
+            border-color: $brand-danger;
+            .node-header {
+                background: $brand-danger;
+                border-color: $brand-danger;
             }
         }
         .workflow-canvas {

From cefd9c115bafdb615f52a3648177d6f975ad1af6 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 21 Feb 2020 16:12:30 -0500
Subject: [PATCH 125/853] Added code to delete all data objects in a
 collection.

---
 lib/galaxy/objectstore/irods.py | 27 ++++++++++++++++++++-------
 1 file changed, 20 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 2ec313d86c36..c77a2ea003a8 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -571,16 +571,29 @@ def delete(self, obj, entire_dir=False, **kwargs):
             # individual files we need to remove the entire directory structure
             # with all the files in it. This is easy for the local file system,
             # but requires iterating through each individual key in irods and deleing it.
-            #
-            # TODO!!!
-            #
             if entire_dir and extra_dir:
                 shutil.rmtree(self._get_cache_path(rel_path))
-                results = self.bucket.get_all_keys(prefix=rel_path)
-                for key in results:
-                    log.debug("Deleting key %s", key.name)
-                    key.delete()
+
+                col_path = self.home + "/" + str(rel_path)
+                col = None
+                try:
+                    col = self.session.collections.get(col_path)
+                except CollectionDoesNotExist:
+                    log.warn("Collection (%s) does not exist!", col_path)
+                    return False
+
+                cols = col.walk()
+                # Traverse the tree only one level deep 
+                for _ in range(2):
+                    # get next result
+                    _, _, data_objects = next(cols)
+
+                    # Delete data objects
+                    for data_object in data_objects:
+                        data_object.unlink(force=True)
+
                 return True
+
             else:
                 # Delete from cache first
                 os.unlink(self._get_cache_path(rel_path))

From 9da6e8e16952a4c0857ce92d3d52e8dfdca491f7 Mon Sep 17 00:00:00 2001
From: Anne Fouilloux <annefou@geo.uio.no>
Date: Sat, 22 Feb 2020 15:21:59 +0100
Subject: [PATCH 126/853] use get to copy data/notebook for jupyterlab (#54)

ITs
---
 interactivetool_climate_notebook.xml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml
index 0ddca7eacb83..f867208bfbe0 100644
--- a/interactivetool_climate_notebook.xml
+++ b/interactivetool_climate_notebook.xml
@@ -23,7 +23,8 @@
 
         #if $input:
             #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
-            cp '$input' './jupyter/data/${cleaned_name}' &&
+	    get -t hid -i '${input.hid}' &&
+	    ln -sf '/import/${input.hid}' './jupyter/data/${cleaned_name}' &&
         #end if
 
         ## change into the directory where the notebooks are located
@@ -32,15 +33,16 @@
 
         #if $mode.mode_select == 'scratch':
             ## copy default notebook
-            cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
+            cp '/home/jovyan/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
             jupyter trust ./ipython_galaxy_notebook.ipynb &&
             jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
             cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
 
         #else:
-            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
-            cp '$mode.ipynb' ./${cleaned_name}.ipynb &&
-            jupyter trust ./${cleaned_name}.ipynb &&
+            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
+	    get -t hid -i '${mode.ipynb.hid}' &&
+	    ln -sf '/import/${mode.ipynb.hid}' './jupyter/data/${cleaned_name}' &&
+            jupyter trust ./${cleaned_name} &&
 
             #if $mode.run_it:
                 jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&

From 69828b837a97d068ab78182f788507e0b35753e1 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 21 Nov 2019 10:16:10 +0100
Subject: [PATCH 127/853] added osw data type

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample |  2 ++
 lib/galaxy/datatypes/binary.py                     | 14 ++++++++++++++
 2 files changed, 16 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index ad5745085cea..09538a00eb82 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -258,6 +258,7 @@
     <datatype extension="ms2" type="galaxy.datatypes.proteomics:Ms2" display_in_upload="true"/>
     <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="mz.sqlite" type="galaxy.datatypes.binary:MzSQlite" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="osw" type="galaxy.datatypes.binary:OSW" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="pqp" type="galaxy.datatypes.binary:PQP" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml" display_in_upload="true"/>
@@ -791,6 +792,7 @@
     <sniffer type="galaxy.datatypes.binary:TwoBit"/>
     <sniffer type="galaxy.datatypes.binary:GeminiSQLite"/>
     <sniffer type="galaxy.datatypes.binary:MzSQlite"/>
+    <sniffer type="galaxy.datatypes.binary:OSW"/>
     <sniffer type="galaxy.datatypes.binary:PQP"/>
     <sniffer type="galaxy.datatypes.binary:IdpDB"/>
     <sniffer type="galaxy.datatypes.binary:ElibSQlite"/>
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index cbfef66ee19e..7520f0e3686a 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -1589,6 +1589,20 @@ def sniff(self, filename):
         return super(PQP, self).sniff(filename) and self.sniff_table_names(filename, table_names)
 
 
+class OSW(PQP):
+    """Class describing OpenSwath output"""
+    file_ext = "osw"
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        super(OSW, self).set_meta(dataset, overwrite=overwrite, **kwd)
+
+    def sniff(self, filename):
+        # osw seems to be an extension of pqp (few tables are added)
+        # see also here https://github.com/OpenMS/OpenMS/issues/4365
+        table_names = ['FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
+        return super(OSW, self).sniff(filename) and self.sniff_table_names(filename, table_names)
+
+
 class BlibSQlite(SQlite):
     """Class describing a Proteomics Spectral Library Sqlite database """
     MetadataElement(name="blib_version", default='1.8', param=MetadataParameter, desc="Blib Version",

From a6b743d85d3183041b4060636b6a961f2fe2c18d Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 20 Nov 2019 22:38:54 +0100
Subject: [PATCH 128/853] added mzTab(2) and TarfoXML

---
 .../config/sample/datatypes_conf.xml.sample   |  7 +-
 lib/galaxy/datatypes/proteomics.py            | 68 +++++++++++++++++++
 2 files changed, 74 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 09538a00eb82..e89381ea88ac 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -233,7 +233,6 @@
     <datatype extension="peptideprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
     <datatype extension="interprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
     <datatype extension="protxml" type="galaxy.datatypes.proteomics:ProtXML" mimetype="application/xml" display_in_upload="true"/>
-    <datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Transformation of retention times"/>
     <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Quality control data in XML format (https://code.google.com/p/qcml/)."/>
     <datatype extension="pepxml.tsv" type="galaxy.datatypes.proteomics:PepXmlReport" display_in_upload="true"/>
     <datatype extension="protxml.tsv" type="galaxy.datatypes.proteomics:ProtXmlReport" display_in_upload="true"/>
@@ -249,6 +248,8 @@
     <datatype extension="watersmasslynx.raw.tar" type="galaxy.datatypes.binary:MassLynxTar" display_in_upload="true"/>
     <datatype extension="wiff.tar" type="galaxy.datatypes.binary:WiffTar" display_in_upload="true"/>
     <datatype extension="mascotxml" type="galaxy.datatypes.proteomics:MascotXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="mztab" type="galaxy.datatypes.proteomics:MzTab" display_in_upload="true"/>
+    <datatype extension="mztab2" type="galaxy.datatypes.proteomics:MzTab2" display_in_upload="true"/>
     <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="nmrml" type="galaxy.datatypes.proteomics:NmrML" mimetype="application/xml" display_in_upload="true" description="nmrML is an open mark-up language for NMR data." description_url="http://nmrml.org/schema/"/>
     <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf" display_in_upload="true"/>
@@ -261,6 +262,7 @@
     <datatype extension="osw" type="galaxy.datatypes.binary:OSW" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="pqp" type="galaxy.datatypes.binary:PQP" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="trafoxml" type="galaxy.datatypes.proteomics:TrafoXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="uniprotxml" type="galaxy.datatypes.proteomics:UniProtXML" mimetype="application/xml" display_in_upload="true"/>
@@ -852,6 +854,8 @@
     <sniffer type="galaxy.datatypes.proteomics:MzIdentML"/>
     <sniffer type="galaxy.datatypes.proteomics:MzML"/>
     <sniffer type="galaxy.datatypes.proteomics:MzQuantML"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzTab"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzTab2"/>
     <sniffer type="galaxy.datatypes.proteomics:MzXML"/>
     <sniffer type="galaxy.datatypes.proteomics:NmrML"/>
     <sniffer type="galaxy.datatypes.proteomics:PepXml"/>
@@ -860,6 +864,7 @@
     <sniffer type="galaxy.datatypes.proteomics:TandemXML"/>
     <sniffer type="galaxy.datatypes.proteomics:ThermoRAW"/>
     <sniffer type="galaxy.datatypes.proteomics:TraML"/>
+    <sniffer type="galaxy.datatypes.proteomics:TrafoXML"/>
     <sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
     <sniffer type="galaxy.datatypes.proteomics:XquestXML"/>
     <sniffer type="galaxy.datatypes.proteomics:Wiff"/>
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 6d36c6456fbd..bc4f5cbcc6a1 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -53,6 +53,68 @@ def generate_primary_file(self, dataset=None):
         return "\n".join(rval)
 
 
+@build_sniff_from_prefix
+class MzTab(Text):
+    """exchange format for proteomics and metabolomics results"""
+    edam_data = "data_3681"
+    file_ext = "mztab"
+    # section names (except MTD)
+    __sections = ["PRH", "PRT", "PEH", "PEP", "PSH", "PSM", "SMH", "SML", "COM"]
+    __version_re = r"([0-9]{1,2})(\.[0-9])?(\.[0-9])?$"
+
+    def __init__(self, **kwd):
+        super(MzTab, self).__init__(**kwd)
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek(dataset.file_name)
+            dataset.blurb = 'mzTab Format'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def sniff_prefix(self, file_prefix):
+        """ Determines whether the file is the correct type. """
+        has_version = False
+        has_mode = False
+        has_type = False
+
+        contents = file_prefix.string_io()
+        while True:
+            line = contents.readline().split("\t")
+            if line[0] == "MTD":
+                if line[1] == "mzTab-version" and re.match(self.__version_re, line) is not None:
+                    has_version = True
+                elif line[1] == "mzTab-mode" and line[2].lowercase() in ["complete", "summary"]:
+                    has_mode = True
+                elif line[1] == "mzTab-type" and line[2].lowercase() in ['quantification', 'identification']:
+                    has_type = True
+            elif not line[0] in self.__sections:
+                return False
+
+        return has_version and has_mode and has_type
+
+
+class MzTab2(MzTab):
+    """exchange format for proteomics and metabolomics results"""
+    file_ext = "mztab2"
+    __sections = ["SMH", "SML", "SFH", "SMF", "SEH", "SME", "COM"]
+    __version_re = r"([0-9]{1,2})(\.[0-9])?(\.[0-9])?-M$"
+
+    def __init__(self, **kwd):
+        super(MzTab2, self).__init__(**kwd)
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek(dataset.file_name)
+            dataset.blurb = 'mzTab2 Format'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+
 class PepXmlReport(Tabular):
     """pepxml converted to tabular report"""
     edam_data = "data_2536"
@@ -187,6 +249,12 @@ class TraML(ProteomicsXml):
     root = "TraML"
 
 
+class TrafoXML(ProteomicsXml):
+    file_ext = "trafoxml"
+    blurb = "RT alignment tranformation"
+    root = "TrafoXML"
+
+
 class MzQuantML(ProteomicsXml):
     edam_format = "format_3248"
     file_ext = "mzq"

From acc7aad6011a451525bfd6d874806c79e13b94e8 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 20 Nov 2019 23:04:10 +0100
Subject: [PATCH 129/853] strip spaces from lines for detecting proteomics xml
 files

to allow for files like https://github.com/OpenMS/OpenMS/blob/develop/src/tests/topp/FileFilter_44_output.mzML
---
 lib/galaxy/datatypes/proteomics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index bc4f5cbcc6a1..572746bebdcd 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -164,7 +164,7 @@ def sniff_prefix(self, file_prefix):
         """ Determines whether the file is the correct XML type. """
         contents = file_prefix.string_io()
         while True:
-            line = contents.readline()
+            line = contents.readline().strip()
             if line is None or not line.startswith('<?'):
                 break
         # pattern match <root or <ns:root for any ns string

From 5ce2025160262573e05d028720bc278ecb1a16c3 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 26 Nov 2019 13:31:19 +0100
Subject: [PATCH 130/853] add sqmass

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample |  2 ++
 lib/galaxy/datatypes/binary.py                     | 14 ++++++++++++++
 2 files changed, 16 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index e89381ea88ac..dd24f068f814 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -350,6 +350,7 @@
     <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="pqp" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true" subclass="true"/>
     <datatype extension="osw" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true" subclass="true"/>
+    <datatype extension="sqmass" type="galaxy.datatypes.binary:SQmass" mimetype="application/octet-stream" display_in_upload="true" subclass="true"/>
     <datatype extension="gemini.sqlite" type="galaxy.datatypes.binary:GeminiSQLite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="cuffdiff.sqlite" type="galaxy.datatypes.binary:CuffDiffSQlite" display_in_upload="true"/>
     <datatype extension="gafa.sqlite" type="galaxy.datatypes.binary:GAFASQLite" mimetype="application/octet-stream" display_in_upload="true"/>
@@ -793,6 +794,7 @@
     <sniffer type="galaxy.datatypes.tabular:Vcf"/>
     <sniffer type="galaxy.datatypes.binary:TwoBit"/>
     <sniffer type="galaxy.datatypes.binary:GeminiSQLite"/>
+    <sniffer type="galaxy.datatypes.binary:SQmass"/>
     <sniffer type="galaxy.datatypes.binary:MzSQlite"/>
     <sniffer type="galaxy.datatypes.binary:OSW"/>
     <sniffer type="galaxy.datatypes.binary:PQP"/>
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 7520f0e3686a..9a48239111a9 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -1603,6 +1603,20 @@ def sniff(self, filename):
         return super(OSW, self).sniff(filename) and self.sniff_table_names(filename, table_names)
 
 
+class SQmass(SQlite):
+    """Class describing a Sqmass database """
+    file_ext = "sqmass"
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        super(SQmass, self).set_meta(dataset, overwrite=overwrite, **kwd)
+
+    def sniff(self, filename):
+        if super(SQmass, self).sniff(filename):
+            table_names = ["CHROMATOGRAM", "PRECURSOR", "RUN", "SPECTRUM", "DATA", "PRODUCT", "RUN_EXTRA"]
+            return self.sniff_table_names(filename, table_names)
+        return False
+
+
 class BlibSQlite(SQlite):
     """Class describing a Proteomics Spectral Library Sqlite database """
     MetadataElement(name="blib_version", default='1.8', param=MetadataParameter, desc="Blib Version",

From b9dda087a97a8d70f4cd483293c6205a7dd4ae67 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 28 Nov 2019 09:52:47 +0100
Subject: [PATCH 131/853] add Kroenik

---
 .../config/sample/datatypes_conf.xml.sample   |  2 ++
 lib/galaxy/datatypes/proteomics.py            | 27 +++++++++++++++++++
 2 files changed, 29 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index dd24f068f814..07c222e78008 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -234,6 +234,7 @@
     <datatype extension="interprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
     <datatype extension="protxml" type="galaxy.datatypes.proteomics:ProtXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Quality control data in XML format (https://code.google.com/p/qcml/)."/>
+    <datatype extension="kroenik" type="galaxy.datatypes.proteomics:Kroenik" display_in_upload="true"/>
     <datatype extension="pepxml.tsv" type="galaxy.datatypes.proteomics:PepXmlReport" display_in_upload="true"/>
     <datatype extension="protxml.tsv" type="galaxy.datatypes.proteomics:ProtXmlReport" display_in_upload="true"/>
     <datatype extension="mascotdat" type="galaxy.datatypes.proteomics:MascotDat" display_in_upload="false"/>
@@ -860,6 +861,7 @@
     <sniffer type="galaxy.datatypes.proteomics:MzTab2"/>
     <sniffer type="galaxy.datatypes.proteomics:MzXML"/>
     <sniffer type="galaxy.datatypes.proteomics:NmrML"/>
+    <sniffer type="galaxy.datatypes.proteomics:Kroenik"/>
     <sniffer type="galaxy.datatypes.proteomics:PepXml"/>
     <sniffer type="galaxy.datatypes.proteomics:ProtXML"/>
     <sniffer type="galaxy.datatypes.proteomics:SPLib"/>
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 572746bebdcd..4b1649a00208 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -115,6 +115,33 @@ def set_peek(self, dataset, is_multi_byte=False):
             dataset.blurb = 'file purged from disk'
 
 
+@build_sniff_from_prefix
+class Kroenik(Tabular):
+    """ Kroenik (HardKloer sibling) files"""
+    file_ext = "kroenik"
+
+    def __init__(self, **kwd):
+        super(Kroenik, self).__init__(**kwd)
+        self.column_names = ["File", "First Scan", "Last Scan", "Num of Scans", "Charge", "Monoisotopic Mass", "Base Isotope Peak", "Best Intensity", "Summed Intensity", "First RTime", "Last RTime", "Best RTime", "Best Correlation", "Modifications"]
+
+    def display_peek(self, dataset):
+        """Returns formated html of peek"""
+        return self.make_html_table(dataset, column_names=self.column_names)
+
+    def sniff_prefix(self, file_prefix):
+        fh = file_prefix.string_io()
+        line = [_.strip() for _ in fh.readline().split("\t")]
+        if len(line) != len(self.column_names) or line != self.column_names:
+            return False
+        line = fh.readline().split("\t")
+        try:
+            [int(_) for _ in line[1:5]]
+            [float(_) for _ in line[5:13]]
+        except ValueError:
+            return False
+        return True
+
+
 class PepXmlReport(Tabular):
     """pepxml converted to tabular report"""
     edam_data = "data_2536"

From 80a7737f71069dc605081130b9c44d8d00552745 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 29 Nov 2019 14:55:25 +0100
Subject: [PATCH 132/853] add dta, dta2d, edta

---
 .../config/sample/datatypes_conf.xml.sample   |   6 +
 lib/galaxy/datatypes/proteomics.py            | 273 +++++++++++++++++-
 2 files changed, 278 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 07c222e78008..f65b7b989c34 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -228,6 +228,9 @@
     <datatype extension="directory" type="galaxy.datatypes.data:Directory">
     </datatype>
     <!-- Proteomics Datatypes -->
+    <datatype extension="dta" type="galaxy.datatypes.proteomics:Dta" display_in_upload="true" />
+    <datatype extension="dta2d" type="galaxy.datatypes.proteomics:Dta2d" display_in_upload="true" />
+    <datatype extension="edta" type="galaxy.datatypes.proteomics:Edta" display_in_upload="true" />
     <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="raw_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
     <datatype extension="peptideprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
@@ -846,6 +849,9 @@
     <sniffer type="galaxy.datatypes.xml:Phyloxml"/>
     <sniffer type="galaxy.datatypes.xml:Owl"/>
     <sniffer type="galaxy.datatypes.xml:Sbml"/>
+    <sniffer type="galaxy.datatypes.proteomics:Dta"/>
+    <sniffer type="galaxy.datatypes.proteomics:Dta2d"/>
+    <sniffer type="galaxy.datatypes.proteomics:Edta"/>
     <sniffer type="galaxy.datatypes.proteomics:ConsensusXML"/>
     <sniffer type="galaxy.datatypes.proteomics:IdXML"/>
     <sniffer type="galaxy.datatypes.proteomics:FeatureXML"/>
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 4b1649a00208..85e86fda4374 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -8,7 +8,7 @@
 from galaxy.datatypes.binary import Binary
 from galaxy.datatypes.data import Text
 from galaxy.datatypes.sniff import build_sniff_from_prefix
-from galaxy.datatypes.tabular import Tabular
+from galaxy.datatypes.tabular import Tabular, TabularData
 from galaxy.datatypes.xml import GenericXml
 from galaxy.util import nice_size
 
@@ -181,6 +181,277 @@ def display_peek(self, dataset):
         return self.make_html_table(dataset, column_names=self.column_names)
 
 
+@build_sniff_from_prefix
+class Dta(TabularData):
+    """dta
+    The first line contains the singly protonated peptide mass (MH+) and the
+    peptide charge state separated by a space. Subsequent lines contain space
+    separated pairs of fragment ion m/z and intensity values.
+    """
+    file_ext = "dta"
+    comment_lines = 0
+
+    def set_meta(self, dataset, **kwd):
+        column_types = []
+        data_row = []
+        data_lines = 0
+        if dataset.has_data():
+            with open(dataset.file_name, 'r') as dtafile:
+                for line in dtafile:
+                    data_lines += 1
+
+        # Guess column types
+        for cell in data_row:
+            column_types.append(self.guess_type(cell))
+
+        # Set metadata
+        dataset.metadata.data_lines = data_lines
+        dataset.metadata.comment_lines = 0
+        dataset.metadata.column_types = ['float', 'float']
+        dataset.metadata.columns = 2
+        dataset.metadata.column_names = ['m/z', 'intensity']
+        dataset.metadata.delimiter = " "
+
+    def sniff_prefix(self, file_prefix):
+        has_data = False
+        for line in file_prefix.line_iterator():
+            line = line.strip().split(" ")
+            if len(line) != 2:
+                return False
+            try:
+                line = [float(_) for _ in line]
+            except ValueError:
+                return False
+            if not all(_ >= 0 for _ in line):
+                return False
+            has_data = True
+        return has_data
+
+
+@build_sniff_from_prefix
+class Dta2d(TabularData):
+    """
+    dta2d: files with three tab/space-separated columns.
+    The default format is: retention time (seconds) , m/z , intensity.
+    If the first line starts with '#', a different order is defined by the the
+    order of the keywords 'MIN' (retention time in minutes) or 'SEC' (retention
+    time in seconds), 'MZ', and 'INT'.
+    Example: '#MZ MIN INT'
+    The peaks of one retention time have to be in subsequent lines.
+
+    Note: sniffer detects
+        - tab separated with correct header and
+        - all space separated variants w/wo correct header
+        Since tab separated wo header would probably cover to much
+    """
+    file_ext = "dta2d"
+    comment_lines = 0
+
+    def _parse_header(self, line):
+        if len(line) != 3 or len(line[0]) < 3 or not line[0].startswith("#"):
+            return None
+        line[0] = line[0].lstrip("#")
+        line = [_.strip() for _ in line]
+        if 'MZ' not in line or 'INT' not in line or ('MIN' not in line and 'SEC' not in line):
+            return None
+        return line
+
+    def _parse_delimiter(self, line):
+        if len(line.split(" ")) == 3:
+            return " "
+        elif len(line.split("\t")) == 3:
+            return "\t"
+        return None
+
+    def _parse_dataline(self, line):
+        try:
+            line = [float(_) for _ in line]
+        except ValueError:
+            return False
+        if not all(_ >= 0 for _ in line):
+            return False
+        return True
+
+    def set_meta(self, dataset, **kwd):
+        data_lines = 0
+        delim = None
+        if dataset.has_data():
+            with open(dataset.file_name, 'r') as dtafile:
+                for line in dtafile:
+                    if delim is None:
+                        delim = self._parse_delimiter(line)
+                        dataset.metadata.column_names = self._parse_header(line.split(delim))
+                    data_lines += 1
+
+        # Set metadata
+        if delim is not None:
+            dataset.metadata.delimiter = delim
+
+        dataset.metadata.data_lines = data_lines
+        dataset.metadata.comment_lines = 0
+        dataset.metadata.column_types = ['float', 'float', 'float']
+        dataset.metadata.columns = 3
+        if dataset.metadata.column_names is None or dataset.metadata.column_names == []:
+            dataset.metadata.comment_lines += 1
+            dataset.metadata.data_lines -= 1
+            dataset.metadata.column_names = ['SEC', 'MZ', 'INT']
+
+    def sniff_prefix(self, file_prefix):
+        sep = None
+        header = None
+        for idx, line in enumerate(file_prefix.line_iterator()):
+            line = line.strip()
+            if sep is None:
+                sep = self._parse_delimiter(line)
+                if sep is None:
+                    return False
+            line = line.split(sep)
+            if len(line) != 3:
+                return False
+            if idx == 0:
+                header = self._parse_header(line)
+                if (header is None) and not self._parse_dataline(line):
+                    return False
+            elif not self._parse_dataline(line):
+                return False
+        if sep is None or (sep == '\t' and header is None):
+            return False
+        return True
+
+
+@build_sniff_from_prefix
+class Edta(TabularData):
+    """
+    Input text file containing tab, space or comma separated columns.
+    The separator between columns is checked in the first line in this order.
+
+    It supports three variants of this format.
+
+    1. Columns are: RT, MZ, Intensity A header is optional.
+    2. Columns are: RT, MZ, Intensity, Charge, <Meta-Data> columns{0,} A header is mandatory.
+    3. Columns are: (RT, MZ, Intensity, Charge){1,}, <Meta-Data> columns{0,}
+       Header is mandatory. First quadruplet is the consensus. All following
+       quadruplets describe the sub-features. This variant is discerned from
+       variant #2 by the name of the fifth column, which is required to be RT1
+       (or rt1). All other column names for sub-features are faithfully ignored.
+    """
+    file_ext = "edta"
+    comment_lines = 0
+
+    def _parse_delimiter(self, line):
+        if len(line.split(" ")) >= 3:
+            return " "
+        elif len(line.split("\t")) >= 3:
+            return "\t"
+        elif len(line.split(",")) >= 3:
+            return "\t"
+        return None
+
+    def _parse_type(self, line):
+        """
+        parse the type from the header line
+        types 1-3 as in the class docs, 0: type 1 wo/wrong header
+        """
+        if len(line) < 3:
+            return None
+        line = [_.lower().replace("/", "") for _ in line]
+        if len(line) == 3:
+            if line[0] == "rt" and line[1] == "mz" and (line[2] == "int" or line[2] == "intensity"):
+                return 1
+            else:
+                return 0
+        if line[0] != "rt" or line[1] != "mz" or (line[2] != "int" and line[2] != "intensity") or line[3] != "charge":
+            return None
+        if not line[4].startswith("rt"):
+            return 2
+        else:
+            return 3
+
+    def _parse_dataline(self, line, tpe):
+        if tpe == 2 or tpe == 3:
+            l = 4
+        else:
+            l = 3
+        try:
+            line = [float(_) for _ in line[:l]]
+        except ValueError:
+            return False
+        if not all(_ >= 0 for _ in line[:l]):
+            return False
+        return True
+
+    def _clean_header(self, line):
+        for idx, el in enumerate(line):
+            el = el.lower()
+            if el.startswith("rt"):
+                line[idx] = "RT"
+            elif el.startswith("int"):
+                line[idx] = "intensity"
+            elif el.startswith("mz"):
+                line[idx] = "m/z"
+            elif el.startswith("charge"):
+                line[idx] = "charge"
+            else:
+                break
+            if idx // 4 > 0:
+                line[idx] += str(idx // 4)
+        return line
+
+    def set_meta(self, dataset, **kwd):
+        data_lines = 0
+        delim = None
+        if dataset.has_data():
+            with open(dataset.file_name, 'r') as dtafile:
+                for idx, line in enumerate(dtafile):
+                    if idx == 0:
+                        delim = self._parse_delimiter(line)
+                        tpe = self._parse_type(line.split(delim))
+                        if tpe == 0:
+                            dataset.metadata.column_names = ["RT", "m/z", "intensity"]
+                        else:
+                            dataset.metadata.column_names = self._clean_header(line.split(delim))
+                    data_lines += 1
+
+        # Set metadata
+        if delim is not None:
+            dataset.metadata.delimiter = delim
+        for c in dataset.metadata.column_names:
+            if any(c.startswith(_) for _ in ["RT", "m/z", "intensity", "charge"]):
+                dataset.metadata.column_types.append("float")
+            else:
+                dataset.metadata.column_types.append("str")
+
+        dataset.metadata.data_lines = data_lines
+        dataset.metadata.comment_lines = 0
+        dataset.metadata.columns = len(dataset.metadata.column_names)
+        if tpe > 0:
+            dataset.metadata.comment_lines += 1
+            dataset.metadata.data_lines -= 1
+
+    def sniff_prefix(self, file_prefix):
+        sep = None
+        tpe = None
+        for idx, line in enumerate(file_prefix.line_iterator()):
+            line = line.strip("\r\n")
+            if sep is None:
+                sep = self._parse_delimiter(line)
+                if sep is None:
+                    return False
+            line = line.split(sep)
+
+            if idx == 0:
+                tpe = self._parse_type(line)
+                if tpe is None:
+                    return False
+                elif tpe == 0 and not self._parse_dataline(line, tpe):
+                    return False
+            elif not self._parse_dataline(line, tpe):
+                return False
+        if tpe is None or (tpe == 0 and sep == '\t'):
+            return False
+        return True
+
+
 class ProteomicsXml(GenericXml):
     """ An enhanced XML datatype used to reuse code across several
     proteomic/mass-spec datatypes. """

From a285b48f54c44aa5908deaba65af8480269beb25 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 14 Jan 2020 15:02:24 +0100
Subject: [PATCH 133/853] dta2d, edta: remove sniffing of to generic types of
 these files

---
 lib/galaxy/datatypes/proteomics.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 85e86fda4374..30c0b8bb2bb0 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -239,10 +239,8 @@ class Dta2d(TabularData):
     Example: '#MZ MIN INT'
     The peaks of one retention time have to be in subsequent lines.
 
-    Note: sniffer detects
-        - tab separated with correct header and
-        - all space separated variants w/wo correct header
-        Since tab separated wo header would probably cover to much
+    Note: sniffer detects (tab or space separated) dta2d files with correct
+    header, wo header seems to generic
     """
     file_ext = "dta2d"
     comment_lines = 0
@@ -314,7 +312,7 @@ def sniff_prefix(self, file_prefix):
                     return False
             elif not self._parse_dataline(line):
                 return False
-        if sep is None or (sep == '\t' and header is None):
+        if sep is None or header is None:
             return False
         return True
 
@@ -334,6 +332,8 @@ class Edta(TabularData):
        quadruplets describe the sub-features. This variant is discerned from
        variant #2 by the name of the fifth column, which is required to be RT1
        (or rt1). All other column names for sub-features are faithfully ignored.
+
+    Note the sniffer only detects files with header.
     """
     file_ext = "edta"
     comment_lines = 0
@@ -359,7 +359,7 @@ def _parse_type(self, line):
             if line[0] == "rt" and line[1] == "mz" and (line[2] == "int" or line[2] == "intensity"):
                 return 1
             else:
-                return 0
+                return None
         if line[0] != "rt" or line[1] != "mz" or (line[2] != "int" and line[2] != "intensity") or line[3] != "charge":
             return None
         if not line[4].startswith("rt"):
@@ -447,7 +447,7 @@ def sniff_prefix(self, file_prefix):
                     return False
             elif not self._parse_dataline(line, tpe):
                 return False
-        if tpe is None or (tpe == 0 and sep == '\t'):
+        if tpe is None:
             return False
         return True
 

From 69644fbfabc7fdd23c5b4c2427b0c8ac078ad2df Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 6 Dec 2019 16:26:51 +0100
Subject: [PATCH 134/853] add paramXML data type

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 2 ++
 lib/galaxy/datatypes/proteomics.py                 | 7 +++++++
 2 files changed, 9 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index f65b7b989c34..5f9502d875ac 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -236,6 +236,7 @@
     <datatype extension="peptideprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
     <datatype extension="interprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
     <datatype extension="protxml" type="galaxy.datatypes.proteomics:ProtXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="paramxml" type="galaxy.datatypes.proteomics:ParamXml" mimetype="application/xml" subclass="true" display_in_upload="true" />
     <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Quality control data in XML format (https://code.google.com/p/qcml/)."/>
     <datatype extension="kroenik" type="galaxy.datatypes.proteomics:Kroenik" display_in_upload="true"/>
     <datatype extension="pepxml.tsv" type="galaxy.datatypes.proteomics:PepXmlReport" display_in_upload="true"/>
@@ -865,6 +866,7 @@
     <sniffer type="galaxy.datatypes.proteomics:MzQuantML"/>
     <sniffer type="galaxy.datatypes.proteomics:MzTab"/>
     <sniffer type="galaxy.datatypes.proteomics:MzTab2"/>
+    <sniffer type="galaxy.datatypes.proteomics:ParamXml"/>
     <sniffer type="galaxy.datatypes.proteomics:MzXML"/>
     <sniffer type="galaxy.datatypes.proteomics:NmrML"/>
     <sniffer type="galaxy.datatypes.proteomics:Kroenik"/>
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 30c0b8bb2bb0..b4e5a8b48266 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -479,6 +479,13 @@ def set_peek(self, dataset, is_multi_byte=False):
             dataset.blurb = 'file purged from disk'
 
 
+class ParamXml(ProteomicsXml):
+    """store Parameters in XML formal"""
+    file_ext = "paramxml"
+    blurb = "parameters in xmls"
+    root = "parameters|PARAMETERS"
+
+
 class PepXml(ProteomicsXml):
     """pepXML data"""
     edam_format = "format_3655"

From 4c7cd6d1e8b055c5f77065f714969064285d3c3f Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 9 Dec 2019 10:55:10 +0100
Subject: [PATCH 135/853] add XQuest Spectra data type

And search root tag not only at the beginning of the line, i.e.
and switch pattern '^<(\w*:)?ROOT' to '<(\w*:)?ROOT' and
search instead of match ("^" in combination with match was not
necessary anyway).
---
 lib/galaxy/config/sample/datatypes_conf.xml.sample |  2 ++
 lib/galaxy/datatypes/proteomics.py                 | 11 +++++++++--
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 5f9502d875ac..70c58d4e0569 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -272,6 +272,7 @@
     <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="uniprotxml" type="galaxy.datatypes.proteomics:UniProtXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="xquest.xml" type="galaxy.datatypes.proteomics:XquestXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="spec.xml" type="galaxy.datatypes.proteomics:XquestSpecXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp" display_in_upload="true"/>
     <datatype extension="splib_noindex" type="galaxy.datatypes.proteomics:SPLibNoIndex" display_in_upload="true"/>
     <datatype extension="splib" type="galaxy.datatypes.proteomics:SPLib" display_in_upload="true"/>
@@ -879,6 +880,7 @@
     <sniffer type="galaxy.datatypes.proteomics:TrafoXML"/>
     <sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
     <sniffer type="galaxy.datatypes.proteomics:XquestXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:XquestSpecXML"/>
     <sniffer type="galaxy.datatypes.proteomics:Wiff"/>
     <sniffer type="galaxy.datatypes.molecules:CML"/>
     <sniffer type="galaxy.datatypes.xml:GenericXml"/>
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index b4e5a8b48266..4aa56df45686 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -466,8 +466,8 @@ def sniff_prefix(self, file_prefix):
             if line is None or not line.startswith('<?'):
                 break
         # pattern match <root or <ns:root for any ns string
-        pattern = r'^<(\w*:)?%s' % self.root
-        return line is not None and re.match(pattern, line) is not None
+        pattern = r'<(\w*:)?%s' % self.root
+        return line is not None and re.search(pattern, line) is not None
 
     def set_peek(self, dataset, is_multi_byte=False):
         """Set the peek and blurb text"""
@@ -604,6 +604,13 @@ class XquestXML(ProteomicsXml):
     root = "xquest_results"
 
 
+class XquestSpecXML(ProteomicsXml):
+    """spec.xml"""
+    file_ext = "spec.xml"
+    blurb = 'xquest_spectra'
+    root = "xquest_spectra"
+
+
 class Mgf(Text):
     """Mascot Generic Format data"""
     edam_data = "data_2536"

From fa2fc3b3a86dafa4051a65f8e310e4ce90ffd0a3 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 9 Dec 2019 11:25:23 +0100
Subject: [PATCH 136/853] add qcML

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample |  2 ++
 lib/galaxy/datatypes/proteomics.py                 | 10 ++++++++++
 2 files changed, 12 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 70c58d4e0569..ea3e55af445f 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -273,6 +273,7 @@
     <datatype extension="uniprotxml" type="galaxy.datatypes.proteomics:UniProtXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="xquest.xml" type="galaxy.datatypes.proteomics:XquestXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="spec.xml" type="galaxy.datatypes.proteomics:XquestSpecXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="qcml" type="galaxy.datatypes.proteomics:QCML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp" display_in_upload="true"/>
     <datatype extension="splib_noindex" type="galaxy.datatypes.proteomics:SPLibNoIndex" display_in_upload="true"/>
     <datatype extension="splib" type="galaxy.datatypes.proteomics:SPLib" display_in_upload="true"/>
@@ -881,6 +882,7 @@
     <sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
     <sniffer type="galaxy.datatypes.proteomics:XquestXML"/>
     <sniffer type="galaxy.datatypes.proteomics:XquestSpecXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:QCML"/>
     <sniffer type="galaxy.datatypes.proteomics:Wiff"/>
     <sniffer type="galaxy.datatypes.molecules:CML"/>
     <sniffer type="galaxy.datatypes.xml:GenericXml"/>
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 4aa56df45686..828dc0d462da 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -611,6 +611,16 @@ class XquestSpecXML(ProteomicsXml):
     root = "xquest_spectra"
 
 
+class QCML(ProteomicsXml):
+    """qcml
+    https://github.com/OpenMS/OpenMS/blob/develop/share/OpenMS/SCHEMAS/mzQCML_0_0_5.xsd
+    https://github.com/OpenMS/OpenMS/blob/develop/share/OpenMS/SCHEMAS/qcML_0.0.7.xsd
+    """
+    file_ext = "qcml"
+    blurb = 'QualityAssessments to runs'
+    root = "qcML|MzQualityML)"
+
+
 class Mgf(Text):
     """Mascot Generic Format data"""
     edam_data = "data_2536"

From aa8d901b3f1a43d674666492cb5635460ca4e7ce Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 18 Dec 2019 12:21:39 +0100
Subject: [PATCH 137/853] add psms and peplist

---
 .../config/sample/datatypes_conf.xml.sample   |  4 ++
 lib/galaxy/datatypes/proteomics.py            | 52 +++++++++++++++++++
 2 files changed, 56 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index ea3e55af445f..5cab3114fc3c 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -239,6 +239,8 @@
     <datatype extension="paramxml" type="galaxy.datatypes.proteomics:ParamXml" mimetype="application/xml" subclass="true" display_in_upload="true" />
     <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Quality control data in XML format (https://code.google.com/p/qcml/)."/>
     <datatype extension="kroenik" type="galaxy.datatypes.proteomics:Kroenik" display_in_upload="true"/>
+    <datatype extension="peplist" type="galaxy.datatypes.proteomics:PepList" display_in_upload="true"/>
+    <datatype extension="psms" type="galaxy.datatypes.proteomics:PSMS" display_in_upload="true"/>
     <datatype extension="pepxml.tsv" type="galaxy.datatypes.proteomics:PepXmlReport" display_in_upload="true"/>
     <datatype extension="protxml.tsv" type="galaxy.datatypes.proteomics:ProtXmlReport" display_in_upload="true"/>
     <datatype extension="mascotdat" type="galaxy.datatypes.proteomics:MascotDat" display_in_upload="false"/>
@@ -872,6 +874,8 @@
     <sniffer type="galaxy.datatypes.proteomics:MzXML"/>
     <sniffer type="galaxy.datatypes.proteomics:NmrML"/>
     <sniffer type="galaxy.datatypes.proteomics:Kroenik"/>
+    <sniffer type="galaxy.datatypes.proteomics:PepList"/>
+    <sniffer type="galaxy.datatypes.proteomics:PSMS"/>
     <sniffer type="galaxy.datatypes.proteomics:PepXml"/>
     <sniffer type="galaxy.datatypes.proteomics:ProtXML"/>
     <sniffer type="galaxy.datatypes.proteomics:SPLib"/>
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 828dc0d462da..536bfc202a4d 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -142,6 +142,58 @@ def sniff_prefix(self, file_prefix):
         return True
 
 
+@build_sniff_from_prefix
+class PepList(Tabular):
+    """
+    Peplist file as used in OpenMS
+    https://github.com/OpenMS/OpenMS/blob/0fc8765670a0ad625c883f328de60f738f7325a4/src/openms/source/FORMAT/FileHandler.cpp#L432
+    """
+    file_ext = "peplist"
+
+    def __init__(self, **kwd):
+        super(PepList, self).__init__(**kwd)
+        self.column_names = ["m/z", "rt(min)", "snr", "charge", "intensity"]
+
+    def display_peek(self, dataset):
+        """Returns formated html of peek"""
+        return self.make_html_table(dataset, column_names=self.column_names)
+
+    def sniff_prefix(self, file_prefix):
+        fh = file_prefix.string_io()
+        line = [_.strip() for _ in fh.readline().split("\t")]
+        if len(line) == 5 and line == self.column_names:
+            return True
+        return False
+
+
+@build_sniff_from_prefix
+class PSMS(Tabular):
+    """
+    Percolator tab-delimited output (PSM level, .psms) as used in OpenMS
+    https://github.com/OpenMS/OpenMS/blob/0fc8765670a0ad625c883f328de60f738f7325a4/src/openms/source/FORMAT/FileHandler.cpp#L453
+    see also http://www.kojak-ms.org/docs/percresults.html
+
+    Note that the data rows can have more columns than the header line
+    since ProteinIds are listed tab-separated.
+    """
+    file_ext = "psms"
+
+    def __init__(self, **kwd):
+        super(PSMS, self).__init__(**kwd)
+        self.column_names = ["PSMId", "score", "q-value", "posterior_error_prob", "peptide", "proteinIds"]
+
+    def display_peek(self, dataset):
+        """Returns formated html of peek"""
+        return self.make_html_table(dataset, column_names=self.column_names)
+
+    def sniff_prefix(self, file_prefix):
+        fh = file_prefix.string_io()
+        line = [_.strip() for _ in fh.readline().split("\t")]
+        if len(line) == 6 and line == self.column_names:
+            return True
+        return False
+
+
 class PepXmlReport(Tabular):
     """pepxml converted to tabular report"""
     edam_data = "data_2536"

From 2dc2eda41f600b148cd4ad44ccb4486d0e4eaf6b Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 14 Jan 2020 16:32:28 +0100
Subject: [PATCH 138/853] mrm: as subclass of Tabular

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 5cab3114fc3c..d5d433ff6012 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -228,6 +228,8 @@
     <datatype extension="directory" type="galaxy.datatypes.data:Directory">
     </datatype>
     <!-- Proteomics Datatypes -->
+    <datatype extension="mrm" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
+    <datatype extension="dta" type="galaxy.datatypes.proteomics:Dta" display_in_upload="true" />
     <datatype extension="dta" type="galaxy.datatypes.proteomics:Dta" display_in_upload="true" />
     <datatype extension="dta2d" type="galaxy.datatypes.proteomics:Dta2d" display_in_upload="true" />
     <datatype extension="edta" type="galaxy.datatypes.proteomics:Edta" display_in_upload="true" />

From 5e084cb351a652d7f87f7b6c995dc0bd2042ef12 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 27 Jan 2020 14:19:35 +0100
Subject: [PATCH 139/853] suggested changes from review

- no sniffing for dta
- remove superficial len checks
- schema links to OpenMS with commit
---
 .../config/sample/datatypes_conf.xml.sample   |  2 --
 lib/galaxy/datatypes/proteomics.py            | 26 ++++---------------
 2 files changed, 5 insertions(+), 23 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index d5d433ff6012..76867b2a7dbc 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -230,7 +230,6 @@
     <!-- Proteomics Datatypes -->
     <datatype extension="mrm" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
     <datatype extension="dta" type="galaxy.datatypes.proteomics:Dta" display_in_upload="true" />
-    <datatype extension="dta" type="galaxy.datatypes.proteomics:Dta" display_in_upload="true" />
     <datatype extension="dta2d" type="galaxy.datatypes.proteomics:Dta2d" display_in_upload="true" />
     <datatype extension="edta" type="galaxy.datatypes.proteomics:Edta" display_in_upload="true" />
     <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" display_in_upload="true"/>
@@ -856,7 +855,6 @@
     <sniffer type="galaxy.datatypes.xml:Phyloxml"/>
     <sniffer type="galaxy.datatypes.xml:Owl"/>
     <sniffer type="galaxy.datatypes.xml:Sbml"/>
-    <sniffer type="galaxy.datatypes.proteomics:Dta"/>
     <sniffer type="galaxy.datatypes.proteomics:Dta2d"/>
     <sniffer type="galaxy.datatypes.proteomics:Edta"/>
     <sniffer type="galaxy.datatypes.proteomics:ConsensusXML"/>
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 536bfc202a4d..7484d416b60f 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -131,7 +131,7 @@ def display_peek(self, dataset):
     def sniff_prefix(self, file_prefix):
         fh = file_prefix.string_io()
         line = [_.strip() for _ in fh.readline().split("\t")]
-        if len(line) != len(self.column_names) or line != self.column_names:
+        if line != self.column_names:
             return False
         line = fh.readline().split("\t")
         try:
@@ -161,7 +161,7 @@ def display_peek(self, dataset):
     def sniff_prefix(self, file_prefix):
         fh = file_prefix.string_io()
         line = [_.strip() for _ in fh.readline().split("\t")]
-        if len(line) == 5 and line == self.column_names:
+        if line == self.column_names:
             return True
         return False
 
@@ -189,7 +189,7 @@ def display_peek(self, dataset):
     def sniff_prefix(self, file_prefix):
         fh = file_prefix.string_io()
         line = [_.strip() for _ in fh.readline().split("\t")]
-        if len(line) == 6 and line == self.column_names:
+        if line == self.column_names:
             return True
         return False
 
@@ -233,7 +233,6 @@ def display_peek(self, dataset):
         return self.make_html_table(dataset, column_names=self.column_names)
 
 
-@build_sniff_from_prefix
 class Dta(TabularData):
     """dta
     The first line contains the singly protonated peptide mass (MH+) and the
@@ -264,21 +263,6 @@ def set_meta(self, dataset, **kwd):
         dataset.metadata.column_names = ['m/z', 'intensity']
         dataset.metadata.delimiter = " "
 
-    def sniff_prefix(self, file_prefix):
-        has_data = False
-        for line in file_prefix.line_iterator():
-            line = line.strip().split(" ")
-            if len(line) != 2:
-                return False
-            try:
-                line = [float(_) for _ in line]
-            except ValueError:
-                return False
-            if not all(_ >= 0 for _ in line):
-                return False
-            has_data = True
-        return has_data
-
 
 @build_sniff_from_prefix
 class Dta2d(TabularData):
@@ -665,8 +649,8 @@ class XquestSpecXML(ProteomicsXml):
 
 class QCML(ProteomicsXml):
     """qcml
-    https://github.com/OpenMS/OpenMS/blob/develop/share/OpenMS/SCHEMAS/mzQCML_0_0_5.xsd
-    https://github.com/OpenMS/OpenMS/blob/develop/share/OpenMS/SCHEMAS/qcML_0.0.7.xsd
+    https://github.com/OpenMS/OpenMS/blob/113c49d01677f7f03343ce7cd542d83c99b351ee/share/OpenMS/SCHEMAS/mzQCML_0_0_5.xsd
+    https://github.com/OpenMS/OpenMS/blob/3cfc57ad1788e7ab2bd6dd9862818b2855234c3f/share/OpenMS/SCHEMAS/qcML_0.0.7.xsd
     """
     file_ext = "qcml"
     blurb = 'QualityAssessments to runs'

From 86eb5dfb1a8f9f93722de444c9cd43969f49cda5 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 14 Feb 2020 15:54:36 +0100
Subject: [PATCH 140/853] sniffer tests for openms related data types

---
 lib/galaxy/datatypes/binary.py         |  36 +++++++-
 lib/galaxy/datatypes/proteomics.py     |  72 ++++++++++++++-
 lib/galaxy/datatypes/test/test.dta2d   |   9 ++
 lib/galaxy/datatypes/test/test.edta    |   7 ++
 lib/galaxy/datatypes/test/test.kroenik |  23 +++++
 lib/galaxy/datatypes/test/test.mztab   |  28 ++++++
 lib/galaxy/datatypes/test/test.mztab2  |  92 +++++++++++++++++++
 lib/galaxy/datatypes/test/test.osw     | Bin 0 -> 102400 bytes
 lib/galaxy/datatypes/test/test.peplist |  36 ++++++++
 lib/galaxy/datatypes/test/test.pqp     | Bin 0 -> 65536 bytes
 lib/galaxy/datatypes/test/test.psms    | 122 +++++++++++++++++++++++++
 lib/galaxy/datatypes/test/test.sqmass  | Bin 0 -> 90112 bytes
 12 files changed, 417 insertions(+), 8 deletions(-)
 create mode 100644 lib/galaxy/datatypes/test/test.dta2d
 create mode 100644 lib/galaxy/datatypes/test/test.edta
 create mode 100644 lib/galaxy/datatypes/test/test.kroenik
 create mode 100644 lib/galaxy/datatypes/test/test.mztab
 create mode 100644 lib/galaxy/datatypes/test/test.mztab2
 create mode 100644 lib/galaxy/datatypes/test/test.osw
 create mode 100644 lib/galaxy/datatypes/test/test.peplist
 create mode 100644 lib/galaxy/datatypes/test/test.pqp
 create mode 100644 lib/galaxy/datatypes/test/test.psms
 create mode 100644 lib/galaxy/datatypes/test/test.sqmass

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 9a48239111a9..16735eb7731b 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -1571,7 +1571,17 @@ def sniff(self, filename):
 
 
 class PQP(SQlite):
-    """Class describing a Peptide query parameters file"""
+    """
+    Class describing a Peptide query parameters file
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.pqp')
+    >>> PQP().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.osw')
+    >>> PQP().sniff(fname)
+    False
+    """
     file_ext = "pqp"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -1590,7 +1600,17 @@ def sniff(self, filename):
 
 
 class OSW(PQP):
-    """Class describing OpenSwath output"""
+    """
+    Class describing OpenSwath output
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.osw')
+    >>> OSW().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.sqmass')
+    >>> OSW().sniff(fname)
+    False
+    """
     file_ext = "osw"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -1604,7 +1624,17 @@ def sniff(self, filename):
 
 
 class SQmass(SQlite):
-    """Class describing a Sqmass database """
+    """
+    Class describing a Sqmass database
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.sqmass')
+    >>> SQmass().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.pqp')
+    >>> SQmass().sniff(fname)
+    False
+    """
     file_ext = "sqmass"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 7484d416b60f..2e6a720e9ae2 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -55,12 +55,22 @@ def generate_primary_file(self, dataset=None):
 
 @build_sniff_from_prefix
 class MzTab(Text):
-    """exchange format for proteomics and metabolomics results"""
+    """
+    exchange format for proteomics and metabolomics results
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.mztab')
+    >>> MzTab().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.mztab2')
+    >>> MzTab().sniff(fname)
+    False
+    """
     edam_data = "data_3681"
     file_ext = "mztab"
     # section names (except MTD)
     __sections = ["PRH", "PRT", "PEH", "PEP", "PSH", "PSM", "SMH", "SML", "COM"]
-    __version_re = r"([0-9]{1,2})(\.[0-9])?(\.[0-9])?$"
+    __version_re = r"(1)(\.[0-9])?(\.[0-9])?"
 
     def __init__(self, **kwd):
         super(MzTab, self).__init__(**kwd)
@@ -97,10 +107,20 @@ def sniff_prefix(self, file_prefix):
 
 
 class MzTab2(MzTab):
-    """exchange format for proteomics and metabolomics results"""
+    """
+    exchange format for proteomics and metabolomics results
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.mztab2')
+    >>> mztab2().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.mztab')
+    >>> mztab2().sniff(fname)
+    False
+    """
     file_ext = "mztab2"
     __sections = ["SMH", "SML", "SFH", "SMF", "SEH", "SME", "COM"]
-    __version_re = r"([0-9]{1,2})(\.[0-9])?(\.[0-9])?-M$"
+    __version_re = r"(2)(\.[0-9])?(\.[0-9])?-M$"
 
     def __init__(self, **kwd):
         super(MzTab2, self).__init__(**kwd)
@@ -117,7 +137,17 @@ def set_peek(self, dataset, is_multi_byte=False):
 
 @build_sniff_from_prefix
 class Kroenik(Tabular):
-    """ Kroenik (HardKloer sibling) files"""
+    """
+    Kroenik (HardKloer sibling) files
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.kroenik')
+    >>> Kroenik().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.peplist')
+    >>> Kroenik().sniff(fname)
+    False
+    """
     file_ext = "kroenik"
 
     def __init__(self, **kwd):
@@ -147,6 +177,14 @@ class PepList(Tabular):
     """
     Peplist file as used in OpenMS
     https://github.com/OpenMS/OpenMS/blob/0fc8765670a0ad625c883f328de60f738f7325a4/src/openms/source/FORMAT/FileHandler.cpp#L432
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.peplist')
+    >>> PepList().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.psms')
+    >>> PepList().sniff(fname)
+    False
     """
     file_ext = "peplist"
 
@@ -175,6 +213,14 @@ class PSMS(Tabular):
 
     Note that the data rows can have more columns than the header line
     since ProteinIds are listed tab-separated.
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.psms')
+    >>> PSMS().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.kroenik')
+    >>> PSMS().sniff(fname)
+    False
     """
     file_ext = "psms"
 
@@ -277,6 +323,14 @@ class Dta2d(TabularData):
 
     Note: sniffer detects (tab or space separated) dta2d files with correct
     header, wo header seems to generic
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.dta2d')
+    >>> Dta2d().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.edta')
+    >>> Dta2d().sniff(fname)
+    False
     """
     file_ext = "dta2d"
     comment_lines = 0
@@ -370,6 +424,14 @@ class Edta(TabularData):
        (or rt1). All other column names for sub-features are faithfully ignored.
 
     Note the sniffer only detects files with header.
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.edta')
+    >>> Edta().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.dta2d')
+    >>> Edta().sniff(fname)
+    False
     """
     file_ext = "edta"
     comment_lines = 0
diff --git a/lib/galaxy/datatypes/test/test.dta2d b/lib/galaxy/datatypes/test/test.dta2d
new file mode 100644
index 000000000000..42840611a976
--- /dev/null
+++ b/lib/galaxy/datatypes/test/test.dta2d
@@ -0,0 +1,9 @@
+#MZ	SEC	INT
+500.0	0	50
+600.0	1	100
+700.0	2	200
+800.0	3	400
+900.0	4	200
+1000.0	5	100
+1100.0	6	50
+900.0	2	200
diff --git a/lib/galaxy/datatypes/test/test.edta b/lib/galaxy/datatypes/test/test.edta
new file mode 100644
index 000000000000..66ae17a2b281
--- /dev/null
+++ b/lib/galaxy/datatypes/test/test.edta
@@ -0,0 +1,7 @@
+RT	mz	Int	charge	Meta2
+10	114	2342	1
+10	115	232	2
+10	116	523	2
+14	220	343	1	value
+14	431.1	343	2
+15	543.2393	343	3	b
diff --git a/lib/galaxy/datatypes/test/test.kroenik b/lib/galaxy/datatypes/test/test.kroenik
new file mode 100644
index 000000000000..b554c1f622d5
--- /dev/null
+++ b/lib/galaxy/datatypes/test/test.kroenik
@@ -0,0 +1,23 @@
+File	First Scan	Last Scan	Num of Scans	Charge	Monoisotopic Mass	Base Isotope Peak	Best Intensity	Summed Intensity	First RTime	Last RTime	Best RTime	Best Correlation	Modifications
+20060502data08_exc_RTf.mzXML	1480	1578	15	3	1345.607960	449.543300	60834.925781	506348.656250	521.106018	553.833008	533.018982	0.991700	_
+20060502data08_exc_RTf.mzXML	1487	1557	11	2	1345.608400	673.811500	26904.589844	199969.046875	523.559998	546.731018	533.018982	0.995300	_
+20060502data08_exc_RTf.mzXML	1557	1620	10	3	2002.810800	668.945100	38904.792969	217929.312500	546.731018	567.784973	553.833008	0.986300	_
+20060502data08_exc_RTf.mzXML	1571	1592	4	2	2002.811525	1002.913800	4603.663086	14353.689453	551.427979	558.577026	556.184998	0.978400	_
+20060502data08_exc_RTf.mzXML	1592	1690	15	3	1772.892100	591.971200	91715.507813	502103.500000	558.577026	590.963013	567.784973	0.986900	_
+20060502data08_exc_RTf.mzXML	1599	1683	13	4	1772.891285	444.230100	72974.398438	417335.125000	560.914001	588.521973	570.002014	0.974700	_
+20060502data08_exc_RTf.mzXML	1599	1676	11	2	1772.889336	887.452600	22342.041016	122096.265625	560.914001	586.155029	567.784973	0.994600	_
+20060502data08_exc_RTf.mzXML	1690	1774	13	2	1401.655615	701.834900	37010.062500	262936.343750	590.963013	619.705017	605.291992	0.995500	_
+20060502data08_exc_RTf.mzXML	1746	1816	11	2	1065.545100	533.779800	48403.296875	347601.562500	610.046997	634.202026	622.135986	0.979800	_
+20060502data08_exc_RTf.mzXML	1816	1851	6	4	2095.873767	525.226300	17985.734375	73192.179688	634.202026	646.385986	641.471008	0.986700	_
+20060502data08_exc_RTf.mzXML	1858	1879	4	4	1904.987400	477.504500	7037.772461	16893.957031	648.786011	656.114014	656.114014	0.962100	_
+20060502data08_exc_RTf.mzXML	1879	1907	4	2	994.581075	498.297700	28557.644531	92082.468750	656.114014	665.525024	660.861023	0.996100	_
+20060502data08_exc_RTf.mzXML	1886	1994	15	3	1506.688193	503.236500	223091.640625	1329185.625000	658.479980	693.369995	670.021973	0.989100	_
+20060502data08_exc_RTf.mzXML	1893	1955	10	2	1506.689740	754.352500	49197.664063	307397.281250	660.861023	680.966003	672.174988	0.990500	_
+20060502data08_exc_RTf.mzXML	1907	2056	23	4	2239.081209	561.027900	189284.390625	1359320.875000	665.525024	713.080994	685.143005	0.973600	_
+20060502data08_exc_RTf.mzXML	1914	1994	13	2	1336.644692	669.329400	174888.703125	994234.375000	667.744019	693.369995	676.612000	0.990700	_
+20060502data08_exc_RTf.mzXML	1921	1988	10	2	1478.675160	740.344800	119720.226563	577115.250000	670.021973	691.309998	678.859985	0.985600	_
+20060502data08_exc_RTf.mzXML	1928	1948	3	2	1697.803500	849.907800	3211.451660	7545.761719	672.174988	678.859985	672.174988	0.927400	_
+20060502data08_exc_RTf.mzXML	1935	1955	4	2	1127.618850	564.816500	67462.703125	183348.593750	674.471985	680.966003	680.966003	0.950400	_
+20060502data08_exc_RTf.mzXML	1941	2021	12	3	2239.081067	747.701800	67137.210938	463090.031250	676.612000	701.872009	683.143982	0.991200	_
+20060502data08_exc_RTf.mzXML	1948	2028	13	2	1583.758454	792.886000	36854.781250	262471.843750	678.859985	704.109009	691.309998	0.993400	_
+20060502data08_exc_RTf.mzXML	1955	2021	11	3	1583.757945	528.926500	128648.492188	829892.062500	680.966003	701.872009	691.309998	0.990400	_
diff --git a/lib/galaxy/datatypes/test/test.mztab b/lib/galaxy/datatypes/test/test.mztab
new file mode 100644
index 000000000000..6c74f6d27ae1
--- /dev/null
+++ b/lib/galaxy/datatypes/test/test.mztab
@@ -0,0 +1,28 @@
+MTD	mzTab-version	1.0 rc5
+MTD	mzTab-mode	Summary
+MTD	mzTab-type	Identification
+MTD	mzTab-ID	Cytidine
+MTD	description	LC-MS/MS Reference Standard
+MTD	sample_processing[1]	[MS, MS:1000544, Conversion to mzML, ]|[MS, MS:1000035, Peak picking, ]|[MS, MS:1001994, Top Hat baseline reduction, ]|[MS, MS:1000782, Savitzky-Golay smoothing, ]|[MS, MS:1000594, Low intensity data point removal, ]
+MTD	instrument[1]-name	[MS, MS:1000483, Thermo Fisher Scientific instrument model, LTQ Orbitrap Velos]
+MTD	instrument[1]-source	[MS, MS:1000008, Ionization Type, ESI]
+MTD	instrument[1]-analyzer[1]	[MS, MS:1000443, Mass Analyzer Type, Orbitrap]
+MTD	instrument[1]-detector	[MS, MS:1000453, Detector, Dynode Detector]
+MTD	software[1]	[MS, MS:1002205, ProteoWizard msconvert, ]
+MTD	software[1]-setting[1]	Peak Picking MS1
+MTD	software[1]	[MS, MS:1001457, data processing software, MassCascade-KNIME]
+MTD	smallmolecule_search_engine_score[1]	[MS, MS:1001153, search engine specific score,]
+MTD	contact[1]-name	Stephan Beisken
+MTD	contact[1]-affiliation	European Bioinformatics Institute (EMBL-EBI)
+MTD	contact[1]-email	beiken@ebi.ac.uk
+MTD	uri[1]	http://www.ebi.ac.uk/metabolights/MTBLS38
+MTD	fixed_mod[1]	[MS, MS:1002453, No fixed modifications searched, ]
+MTD	variable_mod[1]	[ , , CHEMMOD:2M+H, ]
+MTD	variable_mod[2]	[ , , CHEMMOD:M-C5H8O4, ]
+MTD	ms_run[1]-format	[MS, MS:1000584, Proteomics Standards Inititative mzML file format, mzML file]
+MTD	ms_run[1]-location	ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS38/cytidine.mzML
+MTD	ms_run[1]-id_format	[MS, MS:1000767, Native spectrum identifier format, ]
+MTD	ms_run[1]-fragmentation_method	[MS, MS:1000133, Collision-induced dissociation, ]
+
+SMH	identifier	chemical_formula	smiles	inchi_key	description	exp_mass_to_charge	calc_mass_to_charge	charge	retention_time	taxid	species	database	database_version	spectra_ref	search_engine	best_search_engine_score[1]	modifications
+SML	CHEBI:17562	C9H13N3O5	Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)n1	UHDGCWIWMRVCDJ-XVFCMESISA-N	Cytidine	244.0928	null	1	193.25	null	null	ChEBI	109	null	[MS, MS:1001083, ms-ms search, MassBank]	977	CHEMMOD:2M+H,CHEMMOD:M-C5H8O4
diff --git a/lib/galaxy/datatypes/test/test.mztab2 b/lib/galaxy/datatypes/test/test.mztab2
new file mode 100644
index 000000000000..d38a03df9421
--- /dev/null
+++ b/lib/galaxy/datatypes/test/test.mztab2
@@ -0,0 +1,92 @@
+COM	Meta data section																		
+MTD	mzTab-version	2.0.0-M																	
+MTD	mzTab-ID	mzTab-GCxGC-MS																	
+MTD	description	Minimal sample file for GCxGC-MS quantification of small molecules between two experiments																	
+MTD	instrument[1]-name	[MS, MS:1001945, Pegasus 4D, ]																	
+MTD	instrument[1]-source	[MS, MS:1000389, electron Ionization, ]																	
+MTD	instrument[1]-analyzer[1]	[MS, MS:1000084, time-of-flight, ]																	
+MTD	instrument[1]-detector	[MS, MS:1000114, microchannel plate detector, ]																	
+MTD	software[1]	[MS, MS:1001799, ChromaTOF software, 3.21]
+MTD	software[1]-setting[1]	baseline=0.2
+MTD	software[1]-setting[2]	dbMatchTreshold=900
+MTD	sample[1]-species[1]	[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]																	
+MTD	sample[1]-cell_type[1]	[CL, CL:0000233, platelet, ]																	
+MTD	sample[1]-description	Unstimulated human blood platelets																	
+MTD	sample[2]-species[1]	[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]																	
+MTD	sample[2]-cell_type[1]	[CL, CL:0000233, platelet, ]																	
+MTD	sample[2]-description	Unstimulated human blood platelets																	
+MTD	ms_run[1]-location	file://c:/data/control.mzML																	
+MTD	ms_run[1]-format	[MS, MS:1000584, mzML file, ]																	
+MTD	ms_run[1]-id_format	[MS, MS:1000776, scan number only nativeID format, ]
+MTD	ms_run[1]-scan_polarity[1]	[MS, MS:1000130, positive scan, ]																	
+MTD	ms_run[2]-location	file://c:/data/treatment.mzML																	
+MTD	ms_run[2]-format	[MS, MS:1000584, mzML file, ]																	
+MTD	ms_run[2]-id_format	[MS, MS:1000776, scan number only nativeID format, ]
+MTD	ms_run[2]-scan_polarity[1]	[MS, MS:1000130, positive scan, ]																	
+MTD	assay[1]-sample_ref	sample[1]																	
+MTD	assay[1]-ms_run_ref	ms_run[1]																	
+MTD	assay[2]-sample_ref	sample[2]																	
+MTD	assay[2]-ms_run_ref	ms_run[2]																	
+MTD	study_variable[1]	Untreated																	
+MTD	study_variable[1]-assay_refs	assay[1]																	
+MTD	study_variable[1]-description	drug response control																	
+MTD	study_variable[1]-average_function	[MS, MS:1002962, mean, ]																	
+MTD	study_variable[1]-variation_function	[MS, MS:1002885, standard error, ]																	
+MTD	study_variable[2]	Treated																	
+MTD	study_variable[2]-assay_refs	assay[2]																	
+MTD	study_variable[2]-description	drug response treatment																	
+MTD	study_variable[2]-average_function	[MS, MS:1002962, mean, ]																	
+MTD	study_variable[2]-variation_function	[MS, MS:1002885, standard error, ]																	
+MTD	cv[1]-label	MS																	
+MTD	cv[1]-full_name	PSI-MS controlled vocabulary																	
+MTD	cv[1]-version	20-06-2018																	
+MTD	cv[1]-uri	https://www.ebi.ac.uk/ols/ontologies/ms																	
+MTD	cv[2]-label	NCBITaxon																	
+MTD	cv[2]-full_name	An ontology representation of the NCBI organismal taxonomy Ontology																	
+MTD	cv[2]-version	2018-03-02																	
+MTD	cv[2]-uri	https://www.ebi.ac.uk/ols/ontologies/ncbitaxon																	
+MTD	cv[3]-label	CL																	
+MTD	cv[3]-full_name	The Cell Ontology is a structured controlled vocabulary for cell types in animals.																	
+MTD	cv[3]-version	2017-12-11																	
+MTD	cv[3]-uri	https://www.ebi.ac.uk/ols/ontologies/cl																	
+MTD	cv[4]-label	PRIDE																	
+MTD	cv[4]-full_name	PRIDE PRoteomics IDEntifications (PRIDE) database controlled vocabulary																	
+MTD	cv[4]-version	14-06-2018																	
+MTD	cv[4]-uri	https://www.ebi.ac.uk/ols/ontologies/pride																	
+MTD	cv[5]-label	CHEBI																	
+MTD	cv[5]-full_name	Chemical Entities of Biological Interest
+MTD	cv[5]-version	08-02-2019																	
+MTD	cv[5]-uri	https://www.ebi.ac.uk/ols/ontologies/chebi
+MTD	database[1]	[, ,Golm Metabolite Database, ]																	
+MTD	database[1]-prefix	GMD																	
+MTD	database[1]-version	2.3																	
+MTD	database[1]-uri	http://gmd.mpimp-golm.mpg.de/																	
+MTD	database[2]	[, , no database, null]																	
+MTD	database[2]-prefix	null																	
+MTD	database[2]-uri	null																	
+MTD	database[2]-version	Unknown																	
+MTD	derivatization_agent[1]	[,,Methoxylamine hydrochloride,]																	
+MTD	derivatization_agent[2]	[CHEBI, CHEBI:85064, N-methyl-N-(trimethylsilyl)trifluoroacetamide,]																	
+MTD	small_molecule-identification_reliability	[MS, MS:1002896, compound identification confidence level, ]																	
+MTD	id_confidence_measure[1]	[MS, MS:1002890, fragmentation score, ]																	
+MTD	small_molecule-quantification_unit	[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]																	
+MTD	small_molecule_feature-quantification_unit	[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]																	
+MTD	quantification_method	[,,baseline-corrected intensity quantification,]																	
+MTD	custom[1]	[MS, MS:1000901, retention time normalization standard, n-alkanes C10–C36]																	
+																			
+COM	Small molecule summary rows (similar to Protein section). 																		
+COM	Evidences (e.g. multiple modifications, adducts incl. charge variants are summarized). 																		
+COM	For most use cases this summary lines might be sufficient.																		
+SMH	SML_ID	SMF_ID_REFS	database_identifier	chemical_formula	smiles	inchi	chemical_name	uri	theoretical_neutral_mass	adduct_ions	reliability	best_id_confidence_measure	best_id_confidence_value	abundance_assay[1]	abundance_study_variable[1]	abundance_variation_study_variable[1]	abundance_assay[2]	abundance_study_variable[2]	abundance_variation_study_variable[2]
+SML	1	1 | 2	GMD:cd7993ea-ad14-452a-a907-33376cc98790	C18H36O2	CCCCCCCCCCCCCCCCCC(O)=O	InChI=1S/C18H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-17H2,1H3,(H,19,20)	Octadecanoic acid	http://identifiers.org/gmd/cd7993ea-ad14-452a-a907-33376cc98790	284.478	[M+H]1+	2	[MS, MS:1002890, fragmentation score, ]	978	805.16	805.16	0	589.9	589.9	0
+																			
+COM	Small molecule feature rows (only reported in Complete Quantification files and if feature information like e.g. mass traces are important)																		
+SFH	SMF_ID	SME_ID_REFS	SME_ID_REF_ambiguity_code	adduct_ion	isotopomer	exp_mass_to_charge	charge	retention_time_in_seconds	retention_time_in_seconds_start	retention_time_in_seconds_end	abundance_assay[1]	abundance_assay[2]	opt_global_retention_time_nd	opt_global_retention_time_nd_window_start	opt_global_retention_time_nd_window_end				
+SMF	1	1	null	[M+H]1+	null	285.484	1	1564.47	1559.45	1564.48	805.16	805.16	1562 | 2.47 	1557 | 2.45 	1562 | 2.48				
+SMF	2	2	null	[M+H]1+	null	285.484	1	1564.48	1554.45	1569.47	589.9	589.9	1562 | 2.48	1552 | 2.45	1567| 2.47				
+																			
+COM	Small molecule evidence rows for parent ions. Analog to PSM. 																		
+COM	Primary use case: report single hits from spectral library or accurate mass searches without quantification.																		
+SEH	SME_ID	evidence_input_id	database_identifier	chemical_formula	smiles	inchi	chemical_name	uri	derivatized_form	adduct_ion	exp_mass_to_charge	charge	theoretical_mass_to_charge	spectra_ref	identification_method	ms_level	id_confidence_measure[1]	rank	
+SME	1	ms_run[1]:scan=8	GMD:f634c736-39e8-4323-8155-fa3cc26ac9e3	C18H36O2	CCCCCCCCCCCCCCCCCC(O)=O	InChI=1S/C18H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-17H2,1H3,(H,19,20)	Octadecanoic acid (1TMS)	http://identifiers.org/gmd.analyte/f634c736-39e8-4323-8155-fa3cc26ac9e3	[CHEBI, CHEBI:51088, trimethylsilyl group, 1]	[M+H]+	356.6588	1	356.659	ms_run[1]:scan=8	[,, ChromaTOF database search,]	[MS, MS:1000511, ms level, 1]	957	1	
+SME	2	ms_run[2]:scan=23	GMD:f634c736-39e8-4323-8155-fa3cc26ac9e3	C18H36O2	CCCCCCCCCCCCCCCCCC(O)=O	InChI=1S/C18H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-17H2,1H3,(H,19,20)	Octadecanoic acid (1TMS)	http://identifiers.org/gmd.analyte/f634c736-39e8-4323-8155-fa3cc26ac9e3	[CHEBI, CHEBI:51088, trimethylsilyl group, 1]	[M+H]+	356.6589	1	356.659	ms_run[2]:scan=23	[,, ChromaTOF database search,]	[MS, MS:1000511, ms level, 1]	972	1	
diff --git a/lib/galaxy/datatypes/test/test.osw b/lib/galaxy/datatypes/test/test.osw
new file mode 100644
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GIT binary patch
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diff --git a/lib/galaxy/datatypes/test/test.peplist b/lib/galaxy/datatypes/test/test.peplist
new file mode 100644
index 000000000000..af747d21cab9
--- /dev/null
+++ b/lib/galaxy/datatypes/test/test.peplist
@@ -0,0 +1,36 @@
+       m/z	     rt(min)	       snr	      charge	   intensity
+  706.0656	     47.997	     70.443	          3	   3709.630
+  740.4292	     60.127	     28.895	          4	   2153.832
+  708.7055	     63.321	     28.970	          3	   2377.576
+  728.7255	     56.390	     28.530	          3	   1820.929
+  721.3855	     57.410	     25.965	          3	   1332.942
+  740.4400	     64.272	     16.639	          2	   1024.329
+  707.3855	     63.423	     20.248	          3	   1495.899
+  735.7055	     50.275	     29.838	          3	    804.873
+  726.7255	     63.966	     13.282	          3	   1364.349
+  723.4000	     57.647	     13.069	          2	    713.563
+  700.4400	     61.588	     11.435	          2	    579.007
+  736.3400	     61.113	      9.765	          2	    464.364
+  705.4000	     54.454	     12.855	          2	    457.507
+  709.0056	     57.104	     12.614	          3	    454.622
+  710.3000	     49.459	     18.364	          2	    534.519
+  719.4000	     64.714	      7.860	          3	    447.372
+  742.4400	     64.170	      6.799	          2	    357.583
+  752.4000	     55.983	      7.138	          2	    290.348
+  714.1492	     47.114	     22.442	          4	    576.568
+  753.4256	     61.486	      7.788	          3	    318.019
+  730.3800	     53.536	      8.914	          2	    284.038
+  708.8400	     58.836	      6.272	          2	    246.319
+  737.0400	     50.207	     12.257	          3	    309.824
+  716.9200	     58.123	      6.188	          2	    283.297
+  729.7456	     50.308	      9.760	          3	    428.650
+  712.3200	     49.391	      8.749	          2	    235.981
+  748.9400	     51.294	      9.114	          2	    250.202
+  712.8800	     53.672	      6.466	          2	    160.206
+  714.9000	     53.604	      6.417	          2	    202.450
+  716.8800	     54.080	      6.920	          2	    225.521
+  715.7055	     49.017	     10.866	          3	    198.560
+  728.3600	     53.299	      6.913	          3	    156.242
+  753.8800	     49.527	      6.406	          2	    113.352
+  724.0400	     47.997	      6.559	          3	    281.194
+  745.9200	     47.521	      6.732	          2	     87.974
diff --git a/lib/galaxy/datatypes/test/test.pqp b/lib/galaxy/datatypes/test/test.pqp
new file mode 100644
index 0000000000000000000000000000000000000000..bd9d3930e2542ab0eb915fbbb42fc9704e2c81ca
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HcmV?d00001

diff --git a/lib/galaxy/datatypes/test/test.psms b/lib/galaxy/datatypes/test/test.psms
new file mode 100644
index 000000000000..56ef19135142
--- /dev/null
+++ b/lib/galaxy/datatypes/test/test.psms
@@ -0,0 +1,122 @@
+PSMId	score	q-value	posterior_error_prob	peptide	proteinIds
+query:161610;rank:1;spectrum:1093.0258_2187.96_spectrum=40633_uteruspremenopause;rt:2187.96;mz:1093.0258;charge:2	11.0472	0	1.48741e-12	X.SLAGSSGPGASSGTSGDHGELVVR.X	UniProt_E9PI39	UniProt_E9PIZ1	UniProt_E9PK01	UniProt_E9PL12	UniProt_E9PMW7	UniProt_E9PPR1	UniProt_E9PQ49	UniProt_E9PRY8	UniProt_H0YCK7	UniProt_P29692	UniProt_P29692-2	genCDS_ENST00000317198_8_143579792-143586845_-1	genCDS_ENST00000395119_8_143579792-143586845_-1	genCDS_ENST00000419152_8_143579792-143586845_-1	genCDS_ENST00000423316_8_143579792-143590081_-1	genCDS_ENST00000442189_8_143579792-143590081_-1	genCDS_ENST00000524397_8_143580630-143586845_-1	genCDS_ENST00000529007_8_143580630-143586845_-1	genCDS_ENST00000529272_8_143579792-143586845_-1	genCDS_ENST00000530191_8_143580506-143586845_-1	genCDS_ENST00000530445_8_143580620-143586845_-1	genCDS_ENST00000530616_8_143580630-143589222_-1	genCDS_ENST00000531218_8_143580522-143586845_-1	genCDS_ENST00000532741_8_143579792-143590231_-1	genCDS_ENST00000533204_8_143580506-143586845_-1	genCDS_ENST00000533494_8_143580613-143586845_-1	genCDS_ENST00000533749_8_143581079-143599321_-1	genCDS_ENST00000534380_8_143580034-143586845_-1	genCDS_ENST00000618139_8_143580019-143590081_-1
+query:132093;rank:1;spectrum:832.40479_2605.29_spectrum=72602_uteruspremenopause;rt:2605.29;mz:832.40479;charge:2	9.36298	0	7.2763e-11	X.AAAFEEQENETVVVK.X	UniProt_Q5TCU6	UniProt_Q9Y490	genCDS_ENST00000314888_9_35697791-35725694_-1
+query:119552;rank:1;spectrum:769.39142_3320.48_spectrum=167622_uteruspremenopause;rt:3320.48;mz:769.39142;charge:2	8.72204	0	3.19783e-10	X.FALQDLSVEETSAK.X	UniProt_B2RCS5	UniProt_G3V2E8	UniProt_G3V2N5	UniProt_G3V2W4	UniProt_G3V2X9	UniProt_G3V5M4	UniProt_H9KV75	UniProt_O43707	UniProt_P12814	UniProt_P12814-2	UniProt_P12814-3	UniProt_P12814-4	UniProt_P35609	UniProt_Q08043	genCDS_ENST00000193403_14_68874859-68979056_-1	genCDS_ENST00000252699_19_38647746-38729432_1	genCDS_ENST00000366578_1_236686674-236762619_1	genCDS_ENST00000376839_14_68874859-68925582_-1	genCDS_ENST00000394419_14_68874859-68979056_-1	genCDS_ENST00000438964_14_68874859-68979056_-1	genCDS_ENST00000502692_11_66546511-66563193_1	genCDS_ENST00000513398_11_66546938-66563193_1	genCDS_ENST00000538545_14_68874859-68979056_-1	genCDS_ENST00000542672_1_236686674-236762619_1	genCDS_ENST00000553370_14_68904702-68925582_-1	genCDS_ENST00000553779_14_68910020-68925582_-1	genCDS_ENST00000555616_14_68892228-68925582_-1	genCDS_ENST00000556433_14_68893665-68978258_-1	genCDS_ENST00000556571_14_68910022-68978051_-1
+query:105717;rank:1;spectrum:715.89587_3127.2_spectrum=82140_uteruspremenopause;rt:3127.2;mz:715.89587;charge:2	8.58807	0	4.35755e-10	X.LDSLSAQLSQLQK.X	UniProt_P02545	UniProt_P02545-2	UniProt_P02545-3	UniProt_P02545-4	UniProt_P02545-5	UniProt_P02545-6	UniProt_Q5TCI8	genCDS_ENST00000347559_1_156114919-156139106_1	genCDS_ENST00000361308_1_156114919-156137764_1	genCDS_ENST00000368297_1_156126803-156137764_1	genCDS_ENST00000368299_1_156114919-156139106_1	genCDS_ENST00000368300_1_156114919-156139106_1	genCDS_ENST00000368301_1_156114919-156137764_1	genCDS_ENST00000448611_1_156126204-156139839_1	genCDS_ENST00000473598_1_156129850-156139106_1
+query:121144;rank:1;spectrum:776.86639_1943.52_spectrum=62937_uteruspremenopause;rt:1943.52;mz:776.86639;charge:2	8.31993	0	8.09508e-10	X.TSTTSSMVASAEQPR.X	UniProt_E7EMN6	UniProt_E7EUI7	UniProt_P41236	UniProt_Q6NXS1	genCDS_ENST00000413183_3_195527890-195543025_-1	genCDS_ENST00000438848_3_195516925-195543025_-1	genCDS_ENST00000618156_3_195516896-195543025_-1
+query:91084;rank:1;spectrum:661.3443_2685.51_spectrum=127861_uteruspremenopause;rt:2685.51;mz:661.3443;charge:2	7.84396	0	2.43037e-09	X.STSGGTAALGCLVK.X	UniProt_P01857	UniProt_P01860	genCDS_ENST00000390542_14_105741473-105743071_-1	genCDS_ENST00000390548_14_105737762-105743071_-1	genCDS_ENST00000390549_14_105741473-105743071_-1	genCDS_ENST00000390551_14_105769237-105771405_-1	genCDS_ENST00000612473_14_105741473-106005532_-1	genCDS_ENST00000613152_14_105741473-106211391_-1	genCDS_ENST00000615822_14_105741473-106062604_-1	genCDS_ENST00000616127_14_105769237-106038345_-1	genCDS_ENST00000618145_14_105741473-106012356_-1	genCDS_ENST00000618756_14_105668245-106538265_-1	genCDS_ENST00000619212_14_105741473-106211391_-1	genCDS_ENST00000621473_14_105769237-106005532_-1
+query:128131;rank:1;spectrum:813.40948_2244.71_spectrum=40773_uteruspremenopause;rt:2244.71;mz:813.40948;charge:2	7.38397	0	7.03248e-09	X.DALQNPNDLQLQEK.X	UniProt_C9IYV6	UniProt_C9JPE5	UniProt_Q9H0Q0	genCDS_ENST00000381323_2_16552936-16588119_-1	genCDS_ENST00000406434_2_16552936-16588119_-1	genCDS_ENST00000445605_2_16564005-16588119_-1	genCDS_ENST00000451689_2_16564024-16588119_-1
+query:141775;rank:1;spectrum:893.9129_2874.06_spectrum=158864_uteruspremenopause;rt:2874.06;mz:893.9129;charge:2	7.1148	0	1.30952e-08	X.NKDQGTYEDYVEGLR.X	Augustus2_AUGUSTUS00000061902_12_56160654-56153919_1	UniProt_B7Z6Z4	UniProt_F8VPF3	UniProt_F8VZU9	UniProt_F8W180	UniProt_F8W1R7	UniProt_G3V1V0	UniProt_G3V1Y7	UniProt_G8JLA2	UniProt_J3KND3	UniProt_P60660	UniProt_P60660-2	genCDS_ENST00000293422_12_56158402-56161415_1	genCDS_ENST00000348108_12_56158402-56160654_1	genCDS_ENST00000536128_12_56158402-56160331_1	genCDS_ENST00000547408_12_56158402-56162322_1	genCDS_ENST00000547649_12_56158402-56161415_1	genCDS_ENST00000548293_12_56158402-56160654_1	genCDS_ENST00000548400_12_56158402-56160654_1	genCDS_ENST00000548580_12_56158402-56161415_1	genCDS_ENST00000549392_12_56158402-56160320_1	genCDS_ENST00000549566_12_56158402-56161415_1	genCDS_ENST00000550697_12_56158402-56160654_1	genCDS_ENST00000551589_12_56158402-56160331_1
+query:71406;rank:1;spectrum:404.21942_2506.81_spectrum=119549_uteruspremenopause;rt:2506.81;mz:404.21942;charge:3	7.03952	0	1.55822e-08	X.TANDAVELHLK.X	UniProt_Q9P2B2	genCDS_ENST00000393203_1_116910204-116986967_1
+query:129027;rank:1;spectrum:817.40759_3010.12_spectrum=35161_uteruspremenopause;rt:3010.12;mz:817.40759;charge:2	7.02828	0	1.5992e-08	X.EGCTVSPETLSLNVK.X	UniProt_E5KLJ5	UniProt_E5KLJ6	UniProt_E5KLJ9	UniProt_E5KLK1	UniProt_O60313	UniProt_O60313-2	genCDS_ENST00000361150_3_193593378-193692127_1	genCDS_ENST00000361510_3_193593378-193692127_1	genCDS_ENST00000361715_3_193593378-193692127_1	genCDS_ENST00000361828_3_193593378-193692127_1	genCDS_ENST00000361908_3_193593378-193692127_1	genCDS_ENST00000392438_3_193593378-193692127_1
+query:79758;rank:1;spectrum:627.82471_1646.41_spectrum=69987_uteruspremenopause;rt:1646.41;mz:627.82471;charge:2	6.79995	0	2.70985e-08	X.LEPGGGAEAQAVR.X	UniProt_Q14315	UniProt_Q14315-2	genCDS_ENST00000325888_7_128830638-128858523_1	genCDS_ENST00000346177_7_128830638-128858523_1
+query:107233;rank:1;spectrum:721.87775_2878.99_spectrum=96857_uteruspremenopause;rt:2878.99;mz:721.87775;charge:2	6.53355	0	5.01392e-08	X.EAGAGGLSLAVEGPSK.X	UniProt_E7EN95	UniProt_O75369	UniProt_O75369-2	UniProt_O75369-3	UniProt_O75369-6	UniProt_O75369-7	UniProt_O75369-8	UniProt_O75369-9	UniProt_Q14315	UniProt_Q14315-2	genCDS_ENST00000295956_3_58008565-58170762_1	genCDS_ENST00000325888_7_128830638-128858523_1	genCDS_ENST00000346177_7_128830638-128858523_1	genCDS_ENST00000358537_3_58008565-58170762_1	genCDS_ENST00000429972_3_58008565-58170762_1	genCDS_ENST00000490882_3_58008565-58170762_1	genCDS_ENST00000493452_3_58078486-58170762_1
+query:146872;rank:1;spectrum:619.28918_2152.13_spectrum=141583_uteruspremenopause;rt:2152.13;mz:619.28918;charge:3	6.13383	0	1.26226e-07	X.SEETKENEGFTVTAEGK.X	UniProt_M0QYC8	UniProt_P01024	genCDS_ENST00000245907_19_6677882-6720589_-1	genCDS_ENST00000596548_19_6680159-6685038_-1
+query:172404;rank:1;spectrum:871.76086_2726.33_spectrum=42005_uteruspremenopause;rt:2726.33;mz:871.76086;charge:3	5.99128	0	1.75446e-07	X.SEAEEALTSFN(Deamidated)GHKPPGSSEPLTVK.X	UniProt_B4DVB8	UniProt_Q15717	genCDS_ENST00000351593_19_7963483-7991815_-1	genCDS_ENST00000407627_19_7963483-7991815_-1	genCDS_ENST00000596459_19_7963483-7991815_-1
+query:105836;rank:1;spectrum:716.36646_2072.32_spectrum=141400_uteruspremenopause;rt:2072.32;mz:716.36646;charge:2	5.83486	0	2.51791e-07	X.VASSPVM(Oxidation)VSNPATR.X	UniProt_A6NEM2	UniProt_P51610	UniProt_P51610-2	UniProt_P51610-4	genCDS_ENST00000310441_X_153949347-153970840_-1	genCDS_ENST00000369984_X_153949347-153970840_-1
+query:89905;rank:1;spectrum:657.87396_3407.52_spectrum=152816_uteruspremenopause;rt:3407.52;mz:657.87396;charge:2	5.75831	0	3.00493e-07	X.EHALLAYTLGVK.X	Augustus2_AUGUSTUS00000028250_3_184026960-184027756_-1	UniProt_P68104	UniProt_Q05639	UniProt_Q5VTE0	calCuffs_CUFF.68550.1_19_35873852-35875252_1_1_ORF2	ensBodymap_RNASEQT00000006703_5_14651962-14653630_-1	ensBodymap_RNASEQT00000053260_5_14650973-14653630_-1	ensBodymap_RNASEQT00000095825_9_135894020-135896638_1	ensBodymap_RNASEQT00000213862_9_135894020-135896638_1	genCDS_ENST00000217182_20_63488298-63497763_-1	genCDS_ENST00000298049_20_63488298-63497763_-1	genCDS_ENST00000309268_6_73517810-73520026_-1	genCDS_ENST00000316292_6_73517810-73520026_-1	genCDS_ENST00000331523_6_73517810-73520026_-1	genCDS_ENST00000615060_6_73517916-73520026_-1	genpseudogene_ENST00000415278_1_96446930-96448318_1_1_ORF2	genpseudogene_ENST00000419025_3_184026369-184027756_-1_2_ORF4	genpseudogene_ENST00000436459_9_133019486-133020874_1_1_ORF1	genpseudogene_ENST00000514975_4_105484698-105486080_1_1_ORF1	genpseudogene_ENST00000596811_19_35382172-35384052_1_1_ORF5	yalePseudo_PGOHUM00000234671_19_35873074-35874951_1_2_ORF13	yalePseudo_PGOHUM00000237893_3_183744160-183745544_-1_2_ORF4	yalePseudo_PGOHUM00000244804_1_96912486-96913871_1_1_ORF2	yalePseudo_PGOHUM00000246017_4_106405855-106407234_1_1_ORF1
+query:120224;rank:1;spectrum:772.3432_1845.25_spectrum=39781_uteruspremenopause;rt:1845.25;mz:772.3432;charge:2	5.59137	0	4.41859e-07	X.FYEQM(Oxidation)N(Deamidated)GPVAGASR.X	UniProt_E9PI39	UniProt_E9PIZ1	UniProt_E9PK01	UniProt_E9PK06	UniProt_E9PK72	UniProt_E9PKK3	UniProt_E9PL12	UniProt_E9PL71	UniProt_E9PMW7	UniProt_E9PN91	UniProt_E9PPR1	UniProt_E9PQ49	UniProt_E9PQZ1	UniProt_E9PRY8	UniProt_H0YCK7	UniProt_P29692	UniProt_P29692-2	UniProt_P29692-3	UniProt_P29692-4	genCDS_ENST00000317198_8_143579792-143586845_-1	genCDS_ENST00000395119_8_143579792-143586845_-1	genCDS_ENST00000419152_8_143579792-143586845_-1	genCDS_ENST00000423316_8_143579792-143590081_-1	genCDS_ENST00000442189_8_143579792-143590081_-1	genCDS_ENST00000524397_8_143580630-143586845_-1	genCDS_ENST00000524624_8_143579792-143586845_-1	genCDS_ENST00000525223_8_143586729-143586845_-1	genCDS_ENST00000526340_8_143586219-143586845_-1	genCDS_ENST00000526838_8_143579792-143586845_-1	genCDS_ENST00000528610_8_143579792-143586845_-1	genCDS_ENST00000529007_8_143580630-143586845_-1	genCDS_ENST00000529272_8_143579792-143586845_-1	genCDS_ENST00000529516_8_143580642-143586845_-1	genCDS_ENST00000530191_8_143580506-143586845_-1	genCDS_ENST00000530445_8_143580620-143586845_-1	genCDS_ENST00000530616_8_143580630-143589222_-1	genCDS_ENST00000531218_8_143580522-143586845_-1	genCDS_ENST00000531621_8_143579792-143586845_-1	genCDS_ENST00000532543_8_143586729-143586845_-1	genCDS_ENST00000532741_8_143579792-143590231_-1	genCDS_ENST00000533204_8_143580506-143586845_-1	genCDS_ENST00000533494_8_143580613-143586845_-1	genCDS_ENST00000533749_8_143581079-143599321_-1	genCDS_ENST00000533833_8_143580630-143586845_-1	genCDS_ENST00000534377_8_143580186-143586845_-1	genCDS_ENST00000534380_8_143580034-143586845_-1	genCDS_ENST00000618139_8_143580019-143590081_-1	genpseudogene_ENST00000433698_9_92836826-92837668_-1_1_ORF1	yalePseudo_PGOHUM00000236264_9_95599111-95599989_-1_1_ORF1
+query:83950;rank:1;spectrum:640.32916_1950.76_spectrum=62954_uteruspremenopause;rt:1950.76;mz:640.32916;charge:2	5.43278	0	6.3732e-07	X.YLAEVAAGDDKK.X	UniProt_B0AZS6	UniProt_B7Z2E6	UniProt_E7EX29	UniProt_H0YB80	UniProt_P63104	UniProt_P63104-2	genCDS_ENST00000353245_8_100920693-100948889_-1	genCDS_ENST00000395948_8_100920693-100948658_-1	genCDS_ENST00000395951_8_100920693-100948889_-1	genCDS_ENST00000395953_8_100920693-100948889_-1	genCDS_ENST00000395956_8_100920693-100948889_-1	genCDS_ENST00000395957_8_100920693-100948889_-1	genCDS_ENST00000395958_8_100920693-100948889_-1	genCDS_ENST00000419477_8_100920693-100948889_-1	genCDS_ENST00000457309_8_100920693-100948889_-1	genCDS_ENST00000521309_8_100920693-100924973_-1	genCDS_ENST00000521607_8_100920716-100948889_-1	genCDS_ENST00000522542_8_100920693-100948145_-1	genCDS_ENST00000522819_8_100920693-100924973_-1	genCDS_ENST00000523848_8_100920693-100924988_-1	genpseudogene_ENST00000415292_10_23136924-23137661_1_1_ORF1
+query:70327;rank:1;spectrum:602.85034_3098.02_spectrum=159460_uteruspremenopause;rt:3098.02;mz:602.85034;charge:2	5.3382	0	7.92901e-07	X.TLMALGSLAVTK.X	UniProt_H0YCU9	UniProt_Q01995	genCDS_ENST00000278968_11_117203014-117204359_1	genCDS_ENST00000392951_11_117203014-117204359_1	genCDS_ENST00000525531_11_117203014-117204359_1	genCDS_ENST00000529622_11_117203144-117204359_1	genCDS_ENST00000530649_11_117203014-117204359_1	genCDS_ENST00000532870_11_117203014-117204359_1
+query:161278;rank:1;spectrum:725.35535_3439.5_spectrum=82985_uteruspremenopause;rt:3439.5;mz:725.35535;charge:3	5.26056	0	9.48615e-07	X.LEWLESHQDADLEDFKAK.X	UniProt_P11021	genCDS_ENST00000324460_9_125236592-125241126_-1
+query:61382;rank:1;spectrum:578.83197_2603.98_spectrum=142644_uteruspremenopause;rt:2603.98;mz:578.83197;charge:2	5.23568	0	1.00471e-06	X.VKGDVDVSLPK.X	UniProt_Q09666	genCDS_ENST00000378024_11_62516744-62536098_-1
+query:121082;rank:1;spectrum:776.46204_3500.05_spectrum=153073_uteruspremenopause;rt:3500.05;mz:776.46204;charge:2	4.84174	0	2.49494e-06	X.LVQVALNGLENLLR.X	UniProt_F5GYL8	UniProt_F5H4G7	UniProt_H0Y3K0	UniProt_O15131	UniProt_O60684	UniProt_P52294	genCDS_ENST00000344337_3_122426985-122496565_-1	genCDS_ENST00000356348_6_116681335-116732323_1	genCDS_ENST00000368564_6_116681335-116732323_1	genCDS_ENST00000373625_1_32108131-32170894_1	genCDS_ENST00000392517_6_116729563-116732323_1
+query:93986;rank:1;spectrum:671.32318_2044.34_spectrum=17669_uteruspremenopause;rt:2044.34;mz:671.32318;charge:2	4.67543	0	3.66237e-06	X.YELEETETVTK.X	UniProt_C9J813	UniProt_E7EX44	UniProt_E9PGZ1	UniProt_F5H1Z9	UniProt_Q05682	UniProt_Q05682-2	UniProt_Q05682-3	UniProt_Q05682-4	UniProt_Q05682-5	UniProt_Q05682-6	genCDS_ENST00000361675_7_134867734-134968345_1	genCDS_ENST00000361901_7_134867734-134968345_1	genCDS_ENST00000393118_7_134891621-134968345_1	genCDS_ENST00000417172_7_134867734-134968345_1	genCDS_ENST00000422748_7_134867734-134968345_1	genCDS_ENST00000424922_7_134891621-134968345_1	genCDS_ENST00000436461_7_134867734-134960056_1	genCDS_ENST00000443197_7_134891621-134962918_1	genCDS_ENST00000495522_7_134891621-134968345_1
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+query:35867;rank:1;spectrum:503.7821_2660.72_spectrum=19332_uteruspremenopause;rt:2660.72;mz:503.7821;charge:2	2.36667	6.99035e-05	0.000613454	X.LVLEYVDR.X	UniProt_E7ETH0	UniProt_G3XAM2	UniProt_P05156	genCDS_ENST00000394634_4_109740893-109801971_-1	genCDS_ENST00000394635_4_109740893-109801971_-1	genCDS_ENST00000512148_4_109740893-109801971_-1
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+query:175487;rank:1;spectrum:943.40503_1694.59_spectrum=101873_uteruspremenopause;rt:1694.59;mz:943.40503;charge:3	-2.1027	0.100208	1	X.(Acetyl)YEDSQQ(Deamidated)EEAQ(Deamidated)YGAMFQ(Deamidated)EQLM(Oxidation)TLK.X	UniProt_F5H4J1	UniProt_Q14980	UniProt_Q14980-2	UniProt_Q14980-3	UniProt_Q14980-4	genCDS_ENST00000358965_11_72003527-72035943_-1	genCDS_ENST00000393695_11_72003527-72035943_-1	genCDS_ENST00000542977_11_72014948-72035943_-1	genCDS_ENST00000616538_11_72003527-72035943_-1	genCDS_ENST00000620566_11_72003527-72035943_-1
+query:90871;rank:1;spectrum:660.8255_2297.68_spectrum=111599_uteruspremenopause;rt:2297.68;mz:660.8255;charge:2	-2.46345	0.104155	1	X.(Carbamidomethyl)AHN(Deamidated)FDERVFK.X	UniProt_Q96M60	UniProt_Q96M60-2	genCDS_ENST00000299338_15_49328568-49615171_-1	genCDS_ENST00000561064_15_49422710-49615171_-1
diff --git a/lib/galaxy/datatypes/test/test.sqmass b/lib/galaxy/datatypes/test/test.sqmass
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z(CY<=Pxzz2=l}Kkeuf5u00@8p2!H?xfB*=900@8p2!H^B5TEP!Uw{4|6NBsjFnB-!
z1V8`;KmY_l00ck)1V8`;K;Um70N4Nj7Tp9%f&d7B00@8p2!H?xfB*=900@A<pCIsG
HU;qCX3Fb3f

literal 0
HcmV?d00001


From 18efa018bf0a4f94f113fe28780b6e91020d9171 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 19 Feb 2020 17:50:00 +0100
Subject: [PATCH 141/853] openms datatypes: fix mzTab

---
 .../config/sample/datatypes_conf.xml.sample   |  2 +-
 lib/galaxy/datatypes/proteomics.py            | 46 ++++++++++---------
 2 files changed, 26 insertions(+), 22 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 76867b2a7dbc..c6bd174ce252 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -228,7 +228,7 @@
     <datatype extension="directory" type="galaxy.datatypes.data:Directory">
     </datatype>
     <!-- Proteomics Datatypes -->
-    <datatype extension="mrm" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
+    <datatype extension="mrm" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" subclass="true"/>
     <datatype extension="dta" type="galaxy.datatypes.proteomics:Dta" display_in_upload="true" />
     <datatype extension="dta2d" type="galaxy.datatypes.proteomics:Dta2d" display_in_upload="true" />
     <datatype extension="edta" type="galaxy.datatypes.proteomics:Edta" display_in_upload="true" />
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 2e6a720e9ae2..ae3995614853 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -69,8 +69,13 @@ class MzTab(Text):
     edam_data = "data_3681"
     file_ext = "mztab"
     # section names (except MTD)
-    __sections = ["PRH", "PRT", "PEH", "PEP", "PSH", "PSM", "SMH", "SML", "COM"]
-    __version_re = r"(1)(\.[0-9])?(\.[0-9])?"
+    _sections = ["PRH", "PRT", "PEH", "PEP", "PSH", "PSM", "SMH", "SML", "COM"]
+    # mandatory metadata fields and list of allowed entries (in lower case)
+    # (or None if everything is allowed)
+    _man_mtd = {"mzTab-mode": ["complete", "summary"],
+                "mzTab-type": ['quantification', 'identification'],
+                "description": None}
+    _version_re = r"(1)(\.[0-9])?(\.[0-9])?"
 
     def __init__(self, **kwd):
         super(MzTab, self).__init__(**kwd)
@@ -87,23 +92,21 @@ def set_peek(self, dataset, is_multi_byte=False):
     def sniff_prefix(self, file_prefix):
         """ Determines whether the file is the correct type. """
         has_version = False
-        has_mode = False
-        has_type = False
-
+        found_man_mtd = set()
+        cnt = 0
         contents = file_prefix.string_io()
-        while True:
-            line = contents.readline().split("\t")
+        for line in contents:
+            if re.match(r"^\s*$", line):
+                continue
+            line = line.strip("\r\n").split("\t")
             if line[0] == "MTD":
-                if line[1] == "mzTab-version" and re.match(self.__version_re, line) is not None:
+                if line[1] == "mzTab-version" and re.match(self._version_re, line[2]) is not None:
                     has_version = True
-                elif line[1] == "mzTab-mode" and line[2].lowercase() in ["complete", "summary"]:
-                    has_mode = True
-                elif line[1] == "mzTab-type" and line[2].lowercase() in ['quantification', 'identification']:
-                    has_type = True
-            elif not line[0] in self.__sections:
+                elif line[1] in self._man_mtd and (self._man_mtd[line[1]] is None or line[2].lower() in self._man_mtd[line[1]]):
+                    found_man_mtd.add(line[1])
+            elif not line[0] in self._sections:
                 return False
-
-        return has_version and has_mode and has_type
+        return has_version and found_man_mtd == set(self._man_mtd.keys())
 
 
 class MzTab2(MzTab):
@@ -119,8 +122,9 @@ class MzTab2(MzTab):
     False
     """
     file_ext = "mztab2"
-    __sections = ["SMH", "SML", "SFH", "SMF", "SEH", "SME", "COM"]
-    __version_re = r"(2)(\.[0-9])?(\.[0-9])?-M$"
+    _sections = ["SMH", "SML", "SFH", "SMF", "SEH", "SME", "COM"]
+    _version_re = r"(2)(\.[0-9])?(\.[0-9])?-M$"
+    _man_mtd = {"mzTab-ID": None}
 
     def __init__(self, **kwd):
         super(MzTab2, self).__init__(**kwd)
@@ -467,14 +471,14 @@ def _parse_type(self, line):
 
     def _parse_dataline(self, line, tpe):
         if tpe == 2 or tpe == 3:
-            l = 4
+            idx = 4
         else:
-            l = 3
+            idx = 3
         try:
-            line = [float(_) for _ in line[:l]]
+            line = [float(_) for _ in line[:idx]]
         except ValueError:
             return False
-        if not all(_ >= 0 for _ in line[:l]):
+        if not all(_ >= 0 for _ in line[:idx]):
             return False
         return True
 

From 9a2d2f48c6e7819b3d4a5689a481f1a6f2b0d42b Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 20 Feb 2020 11:31:24 +0100
Subject: [PATCH 142/853] MzTab: fix capitalization

---
 lib/galaxy/datatypes/proteomics.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index ae3995614853..fd792e24aea7 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -93,7 +93,6 @@ def sniff_prefix(self, file_prefix):
         """ Determines whether the file is the correct type. """
         has_version = False
         found_man_mtd = set()
-        cnt = 0
         contents = file_prefix.string_io()
         for line in contents:
             if re.match(r"^\s*$", line):
@@ -115,10 +114,10 @@ class MzTab2(MzTab):
 
     >>> from galaxy.datatypes.sniff import get_test_fname
     >>> fname = get_test_fname('test.mztab2')
-    >>> mztab2().sniff(fname)
+    >>> MzTab2().sniff(fname)
     True
     >>> fname = get_test_fname('test.mztab')
-    >>> mztab2().sniff(fname)
+    >>> MzTab2().sniff(fname)
     False
     """
     file_ext = "mztab2"

From 1111e83ff5c144c0a13661152111528982ba143e Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 20 Feb 2020 14:42:11 +0100
Subject: [PATCH 143/853] remove subclass relation between OSW and PQP

---
 lib/galaxy/datatypes/binary.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 16735eb7731b..b93c6d0363fe 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -1596,10 +1596,10 @@ def sniff(self, filename):
         table_names = ['COMPOUND', 'PEPTIDE', 'PEPTIDE_PROTEIN_MAPPING', 'PRECURSOR',
                        'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
                        'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING']
-        return super(PQP, self).sniff(filename) and self.sniff_table_names(filename, table_names)
+        return super(PQP, self).sniff(filename) and self.sniff_table_names(filename, table_names, True)
 
 
-class OSW(PQP):
+class OSW(SQlite):
     """
     Class describing OpenSwath output
 
@@ -1619,8 +1619,11 @@ def set_meta(self, dataset, overwrite=True, **kwd):
     def sniff(self, filename):
         # osw seems to be an extension of pqp (few tables are added)
         # see also here https://github.com/OpenMS/OpenMS/issues/4365
-        table_names = ['FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
-        return super(OSW, self).sniff(filename) and self.sniff_table_names(filename, table_names)
+        table_names = ['COMPOUND', 'PEPTIDE', 'PEPTIDE_PROTEIN_MAPPING', 'PRECURSOR',
+                       'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
+                       'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING',
+                       'FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
+        return super(OSW, self).sniff(filename) and self.sniff_table_names(filename, table_names, True)
 
 
 class SQmass(SQlite):

From 9e785ba3b86207880f063bf918f38ba7d331eb33 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 20 Feb 2020 14:51:29 +0100
Subject: [PATCH 144/853] PQP: just check that the extra OSW tables are not
 included

---
 lib/galaxy/datatypes/binary.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index b93c6d0363fe..cde4e1db2f71 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -1596,7 +1596,8 @@ def sniff(self, filename):
         table_names = ['COMPOUND', 'PEPTIDE', 'PEPTIDE_PROTEIN_MAPPING', 'PRECURSOR',
                        'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
                        'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING']
-        return super(PQP, self).sniff(filename) and self.sniff_table_names(filename, table_names, True)
+        osw_table_names = ['FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
+        return super(PQP, self).sniff(filename) and self.sniff_table_names(filename, table_names) and not self.sniff_table_names(filename, osw_table_names)
 
 
 class OSW(SQlite):
@@ -1623,7 +1624,7 @@ def sniff(self, filename):
                        'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
                        'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING',
                        'FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
-        return super(OSW, self).sniff(filename) and self.sniff_table_names(filename, table_names, True)
+        return super(OSW, self).sniff(filename) and self.sniff_table_names(filename, table_names)
 
 
 class SQmass(SQlite):

From fce58247f60012315df81f2da640527e1c469efc Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 21 Feb 2020 10:58:33 +0100
Subject: [PATCH 145/853] disable sublass="true" for osw, pqp, sqmass

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 6 +++---
 lib/galaxy/datatypes/binary.py                     | 8 ++++++--
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index c6bd174ce252..e7d2da992003 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -358,9 +358,9 @@
     </datatype>
     <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="pqp" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true" subclass="true"/>
-    <datatype extension="osw" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true" subclass="true"/>
-    <datatype extension="sqmass" type="galaxy.datatypes.binary:SQmass" mimetype="application/octet-stream" display_in_upload="true" subclass="true"/>
+    <datatype extension="pqp" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="osw" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="sqmass" type="galaxy.datatypes.binary:SQmass" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="gemini.sqlite" type="galaxy.datatypes.binary:GeminiSQLite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="cuffdiff.sqlite" type="galaxy.datatypes.binary:CuffDiffSQlite" display_in_upload="true"/>
     <datatype extension="gafa.sqlite" type="galaxy.datatypes.binary:GAFASQLite" mimetype="application/octet-stream" display_in_upload="true"/>
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index cde4e1db2f71..7e7c6bc451f3 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -1593,11 +1593,13 @@ def sniff(self, filename):
         for now VERSION GENE PEPTIDE_GENE_MAPPING are excluded, since
         there is test data wo these tables, see also here https://github.com/OpenMS/OpenMS/issues/4365
         """
+        if not super(PQP, self).sniff(filename):
+            return False
         table_names = ['COMPOUND', 'PEPTIDE', 'PEPTIDE_PROTEIN_MAPPING', 'PRECURSOR',
                        'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
                        'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING']
         osw_table_names = ['FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
-        return super(PQP, self).sniff(filename) and self.sniff_table_names(filename, table_names) and not self.sniff_table_names(filename, osw_table_names)
+        return self.sniff_table_names(filename, table_names) and not self.sniff_table_names(filename, osw_table_names)
 
 
 class OSW(SQlite):
@@ -1620,11 +1622,13 @@ def set_meta(self, dataset, overwrite=True, **kwd):
     def sniff(self, filename):
         # osw seems to be an extension of pqp (few tables are added)
         # see also here https://github.com/OpenMS/OpenMS/issues/4365
+        if not super(OSW, self).sniff(filename):
+            return False
         table_names = ['COMPOUND', 'PEPTIDE', 'PEPTIDE_PROTEIN_MAPPING', 'PRECURSOR',
                        'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
                        'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING',
                        'FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
-        return super(OSW, self).sniff(filename) and self.sniff_table_names(filename, table_names)
+        return self.sniff_table_names(filename, table_names)
 
 
 class SQmass(SQlite):

From 274ad1d770f884ca3dd346613f61356429d30bba Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 21 Feb 2020 11:13:35 +0100
Subject: [PATCH 146/853] remove sqlite data types with sniffers from registry

---
 lib/galaxy/datatypes/registry.py | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 67c01e39f579..cfbdd4f8223f 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -770,18 +770,15 @@ def set_default_values(self):
                 'eland'         : tabular.Eland(),
                 'fastq'         : sequence.Fastq(),
                 'fastqsanger'   : sequence.FastqSanger(),
-                'gemini.sqlite' : binary.GeminiSQLite(),
                 'gtf'           : interval.Gtf(),
                 'gff'           : interval.Gff(),
                 'gff3'          : interval.Gff3(),
                 'genetrack'     : tracks.GeneTrack(),
                 'h5'            : binary.H5(),
-                'idpdb'         : binary.IdpDB(),
                 'interval'      : interval.Interval(),
                 'laj'           : images.Laj(),
                 'lav'           : sequence.Lav(),
                 'maf'           : sequence.Maf(),
-                'mz.sqlite'     : binary.MzSQlite(),
                 'pileup'        : tabular.Pileup(),
                 'qualsolid'     : qualityscore.QualityScoreSOLiD(),
                 'qualsolexa'    : qualityscore.QualityScoreSolexa(),
@@ -801,7 +798,6 @@ def set_default_values(self):
                 'axt'           : 'text/plain',
                 'bam'           : 'application/octet-stream',
                 'bed'           : 'text/plain',
-                'blib'          : 'application/octet-stream',
                 'customtrack'   : 'text/plain',
                 'csfasta'       : 'text/plain',
                 'db3'           : 'application/octet-stream',
@@ -809,18 +805,15 @@ def set_default_values(self):
                 'fasta'         : 'text/plain',
                 'fastq'         : 'text/plain',
                 'fastqsanger'   : 'text/plain',
-                'gemini.sqlite' : 'application/octet-stream',
                 'gtf'           : 'text/plain',
                 'gff'           : 'text/plain',
                 'gff3'          : 'text/plain',
                 'h5'            : 'application/octet-stream',
-                'idpdb'         : 'application/octet-stream',
                 'interval'      : 'text/plain',
                 'laj'           : 'text/plain',
                 'lav'           : 'text/plain',
                 'maf'           : 'text/plain',
                 'memexml'       : 'application/xml',
-                'mz.sqlite'     : 'application/octet-stream',
                 'pileup'        : 'text/plain',
                 'qualsolid'     : 'text/plain',
                 'qualsolexa'    : 'text/plain',
@@ -846,10 +839,6 @@ def set_default_values(self):
                 binary.Bam(),
                 binary.Sff(),
                 binary.H5(),
-                binary.GeminiSQLite(),
-                binary.MzSQlite(),
-                binary.IdpDB(),
-                binary.SQlite(),
                 xml.GenericXml(),
                 sequence.Maf(),
                 sequence.Lav(),

From 9d9fa252f2e34428c1e5751d4e96d55e75d81814 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 21 Feb 2020 11:48:29 +0100
Subject: [PATCH 147/853] move SQlite datatype up in the
 datatypes_config.sample

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index e7d2da992003..d4324893da21 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -266,6 +266,7 @@
     <datatype extension="mzdata" type="galaxy.datatypes.proteomics:MzData" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="ms2" type="galaxy.datatypes.proteomics:Ms2" display_in_upload="true"/>
     <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="mz.sqlite" type="galaxy.datatypes.binary:MzSQlite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="osw" type="galaxy.datatypes.binary:OSW" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="pqp" type="galaxy.datatypes.binary:PQP" mimetype="application/octet-stream" display_in_upload="true"/>
@@ -357,7 +358,6 @@
       <converter file="tabular_to_csv.xml" target_datatype="csv"/>
     </datatype>
     <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="pqp" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="osw" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="sqmass" type="galaxy.datatypes.binary:SQmass" mimetype="application/octet-stream" display_in_upload="true"/>

From c6d0955ad22613621b9c78aa53bd52d8400746b8 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 21 Feb 2020 12:15:36 +0100
Subject: [PATCH 148/853] remove db3 from registry

---
 lib/galaxy/datatypes/registry.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index cfbdd4f8223f..5b479baf5fba 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -765,7 +765,6 @@ def set_default_values(self):
                 'coverage'      : coverage.LastzCoverage(),
                 'customtrack'   : interval.CustomTrack(),
                 'csfasta'       : sequence.csFasta(),
-                'db3'           : binary.SQlite(),
                 'fasta'         : sequence.Fasta(),
                 'eland'         : tabular.Eland(),
                 'fastq'         : sequence.Fastq(),
@@ -800,7 +799,6 @@ def set_default_values(self):
                 'bed'           : 'text/plain',
                 'customtrack'   : 'text/plain',
                 'csfasta'       : 'text/plain',
-                'db3'           : 'application/octet-stream',
                 'eland'         : 'application/octet-stream',
                 'fasta'         : 'text/plain',
                 'fastq'         : 'text/plain',

From 0deaf09ad3143a6eaf0f1c466371e4fbabd53a54 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 21 Feb 2020 20:36:17 +0100
Subject: [PATCH 149/853] match thermo.raw extension as in datatypes_conf

---
 lib/galaxy/datatypes/proteomics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index fd792e24aea7..f3a289338444 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -782,7 +782,7 @@ class ThermoRAW(Binary):
     """Class describing a Thermo Finnigan binary RAW file"""
     edam_data = "data_2536"
     edam_format = "format_3712"
-    file_ext = "raw"
+    file_ext = "thermo.raw"
 
     def sniff(self, filename):
         # Thermo Finnigan RAW format is proprietary and hence not well documented.

From ec23d175a7e690e9261bfd2f074edff5793bb8bb Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 21 Feb 2020 22:03:09 +0100
Subject: [PATCH 150/853] add sirius.ms datatype

as subclass of text
---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index d4324893da21..0e5dfcdf2b88 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -248,6 +248,7 @@
     <datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="tandem" type="galaxy.datatypes.proteomics:TandemXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="sirius.ms" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="false"/>
     <datatype extension="thermo.raw" type="galaxy.datatypes.proteomics:ThermoRAW" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="brukerbaf.d.tar" type="galaxy.datatypes.binary:BafTar" display_in_upload="true"/>
     <datatype extension="agilentbrukeryep.d.tar" type="galaxy.datatypes.binary:YepTar" display_in_upload="true"/>

From 68c92b89e73f919d7e6c573ceaa79497586caaec Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Sat, 22 Feb 2020 16:02:26 +0100
Subject: [PATCH 151/853] remove duplicate osw, pqp entries in conf

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 2 --
 1 file changed, 2 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 0e5dfcdf2b88..151062e82e55 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -359,8 +359,6 @@
       <converter file="tabular_to_csv.xml" target_datatype="csv"/>
     </datatype>
     <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="pqp" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="osw" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="sqmass" type="galaxy.datatypes.binary:SQmass" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="gemini.sqlite" type="galaxy.datatypes.binary:GeminiSQLite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="cuffdiff.sqlite" type="galaxy.datatypes.binary:CuffDiffSQlite" display_in_upload="true"/>

From e1a49cc678c4489e31583895fb8bd5126ebe8fd1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sat, 22 Feb 2020 17:57:33 +0100
Subject: [PATCH 152/853] ITs

---
 interactivetool_climate_notebook.xml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml
index f867208bfbe0..d31103dfc2b3 100644
--- a/interactivetool_climate_notebook.xml
+++ b/interactivetool_climate_notebook.xml
@@ -23,8 +23,8 @@
 
         #if $input:
             #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
-	    get -t hid -i '${input.hid}' &&
-	    ln -sf '/import/${input.hid}' './jupyter/data/${cleaned_name}' &&
+            get -t hid -i '${input.hid}' &&
+            ln -sf '/import/${input.hid}' './jupyter/data/${cleaned_name}' &&
         #end if
 
         ## change into the directory where the notebooks are located
@@ -33,15 +33,15 @@
 
         #if $mode.mode_select == 'scratch':
             ## copy default notebook
-            cp '/home/jovyan/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
+            cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
             jupyter trust ./ipython_galaxy_notebook.ipynb &&
             jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
             cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
 
         #else:
             #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
-	    get -t hid -i '${mode.ipynb.hid}' &&
-	    ln -sf '/import/${mode.ipynb.hid}' './jupyter/data/${cleaned_name}' &&
+            get -t hid -i '${mode.ipynb.hid}' &&
+            ln -sf '/import/${mode.ipynb.hid}' './data/${cleaned_name}'
             jupyter trust ./${cleaned_name} &&
 
             #if $mode.run_it:
@@ -51,6 +51,7 @@
             #end if
             cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
         #end if
+
     ]]>
     </command>
     <inputs>

From 6137f9853722fe1a894fff2dfcb6e59366f1bb79 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Sat, 22 Feb 2020 16:27:04 +0100
Subject: [PATCH 153/853] add PEFF data type

---
 .../config/sample/datatypes_conf.xml.sample   |  2 ++
 lib/galaxy/datatypes/proteomics.py            | 26 +++++++++++++++++++
 lib/galaxy/datatypes/test/test.peff           | 11 ++++++++
 3 files changed, 39 insertions(+)
 create mode 100644 lib/galaxy/datatypes/test/test.peff

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 151062e82e55..11d948e64dd8 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -302,6 +302,7 @@
     <datatype extension="kronik" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
     <datatype extension="imzml" type="galaxy.datatypes.proteomics:ImzML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="analyze75" type="galaxy.datatypes.proteomics:Analyze75" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="peff" type="galaxy.datatypes.proteomics:PEFF" display_in_upload="true"/>
     <!-- End Proteomics Datatypes -->
     <datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
@@ -887,6 +888,7 @@
     <sniffer type="galaxy.datatypes.proteomics:XquestSpecXML"/>
     <sniffer type="galaxy.datatypes.proteomics:QCML"/>
     <sniffer type="galaxy.datatypes.proteomics:Wiff"/>
+    <sniffer type="galaxy.datatypes.proteomics:PEFF"/>
     <sniffer type="galaxy.datatypes.molecules:CML"/>
     <sniffer type="galaxy.datatypes.xml:GenericXml"/>
     <sniffer type="galaxy.datatypes.triples:HDT"/>
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index f3a289338444..8abd76f90c62 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -7,6 +7,7 @@
 from galaxy.datatypes import data
 from galaxy.datatypes.binary import Binary
 from galaxy.datatypes.data import Text
+from galaxy.datatypes.sequence import Sequence
 from galaxy.datatypes.sniff import build_sniff_from_prefix
 from galaxy.datatypes.tabular import Tabular, TabularData
 from galaxy.datatypes.xml import GenericXml
@@ -243,6 +244,31 @@ def sniff_prefix(self, file_prefix):
         return False
 
 
+@build_sniff_from_prefix
+class PEFF(Sequence):
+    """
+    PSI Extended FASTA Format
+    https://github.com/HUPO-PSI/PEFF
+    """
+    file_ext = "peff"
+
+    def sniff_prefix(self, file_prefix):
+        """
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname( 'test.peff' )
+        >>> PEFF().sniff( fname )
+        True
+        >>> fname = get_test_fname( 'sequence.fasta' )
+        >>> PEFF().sniff( fname )
+        False
+        """
+        fh = file_prefix.string_io()
+        if re.match(r"# PEFF \d+.\d+", fh.readline()):
+            return True
+        else:
+            return False
+
+
 class PepXmlReport(Tabular):
     """pepxml converted to tabular report"""
     edam_data = "data_2536"
diff --git a/lib/galaxy/datatypes/test/test.peff b/lib/galaxy/datatypes/test/test.peff
new file mode 100644
index 000000000000..a3dc079de2b7
--- /dev/null
+++ b/lib/galaxy/datatypes/test/test.peff
@@ -0,0 +1,11 @@
+# PEFF 1.0
+# //
+# DbName=Minimal Test example PEFF_Minimal_Valid.peff
+# Prefix=sp
+# DbSource=http://www.peptideatlas.org/formats/PEFF/PEFF_Minimal_Valid.peff
+# DbVersion=1
+# SequenceType=AA
+# NumberOfEntries=1
+# //
+>sp:Q9Y2X3 \Length=1
+M

From 16c843145fadde8789fe6ddeb3ef15f806f39dfb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sat, 22 Feb 2020 19:32:28 +0100
Subject: [PATCH 154/853] ITs: fix commandline

---
 interactivetool_climate_notebook.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml
index d31103dfc2b3..096bc0b1ce97 100644
--- a/interactivetool_climate_notebook.xml
+++ b/interactivetool_climate_notebook.xml
@@ -41,7 +41,7 @@
         #else:
             #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
             get -t hid -i '${mode.ipynb.hid}' &&
-            ln -sf '/import/${mode.ipynb.hid}' './data/${cleaned_name}'
+            ln -sf '/import/${mode.ipynb.hid}' './data/${cleaned_name}' &&
             jupyter trust ./${cleaned_name} &&
 
             #if $mode.run_it:

From 0613727e9f869f9ebc5969939053705ed9f1a399 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sat, 22 Feb 2020 20:34:19 +0100
Subject: [PATCH 155/853] ITs: fix an other path issue

---
 interactivetool_climate_notebook.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml
index 096bc0b1ce97..2f7c989bdb1b 100644
--- a/interactivetool_climate_notebook.xml
+++ b/interactivetool_climate_notebook.xml
@@ -42,7 +42,7 @@
             #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
             get -t hid -i '${mode.ipynb.hid}' &&
             ln -sf '/import/${mode.ipynb.hid}' './data/${cleaned_name}' &&
-            jupyter trust ./${cleaned_name} &&
+            jupyter trust ./data/${cleaned_name} &&
 
             #if $mode.run_it:
                 jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&

From 38f0e3755c1a7dd8bfc952b9bbd3712bc715d332 Mon Sep 17 00:00:00 2001
From: Anne Fouilloux <annefou@geo.uio.no>
Date: Sun, 23 Feb 2020 00:03:13 +0100
Subject: [PATCH 156/853] Add panoply version for docker container (#55)

ITs: get it working
---
 interactivetool_panoply.xml | 41 ++++++++++++++++++++++---------------
 1 file changed, 25 insertions(+), 16 deletions(-)

diff --git a/interactivetool_panoply.xml b/interactivetool_panoply.xml
index 5e84abffe8ac..d663ce89b611 100644
--- a/interactivetool_panoply.xml
+++ b/interactivetool_panoply.xml
@@ -1,34 +1,43 @@
-<tool id="interactive_tool_panoply" tool_type="interactive" name="Panoply" version="0.1">
+<tool id="interactive_tool_panoply" tool_type="interactive" name="Panoply" version="@VERSION@">
     <description>interative plotting tool for geo-referenced data</description>
+    <macros>
+    <token name="@VERSION@">4.5.1</token>
+    </macros>
     <requirements>
-        <container type="docker">quay.io/nordicesmhub/docker-panoply</container>
+        <container type="docker">quay.io/nordicesmhub/docker-panoply:@VERSION@</container>
     </requirements>
     <entry_points>
         <entry_point name="Panoply on $infile.display_name" requires_domain="True">
             <port>5800</port>
         </entry_point>
     </entry_points>
-    <command><![CDATA[
-        mkdir output &&
+    <command detect_errors="exit_code">
+    <![CDATA[
+    mkdir output &&
         mkdir /config/home  &&
-	mkdir /config/home/output &&
-	export HOME=/config/home &&
-	cp '$infile' '/config/home/$infile.display_name' &&
-	mkdir /config/home/.gissjava &&
-	cd /config/home/.gissjava    &&
-	tar xvf /opt/PanoplyJ/colorbars.tar &&
-	cd - &&
-	/init &&
-	cp /config/home/output/*.png output/. | true
+        mkdir /config/home/output &&
+        export HOME=/config/home &&
+        cp '$infile' '/config/home/$infile.display_name' &&
+        mkdir /config/home/.gissjava &&
+        cd /config/home/.gissjava    &&
+        tar xvf /opt/PanoplyJ/colorbars.tar &&
+        cd - &&
+        /init ;
+        echo "Galaxy Panoply version @VERSION@" > output/version.txt &&
+        cp /config/home/output/* output/ | true &&
+        cd output &&
+        sleep 2 &&
+        for file in *; do mv "\$file" "\${file// /_}"; done &&
+        for file in *; do mv "\$file" "\$file.\${file\#\#*.}"; done
     ]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="netcdf,h5" label="netcdf"/>
     </inputs>
     <outputs>
-        <data name="outfile" format="png">
-	   <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true"/>
-	</data>
+        <collection name="outputs" type="list" label="Panoply outputs">
+            <discover_datasets pattern="__name_and_ext__" directory="output" />
+        </collection>
     </outputs>
     <tests>
     </tests>

From 0e6ccda1ccd9e4e3be8b66f11feef405891eb065 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Sun, 23 Feb 2020 12:53:33 +0000
Subject: [PATCH 157/853] Handles floats correctly in ByteSize

---
 lib/galaxy/util/bytesize.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/util/bytesize.py b/lib/galaxy/util/bytesize.py
index bd360e05b4dd..60babde05adf 100644
--- a/lib/galaxy/util/bytesize.py
+++ b/lib/galaxy/util/bytesize.py
@@ -45,7 +45,7 @@ def to_unit(self, unit=None, as_string=True):
 
 
 def parse_bytesize(value):
-    if isinstance(value, int):
+    if isinstance(value, int) or isinstance(value, float):
         # Assume bytes
         return value
     value = value.upper()

From f3fd660badf73a2cda23b6201693a0d3b0c4d4c8 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Sun, 23 Feb 2020 12:53:33 +0000
Subject: [PATCH 158/853] Handles floats correctly in ByteSize

---
 lib/galaxy/util/bytesize.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/util/bytesize.py b/lib/galaxy/util/bytesize.py
index bd360e05b4dd..60babde05adf 100644
--- a/lib/galaxy/util/bytesize.py
+++ b/lib/galaxy/util/bytesize.py
@@ -45,7 +45,7 @@ def to_unit(self, unit=None, as_string=True):
 
 
 def parse_bytesize(value):
-    if isinstance(value, int):
+    if isinstance(value, int) or isinstance(value, float):
         # Assume bytes
         return value
     value = value.upper()

From f61ae2c42ae201ff177eb842a693f9488385ff14 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sat, 22 Feb 2020 02:22:17 +0000
Subject: [PATCH 159/853] Don't check if python is from conda when `CONDA_EXE`
 env var is set

Since at least version 3.7.4 of the `python` package from the `defaults`
conda channel, `python -V` doesn't reveal its origin any more.

Also some fixes suggested by `shellcheck`.
---
 scripts/common_startup_functions.sh | 16 ++++++++--------
 tox.ini                             |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/scripts/common_startup_functions.sh b/scripts/common_startup_functions.sh
index 2a1255bd894d..1ec379a2be10 100644
--- a/scripts/common_startup_functions.sh
+++ b/scripts/common_startup_functions.sh
@@ -99,7 +99,7 @@ setup_python() {
     # should run this instance in.
     : ${GALAXY_VIRTUAL_ENV:=.venv}
     # $GALAXY_CONDA_ENV isn't set here to avoid running the version check if not using Conda
-    if [ -d "$GALAXY_VIRTUAL_ENV" -a -z "$skip_venv" ]; then
+    if [ -d "$GALAXY_VIRTUAL_ENV" ] && [ -z "$skip_venv" ]; then
         [ -n "$PYTHONPATH" ] && { echo 'Unsetting $PYTHONPATH'; unset PYTHONPATH; }
         echo "Activating virtualenv at $GALAXY_VIRTUAL_ENV"
         . "$GALAXY_VIRTUAL_ENV/bin/activate"
@@ -148,7 +148,7 @@ find_server() {
     APP_WEBSERVER=${APP_WEBSERVER:-$default_webserver}
     if [ "$APP_WEBSERVER" = "uwsgi" ]; then
         # Look for uwsgi
-        if [ -z "$skip_venv" -a -x $GALAXY_VIRTUAL_ENV/bin/uwsgi ]; then
+        if [ -z "$skip_venv" ] && [ -x $GALAXY_VIRTUAL_ENV/bin/uwsgi ]; then
             UWSGI=$GALAXY_VIRTUAL_ENV/bin/uwsgi
         elif command -v uwsgi >/dev/null 2>&1; then
             UWSGI=uwsgi
@@ -160,7 +160,7 @@ find_server() {
         [ -n "$server_app" ] && arg_getter_args="$arg_getter_args --app $server_app"
         run_server="$UWSGI"
         server_args=
-        if [ -z "$stop_daemon_arg_set" -a -z "$restart_arg_set" ]; then
+        if [ -z "$stop_daemon_arg_set" ] && [ -z "$restart_arg_set" ]; then
             server_args="$(eval python ./scripts/get_uwsgi_args.py $arg_getter_args)"
         fi
         server_args="$server_args $uwsgi_args"
@@ -193,13 +193,13 @@ find_server() {
 # to the `conda` script in the base environment. Thus in Conda 4.4, it may not be possible to locate `conda` even if you
 # are using Conda.
 set_conda_exe() {
-    [ -z "$_CONDA_EXE_SET" ] || return 0
+    [ -n "$CONDA_EXE" ] || [ -n "$_CONDA_EXE_SET" ] && return 0
     if python -V 2>&1 | grep -q -e 'Anaconda' -e 'Continuum Analytics' || \
             python -c 'import sys; print(sys.version.replace("\n", " "))' | grep -q -e 'packaged by conda-forge' ; then
-        : ${CONDA_EXE:=$(command -v conda)}
+        CONDA_EXE=$(command -v conda)
         if [ -z "$CONDA_EXE" ]; then
             echo "WARNING: \`python\` is from conda, but the \`conda\` command cannot be found."
-            pydir="$(dirname $(command -v python))"
+            pydir="$(dirname "$(command -v python)")"
             for CONDA_EXE in $pydir/conda $pydir/../../../bin/conda; do
                 [ -x "$CONDA_EXE" ] && break || unset CONDA_EXE
             done
@@ -209,7 +209,7 @@ set_conda_exe() {
                 echo "         $ conda activate base"
             else
                 echo "Guessed conda location: $CONDA_EXE"
-                PATH="$(dirname $CONDA_EXE):$PATH"
+                PATH="$(dirname "$CONDA_EXE"):$PATH"
             fi
         else
             echo "Found conda at: $CONDA_EXE"
@@ -220,7 +220,7 @@ set_conda_exe() {
 
 set_conda_info() {
     # cache conda info to avoid the cost of running it multiple times
-    if [ -z "$__CONDA_INFO" -o "$1" = "reset" ]; then
+    if [ -z "$__CONDA_INFO" ]; then
         __CONDA_INFO="$(${CONDA_EXE:-conda} info --json)"
     fi
 }
diff --git a/tox.ini b/tox.ini
index 6db822ade1a5..3fe6643ade90 100644
--- a/tox.ini
+++ b/tox.ini
@@ -10,7 +10,7 @@ commands =
     lint: bash .ci/flake8_wrapper.sh
     unit: bash run_tests.sh -u
 whitelist_externals = bash
-passenv = CI
+passenv = CI CONDA_EXE
 setenv =
     py{35,36,37}-first_startup: GALAXY_VIRTUAL_ENV=.venv3
     unit: GALAXY_VIRTUAL_ENV={envdir}

From da256571e679df5e107a02c6c000399d51fe6786 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sun, 23 Feb 2020 01:21:05 +0000
Subject: [PATCH 160/853] Source the full path of conda activate script

Otherwise, if a virtualenv is active on top of conda base env (e.g. when
running py37-first_startup tox test in TravisCI), the wrong `activate`
script is sourced.

Also fix `CONDA_PREFIX` environment variable definition when using a shell
not supported by conda.
---
 scripts/common_startup_functions.sh | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/scripts/common_startup_functions.sh b/scripts/common_startup_functions.sh
index 1ec379a2be10..fef20d27261a 100644
--- a/scripts/common_startup_functions.sh
+++ b/scripts/common_startup_functions.sh
@@ -88,9 +88,9 @@ conda_activate() {
         echo "         starting Galaxy."
         PATH="$(get_conda_env_path $GALAXY_CONDA_ENV)/bin:$PATH"
         CONDA_DEFAULT_ENV="$GALAXY_CONDA_ENV"
-        CONDA_PREFIX="$(get_conda_root_path)"
+        CONDA_PREFIX="$(get_conda_active_prefix)"
     else
-        source activate "$GALAXY_CONDA_ENV"
+        source "$(get_conda_root_prefix)"/bin/activate "$GALAXY_CONDA_ENV"
     fi
 }
 
@@ -225,7 +225,13 @@ set_conda_info() {
     fi
 }
 
-get_conda_root_path() {
+get_conda_active_prefix() {
+    set_conda_info
+    printf "%s" "$__CONDA_INFO" \
+        | python -c "import json, sys; print(json.load(sys.stdin)['active_prefix'])"
+}
+
+get_conda_root_prefix() {
     set_conda_info
     printf "%s" "$__CONDA_INFO" \
         | python -c "import json, sys; print(json.load(sys.stdin)['root_prefix'])"

From acb0674b5e87c6c1c507ae9994387d6bd73cfff4 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 24 Feb 2020 02:11:02 +0000
Subject: [PATCH 161/853] Upgrade Checkout GitHub Action

---
 .github/workflows/converter_tests.yaml | 2 +-
 .github/workflows/integration.yaml     | 2 +-
 .github/workflows/mulled.yaml          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
index a8cd3f3f7a45..64926d007d3d 100644
--- a/.github/workflows/converter_tests.yaml
+++ b/.github/workflows/converter_tests.yaml
@@ -9,7 +9,7 @@ jobs:
       matrix:
         python-version: [3.7]
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v1
diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 4e24129f4827..dc8656359942 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -32,7 +32,7 @@ jobs:
       if: matrix.subset == 'kubernetes'
       run: |
         kubectl get pods
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v1
diff --git a/.github/workflows/mulled.yaml b/.github/workflows/mulled.yaml
index f31e310452b8..4a0ba77ab1f0 100644
--- a/.github/workflows/mulled.yaml
+++ b/.github/workflows/mulled.yaml
@@ -15,7 +15,7 @@ jobs:
       with:
         path: .tox/mulled
         key: tox-mulled-${{ matrix.python-version }}
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v1

From 5f945a36ce6bb876e6eacd23f64e97efcd204e08 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 21 Feb 2020 12:01:36 +0100
Subject: [PATCH 162/853] Fixes for get_estimated_display_viewport

Map objects cannot be unpacked, decrease log level, use context managers
for opening files.

Silences https://sentry.galaxyproject.org/sentry/main/issues/517474/:
```
line (##sequence-regionSL4.0ch07	1	67883646
) uses an unsupported ##sequence-region definition.
```
and similar.
---
 lib/galaxy/datatypes/interval.py | 349 +++++++++++++++----------------
 lib/galaxy/util/__init__.py      |  16 +-
 2 files changed, 181 insertions(+), 184 deletions(-)

diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index ffe6ff9e7d21..92a5eeef4df7 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -167,40 +167,36 @@ def get_estimated_display_viewport(self, dataset, chrom_col=None, start_col=None
             start = sys.maxsize
             end = 0
             max_col = max(chrom_col, start_col, end_col)
-            fh = open(dataset.file_name)
-            while True:
-                line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
-                # Stop if at end of file
-                if not line:
-                    break
-                # Skip comment lines
-                if not line.startswith('#'):
-                    try:
-                        fields = line.rstrip().split('\t')
-                        if len(fields) > max_col:
-                            if chrom is None or chrom == fields[chrom_col]:
-                                start = min(start, int(fields[start_col]))
-                                end = max(end, int(fields[end_col]))
-                                # Set chrom last, in case start and end are not integers
-                                chrom = fields[chrom_col]
-                            viewport_feature_count -= 1
-                    except Exception:
-                        # Most likely a non-integer field has been encountered
-                        # for start / stop. Just ignore and make sure we finish
-                        # reading the line and decrementing the counters.
-                        pass
-                # Make sure we are at the next new line
-                readline_count = VIEWPORT_MAX_READS_PER_LINE
-                while line.rstrip('\n\r') == line:
-                    assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
-                    line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
-                    if not line:
-                        break  # EOF
-                    readline_count -= 1
-                max_line_count -= 1
-                if not viewport_feature_count or not max_line_count:
-                    # exceeded viewport or total line count to check
-                    break
+            with open(dataset.file_name) as fh:
+                for line in util.iter_start_of_line(fh, VIEWPORT_READLINE_BUFFER_SIZE):
+                    # Skip comment lines
+                    if not line.startswith('#'):
+                        try:
+                            fields = line.rstrip().split('\t')
+                            if len(fields) > max_col:
+                                if chrom is None or chrom == fields[chrom_col]:
+                                    start = min(start, int(fields[start_col]))
+                                    end = max(end, int(fields[end_col]))
+                                    # Set chrom last, in case start and end are not integers
+                                    chrom = fields[chrom_col]
+                                viewport_feature_count -= 1
+                        except Exception:
+                            # Most likely a non-integer field has been encountered
+                            # for start / stop. Just ignore and make sure we finish
+                            # reading the line and decrementing the counters.
+                            pass
+                    # Make sure we are at the next new line
+                    readline_count = VIEWPORT_MAX_READS_PER_LINE
+                    while line.rstrip('\n\r') == line:
+                        assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
+                        line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
+                        if not line:
+                            break  # EOF
+                        readline_count -= 1
+                    max_line_count -= 1
+                    if not viewport_feature_count or not max_line_count:
+                        # exceeded viewport or total line count to check
+                        break
             if chrom is not None:
                 return (chrom, str(start), str(end))  # Necessary to return strings?
         except Exception:
@@ -712,66 +708,63 @@ def get_estimated_display_viewport(self, dataset):
                 seqid = None
                 start = sys.maxsize
                 stop = 0
-                fh = open(dataset.file_name)
-                while True:
-                    line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
-                    if not line:
-                        break  # EOF
-                    try:
-                        if line.startswith('##sequence-region'):  # ##sequence-region IV 6000000 6030000
-                            elems = line.rstrip('\n\r').split()
-                            if len(elems) > 3:
-                                # line looks like:
-                                # sequence-region   ctg123 1 1497228
-                                seqid = elems[1]  # IV
-                                start = int(elems[2])  # 6000000
-                                stop = int(elems[3])  # 6030000
-                                break  # use location declared in file
-                            elif len(elems) == 2 and elems[1].find('..') > 0:
-                                # line looks like this:
-                                # sequence-region X:120000..140000
-                                elems = elems[1].split(':')
-                                seqid = elems[0]
-                                start = int(elems[1].split('..')[0])
-                                stop = int(elems[1].split('..')[1])
-                                break  # use location declared in file
-                            else:
-                                log.exception("line (%s) uses an unsupported ##sequence-region definition." % str(line))
-                                # break #no break, if bad definition, we try another method
-                        elif line.startswith("browser position"):
-                            # Allow UCSC style browser and track info in the GFF file
-                            pos_info = line.split()[-1]
-                            seqid, startend = pos_info.split(":")
-                            start, stop = map(int, startend.split("-"))
-                            break  # use location declared in file
-                        elif True not in map(line.startswith, ('#', 'track', 'browser')):  # line.startswith() does not accept iterator in python2.4
-                            viewport_feature_count -= 1
-                            elems = line.rstrip('\n\r').split('\t')
-                            if len(elems) > 3:
-                                if not seqid:
-                                    # We can only set the viewport for a single chromosome
+                with open(dataset.file_name) as fh:
+                    for line in util.iter_start_of_line(fh, VIEWPORT_READLINE_BUFFER_SIZE):
+                        try:
+                            if line.startswith('##sequence-region'):  # ##sequence-region IV 6000000 6030000
+                                elems = line.rstrip('\n\r').split()
+                                if len(elems) > 3:
+                                    # line looks like:
+                                    # sequence-region   ctg123 1 1497228
+                                    seqid = elems[1]  # IV
+                                    start = int(elems[2])  # 6000000
+                                    stop = int(elems[3])  # 6030000
+                                    break  # use location declared in file
+                                elif len(elems) == 2 and elems[1].find('..') > 0:
+                                    # line looks like this:
+                                    # sequence-region X:120000..140000
+                                    elems = elems[1].split(':')
                                     seqid = elems[0]
-                                if seqid == elems[0]:
-                                    # Make sure we have not spanned chromosomes
-                                    start = min(start, int(elems[3]))
-                                    stop = max(stop, int(elems[4]))
-                    except Exception:
-                        # most likely start/stop is not an int or not enough fields
-                        pass
-                    # make sure we are at the next new line
-                    readline_count = VIEWPORT_MAX_READS_PER_LINE
-                    while line.rstrip('\n\r') == line:
-                        assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
-                        line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
-                        if not line:
-                            break  # EOF
-                        readline_count -= 1
-                    max_line_count -= 1
-                    if not viewport_feature_count or not max_line_count:
-                        # exceeded viewport or total line count to check
-                        break
-                if seqid is not None:
-                    return (seqid, str(start), str(stop))  # Necessary to return strings?
+                                    start = int(elems[1].split('..')[0])
+                                    stop = int(elems[1].split('..')[1])
+                                    break  # use location declared in file
+                                else:
+                                    log.debug("line (%s) uses an unsupported ##sequence-region definition." % str(line))
+                                    # break #no break, if bad definition, we try another line
+                            elif line.startswith("browser position"):
+                                # Allow UCSC style browser and track info in the GFF file
+                                pos_info = line.split()[-1]
+                                seqid, startend = pos_info.split(":")
+                                start, stop = list(map(int, startend.split("-")))
+                                break  # use location declared in file
+                            elif not line.startswith(('#', 'track', 'browser')):
+                                viewport_feature_count -= 1
+                                elems = line.rstrip('\n\r').split('\t')
+                                if len(elems) > 3:
+                                    if not seqid:
+                                        # We can only set the viewport for a single chromosome
+                                        seqid = elems[0]
+                                    if seqid == elems[0]:
+                                        # Make sure we have not spanned chromosomes
+                                        start = min(start, int(elems[3]))
+                                        stop = max(stop, int(elems[4]))
+                        except Exception:
+                            # most likely start/stop is not an int or not enough fields
+                            pass
+                        # make sure we are at the next new line
+                        readline_count = VIEWPORT_MAX_READS_PER_LINE
+                        while line.rstrip('\n\r') == line:
+                            assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
+                            line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
+                            if not line:
+                                break  # EOF
+                            readline_count -= 1
+                        max_line_count -= 1
+                        if not viewport_feature_count or not max_line_count:
+                            # exceeded viewport or total line count to check
+                            break
+                    if seqid is not None:
+                        return (seqid, str(start), str(stop))  # Necessary to return strings?
             except Exception:
                 log.exception('Unexpected error')
         return (None, None, None)  # could not determine viewport
@@ -1091,53 +1084,50 @@ def get_estimated_display_viewport(self, dataset):
                 end = 0
                 span = 1
                 step = None
-                fh = open(dataset.file_name)
-                while True:
-                    line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
-                    if not line:
-                        break  # EOF
-                    try:
-                        if line.startswith("browser"):
-                            chr_info = line.rstrip('\n\r').split()[-1]
-                            chrom, coords = chr_info.split(":")
-                            start, end = map(int, coords.split("-"))
-                            break  # use the browser line
-                        # variableStep chrom=chr20
-                        if line and (line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")):
-                            if chrom is not None:
-                                break  # different chrom or different section of the chrom
-                            chrom = line.rstrip('\n\r').split("chrom=")[1].split()[0]
-                            if 'span=' in line:
-                                span = int(line.rstrip('\n\r').split("span=")[1].split()[0])
-                            if 'step=' in line:
-                                step = int(line.rstrip('\n\r').split("step=")[1].split()[0])
-                                start = int(line.rstrip('\n\r').split("start=")[1].split()[0])
-                        else:
-                            fields = line.rstrip('\n\r').split()
-                            if fields:
-                                if step is not None:
-                                    if not end:
-                                        end = start + span
+                with open(dataset.file_name) as fh:
+                    for line in util.iter_readline_count(fh, VIEWPORT_READLINE_BUFFER_SIZE):
+                        try:
+                            if line.startswith("browser"):
+                                chr_info = line.rstrip('\n\r').split()[-1]
+                                chrom, coords = chr_info.split(":")
+                                start, end = list(map(int, coords.split("-")))
+                                break  # use the browser line
+                            # variableStep chrom=chr20
+                            if line and (line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")):
+                                if chrom is not None:
+                                    break  # different chrom or different section of the chrom
+                                chrom = line.rstrip('\n\r').split("chrom=")[1].split()[0]
+                                if 'span=' in line:
+                                    span = int(line.rstrip('\n\r').split("span=")[1].split()[0])
+                                if 'step=' in line:
+                                    step = int(line.rstrip('\n\r').split("step=")[1].split()[0])
+                                    start = int(line.rstrip('\n\r').split("start=")[1].split()[0])
+                            else:
+                                fields = line.rstrip('\n\r').split()
+                                if fields:
+                                    if step is not None:
+                                        if not end:
+                                            end = start + span
+                                        else:
+                                            end += step
                                     else:
-                                        end += step
-                                else:
-                                    start = min(int(fields[0]), start)
-                                    end = max(end, int(fields[0]) + span)
-                                viewport_feature_count -= 1
-                    except Exception:
-                        pass
-                    # make sure we are at the next new line
-                    readline_count = VIEWPORT_MAX_READS_PER_LINE
-                    while line.rstrip('\n\r') == line:
-                        assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
-                        line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
-                        if not line:
-                            break  # EOF
-                        readline_count -= 1
-                    max_line_count -= 1
-                    if not viewport_feature_count or not max_line_count:
-                        # exceeded viewport or total line count to check
-                        break
+                                        start = min(int(fields[0]), start)
+                                        end = max(end, int(fields[0]) + span)
+                                    viewport_feature_count -= 1
+                        except Exception:
+                            pass
+                        # make sure we are at the next new line
+                        readline_count = VIEWPORT_MAX_READS_PER_LINE
+                        while line.rstrip('\n\r') == line:
+                            assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
+                            line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
+                            if not line:
+                                break  # EOF
+                            readline_count -= 1
+                        max_line_count -= 1
+                        if not viewport_feature_count or not max_line_count:
+                            # exceeded viewport or total line count to check
+                            break
                 if chrom is not None:
                     return (chrom, str(start), str(end))  # Necessary to return strings?
             except Exception:
@@ -1278,49 +1268,46 @@ def get_estimated_display_viewport(self, dataset, chrom_col=None, start_col=None
         span = 1
         if self.displayable(dataset):
             try:
-                fh = open(dataset.file_name)
-                while True:
-                    line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
-                    if not line:
-                        break  # EOF
-                    if not line.startswith('#'):
-                        try:
-                            if variable_step_wig:
-                                fields = line.rstrip().split()
-                                if len(fields) == 2:
-                                    start = int(fields[0])
-                                    return (chrom, str(start), str(start + span))
-                            elif line and (line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")):
-                                chrom = line.rstrip('\n\r').split("chrom=")[1].split()[0]
-                                if 'span=' in line:
-                                    span = int(line.rstrip('\n\r').split("span=")[1].split()[0])
-                                if 'start=' in line:
-                                    start = int(line.rstrip('\n\r').split("start=")[1].split()[0])
-                                    return (chrom, str(start), str(start + span))
+                with open(dataset.file_name) as fh:
+                    for line in util.iter_start_of_line(fh, VIEWPORT_READLINE_BUFFER_SIZE):
+                        if not line.startswith('#'):
+                            try:
+                                if variable_step_wig:
+                                    fields = line.rstrip().split()
+                                    if len(fields) == 2:
+                                        start = int(fields[0])
+                                        return (chrom, str(start), str(start + span))
+                                elif line and (line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")):
+                                    chrom = line.rstrip('\n\r').split("chrom=")[1].split()[0]
+                                    if 'span=' in line:
+                                        span = int(line.rstrip('\n\r').split("span=")[1].split()[0])
+                                    if 'start=' in line:
+                                        start = int(line.rstrip('\n\r').split("start=")[1].split()[0])
+                                        return (chrom, str(start), str(start + span))
+                                    else:
+                                        variable_step_wig = True
                                 else:
-                                    variable_step_wig = True
-                            else:
-                                fields = line.rstrip().split('\t')
-                                if len(fields) >= 3:
-                                    chrom = fields[0]
-                                    start = int(fields[1])
-                                    end = int(fields[2])
-                                    return (chrom, str(start), str(end))
-                        except Exception:
-                            # most likely a non-integer field has been encountered for start / stop
-                            continue
-                    # make sure we are at the next new line
-                    readline_count = VIEWPORT_MAX_READS_PER_LINE
-                    while line.rstrip('\n\r') == line:
-                        assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
-                        line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
-                        if not line:
-                            break  # EOF
-                        readline_count -= 1
-                    max_line_count -= 1
-                    if not max_line_count:
-                        # exceeded viewport or total line count to check
-                        break
+                                    fields = line.rstrip().split('\t')
+                                    if len(fields) >= 3:
+                                        chrom = fields[0]
+                                        start = int(fields[1])
+                                        end = int(fields[2])
+                                        return (chrom, str(start), str(end))
+                            except Exception:
+                                # most likely a non-integer field has been encountered for start / stop
+                                continue
+                        # make sure we are at the next new line
+                        readline_count = VIEWPORT_MAX_READS_PER_LINE
+                        while line.rstrip('\n\r') == line:
+                            assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
+                            line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
+                            if not line:
+                                break  # EOF
+                            readline_count -= 1
+                        max_line_count -= 1
+                        if not max_line_count:
+                            # exceeded viewport or total line count to check
+                            break
             except Exception:
                 log.exception('Unexpected error')
         return (None, None, None)  # could not determine viewport
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index 1dcb20b2303d..1a969d66855d 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -26,6 +26,7 @@
 from datetime import datetime
 from email.mime.multipart import MIMEMultipart
 from email.mime.text import MIMEText
+from functools import partial
 from hashlib import md5
 from os.path import relpath
 from xml.etree import ElementInclude, ElementTree
@@ -188,6 +189,14 @@ def caller(*params, **kparams):
     return caller
 
 
+def iter_start_of_line(fh, chunk_size=None):
+    """
+    Iterate over fh and call readline(chunk_size)
+    """
+    for line in iter(partial(fh.readline, chunk_size), ""):
+        yield line
+
+
 def file_iter(fname, sep=None):
     """
     This generator iterates over a file and yields its lines
@@ -198,9 +207,10 @@ def file_iter(fname, sep=None):
     >>> len(lines) !=  0
     True
     """
-    for line in open(fname):
-        if line and line[0] != '#':
-            yield line.split(sep)
+    with open(fname) as fh:
+        for line in fh:
+            if line and line[0] != '#':
+                yield line.split(sep)
 
 
 def file_reader(fp, chunk_size=CHUNK_SIZE):

From 0bf308dff9605de623ed66e28f61c7db5ce91f79 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 24 Feb 2020 10:48:59 +0100
Subject: [PATCH 163/853] Restore map unpacking, skip list casting

---
 lib/galaxy/datatypes/interval.py                    | 4 ++--
 lib/galaxy/webapps/reports/controllers/jobs.py      | 8 ++++----
 lib/galaxy/webapps/reports/controllers/users.py     | 4 ++--
 lib/galaxy/webapps/reports/controllers/workflows.py | 4 ++--
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 92a5eeef4df7..6a2f3e279af1 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -735,7 +735,7 @@ def get_estimated_display_viewport(self, dataset):
                                 # Allow UCSC style browser and track info in the GFF file
                                 pos_info = line.split()[-1]
                                 seqid, startend = pos_info.split(":")
-                                start, stop = list(map(int, startend.split("-")))
+                                start, stop = map(int, startend.split("-"))
                                 break  # use location declared in file
                             elif not line.startswith(('#', 'track', 'browser')):
                                 viewport_feature_count -= 1
@@ -1090,7 +1090,7 @@ def get_estimated_display_viewport(self, dataset):
                             if line.startswith("browser"):
                                 chr_info = line.rstrip('\n\r').split()[-1]
                                 chrom, coords = chr_info.split(":")
-                                start, end = list(map(int, coords.split("-")))
+                                start, end = map(int, coords.split("-"))
                                 break  # use the browser line
                             # variableStep chrom=chr20
                             if line and (line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")):
diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py
index bf346dc18ecd..2c8c2a5a7739 100644
--- a/lib/galaxy/webapps/reports/controllers/jobs.py
+++ b/lib/galaxy/webapps/reports/controllers/jobs.py
@@ -164,11 +164,11 @@ def filter(self, trans, user, query, column_filter):
             # We are either filtering on a date like YYYY-MM-DD or on a month like YYYY-MM,
             # so we need to figure out which type of date we have
             if column_filter.count('-') == 2:  # We are filtering on a date like YYYY-MM-DD
-                year, month, day = list(map(int, column_filter.split("-")))
+                year, month, day = map(int, column_filter.split("-"))
                 start_date = date(year, month, day)
                 end_date = start_date + timedelta(days=1)
             if column_filter.count('-') == 1:  # We are filtering on a month like YYYY-MM
-                year, month = list(map(int, column_filter.split("-")))
+                year, month = map(int, column_filter.split("-"))
                 start_date = date(year, month, 1)
                 end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
 
@@ -371,7 +371,7 @@ def specified_month_all(self, trans, **kwd):
         specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
         specified_month = specified_date[:7]
 
-        year, month = list(map(int, specified_month.split("-")))
+        year, month = map(int, specified_month.split("-"))
         start_date = date(year, month, 1)
         end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
         month_label = start_date.strftime("%B")
@@ -472,7 +472,7 @@ def specified_month_in_error(self, trans, **kwd):
         # If specified_date is not received, we'll default to the current month
         specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
         specified_month = specified_date[:7]
-        year, month = list(map(int, specified_month.split("-")))
+        year, month = map(int, specified_month.split("-"))
         start_date = date(year, month, 1)
         end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
         month_label = start_date.strftime("%B")
diff --git a/lib/galaxy/webapps/reports/controllers/users.py b/lib/galaxy/webapps/reports/controllers/users.py
index e19351e3f8c9..e8bfcfd15766 100644
--- a/lib/galaxy/webapps/reports/controllers/users.py
+++ b/lib/galaxy/webapps/reports/controllers/users.py
@@ -61,7 +61,7 @@ def specified_month(self, trans, **kwd):
         # If specified_date is not received, we'll default to the current month
         specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
         specified_month = specified_date[:7]
-        year, month = list(map(int, specified_month.split("-")))
+        year, month = map(int, specified_month.split("-"))
         start_date = date(year, month, 1)
         end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
         month_label = start_date.strftime("%B")
@@ -91,7 +91,7 @@ def specified_date(self, trans, **kwd):
         message = escape(util.restore_text(kwd.get('message', '')))
         # If specified_date is not received, we'll default to the current month
         specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
-        year, month, day = list(map(int, specified_date.split("-")))
+        year, month, day = map(int, specified_date.split("-"))
         start_date = date(year, month, day)
         end_date = start_date + timedelta(days=1)
         day_of_month = start_date.strftime("%d")
diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py
index 51a34ce3b7ea..a61992333f6d 100644
--- a/lib/galaxy/webapps/reports/controllers/workflows.py
+++ b/lib/galaxy/webapps/reports/controllers/workflows.py
@@ -64,14 +64,14 @@ def filter(self, trans, user, query, column_filter):
             # so we need to figure out which type of date we have
             if column_filter.count('-') == 2:
                 # We are filtering on a date like YYYY-MM-DD
-                year, month, day = list(map(int, column_filter.split("-")))
+                year, month, day = map(int, column_filter.split("-"))
                 start_date = date(year, month, day)
                 end_date = start_date + timedelta(days=1)
                 return query.filter(and_(self.model_class.table.c.create_time >= start_date,
                                          self.model_class.table.c.create_time < end_date))
             if column_filter.count('-') == 1:
                 # We are filtering on a month like YYYY-MM
-                year, month = list(map(int, column_filter.split("-")))
+                year, month = map(int, column_filter.split("-"))
                 start_date = date(year, month, 1)
                 end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
                 return query.filter(and_(self.model_class.table.c.create_time >= start_date,

From 16b2eec5e5a2c172ccfbfae99c1bc73a09977306 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 24 Feb 2020 13:01:21 +0000
Subject: [PATCH 164/853] Use a list comprehension instead of `list(map())`
 with a lambda function

---
 lib/galaxy/managers/sharable.py           | 4 ++--
 lib/galaxy/tool_util/verify/interactor.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index 2bac58cd9e54..4e5c49772aa6 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -152,7 +152,7 @@ def share_with(self, item, user, flush=True):
         # precondition: user has been validated
         # allow user to be a list and call recursivly
         if isinstance(user, list):
-            return list(map(lambda user: self.share_with(item, user, flush=False), user))
+            return [self.share_with(item, _, flush=False) for _ in user]
         # get or create
         existing = self.get_share_assocs(item, user=user)
         if existing:
@@ -181,7 +181,7 @@ def unshare_with(self, item, user, flush=True):
         Delete a user share (or list of shares) from the database.
         """
         if isinstance(user, list):
-            return list(map(lambda user: self.unshare_with(item, user, flush=False), user))
+            return [self.unshare_with(item, _, flush=False) for _ in user]
         # Look for and delete sharing relation for user.
         user_share_assoc = self.get_share_assocs(item, user=user)[0]
         self.session().delete(user_share_assoc)
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index c5d2fbd78085..a606836dc637 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -1088,7 +1088,7 @@ def to_dict(self):
         return {
             "inputs": inputs_dict,
             "outputs": self.outputs,
-            "output_collections": list(map(lambda o: o.to_dict(), self.output_collections)),
+            "output_collections": [_.to_dict() for _ in self.output_collections],
             "num_outputs": self.num_outputs,
             "command_line": self.command_line,
             "command_version": self.command_version,

From 4d98745744305546c4f7b9fa072f3bd0aeb4d51a Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 24 Feb 2020 13:03:06 +0000
Subject: [PATCH 165/853] Use explicit for loop instead of `list(map())`

when used exclusively as a shorthand, with no return value.
---
 lib/galaxy/jobs/dynamic_tool_destination.py | 9 +++++----
 lib/galaxy/tools/__init__.py                | 3 ++-
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/jobs/dynamic_tool_destination.py b/lib/galaxy/jobs/dynamic_tool_destination.py
index 809e3eec9624..be226f37f700 100755
--- a/lib/galaxy/jobs/dynamic_tool_destination.py
+++ b/lib/galaxy/jobs/dynamic_tool_destination.py
@@ -66,12 +66,13 @@ def get_keys_from_dict(dl, keys_list):
     """
     This function builds a list using the keys from nest dictionaries
     """
-    assert isinstance(keys_list, list)
     if isinstance(dl, dict):
-        keys_list += list(dl.keys())
-        list(map(lambda x: get_keys_from_dict(x, keys_list), dl.values()))
+        keys_list.extend(dl.keys())
+        for x in dl.values():
+            get_keys_from_dict(x, keys_list)
     elif isinstance(dl, list):
-        list(map(lambda x: get_keys_from_dict(x, keys_list), dl))
+        for x in dl:
+            get_keys_from_dict(x, keys_list)
 
 
 class RuleValidator(object):
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 19b7a79b0b8b..be156072ef9e 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2637,7 +2637,8 @@ def check_dataset_instance(input_dataset):
                 if not input_dataset_collection.collection.populated:
                     raise ToolInputsNotReadyException("An input collection is not populated.")
 
-            list(map(check_dataset_instance, input_dataset_collection.dataset_instances))
+            for dataset_instance in input_dataset_collection.dataset_instances:
+                check_dataset_instance(dataset_instance)
 
     def _add_datasets_to_history(self, history, elements, datasets_visible=False):
         datasets = []

From dc10309be1bde3b8b0a8d9fa8ef13af32d511e93 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 24 Feb 2020 14:53:15 +0100
Subject: [PATCH 166/853] fix two cases of opening a file binary

might fix https://github.com/galaxyproject/galaxy/issues/9328
---
 .../galaxy_install/tool_dependencies/recipe/step_handler.py   | 4 ++--
 .../galaxy_install/tool_dependencies/recipe/tag_handler.py    | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
index f8ca76ff85de..9f75404c000b 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
@@ -549,9 +549,9 @@ def execute_step(self, tool_dependency, package_name, actions, action_dict, filt
         if is_binary:
             log_file = os.path.join(install_environment.install_dir, basic_util.INSTALLATION_LOG)
             if os.path.exists(log_file):
-                logfile = open(log_file, 'ab')
+                logfile = open(log_file, 'a')
             else:
-                logfile = open(log_file, 'wb')
+                logfile = open(log_file, 'w')
             logfile.write('Successfully downloaded from url: %s\n' % action_dict['url'])
             logfile.close()
         log.debug('Successfully downloaded from url: %s' % action_dict['url'])
diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
index c1ef423a565e..51ce81cb0c26 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
@@ -253,10 +253,10 @@ def create_temporary_tool_dependencies_config(self, tool_shed_url, name, owner,
         text = url_get(tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
         if text:
             # Write the contents to a temporary file on disk so it can be reloaded and parsed.
-            fh = tempfile.NamedTemporaryFile('wb', prefix="tmp-toolshed-cttdc")
+            fh = tempfile.NamedTemporaryFile('w', prefix="tmp-toolshed-cttdc")
             tmp_filename = fh.name
             fh.close()
-            fh = open(tmp_filename, 'wb')
+            fh = open(tmp_filename, 'w')
             fh.write(text)
             fh.close()
             return tmp_filename

From 6d29650673cad6160ae8c26dd546f03ff464eb87 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 24 Feb 2020 14:36:24 -0500
Subject: [PATCH 167/853] Remove '.sample' from default value; rebuild schema

---
 doc/source/admin/galaxy_options.rst         | 4 +++-
 lib/galaxy/config/sample/galaxy.yml.sample  | 4 +++-
 lib/galaxy/webapps/galaxy/config_schema.yml | 4 +++-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 946a2499b604..b26ccd2a90df 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -789,7 +789,9 @@
 :Description:
     File that defines the builds (dbkeys) available at sites used by
     display applications and the URL to those sites.
-:Default: ``config/build_sites.yml.sample``
+    The value of this option will be resolved with respect to
+    <config_dir>.
+:Default: ``build_sites.yml``
 :Type: str
 
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 494a12c44d30..cc3d9ed35694 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -489,7 +489,9 @@ galaxy:
 
   # File that defines the builds (dbkeys) available at sites used by
   # display applications and the URL to those sites.
-  #build_sites_config_file: config/build_sites.yml.sample
+  # The value of this option will be resolved with respect to
+  # <config_dir>.
+  #build_sites_config_file: build_sites.yml
 
   # File containing old-style genome builds.
   # The value of this option will be resolved with respect to
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 34bb16e67147..e21eb5f8ea77 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -591,12 +591,14 @@ mapping:
 
       build_sites_config_file:
         type: str
-        default: config/build_sites.yml.sample
+        default: build_sites.yml
         required: false
         desc: |
           File that defines the builds (dbkeys) available at sites used by display applications
           and the URL to those sites.
 
+          The value of this option will be resolved with respect to <config_dir>.
+
       builds_file_path:
         type: str
         default: shared/ucsc/builds.txt

From c3c0f2d988f1e6c113c68f8b25cb0df2428a9237 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 24 Feb 2020 15:45:48 -0500
Subject: [PATCH 168/853] Check sample config for build_sites

---
 lib/galaxy/config/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 07453d0ca0f7..1f9333adfd41 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -754,7 +754,7 @@ def parse_config_file_options(self, kwargs):
         """
         defaults = dict(
             auth_config_file=[self._in_config_dir('auth_conf.xml')],
-            build_sites_config_file=[self._in_config_dir('build_sites.yml')],
+            build_sites_config_file=[self._in_config_dir('build_sites.yml'), self._in_sample_dir('build_sites.yml.sample')],
             containers_config_file=[self._in_config_dir('containers_conf.yml')],
             data_manager_config_file=[self._in_config_dir('data_manager_conf.xml')],
             datatypes_config_file=[self._in_config_dir('datatypes_conf.xml'), self._in_sample_dir('datatypes_conf.xml.sample')],

From d8773a9598bcab47fb123dd6db54d0d31445c25d Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 24 Feb 2020 16:11:36 +0000
Subject: [PATCH 169/853] Use a Galaxy root path with a space for converters
 and mulled tests

Also:
- Fix integration tests for checkout@v2 action: the working directory is not
  updated any more when `path` is specified
- Use checkout action to clone the galaxy-test-data repo and rsync to move
  them in place
- Install virtualenv<20 when running tests via tox in a directory containing
  spaces, xref. https://github.com/pypa/virtualenv/pull/1660
---
 .github/workflows/converter_tests.yaml | 15 ++++++++++-----
 .github/workflows/integration.yaml     |  4 ++--
 .github/workflows/mulled.yaml          | 17 +++++++++--------
 3 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
index 64926d007d3d..8b20d095f3ae 100644
--- a/.github/workflows/converter_tests.yaml
+++ b/.github/workflows/converter_tests.yaml
@@ -11,7 +11,12 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
-        fetch-depth: 1
+        path: 'galaxy root'
+    - name: Clone galaxyproject/galaxy-test-data
+      uses: actions/checkout@v2
+      with:
+        repository: galaxyproject/galaxy-test-data
+        path: galaxy-test-data
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
@@ -20,10 +25,10 @@ jobs:
       id: pip-cache
       with:
         path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
-    - name: fetch test data
-      run: git clone https://github.com/galaxyproject/galaxy-test-data && cp -R galaxy-test-data/* test-data
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Move test data
+      run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/'
     - name: Install planemo
       run: pip install planemo
     - name: Run tests
-      run: 'planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root .  lib/galaxy/datatypes/converters/*xml'
+      run: planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' 'galaxy root'/lib/galaxy/datatypes/converters/*xml
diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index c2995ae1a3f3..61a2f7d44ddb 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -34,7 +34,6 @@ jobs:
         kubectl get pods
     - uses: actions/checkout@v2
       with:
-        fetch-depth: 1
         path: 'galaxy root'
     - uses: actions/setup-python@v1
       with:
@@ -44,6 +43,7 @@ jobs:
       id: pip-cache
       with:
         path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
+      working-directory: 'galaxy root'
diff --git a/.github/workflows/mulled.yaml b/.github/workflows/mulled.yaml
index 4a0ba77ab1f0..6c96751d1f76 100644
--- a/.github/workflows/mulled.yaml
+++ b/.github/workflows/mulled.yaml
@@ -9,19 +9,20 @@ jobs:
       matrix:
         python-version: [3.7]
     steps:
-    - name: Cache tox dir
-      uses: actions/cache@v1
-      id: cache-tox-mulled
-      with:
-        path: .tox/mulled
-        key: tox-mulled-${{ matrix.python-version }}
     - uses: actions/checkout@v2
       with:
-        fetch-depth: 1
+        path: 'galaxy root'
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Cache pip dir
+      uses: actions/cache@v1
+      id: pip-cache
+      with:
+        path: ~/.cache/pip
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Install tox
-      run: pip install tox
+      run: pip install tox 'virtualenv<20'
     - name: run tests
       run: tox -e mulled
+      working-directory: 'galaxy root'

From ead6bb4c82bf7d0ec6dc969fac0f4be57c521937 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 25 Feb 2020 09:48:00 +0100
Subject: [PATCH 170/853] Strip unicode null characters from traceback and
 job_messages

May or may not help with
https://github.com/galaxyproject/galaxy/issues/9428.
---
 lib/galaxy/jobs/__init__.py            | 2 +-
 lib/galaxy/tool_util/output_checker.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index f9cce38d98db..f485b52e88bb 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1235,7 +1235,7 @@ def fail(self, message, exception=False, tool_stdout="", tool_stderr="", exit_co
             if exception:
                 # Save the traceback immediately in case we generate another
                 # below
-                job.traceback = traceback.format_exc()
+                job.traceback = unicodify(traceback.format_exc(), strip_null=True)
                 # Get the exception and let the tool attempt to generate
                 # a better message
                 etype, evalue, tb = sys.exc_info()
diff --git a/lib/galaxy/tool_util/output_checker.py b/lib/galaxy/tool_util/output_checker.py
index 7e22242092ab..c89f471c9fc5 100644
--- a/lib/galaxy/tool_util/output_checker.py
+++ b/lib/galaxy/tool_util/output_checker.py
@@ -50,8 +50,8 @@ def check_output(stdio_regexes, stdio_exit_codes, stdout, stderr, tool_exit_code
     # has a bug but the tool was ok, and it lets a workflow continue.
     state = DETECTED_JOB_STATE.OK
 
-    stdout = unicodify(stdout)
-    stderr = unicodify(stderr)
+    stdout = unicodify(stdout, strip_null=True)
+    stderr = unicodify(stderr, strip_null=True)
 
     # messages (descriptions of the detected exit_code and regexes)
     # to be prepended to the stdout/stderr after all exit code and regex tests

From c54836e98436d3a4798c93e402e1931e9b855f17 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 24 Feb 2020 14:36:24 -0500
Subject: [PATCH 171/853] Remove '.sample' from default value; rebuild schema

---
 doc/source/admin/galaxy_options.rst         | 4 +++-
 lib/galaxy/config/sample/galaxy.yml.sample  | 4 +++-
 lib/galaxy/webapps/galaxy/config_schema.yml | 4 +++-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index f383d23db9cb..f4948b3c19e4 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -789,7 +789,9 @@
 :Description:
     File that defines the builds (dbkeys) available at sites used by
     display applications and the URL to those sites.
-:Default: ``config/build_sites.yml.sample``
+    The value of this option will be resolved with respect to
+    <config_dir>.
+:Default: ``build_sites.yml``
 :Type: str
 
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 4b13f5fa059d..1263f0d1b1f1 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -492,7 +492,9 @@ galaxy:
 
   # File that defines the builds (dbkeys) available at sites used by
   # display applications and the URL to those sites.
-  #build_sites_config_file: config/build_sites.yml.sample
+  # The value of this option will be resolved with respect to
+  # <config_dir>.
+  #build_sites_config_file: build_sites.yml
 
   # File containing old-style genome builds.
   # The value of this option will be resolved with respect to
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index e60025b39977..a723a9aec954 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -591,12 +591,14 @@ mapping:
 
       build_sites_config_file:
         type: str
-        default: config/build_sites.yml.sample
+        default: build_sites.yml
         required: false
         desc: |
           File that defines the builds (dbkeys) available at sites used by display applications
           and the URL to those sites.
 
+          The value of this option will be resolved with respect to <config_dir>.
+
       builds_file_path:
         type: str
         default: shared/ucsc/builds.txt

From 24a97be15480f545655bcc2dd7d6681899ca32f3 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 24 Feb 2020 15:45:48 -0500
Subject: [PATCH 172/853] Check sample config for build_sites

---
 lib/galaxy/config/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 2c631cad3646..47fe8b74cdfd 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -741,7 +741,7 @@ def parse_config_file_options(self, kwargs):
         """
         defaults = dict(
             auth_config_file=[self._in_config_dir('auth_conf.xml')],
-            build_sites_config_file=[self._in_config_dir('build_sites.yml')],
+            build_sites_config_file=[self._in_config_dir('build_sites.yml'), self._in_sample_dir('build_sites.yml.sample')],
             containers_config_file=[self._in_config_dir('containers_conf.yml')],
             data_manager_config_file=[self._in_config_dir('data_manager_conf.xml')],
             datatypes_config_file=[self._in_config_dir('datatypes_conf.xml'), self._in_sample_dir('datatypes_conf.xml.sample')],

From c86c75cc2b8f5440b4fdaa021e9ff06410c3d3b9 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 25 Feb 2020 11:31:58 +0100
Subject: [PATCH 173/853] Fix login to accounts using different email
 capitalization

https://github.com/galaxyproject/galaxy/pull/8631 added case-insensitive
matches to user emails. If two accounts with different email
capitalizations exist one of them will be picked at random for login.
To fix this we first check for exact match and only if there is no
direct match we lowercase the comparison.
---
 lib/galaxy/managers/users.py                  | 4 +++-
 lib/galaxy/webapps/galaxy/controllers/user.py | 7 ++++++-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index f3f9ba94d0f5..2ad6457a2c00 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -489,7 +489,9 @@ def send_reset_email(self, trans, payload={}, **kwd):
                 return "Failed to produce password reset token. User not found."
 
     def get_reset_token(self, trans, email):
-        reset_user = trans.sa_session.query(self.app.model.User).filter(func.lower(self.app.model.User.table.c.email) == email.lower()).first()
+        reset_user = trans.sa_session.query(self.app.model.User).filter(self.app.model.User.table.c.email == email.lower()).first()
+        if not reset_user and email != email.lower():
+            reset_user = trans.sa_session.query(self.app.model.User).filter(func.lower(self.app.model.User.table.c.email) == email.lower()).first()
         if reset_user:
             prt = self.app.model.PasswordResetToken(reset_user)
             trans.sa_session.add(prt)
diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index 4e75d5a91ea4..071ee286de33 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -135,9 +135,14 @@ def __validate_login(self, trans, payload={}, **kwd):
         if not login or not password:
             return self.message_exception(trans, "Please specify a username and password.")
         user = trans.sa_session.query(trans.app.model.User).filter(or_(
-            func.lower(trans.app.model.User.table.c.email) == login.lower(),
+            trans.app.model.User.table.c.email == login,
             trans.app.model.User.table.c.username == login
         )).first()
+        if not user and login.lower() != login:
+            user = trans.sa_session.query(trans.app.model.User).filter(or_(
+                func.lower(trans.app.model.User.table.c.email) == login.lower(),
+                trans.app.model.User.table.c.username == login
+            )).first()
         log.debug("trans.app.config.auth_config_file: %s" % trans.app.config.auth_config_file)
         if user is None:
             message, user = self.__autoregistration(trans, login, password)

From d649338297e89ebcbbd654a4836b5f48b2f131bc Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 25 Feb 2020 12:13:14 +0100
Subject: [PATCH 174/853] Fix TwoBitFile handle not opened in binary mode

Fixes https://sentry.galaxyproject.org/sentry/main/issues/501741/:
```
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd7 in position 77: invalid continuation byte
  File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__
    iterable = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/middleware/statsd.py", line 34, in __call__
    req = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 143, in __call__
    return self.handle_request(environ, start_response)
  File "galaxy/web/framework/base.py", line 222, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/web/framework/decorators.py", line 57, in call_and_format
    rval = func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/api/genomes.py", line 41, in show
    region = self.app.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high)
  File "galaxy/visualization/genomes.py", line 395, in reference
    twobit = TwoBitFile(open(twobit_file_name))
  File "bx/seq/twobit.py", line 56, in __init__
    strng = file.read(TWOBIT_MAGIC_SIZE)
  File "python3.6/codecs.py", line 321, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
```
---
 lib/galaxy/visualization/genomes.py  | 2 +-
 tools/extract/extract_genomic_dna.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index 6c81630fa8ac..9aeb74ac1a87 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -392,7 +392,7 @@ def reference(self, trans, dbkey, chrom, low, high):
 
         # Read and return reference data.
         try:
-            twobit = TwoBitFile(open(twobit_file_name))
+            twobit = TwoBitFile(open(twobit_file_name, 'rb'))
             if chrom in twobit:
                 seq_data = twobit[chrom].get(int(low), int(high))
                 return GenomeRegion(chrom=chrom, start=low, end=high, sequence=seq_data)
diff --git a/tools/extract/extract_genomic_dna.py b/tools/extract/extract_genomic_dna.py
index b42f7b127a88..3ae993223492 100755
--- a/tools/extract/extract_genomic_dna.py
+++ b/tools/extract/extract_genomic_dna.py
@@ -222,7 +222,7 @@ def get_lines(feature):
                 continue
         elif seq_path and os.path.isfile(seq_path):
             if not(twobitfile):
-                twobitfile = bx.seq.twobit.TwoBitFile(open(seq_path))
+                twobitfile = bx.seq.twobit.TwoBitFile(open(seq_path, 'rb'))
             try:
                 if options.gff and interpret_features:
                     # Create sequence from intervals within a feature.

From 382b6a41bc550056f2faa3cccf5c7a964321fd56 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 25 Feb 2020 12:31:16 +0100
Subject: [PATCH 175/853] Fix uploading workflow archives

This fixes https://sentry.galaxyproject.org/sentry/main/issues/502038/:
```
TypeError: a bytes-like object is required, not 'str'
  File "galaxy/web/framework/decorators.py", line 282, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/api/workflows.py", line 361, in create
    return self.__api_import_from_archive(trans, archive_data, "uploaded file")
  File "galaxy/webapps/galaxy/api/workflows.py", line 640, in __api_import_from_archive
    if "GalaxyWorkflow" in archive_data:
```
The actual uploaded data is still invalid, but a more meaningful message
will be raised with this fix.
---
 lib/galaxy/webapps/galaxy/api/workflows.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index d529e58d54d6..e45d536e9dae 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -353,7 +353,7 @@ def create(self, trans, payload, **kwd):
                 uploaded_file = archive_file.file
                 uploaded_file_name = uploaded_file.name
                 if os.path.getsize(os.path.abspath(uploaded_file_name)) > 0:
-                    archive_data = uploaded_file.read()
+                    archive_data = util.unicodify(uploaded_file.read())
                 else:
                     raise exceptions.MessageException("You attempted to upload an empty file.")
             else:

From 2c3f63751ac0bf7251d8e8f7c3b04237fafa905c Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 11 Feb 2020 11:35:51 +0000
Subject: [PATCH 176/853] Fix py27-first_startup Travis job to actually use
 Python 2

`scripts/common_startup.sh` now prefers python3 when creating Galaxy's
virtual environment, so it needs to be run when inside the tox virtualenv,
where `GALAXY_PYTHON` is defined.
---
 .travis.yml               |  8 ++++----
 scripts/common_startup.sh | 13 +++++++------
 tox.ini                   |  1 +
 3 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 942e8625b469..7df63e0f77a5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,11 +11,11 @@ install:
   - pip install tox
   - |
     if [ "$TOX_ENV" == "py27-first_startup" ]; then
-        sh scripts/common_startup.sh
-        wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite
-        mv db_gx_rev_0127.sqlite database/universe.sqlite
-        sh manage_db.sh upgrade
+        # Use this job to test the latest migrations
+        wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite
+        mv db_gx_rev_0141.sqlite database/universe.sqlite
     elif [ "$TOX_ENV" == "py35-first_startup" ]; then
+        # There is now a pre-installed python3 on osx Travis workers, but use this job to test using a conda environment
         MINICONDA_URL="https://repo.anaconda.com/miniconda"
         MINICONDA_FILE="Miniconda3-latest-MacOSX-x86_64.sh"
         curl -L -O "${MINICONDA_URL}/${MINICONDA_FILE}"
diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh
index 51a574de2c1f..bba0815904b7 100755
--- a/scripts/common_startup.sh
+++ b/scripts/common_startup.sh
@@ -128,11 +128,7 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
             fi
             virtualenv "$GALAXY_VIRTUAL_ENV"
         else
-            # If .venv does not exist, and there is no conda available, attempt to create it.
-            # Ensure Python is a supported version before creating .venv
-            echo "Creating Python virtual environment for Galaxy: $GALAXY_VIRTUAL_ENV"
-            echo "To avoid this, use the --no-create-venv flag or set \$GALAXY_VIRTUAL_ENV to an"
-            echo "existing environment before starting Galaxy."
+            # If $GALAXY_VIRTUAL_ENV does not exist, and there is no conda available, attempt to create it.
             if [ -z "$GALAXY_PYTHON" ]; then
                 if command -v python3 >/dev/null; then
                     GALAXY_PYTHON=python3
@@ -140,7 +136,12 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
                     GALAXY_PYTHON=python
                 fi
             fi
+            # Ensure Python is a supported version before creating $GALAXY_VIRTUAL_ENV
             "$GALAXY_PYTHON" ./scripts/check_python.py || exit 1
+            echo "Creating Python virtual environment for Galaxy: $GALAXY_VIRTUAL_ENV"
+            echo "using Python: $GALAXY_PYTHON"
+            echo "To avoid this, use the --no-create-venv flag or set \$GALAXY_VIRTUAL_ENV to an"
+            echo "existing environment before starting Galaxy."
             if command -v virtualenv >/dev/null; then
                 virtualenv -p "$GALAXY_PYTHON" "$GALAXY_VIRTUAL_ENV"
             else
@@ -186,7 +187,7 @@ fi
 : ${PYPI_INDEX_URL:="https://pypi.python.org/simple"}
 : ${GALAXY_DEV_REQUIREMENTS:="./lib/galaxy/dependencies/dev-requirements.txt"}
 if [ $REPLACE_PIP -eq 1 ]; then
-    pip install 'pip>=8.1'
+    python -m pip install 'pip>=8.1'
 fi
 
 requirement_args="-r requirements.txt"
diff --git a/tox.ini b/tox.ini
index fd02ce81ddaf..65f753592933 100644
--- a/tox.ini
+++ b/tox.ini
@@ -16,6 +16,7 @@ whitelist_externals = bash
 passenv = CI CONDA_EXE
 setenv =
     first_startup: GALAXY_PYTHON=python
+    first_startup: GALAXY_CONFIG_DATABASE_AUTO_MIGRATE=true
     py{35,36,37}-first_startup: GALAXY_VIRTUAL_ENV=.venv3
     unit: GALAXY_VIRTUAL_ENV={envdir}
     unit: GALAXY_ENABLE_BETA_COMPRESSED_GENBANK_SNIFFING=1

From 6f18c2eca97bb182ba5158ccc5235cbb19e32ba3 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 21 Feb 2020 20:04:29 +0000
Subject: [PATCH 177/853] Let Galaxy create the `_galaxy_` conda env

---
 .travis.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 7df63e0f77a5..0f690edec63f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,7 +4,7 @@ language: generic
 
 env:
   - TOX_ENV=py27-first_startup
-  - TOX_ENV=py35-first_startup
+  - TOX_ENV=py37-first_startup
 
 install:
   - set -e
@@ -14,14 +14,13 @@ install:
         # Use this job to test the latest migrations
         wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite
         mv db_gx_rev_0141.sqlite database/universe.sqlite
-    elif [ "$TOX_ENV" == "py35-first_startup" ]; then
+    elif [ "$TOX_ENV" == "py37-first_startup" ]; then
         # There is now a pre-installed python3 on osx Travis workers, but use this job to test using a conda environment
         MINICONDA_URL="https://repo.anaconda.com/miniconda"
         MINICONDA_FILE="Miniconda3-latest-MacOSX-x86_64.sh"
         curl -L -O "${MINICONDA_URL}/${MINICONDA_FILE}"
         bash $MINICONDA_FILE -b
-        ~/miniconda3/bin/conda create --yes --override-channels --channel conda-forge --channel defaults --name _galaxy_ 'python=3.5' 'pip>=9' 'virtualenv>=16'
-        . ~/miniconda3/bin/activate _galaxy_
+        . ~/miniconda3/bin/activate
     fi
 
 script: tox -e $TOX_ENV

From 6be7ac8eee54fac0af75f8f56dece32aa059d8d0 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 24 Feb 2020 14:53:15 +0100
Subject: [PATCH 178/853] fix two cases of opening a file binary

might fix https://github.com/galaxyproject/galaxy/issues/9328
---
 .../galaxy_install/tool_dependencies/recipe/step_handler.py   | 4 ++--
 .../galaxy_install/tool_dependencies/recipe/tag_handler.py    | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
index 6b7176dee3ae..f44b144f8604 100644
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
@@ -549,9 +549,9 @@ def execute_step(self, tool_dependency, package_name, actions, action_dict, filt
         if is_binary:
             log_file = os.path.join(install_environment.install_dir, basic_util.INSTALLATION_LOG)
             if os.path.exists(log_file):
-                logfile = open(log_file, 'ab')
+                logfile = open(log_file, 'a')
             else:
-                logfile = open(log_file, 'wb')
+                logfile = open(log_file, 'w')
             logfile.write('Successfully downloaded from url: %s\n' % action_dict['url'])
             logfile.close()
         log.debug('Successfully downloaded from url: %s' % action_dict['url'])
diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
index a7e6b0f1d760..b63e051a78b8 100644
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
@@ -253,10 +253,10 @@ def create_temporary_tool_dependencies_config(self, tool_shed_url, name, owner,
         text = url_get(tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
         if text:
             # Write the contents to a temporary file on disk so it can be reloaded and parsed.
-            fh = tempfile.NamedTemporaryFile('wb', prefix="tmp-toolshed-cttdc")
+            fh = tempfile.NamedTemporaryFile('w', prefix="tmp-toolshed-cttdc")
             tmp_filename = fh.name
             fh.close()
-            fh = open(tmp_filename, 'wb')
+            fh = open(tmp_filename, 'w')
             fh.write(text)
             fh.close()
             return tmp_filename

From f344dd85d38761f87bfb02fadb543e4ec5d6923f Mon Sep 17 00:00:00 2001
From: Alexander OSTROVSKY <alexanderostrovsky@Caroline.local>
Date: Wed, 7 Aug 2019 14:46:41 -0400
Subject: [PATCH 179/853] parent 207f4c5fb0423c13a2afcf34c78b9629a0c0ca75
 author Alexander OSTROVSKY <alexanderostrovsky@Caroline.local> 1565203601
 -0400 committer Alexander OSTROVSKY
 <alexanderostrovsky@p-body.win.ad.jhu.edu> 1582640692 -0500

Notifications on job completion

JS lint for var notification

Altered to accomodate job failures and user cancellations

Added an icon to easily differentiate job success from failure

Tab updates when window is hidden.

Better completion message, removed console.log

Notification grammar, and linking tab icon change with notification permissions

tab fix

Tab resets on view

js lint
---
 .../scripts/mvc/dataset/dataset-model.js      |  28 ++++++++++
 client/galaxy/scripts/mvc/user/tab-updates.js |  52 ++++++++++++++++++
 static/erricon.ico                            | Bin 0 -> 2253 bytes
 3 files changed, 80 insertions(+)
 create mode 100644 client/galaxy/scripts/mvc/user/tab-updates.js
 create mode 100644 static/erricon.ico

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-model.js b/client/galaxy/scripts/mvc/dataset/dataset-model.js
index 69f18aa6ce03..b16aae7a0bd1 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-model.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-model.js
@@ -5,8 +5,10 @@ import { getAppRoot } from "onload/loadConfig";
 import STATES from "mvc/dataset/states";
 import BASE_MVC from "mvc/base-mvc";
 import _l from "utils/localization";
+import TAB_UPDATES from "mvc/user/tab-updates";
 
 var logNamespace = "dataset";
+var hiddenupdates = 1;
 //==============================================================================
 var searchableMixin = BASE_MVC.SearchableModelMixin;
 /** @class base model for any DatasetAssociation (HDAs, LDDAs, DatasetCollectionDAs).
@@ -99,6 +101,25 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                     this.log(`${this} has changed state:`, currModel, newState);
                     if (this.inReadyState()) {
                         this.trigger("state:ready", currModel, newState, this.previous("state"));
+                        if (newState != "discarded"){
+                            if(newState === "ok"){
+                                new Notification(`Job complete: ${this.get("name")}`, {
+                                icon: "static/favicon.ico"
+                                      });
+                                if(TAB_UPDATES.is_hidden()){
+                                    TAB_UPDATES.hidden_count(hiddenupdates);
+                                    hiddenupdates++;
+                                }
+                            } else if(newState == "error"){
+                                new Notification(`Job failure: ${this.get("name")}`, {
+                                icon: "static/erricon.ico"
+                                      });
+                                if(TAB_UPDATES.is_hidden() && Notification.permission == "granted"){
+                                    TAB_UPDATES.change_favicon("static/erricon.ico")
+                                }
+                            }
+
+                          }
                     }
                 });
                 // the download url (currently) relies on having a correct file extension
@@ -349,6 +370,13 @@ var DatasetAssociationCollection = Backbone.Collection.extend(BASE_MVC.LoggableM
     }
 );
 
+window.addEventListener("focus", function(){
+    if(document.getElementById('tabicon').href.search("erricon") != -1){
+        TAB_UPDATES.change_favicon("static/favicon.ico");
+    }
+    document.title = "Galaxy";
+    hiddenupdates = 1;
+});
 //==============================================================================
 export default {
     DatasetAssociation: DatasetAssociation,
diff --git a/client/galaxy/scripts/mvc/user/tab-updates.js b/client/galaxy/scripts/mvc/user/tab-updates.js
new file mode 100644
index 000000000000..b098eae4fa9f
--- /dev/null
+++ b/client/galaxy/scripts/mvc/user/tab-updates.js
@@ -0,0 +1,52 @@
+//Allow change tab on event=====================================================
+function change_favicon(img){
+    var favicon = document.createElement("link");
+    favicon.id = "tabicon";
+    favicon.setAttribute("rel", "shortcut icon");
+    var head = document.querySelector("head");
+    head.appendChild(favicon);
+    favicon.setAttribute("type", "image/png");
+    favicon.setAttribute("href", img);
+}
+
+//Check if browser is hidden-aware==============================================
+function hidden_permit(){
+    var browsers = ["webkit","moz","ms","o"];
+    if ("hidden" in document){
+        return "hidden";
+    }
+    for (var i=0; i < browsers.length; i++){
+        if ((browsers[i] + "Hidden") in document){
+            return browsers[i] + "Hidden";
+        }
+    }
+    return null;
+}
+
+//Find out if browser tab is hidden=============================================
+function is_hidden(){
+    var state = hidden_permit();
+    if (!state){
+        return false;
+    }
+    return document[state];
+}
+
+//Generate new tab message to display on update in window=======================
+function hidden_count(current){
+    if(is_hidden()){
+        if(current === 1){
+            document.title = "Galaxy (1 job completed)";
+        }else{
+        document.title = "Galaxy (" + current + " jobs completed)";
+        }
+    }
+}
+
+
+export default{
+    change_favicon: change_favicon,
+    hidden_permit: hidden_permit,
+    is_hidden: is_hidden,
+    hidden_count: hidden_count
+};
diff --git a/static/erricon.ico b/static/erricon.ico
new file mode 100644
index 0000000000000000000000000000000000000000..c5ee4d32e54a720ba16fd2a49149cface7122767
GIT binary patch
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zK%8KUcj1m`o(V&_e>cAMB<=vAx!70&72S$c+=U3$)`JEBqS8Er06Dp`0Kg9f5#8zT
z_Q$Y(V5lC+AM_>bF+-_bGyve3Snf2GOeZ0jp&=9+mT9KCjlgo}JU2=eu??XIo2k0n
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jAvz~Udvo{BqvPf!6Q@h_ieiZFyf+5H+5ul->67q(P{pnO

literal 0
HcmV?d00001


From 229e04a5fde7d43e9ba9df231dad704d8feee565 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 25 Feb 2020 15:57:40 +0100
Subject: [PATCH 180/853] fix searchgui_archive set_meta

probably with py3 reading a file from a zip file is binary.
hence startswith and split fail.
---
 lib/galaxy/datatypes/binary.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 1ba208f2c6f3..f9193e864320 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -2112,6 +2112,7 @@ def set_meta(self, dataset, overwrite=True, **kwd):
                     if 'searchgui.properties' in tempzip.namelist():
                         with tempzip.open('searchgui.properties') as fh:
                             for line in fh:
+                                line = line.decode()
                                 if line.startswith('searchgui.version'):
                                     version = line.split('=')[1].strip()
                                     dataset.metadata.searchgui_version = version

From 1b762945899c2b2972473234947678fc94587b50 Mon Sep 17 00:00:00 2001
From: Andreas Skorczyk <me@andreas-sk.de>
Date: Tue, 4 Feb 2020 15:22:51 +0100
Subject: [PATCH 181/853] Allow setting container path for containers

`preprocess_volumes` only allowed to set the host path
(HOST:MODE),
which in some cases might not be enough. With this
change it is also possible to set the container path
(HOST:CONTAINER:MODE), as described in
https://docs.docker.com/storage/bind-mounts/
described
---
 lib/galaxy/tool_util/deps/container_classes.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/deps/container_classes.py b/lib/galaxy/tool_util/deps/container_classes.py
index 9970334fdea2..0d5f53ed939a 100644
--- a/lib/galaxy/tool_util/deps/container_classes.py
+++ b/lib/galaxy/tool_util/deps/container_classes.py
@@ -103,6 +103,8 @@ def preprocess_volumes(volumes_raw_str, container_type):
     ['/a/b:rw']
     >>> preprocess_volumes("/a/b:ro,/a/b/c:rw", DOCKER_CONTAINER_TYPE)
     ['/a/b:ro', '/a/b/c:rw']
+    >>> preprocess_volumes("/a/b:/a:ro,/a/b/c:/a/b:rw", DOCKER_CONTAINER_TYPE)
+    ['/a/b:/a:ro', '/a/b/c:/a/b:rw']
     >>> preprocess_volumes("/a/b:default_ro,/a/b/c:rw", DOCKER_CONTAINER_TYPE)
     ['/a/b:ro', '/a/b/c:rw']
     >>> preprocess_volumes("/a/b:default_ro,/a/b/c:rw", SINGULARITY_CONTAINER_TYPE)
@@ -115,8 +117,12 @@ def preprocess_volumes(volumes_raw_str, container_type):
 
     for volume_raw_str in volumes_raw_strs:
         volume_parts = volume_raw_str.split(":")
-        if len(volume_parts) > 2:
+        if len(volume_parts) > 3:
             raise Exception("Unparsable volumes string in configuration [%s]" % volumes_raw_str)
+        if len(volume_parts) == 3:
+            volume_parts = ["%s:%s" % (volume_parts[0], volume_parts[1]), volume_parts[2]]
+        if len(volume_parts) == 2 and volume_parts[1] not in ("rw", "ro", "default_ro"):
+            volume_parts = ["%s:%s" % (volume_parts[0], volume_parts[1]), "rw"]
         if len(volume_parts) == 1:
             volume_parts.append("rw")
         volumes.append(volume_parts)

From d5be9b3ae5cf091bb518a717b9c7fda8204973ef Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Tue, 25 Feb 2020 16:29:32 +0100
Subject: [PATCH 182/853] Don't check username again

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/webapps/galaxy/controllers/user.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index 071ee286de33..7cf207f7a8b9 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -139,10 +139,9 @@ def __validate_login(self, trans, payload={}, **kwd):
             trans.app.model.User.table.c.username == login
         )).first()
         if not user and login.lower() != login:
-            user = trans.sa_session.query(trans.app.model.User).filter(or_(
-                func.lower(trans.app.model.User.table.c.email) == login.lower(),
-                trans.app.model.User.table.c.username == login
-            )).first()
+            user = trans.sa_session.query(trans.app.model.User).filter(
+                func.lower(trans.app.model.User.table.c.email) == login.lower()
+            ).first()
         log.debug("trans.app.config.auth_config_file: %s" % trans.app.config.auth_config_file)
         if user is None:
             message, user = self.__autoregistration(trans, login, password)

From c673eb4a3fc0866d48cbd8ace6bbc577a14c7960 Mon Sep 17 00:00:00 2001
From: Alexander OSTROVSKY <alexanderostrovsky@p-body.win.ad.jhu.edu>
Date: Tue, 25 Feb 2020 11:03:00 -0500
Subject: [PATCH 183/853] incremental

---
 .../components/User/UserPreferences.vue       | 19 ++++++++++++
 .../scripts/mvc/dataset/dataset-model.js      | 31 ++++++++++---------
 client/galaxy/scripts/mvc/user/tab-updates.js | 29 +++++++++--------
 3 files changed, 50 insertions(+), 29 deletions(-)

diff --git a/client/galaxy/scripts/components/User/UserPreferences.vue b/client/galaxy/scripts/components/User/UserPreferences.vue
index 6bc0e467dd5f..dc86e9b09f1d 100644
--- a/client/galaxy/scripts/components/User/UserPreferences.vue
+++ b/client/galaxy/scripts/components/User/UserPreferences.vue
@@ -22,6 +22,13 @@
                 </div>
             </div>
         </b-row>
+        <b-row class="ml-3 mb-1">
+            <i class="fa-plus-square-o" />
+            <div class="pref-content pr-1">
+                <a @click="toggleNotifications" href="javascript:void(0)"><b>Enable notifications</b></a>
+                <div class="form-text text-muted">Allow push and tab notifcations on job completion/failure</div>
+            </div>
+        </b-row>
         <p class="mt-2">
             You are using <strong>{{ diskUsage }}</strong> of disk space in this Galaxy instance.
             <span v-html="quotaUsageString"></span>
@@ -107,6 +114,18 @@ export default {
         }
     },
     methods: {
+        toggleNotifications() {
+            Notification.requestPermission().then(function(permission) {
+                //If the user accepts, let's create a notification
+                if (permission === "granted") {
+                    new Notification("Notifications enabled", {
+                        icon: "static/favicon.ico"
+                    });
+                } else {
+                    alert("Notifications disabled, please re-enable through browser settings.");
+                }
+            });
+        },
         openManageCustomBuilds() {
             const Galaxy = getGalaxyInstance();
             Galaxy.page.router.push(`${getAppRoot()}custom_builds`);
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-model.js b/client/galaxy/scripts/mvc/dataset/dataset-model.js
index b16aae7a0bd1..fa781f13b4ea 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-model.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-model.js
@@ -101,25 +101,27 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                     this.log(`${this} has changed state:`, currModel, newState);
                     if (this.inReadyState()) {
                         this.trigger("state:ready", currModel, newState, this.previous("state"));
-                        if (newState != "discarded"){
-                            if(newState === "ok"){
+                        if (newState != "discarded") {
+                            if (newState === "ok") {
+                                console.log("helloworld");
                                 new Notification(`Job complete: ${this.get("name")}`, {
-                                icon: "static/favicon.ico"
-                                      });
-                                if(TAB_UPDATES.is_hidden()){
+                                    icon: "static/favicon.ico"
+                                });
+                                new Notification("HELLO");
+                                if (TAB_UPDATES.is_hidden()) {
                                     TAB_UPDATES.hidden_count(hiddenupdates);
                                     hiddenupdates++;
                                 }
-                            } else if(newState == "error"){
+                            } else if (newState == "error") {
+                                console.log("goodbye");
                                 new Notification(`Job failure: ${this.get("name")}`, {
-                                icon: "static/erricon.ico"
-                                      });
-                                if(TAB_UPDATES.is_hidden() && Notification.permission == "granted"){
-                                    TAB_UPDATES.change_favicon("static/erricon.ico")
+                                    icon: "static/erricon.ico"
+                                });
+                                if (TAB_UPDATES.is_hidden() && Notification.permission == "granted") {
+                                    TAB_UPDATES.change_favicon("static/erricon.ico");
                                 }
                             }
-
-                          }
+                        }
                     }
                 });
                 // the download url (currently) relies on having a correct file extension
@@ -370,8 +372,9 @@ var DatasetAssociationCollection = Backbone.Collection.extend(BASE_MVC.LoggableM
     }
 );
 
-window.addEventListener("focus", function(){
-    if(document.getElementById('tabicon').href.search("erricon") != -1){
+window.addEventListener("focus", function() {
+    const testing = document.getElementById("tabicon");
+    if (testing && testing.href.search("erricon") != -1) {
         TAB_UPDATES.change_favicon("static/favicon.ico");
     }
     document.title = "Galaxy";
diff --git a/client/galaxy/scripts/mvc/user/tab-updates.js b/client/galaxy/scripts/mvc/user/tab-updates.js
index b098eae4fa9f..5b32f63d7eab 100644
--- a/client/galaxy/scripts/mvc/user/tab-updates.js
+++ b/client/galaxy/scripts/mvc/user/tab-updates.js
@@ -1,5 +1,5 @@
 //Allow change tab on event=====================================================
-function change_favicon(img){
+function change_favicon(img) {
     var favicon = document.createElement("link");
     favicon.id = "tabicon";
     favicon.setAttribute("rel", "shortcut icon");
@@ -10,13 +10,13 @@ function change_favicon(img){
 }
 
 //Check if browser is hidden-aware==============================================
-function hidden_permit(){
-    var browsers = ["webkit","moz","ms","o"];
-    if ("hidden" in document){
+function hidden_permit() {
+    var browsers = ["webkit", "moz", "ms", "o"];
+    if ("hidden" in document) {
         return "hidden";
     }
-    for (var i=0; i < browsers.length; i++){
-        if ((browsers[i] + "Hidden") in document){
+    for (var i = 0; i < browsers.length; i++) {
+        if (browsers[i] + "Hidden" in document) {
             return browsers[i] + "Hidden";
         }
     }
@@ -24,27 +24,26 @@ function hidden_permit(){
 }
 
 //Find out if browser tab is hidden=============================================
-function is_hidden(){
+function is_hidden() {
     var state = hidden_permit();
-    if (!state){
+    if (!state) {
         return false;
     }
     return document[state];
 }
 
 //Generate new tab message to display on update in window=======================
-function hidden_count(current){
-    if(is_hidden()){
-        if(current === 1){
+function hidden_count(current) {
+    if (is_hidden()) {
+        if (current === 1) {
             document.title = "Galaxy (1 job completed)";
-        }else{
-        document.title = "Galaxy (" + current + " jobs completed)";
+        } else {
+            document.title = "Galaxy (" + current + " jobs completed)";
         }
     }
 }
 
-
-export default{
+export default {
     change_favicon: change_favicon,
     hidden_permit: hidden_permit,
     is_hidden: is_hidden,

From 4717e621e6f75107831ef3d1f7436f12cbb41d10 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 25 Feb 2020 11:12:35 -0500
Subject: [PATCH 184/853] Fix styling of entry in preferences list, add info on
 how to unset

---
 client/galaxy/scripts/components/User/UserPreferences.vue | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/User/UserPreferences.vue b/client/galaxy/scripts/components/User/UserPreferences.vue
index dc86e9b09f1d..31d081bc3563 100644
--- a/client/galaxy/scripts/components/User/UserPreferences.vue
+++ b/client/galaxy/scripts/components/User/UserPreferences.vue
@@ -23,10 +23,13 @@
             </div>
         </b-row>
         <b-row class="ml-3 mb-1">
-            <i class="fa-plus-square-o" />
+            <i class="pref-icon pt-1 fa fa-lg fa-plus-square-o" />
             <div class="pref-content pr-1">
                 <a @click="toggleNotifications" href="javascript:void(0)"><b>Enable notifications</b></a>
-                <div class="form-text text-muted">Allow push and tab notifcations on job completion/failure</div>
+                <div class="form-text text-muted">
+                    Allow push and tab notifcations on job completion. To disable, revoke the site notification
+                    privilege in your browser.
+                </div>
             </div>
         </b-row>
         <p class="mt-2">

From 64a741b247917f97ea4b3a8d77f0da9cac574cc6 Mon Sep 17 00:00:00 2001
From: Alexander OSTROVSKY <alexanderostrovsky@p-body.win.ad.jhu.edu>
Date: Tue, 25 Feb 2020 11:14:38 -0500
Subject: [PATCH 185/853] final tweaks

---
 client/galaxy/scripts/mvc/dataset/dataset-model.js | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-model.js b/client/galaxy/scripts/mvc/dataset/dataset-model.js
index fa781f13b4ea..85a8559bea57 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-model.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-model.js
@@ -103,17 +103,14 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                         this.trigger("state:ready", currModel, newState, this.previous("state"));
                         if (newState != "discarded") {
                             if (newState === "ok") {
-                                console.log("helloworld");
                                 new Notification(`Job complete: ${this.get("name")}`, {
                                     icon: "static/favicon.ico"
                                 });
-                                new Notification("HELLO");
                                 if (TAB_UPDATES.is_hidden()) {
                                     TAB_UPDATES.hidden_count(hiddenupdates);
                                     hiddenupdates++;
                                 }
                             } else if (newState == "error") {
-                                console.log("goodbye");
                                 new Notification(`Job failure: ${this.get("name")}`, {
                                     icon: "static/erricon.ico"
                                 });

From 91c2676946e6893cd25ce021435d3e4a513987a5 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Tue, 25 Feb 2020 17:28:31 +0100
Subject: [PATCH 186/853] Add tool recommendations for tool run

---
 .../galaxy/scripts/mvc/tool-recommendation.js | 197 +++++++++++++++
 client/galaxy/scripts/mvc/tool/tool-form.js   |   9 +
 client/galaxy/style/scss/base.scss            |  20 ++
 .../tool_recommendations_overwrite.yml.sample |  48 ++++
 doc/source/admin/galaxy_options.rst           |  64 +++++
 lib/galaxy/config/sample/galaxy.yml.sample    |  29 +++
 .../pipfiles/default/pinned-requirements.txt  |   2 +
 lib/galaxy/managers/configuration.py          |   5 +
 lib/galaxy/webapps/galaxy/api/workflows.py    | 224 ++++++++++++++++++
 lib/galaxy/webapps/galaxy/buildapp.py         |   1 +
 lib/galaxy/webapps/galaxy/config_schema.yml   |  40 ++++
 lib/galaxy_test/api/test_workflows.py         |  18 ++
 12 files changed, 657 insertions(+)
 create mode 100644 client/galaxy/scripts/mvc/tool-recommendation.js
 create mode 100644 config/tool_recommendations_overwrite.yml.sample

diff --git a/client/galaxy/scripts/mvc/tool-recommendation.js b/client/galaxy/scripts/mvc/tool-recommendation.js
new file mode 100644
index 000000000000..9751d21db299
--- /dev/null
+++ b/client/galaxy/scripts/mvc/tool-recommendation.js
@@ -0,0 +1,197 @@
+import Backbone from "backbone";
+import Utils from "utils/utils";
+import * as d3 from "d3";
+import { getAppRoot } from "onload/loadConfig";
+import $ from "jquery";
+
+
+var ToolRecommendationView = Backbone.View.extend({
+    el: "#tool-recommendation-view",
+
+    initialize: function(options) {
+        let toolId = options.toolId || "";
+        let self = this;
+        if (toolId.indexOf("/") > 0) {
+            let toolIdSlash = toolId.split("/");
+            toolId = toolIdSlash[toolIdSlash.length - 2];
+        }
+        Utils.request({
+            type: "POST",
+            url: `${getAppRoot()}api/workflows/get_tool_predictions`,
+            data: {"tool_sequence": toolId},
+            success: data => {
+                // get datatypes mapping
+                let datatypes_mapping = JSON.parse(
+                    $.ajax({
+                        url: `${getAppRoot()}api/datatypes/mapping`,
+                        async: false
+                    }).responseText
+                );
+                let extToType = datatypes_mapping.ext_to_class_name;
+                let typeToType = datatypes_mapping.class_to_classes;
+                let predData = data.predicted_data;
+                if (data !== null && predData.children.length > 0) {
+                    let filteredData = {};
+                    let compatibleTools = {};
+                    let filteredChildren = [];
+                    let outputDatatypes = predData["o_extensions"];
+                    for (const [index, nameObj] of predData.children.entries()) {
+                        let inputDatatypes = nameObj["i_extensions"];
+                        for (const out_t of outputDatatypes.entries()) {
+                            for(const in_t of inputDatatypes.entries()) {
+                                let child = extToType[out_t[1]];
+                                let parent = extToType[in_t[1]];
+                                if (((typeToType[child] && parent in typeToType[child]) === true) ||
+                                     out_t[1] === "input" ||
+                                     out_t[1] === "_sniff_" ||
+                                     out_t[1] === "input_collection") {
+                                    compatibleTools[nameObj["tool_id"]] = nameObj["name"];
+                                    break
+                                }
+                            }
+                        }
+                    }
+                    for (let id in compatibleTools) {
+                        for (const [index, nameObj] of predData.children.entries()) {
+                            if (nameObj["tool_id"] === id) {
+                                filteredChildren.push(nameObj);
+                                break
+                            }
+                        }
+                    }
+                    filteredData["o_extensions"] = predData["o_extensions"];
+                    filteredData["name"] = predData["name"];
+                    filteredData["children"] = filteredChildren;
+                    if (filteredChildren.length > 0 && predData["is_deprecated"] === false) {
+                        self.$el.append("<div class='infomessagelarge'>You have used " + filteredData.name + " tool. For further analysis, you could try using the following/recommended tools. The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to open its definition. </div>");
+                        self.render_tree(filteredData);
+                    }
+                    else if(predData["is_deprecated"] === true) {
+                        self.$el.append("<div class='warningmessagelarge'>You have used " + predData.name + " tool. " + predData["message"] + ". </div>");
+                    }
+                }
+            }
+        });
+    },
+
+    render_tree: function(predicted_data) {
+        let margin = {top: 20, right: 30, bottom: 20, left: 250},
+            width = 900 - margin.right - margin.left,
+            height = 300 - margin.top - margin.bottom;
+        let i = 0,
+            duration = 750,
+            root;
+        let tree = d3.layout.tree()
+            .size([height, width]);
+        let diagonal = d3.svg.diagonal()
+            .projection(d => { return [d.y, d.x]; });
+        let svg = d3.select("#tool-recommendation-view").append("svg")
+            .attr("width", width + margin.right + margin.left)
+            .attr("height", height + margin.top + margin.bottom)
+            .append("g")
+            .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+
+        function update(source) {
+            // Compute the new tree layout.
+            let nodes = tree.nodes(root).reverse(),
+                links = tree.links(nodes);
+            // Normalize for fixed-depth.
+            nodes.forEach(d => { d.y = d.depth * 180; });
+            // Update the nodes…
+            let node = svg.selectAll("g.node")
+                .data(nodes, d => { return d.id || (d.id = ++i); });
+            // Enter any new nodes at the parent's previous position.
+            let nodeEnter = node.enter().append("g")
+                .attr("class", "node")
+                .attr("transform", d => { return "translate(" + source.y0 + "," + source.x0 + ")"; })
+                .on("click", click);
+            nodeEnter.append("circle")
+                .attr("r", 1e-6)
+                .style("fill", d => { return d._children ? "lightsteelblue" : "#fff"; });
+            nodeEnter.append("text")
+                .attr("x", d => { return d.children || d._children ? -10 : 10; })
+                .attr("dy", ".35em")
+                .attr("text-anchor", d => { return d.children || d._children ? "end" : "start"; })
+                .text(d => { return d.name; })
+                .style("fill-opacity", 1e-6);
+            nodeEnter.append("title")
+                .text(d => { return d.children || d._children ? "Click to collapse" : "Click to open tool definition"; })
+            // Transition nodes to their new position.
+            let nodeUpdate = node.transition()
+                .duration(duration)
+                .attr("transform", d => { return "translate(" + d.y + "," + d.x + ")"; });
+            nodeUpdate.select("circle")
+                .attr("r", 4.5)
+                .style("fill", d => { return d._children ? "lightsteelblue" : "#fff"; });
+            nodeUpdate.select("text")
+                .style("fill-opacity", 1);
+            // Transition exiting nodes to the parent's new position.
+            let nodeExit = node.exit().transition()
+                .duration(duration)
+                .attr("transform", d => { return "translate(" + source.y + "," + source.x + ")"; })
+                .remove();
+            nodeExit.select("circle")
+                .attr("r", 1e-6);
+            nodeExit.select("text")
+                .style("fill-opacity", 1e-6);
+            // Update the links…
+            let link = svg.selectAll("path.link")
+                .data(links, d => { return d.target.id; });
+            // Enter any new links at the parent's previous position.
+            link.enter().insert("path", "g")
+                .attr("class", "link")
+                .attr("d", d => {
+                    let o = {x: source.x0, y: source.y0};
+                    return diagonal({source: o, target: o});
+                });
+            // Transition links to their new position.
+            link.transition()
+                .duration(duration)
+                .attr("d", diagonal);
+            // Transition exiting nodes to the parent's new position.
+            link.exit().transition()
+                .duration(duration)
+                .attr("d", d => {
+                    let o = {x: source.x, y: source.y};
+                    return diagonal({source: o, target: o});
+                })
+                .remove();
+            // Stash the old positions for transition.
+            nodes.forEach(d => {
+                d.x0 = d.x;
+                d.y0 = d.y;
+            });
+        }
+        // Toggle children on click.
+        function click(d) {
+            if (d.children) {
+                d._children = d.children;
+                d.children = null;
+            } else {
+                d.children = d._children;
+                d._children = null;
+            }
+            update(d);
+            if (d.tool_id !== undefined && d.tool_id !== "undefined" && d.tool_id !== null && d.tool_id !== "") {
+                document.location.href = `${getAppRoot()}` + 'tool_runner?tool_id=' + d.tool_id;
+            }
+        }
+        function collapse(d) {
+            if (d.children) {
+                d._children = d.children;
+                d._children.forEach(collapse);
+                d.children = null;
+            }
+        }
+        d3.select(self.frameElement).style("height", "400px");
+        root = predicted_data;
+        root.x0 = height / 2;
+        root.y0 = 0;
+        root.children.forEach(collapse);
+        update(root);
+    }
+});
+
+export default {
+    ToolRecommendationView: ToolRecommendationView
+};
diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index 89bdb4d3f289..93e7f2bc3f1b 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -13,6 +13,7 @@ import ToolFormBase from "mvc/tool/tool-form-base";
 import Webhooks from "mvc/webhooks";
 import Vue from "vue";
 import ToolEntryPoints from "components/ToolEntryPoints/ToolEntryPoints";
+import ToolRecommendation from "mvc/tool-recommendation";
 
 const View = Backbone.View.extend({
     initialize: function(options) {
@@ -267,6 +268,14 @@ const View = Backbone.View.extend({
                     }
                 }
                 this.$el.append(this._templateSuccess(response, job_def));
+                let enable_tool_recommendations = window.Galaxy.config.enable_tool_recommendations;
+                if (enable_tool_recommendations === true || enable_tool_recommendations === 'true') {
+                    // show tool recommendations
+                    this.$el.append($("<div/>", { id: "tool-recommendation-view" }));
+                    var toolRecommendation = new ToolRecommendation.ToolRecommendationView({
+                        toolId: job_def.tool_id
+                    });
+                }
                 this.$el.parent().scrollTop(0);
                 // Show Webhook if job is running
                 if (response.jobs && response.jobs.length > 0) {
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index ed488b4f892e..c6b0e3f2e19d 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1650,3 +1650,23 @@ body.reports {
     bottom: 0;
     background: url(../../images/largespinner.gif) no-repeat center center fixed;
 }
+
+/* For collapsible D3 tree */
+
+.node {
+    cursor: pointer;
+}
+.node circle {
+    fill: #000;
+    stroke: #c2ebc2;
+    stroke-width: 0.3rem;
+}
+.node text {
+    font: 0.75rem sans-serif;
+}
+
+.link {
+    fill: none;
+    stroke: #c2ebc2;
+    stroke-width: 0.3rem;
+}
diff --git a/config/tool_recommendations_overwrite.yml.sample b/config/tool_recommendations_overwrite.yml.sample
new file mode 100644
index 000000000000..b1fc424a766d
--- /dev/null
+++ b/config/tool_recommendations_overwrite.yml.sample
@@ -0,0 +1,48 @@
+# Provide a list of tools which are deprecated. These tools would be removed the list of 
+# recommended tools by the deep learning model. These tools will be removed from the recommendations and a warning message, set as the 'text_message', 
+# is shown instead of their recommendations and when they are executed.
+# Format:
+# <<tool id>>:
+#   - is_deprecate: True
+#   - text_message: <<message to show once they are recommended by the deep learning model>>
+#
+# For the following example, the tool 'cufflinks' is deprecated. It will be removed from the recommendations and a warning message, set as the 'text_message', 
+# is shown instead of its recommendations and when it is executed:
+#
+# cufflinks:
+#  - is_deprecated: True
+#    text_message: It is deprecated
+#
+#
+#
+# Provide list of tools to be recommended. These tools will either be appended to the tools recommended by deep learning model or 
+# completely overwrite them with these tools.
+# Format:
+# <<tool id>>:
+#   - tool_id: <<recommended tool id 1>>
+#     name: <<display text: name and description of the tool>>
+#     i_extensions:
+#       - <<input file extension>>
+#       - <<input file extension>>
+#   - tool_id: <<recommended tool id 2>>
+#     name: <<display text: name and description of the tool>>
+#     i_extensions:
+#       - <<input file extension of this tool>>
+#       - <<input file extension of this tool>>
+# <<tool id>>:
+#   - tool_id ...
+#
+# For the following example, the tools 'cat1' and 'sort1' are shown as the recommendations for tool 'Filter1':
+#
+# Filter1:
+#  - tool_id: 'cat1'
+#    name: 'Concatenate datasets tail-to-head'
+#    i_extensions: 
+#      - tabular
+#      - txt
+#  - tool_id: 'sort1'
+#    name: 'Sort data in ascending or descending order'
+#    i_extensions: 
+#      - tabular
+#      - txt
+
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index b26ccd2a90df..fdc5c4693492 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -4011,4 +4011,68 @@
 :Type: int
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``enable_tool_recommendations``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Allow the display of tool recommendations in workflow editor and
+    after tool execution. If it is enabled and set to true, please
+    enable 'tool_recommendation_model_path' as well
+:Default: ``false``
+:Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``tool_recommendation_model_path``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Set remote path of the trained model (HDF5 file) for tool
+    recommendation. It is required to be set if
+    'enable_tool_recommendations' property is enabled and set to true.
+:Default: ``https://github.com/anuprulez/download_store/raw/tool_recommendation_model/tool_recommendation_model/tool_recommendation_model.hdf5``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~
+``topk_recommendations``
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Set the number of predictions/recommendations to be made by the
+    model
+:Default: ``20``
+:Type: int
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``admin_tool_recommendations_path``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Set path to the additional tool preferences from Galaxy admins. It
+    has two blocks. One for listing deprecated tools which will be
+    removed from the recommendations and another is for adding
+    additional tools to be recommended along side those from the deep
+    learning model.
+:Default: ``None``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``overwrite_model_recommendations``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Overwrite or append to the tool recommendations by the deep
+    learning model. When set to true, all the recommendations by the
+    deep learning model are overwritten by the recommendations set by
+    an admin in a config file 'tool_recommendations_overwrite.yml'.
+    When set to false, the recommended tools by admins and predicted
+    by the deep learning model are shown.
+:Default: ``false``
+:Type: bool
+
+
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index cc3d9ed35694..b57de1ff1294 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1960,3 +1960,32 @@ galaxy:
   # as threshold (above threshold: regular select fields will be used)
   #select_type_workflow_threshold: -1
 
+  # Allow the display of tool recommendations in workflow editor and
+  # after tool execution. If it is enabled and set to true, please
+  # enable 'tool_recommendation_model_path' as well
+  #enable_tool_recommendations: false
+
+  # Set remote path of the trained model (HDF5 file) for tool
+  # recommendation. It is required to be set if
+  # 'enable_tool_recommendations' property is enabled and set to true.
+  #tool_recommendation_model_path: https://github.com/anuprulez/download_store/raw/tool_recommendation_model/tool_recommendation_model/tool_recommendation_model.hdf5
+
+  # Set the number of predictions/recommendations to be made by the
+  # model
+  #topk_recommendations: 20
+
+  # Set path to the additional tool preferences from Galaxy admins. It
+  # has two blocks. One for listing deprecated tools which will be
+  # removed from the recommendations and another is for adding
+  # additional tools to be recommended along side those from the deep
+  # learning model.
+  #admin_tool_recommendations_path: null
+
+  # Overwrite or append to the tool recommendations by the deep learning
+  # model. When set to true, all the recommendations by the deep
+  # learning model are overwritten by the recommendations set by an
+  # admin in a config file 'tool_recommendations_overwrite.yml'. When
+  # set to false, the recommended tools by admins and predicted by the
+  # deep learning model are shown.
+  #overwrite_model_recommendations: false
+
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 61ceec85d97a..183dfb77fc81 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -78,6 +78,7 @@ jmespath==0.9.4
 jsonpatch==1.25
 jsonpointer==2.0
 jsonschema==3.2.0
+keras==2.2.4
 keystoneauth1==3.18.0
 kombu==4.6.7
 lockfile==0.12.2
@@ -180,6 +181,7 @@ subprocess32==3.5.4 ; python_version < '3.0'
 svgwrite==1.3.1
 tempita==0.5.2
 tenacity==4.12.0
+tensorflow==1.12.2
 typing-extensions==3.7.4.1
 typing==3.7.4.1 ; python_version < '3.5'
 tzlocal==2.0.0
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index 6df4ace6bbe8..4812e33091fb 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -62,6 +62,11 @@ def _use_config(config, key, **context):
             'communication_server_port'         : _use_config,
             'communication_server_host'         : _use_config,
             'persistent_communication_rooms'    : _use_config,
+            'enable_tool_recommendations'       : _use_config,
+            'tool_recommendation_model_path'    : _use_config,
+            'admin_tool_recommendations_path'   : _use_config,
+            'overwrite_model_recommendations'   : _use_config,
+            'topk_recommendations'              : _use_config,
             'allow_user_impersonation'          : _use_config,
             'allow_user_creation'               : _defaults_to(False),  # schema default is True
             'use_remote_user'                   : _defaults_to(None),  # schema default is False; or config.single_user
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 15ed31f2f861..5a5fbb594ff1 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -14,6 +14,10 @@
 from sqlalchemy import desc, false, or_, true
 from sqlalchemy.orm import joinedload
 
+import numpy as np
+import h5py
+from keras.models import model_from_json
+
 from galaxy import (
     exceptions,
     model,
@@ -57,6 +61,10 @@ def __init__(self, app):
         self.history_manager = histories.HistoryManager(app)
         self.workflow_manager = workflows.WorkflowsManager(app)
         self.workflow_contents_manager = workflows.WorkflowContentsManager(app)
+        self.tool_recommendation_model_path = None
+        self.admin_tool_recommendations_path = None
+        self.deprecated_tools = dict()
+        self.admin_recommendations = dict()
 
     def __get_full_shed_url(self, url):
         for name, shed_url in self.app.tool_shed_registry.tool_sheds.items():
@@ -631,6 +639,222 @@ def build_module(self, trans, payload={}):
             'post_job_actions'  : module.get_post_job_actions(inputs)
         }
 
+    @expose_api
+    def get_tool_predictions(self, trans, payload, **kwd):
+        """
+        POST /api/workflows/get_tool_predictions
+        Fetch predicted tools for a workflow
+        :type   payload: dict
+        :param  payload: a dictionary containing two parameters:
+                         'tool_sequence' - comma separated sequence of tool ids
+                         'remote_model_url' - (optional) path to the deep learning model
+        """
+        remote_model_url = payload.get('remote_model_url', None)
+        if remote_model_url is None:
+            remote_model_url = trans.app.config.tool_recommendation_model_path
+        if 'tool_sequence' not in payload or remote_model_url is None:
+            return
+        tool_sequence = payload.get('tool_sequence', "")
+        # collect tool recommendation preferences if set by admin
+        self.__collect_admin_preferences(trans.app.config.admin_tool_recommendations_path)
+        # recreate the neural network model to be used for prediction
+        self.__set_model(trans, remote_model_url)
+        # get the recommended tools for a tool sequence
+        recommended_tools = self.__compute_tool_prediction(trans, tool_sequence)
+        return {
+            "current_tool": tool_sequence,
+            "predicted_data": recommended_tools
+        }
+
+    #
+    # -- Helper methods --
+    #
+
+    def __set_model(self, trans, remote_model_url):
+        """
+        Create model and associated dictionaries for recommendations
+        """
+        if not self.tool_recommendation_model_path:
+            self.tool_recommendation_model_path = self.__download_model(remote_model_url)
+            self.all_tools = dict()
+            model_weights = list()
+            counter_layer_weights = 0
+            # collect ids and names of all the installed tools
+            for tool_id, tool in trans.app.toolbox.tools():
+                t_id_renamed = tool_id
+                if t_id_renamed.find("/") > -1:
+                    t_id_renamed = t_id_renamed.split("/")[-2]
+                self.all_tools[t_id_renamed] = (tool_id, tool.name)
+            # read the hdf5 attributes
+            trained_model = h5py.File(self.tool_recommendation_model_path, 'r')
+            model_config = json.loads(trained_model.get('model_config').value)
+            self.loaded_model = model_from_json(model_config)
+            # set the dictionary of tools
+            self.model_data_dictionary = json.loads(trained_model.get('data_dictionary').value)
+            self.reverse_dictionary = dict((v, k) for k, v in self.model_data_dictionary.items())
+            # set the list of compatible tools
+            self.compatible_tools = json.loads(trained_model.get('compatible_tools').value)
+            self.tool_weights = json.loads(trained_model.get('class_weights').value)
+            self.tool_weights_sorted = dict()
+            # sort the tools' usage dictionary
+            tool_pos_sorted = [int(key) for key in self.tool_weights.keys()]
+            for k in tool_pos_sorted:
+                self.tool_weights_sorted[k] = self.tool_weights[str(k)]
+            # iterate through all the attributes of the model to find weights of neural network layers
+            for item in trained_model.keys():
+                if "weight_" in item:
+                    d_key = "weight_" + str(counter_layer_weights)
+                    weights = trained_model.get(d_key).value
+                    model_weights.append(weights)
+                    counter_layer_weights += 1
+            # set the model weights
+            self.loaded_model.set_weights(model_weights)
+
+    def __collect_admin_preferences(self, admin_path):
+        """
+        Collect preferences for recommendations of tools
+        set by admins as dictionaries of deprecated tools and
+        additional recommendations
+        """
+        if not self.admin_tool_recommendations_path and admin_path is not None:
+            self.admin_tool_recommendations_path = os.path.join(os.getcwd(), admin_path)
+            with open(self.admin_tool_recommendations_path) as admin_recommendations:
+                admin_recommendation_preferences = yaml.safe_load(admin_recommendations)
+                if admin_recommendation_preferences:
+                    for tool_id in admin_recommendation_preferences:
+                        tool_info = admin_recommendation_preferences[tool_id]
+                        if 'is_deprecated' in tool_info[0]:
+                            self.deprecated_tools[tool_id] = tool_info[0]["text_message"]
+                        else:
+                            if tool_id not in self.admin_recommendations:
+                                self.admin_recommendations[tool_id] = tool_info
+
+    def __download_model(self, model_url, download_local='database/'):
+        """
+        Download the model from remote server
+        """
+        local_dir = os.path.join(os.getcwd(), download_local, 'tool_recommendation_model.hdf5')
+        # read model from remote
+        model_binary = requests.get(model_url)
+        # save model to a local directory
+        with open(local_dir, 'wb') as model_file:
+            model_file.write(model_binary.content)
+            return local_dir
+
+    def __get_tool_extensions(self, trans, tool_id):
+        """
+        Get the input and output extensions of a tool
+        """
+        payload = {'type': 'tool', 'tool_id': tool_id, '_': 'true'}
+        inputs = payload.get('inputs', {})
+        trans.workflow_building_mode = workflow_building_modes.ENABLED
+        module = module_factory.from_dict(trans, payload)
+        if 'tool_state' not in payload:
+            module_state = {}
+            populate_state(trans, module.get_inputs(), inputs, module_state, check=False)
+            module.recover_state(module_state)
+        inputs = module.get_all_inputs(connectable_only=True)
+        outputs = module.get_all_outputs()
+        input_extensions = list()
+        output_extensions = list()
+        for i_ext in inputs:
+            input_extensions.extend(i_ext['extensions'])
+        for o_ext in outputs:
+            output_extensions.extend(o_ext['extensions'])
+        return input_extensions, output_extensions
+
+    def __filter_tool_predictions(self, trans, prediction_data, tool_ids, tool_scores, last_tool_name):
+        """
+        Filter tool predictions based on datatype compatibility and tool connections.
+        Add admin preferences to recommendations.
+        """
+        last_compatible_tools = list()
+        if last_tool_name in self.compatible_tools:
+            last_compatible_tools = self.compatible_tools[last_tool_name].split(",")
+        prediction_data["is_deprecated"] = False
+        t_ids_scores = zip(tool_ids, tool_scores)
+        # form the payload of the predicted tools to be shown
+        for child, score in t_ids_scores:
+            c_dict = dict()
+            for t_id in self.all_tools:
+                # select the name and tool id if it is installed in Galaxy
+                if t_id == child and score > 0.0 and child in last_compatible_tools and child not in self.deprecated_tools:
+                    full_tool_id = self.all_tools[t_id][0]
+                    pred_input_extensions, _ = self.__get_tool_extensions(trans, full_tool_id)
+                    c_dict["name"] = self.all_tools[t_id][1] + " (" + str(score) + "%)"
+                    c_dict["tool_id"] = full_tool_id
+                    c_dict["i_extensions"] = list(set(pred_input_extensions))
+                    prediction_data["children"].append(c_dict)
+                    break
+        # incorporate preferences set by admins
+        if self.admin_tool_recommendations_path:
+            # filter out deprecated tools
+            t_ids_scores = [(tid, score) for tid, score in zip(tool_ids, tool_scores) if tid not in self.deprecated_tools]
+            # set the property if the last tool of the sequence is deprecated
+            if last_tool_name in self.deprecated_tools:
+                prediction_data["is_deprecated"] = True
+                prediction_data["message"] = self.deprecated_tools[last_tool_name]
+            # add the recommendations given by admins
+            for tool_id in self.admin_recommendations:
+                if last_tool_name == tool_id:
+                    admin_recommendations = self.admin_recommendations[tool_id]
+                    if trans.app.config.overwrite_model_recommendations is True:
+                        prediction_data["children"] = admin_recommendations
+                    else:
+                        prediction_data["children"].extend(admin_recommendations)
+                    break
+        # get the root name for displaying after tool run
+        for t_id in self.all_tools:
+            if t_id == last_tool_name:
+                prediction_data["name"] = self.all_tools[t_id][1]
+                break
+        return prediction_data
+
+    def __compute_tool_prediction(self, trans, tool_sequence):
+        """
+        Compute the predicted tools for a tool sequences
+        Return a payload with the tool sequences and recommended tools
+        Return an empty payload with just the tool sequence if anything goes wrong within the try block
+        """
+        max_seq_len = 25
+        topk = trans.app.config.topk_recommendations
+        prediction_data = dict()
+        tool_sequence = tool_sequence.split(",")[::-1]
+        prediction_data["name"] = ",".join(tool_sequence)
+        prediction_data["children"] = list()
+        last_tool_name = tool_sequence[-1]
+        # do prediction only if the last is present in the collections of tools
+        if last_tool_name in self.model_data_dictionary:
+            sample = np.zeros(max_seq_len)
+            # get the list of datatype extensions of the last tool of the tool sequence
+            _, last_output_extensions = self.__get_tool_extensions(trans, self.all_tools[last_tool_name][0])
+            prediction_data["o_extensions"] = list(set(last_output_extensions))
+            # get tool names without slashes and create a sequence vector
+            for idx, tool_name in enumerate(tool_sequence):
+                if tool_name.find("/") > -1:
+                    tool_name = tool_name.split("/")[-2]
+                sample[idx] = int(self.model_data_dictionary[tool_name])
+            sample = np.reshape(sample, (1, max_seq_len))
+            # predict next tools for a test path
+            prediction = self.loaded_model.predict(sample, verbose=0)
+            prediction = np.reshape(prediction, (prediction.shape[1],))
+            # boost the predicted scores using tools' usage
+            weight_values = list(self.tool_weights_sorted.values())
+            prediction = prediction * weight_values
+            # normalize the predicted scores with max and sort the predictions
+            max_prediction = float(np.max(prediction))
+            if max_prediction == 0.0:
+                max_prediction = 1.0
+            prediction = prediction / max_prediction
+            prediction_pos = np.argsort(prediction, axis=-1)
+            # get topk prediction
+            topk_prediction_pos = prediction_pos[-topk:]
+            # read tool names using reverse dictionary
+            pred_tool_ids = [self.reverse_dictionary[int(tool_pos)] for tool_pos in topk_prediction_pos]
+            predicted_scores = [int(prediction[pos] * 100) for pos in topk_prediction_pos]
+            prediction_data = self.__filter_tool_predictions(trans, prediction_data, pred_tool_ids[::-1], predicted_scores[::-1], last_tool_name)
+        return prediction_data
+
     #
     # -- Helper methods --
     #
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 7281d8240af3..90485e2b23e7 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -402,6 +402,7 @@ def populate_api_routes(webapp, app):
     webapp.mapper.connect('/api/container_resolvers/{index}/toolbox', action="resolve_toolbox", controller="container_resolution", conditions=dict(method=["GET"]))
     webapp.mapper.connect('/api/container_resolvers/{index}/resolve/install', action="resolve_with_install", controller="container_resolution", conditions=dict(method=["POST"]))
     webapp.mapper.connect('/api/container_resolvers/{index}/toolbox/install', action="resolve_toolbox_with_install", controller="container_resolution", conditions=dict(method=["POST"]))
+    webapp.mapper.connect('/api/workflows/get_tool_predictions', action='get_tool_predictions', controller="workflows", conditions=dict(method=["POST"]))
 
     webapp.mapper.resource_with_deleted('user', 'users', path_prefix='/api')
     webapp.mapper.resource('genome', 'genomes', path_prefix='/api')
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index e21eb5f8ea77..bc646a13b631 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2959,3 +2959,43 @@ mapping:
           use 0 in order to always use select2 fields,
           use -1 (default) in order to always use the regular select fields,
           use any other positive number as threshold (above threshold: regular select fields will be used)
+
+      enable_tool_recommendations:
+        type: bool
+        default: false
+        required: false
+        desc: |
+          Allow the display of tool recommendations in workflow editor and after tool execution.
+          If it is enabled and set to true, please enable 'tool_recommendation_model_path' as well
+
+      tool_recommendation_model_path:
+        type: str
+        default: 'https://github.com/anuprulez/download_store/raw/tool_recommendation_model/tool_recommendation_model/tool_recommendation_model.hdf5'
+        required: false
+        desc: |
+          Set remote path of the trained model (HDF5 file) for tool recommendation.
+          It is required to be set if 'enable_tool_recommendations' property is enabled and set to true.
+
+      topk_recommendations:
+        type: int
+        default: 20
+        required: false
+        desc: |
+          Set the number of predictions/recommendations to be made by the model
+
+      admin_tool_recommendations_path:
+        type: str
+        required: false
+        desc: |
+          Set path to the additional tool preferences from Galaxy admins.
+          It has two blocks. One for listing deprecated tools which will be removed from the recommendations and
+          another is for adding additional tools to be recommended along side those from the deep learning model.
+
+      overwrite_model_recommendations:
+        type: bool
+        default: false
+        required: false
+        desc: |
+          Overwrite or append to the tool recommendations by the deep learning model. When set to true, all the recommendations by the deep learning model
+          are overwritten by the recommendations set by an admin in a config file 'tool_recommendations_overwrite.yml'. When set to false, the recommended tools
+          by admins and predicted by the deep learning model are shown.
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index a40ab737f8a2..5e957cec22ce 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -331,6 +331,24 @@ def __test_upload(self, use_deprecated_route=False, name="test_import", workflow
             self._assert_user_has_workflow_with_name(name)
         return upload_response
 
+    def test_get_tool_predictions(self):
+        request = {"tool_sequence": "Cut1", "remote_model_url": "https://github.com/anuprulez/download_store/raw/tool_recommendation_model/tool_recommendation_model/tool_recommendation_model.hdf5"}
+        actual_recommendations = ['Filter1', 'cat1', 'addValue', 'comp1', 'Grep1']
+        route = "workflows/get_tool_predictions"
+        response = self._post(route, data=request)
+        recommendation_response = response.json()
+        # check Ok response from the API
+        self._assert_status_code_is(response, 200)
+        # check the input tool sequence
+        assert recommendation_response["current_tool"] == request["tool_sequence"]
+        # check non-empty predictions list
+        predicted_tools = recommendation_response["predicted_data"]["children"]
+        assert len(predicted_tools) > 0
+        # check for the correct predictions
+        for tool in predicted_tools:
+            assert tool["tool_id"] in actual_recommendations
+            break
+
     def test_update(self):
         original_workflow = self.workflow_populator.load_workflow(name="test_import")
         uuids = {}

From 10c2715d7ab57f76477b3e3fab72bd6cadeb9767 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 24 Feb 2020 15:44:31 +0100
Subject: [PATCH 187/853] make delta (sim_size) default consistent

---
 lib/galaxy/tool_util/verify/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/verify/__init__.py b/lib/galaxy/tool_util/verify/__init__.py
index 0a2a554da0d2..0b36227e8406 100644
--- a/lib/galaxy/tool_util/verify/__init__.py
+++ b/lib/galaxy/tool_util/verify/__init__.py
@@ -131,7 +131,7 @@ def get_filename(filename):
             elif compare == 're_match_multiline':
                 files_re_match_multiline(local_name, temp_name, attributes=attributes)
             elif compare == 'sim_size':
-                delta = attributes.get('delta', '100')
+                delta = attributes.get('delta', '10000')
                 s1 = len(output_content)
                 s2 = os.path.getsize(local_name)
                 if abs(s1 - s2) > int(delta):

From e47ab7a13aac8f1d85fac267f98a761fd5554e3e Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 24 Feb 2020 17:42:30 +0100
Subject: [PATCH 188/853] use a constant to specify default

---
 lib/galaxy/tool_util/parser/util.py     | 2 ++
 lib/galaxy/tool_util/parser/xml.py      | 2 ++
 lib/galaxy/tool_util/verify/__init__.py | 3 ++-
 3 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/parser/util.py b/lib/galaxy/tool_util/parser/util.py
index 41c25186c14d..b2cdfd2bac32 100644
--- a/lib/galaxy/tool_util/parser/util.py
+++ b/lib/galaxy/tool_util/parser/util.py
@@ -1,5 +1,7 @@
 from collections import OrderedDict
 
+DEFAULT_DELTA = "10000"
+
 
 def is_dict(item):
     return isinstance(item, dict) or isinstance(item, OrderedDict)
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index f38301762e02..90a3ec450830 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -9,6 +9,7 @@
 import packaging.version
 
 from galaxy.tool_util.deps import requirements
+from galaxy.tool_util.parser import DEFAULT_DELTA
 from galaxy.util import string_as_bool, xml_text, xml_to_string
 from .interface import (
     InputSource,
@@ -613,6 +614,7 @@ def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_dis
     attributes['lines_diff'] = int(attrib.pop('lines_diff', '0'))
     # Allow a file size to vary if sim_size compare
     attributes['delta'] = int(attrib.pop('delta', '10000'))
+    attributes['delta'] = int(attrib.pop('delta', DEFAULT_DELTA))
     attributes['sort'] = string_as_bool(attrib.pop('sort', False))
     attributes['decompress'] = string_as_bool(attrib.pop('decompress', False))
     extra_files = []
diff --git a/lib/galaxy/tool_util/verify/__init__.py b/lib/galaxy/tool_util/verify/__init__.py
index 0b36227e8406..5c8bb414f297 100644
--- a/lib/galaxy/tool_util/verify/__init__.py
+++ b/lib/galaxy/tool_util/verify/__init__.py
@@ -16,6 +16,7 @@
 except ImportError:
     pysam = None
 
+from galaxy.tool_util.parser import DEFAULT_DELTA
 from galaxy.util import unicodify
 from galaxy.util.compression_utils import get_fileobj
 from .asserts import verify_assertions
@@ -131,7 +132,7 @@ def get_filename(filename):
             elif compare == 're_match_multiline':
                 files_re_match_multiline(local_name, temp_name, attributes=attributes)
             elif compare == 'sim_size':
-                delta = attributes.get('delta', '10000')
+                delta = int(attributes.get('delta', DEFAULT_DELTA))
                 s1 = len(output_content)
                 s2 = os.path.getsize(local_name)
                 if abs(s1 - s2) > int(delta):

From 0e98dbd778fbef80a2c48bc3fd2816b24cbe22de Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 24 Feb 2020 17:57:28 +0100
Subject: [PATCH 189/853] fix imports

---
 lib/galaxy/tool_util/parser/xml.py      | 2 +-
 lib/galaxy/tool_util/verify/__init__.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index 90a3ec450830..9bdc060cfa16 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -9,7 +9,7 @@
 import packaging.version
 
 from galaxy.tool_util.deps import requirements
-from galaxy.tool_util.parser import DEFAULT_DELTA
+from galaxy.tool_util.parser.util import DEFAULT_DELTA
 from galaxy.util import string_as_bool, xml_text, xml_to_string
 from .interface import (
     InputSource,
diff --git a/lib/galaxy/tool_util/verify/__init__.py b/lib/galaxy/tool_util/verify/__init__.py
index 5c8bb414f297..966f13f9060f 100644
--- a/lib/galaxy/tool_util/verify/__init__.py
+++ b/lib/galaxy/tool_util/verify/__init__.py
@@ -16,7 +16,7 @@
 except ImportError:
     pysam = None
 
-from galaxy.tool_util.parser import DEFAULT_DELTA
+from galaxy.tool_util.parser.util import DEFAULT_DELTA
 from galaxy.util import unicodify
 from galaxy.util.compression_utils import get_fileobj
 from .asserts import verify_assertions

From dc3c9009f13b2b944c301ff1766ba3b6afccf12e Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 24 Feb 2020 18:30:37 +0100
Subject: [PATCH 190/853] also use the default for yaml parser

---
 lib/galaxy/tool_util/parser/yaml.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index c271a9a1cc65..ce2a910c4d03 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -1,8 +1,8 @@
 from collections import OrderedDict
 
 import packaging.version
-
 from galaxy.tool_util.deps import requirements
+from galaxy.tool_util.parser.util import DEFAULT_DELTA
 from .interface import (
     InputSource,
     PageSource,
@@ -218,7 +218,7 @@ def _parse_test(i, test_dict):
         defaults = {
             'compare': 'diff',
             'lines_diff': 0,
-            'delta': 1000,
+            'delta': DEFAULT_DELTA,
             'sort': False,
         }
         # TODO

From dd09df0ab9b500d84c1cabec8eeb478dce8c147c Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Tue, 25 Feb 2020 18:22:08 +0100
Subject: [PATCH 191/853] Update tensorflow requirements

---
 .../dependencies/pipfiles/default/pinned-requirements.txt       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 183dfb77fc81..dc64eec6383d 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -181,7 +181,7 @@ subprocess32==3.5.4 ; python_version < '3.0'
 svgwrite==1.3.1
 tempita==0.5.2
 tenacity==4.12.0
-tensorflow==1.12.2
+tensorflow==1.15.0
 typing-extensions==3.7.4.1
 typing==3.7.4.1 ; python_version < '3.5'
 tzlocal==2.0.0

From 915b3afa61285235a8df416f97490ad2bf67ffde Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Tue, 25 Feb 2020 18:32:39 +0100
Subject: [PATCH 192/853] Fix deprecation warning for H5py

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 5a5fbb594ff1..62a67c17b3e8 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -687,14 +687,14 @@ def __set_model(self, trans, remote_model_url):
                 self.all_tools[t_id_renamed] = (tool_id, tool.name)
             # read the hdf5 attributes
             trained_model = h5py.File(self.tool_recommendation_model_path, 'r')
-            model_config = json.loads(trained_model.get('model_config').value)
+            model_config = json.loads(trained_model['model_config'].value)
             self.loaded_model = model_from_json(model_config)
             # set the dictionary of tools
-            self.model_data_dictionary = json.loads(trained_model.get('data_dictionary').value)
+            self.model_data_dictionary = json.loads(trained_model['data_dictionary'].value)
             self.reverse_dictionary = dict((v, k) for k, v in self.model_data_dictionary.items())
             # set the list of compatible tools
-            self.compatible_tools = json.loads(trained_model.get('compatible_tools').value)
-            self.tool_weights = json.loads(trained_model.get('class_weights').value)
+            self.compatible_tools = json.loads(trained_model['compatible_tools'].value)
+            self.tool_weights = json.loads(trained_model['class_weights'].value)
             self.tool_weights_sorted = dict()
             # sort the tools' usage dictionary
             tool_pos_sorted = [int(key) for key in self.tool_weights.keys()]
@@ -704,7 +704,7 @@ def __set_model(self, trans, remote_model_url):
             for item in trained_model.keys():
                 if "weight_" in item:
                     d_key = "weight_" + str(counter_layer_weights)
-                    weights = trained_model.get(d_key).value
+                    weights = trained_model[d_key].value
                     model_weights.append(weights)
                     counter_layer_weights += 1
             # set the model weights

From 5cac6a706ff9046dd0373ab605a1fc93193f23ae Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 25 Feb 2020 19:16:25 +0100
Subject: [PATCH 193/853] Fix to_dict for upload1 tool

This used to happen in tool_form.mako (https://github.com/galaxyproject/galaxy/blob/0637e0adeeafde44405f69581c3e9b2ae7123ef7/templates/webapps/galaxy/tool_form.mako#L299),
where the code was:
```
    # Handle calculating the redirect url for the special case where we have nginx proxy
    # upload and need to do url_for on the redirect portion of the tool action.
    try:
        tool_url = h.url_for(tool.action)
    except AttributeError:
        assert len(tool.action) == 2
        tool_url = tool.action[0] + h.url_for(tool.action[1])
```
Fixes https://sentry.galaxyproject.org/sentry/main/issues/300358/:
```
AttributeError: 'tuple' object has no attribute 'startswith'
  File "galaxy/web/framework/decorators.py", line 282, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/api/tools.py", line 124, in build
    return tool.to_json(trans, kwd.get('inputs', kwd))
  File "galaxy/tools/__init__.py", line 2057, in to_json
    'action'        : self.app.url_for(self.action),
  File "routes/util.py", line 211, in url_for
    if url.startswith('/') and hasattr(config, 'environ') \
```
---
 lib/galaxy/tools/__init__.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index be156072ef9e..711b52c977bb 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2038,6 +2038,11 @@ def to_json(self, trans, kwd={}, job=None, workflow_building_mode=False):
             tool_help = self.help.render(static_path=self.app.url_for('/static'), host_url=self.app.url_for('/', qualified=True))
             tool_help = unicodify(tool_help, 'utf-8')
 
+        if isinstance(self.action, tuple):
+            action = self.action[0] + self.app.url_for(self.action[1])
+        else:
+            action = self.app.url_for(self.action)
+
         # update tool model
         tool_model.update({
             'id'            : self.id,
@@ -2055,7 +2060,7 @@ def to_json(self, trans, kwd={}, job=None, workflow_building_mode=False):
             'job_remap'     : self._get_job_remap(job),
             'history_id'    : trans.security.encode_id(history.id) if history else None,
             'display'       : self.display_interface,
-            'action'        : self.app.url_for(self.action),
+            'action'        : action,
             'method'        : self.method,
             'enctype'       : self.enctype
         })

From 487964483960fd33e31df1344c1de779e1ea1e76 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 25 Feb 2020 15:14:42 -0500
Subject: [PATCH 194/853] Added datatype upload test to iRODS.

---
 .gitignore                                    |   1 -
 test/integration/object_store_conf.xml        |  11 ++
 .../integration/test_datatype_upload_irods.py | 109 ++++++++++++++++++
 3 files changed, 120 insertions(+), 1 deletion(-)
 create mode 100644 test/integration/object_store_conf.xml
 create mode 100644 test/integration/test_datatype_upload_irods.py

diff --git a/.gitignore b/.gitignore
index 31f42a911440..35207905f933 100644
--- a/.gitignore
+++ b/.gitignore
@@ -79,7 +79,6 @@ shed_tool_data_table_conf.xml
 job_conf.xml
 data_manager_conf.xml
 shed_data_manager_conf.xml
-object_store_conf.xml
 job_metrics_conf.xml
 workflow_schedulers_conf.xml
 config/*
diff --git a/test/integration/object_store_conf.xml b/test/integration/object_store_conf.xml
new file mode 100644
index 000000000000..e87548784cc0
--- /dev/null
+++ b/test/integration/object_store_conf.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<object_store type="irods"> 
+    <files_dir path="database/files3"/>
+    <auth username="rods" password="rods" />
+    <resource name="demoResc" />
+    <zone name="tempZone" />
+    <connection host="localhost" port="1247"/>
+    <cache path="database/object_store_cache" size="1000" />
+    <extra_dir type="job_work" path="database/job_working_directory_irods"/>
+    <extra_dir type="temp" path="database/tmp_irods"/>
+</object_store>
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
new file mode 100644
index 000000000000..575628a8aa01
--- /dev/null
+++ b/test/integration/test_datatype_upload_irods.py
@@ -0,0 +1,109 @@
+import collections
+import os
+import tempfile
+
+import pytest
+
+from galaxy.datatypes.registry import Registry
+from galaxy.util.checkers import (
+    is_bz2,
+    is_gzip,
+    is_zip
+)
+from galaxy.util.hash_util import md5_hash_file
+from galaxy_test.driver import integration_util
+from .test_upload_configuration_options import BaseUploadContentConfigurationInstance
+
+SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
+TEST_FILE_DIR = '%s/../../lib/galaxy/datatypes/test' % SCRIPT_DIRECTORY
+TestData = collections.namedtuple('UploadDatatypesData', 'path datatype uploadable')
+GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
+DATATYPES_CONFIG = os.path.join(GALAXY_ROOT, 'lib/galaxy/config/sample/datatypes_conf.xml.sample')
+PARENT_SNIFFER_MAP = {'fastqsolexa': 'fastq'}
+OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "object_store_conf.xml")
+
+
+def find_datatype(registry, filename):
+    # match longest extension first
+    sorted_extensions = sorted(registry.datatypes_by_extension.keys(), key=len, reverse=True)
+    for extension in sorted_extensions:
+        if filename.endswith(extension) or filename.startswith(extension):
+            return registry.datatypes_by_extension[extension]
+    raise Exception("Couldn't guess datatype for file '%s'" % filename)
+
+
+def collect_test_data(registry):
+    test_files = [f for f in os.listdir(TEST_FILE_DIR) if "." in f]
+    files = [os.path.join(TEST_FILE_DIR, f) for f in test_files]
+    datatypes = [find_datatype(registry, f) for f in test_files]
+    uploadable = [datatype.file_ext in registry.upload_file_formats for datatype in datatypes]
+    test_data_description = [TestData(*items) for items in zip(files, datatypes, uploadable)]
+    return {os.path.basename(data.path): data for data in test_data_description}
+
+
+class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
+    framework_tool_and_types = False
+    datatypes_conf_override = DATATYPES_CONFIG
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["object_store_config_file"] = OBJECT_STORE_CONFIG_FILE
+
+
+instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
+
+
+@pytest.fixture
+def temp_file():
+    with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
+        yield fh
+
+
+registry = Registry()
+registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG)
+TEST_CASES = collect_test_data(registry)
+
+
+@pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))
+def test_upload_datatype_auto(instance, test_data, temp_file):
+    is_compressed = False
+    for is_method in (is_bz2, is_gzip, is_zip):
+        is_compressed = is_method(test_data.path)
+        if is_compressed:
+            break
+    with open(test_data.path, 'rb') as content:
+        if hasattr(test_data.datatype, 'sniff') or 'false' in test_data.path:
+            file_type = 'auto'
+        else:
+            file_type = test_data.datatype.file_ext
+        dataset = instance.dataset_populator.new_dataset(instance.history_id, content=content, wait=False, file_type=file_type)
+    dataset = instance.dataset_populator.get_history_dataset_details(instance.history_id, dataset=dataset, assert_ok=False)
+    expected_file_ext = test_data.datatype.file_ext
+    # State might be error if the datatype can't be uploaded
+    if dataset['state'] == 'error' and not test_data.uploadable:
+        # Some things can't be uploaded, if attempting to upload these datasets we mention why
+        assert 'invalid' in dataset['misc_info'] or 'unsupported' in dataset['misc_info']
+        return
+    elif dataset['state'] == 'error' and 'empty' in dataset['misc_info']:
+        return
+    else:
+        # state should be OK
+        assert dataset['state'] == 'ok'
+    # Check that correct datatype has been detected
+    file_ext = dataset['file_ext']
+    if 'false' in test_data.path:
+        # datasets with false in their name are not of a specific datatype
+        assert file_ext != PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
+    else:
+        assert file_ext == PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
+    datatype = registry.datatypes_by_extension[file_ext]
+    datatype_compressed = getattr(datatype, "compressed", False)
+    if not is_compressed or datatype_compressed:
+        # download file and verify it hasn't been manipulated
+        temp_file.write(instance.dataset_populator.get_history_dataset_content(history_id=instance.history_id,
+                                                                               dataset=dataset,
+                                                                               type='bytes',
+                                                                               assert_ok=False,
+                                                                               raw=True))
+        temp_file.flush()
+        assert md5_hash_file(test_data.path) == md5_hash_file(temp_file.name)

From 80cf8acceed947b98c2c505af092c7730486f5cf Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 25 Feb 2020 17:09:25 -0500
Subject: [PATCH 195/853] Fix data tables vue display

---
 .../components/admin/DataTablesGrid.vue       | 20 ++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/client/galaxy/scripts/components/admin/DataTablesGrid.vue b/client/galaxy/scripts/components/admin/DataTablesGrid.vue
index 1ae5c4019cac..fe898d7af410 100644
--- a/client/galaxy/scripts/components/admin/DataTablesGrid.vue
+++ b/client/galaxy/scripts/components/admin/DataTablesGrid.vue
@@ -3,15 +3,17 @@
         <template v-slot:title>
             Current data table registry contains {{ rows.length }} data tables
         </template>
-        <template slot:rows v-for="(row, index) in rows">
-            <tr :key="row.id" :class="[index % 2 === 0 ? 'tr' : 'odd_row']">
-                <td>
-                    <a href="javascript:void(0)" @click="handleTableNameClick">{{ row.name }}</a>
-                </td>
-                <td>{{ row.filename }}</td>
-                <td>{{ row.tool_data_path }}</td>
-                <td>{{ row.errors }}</td>
-            </tr>
+        <template v-slot:rows>
+            <template v-for="(row, index) in rows">
+                <tr :key="row.id" :class="[index % 2 === 0 ? 'tr' : 'odd_row']">
+                    <td>
+                        <a href="javascript:void(0)" @click="handleTableNameClick">{{ row.name }}</a>
+                    </td>
+                    <td>{{ row.filename }}</td>
+                    <td>{{ row.tool_data_path }}</td>
+                    <td>{{ row.errors }}</td>
+                </tr>
+            </template>
         </template>
     </base-grid>
 </template>

From 7e447ba15f20ed41f4e9519e8090253230570c90 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 25 Feb 2020 21:30:18 -0500
Subject: [PATCH 196/853] Update vue slot syntax in admin/dependencies and the
 toolshed installed list components.

---
 .../galaxy/scripts/components/Toolshed/InstalledList/Index.vue  | 2 +-
 .../scripts/components/admin/Dependencies/ContainerIndex.vue    | 2 +-
 .../scripts/components/admin/Dependencies/ResolutionIndex.vue   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/components/Toolshed/InstalledList/Index.vue b/client/galaxy/scripts/components/Toolshed/InstalledList/Index.vue
index 8e577c0dddd9..a72225f47625 100644
--- a/client/galaxy/scripts/components/Toolshed/InstalledList/Index.vue
+++ b/client/galaxy/scripts/components/Toolshed/InstalledList/Index.vue
@@ -41,7 +41,7 @@
                         </b-link>
                         <div>{{ row.item.description }}</div>
                     </template>
-                    <template slot="row-details" slot-scope="row">
+                    <template v-slot:row-details="row">
                         <RepositoryDetails :repo="row.item" />
                     </template>
                 </b-table>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/ContainerIndex.vue b/client/galaxy/scripts/components/admin/Dependencies/ContainerIndex.vue
index cf49f0765b06..a568b4a87334 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/ContainerIndex.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/ContainerIndex.vue
@@ -89,7 +89,7 @@
                 <template v-slot:cell(tool)="row">
                     <tool-display :tool-id="row.item.tool_id" />
                 </template>
-                <template slot="row-details" slot-scope="row">
+                <template v-slot:row-details="row">
                     <container-resolution-details :resolution="row.item" />
                 </template>
             </b-table>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/ResolutionIndex.vue b/client/galaxy/scripts/components/admin/Dependencies/ResolutionIndex.vue
index c66aed906dbc..7836212940d8 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/ResolutionIndex.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/ResolutionIndex.vue
@@ -50,7 +50,7 @@
                 <template v-slot:cell(tool)="row">
                     <tool-display :tool-id="row.item.tool" />
                 </template>
-                <template slot="row-details" slot-scope="row">
+                <template v-slot:row-details="row">
                     <resolution-details :resolution="row.item" />
                 </template>
             </b-table>

From 23ad85061e7e892d4056e895bae8d5495a8431f4 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 25 Feb 2020 21:39:59 -0500
Subject: [PATCH 197/853] Drop unused slot from DataManagerJobs

---
 .../scripts/components/admin/DataManager/DataManagerJobs.vue    | 2 --
 1 file changed, 2 deletions(-)

diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue b/client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
index 4f1931a7d677..69e5756e8c57 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
@@ -40,8 +40,6 @@
                 striped
                 id="jobs-table"
             >
-                <!-- Enable cell formatting for the command line column -->
-                <span slot="html" slot-scope="data" v-html="data.value"> </span>
                 <template v-slot:cell(actions)="row">
                     <b-button-group>
                         <b-button v-b-tooltip.hover title="Rerun" target="_top" :href="jobs[row.index]['runUrl']">

From 2f264977f12a4daf61530ef912cf7fbffb0a3c78 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Tue, 25 Feb 2020 22:21:42 -0500
Subject: [PATCH 198/853] Make mutable_config_dir configurable + rename

Also: do not run integration test on managed_config_dir: it depends on
config_dir, which is modified for testing.

Note: replaces previous commit from 9377
---
 lib/galaxy/config/__init__.py               | 29 ++++++++++-----------
 lib/galaxy/webapps/galaxy/config_schema.yml | 19 ++++++++++----
 lib/tool_shed/webapp/config.py              |  2 +-
 test/integration/test_config_defaults.py    | 14 +++++-----
 4 files changed, 37 insertions(+), 27 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 07453d0ca0f7..6416c96ad4cf 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -133,37 +133,36 @@ def _set_config_directories():
                 self.config_dir = os.path.abspath(self.config_dir)
 
             self.data_dir = config_kwargs.get('data_dir')
-            # mutable_config_dir is intentionally not configurable. You can
-            # override individual mutable configs with config options, but they
-            # should be considered Galaxy-controlled data files and will by default
-            # just live in the data dir
             self.sample_config_dir = os.path.join(os.path.dirname(__file__), 'sample')
+            self.managed_config_dir = config_kwargs.get('managed_config_dir')
 
             if running_from_source:
                 if self.config_dir is None:
                     self.config_dir = os.path.join(self.root, 'config')
                 if self.data_dir is None:
                     self.data_dir = os.path.join(self.root, 'database')
-                self.mutable_config_dir = self.config_dir
+                if self.managed_config_dir is None:
+                    self.managed_config_dir = self.config_dir
             else:
                 if self.config_dir is None:
                     self.config_dir = os.getcwd()
                 if self.data_dir is None:
                     self.data_dir = os.path.join(self.config_dir, 'data')
-                self.mutable_config_dir = os.path.join(self.data_dir, 'config')
+                if self.managed_config_dir is None:
+                    self.managed_config_dir = os.path.join(self.data_dir, 'config')
 
             # TODO: do we still need to support ../shed_tools when running_from_source?
             self.shed_tools_dir = os.path.join(self.data_dir, 'shed_tools')
 
             log.debug("Configuration directory is %s", self.config_dir)
             log.debug("Data directory is %s", self.data_dir)
-            log.debug("Mutable config directory is %s", self.mutable_config_dir)
+            log.debug("Managed config directory is %s", self.managed_config_dir)
 
         _set_global_conf()
         _set_config_directories()
 
-    def _in_mutable_config_dir(self, path):
-        return os.path.join(self.mutable_config_dir, path)
+    def _in_managed_config_dir(self, path):
+        return os.path.join(self.managed_config_dir, path)
 
     def _in_config_dir(self, path):
         return os.path.join(self.config_dir, path)
@@ -380,7 +379,7 @@ def _process_config(self, kwargs):
         self.oidc_config = kwargs.get("oidc_config_file", self.oidc_config_file)
         self.oidc_backends_config = kwargs.get("oidc_backends_config_file", self.oidc_backends_config_file)
         self.oidc = []
-        self.integrated_tool_panel_config = os.path.join(self.mutable_config_dir, self.integrated_tool_panel_config)
+        self.integrated_tool_panel_config = os.path.join(self.managed_config_dir, self.integrated_tool_panel_config)
         integrated_tool_panel_tracking_directory = kwargs.get('integrated_tool_panel_tracking_directory')
         if integrated_tool_panel_tracking_directory:
             self.integrated_tool_panel_tracking_directory = os.path.join(self.root, integrated_tool_panel_tracking_directory)
@@ -764,14 +763,14 @@ def parse_config_file_options(self, kwargs):
             job_metrics_config_file=[self._in_config_dir('job_metrics_conf.xml'), self._in_sample_dir('job_metrics_conf.xml.sample')],
             job_resource_params_file=[self._in_config_dir('job_resource_params_conf.xml')],
             local_conda_mapping_file=[self._in_config_dir('local_conda_mapping.yml')],
-            migrated_tools_config=[self._in_mutable_config_dir('migrated_tools_conf.xml')],
+            migrated_tools_config=[self._in_managed_config_dir('migrated_tools_conf.xml')],
             modules_mapping_files=[self._in_config_dir('environment_modules_mapping.yml')],
             object_store_config_file=[self._in_config_dir('object_store_conf.xml')],
             oidc_backends_config_file=[self._in_config_dir('oidc_backends_config.xml')],
             oidc_config_file=[self._in_config_dir('oidc_config.xml')],
-            shed_data_manager_config_file=[self._in_mutable_config_dir('shed_data_manager_conf.xml')],
-            shed_tool_config_file=[self._in_mutable_config_dir('shed_tool_conf.xml')],
-            shed_tool_data_table_config=[self._in_mutable_config_dir('shed_tool_data_table_conf.xml')],
+            shed_data_manager_config_file=[self._in_managed_config_dir('shed_data_manager_conf.xml')],
+            shed_tool_config_file=[self._in_managed_config_dir('shed_tool_conf.xml')],
+            shed_tool_data_table_config=[self._in_managed_config_dir('shed_tool_data_table_conf.xml')],
             tool_destinations_config_file=[self._in_config_dir('tool_destinations.yml')],
             tool_sheds_config_file=[self._in_config_dir('tool_sheds_conf.xml')],
             user_preferences_extra_conf_path=[self._in_config_dir('user_preferences_extra_conf.yml')],
@@ -829,7 +828,7 @@ def _ensure_directory(self, path):
                 raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, unicodify(e)))
 
     def check(self):
-        paths_to_check = [self.tool_data_path, self.data_dir, self.mutable_config_dir]
+        paths_to_check = [self.tool_data_path, self.data_dir, self.managed_config_dir]
         # Check that required directories exist
         for path in paths_to_check:
             if path not in [None, False] and not os.path.isdir(path):
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 34bb16e67147..c30e8e33b758 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -34,6 +34,15 @@ mapping:
           other Galaxy config files (e.g. datatypes_config_file). Defaults to the
           directory in which galaxy.yml is located.
 
+      managed_config_dir:
+        type: str
+        required: false
+        desc: |
+          The directory that will be prepended to relative paths in options specifying
+          config files controlled by Galaxy (such as shed_tool_config_file, etc.). Must be
+          writable by the user running Galaxy.  Defaults to `<config_dir>/` if running
+          Galaxy from source or `<data_dir>/config` otherwise.
+
       data_dir:
         type: str
         required: false
@@ -223,7 +232,7 @@ mapping:
           installation, whereas Galaxy will fail to start if any files in
           tool_config_file cannot be read.
 
-          The value of this option will be resolved with respect to <mutable_config_dir>.
+          The value of this option will be resolved with respect to <managed_config_dir>.
 
       check_migrate_tools:
         type: bool
@@ -245,7 +254,7 @@ mapping:
           scripts to install tools that have been migrated to the tool shed upon a new
           release, they will be added to this tool config file.
 
-          The value of this option will be resolved with respect to <mutable_config_dir>.
+          The value of this option will be resolved with respect to <managed_config_dir>.
 
       integrated_tool_panel_config:
         type: str
@@ -257,7 +266,7 @@ mapping:
           file can be changed by the Galaxy administrator to alter the layout of the
           tool panel.  If not present, Galaxy will create it.
 
-          The value of this option will be resolved with respect to <mutable_config_dir>.
+          The value of this option will be resolved with respect to <managed_config_dir>.
 
       tool_path:
         type: str
@@ -558,7 +567,7 @@ mapping:
           entries are automatically added to the following file, which is parsed and
           applied to the ToolDataTableManager at server start up.
 
-          The value of this option will be resolved with respect to <mutable_config_dir>.
+          The value of this option will be resolved with respect to <managed_config_dir>.
 
       tool_data_path:
         type: str
@@ -2444,7 +2453,7 @@ mapping:
           File where Tool Shed based Data Managers are configured. This file will be created
           automatically upon data manager installation.
 
-          The value of this option will be resolved with respect to <mutable_config_dir>.
+          The value of this option will be resolved with respect to <managed_config_dir>.
 
       galaxy_data_manager_data_path:
         type: str
diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index d58a91ace5e8..424207d353f4 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -181,7 +181,7 @@ def parse_config_file_options(self, kwargs):
         defaults = dict(
             auth_config_file=[self._in_config_dir('config/auth_conf.xml')],
             datatypes_config_file=[self._in_config_dir('datatypes_conf.xml'), self._in_sample_dir('datatypes_conf.xml.sample')],
-            shed_tool_data_table_config=[self._in_mutable_config_dir('shed_tool_data_table_conf.xml')],
+            shed_tool_data_table_config=[self._in_managed_config_dir('shed_tool_data_table_conf.xml')],
         )
 
         self._parse_config_file_options(defaults, dict(), kwargs)
diff --git a/test/integration/test_config_defaults.py b/test/integration/test_config_defaults.py
index b8249f45708f..c8d2ff5f26e9 100644
--- a/test/integration/test_config_defaults.py
+++ b/test/integration/test_config_defaults.py
@@ -19,6 +19,7 @@
 Configuration options NOT tested:
 - config_dir (value overridden for testing)
 - data_dir (value overridden for testing)
+- managed_config_dir (value depends on config_dir: see note above)
 - new_file_path (value overridden for testing)
 - logging (mapping loaded in config/; TODO)
 - dependency_resolution (nested properties; TODO)
@@ -42,7 +43,7 @@
     'root',
     'config_file',
     'config_dir',
-    'mutable_config_dir',
+    'managed_config_dir',
     'data_dir',
     'auth_config_file',
     'blacklist_file',
@@ -107,7 +108,7 @@
     'auth_config_file': 'config_dir',
     'builds_file_path': 'tool_data_path',
     'dependency_resolvers_config_file': 'config_dir',
-    'integrated_tool_panel_config': 'config_dir',
+    'integrated_tool_panel_config': 'managed_config_dir',
     'involucro_path': 'root_dir',
     'job_resource_params_file': 'config_dir',
     'len_file_path': 'tool_data_path',
@@ -115,10 +116,10 @@
     'oidc_backends_config_file': 'config_dir',
     'oidc_config_file': 'config_dir',
     'sanitize_whitelist_file': 'root_dir',
-    'shed_data_manager_config_file': 'mutable_config_dir',
-    'shed_tool_config_file': 'mutable_config_dir',
+    'shed_data_manager_config_file': 'managed_config_dir',
+    'shed_tool_config_file': 'managed_config_dir',
     'shed_tool_data_path': 'tool_data_path',
-    'shed_tool_data_table_config': 'mutable_config_dir',
+    'shed_tool_data_table_config': 'managed_config_dir',
     'tool_data_path': 'root_dir',
     'tool_path': 'root_dir',
     'tool_sheds_config_file': 'config_dir',
@@ -180,6 +181,7 @@ def expected_default_config_dir(value):
     'job_working_directory',  # broken; may or may not be able to test
     'library_import_dir',  # broken: default overridden
     'logging',  # mapping loaded in config/
+    'managed_config_dir',  # depends on config_dir: see note above
     'markdown_export_css',  # default not used?
     'markdown_export_css_pages',  # default not used?
     'markdown_export_css_invocation_reports',  # default not used?
@@ -229,7 +231,7 @@ def load_parent_dirs():
         return {
             'root_dir': DRIVER.app.config.root,
             'config_dir': DRIVER.app.config.config_dir,
-            'mutable_config_dir': DRIVER.app.config.mutable_config_dir,
+            'managed_config_dir': DRIVER.app.config.managed_config_dir,
             'data_dir': DRIVER.app.config.data_dir,
             'tool_data_path': DRIVER.app.config.tool_data_path,
         }

From ed19b91941542e7011b6657275854645adbaa257 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Tue, 25 Feb 2020 22:28:46 -0500
Subject: [PATCH 199/853] Run make config-rebuild

---
 doc/source/admin/galaxy_options.rst        | 24 +++++++++++++++++-----
 lib/galaxy/config/sample/galaxy.yml.sample | 17 ++++++++++-----
 2 files changed, 31 insertions(+), 10 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 946a2499b604..38a2ccfc59a5 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -10,6 +10,20 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~
+``managed_config_dir``
+~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    The directory that will be prepended to relative paths in options
+    specifying config files controlled by Galaxy (such as
+    shed_tool_config_file, etc.). Must be writable by the user running
+    Galaxy.  Defaults to `<config_dir>/` if running Galaxy from source
+    or `<data_dir>/config` otherwise.
+:Default: ``None``
+:Type: str
+
+
 ~~~~~~~~~~~~
 ``data_dir``
 ~~~~~~~~~~~~
@@ -272,7 +286,7 @@
     upon tool installation, whereas Galaxy will fail to start if any
     files in tool_config_file cannot be read.
     The value of this option will be resolved with respect to
-    <mutable_config_dir>.
+    <managed_config_dir>.
 :Default: ``shed_tool_conf.xml``
 :Type: str
 
@@ -303,7 +317,7 @@
     tool shed upon a new release, they will be added to this tool
     config file.
     The value of this option will be resolved with respect to
-    <mutable_config_dir>.
+    <managed_config_dir>.
 :Default: ``migrated_tools_conf.xml``
 :Type: str
 
@@ -319,7 +333,7 @@
     administrator to alter the layout of the tool panel.  If not
     present, Galaxy will create it.
     The value of this option will be resolved with respect to
-    <mutable_config_dir>.
+    <managed_config_dir>.
 :Default: ``integrated_tool_panel.xml``
 :Type: str
 
@@ -735,7 +749,7 @@
     following file, which is parsed and applied to the
     ToolDataTableManager at server start up.
     The value of this option will be resolved with respect to
-    <mutable_config_dir>.
+    <managed_config_dir>.
 :Default: ``shed_tool_data_table_conf.xml``
 :Type: str
 
@@ -3305,7 +3319,7 @@
     File where Tool Shed based Data Managers are configured. This file
     will be created automatically upon data manager installation.
     The value of this option will be resolved with respect to
-    <mutable_config_dir>.
+    <managed_config_dir>.
 :Default: ``shed_data_manager_conf.xml``
 :Type: str
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 494a12c44d30..075c7f98fdc7 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -112,6 +112,13 @@ galaxy:
   # Defaults to the directory in which galaxy.yml is located.
   #config_dir: null
 
+  # The directory that will be prepended to relative paths in options
+  # specifying config files controlled by Galaxy (such as
+  # shed_tool_config_file, etc.). Must be writable by the user running
+  # Galaxy.  Defaults to `<config_dir>/` if running Galaxy from source
+  # or `<data_dir>/config` otherwise.
+  #managed_config_dir: null
+
   # The directory that will be prepended to relative paths in options
   # specifying Galaxy data/cache directories and files (such as the
   # default SQLite database, file_path, etc.). Defaults to `database/`
@@ -233,7 +240,7 @@ galaxy:
   # installation, whereas Galaxy will fail to start if any files in
   # tool_config_file cannot be read.
   # The value of this option will be resolved with respect to
-  # <mutable_config_dir>.
+  # <managed_config_dir>.
   #shed_tool_config_file: shed_tool_conf.xml
 
   # Enable / disable checking if any tools defined in the above non-shed
@@ -249,7 +256,7 @@ galaxy:
   # tool shed upon a new release, they will be added to this tool config
   # file.
   # The value of this option will be resolved with respect to
-  # <mutable_config_dir>.
+  # <managed_config_dir>.
   #migrated_tools_config: migrated_tools_conf.xml
 
   # File that contains the XML section and tool tags from all tool panel
@@ -258,7 +265,7 @@ galaxy:
   # to alter the layout of the tool panel.  If not present, Galaxy will
   # create it.
   # The value of this option will be resolved with respect to
-  # <mutable_config_dir>.
+  # <managed_config_dir>.
   #integrated_tool_panel_config: integrated_tool_panel.xml
 
   # Default path to the directory containing the tools defined in
@@ -463,7 +470,7 @@ galaxy:
   # is parsed and applied to the ToolDataTableManager at server start
   # up.
   # The value of this option will be resolved with respect to
-  # <mutable_config_dir>.
+  # <managed_config_dir>.
   #shed_tool_data_table_config: shed_tool_data_table_conf.xml
 
   # Directory where data used by tools is located.  See the samples in
@@ -1619,7 +1626,7 @@ galaxy:
   # File where Tool Shed based Data Managers are configured. This file
   # will be created automatically upon data manager installation.
   # The value of this option will be resolved with respect to
-  # <mutable_config_dir>.
+  # <managed_config_dir>.
   #shed_data_manager_config_file: shed_data_manager_conf.xml
 
   # Directory to store Data Manager based tool-data. Defaults to the

From 2dc072609f2a9ca83348fa822dffa89886ef6dba Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 28 Jan 2020 16:28:38 +0100
Subject: [PATCH 200/853] Update scripts/bootstrap_history.py for python 3 /
 pygithub

---
 scripts/bootstrap_history.py | 55 ++++++++++++++++++++----------------
 1 file changed, 30 insertions(+), 25 deletions(-)

diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index 216595bc6fff..4440138f7b87 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -6,6 +6,7 @@
 import calendar
 import datetime
 import json
+import logging
 import os
 import re
 import string
@@ -18,12 +19,14 @@
 except ImportError:
     requests = None
 try:
-    from pygithub3 import Github
+    from github import Github
 except ImportError:
     Github = None
 from six import string_types
 from six.moves.urllib.parse import urljoin
 
+log = logging.getLogger(__name__)
+
 PROJECT_DIRECTORY = os.path.join(os.path.dirname(__file__), os.pardir)
 GALAXY_VERSION_FILE = os.path.join(PROJECT_DIRECTORY, "lib", "galaxy", "version.py")
 PROJECT_OWNER = "galaxyproject"
@@ -40,7 +43,7 @@
     "tnabtaf", "natefoo", "jgoecks",
     "guerler", "jennaj", "nekrut", "jxtx",
     "VJalili", "WilliamHolden", "Nerdinacan",
-    "ic4f",
+    "ic4f", "mvdbeek"
 ]
 
 TEMPLATE = """
@@ -350,7 +353,7 @@ def do_release(argv):
     template = template.replace(".. enhancement", "%s\n\n.. enhancement" % enhancement_targets)
     template = template.replace(".. bug", "%s\n\n.. bug" % bug_targets)
     release_info = string.Template(template).safe_substitute(release=release_name)
-    open(release_file, "w").write(release_info.encode("utf-8"))
+    open(release_file, "w").write(release_info)
     month = int(release_name.split(".")[1])
     month_name = calendar.month_name[month]
     year = release_name.split(".")[0]
@@ -379,7 +382,7 @@ def do_release(argv):
     next_release_file = _release_file(next_version + "_announce.rst")
 
     next_announce = NEXT_TEMPLATE.substitute(**next_version_params)
-    open(next_release_file, "w").write(next_announce.encode("utf-8"))
+    open(next_release_file, "w").write(next_announce)
     releases_index = _release_file("index.rst")
     releases_index_contents = _read_file(releases_index)
     releases_index_contents = releases_index_contents.replace(".. announcements\n", ".. announcements\n   " + next_version + "_announce\n")
@@ -471,29 +474,30 @@ def _release_dates(version):
     return freeze_date, release_date
 
 
-def _get_prs(release_name, state="closed"):
+def _get_prs(release_name, state="closed", pr_cache=[]):
     github = _github_client()
-    pull_requests = github.pull_requests.list(
+    repo = github.get_repo("%s/%s" % (PROJECT_OWNER, PROJECT_NAME))
+    add_to_cache = not pr_cache
+    pull_requests = pr_cache or repo.get_pulls(
         state=state,
-        user=PROJECT_OWNER,
-        repo=PROJECT_NAME,
     )
     reached_old_prs = False
 
-    for page in pull_requests:
+    for pr in pull_requests:
         if reached_old_prs:
             break
 
-        for pr in page:
-            if pr.created_at < datetime.datetime(2016, 11, 1, 0, 0):
-                reached_old_prs = True
-                pass
-            merged_at = pr.merged_at
-            milestone = pr.milestone
-            proper_state = state != "closed" or merged_at
-            if not proper_state or not milestone or milestone['title'] != release_name:
-                continue
-            yield pr
+        if pr.created_at < datetime.datetime(2018, 11, 1, 0, 0):
+            reached_old_prs = True
+            pass
+        merged_at = pr.merged_at
+        milestone = pr.milestone
+        proper_state = state != "closed" or merged_at
+        if not proper_state or not milestone or milestone.title != release_name:
+            continue
+        if add_to_cache:
+            pr_cache.append(pr)
+        yield pr
 
 
 def main(argv):
@@ -585,8 +589,8 @@ def extend_target(target, line, source=history):
     owner = None
     if ident.startswith("pr"):
         pull_request = ident[len("pr"):]
-        user = req["head"]["user"]
-        owner = user["login"]
+        user = req["head"].user
+        owner = user.login
         if owner in DEVTEAM:
             owner = None
         text = ".. _Pull Request {0}: {1}/pull/{0}".format(pull_request, PROJECT_URL)
@@ -615,7 +619,7 @@ def extend_target(target, line, source=history):
     to_doc = wrap(to_doc)
     if text_target is not None:
         history = extend_target(text_target, to_doc, history)
-    if req and 'labels' in req:
+    if req and req['labels']:
         labels = req['labels']
         if 'area/datatypes' in labels:
             user_announce = extend_target("datatypes", to_doc, user_announce)
@@ -630,12 +634,12 @@ def extend_target(target, line, source=history):
 
 def _read_file(path):
     with open(path, "r") as f:
-        return f.read().decode("utf-8")
+        return f.read()
 
 
 def _write_file(path, contents):
     with open(path, "w") as f:
-        f.write(contents.encode("utf-8"))
+        f.write(contents)
 
 
 def _text_target(github, pull_request, labels=None):
@@ -713,7 +717,7 @@ def _text_target(github, pull_request, labels=None):
 
 
 def _pr_to_labels(pr):
-    labels = [l["name"].lower() for l in pr.labels]
+    labels = [l.name.lower() for l in pr.labels]
     return labels
 
 
@@ -740,6 +744,7 @@ def _github_client():
         github_json = os.path.expanduser("~/.github.json")
         github = Github(**json.load(open(github_json, "r")))
     except Exception:
+        log.exception()
         github = None
     return github
 

From 08e97198c935dbef8965e383f62bd073c38c6190 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 28 Jan 2020 19:41:06 +0100
Subject: [PATCH 201/853] Release notes for 20.01

---
 doc/source/releases/20.01.rst               | 655 ++++++++++++++++++++
 doc/source/releases/20.01_announce.rst      |  62 +-
 doc/source/releases/20.01_announce_user.rst |  93 +++
 doc/source/releases/20.01_prs.rst           | 277 +++++++++
 4 files changed, 1084 insertions(+), 3 deletions(-)
 create mode 100644 doc/source/releases/20.01.rst
 create mode 100644 doc/source/releases/20.01_announce_user.rst
 create mode 100644 doc/source/releases/20.01_prs.rst

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
new file mode 100644
index 000000000000..db6791476c2a
--- /dev/null
+++ b/doc/source/releases/20.01.rst
@@ -0,0 +1,655 @@
+
+.. to_doc
+
+20.01
+===============================
+
+.. announce_start
+
+Enhancements
+-------------------------------
+
+.. major_feature
+
+
+.. feature
+* CLI tools for installing/testing Docker and Singularity containers
+  (thanks to `@simonbray <https://github.com/simonbray>`__).
+  `Pull Request 7936`_
+* Markdown-based Galaxy Pages.
+  `Pull Request 8512`_
+* Make Masthead and workflow page screenreader friendly
+  `Pull Request 8700`_
+* Add data dialog input element to client form parameter list
+  `Pull Request 8774`_
+* Add has_size option
+  (thanks to `@simonbray <https://github.com/simonbray>`__).
+  `Pull Request 8852`_
+* Email notifications on job completion
+  `Pull Request 8948`_
+* Make tours reloadable
+  `Pull Request 9032`_
+* Add a config option to allow customizing the brand title
+  `Pull Request 9062`_
+* IT fixes and 3 new ITs
+  `Pull Request 9141`_
+
+.. enhancement_tag_viz
+
+.. enhancement_tag_datatypes
+* Datatypes for MassSpec DIA dlib,elib
+  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
+  `Pull Request 8657`_
+* Add bus as binary, remove extra datatype
+  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
+  `Pull Request 8705`_
+* remove dada2_derep data type
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 8902`_
+* Add new GROMACS datatypes: ndx, xvg, edr
+  (thanks to `@simonbray <https://github.com/simonbray>`__).
+  `Pull Request 8964`_
+* add gff3.gz and gff3.bz2 datatypes
+  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
+  `Pull Request 8967`_
+* Make mol2 visible
+  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
+  `Pull Request 8995`_
+* Add a datatype subclass for CAT (Contig Annotation Tool)
+  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
+  `Pull Request 9087`_
+
+.. enhancement_tag_tools
+* Upgrade askomics interactive tool
+  (thanks to `@xgaia <https://github.com/xgaia>`__).
+  `Pull Request 8517`_
+* Remove collection ID character restriction from 'Relabel collection from
+  file' tool
+  (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
+  `Pull Request 8571`_
+* Allow space, dot and comma in relabel identifier tool
+  `Pull Request 8757`_
+* Fix script shebangs
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8888`_
+* Allow admins to import tools/workflows from paths.
+  `Pull Request 9003`_
+
+.. enhancement_tag_workflows
+* Interactive modification of invocation report.
+  `Pull Request 8691`_
+* User-facing Workflow Invocation Grid
+  `Pull Request 8699`_
+* PDF Export of Galaxy Markdown
+  `Pull Request 8893`_
+* Refactor some workflow editor plumbing to VueJS
+  `Pull Request 8931`_
+* Track non-history content outputs.
+  `Pull Request 9009`_
+* Default format 2 workflows to be downloaded as YAML.
+  `Pull Request 9023`_
+* Even Richer Workflow Inputs
+  `Pull Request 9086`_
+* Separate Markdown Validation into its own module.
+  `Pull Request 9099`_
+* add option select_type_workflow_threshold (rebase)
+  `Pull Request 9105`_
+
+.. enhancement_tag_ui
+* Upgrade eslint (major version), fix compliance with new standard rules.
+  `Pull Request 8708`_
+* JobMetrics.vue unit test.
+  `Pull Request 8732`_
+* Fix the flexible Data Dialog to work independent of the page layout
+  initialization hooks.
+  `Pull Request 8744`_
+* axios-mock-adapter for cleaner, more expansive testing
+  `Pull Request 8749`_
+* Added client-side application configs for each target environment
+  `Pull Request 8827`_
+
+.. enhancement_tag_jobs
+* Small cleanup for job runners kill
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8523`_
+* Improvements to Galaxy and Pulsar job execution
+  `Pull Request 8625`_
+* Allow assigning UUID job ids with Pulsar in MQ mode.
+  `Pull Request 8718`_
+* Do not re-compute job input_ext/dbkey in job finish.
+  `Pull Request 8910`_
+* Implement extended job metadata collection
+  `Pull Request 8930`_
+* Move Jobs updated time display logic to client.
+  `Pull Request 8943`_
+* Implement extended job metadata collection + fixes
+  `Pull Request 8984`_
+* Place version output file in a writable directory for containerized jobs.
+  `Pull Request 8997`_
+* Fix deletion of outputs and working before job
+  `Pull Request 9245`_
+
+.. enhancement_tag_admin
+* Add Tool Manager Component for Admin Panel
+  `Pull Request 8601`_
+* Add process ID to worker_process table
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8972`_
+
+.. enhancement
+* Use official "login with" buttons for OIDC
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
+  `Pull Request 8107`_
+* Add data types to docs.galaxyproject.org
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8531`_
+* python-ldap python3 update and documentation change
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8618`_
+* GitLab error reporting
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8620`_
+* Extend the list of attributes to be reported.
+  `Pull Request 8661`_
+* Have CI ensure client PRs are formatted.
+  `Pull Request 8662`_
+* Add area/configuration label
+  `Pull Request 8665`_
+* Update BootstrapVue to 2.0.1
+  `Pull Request 8666`_
+* add .gitattributes file and normalize line endings to use LF in…
+  `Pull Request 8677`_
+* Improve CI reliability by annotating external resources.
+  `Pull Request 8678`_
+* Restrict `/api/histories/shared_with_me` to logged-in users
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8685`_
+* Automate path resolution for config options
+  `Pull Request 8689`_
+* Remove unused Docker Swarm options
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8690`_
+* LDAP search member of filter
+  (thanks to `@BioinformaticsPlatformWIV-ISP
+  <https://github.com/BioinformaticsPlatformWIV-ISP>`__).
+  `Pull Request 8697`_
+* Rebuild and prettify config sample and doc
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8713`_
+* Update zh/locale.js
+  (thanks to `@shenweiyan <https://github.com/shenweiyan>`__).
+  `Pull Request 8725`_
+* Start using path_resolves_to; add integration tests
+  `Pull Request 8737`_
+* Significant overhaul to container+dependency management
+  `Pull Request 8741`_
+* Multi subdomains cookie support
+  (thanks to `@julozi <https://github.com/julozi>`__).
+  `Pull Request 8746`_
+* One test case to rule them all
+  `Pull Request 8793`_
+* Allow recording more performance statistics to statsd.
+  `Pull Request 8800`_
+* Add installation monitor popup to toolshed client
+  `Pull Request 8810`_
+* General server dependency updates (was/including catalina fix)
+  `Pull Request 8843`_
+* Add badge to indicate availability of a newer toolshed repository version
+  `Pull Request 8860`_
+* Add config options to integration test for abs path
+  `Pull Request 8862`_
+* Make message_box style and visible options reloadable
+  `Pull Request 8863`_
+* Remove 'area/cleanup', edit 'kind/refactoring'
+  `Pull Request 8874`_
+* Unpin bdbag.
+  `Pull Request 8883`_
+* Add separate knob for masthead colors
+  `Pull Request 8904`_
+* Refactor galaxy_install and required dependencies into Galaxy's namespace.
+  `Pull Request 8905`_
+* Enable interactivetools with other beta tools...
+  `Pull Request 8913`_
+* Simplify logo replacement, fix height and alignment
+  `Pull Request 8914`_
+* Simplify Python deps installation in `testing-base` Dockerfile
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8921`_
+* Config: drop redundant `template_cache` attribute
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8924`_
+* Enable secondary authorization
+  `Pull Request 8926`_
+* Set up a cache dir for pip when running tests with Docker
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8929`_
+* Add link for interactive tools
+  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
+  `Pull Request 8936`_
+* Remove deprecated tool dependency scripts.
+  `Pull Request 8955`_
+* Remove tool shed API examples.
+  `Pull Request 8956`_
+* Remove script for migrating tools to the tool shed...
+  `Pull Request 8957`_
+* Move galaxy testing utilities into cleaner package structure.
+  `Pull Request 8960`_
+* Create packages for Galaxy tests and infrastructure.
+  `Pull Request 8962`_
+* Remove workflow support from tool shed.
+  `Pull Request 8978`_
+* Remove capsule feature from tool shed.
+  `Pull Request 8979`_
+* trim long ldda messages; improve fluid media css
+  `Pull Request 9000`_
+* Expose python version in api/config
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
+  `Pull Request 9010`_
+* Hot module reloading using webpack-dev-server for client dev
+  `Pull Request 9029`_
+* when building ts index log parse errors at debug level
+  `Pull Request 9033`_
+* Update quickstart.rst
+  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
+  `Pull Request 9044`_
+* Add Sergey Golitsynskiy to committers group
+  `Pull Request 9056`_
+* Update Mercurial to Py3-compatible v5.2, and all other deps
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9065`_
+* Automatically redirect to OIDC provider when only auth option
+  (thanks to `@machristie <https://github.com/machristie>`__).
+  `Pull Request 9115`_
+* Automatically use extended-base-image if necessary
+  `Pull Request 9116`_
+* Add HMR to client readme.
+  `Pull Request 9121`_
+* Add admin functionality to histories API
+  (thanks to `@thomcuddihy <https://github.com/thomcuddihy>`__).
+  `Pull Request 9124`_
+* Don't break generated reStructuredText and YAML on hyphens
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9128`_
+* mulled: use threading.Event in PrintProgress to avoid unnecessary wai…
+  `Pull Request 9163`_
+* Update my username
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
+  `Pull Request 9195`_
+* Add base_image column to mulled-build-files
+  `Pull Request 9199`_
+* Allow passing conda_context to any_target_requires_extended_base
+  `Pull Request 9202`_
+* Backport 9175: Update galaxy.tool_util.cwl for latest changes in CWL branch.
+  `Pull Request 9210`_
+* Extended base annotation fixes
+  `Pull Request 9224`_
+
+.. small_enhancement
+* Factor out yaml read/write from config_manage.py
+  `Pull Request 8509`_
+* Implementation of the workflow list as vue component
+  `Pull Request 8551`_
+* Refactor config loading
+  `Pull Request 8573`_
+* Change reloadable config + misc cleanup
+  `Pull Request 8600`_
+* Case-insensitive match user-supplied email when logging in
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8631`_
+* Modify schema defaults and their loading
+  `Pull Request 8639`_
+* Replace resolve_path() with os.path.join()
+  `Pull Request 8646`_
+* Simplify config code (minor edits)
+  `Pull Request 8648`_
+* Refactor/cleanup config loading (misc edits)
+  `Pull Request 8651`_
+* Remove unused Tags file since it was converted to a Vue component
+  `Pull Request 8722`_
+* Update slot syntax to v-slot across the board.
+  `Pull Request 8730`_
+* Remove deprecated Toolshed API endpoints
+  `Pull Request 8734`_
+* Client build process refinement
+  `Pull Request 8742`_
+* Add vue component and endpoint to reset repository metadata
+  `Pull Request 8754`_
+* Cleanup SQL query in ``_calculate_or_set_disk_usage()``
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8776`_
+* Drop DetachedInstanceError workaround
+  `Pull Request 8785`_
+* Simplify code for expand_meta_parameters
+  (thanks to `@qiagu <https://github.com/qiagu>`__).
+  `Pull Request 8794`_
+* Convert User Preferences page to Vue Component
+  `Pull Request 8803`_
+* client-side current user store module
+  `Pull Request 8813`_
+* Refactor database_connection config loading
+  `Pull Request 8855`_
+* Refactor default_locale config option; test
+  `Pull Request 8856`_
+* Refactor infrastructure_url/port values; fix tests
+  `Pull Request 8857`_
+* Refactor pretty-datatime_format config loading
+  `Pull Request 8858`_
+* Fix misc. integration tests for config values
+  `Pull Request 8859`_
+* Do not specify None as default in dict.get()
+  `Pull Request 8865`_
+* Delete 'resolve path' integration tests
+  `Pull Request 8870`_
+* Do not raise Exception to manage control flow
+  `Pull Request 8876`_
+* Eliminate interactive debugging middleware
+  `Pull Request 8877`_
+* Normalize myexperiment_target_url / myexperiment_url
+  `Pull Request 8882`_
+* Do not override schema defaults if they exist
+  `Pull Request 8884`_
+* Use schema defaults in galaxy masthead
+  `Pull Request 8885`_
+* Cleanup config loading (minor fixes)
+  `Pull Request 8890`_
+* Refactor _set_config_base; fix config_dir value
+  `Pull Request 8915`_
+* Library tags tweaks and tests
+  `Pull Request 8947`_
+* Refactor Toolshed webapp into tool_shed package.
+  `Pull Request 8949`_
+* Separate Shed and Galaxy makos, package shed makos.
+  `Pull Request 8958`_
+* Remove admin tool shed controller code (Part 1)
+  `Pull Request 8988`_
+* Remove unused helper code from twilltestcase.
+  `Pull Request 8989`_
+* Fix tool image loading (was broken due to failing repo dir resolution)
+  `Pull Request 9006`_
+* Convert Custom builds vue
+  `Pull Request 9016`_
+* Implement datasets grid as vue component
+  `Pull Request 9018`_
+* remove unused toolshed template code
+  `Pull Request 9084`_
+* Default the authnz_manager to None
+  `Pull Request 9117`_
+* Update github username @erasche to @hexylena and correct inconsistencies
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
+  `Pull Request 9194`_
+
+
+
+Fixes
+-------------------------------
+
+.. major_bug
+
+
+.. bug_tag_viz
+* Wrap SQL statement in a text() function as required by sqlalchemy
+  (thanks to `@kaukrise <https://github.com/kaukrise>`__).
+  `Pull Request 9216`_
+* Ensure visible overflow on navbar container
+  (thanks to `@kaukrise <https://github.com/kaukrise>`__).
+  `Pull Request 9217`_
+
+.. bug_tag_datatypes
+* Fix cool sniffing on python3
+  `Pull Request 9153`_
+
+.. bug_tag_tools
+* grouping: strip newlines
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 8953`_
+* Add requirements to interval_to_bed_converter.xml
+  `Pull Request 9041`_
+
+.. bug_tag_workflows
+* Exports reports with workflows (if configured).
+  `Pull Request 9055`_
+* Rev gxformat2 dependency to fix various export issues.
+  `Pull Request 9075`_
+
+.. bug_tag_ui
+* Run prettier after `#8107
+  <https://github.com/galaxyproject/galaxy/issues/8107>`__
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9102`_
+
+.. bug_tag_jobs
+* Small fixes for k8s.
+  `Pull Request 8759`_
+* Fix output.file_path writing to read-only path on Docker
+  `Pull Request 9048`_
+* Add job home to writable paths
+  `Pull Request 9051`_
+* Fix LocalShell returncode
+  `Pull Request 9171`_
+* Fix: Added support for specifying k8s job pod priority class
+  (thanks to `@nuwang <https://github.com/nuwang>`__).
+  `Pull Request 9219`_
+* Fix: Added support for specifying k8s job affinity and tolerations
+  (thanks to `@nuwang <https://github.com/nuwang>`__).
+  `Pull Request 9225`_
+* Mount job_working_directory/configs rw
+  `Pull Request 9234`_
+* Limit async hack to async tools
+  `Pull Request 9242`_
+* Fix moving of data manager output for entries
+  `Pull Request 9243`_
+* python3 fixes for setups using drmaa and realuser setups
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 9246`_
+* fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 9253`_
+
+.. bug_tag_admin
+* Encode lines in filter_file_fields
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8652`_
+* Git error reporting - bug fixes and better error handling
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8900`_
+* Assorted admin panel fixes
+  `Pull Request 9097`_
+* Run integration tests on github, fix various bugs (interactive tools,
+  kubernetes, test framework)
+  `Pull Request 9193`_
+
+.. bug
+* Documentation update
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8508`_
+* Asynchronous data source: unable to create the file
+  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
+  `Pull Request 8515`_
+* OIDC config patch
+  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
+  `Pull Request 8572`_
+* set uwsgi umask default
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 8581`_
+* Fix `test_validate_simple_config` unit test
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8632`_
+* Fix a bug that occurs while installing a data manager.
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8634`_
+* Fix bug in build_dependency_manager()
+  `Pull Request 8660`_
+* Get rid of fix timeout in admin app Selenium test.
+  `Pull Request 8667`_
+* More robust login/logout with Selenium.
+  `Pull Request 8676`_
+* Fixes for BootstrapVue Tables
+  `Pull Request 8684`_
+* More bootstrap vue upgrade fixes.
+  `Pull Request 8692`_
+* GRT: Ensure correct encoding, no partial lines
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
+  `Pull Request 8712`_
+* Revise toolshed config dependency check error message in repository install
+  manager
+  `Pull Request 8720`_
+* Fix data dialog height, modal test case and table slots
+  `Pull Request 8724`_
+* Do not overwrite existing attributes
+  `Pull Request 8728`_
+* Replace hardcoded configuration
+  `Pull Request 8731`_
+* Fix `new_secure_hash()` when passed an empty string
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8739`_
+* data_manager_conf.xml.sample is missing
+  (thanks to `@lecorguille <https://github.com/lecorguille>`__).
+  `Pull Request 8784`_
+* Revert "[19.09] Fix detached parent instance error in 8769"
+  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
+  `Pull Request 8791`_
+* Handles k8s job recently created with no status set yet
+  (thanks to `@pcm32 <https://github.com/pcm32>`__).
+  `Pull Request 8799`_
+* Add postcss-loader and autoprefixer dependencies
+  `Pull Request 8821`_
+* LDAP fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8823`_
+* Ensure app.config.config_file is an absolute path
+  `Pull Request 8836`_
+* Fix rare bug in config loading + add unit test
+  `Pull Request 8837`_
+* fix plugin name
+  (thanks to `@gmauro <https://github.com/gmauro>`__).
+  `Pull Request 8840`_
+* Restore portlet section style for repeat blocks
+  `Pull Request 8864`_
+* Prevent potential bug in config loading; test
+  `Pull Request 8866`_
+* Fix authnz manager's oidc config parsing for python3
+  `Pull Request 8871`_
+* Update check_py3_compatibility script for new ack versions.
+  `Pull Request 8872`_
+* If config_file is None, use cwd, not its parent
+  `Pull Request 8894`_
+* Log LDAP authenticate exceptions at the right level
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8907`_
+* make pgcleanup also delete HDAs
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 8908`_
+* Fix unbounded variable error in `GET /api/datasets/{encoded_dataset_id}`
+  exception handling
+  `Pull Request 8935`_
+* Set `deleted` attribute of history datasets when purging histories from grid
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8940`_
+* Fix default logo path in configuration manager
+  `Pull Request 8941`_
+* Fix API decorator order
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9015`_
+* do not use var from inner scope
+  `Pull Request 9026`_
+* escape double hyphen in IT sample config, making it valid XML
+  `Pull Request 9034`_
+* Fix input parameter comparisons
+  `Pull Request 9047`_
+* Restore casting a boolean param to str when comparing with one
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9052`_
+* Fix comparison if parameter is optional and value is not provided
+  `Pull Request 9054`_
+* Small refactor of ``InputValueWrapper`` comparison methods
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9059`_
+* Add create_time to the signature of Repository constructor.
+  `Pull Request 9063`_
+* Listify value for multiple SelectToolParameterWrapper
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9067`_
+* Use newer psycopg2 conditional requirement for wheels on 3.7
+  `Pull Request 9068`_
+* Fix mulled version comparison
+  `Pull Request 9078`_
+* linter: accept outputs with auto_format only
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 9081`_
+* Create temporary files for cgi.FieldsStorage with delete=False
+  `Pull Request 9082`_
+* Fix importing a directory from user_library_import_dir
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9090`_
+* Make callbacks for tour and config watchers a control task
+  `Pull Request 9092`_
+* Don't watch tool files through watchdog
+  `Pull Request 9094`_
+* Allow html in registration warning message.
+  `Pull Request 9098`_
+* Admin job info display fix
+  `Pull Request 9120`_
+* Client build readme followup
+  `Pull Request 9122`_
+* Fix mulled cache/data locations, rebuild schema
+  `Pull Request 9125`_
+* More fixes for publishing decomposed packages.
+  `Pull Request 9126`_
+* fix url for workflow sharing
+  `Pull Request 9132`_
+* Add click prevent to workflow list dropdowns
+  `Pull Request 9133`_
+* Remove legacy admin panel entry for installation monitor, fix typo
+  `Pull Request 9134`_
+* Parse brand label option in legacy mako
+  `Pull Request 9136`_
+* Restore returning "None" when casting unselected multiselect param to str
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9144`_
+* Misc fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9145`_
+* Add implementation of `parse_interactivetool` to `CwlToolSource` class
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9146`_
+* Fix optional unset integer and float params
+  `Pull Request 9149`_
+* Assorted OIDC fixes
+  `Pull Request 9150`_
+* Cast to None for optional params if not comparing strings
+  `Pull Request 9156`_
+* Ensure that users have a private role before login
+  `Pull Request 9168`_
+* Add static-safe mapping to config management
+  `Pull Request 9179`_
+* Fix tool shed tests for `#9168
+  <https://github.com/galaxyproject/galaxy/issues/9168>`__.
+  `Pull Request 9182`_
+* Add require_login bypass for entire authnz controller.
+  `Pull Request 9192`_
+* Fix runtime error in ToolConfWatcher
+  `Pull Request 9212`_
+* Fix extended base for singularity and add base_image_for_targets
+  `Pull Request 9215`_
+* More mulled-build-files fixes
+  `Pull Request 9228`_
+* Fix mailto hrefs in menus
+  `Pull Request 9232`_
+* Move meme_fimo out of unversioned lib tools
+  `Pull Request 9237`_
+* Fallback to binary download if header lies about content encoding
+  `Pull Request 9239`_
+* Fix lint warning string formatting
+  `Pull Request 9240`_
+* Fix unselected select parameter comparison to empty string
+  `Pull Request 9260`_
+* Fix iteritems use in build_from_current_history.mako
+  `Pull Request 9266`_
+* Fix suffix for single target mulled builds
+  `Pull Request 9267`_
+* backport 9268: Fix target_str_to_targets
+  `Pull Request 9269`_
+
+
+.. include:: 20.01_prs.rst
+
diff --git a/doc/source/releases/20.01_announce.rst b/doc/source/releases/20.01_announce.rst
index 2c7a6a98ff50..406a076c09a2 100644
--- a/doc/source/releases/20.01_announce.rst
+++ b/doc/source/releases/20.01_announce.rst
@@ -3,8 +3,64 @@
 January 2020 Galaxy Release (v 20.01)
 ===========================================================
 
+.. include:: _header.rst
 
-Schedule
+Highlights
 ===========================================================
- * Planned Freeze Date: 2020-01-06
- * Planned Release Date: 2020-01-27
+
+**Enhanced workflow functionality** 
+  Workflows can now now make use of optional datasets and optional parameters,
+  optional parameter default values and dataset inputs can now be restricted to
+  user-defined datatypes. The workflow editor and execution engine have been
+  enhanced to allow defining options to choose from, and these options can be
+  connected to compatible text, integer, float, color and select tool parameters
+  for more flexible and universally re-usable workflows (`Pull Request 9086`_, `Pull Request 9073`_, `Pull Request 8264`_). 
+
+**Major update to container and dependency management interface**
+  The manage dependencies interface has been ported to vue.js and displays
+  additional information about installed, missing and available dependencies
+  and conveniently summarizes dependency status for all installed tools.
+  Additionally the user interface now displays whether a `Biocontainers <https://biocontainers.pro/#/registry>`__ image
+  is available at `quay.io <https://quay.io>`__ (`Pull Request 8741`_).
+
+**Extended job metadata collection**
+  Creating Job metadata has been reworked so that the dataset transfer that
+  occurs after a Galaxy job can be initiated by the compute node that runs a
+  Galaxy job. Previously the transfer was done by Galaxy under many production
+  scenarios.  This reduces IO load on Galaxy instances and should allow running
+  many more jobs in parallel. This work will also make jobs running on remote
+  compute resources much more efficient if the remote resources can write to
+  Galaxy'so object store. To benefit from this new metadata setting Galaxy needs
+  to use object stores that use uuids for storing datasets and set the
+  ``metadata_strategy`` configuration value to ``extended``. This feature is in beta
+  testing, but work is ongoing to mix existing object store configuration and
+  choose the most efficient way of transfering datasets automatically (`Pull
+  Request 8930`_ ).
+
+
+Also check out the `20.01 user release notes <https://docs.galaxyproject.org/en/release_20.01/releases/20.01_announce_user.html>`__
+
+Get Galaxy
+==========
+
+The code lives at `GitHub <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
+
+To get a new Galaxy repository run:
+  .. code-block:: shell
+
+      $ git clone -b release_20.01 https://github.com/galaxyproject/galaxy.git
+
+To update an existing Galaxy repository run:
+  .. code-block:: shell
+
+      $ git fetch origin && git checkout release_20.01 && git pull --ff-only origin release_20.01
+
+See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
+
+Release Notes
+===========================================================
+
+.. include:: 20.01.rst
+   :start-after: announce_start
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/20.01_announce_user.rst b/doc/source/releases/20.01_announce_user.rst
new file mode 100644
index 000000000000..c4d19b4cedd2
--- /dev/null
+++ b/doc/source/releases/20.01_announce_user.rst
@@ -0,0 +1,93 @@
+
+===========================================================
+January 2020 Galaxy Release (v 20.01)
+===========================================================
+
+.. include:: _header.rst
+
+Highlights
+===========================================================
+
+**Feature1**
+  Feature description.
+
+**Feature2**
+  Feature description.
+
+**Feature3**
+  Feature description.
+
+
+New Visualizations
+===========================================================
+
+.. visualizations
+* Add data dialog input element to client form parameter list
+  `Pull Request 8774`_
+* Wrap SQL statement in a text() function as required by sqlalchemy
+  (thanks to `@kaukrise <https://github.com/kaukrise>`__).
+  `Pull Request 9216`_
+* Ensure visible overflow on navbar container
+  (thanks to `@kaukrise <https://github.com/kaukrise>`__).
+  `Pull Request 9217`_
+
+New Datatypes
+===========================================================
+
+.. datatypes
+* Datatypes for MassSpec DIA dlib,elib
+  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
+  `Pull Request 8657`_
+* Add bus as binary, remove extra datatype
+  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
+  `Pull Request 8705`_
+* remove dada2_derep data type
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 8902`_
+* Add new GROMACS datatypes: ndx, xvg, edr
+  (thanks to `@simonbray <https://github.com/simonbray>`__).
+  `Pull Request 8964`_
+* add gff3.gz and gff3.bz2 datatypes
+  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
+  `Pull Request 8967`_
+* Make mol2 visible
+  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
+  `Pull Request 8995`_
+* Add a datatype subclass for CAT (Contig Annotation Tool)
+  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
+  `Pull Request 9087`_
+* Fix cool sniffing on python3
+  `Pull Request 9153`_
+
+Builtin Tool Updates
+===========================================================
+
+.. tools
+* Upgrade askomics interactive tool
+  (thanks to `@xgaia <https://github.com/xgaia>`__).
+  `Pull Request 8517`_
+* Remove collection ID character restriction from 'Relabel collection from
+  file' tool
+  (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
+  `Pull Request 8571`_
+* Allow space, dot and comma in relabel identifier tool
+  `Pull Request 8757`_
+* Fix script shebangs
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8888`_
+* grouping: strip newlines
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 8953`_
+* Allow admins to import tools/workflows from paths.
+  `Pull Request 9003`_
+* Add requirements to interval_to_bed_converter.xml
+  `Pull Request 9041`_
+
+Release Notes
+===========================================================
+
+Please see the `full release notes <20.01_announce.html>`_ for more details.
+
+.. include:: 20.01_prs.rst
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/20.01_prs.rst b/doc/source/releases/20.01_prs.rst
new file mode 100644
index 000000000000..8911eb66e408
--- /dev/null
+++ b/doc/source/releases/20.01_prs.rst
@@ -0,0 +1,277 @@
+
+.. github_links
+.. _Pull Request 7936: https://github.com/galaxyproject/galaxy/pull/7936
+.. _Pull Request 8107: https://github.com/galaxyproject/galaxy/pull/8107
+.. _Pull Request 8508: https://github.com/galaxyproject/galaxy/pull/8508
+.. _Pull Request 8509: https://github.com/galaxyproject/galaxy/pull/8509
+.. _Pull Request 8512: https://github.com/galaxyproject/galaxy/pull/8512
+.. _Pull Request 8515: https://github.com/galaxyproject/galaxy/pull/8515
+.. _Pull Request 8517: https://github.com/galaxyproject/galaxy/pull/8517
+.. _Pull Request 8523: https://github.com/galaxyproject/galaxy/pull/8523
+.. _Pull Request 8531: https://github.com/galaxyproject/galaxy/pull/8531
+.. _Pull Request 8551: https://github.com/galaxyproject/galaxy/pull/8551
+.. _Pull Request 8571: https://github.com/galaxyproject/galaxy/pull/8571
+.. _Pull Request 8572: https://github.com/galaxyproject/galaxy/pull/8572
+.. _Pull Request 8573: https://github.com/galaxyproject/galaxy/pull/8573
+.. _Pull Request 8581: https://github.com/galaxyproject/galaxy/pull/8581
+.. _Pull Request 8600: https://github.com/galaxyproject/galaxy/pull/8600
+.. _Pull Request 8601: https://github.com/galaxyproject/galaxy/pull/8601
+.. _Pull Request 8618: https://github.com/galaxyproject/galaxy/pull/8618
+.. _Pull Request 8620: https://github.com/galaxyproject/galaxy/pull/8620
+.. _Pull Request 8625: https://github.com/galaxyproject/galaxy/pull/8625
+.. _Pull Request 8631: https://github.com/galaxyproject/galaxy/pull/8631
+.. _Pull Request 8632: https://github.com/galaxyproject/galaxy/pull/8632
+.. _Pull Request 8634: https://github.com/galaxyproject/galaxy/pull/8634
+.. _Pull Request 8639: https://github.com/galaxyproject/galaxy/pull/8639
+.. _Pull Request 8646: https://github.com/galaxyproject/galaxy/pull/8646
+.. _Pull Request 8648: https://github.com/galaxyproject/galaxy/pull/8648
+.. _Pull Request 8651: https://github.com/galaxyproject/galaxy/pull/8651
+.. _Pull Request 8652: https://github.com/galaxyproject/galaxy/pull/8652
+.. _Pull Request 8657: https://github.com/galaxyproject/galaxy/pull/8657
+.. _Pull Request 8660: https://github.com/galaxyproject/galaxy/pull/8660
+.. _Pull Request 8661: https://github.com/galaxyproject/galaxy/pull/8661
+.. _Pull Request 8662: https://github.com/galaxyproject/galaxy/pull/8662
+.. _Pull Request 8665: https://github.com/galaxyproject/galaxy/pull/8665
+.. _Pull Request 8666: https://github.com/galaxyproject/galaxy/pull/8666
+.. _Pull Request 8667: https://github.com/galaxyproject/galaxy/pull/8667
+.. _Pull Request 8676: https://github.com/galaxyproject/galaxy/pull/8676
+.. _Pull Request 8677: https://github.com/galaxyproject/galaxy/pull/8677
+.. _Pull Request 8678: https://github.com/galaxyproject/galaxy/pull/8678
+.. _Pull Request 8684: https://github.com/galaxyproject/galaxy/pull/8684
+.. _Pull Request 8685: https://github.com/galaxyproject/galaxy/pull/8685
+.. _Pull Request 8689: https://github.com/galaxyproject/galaxy/pull/8689
+.. _Pull Request 8690: https://github.com/galaxyproject/galaxy/pull/8690
+.. _Pull Request 8691: https://github.com/galaxyproject/galaxy/pull/8691
+.. _Pull Request 8692: https://github.com/galaxyproject/galaxy/pull/8692
+.. _Pull Request 8694: https://github.com/galaxyproject/galaxy/pull/8694
+.. _Pull Request 8697: https://github.com/galaxyproject/galaxy/pull/8697
+.. _Pull Request 8699: https://github.com/galaxyproject/galaxy/pull/8699
+.. _Pull Request 8700: https://github.com/galaxyproject/galaxy/pull/8700
+.. _Pull Request 8705: https://github.com/galaxyproject/galaxy/pull/8705
+.. _Pull Request 8708: https://github.com/galaxyproject/galaxy/pull/8708
+.. _Pull Request 8709: https://github.com/galaxyproject/galaxy/pull/8709
+.. _Pull Request 8712: https://github.com/galaxyproject/galaxy/pull/8712
+.. _Pull Request 8713: https://github.com/galaxyproject/galaxy/pull/8713
+.. _Pull Request 8718: https://github.com/galaxyproject/galaxy/pull/8718
+.. _Pull Request 8720: https://github.com/galaxyproject/galaxy/pull/8720
+.. _Pull Request 8722: https://github.com/galaxyproject/galaxy/pull/8722
+.. _Pull Request 8724: https://github.com/galaxyproject/galaxy/pull/8724
+.. _Pull Request 8725: https://github.com/galaxyproject/galaxy/pull/8725
+.. _Pull Request 8726: https://github.com/galaxyproject/galaxy/pull/8726
+.. _Pull Request 8728: https://github.com/galaxyproject/galaxy/pull/8728
+.. _Pull Request 8730: https://github.com/galaxyproject/galaxy/pull/8730
+.. _Pull Request 8731: https://github.com/galaxyproject/galaxy/pull/8731
+.. _Pull Request 8732: https://github.com/galaxyproject/galaxy/pull/8732
+.. _Pull Request 8734: https://github.com/galaxyproject/galaxy/pull/8734
+.. _Pull Request 8735: https://github.com/galaxyproject/galaxy/pull/8735
+.. _Pull Request 8737: https://github.com/galaxyproject/galaxy/pull/8737
+.. _Pull Request 8739: https://github.com/galaxyproject/galaxy/pull/8739
+.. _Pull Request 8741: https://github.com/galaxyproject/galaxy/pull/8741
+.. _Pull Request 8742: https://github.com/galaxyproject/galaxy/pull/8742
+.. _Pull Request 8744: https://github.com/galaxyproject/galaxy/pull/8744
+.. _Pull Request 8746: https://github.com/galaxyproject/galaxy/pull/8746
+.. _Pull Request 8749: https://github.com/galaxyproject/galaxy/pull/8749
+.. _Pull Request 8754: https://github.com/galaxyproject/galaxy/pull/8754
+.. _Pull Request 8757: https://github.com/galaxyproject/galaxy/pull/8757
+.. _Pull Request 8759: https://github.com/galaxyproject/galaxy/pull/8759
+.. _Pull Request 8762: https://github.com/galaxyproject/galaxy/pull/8762
+.. _Pull Request 8774: https://github.com/galaxyproject/galaxy/pull/8774
+.. _Pull Request 8776: https://github.com/galaxyproject/galaxy/pull/8776
+.. _Pull Request 8784: https://github.com/galaxyproject/galaxy/pull/8784
+.. _Pull Request 8785: https://github.com/galaxyproject/galaxy/pull/8785
+.. _Pull Request 8791: https://github.com/galaxyproject/galaxy/pull/8791
+.. _Pull Request 8793: https://github.com/galaxyproject/galaxy/pull/8793
+.. _Pull Request 8794: https://github.com/galaxyproject/galaxy/pull/8794
+.. _Pull Request 8799: https://github.com/galaxyproject/galaxy/pull/8799
+.. _Pull Request 8800: https://github.com/galaxyproject/galaxy/pull/8800
+.. _Pull Request 8803: https://github.com/galaxyproject/galaxy/pull/8803
+.. _Pull Request 8810: https://github.com/galaxyproject/galaxy/pull/8810
+.. _Pull Request 8813: https://github.com/galaxyproject/galaxy/pull/8813
+.. _Pull Request 8821: https://github.com/galaxyproject/galaxy/pull/8821
+.. _Pull Request 8823: https://github.com/galaxyproject/galaxy/pull/8823
+.. _Pull Request 8827: https://github.com/galaxyproject/galaxy/pull/8827
+.. _Pull Request 8836: https://github.com/galaxyproject/galaxy/pull/8836
+.. _Pull Request 8837: https://github.com/galaxyproject/galaxy/pull/8837
+.. _Pull Request 8839: https://github.com/galaxyproject/galaxy/pull/8839
+.. _Pull Request 8840: https://github.com/galaxyproject/galaxy/pull/8840
+.. _Pull Request 8843: https://github.com/galaxyproject/galaxy/pull/8843
+.. _Pull Request 8852: https://github.com/galaxyproject/galaxy/pull/8852
+.. _Pull Request 8855: https://github.com/galaxyproject/galaxy/pull/8855
+.. _Pull Request 8856: https://github.com/galaxyproject/galaxy/pull/8856
+.. _Pull Request 8857: https://github.com/galaxyproject/galaxy/pull/8857
+.. _Pull Request 8858: https://github.com/galaxyproject/galaxy/pull/8858
+.. _Pull Request 8859: https://github.com/galaxyproject/galaxy/pull/8859
+.. _Pull Request 8860: https://github.com/galaxyproject/galaxy/pull/8860
+.. _Pull Request 8862: https://github.com/galaxyproject/galaxy/pull/8862
+.. _Pull Request 8863: https://github.com/galaxyproject/galaxy/pull/8863
+.. _Pull Request 8864: https://github.com/galaxyproject/galaxy/pull/8864
+.. _Pull Request 8865: https://github.com/galaxyproject/galaxy/pull/8865
+.. _Pull Request 8866: https://github.com/galaxyproject/galaxy/pull/8866
+.. _Pull Request 8870: https://github.com/galaxyproject/galaxy/pull/8870
+.. _Pull Request 8871: https://github.com/galaxyproject/galaxy/pull/8871
+.. _Pull Request 8872: https://github.com/galaxyproject/galaxy/pull/8872
+.. _Pull Request 8873: https://github.com/galaxyproject/galaxy/pull/8873
+.. _Pull Request 8874: https://github.com/galaxyproject/galaxy/pull/8874
+.. _Pull Request 8876: https://github.com/galaxyproject/galaxy/pull/8876
+.. _Pull Request 8877: https://github.com/galaxyproject/galaxy/pull/8877
+.. _Pull Request 8882: https://github.com/galaxyproject/galaxy/pull/8882
+.. _Pull Request 8883: https://github.com/galaxyproject/galaxy/pull/8883
+.. _Pull Request 8884: https://github.com/galaxyproject/galaxy/pull/8884
+.. _Pull Request 8885: https://github.com/galaxyproject/galaxy/pull/8885
+.. _Pull Request 8888: https://github.com/galaxyproject/galaxy/pull/8888
+.. _Pull Request 8890: https://github.com/galaxyproject/galaxy/pull/8890
+.. _Pull Request 8893: https://github.com/galaxyproject/galaxy/pull/8893
+.. _Pull Request 8894: https://github.com/galaxyproject/galaxy/pull/8894
+.. _Pull Request 8900: https://github.com/galaxyproject/galaxy/pull/8900
+.. _Pull Request 8902: https://github.com/galaxyproject/galaxy/pull/8902
+.. _Pull Request 8904: https://github.com/galaxyproject/galaxy/pull/8904
+.. _Pull Request 8905: https://github.com/galaxyproject/galaxy/pull/8905
+.. _Pull Request 8907: https://github.com/galaxyproject/galaxy/pull/8907
+.. _Pull Request 8908: https://github.com/galaxyproject/galaxy/pull/8908
+.. _Pull Request 8910: https://github.com/galaxyproject/galaxy/pull/8910
+.. _Pull Request 8913: https://github.com/galaxyproject/galaxy/pull/8913
+.. _Pull Request 8914: https://github.com/galaxyproject/galaxy/pull/8914
+.. _Pull Request 8915: https://github.com/galaxyproject/galaxy/pull/8915
+.. _Pull Request 8921: https://github.com/galaxyproject/galaxy/pull/8921
+.. _Pull Request 8922: https://github.com/galaxyproject/galaxy/pull/8922
+.. _Pull Request 8924: https://github.com/galaxyproject/galaxy/pull/8924
+.. _Pull Request 8926: https://github.com/galaxyproject/galaxy/pull/8926
+.. _Pull Request 8929: https://github.com/galaxyproject/galaxy/pull/8929
+.. _Pull Request 8930: https://github.com/galaxyproject/galaxy/pull/8930
+.. _Pull Request 8931: https://github.com/galaxyproject/galaxy/pull/8931
+.. _Pull Request 8935: https://github.com/galaxyproject/galaxy/pull/8935
+.. _Pull Request 8936: https://github.com/galaxyproject/galaxy/pull/8936
+.. _Pull Request 8940: https://github.com/galaxyproject/galaxy/pull/8940
+.. _Pull Request 8941: https://github.com/galaxyproject/galaxy/pull/8941
+.. _Pull Request 8943: https://github.com/galaxyproject/galaxy/pull/8943
+.. _Pull Request 8947: https://github.com/galaxyproject/galaxy/pull/8947
+.. _Pull Request 8948: https://github.com/galaxyproject/galaxy/pull/8948
+.. _Pull Request 8949: https://github.com/galaxyproject/galaxy/pull/8949
+.. _Pull Request 8953: https://github.com/galaxyproject/galaxy/pull/8953
+.. _Pull Request 8955: https://github.com/galaxyproject/galaxy/pull/8955
+.. _Pull Request 8956: https://github.com/galaxyproject/galaxy/pull/8956
+.. _Pull Request 8957: https://github.com/galaxyproject/galaxy/pull/8957
+.. _Pull Request 8958: https://github.com/galaxyproject/galaxy/pull/8958
+.. _Pull Request 8960: https://github.com/galaxyproject/galaxy/pull/8960
+.. _Pull Request 8962: https://github.com/galaxyproject/galaxy/pull/8962
+.. _Pull Request 8964: https://github.com/galaxyproject/galaxy/pull/8964
+.. _Pull Request 8967: https://github.com/galaxyproject/galaxy/pull/8967
+.. _Pull Request 8972: https://github.com/galaxyproject/galaxy/pull/8972
+.. _Pull Request 8978: https://github.com/galaxyproject/galaxy/pull/8978
+.. _Pull Request 8979: https://github.com/galaxyproject/galaxy/pull/8979
+.. _Pull Request 8984: https://github.com/galaxyproject/galaxy/pull/8984
+.. _Pull Request 8988: https://github.com/galaxyproject/galaxy/pull/8988
+.. _Pull Request 8989: https://github.com/galaxyproject/galaxy/pull/8989
+.. _Pull Request 8990: https://github.com/galaxyproject/galaxy/pull/8990
+.. _Pull Request 8991: https://github.com/galaxyproject/galaxy/pull/8991
+.. _Pull Request 8994: https://github.com/galaxyproject/galaxy/pull/8994
+.. _Pull Request 8995: https://github.com/galaxyproject/galaxy/pull/8995
+.. _Pull Request 8997: https://github.com/galaxyproject/galaxy/pull/8997
+.. _Pull Request 9000: https://github.com/galaxyproject/galaxy/pull/9000
+.. _Pull Request 9003: https://github.com/galaxyproject/galaxy/pull/9003
+.. _Pull Request 9006: https://github.com/galaxyproject/galaxy/pull/9006
+.. _Pull Request 9009: https://github.com/galaxyproject/galaxy/pull/9009
+.. _Pull Request 9010: https://github.com/galaxyproject/galaxy/pull/9010
+.. _Pull Request 9013: https://github.com/galaxyproject/galaxy/pull/9013
+.. _Pull Request 9015: https://github.com/galaxyproject/galaxy/pull/9015
+.. _Pull Request 9016: https://github.com/galaxyproject/galaxy/pull/9016
+.. _Pull Request 9018: https://github.com/galaxyproject/galaxy/pull/9018
+.. _Pull Request 9019: https://github.com/galaxyproject/galaxy/pull/9019
+.. _Pull Request 9023: https://github.com/galaxyproject/galaxy/pull/9023
+.. _Pull Request 9026: https://github.com/galaxyproject/galaxy/pull/9026
+.. _Pull Request 9029: https://github.com/galaxyproject/galaxy/pull/9029
+.. _Pull Request 9032: https://github.com/galaxyproject/galaxy/pull/9032
+.. _Pull Request 9033: https://github.com/galaxyproject/galaxy/pull/9033
+.. _Pull Request 9034: https://github.com/galaxyproject/galaxy/pull/9034
+.. _Pull Request 9041: https://github.com/galaxyproject/galaxy/pull/9041
+.. _Pull Request 9044: https://github.com/galaxyproject/galaxy/pull/9044
+.. _Pull Request 9047: https://github.com/galaxyproject/galaxy/pull/9047
+.. _Pull Request 9048: https://github.com/galaxyproject/galaxy/pull/9048
+.. _Pull Request 9051: https://github.com/galaxyproject/galaxy/pull/9051
+.. _Pull Request 9052: https://github.com/galaxyproject/galaxy/pull/9052
+.. _Pull Request 9054: https://github.com/galaxyproject/galaxy/pull/9054
+.. _Pull Request 9055: https://github.com/galaxyproject/galaxy/pull/9055
+.. _Pull Request 9056: https://github.com/galaxyproject/galaxy/pull/9056
+.. _Pull Request 9059: https://github.com/galaxyproject/galaxy/pull/9059
+.. _Pull Request 9062: https://github.com/galaxyproject/galaxy/pull/9062
+.. _Pull Request 9063: https://github.com/galaxyproject/galaxy/pull/9063
+.. _Pull Request 9064: https://github.com/galaxyproject/galaxy/pull/9064
+.. _Pull Request 9065: https://github.com/galaxyproject/galaxy/pull/9065
+.. _Pull Request 9067: https://github.com/galaxyproject/galaxy/pull/9067
+.. _Pull Request 9068: https://github.com/galaxyproject/galaxy/pull/9068
+.. _Pull Request 9075: https://github.com/galaxyproject/galaxy/pull/9075
+.. _Pull Request 9078: https://github.com/galaxyproject/galaxy/pull/9078
+.. _Pull Request 9081: https://github.com/galaxyproject/galaxy/pull/9081
+.. _Pull Request 9082: https://github.com/galaxyproject/galaxy/pull/9082
+.. _Pull Request 9084: https://github.com/galaxyproject/galaxy/pull/9084
+.. _Pull Request 9086: https://github.com/galaxyproject/galaxy/pull/9086
+.. _Pull Request 9087: https://github.com/galaxyproject/galaxy/pull/9087
+.. _Pull Request 9089: https://github.com/galaxyproject/galaxy/pull/9089
+.. _Pull Request 9090: https://github.com/galaxyproject/galaxy/pull/9090
+.. _Pull Request 9092: https://github.com/galaxyproject/galaxy/pull/9092
+.. _Pull Request 9094: https://github.com/galaxyproject/galaxy/pull/9094
+.. _Pull Request 9097: https://github.com/galaxyproject/galaxy/pull/9097
+.. _Pull Request 9098: https://github.com/galaxyproject/galaxy/pull/9098
+.. _Pull Request 9099: https://github.com/galaxyproject/galaxy/pull/9099
+.. _Pull Request 9102: https://github.com/galaxyproject/galaxy/pull/9102
+.. _Pull Request 9104: https://github.com/galaxyproject/galaxy/pull/9104
+.. _Pull Request 9105: https://github.com/galaxyproject/galaxy/pull/9105
+.. _Pull Request 9115: https://github.com/galaxyproject/galaxy/pull/9115
+.. _Pull Request 9116: https://github.com/galaxyproject/galaxy/pull/9116
+.. _Pull Request 9117: https://github.com/galaxyproject/galaxy/pull/9117
+.. _Pull Request 9120: https://github.com/galaxyproject/galaxy/pull/9120
+.. _Pull Request 9121: https://github.com/galaxyproject/galaxy/pull/9121
+.. _Pull Request 9122: https://github.com/galaxyproject/galaxy/pull/9122
+.. _Pull Request 9124: https://github.com/galaxyproject/galaxy/pull/9124
+.. _Pull Request 9125: https://github.com/galaxyproject/galaxy/pull/9125
+.. _Pull Request 9126: https://github.com/galaxyproject/galaxy/pull/9126
+.. _Pull Request 9128: https://github.com/galaxyproject/galaxy/pull/9128
+.. _Pull Request 9132: https://github.com/galaxyproject/galaxy/pull/9132
+.. _Pull Request 9133: https://github.com/galaxyproject/galaxy/pull/9133
+.. _Pull Request 9134: https://github.com/galaxyproject/galaxy/pull/9134
+.. _Pull Request 9136: https://github.com/galaxyproject/galaxy/pull/9136
+.. _Pull Request 9137: https://github.com/galaxyproject/galaxy/pull/9137
+.. _Pull Request 9141: https://github.com/galaxyproject/galaxy/pull/9141
+.. _Pull Request 9144: https://github.com/galaxyproject/galaxy/pull/9144
+.. _Pull Request 9145: https://github.com/galaxyproject/galaxy/pull/9145
+.. _Pull Request 9146: https://github.com/galaxyproject/galaxy/pull/9146
+.. _Pull Request 9149: https://github.com/galaxyproject/galaxy/pull/9149
+.. _Pull Request 9150: https://github.com/galaxyproject/galaxy/pull/9150
+.. _Pull Request 9153: https://github.com/galaxyproject/galaxy/pull/9153
+.. _Pull Request 9155: https://github.com/galaxyproject/galaxy/pull/9155
+.. _Pull Request 9156: https://github.com/galaxyproject/galaxy/pull/9156
+.. _Pull Request 9163: https://github.com/galaxyproject/galaxy/pull/9163
+.. _Pull Request 9168: https://github.com/galaxyproject/galaxy/pull/9168
+.. _Pull Request 9171: https://github.com/galaxyproject/galaxy/pull/9171
+.. _Pull Request 9179: https://github.com/galaxyproject/galaxy/pull/9179
+.. _Pull Request 9182: https://github.com/galaxyproject/galaxy/pull/9182
+.. _Pull Request 9192: https://github.com/galaxyproject/galaxy/pull/9192
+.. _Pull Request 9193: https://github.com/galaxyproject/galaxy/pull/9193
+.. _Pull Request 9194: https://github.com/galaxyproject/galaxy/pull/9194
+.. _Pull Request 9195: https://github.com/galaxyproject/galaxy/pull/9195
+.. _Pull Request 9199: https://github.com/galaxyproject/galaxy/pull/9199
+.. _Pull Request 9202: https://github.com/galaxyproject/galaxy/pull/9202
+.. _Pull Request 9210: https://github.com/galaxyproject/galaxy/pull/9210
+.. _Pull Request 9212: https://github.com/galaxyproject/galaxy/pull/9212
+.. _Pull Request 9215: https://github.com/galaxyproject/galaxy/pull/9215
+.. _Pull Request 9216: https://github.com/galaxyproject/galaxy/pull/9216
+.. _Pull Request 9217: https://github.com/galaxyproject/galaxy/pull/9217
+.. _Pull Request 9219: https://github.com/galaxyproject/galaxy/pull/9219
+.. _Pull Request 9224: https://github.com/galaxyproject/galaxy/pull/9224
+.. _Pull Request 9225: https://github.com/galaxyproject/galaxy/pull/9225
+.. _Pull Request 9228: https://github.com/galaxyproject/galaxy/pull/9228
+.. _Pull Request 9232: https://github.com/galaxyproject/galaxy/pull/9232
+.. _Pull Request 9234: https://github.com/galaxyproject/galaxy/pull/9234
+.. _Pull Request 9237: https://github.com/galaxyproject/galaxy/pull/9237
+.. _Pull Request 9239: https://github.com/galaxyproject/galaxy/pull/9239
+.. _Pull Request 9240: https://github.com/galaxyproject/galaxy/pull/9240
+.. _Pull Request 9242: https://github.com/galaxyproject/galaxy/pull/9242
+.. _Pull Request 9243: https://github.com/galaxyproject/galaxy/pull/9243
+.. _Pull Request 9245: https://github.com/galaxyproject/galaxy/pull/9245
+.. _Pull Request 9246: https://github.com/galaxyproject/galaxy/pull/9246
+.. _Pull Request 9253: https://github.com/galaxyproject/galaxy/pull/9253
+.. _Pull Request 9260: https://github.com/galaxyproject/galaxy/pull/9260
+.. _Pull Request 9263: https://github.com/galaxyproject/galaxy/pull/9263
+.. _Pull Request 9266: https://github.com/galaxyproject/galaxy/pull/9266
+.. _Pull Request 9267: https://github.com/galaxyproject/galaxy/pull/9267
+.. _Pull Request 9269: https://github.com/galaxyproject/galaxy/pull/9269

From 8619c2d01f842c048ecee69fa295f0ec938e7f6f Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Wed, 29 Jan 2020 10:24:14 +0100
Subject: [PATCH 202/853] Update doc/source/releases/20.01_announce.rst

Co-Authored-By: Helena Rasche <hxr@hx42.org>
---
 doc/source/releases/20.01_announce.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/releases/20.01_announce.rst b/doc/source/releases/20.01_announce.rst
index 406a076c09a2..fe32dee8759a 100644
--- a/doc/source/releases/20.01_announce.rst
+++ b/doc/source/releases/20.01_announce.rst
@@ -30,7 +30,7 @@ Highlights
   scenarios.  This reduces IO load on Galaxy instances and should allow running
   many more jobs in parallel. This work will also make jobs running on remote
   compute resources much more efficient if the remote resources can write to
-  Galaxy'so object store. To benefit from this new metadata setting Galaxy needs
+  Galaxy's object store. To benefit from this new metadata setting Galaxy needs
   to use object stores that use uuids for storing datasets and set the
   ``metadata_strategy`` configuration value to ``extended``. This feature is in beta
   testing, but work is ongoing to mix existing object store configuration and

From d217b6d117dd268093a3ddd73ad956bc25b6cc95 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 29 Jan 2020 10:33:45 +0100
Subject: [PATCH 203/853] Edit to 20.01_announce.rst

---
 doc/source/releases/20.01_announce.rst | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/doc/source/releases/20.01_announce.rst b/doc/source/releases/20.01_announce.rst
index fe32dee8759a..b54341b31157 100644
--- a/doc/source/releases/20.01_announce.rst
+++ b/doc/source/releases/20.01_announce.rst
@@ -8,13 +8,13 @@ January 2020 Galaxy Release (v 20.01)
 Highlights
 ===========================================================
 
-**Enhanced workflow functionality** 
-  Workflows can now now make use of optional datasets and optional parameters,
+**Enhanced workflow functionality**
+  Workflows can now make use of optional datasets and optional parameters,
   optional parameter default values and dataset inputs can now be restricted to
   user-defined datatypes. The workflow editor and execution engine have been
   enhanced to allow defining options to choose from, and these options can be
   connected to compatible text, integer, float, color and select tool parameters
-  for more flexible and universally re-usable workflows (`Pull Request 9086`_, `Pull Request 9073`_, `Pull Request 8264`_). 
+  for more flexible and universally re-usable workflows (`Pull Request 9086`_).
 
 **Major update to container and dependency management interface**
   The manage dependencies interface has been ported to vue.js and displays
@@ -26,16 +26,15 @@ Highlights
 **Extended job metadata collection**
   Creating Job metadata has been reworked so that the dataset transfer that
   occurs after a Galaxy job can be initiated by the compute node that runs a
-  Galaxy job. Previously the transfer was done by Galaxy under many production
-  scenarios.  This reduces IO load on Galaxy instances and should allow running
-  many more jobs in parallel. This work will also make jobs running on remote
-  compute resources much more efficient if the remote resources can write to
-  Galaxy's object store. To benefit from this new metadata setting Galaxy needs
-  to use object stores that use uuids for storing datasets and set the
-  ``metadata_strategy`` configuration value to ``extended``. This feature is in beta
-  testing, but work is ongoing to mix existing object store configuration and
-  choose the most efficient way of transfering datasets automatically (`Pull
-  Request 8930`_ ).
+  Galaxy job. Previously the transfer was often done by Galaxy. Offloading this
+  task to the compute node should allow handling many more jobs in parallel. This
+  work will also make jobs running on remote compute resources much more
+  efficient if the remote resources can write to Galaxy's object store. To
+  benefit from this new metadata setting Galaxy needs to use object stores that
+  use uuids for storing datasets and set the ``metadata_strategy`` configuration
+  value to ``extended``. This feature is in beta testing, but work is ongoing to
+  mix existing object store configuration and choose the most efficient way of
+  transfering datasets automatically (`Pull Request 8930`_ ).
 
 
 Also check out the `20.01 user release notes <https://docs.galaxyproject.org/en/release_20.01/releases/20.01_announce_user.html>`__

From 722c2f251a88978828eba25a5658ae526db68110 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 4 Feb 2020 11:47:25 +0100
Subject: [PATCH 204/853] First pass at user announements

---
 doc/source/releases/20.01_announce_user.rst | 31 +++++++++++++++++----
 1 file changed, 25 insertions(+), 6 deletions(-)

diff --git a/doc/source/releases/20.01_announce_user.rst b/doc/source/releases/20.01_announce_user.rst
index c4d19b4cedd2..367b2c552d9b 100644
--- a/doc/source/releases/20.01_announce_user.rst
+++ b/doc/source/releases/20.01_announce_user.rst
@@ -8,20 +8,37 @@ January 2020 Galaxy Release (v 20.01)
 Highlights
 ===========================================================
 
-**Feature1**
-  Feature description.
+**Workflow Executions Menu**
+  This menu can be reached from the User menu -> Workflow Invocations
+  and lists your recent Workflow executions, their status and links
+  to the Workflow Editor and the History with the results of the
+  Workflow run.
 
-**Feature2**
-  Feature description.
+.. figure:: https://user-images.githubusercontent.com/216771/65520097-0a041f80-deb5-11e9-80ac-2557b36c252f.png
+   :alt: Workflow invocation menu
 
-**Feature3**
-  Feature description.
+.. figure:: https://user-images.githubusercontent.com/6804901/73737075-345ac900-4742-11ea-9f50-0f0e4c3d9271.png
+   :alt: Workflow invocatios
+
+**Galay Markdown Pages and Workflow Reports as PDF**
+  An additional link has been added to Galaxy Markdown Pahes and Workflow reports
+  that exports your document as a standalone PDF.
+
+**Screenreader-friendly Navigation**
+  The top menu and the Workflow Editor have been improved for easier navigation
+  using Screenreaders and the Keyboard.
+  Thanks goes to `@WilliamHolden  <https://github.com/WilliamHolden>`__
+
+**Email-notification for completed jobs**
+  You can now select to be notified by email when a tool run has finished.
+  Thanks goes to `@astrovsky01 <https://github.com/astrovsky01>`__
 
 
 New Visualizations
 ===========================================================
 
 .. visualizations
+
 * Add data dialog input element to client form parameter list
   `Pull Request 8774`_
 * Wrap SQL statement in a text() function as required by sqlalchemy
@@ -35,6 +52,7 @@ New Datatypes
 ===========================================================
 
 .. datatypes
+
 * Datatypes for MassSpec DIA dlib,elib
   (thanks to `@jj-umn <https://github.com/jj-umn>`__).
   `Pull Request 8657`_
@@ -63,6 +81,7 @@ Builtin Tool Updates
 ===========================================================
 
 .. tools
+
 * Upgrade askomics interactive tool
   (thanks to `@xgaia <https://github.com/xgaia>`__).
   `Pull Request 8517`_

From b76e29a267d9dec714316053b8fef54562c70dc1 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 4 Feb 2020 20:29:00 +0100
Subject: [PATCH 205/853] Add workflow report and email button screenshots

---
 doc/source/releases/20.01_announce_user.rst | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/doc/source/releases/20.01_announce_user.rst b/doc/source/releases/20.01_announce_user.rst
index 367b2c552d9b..7bbad894bdc8 100644
--- a/doc/source/releases/20.01_announce_user.rst
+++ b/doc/source/releases/20.01_announce_user.rst
@@ -24,6 +24,9 @@ Highlights
   An additional link has been added to Galaxy Markdown Pahes and Workflow reports
   that exports your document as a standalone PDF.
 
+.. figure:: https://user-images.githubusercontent.com/6804901/73776256-b7524280-4787-11ea-821f-d9a8c6339ee9.png
+   :alt: Example PDF export
+
 **Screenreader-friendly Navigation**
   The top menu and the Workflow Editor have been improved for easier navigation
   using Screenreaders and the Keyboard.
@@ -33,6 +36,8 @@ Highlights
   You can now select to be notified by email when a tool run has finished.
   Thanks goes to `@astrovsky01 <https://github.com/astrovsky01>`__
 
+.. figure:: https://user-images.githubusercontent.com/6804901/73779180-a2c47900-478c-11ea-98ab-7355276b6f6d.png
+   :alt: Example of email button
 
 New Visualizations
 ===========================================================

From 090bef14fb595fffdb69ca55621fcac487e543b6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 4 Feb 2020 21:32:35 +0100
Subject: [PATCH 206/853] Tweak image size and add 20.01_annouce to index

---
 doc/source/releases/20.01_announce_user.rst | 2 ++
 doc/source/releases/index.rst               | 1 +
 2 files changed, 3 insertions(+)

diff --git a/doc/source/releases/20.01_announce_user.rst b/doc/source/releases/20.01_announce_user.rst
index 7bbad894bdc8..c33c887f3386 100644
--- a/doc/source/releases/20.01_announce_user.rst
+++ b/doc/source/releases/20.01_announce_user.rst
@@ -16,6 +16,7 @@ Highlights
 
 .. figure:: https://user-images.githubusercontent.com/216771/65520097-0a041f80-deb5-11e9-80ac-2557b36c252f.png
    :alt: Workflow invocation menu
+   :width: 400px
 
 .. figure:: https://user-images.githubusercontent.com/6804901/73737075-345ac900-4742-11ea-9f50-0f0e4c3d9271.png
    :alt: Workflow invocatios
@@ -38,6 +39,7 @@ Highlights
 
 .. figure:: https://user-images.githubusercontent.com/6804901/73779180-a2c47900-478c-11ea-98ab-7355276b6f6d.png
    :alt: Example of email button
+   :width: 300px
 
 New Visualizations
 ===========================================================
diff --git a/doc/source/releases/index.rst b/doc/source/releases/index.rst
index 98c88cbf52a7..044163d7f083 100644
--- a/doc/source/releases/index.rst
+++ b/doc/source/releases/index.rst
@@ -4,6 +4,7 @@ Releases
 .. toctree::
    :maxdepth: 1
 
+   20.01_announce
    19.09_announce
    19.05_announce
    19.01_announce

From 3d22c726fc3c4a78ce3598da7af80b33c5b4b50d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 4 Feb 2020 21:34:11 +0100
Subject: [PATCH 207/853] Fix RST formatting

---
 doc/source/releases/20.01.rst | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
index db6791476c2a..651138e8ac47 100644
--- a/doc/source/releases/20.01.rst
+++ b/doc/source/releases/20.01.rst
@@ -13,6 +13,7 @@ Enhancements
 
 
 .. feature
+
 * CLI tools for installing/testing Docker and Singularity containers
   (thanks to `@simonbray <https://github.com/simonbray>`__).
   `Pull Request 7936`_
@@ -37,6 +38,7 @@ Enhancements
 .. enhancement_tag_viz
 
 .. enhancement_tag_datatypes
+
 * Datatypes for MassSpec DIA dlib,elib
   (thanks to `@jj-umn <https://github.com/jj-umn>`__).
   `Pull Request 8657`_
@@ -60,6 +62,7 @@ Enhancements
   `Pull Request 9087`_
 
 .. enhancement_tag_tools
+
 * Upgrade askomics interactive tool
   (thanks to `@xgaia <https://github.com/xgaia>`__).
   `Pull Request 8517`_
@@ -76,6 +79,7 @@ Enhancements
   `Pull Request 9003`_
 
 .. enhancement_tag_workflows
+
 * Interactive modification of invocation report.
   `Pull Request 8691`_
 * User-facing Workflow Invocation Grid
@@ -96,6 +100,7 @@ Enhancements
   `Pull Request 9105`_
 
 .. enhancement_tag_ui
+
 * Upgrade eslint (major version), fix compliance with new standard rules.
   `Pull Request 8708`_
 * JobMetrics.vue unit test.
@@ -109,6 +114,7 @@ Enhancements
   `Pull Request 8827`_
 
 .. enhancement_tag_jobs
+
 * Small cleanup for job runners kill
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 8523`_
@@ -130,6 +136,7 @@ Enhancements
   `Pull Request 9245`_
 
 .. enhancement_tag_admin
+
 * Add Tool Manager Component for Admin Panel
   `Pull Request 8601`_
 * Add process ID to worker_process table
@@ -137,6 +144,7 @@ Enhancements
   `Pull Request 8972`_
 
 .. enhancement
+
 * Use official "login with" buttons for OIDC
   (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 8107`_
@@ -285,6 +293,7 @@ Enhancements
   `Pull Request 9224`_
 
 .. small_enhancement
+
 * Factor out yaml read/write from config_manage.py
   `Pull Request 8509`_
 * Implementation of the workflow list as vue component
@@ -387,6 +396,7 @@ Fixes
 
 
 .. bug_tag_viz
+
 * Wrap SQL statement in a text() function as required by sqlalchemy
   (thanks to `@kaukrise <https://github.com/kaukrise>`__).
   `Pull Request 9216`_
@@ -394,30 +404,38 @@ Fixes
   (thanks to `@kaukrise <https://github.com/kaukrise>`__).
   `Pull Request 9217`_
 
+
 .. bug_tag_datatypes
+
 * Fix cool sniffing on python3
   `Pull Request 9153`_
 
+
 .. bug_tag_tools
+
 * grouping: strip newlines
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 8953`_
 * Add requirements to interval_to_bed_converter.xml
   `Pull Request 9041`_
 
+
 .. bug_tag_workflows
+
 * Exports reports with workflows (if configured).
   `Pull Request 9055`_
 * Rev gxformat2 dependency to fix various export issues.
   `Pull Request 9075`_
 
 .. bug_tag_ui
+
 * Run prettier after `#8107
   <https://github.com/galaxyproject/galaxy/issues/8107>`__
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 9102`_
 
 .. bug_tag_jobs
+
 * Small fixes for k8s.
   `Pull Request 8759`_
 * Fix output.file_path writing to read-only path on Docker
@@ -446,6 +464,7 @@ Fixes
   `Pull Request 9253`_
 
 .. bug_tag_admin
+
 * Encode lines in filter_file_fields
   (thanks to `@selten <https://github.com/selten>`__).
   `Pull Request 8652`_
@@ -459,6 +478,7 @@ Fixes
   `Pull Request 9193`_
 
 .. bug
+
 * Documentation update
   (thanks to `@selten <https://github.com/selten>`__).
   `Pull Request 8508`_

From 6b304586c46e7382903e04d7b3e1bbacc83392af Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 4 Feb 2020 22:04:31 +0100
Subject: [PATCH 208/853] Fix missing newline after section

---
 scripts/bootstrap_history.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index 4440138f7b87..dde83dd5c605 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -713,6 +713,8 @@ def _text_target(github, pull_request, labels=None):
     else:
         print("Logic problem, cannot determine section for %s" % _pr_to_str(pull_request))
         text_target = None
+    if text_target:
+        text_target += "\n"
     return text_target
 
 
@@ -775,7 +777,7 @@ def wrap(message):
     message = process_sentence(message)
     wrapper = textwrap.TextWrapper(initial_indent="* ")
     wrapper.subsequent_indent = '  '
-    wrapper.width = 78
+    wrapper.width = 160
     message_lines = message.splitlines()
     first_lines = "\n".join(wrapper.wrap(message_lines[0]))
     wrapper.initial_indent = "  "

From fe68dede4dc5c0dfa83722236d6df995713df432 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 11 Feb 2020 19:39:46 +0100
Subject: [PATCH 209/853] Pahes typo

---
 doc/source/releases/20.01_announce_user.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/releases/20.01_announce_user.rst b/doc/source/releases/20.01_announce_user.rst
index c33c887f3386..5d5dbda7235c 100644
--- a/doc/source/releases/20.01_announce_user.rst
+++ b/doc/source/releases/20.01_announce_user.rst
@@ -22,7 +22,7 @@ Highlights
    :alt: Workflow invocatios
 
 **Galay Markdown Pages and Workflow Reports as PDF**
-  An additional link has been added to Galaxy Markdown Pahes and Workflow reports
+  An additional link has been added to Galaxy Markdown Pages and Workflow reports
   that exports your document as a standalone PDF.
 
 .. figure:: https://user-images.githubusercontent.com/6804901/73776256-b7524280-4787-11ea-821f-d9a8c6339ee9.png

From 07a69221059064b964e48c040ac265b0bcd1223d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 21 Feb 2020 17:57:08 +0100
Subject: [PATCH 210/853] Update with new 20.01 PRs

---
 doc/source/releases/20.01.rst               | 139 ++++++++++++++++----
 doc/source/releases/20.01_announce_user.rst |  23 +++-
 doc/source/releases/20.01_prs.rst           |  51 +++++++
 3 files changed, 183 insertions(+), 30 deletions(-)

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
index 651138e8ac47..3aed23a42705 100644
--- a/doc/source/releases/20.01.rst
+++ b/doc/source/releases/20.01.rst
@@ -34,9 +34,15 @@ Enhancements
   `Pull Request 9062`_
 * IT fixes and 3 new ITs
   `Pull Request 9141`_
+* Remove GenomeSpace tools, OpenID, UI and requirements
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9363`_
 
 .. enhancement_tag_viz
 
+* Hyphy-vision fixes and updates.
+  `Pull Request 9384`_
+
 .. enhancement_tag_datatypes
 
 * Datatypes for MassSpec DIA dlib,elib
@@ -51,7 +57,7 @@ Enhancements
 * Add new GROMACS datatypes: ndx, xvg, edr
   (thanks to `@simonbray <https://github.com/simonbray>`__).
   `Pull Request 8964`_
-* add gff3.gz and gff3.bz2 datatypes
+* Add gff3.gz and gff3.bz2 datatypes
   (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
   `Pull Request 8967`_
 * Make mol2 visible
@@ -60,14 +66,15 @@ Enhancements
 * Add a datatype subclass for CAT (Contig Annotation Tool)
   (thanks to `@jj-umn <https://github.com/jj-umn>`__).
   `Pull Request 9087`_
+* Add tabular.gz datatype and add embl to uploadable formats
+  `Pull Request 9293`_
 
 .. enhancement_tag_tools
 
 * Upgrade askomics interactive tool
   (thanks to `@xgaia <https://github.com/xgaia>`__).
   `Pull Request 8517`_
-* Remove collection ID character restriction from 'Relabel collection from
-  file' tool
+* Remove collection ID character restriction from 'Relabel collection from file' tool
   (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
   `Pull Request 8571`_
 * Allow space, dot and comma in relabel identifier tool
@@ -77,6 +84,8 @@ Enhancements
   `Pull Request 8888`_
 * Allow admins to import tools/workflows from paths.
   `Pull Request 9003`_
+* Move sam_pileup to GALAXY_LIB_TOOLS_VERSIONED
+  `Pull Request 9320`_
 
 .. enhancement_tag_workflows
 
@@ -105,8 +114,7 @@ Enhancements
   `Pull Request 8708`_
 * JobMetrics.vue unit test.
   `Pull Request 8732`_
-* Fix the flexible Data Dialog to work independent of the page layout
-  initialization hooks.
+* Fix the flexible Data Dialog to work independent of the page layout initialization hooks.
   `Pull Request 8744`_
 * axios-mock-adapter for cleaner, more expansive testing
   `Pull Request 8749`_
@@ -134,6 +142,10 @@ Enhancements
   `Pull Request 8997`_
 * Fix deletion of outputs and working before job
   `Pull Request 9245`_
+* Mount tool_data_path (ro) when running containerized tools
+  `Pull Request 9314`_
+* Allow remote jobs to configure Interactive Tool entry points.
+  `Pull Request 9349`_
 
 .. enhancement_tag_admin
 
@@ -147,7 +159,7 @@ Enhancements
 
 * Use official "login with" buttons for OIDC
   (thanks to `@hexylena <https://github.com/hexylena>`__).
-  `Pull Request 8107`_
+  `Pull Request 8107`_, `Pull Request 9102`_
 * Add data types to docs.galaxyproject.org
   (thanks to `@selten <https://github.com/selten>`__).
   `Pull Request 8531`_
@@ -178,8 +190,7 @@ Enhancements
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 8690`_
 * LDAP search member of filter
-  (thanks to `@BioinformaticsPlatformWIV-ISP
-  <https://github.com/BioinformaticsPlatformWIV-ISP>`__).
+  (thanks to `@BioinformaticsPlatformWIV-ISP <https://github.com/BioinformaticsPlatformWIV-ISP>`__).
   `Pull Request 8697`_
 * Rebuild and prettify config sample and doc
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -280,6 +291,8 @@ Enhancements
   `Pull Request 9128`_
 * mulled: use threading.Event in PrintProgress to avoid unnecessary wai…
   `Pull Request 9163`_
+* Set Conda environment variables  when running biocontainers
+  `Pull Request 9170`_
 * Update my username
   (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 9195`_
@@ -291,6 +304,10 @@ Enhancements
   `Pull Request 9210`_
 * Extended base annotation fixes
   `Pull Request 9224`_
+* External auth login refinement
+  `Pull Request 9233`_
+* Fixes for IGV GEDA handling of genomes
+  `Pull Request 9413`_
 
 .. small_enhancement
 
@@ -386,7 +403,10 @@ Enhancements
 * Update github username @erasche to @hexylena and correct inconsistencies
   (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 9194`_
-
+* Add requirements, fix legacy tools and move them out of GALAXY_LIB_TOOLS_UNVERSIONED
+  `Pull Request 9336`_
+* Add requirements to (almost) all converters, profile and minor fixes
+  `Pull Request 9345`_
 
 
 Fixes
@@ -403,14 +423,14 @@ Fixes
 * Ensure visible overflow on navbar container
   (thanks to `@kaukrise <https://github.com/kaukrise>`__).
   `Pull Request 9217`_
-
+* Various python 3 fixes from sentry
+  `Pull Request 9337`_
 
 .. bug_tag_datatypes
 
 * Fix cool sniffing on python3
   `Pull Request 9153`_
 
-
 .. bug_tag_tools
 
 * grouping: strip newlines
@@ -418,7 +438,13 @@ Fixes
   `Pull Request 8953`_
 * Add requirements to interval_to_bed_converter.xml
   `Pull Request 9041`_
-
+* Fix version in which ``sam_pileup`` was fixed
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9350`_
+* Expunge tool shed repository objects, prevents ParentInstanceDetachedError
+  `Pull Request 9354`_
+* Fix maf tools
+  `Pull Request 9393`_
 
 .. bug_tag_workflows
 
@@ -426,13 +452,10 @@ Fixes
   `Pull Request 9055`_
 * Rev gxformat2 dependency to fix various export issues.
   `Pull Request 9075`_
-
-.. bug_tag_ui
-
-* Run prettier after `#8107
-  <https://github.com/galaxyproject/galaxy/issues/8107>`__
-  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
-  `Pull Request 9102`_
+* Fix workflow editor save as functionality
+  `Pull Request 9315`_
+* Various fixes and enhancements to reports
+  `Pull Request 9316`_
 
 .. bug_tag_jobs
 
@@ -462,6 +485,13 @@ Fixes
 * fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 9253`_
+* Email notifications aren't used from just workflow steps anymore.
+  `Pull Request 9276`_
+* Use requests for slots instead of limit
+  (thanks to `@nuwang <https://github.com/nuwang>`__).
+  `Pull Request 9322`_
+* Make set metadata exec after process more robust
+  `Pull Request 9395`_
 
 .. bug_tag_admin
 
@@ -473,9 +503,10 @@ Fixes
   `Pull Request 8900`_
 * Assorted admin panel fixes
   `Pull Request 9097`_
-* Run integration tests on github, fix various bugs (interactive tools,
-  kubernetes, test framework)
+* Run integration tests on github, fix various bugs (interactive tools, kubernetes, test framework)
   `Pull Request 9193`_
+* Always add shed_tool_config file to tool_configs
+  `Pull Request 9364`_
 
 .. bug
 
@@ -510,8 +541,7 @@ Fixes
 * GRT: Ensure correct encoding, no partial lines
   (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 8712`_
-* Revise toolshed config dependency check error message in repository install
-  manager
+* Revise toolshed config dependency check error message in repository install manager
   `Pull Request 8720`_
 * Fix data dialog height, modal test case and table slots
   `Pull Request 8724`_
@@ -559,8 +589,7 @@ Fixes
 * make pgcleanup also delete HDAs
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 8908`_
-* Fix unbounded variable error in `GET /api/datasets/{encoded_dataset_id}`
-  exception handling
+* Fix unbounded variable error in `GET /api/datasets/{encoded_dataset_id}` exception handling
   `Pull Request 8935`_
 * Set `deleted` attribute of history datasets when purging histories from grid
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -642,8 +671,7 @@ Fixes
   `Pull Request 9168`_
 * Add static-safe mapping to config management
   `Pull Request 9179`_
-* Fix tool shed tests for `#9168
-  <https://github.com/galaxyproject/galaxy/issues/9168>`__.
+* Fix tool shed tests for `#9168 <https://github.com/galaxyproject/galaxy/issues/9168>`__.
   `Pull Request 9182`_
 * Add require_login bypass for entire authnz controller.
   `Pull Request 9192`_
@@ -669,7 +697,62 @@ Fixes
   `Pull Request 9267`_
 * backport 9268: Fix target_str_to_targets
   `Pull Request 9269`_
-
+* Backwards compatible build number parsing
+  `Pull Request 9278`_
+* Tag display fixes for ui-select.
+  `Pull Request 9281`_
+* Python3: don't check for has_key attribute
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9290`_
+* Prevent caching of bootstrapped client data
+  `Pull Request 9294`_
+* Add build_sites_config_file option to config_schema
+  `Pull Request 9297`_
+* Backport reports config/py3 fix
+  `Pull Request 9309`_
+* Python3: unicodify the output of ``subprocess.check_output()``
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9319`_
+* Fix reports disk usage query for python 3
+  `Pull Request 9321`_
+* Fix string module use
+  `Pull Request 9327`_
+* Fix Python 3 error in containers lib
+  `Pull Request 9329`_
+* Fix use of next() as a meethod instead of a function
+  `Pull Request 9330`_
+* Automatically resolve and add static-safe mappings for client-based images
+  `Pull Request 9331`_
+* Various doc fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9334`_
+* Fix app reference in guess_shed_config
+  `Pull Request 9339`_
+* Make linters more robust on python 3
+  `Pull Request 9348`_
+* Use RenamedTemporaryFile for safer integrated_tool_panel_file writing
+  `Pull Request 9359`_
+* Only get non-deleted datasets when listing custom dbkeys
+  `Pull Request 9360`_
+* Prevent duplicate listing of doi link and link (text, with href doi link)
+  `Pull Request 9366`_
+* Styleguide fixes
+  `Pull Request 9367`_
+* Prevent tool execution getting stuck in history when a chromInfo data…
+  `Pull Request 9385`_
+* Move migrated_tools_conf > mutable_config_dir (`#9376 <https://github.com/galaxyproject/galaxy/issues/9376>`__)
+  `Pull Request 9388`_
+* Fix dependency for CONVERTER_tar_to_directory
+  `Pull Request 9389`_
+* Fix for qp method used in GEDAs.
+  `Pull Request 9391`_
+* Fix hid comparison failing with hdas without hid
+  `Pull Request 9398`_
+* Don't raise exception if anon goes to <galaxy_url>/user/resend_verification
+  `Pull Request 9404`_
+* Update bleach to 3.1.1
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9408`_
 
 .. include:: 20.01_prs.rst
 
diff --git a/doc/source/releases/20.01_announce_user.rst b/doc/source/releases/20.01_announce_user.rst
index 5d5dbda7235c..62da797d5e95 100644
--- a/doc/source/releases/20.01_announce_user.rst
+++ b/doc/source/releases/20.01_announce_user.rst
@@ -83,6 +83,8 @@ New Datatypes
   `Pull Request 9087`_
 * Fix cool sniffing on python3
   `Pull Request 9153`_
+* Allow tabular.gz / add embl to uploadable formats
+  `Pull Request 9293`_
 
 Builtin Tool Updates
 ===========================================================
@@ -92,8 +94,7 @@ Builtin Tool Updates
 * Upgrade askomics interactive tool
   (thanks to `@xgaia <https://github.com/xgaia>`__).
   `Pull Request 8517`_
-* Remove collection ID character restriction from 'Relabel collection from
-  file' tool
+* Remove collection ID character restriction from 'Relabel collection from file' tool
   (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
   `Pull Request 8571`_
 * Allow space, dot and comma in relabel identifier tool
@@ -108,6 +109,24 @@ Builtin Tool Updates
   `Pull Request 9003`_
 * Add requirements to interval_to_bed_converter.xml
   `Pull Request 9041`_
+* Move sam_pileup to GALAXY_LIB_TOOLS_VERSIONED
+  `Pull Request 9320`_
+* Add requirements, fix legacy tools and move them out of GALAXY_LIB_TOOLS_UNVERSIONED
+  `Pull Request 9336`_
+* Add requirements to (almost) all converters, profile and minor fixes
+  `Pull Request 9345`_
+* Fix version in which ``sam_pileup`` was fixed
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9350`_
+* Expunge tool shed repository objects, prevents ParentInstanceDetachedError
+  `Pull Request 9354`_
+* Remove GenomeSpace tools, OpenID, UI and requirements
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9363`_
+* Fix maf tools
+  `Pull Request 9393`_
+* XML fix for joiner.xml.
+  `Pull Request 9399`_
 
 Release Notes
 ===========================================================
diff --git a/doc/source/releases/20.01_prs.rst b/doc/source/releases/20.01_prs.rst
index 8911eb66e408..93605645687f 100644
--- a/doc/source/releases/20.01_prs.rst
+++ b/doc/source/releases/20.01_prs.rst
@@ -242,6 +242,7 @@
 .. _Pull Request 9156: https://github.com/galaxyproject/galaxy/pull/9156
 .. _Pull Request 9163: https://github.com/galaxyproject/galaxy/pull/9163
 .. _Pull Request 9168: https://github.com/galaxyproject/galaxy/pull/9168
+.. _Pull Request 9170: https://github.com/galaxyproject/galaxy/pull/9170
 .. _Pull Request 9171: https://github.com/galaxyproject/galaxy/pull/9171
 .. _Pull Request 9179: https://github.com/galaxyproject/galaxy/pull/9179
 .. _Pull Request 9182: https://github.com/galaxyproject/galaxy/pull/9182
@@ -261,6 +262,7 @@
 .. _Pull Request 9225: https://github.com/galaxyproject/galaxy/pull/9225
 .. _Pull Request 9228: https://github.com/galaxyproject/galaxy/pull/9228
 .. _Pull Request 9232: https://github.com/galaxyproject/galaxy/pull/9232
+.. _Pull Request 9233: https://github.com/galaxyproject/galaxy/pull/9233
 .. _Pull Request 9234: https://github.com/galaxyproject/galaxy/pull/9234
 .. _Pull Request 9237: https://github.com/galaxyproject/galaxy/pull/9237
 .. _Pull Request 9239: https://github.com/galaxyproject/galaxy/pull/9239
@@ -275,3 +277,52 @@
 .. _Pull Request 9266: https://github.com/galaxyproject/galaxy/pull/9266
 .. _Pull Request 9267: https://github.com/galaxyproject/galaxy/pull/9267
 .. _Pull Request 9269: https://github.com/galaxyproject/galaxy/pull/9269
+.. _Pull Request 9276: https://github.com/galaxyproject/galaxy/pull/9276
+.. _Pull Request 9278: https://github.com/galaxyproject/galaxy/pull/9278
+.. _Pull Request 9281: https://github.com/galaxyproject/galaxy/pull/9281
+.. _Pull Request 9290: https://github.com/galaxyproject/galaxy/pull/9290
+.. _Pull Request 9293: https://github.com/galaxyproject/galaxy/pull/9293
+.. _Pull Request 9294: https://github.com/galaxyproject/galaxy/pull/9294
+.. _Pull Request 9297: https://github.com/galaxyproject/galaxy/pull/9297
+.. _Pull Request 9309: https://github.com/galaxyproject/galaxy/pull/9309
+.. _Pull Request 9314: https://github.com/galaxyproject/galaxy/pull/9314
+.. _Pull Request 9315: https://github.com/galaxyproject/galaxy/pull/9315
+.. _Pull Request 9316: https://github.com/galaxyproject/galaxy/pull/9316
+.. _Pull Request 9319: https://github.com/galaxyproject/galaxy/pull/9319
+.. _Pull Request 9320: https://github.com/galaxyproject/galaxy/pull/9320
+.. _Pull Request 9321: https://github.com/galaxyproject/galaxy/pull/9321
+.. _Pull Request 9322: https://github.com/galaxyproject/galaxy/pull/9322
+.. _Pull Request 9327: https://github.com/galaxyproject/galaxy/pull/9327
+.. _Pull Request 9329: https://github.com/galaxyproject/galaxy/pull/9329
+.. _Pull Request 9330: https://github.com/galaxyproject/galaxy/pull/9330
+.. _Pull Request 9331: https://github.com/galaxyproject/galaxy/pull/9331
+.. _Pull Request 9334: https://github.com/galaxyproject/galaxy/pull/9334
+.. _Pull Request 9336: https://github.com/galaxyproject/galaxy/pull/9336
+.. _Pull Request 9337: https://github.com/galaxyproject/galaxy/pull/9337
+.. _Pull Request 9339: https://github.com/galaxyproject/galaxy/pull/9339
+.. _Pull Request 9345: https://github.com/galaxyproject/galaxy/pull/9345
+.. _Pull Request 9348: https://github.com/galaxyproject/galaxy/pull/9348
+.. _Pull Request 9349: https://github.com/galaxyproject/galaxy/pull/9349
+.. _Pull Request 9350: https://github.com/galaxyproject/galaxy/pull/9350
+.. _Pull Request 9354: https://github.com/galaxyproject/galaxy/pull/9354
+.. _Pull Request 9359: https://github.com/galaxyproject/galaxy/pull/9359
+.. _Pull Request 9360: https://github.com/galaxyproject/galaxy/pull/9360
+.. _Pull Request 9363: https://github.com/galaxyproject/galaxy/pull/9363
+.. _Pull Request 9364: https://github.com/galaxyproject/galaxy/pull/9364
+.. _Pull Request 9366: https://github.com/galaxyproject/galaxy/pull/9366
+.. _Pull Request 9367: https://github.com/galaxyproject/galaxy/pull/9367
+.. _Pull Request 9375: https://github.com/galaxyproject/galaxy/pull/9375
+.. _Pull Request 9384: https://github.com/galaxyproject/galaxy/pull/9384
+.. _Pull Request 9385: https://github.com/galaxyproject/galaxy/pull/9385
+.. _Pull Request 9388: https://github.com/galaxyproject/galaxy/pull/9388
+.. _Pull Request 9389: https://github.com/galaxyproject/galaxy/pull/9389
+.. _Pull Request 9391: https://github.com/galaxyproject/galaxy/pull/9391
+.. _Pull Request 9393: https://github.com/galaxyproject/galaxy/pull/9393
+.. _Pull Request 9395: https://github.com/galaxyproject/galaxy/pull/9395
+.. _Pull Request 9397: https://github.com/galaxyproject/galaxy/pull/9397
+.. _Pull Request 9398: https://github.com/galaxyproject/galaxy/pull/9398
+.. _Pull Request 9399: https://github.com/galaxyproject/galaxy/pull/9399
+.. _Pull Request 9400: https://github.com/galaxyproject/galaxy/pull/9400
+.. _Pull Request 9404: https://github.com/galaxyproject/galaxy/pull/9404
+.. _Pull Request 9408: https://github.com/galaxyproject/galaxy/pull/9408
+.. _Pull Request 9413: https://github.com/galaxyproject/galaxy/pull/9413

From 4f8ce5ecbf5cfc7b44e7f1938dbe8d8b98160e63 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 26 Feb 2020 10:22:30 +0100
Subject: [PATCH 211/853] use TextIOWrapper instead of decode

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/datatypes/binary.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index f9193e864320..0a03fca23e02 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -2111,8 +2111,7 @@ def set_meta(self, dataset, overwrite=True, **kwd):
                 with zipfile.ZipFile(dataset.file_name) as tempzip:
                     if 'searchgui.properties' in tempzip.namelist():
                         with tempzip.open('searchgui.properties') as fh:
-                            for line in fh:
-                                line = line.decode()
+                            for line in io.TextIOWrapper(fh):
                                 if line.startswith('searchgui.version'):
                                     version = line.split('=')[1].strip()
                                     dataset.metadata.searchgui_version = version

From 05d5fd1da84de9d357e38b797d44d3a57c75b836 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 10:21:46 +0100
Subject: [PATCH 212/853] Update with latest PRs

---
 doc/source/releases/20.01.rst     | 28 ++++++++++++++++++++++++++++
 doc/source/releases/20.01_prs.rst | 13 +++++++++++++
 2 files changed, 41 insertions(+)

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
index 3aed23a42705..6f4f15389891 100644
--- a/doc/source/releases/20.01.rst
+++ b/doc/source/releases/20.01.rst
@@ -492,6 +492,10 @@ Fixes
   `Pull Request 9322`_
 * Make set metadata exec after process more robust
   `Pull Request 9395`_
+* Make dataset discovery respect final_job_state
+  `Pull Request 9406`_
+* Strip unicode null characters from traceback and job_messages
+  `Pull Request 9430`_
 
 .. bug_tag_admin
 
@@ -753,6 +757,30 @@ Fixes
 * Update bleach to 3.1.1
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 9408`_
+* Fix shed image resolution
+  `Pull Request 9411`_
+* Fixes for get_estimated_display_viewport
+  `Pull Request 9415`_
+* Fix wrong map use in many places
+  `Pull Request 9416`_
+* Conda startup fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9421`_
+* fix two cases of opening a file binary
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 9424`_
+* Remove '.sample' from default value; rebuild schema
+  `Pull Request 9427`_
+* Fix login to accounts using different email capitalization
+  `Pull Request 9432`_
+* Fix TwoBitFile handle not opened in binary mode
+  `Pull Request 9433`_
+* Fix uploading workflow archives
+  `Pull Request 9434`_
+* Fix to_dict for upload1 tool
+  `Pull Request 9441`_
+* Fix data tables vue display
+  `Pull Request 9442`_
 
 .. include:: 20.01_prs.rst
 
diff --git a/doc/source/releases/20.01_prs.rst b/doc/source/releases/20.01_prs.rst
index 93605645687f..b59e8a524b59 100644
--- a/doc/source/releases/20.01_prs.rst
+++ b/doc/source/releases/20.01_prs.rst
@@ -324,5 +324,18 @@
 .. _Pull Request 9399: https://github.com/galaxyproject/galaxy/pull/9399
 .. _Pull Request 9400: https://github.com/galaxyproject/galaxy/pull/9400
 .. _Pull Request 9404: https://github.com/galaxyproject/galaxy/pull/9404
+.. _Pull Request 9406: https://github.com/galaxyproject/galaxy/pull/9406
 .. _Pull Request 9408: https://github.com/galaxyproject/galaxy/pull/9408
+.. _Pull Request 9411: https://github.com/galaxyproject/galaxy/pull/9411
 .. _Pull Request 9413: https://github.com/galaxyproject/galaxy/pull/9413
+.. _Pull Request 9415: https://github.com/galaxyproject/galaxy/pull/9415
+.. _Pull Request 9416: https://github.com/galaxyproject/galaxy/pull/9416
+.. _Pull Request 9421: https://github.com/galaxyproject/galaxy/pull/9421
+.. _Pull Request 9424: https://github.com/galaxyproject/galaxy/pull/9424
+.. _Pull Request 9427: https://github.com/galaxyproject/galaxy/pull/9427
+.. _Pull Request 9430: https://github.com/galaxyproject/galaxy/pull/9430
+.. _Pull Request 9432: https://github.com/galaxyproject/galaxy/pull/9432
+.. _Pull Request 9433: https://github.com/galaxyproject/galaxy/pull/9433
+.. _Pull Request 9434: https://github.com/galaxyproject/galaxy/pull/9434
+.. _Pull Request 9441: https://github.com/galaxyproject/galaxy/pull/9441
+.. _Pull Request 9442: https://github.com/galaxyproject/galaxy/pull/9442

From 9748452b1b5321c533db81832fa8dde4dc569306 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 10:24:49 +0100
Subject: [PATCH 213/853] Merge followup PR into original announcement

---
 doc/source/releases/20.01.rst | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
index 6f4f15389891..c20608d61f13 100644
--- a/doc/source/releases/20.01.rst
+++ b/doc/source/releases/20.01.rst
@@ -481,10 +481,7 @@ Fixes
   `Pull Request 9243`_
 * python3 fixes for setups using drmaa and realuser setups
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
-  `Pull Request 9246`_
-* fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246
-  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
-  `Pull Request 9253`_
+  `Pull Request 9246`_, `Pull Request 9253`_
 * Email notifications aren't used from just workflow steps anymore.
   `Pull Request 9276`_
 * Use requests for slots instead of limit

From 28aaa8834445071096635bb378d6ae79e5856c6b Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 26 Feb 2020 10:37:01 +0100
Subject: [PATCH 214/853] apply int to default also in yaml parser

---
 lib/galaxy/tool_util/parser/yaml.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index ce2a910c4d03..bcdd9528c9b0 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -218,7 +218,7 @@ def _parse_test(i, test_dict):
         defaults = {
             'compare': 'diff',
             'lines_diff': 0,
-            'delta': DEFAULT_DELTA,
+            'delta': int(DEFAULT_DELTA),
             'sort': False,
         }
         # TODO

From 7624a4dc663c0d31d4017c6b4477e242c5cf3509 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 26 Feb 2020 10:52:11 +0100
Subject: [PATCH 215/853] add missing import

---
 lib/galaxy/datatypes/binary.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 0a03fca23e02..33cb382d87b3 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -3,6 +3,7 @@
 
 import binascii
 import gzip
+import io
 import logging
 import os
 import shutil

From 765f59175c3b3bdb1d83a1d1cdf824f3d522b96d Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 7 Feb 2020 20:01:42 +0000
Subject: [PATCH 216/853] Create Python3 virtualenv by default

- Allow specifying Python to use to create virtualenv using GALAXY_PYTHON
  environment variable.
- Integrate Python support docs from https://galaxyproject.org/admin/python/
- Update virtualenv installation to use v16.7.9
---
 .circleci/config.yml                        | 12 +++----
 doc/source/admin/framework_dependencies.rst |  2 +-
 doc/source/admin/index.rst                  |  9 ++---
 doc/source/admin/python.md                  | 37 +++++++++++++++++++++
 run_tests.sh                                |  3 +-
 scripts/check_python.py                     | 26 ++++++++++-----
 scripts/common_startup.sh                   | 23 ++++++++-----
 tox.ini                                     | 12 +++----
 8 files changed, 85 insertions(+), 39 deletions(-)
 create mode 100644 doc/source/admin/python.md

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 833e897606c3..7904c41fac37 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -97,24 +97,20 @@ jobs:
       - *restore_repo_cache
       - *install_tox
       - run: tox -e py27-unit
-  py27_docstring:
+  py35_docstring:
     docker:
-      - image: circleci/python:2.7
+      - image: circleci/python:3.5
     <<: *set_workdir
     steps:
       - *restore_repo_cache
       - *install_tox
-      - run: tox -e py27-lint_docstring_include_list
+      - run: tox -e py35-lint_docstring_include_list
   py27_first_startup:
     docker:
       - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
-      - run: sh scripts/common_startup.sh
-      - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite
-      - run: mv db_gx_rev_0127.sqlite database/universe.sqlite
-      - run: sh manage_db.sh -c ./config/galaxy.yml.sample upgrade
       - *install_tox
       - run: tox -e py27-first_startup
   py35_lint:
@@ -200,7 +196,7 @@ workflows:
           <<: *requires_get_code
       - py27_first_startup:
           <<: *requires_get_code
-      - py27_docstring:
+      - py35_docstring:
           <<: *requires_get_code
       - py35_lint:
           <<: *requires_get_code
diff --git a/doc/source/admin/framework_dependencies.rst b/doc/source/admin/framework_dependencies.rst
index fa1c0e9f8f66..8d7bb7aafcb6 100644
--- a/doc/source/admin/framework_dependencies.rst
+++ b/doc/source/admin/framework_dependencies.rst
@@ -181,7 +181,7 @@ Galaxy can create a virtualenv using the adapted virtualenv package. Once a vali
         3. Start galaxy using ``sh run.sh`` or execute ``sh scripts/common_startup.sh``.
 
 
-    A Conda environment named ``_galaxy_`` will be created using python 2 and the appropriate virtualenv package will be installed into this environment.
+    A Conda environment named ``_galaxy_`` will be created and the appropriate virtualenv package will be installed into this environment.
     Using this environment a ``.venv`` is initialized. This is a one-time setup, and all other activation and dependency
     management happens exactly as if a system Python was used for creating ``.venv``.
 
diff --git a/doc/source/admin/index.rst b/doc/source/admin/index.rst
index e667df8cabe1..690774a1e662 100644
--- a/doc/source/admin/index.rst
+++ b/doc/source/admin/index.rst
@@ -6,19 +6,20 @@ This documentation is in the midst of being ported and unified based on resource
 .. toctree::
    :maxdepth: 2
 
+   python
+   framework_dependencies
    config
    config_logging
    production
-   scaling
    nginx
    apache
+   scaling
    cluster
    jobs
-   tool_panel
    authentication
+   tool_panel
    dependency_resolvers
    conda_faq
-   framework_dependencies
-   options
    reports
    useful_scripts
+   options
diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md
new file mode 100644
index 000000000000..018bff5319ab
--- /dev/null
+++ b/doc/source/admin/python.md
@@ -0,0 +1,37 @@
+# Supported Python versions
+
+Galaxy's core functionality is currently supported on Python **2.7** (although
+deprecated) and **>=3.5** .
+
+If Galaxy complains about the version of Python you are using, check that
+`python --version` reports a supported version. If this is not the case:
+
+1. Completely remove the virtualenv used by Galaxy, e.g. with:
+   `rm -rf /path/to/galaxy/.venv`
+
+2. Let Galaxy know the path of the correct version of Python.
+
+    - If you are using Galaxy >= 20.05, just execute:
+      `export GALAXY_PYTHON=/path/to/python`
+    - If instead you are using an older version of Galaxy, you can manipulate
+      your shell's `$PATH` variable to place the correct version first. This can
+      be done for just Python by creating a new directory, adding a symbolic
+      link to python in there, and putting that directory at the front of
+      `$PATH`:
+
+        ```sh
+        % mkdir ~/galaxy-python
+        % ln -s /path/to/python ~/galaxy-python/python
+        % export PATH=~/galaxy-python:$PATH
+        ```
+
+3. Start Galaxy again.
+
+N.B. If you have compiled your own Python interpreter from source, please ensure
+that the `ssl`, `sqlite3`, `curses` and `bz2` modules were built and can be
+imported after installation. These "extra" modules are built at the end of the
+compilation process and are required by the Galaxy framework. If building on
+Linux, you may need to install the appropriate `-dev` packages for OpenSSL and
+Bzip2. You may also need to build Python with shared libraries
+(`--enable-shared`).
+
diff --git a/run_tests.sh b/run_tests.sh
index 77c7871043c8..7e6bdb798f2b 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -1,4 +1,3 @@
-
 #!/bin/sh
 
 cd "$(dirname "$0")"
@@ -313,7 +312,7 @@ then
     echo "Docker version:"
     docker --version
     echo "Launching docker container for testing with extra args ${DOCKER_RUN_EXTRA_ARGS}..."
-    name=$(python -c 'import re; import uuid; print re.sub("-","",str(uuid.uuid4()))')
+    name=$(python -c 'import re; import uuid; print re.sub("-", "", str(uuid.uuid4()))')
     # Create a cache dir for pip, so it has the right owner
     DOCKER_PIP_CACHE_DIR="$HOME"/.cache/docker_galaxy_pip
     mkdir -p "$DOCKER_PIP_CACHE_DIR"
diff --git a/scripts/check_python.py b/scripts/check_python.py
index 2a5175e29e65..adccedf27b0b 100644
--- a/scripts/check_python.py
+++ b/scripts/check_python.py
@@ -6,20 +6,28 @@
 
 import sys
 
-version_string = '.'.join(str(_) for _ in sys.version_info[:3])
-
-msg = """ERROR: Your Python version is: %s
-Galaxy is currently supported on Python 2.7 and >=3.5 . To run Galaxy, please
-install a supported Python version. If a supported version is already
-installed but is not your default, https://galaxyproject.org/admin/python/
-contains instructions on how to force Galaxy to use a different version.""" % version_string
-
 
 def check_python():
-    if sys.version_info[:2] == (2, 7) or sys.version_info[:2] >= (3, 5):
+    if sys.version_info[:2] >= (3, 5):
         # supported
         return
+    elif sys.version_info[:2] == (2, 7):
+        msg = """\
+Galaxy support for Python 2.7 is deprecated, please consider moving to
+Python >= 3.5 .
+https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
+on how to force Galaxy to use a different version."""
+        print(msg, file=sys.stderr)
+        return
     else:
+        version_string = '.'.join(str(_) for _ in sys.version_info[:3])
+        msg = """\
+ERROR: Your Python version is: %s
+Galaxy is currently supported on Python 2.7 (although deprecated) and >=3.5 .
+To run Galaxy, please install a supported Python version.
+If a supported version is already installed but is not your default,
+https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
+on how to force Galaxy to use a different version.""" % version_string
         print(msg, file=sys.stderr)
         raise Exception(msg)
 
diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh
index df3656e9cf41..51a574de2c1f 100755
--- a/scripts/common_startup.sh
+++ b/scripts/common_startup.sh
@@ -121,7 +121,7 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
                     echo "Creating Conda environment for Galaxy: $GALAXY_CONDA_ENV"
                     echo "To avoid this, use the --no-create-venv flag or set \$GALAXY_CONDA_ENV to an"
                     echo "existing environment before starting Galaxy."
-                    $CONDA_EXE create --yes --override-channels --channel conda-forge --channel defaults --name "$GALAXY_CONDA_ENV" 'python=2.7' 'pip>=9' 'virtualenv>=16'
+                    $CONDA_EXE create --yes --override-channels --channel conda-forge --channel defaults --name "$GALAXY_CONDA_ENV" 'python=3.6' 'pip>=9' 'virtualenv>=16'
                     unset __CONDA_INFO
                 fi
                 conda_activate
@@ -133,13 +133,20 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
             echo "Creating Python virtual environment for Galaxy: $GALAXY_VIRTUAL_ENV"
             echo "To avoid this, use the --no-create-venv flag or set \$GALAXY_VIRTUAL_ENV to an"
             echo "existing environment before starting Galaxy."
-            python ./scripts/check_python.py || exit 1
+            if [ -z "$GALAXY_PYTHON" ]; then
+                if command -v python3 >/dev/null; then
+                    GALAXY_PYTHON=python3
+                else
+                    GALAXY_PYTHON=python
+                fi
+            fi
+            "$GALAXY_PYTHON" ./scripts/check_python.py || exit 1
             if command -v virtualenv >/dev/null; then
-                virtualenv -p "$(command -v python)" "$GALAXY_VIRTUAL_ENV"
+                virtualenv -p "$GALAXY_PYTHON" "$GALAXY_VIRTUAL_ENV"
             else
-                vvers=16.1.0
+                vvers=16.7.9
                 vurl="https://files.pythonhosted.org/packages/source/v/virtualenv/virtualenv-${vvers}.tar.gz"
-                vsha=f899fafcd92e1150f40c8215328be38ff24b519cd95357fa6e78e006c7638208
+                vsha=0d62c70883c0342d59c11d0ddac0d954d0431321a41ab20851facf2b222598f3
                 vtmp=$(mktemp -d -t galaxy-virtualenv-XXXXXX)
                 vsrc="$vtmp/$(basename $vurl)"
                 # SSL certificates are not checked to prevent problems with messed
@@ -151,16 +158,16 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
                 elif command -v wget >/dev/null; then
                     wget --no-check-certificate -O "$vsrc" "$vurl"
                 else
-                    python -c "try:
+                    "$GALAXY_PYTHON" -c "try:
     from urllib import urlretrieve
 except:
     from urllib.request import urlretrieve
 urlretrieve('$vurl', '$vsrc')"
                 fi
                 echo "Verifying $vsrc checksum is $vsha"
-                python -c "import hashlib; assert hashlib.sha256(open('$vsrc', 'rb').read()).hexdigest() == '$vsha', '$vsrc: invalid checksum'"
+                "$GALAXY_PYTHON" -c "import hashlib; assert hashlib.sha256(open('$vsrc', 'rb').read()).hexdigest() == '$vsha', '$vsrc: invalid checksum'"
                 tar zxf "$vsrc" -C "$vtmp"
-                python "$vtmp/virtualenv-$vvers/src/virtualenv.py" "$GALAXY_VIRTUAL_ENV"
+                "$GALAXY_PYTHON" "$vtmp/virtualenv-$vvers/virtualenv.py" "$GALAXY_VIRTUAL_ENV"
                 rm -rf "$vtmp"
             fi
         fi
diff --git a/tox.ini b/tox.ini
index 3fe6643ade90..fd02ce81ddaf 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,17 +1,21 @@
 [tox]
 # envlist is the list of environments that are tested when `tox` is run without any option
 # hyphens in an environment name are used to delimit factors
-envlist = check_py3_compatibility, py{27,35}-first_startup, py{27,35}-lint, py27-lint_docstring_include_list, py{27,35}-unit, test_galaxy_packages, validate_test_tools
+envlist = check_py3_compatibility, py{27,35}-first_startup, py{27,35}-lint, py35-lint_docstring_include_list, py{27,35}-unit, test_galaxy_packages, validate_test_tools
 skipsdist = True
 
 [testenv]
 commands =
     first_startup: bash .ci/first_startup.sh
     lint: bash .ci/flake8_wrapper.sh
+    lint_docstring: bash .ci/flake8_wrapper_docstrings.sh --exclude
+    lint_docstring_include_list: bash .ci/flake8_wrapper_docstrings.sh --include
+
     unit: bash run_tests.sh -u
 whitelist_externals = bash
 passenv = CI CONDA_EXE
 setenv =
+    first_startup: GALAXY_PYTHON=python
     py{35,36,37}-first_startup: GALAXY_VIRTUAL_ENV=.venv3
     unit: GALAXY_VIRTUAL_ENV={envdir}
     unit: GALAXY_ENABLE_BETA_COMPRESSED_GENBANK_SNIFFING=1
@@ -34,12 +38,6 @@ whitelist_externals = make
 [testenv:mako_count]
 commands = bash .ci/check_mako.sh
 
-[testenv:py27-lint_docstring]
-commands = bash .ci/flake8_wrapper_docstrings.sh --exclude
-
-[testenv:py27-lint_docstring_include_list]
-commands = bash .ci/flake8_wrapper_docstrings.sh --include
-
 [testenv:test_galaxy_packages]
 commands = bash packages/test.sh
 

From 58ae3e43e3bc053c93406fd19a7b1fb523b10831 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sun, 9 Feb 2020 16:03:28 +0000
Subject: [PATCH 217/853] Python3: decode the output of
 ``subprocess.check_output()``

---
 doc/source/conf.versioning.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/doc/source/conf.versioning.py b/doc/source/conf.versioning.py
index 65a85d7fd2dd..8b112f7afcad 100644
--- a/doc/source/conf.versioning.py
+++ b/doc/source/conf.versioning.py
@@ -43,7 +43,8 @@
     _target_ver = TARGET_GIT_BRANCH[len('release_'):]
 
 # Use tags to determine versions - a stable version will have a branch before it's released, but not a tag.
-for _tag in reversed(check_output(('git', 'tag')).splitlines()):
+tags = check_output(('git', 'tag')).decode().splitlines()
+for _tag in reversed(tags):
     if _tag.startswith('v') and _tag.count('.') == 1:
         # this version is released
         _ver = _tag[1:]

From 4c712f0f2d6386873e322de5efb64a236631fe7b Mon Sep 17 00:00:00 2001
From: Alex Ostrovsky <40246333+astrovsky01@users.noreply.github.com>
Date: Tue, 18 Feb 2020 15:31:29 -0500
Subject: [PATCH 218/853] Added conda python update

---
 doc/source/admin/python.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md
index 018bff5319ab..228af9e9fd1e 100644
--- a/doc/source/admin/python.md
+++ b/doc/source/admin/python.md
@@ -24,6 +24,8 @@ If Galaxy complains about the version of Python you are using, check that
         % ln -s /path/to/python ~/galaxy-python/python
         % export PATH=~/galaxy-python:$PATH
         ```
+        
+    - If using Galaxy with a conda environment, remove conda environment (e.g. ```rm -rf /path/to/conda/__galaxy__```)
 
 3. Start Galaxy again.
 

From 99bc25f4ccabf29b4fdaf2e8fd35e9d4abe617a5 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 19 Feb 2020 16:09:12 +0000
Subject: [PATCH 219/853] Add more details

---
 doc/source/admin/python.md | 59 ++++++++++++++++++++++----------------
 1 file changed, 34 insertions(+), 25 deletions(-)

diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md
index 228af9e9fd1e..6209bebba8e8 100644
--- a/doc/source/admin/python.md
+++ b/doc/source/admin/python.md
@@ -3,31 +3,40 @@
 Galaxy's core functionality is currently supported on Python **2.7** (although
 deprecated) and **>=3.5** .
 
-If Galaxy complains about the version of Python you are using, check that
-`python --version` reports a supported version. If this is not the case:
-
-1. Completely remove the virtualenv used by Galaxy, e.g. with:
-   `rm -rf /path/to/galaxy/.venv`
-
-2. Let Galaxy know the path of the correct version of Python.
-
-    - If you are using Galaxy >= 20.05, just execute:
-      `export GALAXY_PYTHON=/path/to/python`
-    - If instead you are using an older version of Galaxy, you can manipulate
-      your shell's `$PATH` variable to place the correct version first. This can
-      be done for just Python by creating a new directory, adding a symbolic
-      link to python in there, and putting that directory at the front of
-      `$PATH`:
-
-        ```sh
-        % mkdir ~/galaxy-python
-        % ln -s /path/to/python ~/galaxy-python/python
-        % export PATH=~/galaxy-python:$PATH
-        ```
-        
-    - If using Galaxy with a conda environment, remove conda environment (e.g. ```rm -rf /path/to/conda/__galaxy__```)
-
-3. Start Galaxy again.
+If Galaxy complains about the version of Python you are using:
+
+1. Completely remove the Python virtualenv used by Galaxy (which can be
+   configured with the `GALAXY_VIRTUAL_ENV` environment variable and defaults to
+   `.venv`), e.g. with: `rm -rf /path/to/galaxy/.venv`
+
+2. If you were using a Python from a conda environment (which can be configured
+   with the `GALAXY_CONDA_ENV` environment variable and defaults to `_galaxy_`),
+   remove it, e.g. with: `conda env remove -n _galaxy_`
+
+3. Let Galaxy know which Python to use in one of the following methods:
+
+    - If you want to use Python from conda, just activate the `base` environment
+      and Galaxy will create a new conda environment for itself.
+    - Otherwise:
+        1. Make sure a supported version of Python is installed.
+        2. Verify that the Python interpreter you want to use is first in the
+           output of `which -a python3 python` (or `which -a python` if you are
+           using Galaxy <=20.01). If this is not the case:
+           - If you are using Galaxy >= 20.05, just execute:
+             `export GALAXY_PYTHON=/path/to/python`
+           - If instead you are using an older version of Galaxy, you can
+            manipulate your shell's `PATH` variable to place the correct version
+            first. This can be done for just Python by creating a new directory,
+            adding a symbolic link to `python` in there, and putting that
+            directory at the front of `PATH`:
+
+              ```sh
+              % mkdir ~/galaxy-python
+              % ln -s /path/to/python ~/galaxy-python/python
+              % export PATH=~/galaxy-python:$PATH
+              ```
+
+4. Start Galaxy again.
 
 N.B. If you have compiled your own Python interpreter from source, please ensure
 that the `ssl`, `sqlite3`, `curses` and `bz2` modules were built and can be

From 35ae3f375beae5e925be10eb774899ef14b8e6f2 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 26 Feb 2020 10:56:28 +0100
Subject: [PATCH 220/853] Fix linting issues

---
 .../galaxy/scripts/mvc/tool-recommendation.js | 67 +++++++++----------
 client/galaxy/scripts/mvc/tool/tool-form.js   |  4 +-
 lib/galaxy/webapps/galaxy/api/workflows.py    |  5 +-
 3 files changed, 38 insertions(+), 38 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool-recommendation.js b/client/galaxy/scripts/mvc/tool-recommendation.js
index 9751d21db299..2e06e89b7242 100644
--- a/client/galaxy/scripts/mvc/tool-recommendation.js
+++ b/client/galaxy/scripts/mvc/tool-recommendation.js
@@ -10,9 +10,9 @@ var ToolRecommendationView = Backbone.View.extend({
 
     initialize: function(options) {
         let toolId = options.toolId || "";
-        let self = this;
+        const self = this;
         if (toolId.indexOf("/") > 0) {
-            let toolIdSlash = toolId.split("/");
+            const toolIdSlash = toolId.split("/");
             toolId = toolIdSlash[toolIdSlash.length - 2];
         }
         Utils.request({
@@ -21,26 +21,26 @@ var ToolRecommendationView = Backbone.View.extend({
             data: {"tool_sequence": toolId},
             success: data => {
                 // get datatypes mapping
-                let datatypes_mapping = JSON.parse(
+                const datatypes_mapping = JSON.parse(
                     $.ajax({
                         url: `${getAppRoot()}api/datatypes/mapping`,
                         async: false
                     }).responseText
                 );
-                let extToType = datatypes_mapping.ext_to_class_name;
-                let typeToType = datatypes_mapping.class_to_classes;
-                let predData = data.predicted_data;
+                const extToType = datatypes_mapping.ext_to_class_name;
+                const typeToType = datatypes_mapping.class_to_classes;
+                const predData = data.predicted_data;
                 if (data !== null && predData.children.length > 0) {
-                    let filteredData = {};
-                    let compatibleTools = {};
-                    let filteredChildren = [];
-                    let outputDatatypes = predData["o_extensions"];
-                    for (const [index, nameObj] of predData.children.entries()) {
-                        let inputDatatypes = nameObj["i_extensions"];
+                    const filteredData = {};
+                    const compatibleTools = {};
+                    const filteredChildren = [];
+                    const outputDatatypes = predData["o_extensions"];
+                    for (const [_, nameObj] of predData.children.entries()) {
+                        const inputDatatypes = nameObj["i_extensions"];
                         for (const out_t of outputDatatypes.entries()) {
                             for(const in_t of inputDatatypes.entries()) {
-                                let child = extToType[out_t[1]];
-                                let parent = extToType[in_t[1]];
+                                const child = extToType[out_t[1]];
+                                const parent = extToType[in_t[1]];
                                 if (((typeToType[child] && parent in typeToType[child]) === true) ||
                                      out_t[1] === "input" ||
                                      out_t[1] === "_sniff_" ||
@@ -51,8 +51,8 @@ var ToolRecommendationView = Backbone.View.extend({
                             }
                         }
                     }
-                    for (let id in compatibleTools) {
-                        for (const [index, nameObj] of predData.children.entries()) {
+                    for (const id in compatibleTools) {
+                        for (const [_, nameObj] of predData.children.entries()) {
                             if (nameObj["tool_id"] === id) {
                                 filteredChildren.push(nameObj);
                                 break
@@ -75,33 +75,32 @@ var ToolRecommendationView = Backbone.View.extend({
     },
 
     render_tree: function(predicted_data) {
-        let margin = {top: 20, right: 30, bottom: 20, left: 250},
+        const margin = {top: 20, right: 30, bottom: 20, left: 250},
             width = 900 - margin.right - margin.left,
-            height = 300 - margin.top - margin.bottom;
-        let i = 0,
-            duration = 750,
-            root;
-        let tree = d3.layout.tree()
+            height = 300 - margin.top - margin.bottom,
+            duration = 750;
+        const tree = d3.layout.tree()
             .size([height, width]);
-        let diagonal = d3.svg.diagonal()
-            .projection(d => { return [d.y, d.x]; });
-        let svg = d3.select("#tool-recommendation-view").append("svg")
+        const diagonal = d3.svg.diagonal()
+            .projection(d => { return [d.y, d.x]; })
+        const svg = d3.select("#tool-recommendation-view").append("svg")
             .attr("width", width + margin.right + margin.left)
             .attr("height", height + margin.top + margin.bottom)
             .append("g")
             .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
-
+        let i = 0,
+            root = null;
         function update(source) {
             // Compute the new tree layout.
-            let nodes = tree.nodes(root).reverse(),
-                links = tree.links(nodes);
+            const nodes = tree.nodes(root).reverse();
+            const links = tree.links(nodes);
             // Normalize for fixed-depth.
             nodes.forEach(d => { d.y = d.depth * 180; });
             // Update the nodes…
-            let node = svg.selectAll("g.node")
+            const node = svg.selectAll("g.node")
                 .data(nodes, d => { return d.id || (d.id = ++i); });
             // Enter any new nodes at the parent's previous position.
-            let nodeEnter = node.enter().append("g")
+            const nodeEnter = node.enter().append("g")
                 .attr("class", "node")
                 .attr("transform", d => { return "translate(" + source.y0 + "," + source.x0 + ")"; })
                 .on("click", click);
@@ -117,7 +116,7 @@ var ToolRecommendationView = Backbone.View.extend({
             nodeEnter.append("title")
                 .text(d => { return d.children || d._children ? "Click to collapse" : "Click to open tool definition"; })
             // Transition nodes to their new position.
-            let nodeUpdate = node.transition()
+            const nodeUpdate = node.transition()
                 .duration(duration)
                 .attr("transform", d => { return "translate(" + d.y + "," + d.x + ")"; });
             nodeUpdate.select("circle")
@@ -126,7 +125,7 @@ var ToolRecommendationView = Backbone.View.extend({
             nodeUpdate.select("text")
                 .style("fill-opacity", 1);
             // Transition exiting nodes to the parent's new position.
-            let nodeExit = node.exit().transition()
+            const nodeExit = node.exit().transition()
                 .duration(duration)
                 .attr("transform", d => { return "translate(" + source.y + "," + source.x + ")"; })
                 .remove();
@@ -135,7 +134,7 @@ var ToolRecommendationView = Backbone.View.extend({
             nodeExit.select("text")
                 .style("fill-opacity", 1e-6);
             // Update the links…
-            let link = svg.selectAll("path.link")
+            const link = svg.selectAll("path.link")
                 .data(links, d => { return d.target.id; });
             // Enter any new links at the parent's previous position.
             link.enter().insert("path", "g")
@@ -152,7 +151,7 @@ var ToolRecommendationView = Backbone.View.extend({
             link.exit().transition()
                 .duration(duration)
                 .attr("d", d => {
-                    let o = {x: source.x, y: source.y};
+                    const o = {x: source.x, y: source.y};
                     return diagonal({source: o, target: o});
                 })
                 .remove();
diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index 93e7f2bc3f1b..3cd3e4ddc704 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -268,11 +268,11 @@ const View = Backbone.View.extend({
                     }
                 }
                 this.$el.append(this._templateSuccess(response, job_def));
-                let enable_tool_recommendations = window.Galaxy.config.enable_tool_recommendations;
+                const enable_tool_recommendations = window.Galaxy.config.enable_tool_recommendations;
                 if (enable_tool_recommendations === true || enable_tool_recommendations === 'true') {
                     // show tool recommendations
                     this.$el.append($("<div/>", { id: "tool-recommendation-view" }));
-                    var toolRecommendation = new ToolRecommendation.ToolRecommendationView({
+                    const toolRecommendation = new ToolRecommendation.ToolRecommendationView({
                         toolId: job_def.tool_id
                     });
                 }
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 62a67c17b3e8..c8b8e04d8089 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -5,6 +5,7 @@
 
 import io
 import json
+import yaml
 import logging
 import os
 
@@ -12,10 +13,10 @@
 from gxformat2._yaml import ordered_dump
 from markupsafe import escape
 from sqlalchemy import desc, false, or_, true
+import h5py
+import numpy as np
 from sqlalchemy.orm import joinedload
 
-import numpy as np
-import h5py
 from keras.models import model_from_json
 
 from galaxy import (

From 1169db7c9ee25c5bfcf7f2e8312e0ba0624760b0 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 11:02:24 +0100
Subject: [PATCH 221/853] Mention that database/compiled_templates needs to be
 removed when upgrading python

---
 doc/source/admin/python.md | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md
index 6209bebba8e8..ba75e2f1e4f5 100644
--- a/doc/source/admin/python.md
+++ b/doc/source/admin/python.md
@@ -36,7 +36,13 @@ If Galaxy complains about the version of Python you are using:
               % export PATH=~/galaxy-python:$PATH
               ```
 
-4. Start Galaxy again.
+4. Remove compiled mako templates when upgrading from Python 2:
+     ```sh
+     % rm -rf /path/to/galaxy/database/compiled_templates/
+     ```
+   These templated will be regenerated automatically when starting Galaxy.
+
+5. Start Galaxy again.
 
 N.B. If you have compiled your own Python interpreter from source, please ensure
 that the `ssl`, `sqlite3`, `curses` and `bz2` modules were built and can be

From 48e015d362bcb131d644409952e9fff0c12dffae Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 11:02:39 +0100
Subject: [PATCH 222/853] Link to Python upgrade instructions

---
 doc/source/releases/20.01_announce.rst | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/doc/source/releases/20.01_announce.rst b/doc/source/releases/20.01_announce.rst
index b54341b31157..065f1b66cead 100644
--- a/doc/source/releases/20.01_announce.rst
+++ b/doc/source/releases/20.01_announce.rst
@@ -56,6 +56,13 @@ To update an existing Galaxy repository run:
 
 See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
 
+Deprecation Notice
+==================
+
+With the release of Galaxy 20.01 we strongly encourage all deployers to run Galaxy under Python 3.
+For instructions on how to transition to Python 3 please see `here <https://docs.galaxyproject.org/en/release_20.01/admin/python.html>`__.
+
+
 Release Notes
 ===========================================================
 

From 9fdbad72471631284b2418c5b844d1bcc45bc4d6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 11:13:45 +0100
Subject: [PATCH 223/853] Mention that more distribution tools/converters need
 dependencies now

---
 doc/source/releases/20.01_announce.rst | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/doc/source/releases/20.01_announce.rst b/doc/source/releases/20.01_announce.rst
index 065f1b66cead..cc8ff3f0c7ab 100644
--- a/doc/source/releases/20.01_announce.rst
+++ b/doc/source/releases/20.01_announce.rst
@@ -56,6 +56,13 @@ To update an existing Galaxy repository run:
 
 See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
 
+Updates to Tools and Converters in the Galaxy distribution
+==========================================================
+
+Many tools and Converters have been updated in the 20.01 release.
+As a consequence deployers need to install dependencies for these in the
+Admin Menu -> Manage Dependencies.
+
 Deprecation Notice
 ==================
 

From cf54ae1bebcf9c8aaea67ce634e887794777752d Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 26 Feb 2020 12:29:46 +0100
Subject: [PATCH 224/853] Fix linting issues

---
 .../galaxy/scripts/mvc/tool-recommendation.js | 39 +++++++-------
 client/galaxy/scripts/mvc/tool/tool-form.js   |  2 +-
 doc/source/admin/galaxy_options.rst           |  2 +-
 lib/galaxy/config/sample/galaxy.yml.sample    |  2 +-
 lib/galaxy/webapps/galaxy/api/workflows.py    | 51 ++++++++++---------
 lib/galaxy/webapps/galaxy/config_schema.yml   |  2 +
 6 files changed, 51 insertions(+), 47 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool-recommendation.js b/client/galaxy/scripts/mvc/tool-recommendation.js
index 2e06e89b7242..b2254a573b6a 100644
--- a/client/galaxy/scripts/mvc/tool-recommendation.js
+++ b/client/galaxy/scripts/mvc/tool-recommendation.js
@@ -26,35 +26,36 @@ var ToolRecommendationView = Backbone.View.extend({
                         url: `${getAppRoot()}api/datatypes/mapping`,
                         async: false
                     }).responseText
-                );
-                const extToType = datatypes_mapping.ext_to_class_name;
-                const typeToType = datatypes_mapping.class_to_classes;
-                const predData = data.predicted_data;
+                ),
+                extToType = datatypes_mapping.ext_to_class_name,
+                typeToType = datatypes_mapping.class_to_classes,
+                predData = data.predicted_data;
                 if (data !== null && predData.children.length > 0) {
-                    const filteredData = {};
-                    const compatibleTools = {};
-                    const filteredChildren = [];
-                    const outputDatatypes = predData["o_extensions"];
-                    for (const [_, nameObj] of predData.children.entries()) {
-                        const inputDatatypes = nameObj["i_extensions"];
+                    const filteredData = {},
+                        compatibleTools = {},
+                        filteredChildren = [],
+                        outputDatatypes = predData["o_extensions"],
+                        children = predData.children;
+                    for (const nameObj of children.entries()) {
+                        const inputDatatypes = nameObj[1]["i_extensions"];
                         for (const out_t of outputDatatypes.entries()) {
                             for(const in_t of inputDatatypes.entries()) {
-                                const child = extToType[out_t[1]];
-                                const parent = extToType[in_t[1]];
+                                const child = extToType[out_t[1]],
+                                    parent = extToType[in_t[1]];
                                 if (((typeToType[child] && parent in typeToType[child]) === true) ||
                                      out_t[1] === "input" ||
                                      out_t[1] === "_sniff_" ||
                                      out_t[1] === "input_collection") {
-                                    compatibleTools[nameObj["tool_id"]] = nameObj["name"];
+                                    compatibleTools[nameObj[1]["tool_id"]] = nameObj[1]["name"];
                                     break
                                 }
                             }
                         }
                     }
                     for (const id in compatibleTools) {
-                        for (const [_, nameObj] of predData.children.entries()) {
-                            if (nameObj["tool_id"] === id) {
-                                filteredChildren.push(nameObj);
+                        for (const nameObj of children.entries()) {
+                            if (nameObj[1]["tool_id"] === id) {
+                                filteredChildren.push(nameObj[1]);
                                 break
                             }
                         }
@@ -92,8 +93,8 @@ var ToolRecommendationView = Backbone.View.extend({
             root = null;
         function update(source) {
             // Compute the new tree layout.
-            const nodes = tree.nodes(root).reverse();
-            const links = tree.links(nodes);
+            const nodes = tree.nodes(root).reverse(),
+                links = tree.links(nodes);
             // Normalize for fixed-depth.
             nodes.forEach(d => { d.y = d.depth * 180; });
             // Update the nodes…
@@ -140,7 +141,7 @@ var ToolRecommendationView = Backbone.View.extend({
             link.enter().insert("path", "g")
                 .attr("class", "link")
                 .attr("d", d => {
-                    let o = {x: source.x0, y: source.y0};
+                    const o = {x: source.x0, y: source.y0};
                     return diagonal({source: o, target: o});
                 });
             // Transition links to their new position.
diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index 3cd3e4ddc704..82c7dc820346 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -272,7 +272,7 @@ const View = Backbone.View.extend({
                 if (enable_tool_recommendations === true || enable_tool_recommendations === 'true') {
                     // show tool recommendations
                     this.$el.append($("<div/>", { id: "tool-recommendation-view" }));
-                    const toolRecommendation = new ToolRecommendation.ToolRecommendationView({
+                    new ToolRecommendation.ToolRecommendationView({
                         toolId: job_def.tool_id
                     });
                 }
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index fdc5c4693492..4920d8ae8f95 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -4056,7 +4056,7 @@
     removed from the recommendations and another is for adding
     additional tools to be recommended along side those from the deep
     learning model.
-:Default: ``None``
+:Default: ``tool_recommendations_overwrite.yml``
 :Type: str
 
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index b57de1ff1294..41310e3d20c8 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1979,7 +1979,7 @@ galaxy:
   # removed from the recommendations and another is for adding
   # additional tools to be recommended along side those from the deep
   # learning model.
-  #admin_tool_recommendations_path: null
+  #admin_tool_recommendations_path: tool_recommendations_overwrite.yml
 
   # Overwrite or append to the tool recommendations by the deep learning
   # model. When set to true, all the recommendations by the deep
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index c8b8e04d8089..32186d785f68 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -5,20 +5,11 @@
 
 import io
 import json
-import yaml
 import logging
 import os
 
 import requests
-from gxformat2._yaml import ordered_dump
-from markupsafe import escape
-from sqlalchemy import desc, false, or_, true
-import h5py
-import numpy as np
-from sqlalchemy.orm import joinedload
-
-from keras.models import model_from_json
-
+import yaml
 from galaxy import (
     exceptions,
     model,
@@ -46,11 +37,20 @@
     url_for,
     UsesStoredWorkflowMixin
 )
+
 from galaxy.workflow.extract import extract_workflow
 from galaxy.workflow.modules import module_factory
 from galaxy.workflow.reports import generate_report
 from galaxy.workflow.run import invoke, queue_invoke
 from galaxy.workflow.run_request import build_workflow_run_configs
+from gxformat2._yaml import ordered_dump
+from markupsafe import escape
+
+import h5py
+import numpy as np
+from keras.models import model_from_json
+from sqlalchemy import desc, false, or_, true
+from sqlalchemy.orm import joinedload
 
 log = logging.getLogger(__name__)
 
@@ -688,14 +688,14 @@ def __set_model(self, trans, remote_model_url):
                 self.all_tools[t_id_renamed] = (tool_id, tool.name)
             # read the hdf5 attributes
             trained_model = h5py.File(self.tool_recommendation_model_path, 'r')
-            model_config = json.loads(trained_model['model_config'].value)
+            model_config = json.loads(trained_model['model_config'][()])
             self.loaded_model = model_from_json(model_config)
             # set the dictionary of tools
-            self.model_data_dictionary = json.loads(trained_model['data_dictionary'].value)
+            self.model_data_dictionary = json.loads(trained_model['data_dictionary'][()])
             self.reverse_dictionary = dict((v, k) for k, v in self.model_data_dictionary.items())
             # set the list of compatible tools
-            self.compatible_tools = json.loads(trained_model['compatible_tools'].value)
-            self.tool_weights = json.loads(trained_model['class_weights'].value)
+            self.compatible_tools = json.loads(trained_model['compatible_tools'][()])
+            self.tool_weights = json.loads(trained_model['class_weights'][()])
             self.tool_weights_sorted = dict()
             # sort the tools' usage dictionary
             tool_pos_sorted = [int(key) for key in self.tool_weights.keys()]
@@ -705,7 +705,7 @@ def __set_model(self, trans, remote_model_url):
             for item in trained_model.keys():
                 if "weight_" in item:
                     d_key = "weight_" + str(counter_layer_weights)
-                    weights = trained_model[d_key].value
+                    weights = trained_model[d_key][()]
                     model_weights.append(weights)
                     counter_layer_weights += 1
             # set the model weights
@@ -719,16 +719,17 @@ def __collect_admin_preferences(self, admin_path):
         """
         if not self.admin_tool_recommendations_path and admin_path is not None:
             self.admin_tool_recommendations_path = os.path.join(os.getcwd(), admin_path)
-            with open(self.admin_tool_recommendations_path) as admin_recommendations:
-                admin_recommendation_preferences = yaml.safe_load(admin_recommendations)
-                if admin_recommendation_preferences:
-                    for tool_id in admin_recommendation_preferences:
-                        tool_info = admin_recommendation_preferences[tool_id]
-                        if 'is_deprecated' in tool_info[0]:
-                            self.deprecated_tools[tool_id] = tool_info[0]["text_message"]
-                        else:
-                            if tool_id not in self.admin_recommendations:
-                                self.admin_recommendations[tool_id] = tool_info
+            if os.path.exists(self.admin_tool_recommendations_path):
+                with open(self.admin_tool_recommendations_path) as admin_recommendations:
+                    admin_recommendation_preferences = yaml.safe_load(admin_recommendations)
+                    if admin_recommendation_preferences:
+                        for tool_id in admin_recommendation_preferences:
+                            tool_info = admin_recommendation_preferences[tool_id]
+                            if 'is_deprecated' in tool_info[0]:
+                                self.deprecated_tools[tool_id] = tool_info[0]["text_message"]
+                            else:
+                                if tool_id not in self.admin_recommendations:
+                                    self.admin_recommendations[tool_id] = tool_info
 
     def __download_model(self, model_url, download_local='database/'):
         """
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index bc646a13b631..3fdd1ba0fee8 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2986,6 +2986,8 @@ mapping:
       admin_tool_recommendations_path:
         type: str
         required: false
+        default: 'tool_recommendations_overwrite.yml'
+        path_resolves_to: config_dir
         desc: |
           Set path to the additional tool preferences from Galaxy admins.
           It has two blocks. One for listing deprecated tools which will be removed from the recommendations and

From cfeff793782c9a984e8f0b64c1b68323bc0dc265 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 26 Feb 2020 12:51:56 +0100
Subject: [PATCH 225/853] remove remnant line

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/tool_util/parser/xml.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index 9bdc060cfa16..110524b46590 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -613,7 +613,6 @@ def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_dis
     # Number of lines to allow to vary in logs (for dates, etc)
     attributes['lines_diff'] = int(attrib.pop('lines_diff', '0'))
     # Allow a file size to vary if sim_size compare
-    attributes['delta'] = int(attrib.pop('delta', '10000'))
     attributes['delta'] = int(attrib.pop('delta', DEFAULT_DELTA))
     attributes['sort'] = string_as_bool(attrib.pop('sort', False))
     attributes['decompress'] = string_as_bool(attrib.pop('decompress', False))

From 45eb41a80eddb842f0d41ae218d82dbaa43437f5 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 26 Feb 2020 12:53:56 +0100
Subject: [PATCH 226/853] add default to docs

and restore empty line to separate third-party from "internal" imports
---
 lib/galaxy/tool_util/parser/yaml.py | 1 +
 lib/galaxy/tool_util/xsd/galaxy.xsd | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index bcdd9528c9b0..4ee12798997d 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -1,6 +1,7 @@
 from collections import OrderedDict
 
 import packaging.version
+
 from galaxy.tool_util.deps import requirements
 from galaxy.tool_util.parser.util import DEFAULT_DELTA
 from .interface import (
diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index 6ae0e3e102cd..5d4fd5253d28 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -1314,7 +1314,7 @@ When this attribute is true and ``compare`` is set to ``diff``, try to decompres
     </xs:attribute>
     <xs:attribute name="delta" type="xs:integer">
       <xs:annotation>
-        <xs:documentation xml:lang="en">If ``compare`` is set to ``sim_size``, this is the number of bytes different allowed.</xs:documentation>
+        <xs:documentation xml:lang="en">If ``compare`` is set to ``sim_size``, this is the number of bytes different allowed (default 10.000).</xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>

From 04515f11bd5d5a3f046f6247445d9f843bb597e6 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 26 Feb 2020 12:57:23 +0100
Subject: [PATCH 227/853] Correct number

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/tool_util/xsd/galaxy.xsd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index 5d4fd5253d28..a812c6dc04d2 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -1314,7 +1314,7 @@ When this attribute is true and ``compare`` is set to ``diff``, try to decompres
     </xs:attribute>
     <xs:attribute name="delta" type="xs:integer">
       <xs:annotation>
-        <xs:documentation xml:lang="en">If ``compare`` is set to ``sim_size``, this is the number of bytes different allowed (default 10.000).</xs:documentation>
+        <xs:documentation xml:lang="en">If ``compare`` is set to ``sim_size``, this is the number of bytes different allowed (default 10000).</xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>

From 4066d1bd757732fa7893f62e08e565a0a76d7331 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 14:01:33 +0100
Subject: [PATCH 228/853] Restore database migration test

---
 .circleci/config.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 7904c41fac37..a87c6269b746 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -135,6 +135,10 @@ jobs:
     <<: *set_workdir
     steps:
       - *restore_repo_cache
+      - run: sh scripts/common_startup.sh
+      - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite
+      - run: mv db_gx_rev_0127.sqlite database/universe.sqlite
+      - run: sh manage_db.sh -c ./config/galaxy.yml.sample upgrade
       - *install_tox
       - run: tox -e py35-first_startup
   validate_test_tools:

From 4f0cce0c270e2c0feaa1b8302e91d497b9653fe4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 14:06:55 +0100
Subject: [PATCH 229/853] Adjust docs for when we started preferring python3

---
 doc/source/admin/python.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md
index ba75e2f1e4f5..691cf8bd8472 100644
--- a/doc/source/admin/python.md
+++ b/doc/source/admin/python.md
@@ -21,7 +21,7 @@ If Galaxy complains about the version of Python you are using:
         1. Make sure a supported version of Python is installed.
         2. Verify that the Python interpreter you want to use is first in the
            output of `which -a python3 python` (or `which -a python` if you are
-           using Galaxy <=20.01). If this is not the case:
+           using Galaxy <=19.09). If this is not the case:
            - If you are using Galaxy >= 20.05, just execute:
              `export GALAXY_PYTHON=/path/to/python`
            - If instead you are using an older version of Galaxy, you can

From e409cdbc9de76c22bbb9adce752ca349f18def0a Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 26 Feb 2020 14:17:44 +0100
Subject: [PATCH 230/853] Run prettier

---
 .../galaxy/scripts/mvc/tool-recommendation.js | 162 +++++++++++-------
 client/galaxy/scripts/mvc/tool/tool-form.js   |   2 +-
 2 files changed, 102 insertions(+), 62 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool-recommendation.js b/client/galaxy/scripts/mvc/tool-recommendation.js
index b2254a573b6a..09e9a29812f3 100644
--- a/client/galaxy/scripts/mvc/tool-recommendation.js
+++ b/client/galaxy/scripts/mvc/tool-recommendation.js
@@ -4,7 +4,6 @@ import * as d3 from "d3";
 import { getAppRoot } from "onload/loadConfig";
 import $ from "jquery";
 
-
 var ToolRecommendationView = Backbone.View.extend({
     el: "#tool-recommendation-view",
 
@@ -18,18 +17,18 @@ var ToolRecommendationView = Backbone.View.extend({
         Utils.request({
             type: "POST",
             url: `${getAppRoot()}api/workflows/get_tool_predictions`,
-            data: {"tool_sequence": toolId},
+            data: { tool_sequence: toolId },
             success: data => {
                 // get datatypes mapping
                 const datatypes_mapping = JSON.parse(
-                    $.ajax({
-                        url: `${getAppRoot()}api/datatypes/mapping`,
-                        async: false
-                    }).responseText
-                ),
-                extToType = datatypes_mapping.ext_to_class_name,
-                typeToType = datatypes_mapping.class_to_classes,
-                predData = data.predicted_data;
+                        $.ajax({
+                            url: `${getAppRoot()}api/datatypes/mapping`,
+                            async: false
+                        }).responseText
+                    ),
+                    extToType = datatypes_mapping.ext_to_class_name,
+                    typeToType = datatypes_mapping.class_to_classes,
+                    predData = data.predicted_data;
                 if (data !== null && predData.children.length > 0) {
                     const filteredData = {},
                         compatibleTools = {},
@@ -39,15 +38,17 @@ var ToolRecommendationView = Backbone.View.extend({
                     for (const nameObj of children.entries()) {
                         const inputDatatypes = nameObj[1]["i_extensions"];
                         for (const out_t of outputDatatypes.entries()) {
-                            for(const in_t of inputDatatypes.entries()) {
+                            for (const in_t of inputDatatypes.entries()) {
                                 const child = extToType[out_t[1]],
                                     parent = extToType[in_t[1]];
-                                if (((typeToType[child] && parent in typeToType[child]) === true) ||
-                                     out_t[1] === "input" ||
-                                     out_t[1] === "_sniff_" ||
-                                     out_t[1] === "input_collection") {
+                                if (
+                                    (typeToType[child] && parent in typeToType[child]) === true ||
+                                    out_t[1] === "input" ||
+                                    out_t[1] === "_sniff_" ||
+                                    out_t[1] === "input_collection"
+                                ) {
                                     compatibleTools[nameObj[1]["tool_id"]] = nameObj[1]["name"];
-                                    break
+                                    break;
                                 }
                             }
                         }
@@ -56,7 +57,7 @@ var ToolRecommendationView = Backbone.View.extend({
                         for (const nameObj of children.entries()) {
                             if (nameObj[1]["tool_id"] === id) {
                                 filteredChildren.push(nameObj[1]);
-                                break
+                                break;
                             }
                         }
                     }
@@ -64,11 +65,20 @@ var ToolRecommendationView = Backbone.View.extend({
                     filteredData["name"] = predData["name"];
                     filteredData["children"] = filteredChildren;
                     if (filteredChildren.length > 0 && predData["is_deprecated"] === false) {
-                        self.$el.append("<div class='infomessagelarge'>You have used " + filteredData.name + " tool. For further analysis, you could try using the following/recommended tools. The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to open its definition. </div>");
+                        self.$el.append(
+                            "<div class='infomessagelarge'>You have used " +
+                                filteredData.name +
+                                " tool. For further analysis, you could try using the following/recommended tools. The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to open its definition. </div>"
+                        );
                         self.render_tree(filteredData);
-                    }
-                    else if(predData["is_deprecated"] === true) {
-                        self.$el.append("<div class='warningmessagelarge'>You have used " + predData.name + " tool. " + predData["message"] + ". </div>");
+                    } else if (predData["is_deprecated"] === true) {
+                        self.$el.append(
+                            "<div class='warningmessagelarge'>You have used " +
+                                predData.name +
+                                " tool. " +
+                                predData["message"] +
+                                ". </div>"
+                        );
                     }
                 }
             }
@@ -76,15 +86,17 @@ var ToolRecommendationView = Backbone.View.extend({
     },
 
     render_tree: function(predicted_data) {
-        const margin = {top: 20, right: 30, bottom: 20, left: 250},
+        const margin = { top: 20, right: 30, bottom: 20, left: 250 },
             width = 900 - margin.right - margin.left,
             height = 300 - margin.top - margin.bottom,
             duration = 750;
-        const tree = d3.layout.tree()
-            .size([height, width]);
-        const diagonal = d3.svg.diagonal()
-            .projection(d => { return [d.y, d.x]; })
-        const svg = d3.select("#tool-recommendation-view").append("svg")
+        const tree = d3.layout.tree().size([height, width]);
+        const diagonal = d3.svg.diagonal().projection(d => {
+            return [d.y, d.x];
+        });
+        const svg = d3
+            .select("#tool-recommendation-view")
+            .append("svg")
             .attr("width", width + margin.right + margin.left)
             .attr("height", height + margin.top + margin.bottom)
             .append("g")
@@ -96,64 +108,92 @@ var ToolRecommendationView = Backbone.View.extend({
             const nodes = tree.nodes(root).reverse(),
                 links = tree.links(nodes);
             // Normalize for fixed-depth.
-            nodes.forEach(d => { d.y = d.depth * 180; });
+            nodes.forEach(d => {
+                d.y = d.depth * 180;
+            });
             // Update the nodes…
-            const node = svg.selectAll("g.node")
-                .data(nodes, d => { return d.id || (d.id = ++i); });
+            const node = svg.selectAll("g.node").data(nodes, d => {
+                return d.id || (d.id = ++i);
+            });
             // Enter any new nodes at the parent's previous position.
-            const nodeEnter = node.enter().append("g")
+            const nodeEnter = node
+                .enter()
+                .append("g")
                 .attr("class", "node")
-                .attr("transform", d => { return "translate(" + source.y0 + "," + source.x0 + ")"; })
+                .attr("transform", d => {
+                    return "translate(" + source.y0 + "," + source.x0 + ")";
+                })
                 .on("click", click);
-            nodeEnter.append("circle")
+            nodeEnter
+                .append("circle")
                 .attr("r", 1e-6)
-                .style("fill", d => { return d._children ? "lightsteelblue" : "#fff"; });
-            nodeEnter.append("text")
-                .attr("x", d => { return d.children || d._children ? -10 : 10; })
+                .style("fill", d => {
+                    return d._children ? "lightsteelblue" : "#fff";
+                });
+            nodeEnter
+                .append("text")
+                .attr("x", d => {
+                    return d.children || d._children ? -10 : 10;
+                })
                 .attr("dy", ".35em")
-                .attr("text-anchor", d => { return d.children || d._children ? "end" : "start"; })
-                .text(d => { return d.name; })
+                .attr("text-anchor", d => {
+                    return d.children || d._children ? "end" : "start";
+                })
+                .text(d => {
+                    return d.name;
+                })
                 .style("fill-opacity", 1e-6);
-            nodeEnter.append("title")
-                .text(d => { return d.children || d._children ? "Click to collapse" : "Click to open tool definition"; })
+            nodeEnter.append("title").text(d => {
+                return d.children || d._children ? "Click to collapse" : "Click to open tool definition";
+            });
             // Transition nodes to their new position.
-            const nodeUpdate = node.transition()
+            const nodeUpdate = node
+                .transition()
                 .duration(duration)
-                .attr("transform", d => { return "translate(" + d.y + "," + d.x + ")"; });
-            nodeUpdate.select("circle")
+                .attr("transform", d => {
+                    return "translate(" + d.y + "," + d.x + ")";
+                });
+            nodeUpdate
+                .select("circle")
                 .attr("r", 4.5)
-                .style("fill", d => { return d._children ? "lightsteelblue" : "#fff"; });
-            nodeUpdate.select("text")
-                .style("fill-opacity", 1);
+                .style("fill", d => {
+                    return d._children ? "lightsteelblue" : "#fff";
+                });
+            nodeUpdate.select("text").style("fill-opacity", 1);
             // Transition exiting nodes to the parent's new position.
-            const nodeExit = node.exit().transition()
+            const nodeExit = node
+                .exit()
+                .transition()
                 .duration(duration)
-                .attr("transform", d => { return "translate(" + source.y + "," + source.x + ")"; })
+                .attr("transform", d => {
+                    return "translate(" + source.y + "," + source.x + ")";
+                })
                 .remove();
-            nodeExit.select("circle")
-                .attr("r", 1e-6);
-            nodeExit.select("text")
-                .style("fill-opacity", 1e-6);
+            nodeExit.select("circle").attr("r", 1e-6);
+            nodeExit.select("text").style("fill-opacity", 1e-6);
             // Update the links…
-            const link = svg.selectAll("path.link")
-                .data(links, d => { return d.target.id; });
+            const link = svg.selectAll("path.link").data(links, d => {
+                return d.target.id;
+            });
             // Enter any new links at the parent's previous position.
-            link.enter().insert("path", "g")
+            link.enter()
+                .insert("path", "g")
                 .attr("class", "link")
                 .attr("d", d => {
-                    const o = {x: source.x0, y: source.y0};
-                    return diagonal({source: o, target: o});
+                    const o = { x: source.x0, y: source.y0 };
+                    return diagonal({ source: o, target: o });
                 });
             // Transition links to their new position.
             link.transition()
                 .duration(duration)
                 .attr("d", diagonal);
             // Transition exiting nodes to the parent's new position.
-            link.exit().transition()
+            link.exit()
+                .transition()
                 .duration(duration)
                 .attr("d", d => {
-                    const o = {x: source.x, y: source.y};
-                    return diagonal({source: o, target: o});
+                    const o = { x: source.x, y: source.y };
+                    return diagonal({ source: o, target: o });
                 })
                 .remove();
             // Stash the old positions for transition.
@@ -173,7 +213,7 @@ var ToolRecommendationView = Backbone.View.extend({
             }
             update(d);
             if (d.tool_id !== undefined && d.tool_id !== "undefined" && d.tool_id !== null && d.tool_id !== "") {
-                document.location.href = `${getAppRoot()}` + 'tool_runner?tool_id=' + d.tool_id;
+                document.location.href = `${getAppRoot()}` + "tool_runner?tool_id=" + d.tool_id;
             }
         }
         function collapse(d) {
diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index 82c7dc820346..f973f10b2880 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -269,7 +269,7 @@ const View = Backbone.View.extend({
                 }
                 this.$el.append(this._templateSuccess(response, job_def));
                 const enable_tool_recommendations = window.Galaxy.config.enable_tool_recommendations;
-                if (enable_tool_recommendations === true || enable_tool_recommendations === 'true') {
+                if (enable_tool_recommendations === true || enable_tool_recommendations === "true") {
                     // show tool recommendations
                     this.$el.append($("<div/>", { id: "tool-recommendation-view" }));
                     new ToolRecommendation.ToolRecommendationView({

From 8735e9ad0d218fd628982015a5874c5095a33c9f Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 26 Feb 2020 14:23:27 +0100
Subject: [PATCH 231/853] sort imports

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 31 ++++++----------------
 1 file changed, 8 insertions(+), 23 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 32186d785f68..d40fb7412791 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -10,34 +10,19 @@
 
 import requests
 import yaml
-from galaxy import (
-    exceptions,
-    model,
-    util
-)
-from galaxy.managers import (
-    histories,
-    workflows
-)
+from galaxy import exceptions, model, util
+from galaxy.managers import histories, workflows
 from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter
 from galaxy.model.item_attrs import UsesAnnotations
-from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
+from galaxy.tool_shed.galaxy_install.install_manager import \
+    InstallRepositoryManager
 from galaxy.tools.parameters import populate_state
 from galaxy.tools.parameters.basic import workflow_building_modes
 from galaxy.util.sanitize_html import sanitize_html
-from galaxy.web import (
-    expose_api,
-    expose_api_anonymous_and_sessionless,
-    expose_api_raw,
-    format_return_as_json,
-)
-from galaxy.webapps.base.controller import (
-    BaseAPIController,
-    SharableMixin,
-    url_for,
-    UsesStoredWorkflowMixin
-)
-
+from galaxy.web import (expose_api, expose_api_anonymous_and_sessionless,
+                        expose_api_raw, format_return_as_json)
+from galaxy.webapps.base.controller import (BaseAPIController, SharableMixin,
+                                            UsesStoredWorkflowMixin, url_for)
 from galaxy.workflow.extract import extract_workflow
 from galaxy.workflow.modules import module_factory
 from galaxy.workflow.reports import generate_report

From 0aa5c4b21c5e76dfc08f918b667a82508f8f50d1 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 14:25:10 +0100
Subject: [PATCH 232/853] One more version change

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 doc/source/admin/python.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md
index 691cf8bd8472..a8ef04c7669d 100644
--- a/doc/source/admin/python.md
+++ b/doc/source/admin/python.md
@@ -22,7 +22,7 @@ If Galaxy complains about the version of Python you are using:
         2. Verify that the Python interpreter you want to use is first in the
            output of `which -a python3 python` (or `which -a python` if you are
            using Galaxy <=19.09). If this is not the case:
-           - If you are using Galaxy >= 20.05, just execute:
+           - If you are using Galaxy >= 20.01, just execute:
              `export GALAXY_PYTHON=/path/to/python`
            - If instead you are using an older version of Galaxy, you can
             manipulate your shell's `PATH` variable to place the correct version
@@ -51,4 +51,3 @@ compilation process and are required by the Galaxy framework. If building on
 Linux, you may need to install the appropriate `-dev` packages for OpenSSL and
 Bzip2. You may also need to build Python with shared libraries
 (`--enable-shared`).
-

From 865ba235d1050274ec26a29145ea0a5f147da4a1 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 26 Feb 2020 14:32:39 +0100
Subject: [PATCH 233/853] Fix `UserManager.get_reset_token()` after #9432

Remove `lower()` also from the right side.
---
 lib/galaxy/managers/users.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 2ad6457a2c00..9553698ee92e 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -489,7 +489,7 @@ def send_reset_email(self, trans, payload={}, **kwd):
                 return "Failed to produce password reset token. User not found."
 
     def get_reset_token(self, trans, email):
-        reset_user = trans.sa_session.query(self.app.model.User).filter(self.app.model.User.table.c.email == email.lower()).first()
+        reset_user = trans.sa_session.query(self.app.model.User).filter(self.app.model.User.table.c.email == email).first()
         if not reset_user and email != email.lower():
             reset_user = trans.sa_session.query(self.app.model.User).filter(func.lower(self.app.model.User.table.c.email) == email.lower()).first()
         if reset_user:

From bb36a58179bea13ba4684f55fbb8d5b481431a9c Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 26 Feb 2020 15:29:09 +0100
Subject: [PATCH 234/853] Update import order

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index d40fb7412791..af2f9a552dfb 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -10,6 +10,9 @@
 
 import requests
 import yaml
+
+from gxformat2._yaml import ordered_dump
+
 from galaxy import exceptions, model, util
 from galaxy.managers import histories, workflows
 from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter
@@ -22,16 +25,16 @@
 from galaxy.web import (expose_api, expose_api_anonymous_and_sessionless,
                         expose_api_raw, format_return_as_json)
 from galaxy.webapps.base.controller import (BaseAPIController, SharableMixin,
-                                            UsesStoredWorkflowMixin, url_for)
+                                            url_for, UsesStoredWorkflowMixin)
 from galaxy.workflow.extract import extract_workflow
 from galaxy.workflow.modules import module_factory
 from galaxy.workflow.reports import generate_report
 from galaxy.workflow.run import invoke, queue_invoke
 from galaxy.workflow.run_request import build_workflow_run_configs
-from gxformat2._yaml import ordered_dump
-from markupsafe import escape
 
 import h5py
+
+from markupsafe import escape
 import numpy as np
 from keras.models import model_from_json
 from sqlalchemy import desc, false, or_, true

From b6d05e3d0959a6590910e637372598a3b12b729e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 16:17:08 +0100
Subject: [PATCH 235/853] Update for new 20.01 PRs

---
 doc/source/releases/20.01.rst     | 6 ++++++
 doc/source/releases/20.01_prs.rst | 2 ++
 2 files changed, 8 insertions(+)

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
index c20608d61f13..fffe8a32f5e4 100644
--- a/doc/source/releases/20.01.rst
+++ b/doc/source/releases/20.01.rst
@@ -430,6 +430,9 @@ Fixes
 
 * Fix cool sniffing on python3
   `Pull Request 9153`_
+* Fix `SearchGuiArchive.set_meta()`
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 9437`_
 
 .. bug_tag_tools
 
@@ -778,6 +781,9 @@ Fixes
   `Pull Request 9441`_
 * Fix data tables vue display
   `Pull Request 9442`_
+* Fix `UserManager.get_reset_token()` after `#9432 <https://github.com/galaxyproject/galaxy/issues/9432>`__
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9446`_
 
 .. include:: 20.01_prs.rst
 
diff --git a/doc/source/releases/20.01_prs.rst b/doc/source/releases/20.01_prs.rst
index b59e8a524b59..0a6d9e4ee35c 100644
--- a/doc/source/releases/20.01_prs.rst
+++ b/doc/source/releases/20.01_prs.rst
@@ -337,5 +337,7 @@
 .. _Pull Request 9432: https://github.com/galaxyproject/galaxy/pull/9432
 .. _Pull Request 9433: https://github.com/galaxyproject/galaxy/pull/9433
 .. _Pull Request 9434: https://github.com/galaxyproject/galaxy/pull/9434
+.. _Pull Request 9437: https://github.com/galaxyproject/galaxy/pull/9437
 .. _Pull Request 9441: https://github.com/galaxyproject/galaxy/pull/9441
 .. _Pull Request 9442: https://github.com/galaxyproject/galaxy/pull/9442
+.. _Pull Request 9446: https://github.com/galaxyproject/galaxy/pull/9446

From 35e9af18af55e8dbdcaf049438f3e36bcd6d2e02 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 26 Feb 2020 10:36:45 -0500
Subject: [PATCH 236/853] Update lib/galaxy/config/__init__.py

Use helper method

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/config/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 6416c96ad4cf..bf781b8cc466 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -152,7 +152,7 @@ def _set_config_directories():
                     self.managed_config_dir = os.path.join(self.data_dir, 'config')
 
             # TODO: do we still need to support ../shed_tools when running_from_source?
-            self.shed_tools_dir = os.path.join(self.data_dir, 'shed_tools')
+            self.shed_tools_dir = self._in_data_dir('shed_tools')
 
             log.debug("Configuration directory is %s", self.config_dir)
             log.debug("Data directory is %s", self.data_dir)

From 3d907241a7926161083b9498573dee04d715d32c Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 26 Feb 2020 10:44:45 -0500
Subject: [PATCH 237/853] Use helper method

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/config/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index bf781b8cc466..8c97f0743573 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -149,7 +149,7 @@ def _set_config_directories():
                 if self.data_dir is None:
                     self.data_dir = os.path.join(self.config_dir, 'data')
                 if self.managed_config_dir is None:
-                    self.managed_config_dir = os.path.join(self.data_dir, 'config')
+                    self.managed_config_dir = self._in_data_dir('config')
 
             # TODO: do we still need to support ../shed_tools when running_from_source?
             self.shed_tools_dir = self._in_data_dir('shed_tools')

From 738566ec9e845305908354f8449b0fd8ac94eb79 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 26 Feb 2020 10:46:05 -0500
Subject: [PATCH 238/853] Use helper method

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/config/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 8c97f0743573..d9f04be624d5 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -147,7 +147,7 @@ def _set_config_directories():
                 if self.config_dir is None:
                     self.config_dir = os.getcwd()
                 if self.data_dir is None:
-                    self.data_dir = os.path.join(self.config_dir, 'data')
+                    self.data_dir = self._in_config_dir('data')
                 if self.managed_config_dir is None:
                     self.managed_config_dir = self._in_data_dir('config')
 

From 823526a1fc6c14c868f473f067e68c37ecd5197a Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 26 Feb 2020 10:57:48 -0500
Subject: [PATCH 239/853] Use helper method

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/config/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index d9f04be624d5..741b50c360a4 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -379,7 +379,7 @@ def _process_config(self, kwargs):
         self.oidc_config = kwargs.get("oidc_config_file", self.oidc_config_file)
         self.oidc_backends_config = kwargs.get("oidc_backends_config_file", self.oidc_backends_config_file)
         self.oidc = []
-        self.integrated_tool_panel_config = os.path.join(self.managed_config_dir, self.integrated_tool_panel_config)
+        self.integrated_tool_panel_config = self._in_managed_config_dir(self.integrated_tool_panel_config)
         integrated_tool_panel_tracking_directory = kwargs.get('integrated_tool_panel_tracking_directory')
         if integrated_tool_panel_tracking_directory:
             self.integrated_tool_panel_tracking_directory = os.path.join(self.root, integrated_tool_panel_tracking_directory)

From a9113698b0abc8ea1966268c4182e8e1b9d5f442 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Wed, 26 Feb 2020 11:59:41 -0500
Subject: [PATCH 240/853] Revised code based on code review feedback

---
 .../dependencies/conditional-requirements.txt      |  2 +-
 lib/galaxy/objectstore/irods.py                    |  7 ++++---
 test/integration/object_store_conf.xml             |  1 -
 test/integration/objectstore/test_irods.py         | 14 +++++++-------
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index b57b56bfcbb1..8bb87c708ae8 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -8,7 +8,7 @@ drmaa
 statsd
 docker
 azure-storage==0.32.0
-# PyRods not in PyPI
+python-irodsclient==0.8.2
 python-ldap==3.2.0
 python-pam
 galaxycloudrunner
diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index c77a2ea003a8..a0d8085ffe22 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -24,6 +24,7 @@
     ObjectNotFound
 )
 from galaxy.util import (
+    bytesize,
     directory_hash_id,
     umask_fix_perms,
 )
@@ -172,10 +173,10 @@ def _initialize(self):
         self.home =  "/" + self.zone + "/home/" + self.username
 
         self.session = self._configure_connection(host=self.host, port=self.port, user=self.username, password=self.password, zone=self.zone)
-        # Clean cache only if value is set in galaxy.ini
+        # Clean cache only if value is set in galaxy config file
         if self.cache_size != -1:
             # Convert GBs to bytes for comparison
-            self.cache_size = self.cache_size * 1073741824
+            self.cache_size = self.cache_size * bytesize.SUFFIX_TO_BYTES['GI']
             # Helper for interruptable sleep
             self.sleeper = Sleeper()
             self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
@@ -686,7 +687,7 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
                     log.exception("Trouble copying source file '%s' to cache '%s'", source_file, cache_file)
             else:
                 source_file = self._get_cache_path(rel_path)
-            # Update the file on S3
+            # Update the file on iRODS 
             self._push_to_os(rel_path, source_file)
         else:
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
diff --git a/test/integration/object_store_conf.xml b/test/integration/object_store_conf.xml
index e87548784cc0..778b42f4083e 100644
--- a/test/integration/object_store_conf.xml
+++ b/test/integration/object_store_conf.xml
@@ -1,6 +1,5 @@
 <?xml version="1.0"?>
 <object_store type="irods"> 
-    <files_dir path="database/files3"/>
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
diff --git a/test/integration/objectstore/test_irods.py b/test/integration/objectstore/test_irods.py
index 636b73ee7ed6..19bf3a388e24 100644
--- a/test/integration/objectstore/test_irods.py
+++ b/test/integration/objectstore/test_irods.py
@@ -17,26 +17,26 @@ class IrodsObjectStoreIntegrationTestCase(integration_util.IntegrationTestCase):
 
     container_name = "irods_server"
 
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["object_store_config_file"] = "object_store_conf.xml" 
+
     @classmethod
     def setUpClass(cls):
-        print('Starting setUpClass')
         super(IrodsObjectStoreIntegrationTestCase, cls).setUpClass()
         IrodsObjectStoreIntegrationTestCase.start_irods_server(container_name=IrodsObjectStoreIntegrationTestCase.container_name)
 
         # Let the server start before running the test
         time.sleep(10)
-        print('Finishing setUpClass')
 
     @classmethod
     def tearDownClass(cls): 
-        print('Starting tearDownClass')
         super(IrodsObjectStoreIntegrationTestCase, cls).tearDownClass()
         IrodsObjectStoreIntegrationTestCase.stop_irods_server(container_name=IrodsObjectStoreIntegrationTestCase.container_name)       
-        print('Finishing tearDownClass')
 
     @classmethod
-    def start_irods_server(cls, container_name, postgres_port=5432, irods_port=1247, docker_image='kxk302/irods-server:0.1'):
-        start_server = ['docker', 'run', '-h', 'localhost', '-p', '{port}:5432'.format(port=postgres_port), '-p', '{port}:1247'.format(port=irods_port), '-d', '--name', container_name, docker_image]
+    def start_irods_server(cls, container_name, irods_port=1247, docker_image='kxk302/irods-server:0.1'):
+        start_server = ['docker', 'run', '-h', 'localhost', '-p', '{port}:1247'.format(port=irods_port), '-d', '--name', container_name, docker_image]
         subprocess.check_call(start_server) 
         
     @classmethod
@@ -117,7 +117,7 @@ def test_create_delete_new_data_object(self):
 
             with pytest.raises(CollectionDoesNotExist):
                 coll = session.collections.get(newCollection)
-
+ 
     def test_populate_fetch_new_data_object(self):
         with iRODSSession(host='localhost', 
             port='1247', 

From 997764e5c48a7ef2444e28a793352ca2f030510f Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 26 Feb 2020 17:18:26 +0000
Subject: [PATCH 241/853] Remove `virtualenv<20` requirement for mulled tests

Introduced in commit d8773a9598bcab47fb123dd6db54d0d31445c25d , it is not
needed any more since virtualenv 20.0.6 fixed the issue.
---
 .github/workflows/mulled.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/mulled.yaml b/.github/workflows/mulled.yaml
index 6c96751d1f76..1bdcd1dfde06 100644
--- a/.github/workflows/mulled.yaml
+++ b/.github/workflows/mulled.yaml
@@ -22,7 +22,7 @@ jobs:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Install tox
-      run: pip install tox 'virtualenv<20'
+      run: pip install tox
     - name: run tests
       run: tox -e mulled
       working-directory: 'galaxy root'

From ed8e71d1592504e8137890a3408c693ed72f3f19 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Wed, 26 Feb 2020 13:29:49 -0500
Subject: [PATCH 242/853] More code review changes

---
 .gitignore                                                      | 1 +
 .../{object_store_conf.xml => irods_object_store_conf.xml}      | 0
 test/integration/test_datatype_upload_irods.py                  | 2 +-
 test/unit/objectstore/test_irods.py                             | 0
 4 files changed, 2 insertions(+), 1 deletion(-)
 rename test/integration/{object_store_conf.xml => irods_object_store_conf.xml} (100%)
 create mode 100644 test/unit/objectstore/test_irods.py

diff --git a/.gitignore b/.gitignore
index 35207905f933..31f42a911440 100644
--- a/.gitignore
+++ b/.gitignore
@@ -79,6 +79,7 @@ shed_tool_data_table_conf.xml
 job_conf.xml
 data_manager_conf.xml
 shed_data_manager_conf.xml
+object_store_conf.xml
 job_metrics_conf.xml
 workflow_schedulers_conf.xml
 config/*
diff --git a/test/integration/object_store_conf.xml b/test/integration/irods_object_store_conf.xml
similarity index 100%
rename from test/integration/object_store_conf.xml
rename to test/integration/irods_object_store_conf.xml
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 575628a8aa01..c1de59b14762 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -20,7 +20,7 @@
 GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
 DATATYPES_CONFIG = os.path.join(GALAXY_ROOT, 'lib/galaxy/config/sample/datatypes_conf.xml.sample')
 PARENT_SNIFFER_MAP = {'fastqsolexa': 'fastq'}
-OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "object_store_conf.xml")
+OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "irods_object_store_conf.xml")
 
 
 def find_datatype(registry, filename):
diff --git a/test/unit/objectstore/test_irods.py b/test/unit/objectstore/test_irods.py
new file mode 100644
index 000000000000..e69de29bb2d1

From 74cd45d2adc1dc7f01c73f1331a5728e88d97e14 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 26 Feb 2020 13:34:45 -0500
Subject: [PATCH 243/853] Update migration version number, fix typo

---
 ...d_content_update_time.py => 0165_add_content_update_time.py} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename lib/galaxy/model/migrate/versions/{0162_add_content_update_time.py => 0165_add_content_update_time.py} (95%)

diff --git a/lib/galaxy/model/migrate/versions/0162_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0165_add_content_update_time.py
similarity index 95%
rename from lib/galaxy/model/migrate/versions/0162_add_content_update_time.py
rename to lib/galaxy/model/migrate/versions/0165_add_content_update_time.py
index 7b85a4f68867..734e41aefb06 100644
--- a/lib/galaxy/model/migrate/versions/0162_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0165_add_content_update_time.py
@@ -1,5 +1,5 @@
 """
-Adds timestamps to hdac table. Adds triggers to dataset, hda, hdac tables
+Adds timestamps to hdca table. Adds triggers to dataset, hda, hdca tables
 to update history.update_time when contents are changed.
 """
 from __future__ import print_function

From b2e00afbaf4713125a833548642bec3ce3573829 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 26 Feb 2020 15:35:03 -0500
Subject: [PATCH 244/853] Followup to shed tool static fixes; change order of
 lookup preferring to check static/images first.

---
 .../galaxy/controllers/shed_tool_static.py    | 28 +++++++++----------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py b/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py
index 7f659ad85bf0..5560b1cc2517 100644
--- a/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py
+++ b/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py
@@ -33,24 +33,24 @@ def index(self, trans, shed, owner, repo, tool, version, image_file):
         guid = '/'.join((shed, 'repos', owner, repo, tool, version))
         tool = trans.app.toolbox.get_tool(guid)
         repo_path = os.path.abspath(tool._repository_dir)
-        asset_path = os.path.abspath(join(repo_path, image_file))
-
-        # test specified image_file path exactly first, then fail through to
-        # other locations.
-        # Might want to swap this around and check for static/images first if
-        # that's the new(?) standard.
-        if not _asset_exists_and_is_safe(repo_path, asset_path):
-            if 'static/images' not in image_file:
-                asset_path = join(repo_path, 'static', 'images', image_file)
-                if not _asset_exists_and_is_safe(repo_path, asset_path):
-                    asset_path = None
-
-        if asset_path:
+        found_path = None
+
+        if 'static/images' not in image_file:
+            asset_path = os.path.abspath(join(repo_path, 'static', 'images', image_file))
+            if _asset_exists_and_is_safe(repo_path, asset_path):
+                found_path = asset_path
+
+        if not found_path:
+            asset_path = os.path.abspath(join(repo_path, image_file))
+            if _asset_exists_and_is_safe(repo_path, asset_path):
+                found_path = asset_path
+
+        if found_path:
             ext = os.path.splitext(image_file)[-1].lstrip('.')
             if ext:
                 mime = trans.app.datatypes_registry.get_mimetype_by_extension(ext)
                 if mime:
                     trans.response.set_content_type(mime)
-            return open(asset_path, 'rb')
+            return open(found_path, 'rb')
         else:
             raise RequestParameterInvalidException()

From 4e96e3edce5147aba68afde48bbbca61a4560417 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 27 Feb 2020 11:49:49 +0000
Subject: [PATCH 245/853] Use `with` statement to open file

---
 scripts/bootstrap_history.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index dde83dd5c605..87c471a42896 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -743,8 +743,10 @@ def _releases():
 
 def _github_client():
     try:
-        github_json = os.path.expanduser("~/.github.json")
-        github = Github(**json.load(open(github_json, "r")))
+        github_json_path = os.path.expanduser("~/.github.json")
+        with open(github_json_path, "r") as fh:
+            github_json_dict = json.load(fh)
+        github = Github(**github_json_dict)
     except Exception:
         log.exception()
         github = None

From 2b5efd7960974df0c3268152655b171777755948 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 27 Feb 2020 08:32:38 -0500
Subject: [PATCH 246/853] Fix import order in api/workflows.

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index af2f9a552dfb..a9cb1f469e27 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -8,17 +8,21 @@
 import logging
 import os
 
+import h5py
+import numpy as np
 import requests
 import yaml
-
 from gxformat2._yaml import ordered_dump
+from keras.models import model_from_json
+from markupsafe import escape
+from sqlalchemy import desc, false, or_, true
+from sqlalchemy.orm import joinedload
 
 from galaxy import exceptions, model, util
 from galaxy.managers import histories, workflows
 from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter
 from galaxy.model.item_attrs import UsesAnnotations
-from galaxy.tool_shed.galaxy_install.install_manager import \
-    InstallRepositoryManager
+from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
 from galaxy.tools.parameters import populate_state
 from galaxy.tools.parameters.basic import workflow_building_modes
 from galaxy.util.sanitize_html import sanitize_html
@@ -32,13 +36,6 @@
 from galaxy.workflow.run import invoke, queue_invoke
 from galaxy.workflow.run_request import build_workflow_run_configs
 
-import h5py
-
-from markupsafe import escape
-import numpy as np
-from keras.models import model_from_json
-from sqlalchemy import desc, false, or_, true
-from sqlalchemy.orm import joinedload
 
 log = logging.getLogger(__name__)
 

From 5e3750d9a781dcaa65df87e419d14cb42c9e3685 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Thu, 27 Feb 2020 11:03:47 -0500
Subject: [PATCH 247/853] Interpret empty string as 'value not set'

Based on code review discussion
---
 lib/galaxy/config/__init__.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 741b50c360a4..96d31a47fd37 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -137,18 +137,18 @@ def _set_config_directories():
             self.managed_config_dir = config_kwargs.get('managed_config_dir')
 
             if running_from_source:
-                if self.config_dir is None:
+                if not self.config_dir:
                     self.config_dir = os.path.join(self.root, 'config')
-                if self.data_dir is None:
+                if not self.data_dir:
                     self.data_dir = os.path.join(self.root, 'database')
-                if self.managed_config_dir is None:
+                if not self.managed_config_dir:
                     self.managed_config_dir = self.config_dir
             else:
-                if self.config_dir is None:
+                if not self.config_dir:
                     self.config_dir = os.getcwd()
-                if self.data_dir is None:
+                if not self.data_dir:
                     self.data_dir = self._in_config_dir('data')
-                if self.managed_config_dir is None:
+                if not self.managed_config_dir:
                     self.managed_config_dir = self._in_data_dir('config')
 
             # TODO: do we still need to support ../shed_tools when running_from_source?

From 2bfeeec299990e154b56438a80869b09325e271e Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 27 Feb 2020 16:04:40 +0000
Subject: [PATCH 248/853] Drop pygithub3 dev requirement

---
 lib/galaxy/dependencies/pipfiles/default/Pipfile                 | 1 -
 .../dependencies/pipfiles/default/pinned-dev-requirements.txt    | 1 -
 2 files changed, 2 deletions(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/lib/galaxy/dependencies/pipfiles/default/Pipfile
index 3c3ce61385ae..67964f856123 100644
--- a/lib/galaxy/dependencies/pipfiles/default/Pipfile
+++ b/lib/galaxy/dependencies/pipfiles/default/Pipfile
@@ -13,7 +13,6 @@ gunicorn = "*"
 lxml = "!=4.2.2"
 mock = "*"
 NoseHTML = "*"
-pygithub3 = {version = "*", markers = "python_version < '3'"}
 pytest = "*"
 pytest-cov = "*"
 pytest-html = "*"
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index 7388ad1a6918..cbf02baf09f8 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -34,7 +34,6 @@ pluggy==0.13.1
 port-for==0.4
 psutil==5.6.7
 py==1.8.0
-pygithub3==0.5.1 ; python_version < '3'
 pygments==2.5.2
 pyparsing==2.4.5
 pytest-cov==2.8.1

From 5d4d4c6707da0c75171bcce3ba53cadb31807a15 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Thu, 27 Feb 2020 11:50:42 -0500
Subject: [PATCH 249/853] If managed_config_dir is set by user, ensure path is
 absolute.

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/config/__init__.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 96d31a47fd37..ab2e74ff85dc 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -135,6 +135,8 @@ def _set_config_directories():
             self.data_dir = config_kwargs.get('data_dir')
             self.sample_config_dir = os.path.join(os.path.dirname(__file__), 'sample')
             self.managed_config_dir = config_kwargs.get('managed_config_dir')
+            if self.managed_config_dir:
+                self.managed_config_dir = os.path.abspath(self.managed_config_dir)
 
             if running_from_source:
                 if not self.config_dir:

From a117a9a6627507b30a7953f9626930633dc54316 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 27 Feb 2020 18:09:03 +0100
Subject: [PATCH 250/853] Update version to 20.01.rc1

---
 lib/galaxy/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py
index c6f9ae3dcc78..a7147a4caba4 100644
--- a/lib/galaxy/version.py
+++ b/lib/galaxy/version.py
@@ -1,3 +1,3 @@
 VERSION_MAJOR = "20.01"
-VERSION_MINOR = "dev"
+VERSION_MINOR = "rc1"
 VERSION = VERSION_MAJOR + ('.' + VERSION_MINOR if VERSION_MINOR else '')

From 4759d3d33d78b8c6f7a831a396afe72f5a7ffb64 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 27 Feb 2020 18:09:04 +0100
Subject: [PATCH 251/853] Update version to 20.05.dev

---
 lib/galaxy/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py
index c6f9ae3dcc78..f3f1e9c320cd 100644
--- a/lib/galaxy/version.py
+++ b/lib/galaxy/version.py
@@ -1,3 +1,3 @@
-VERSION_MAJOR = "20.01"
+VERSION_MAJOR = "20.05"
 VERSION_MINOR = "dev"
 VERSION = VERSION_MAJOR + ('.' + VERSION_MINOR if VERSION_MINOR else '')

From 2faef5510fc86c2454ed72d65c70302b5bd050a0 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 27 Feb 2020 19:42:00 +0100
Subject: [PATCH 252/853] Update version to 20.01

---
 lib/galaxy/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py
index a7147a4caba4..74e8bc6cc835 100644
--- a/lib/galaxy/version.py
+++ b/lib/galaxy/version.py
@@ -1,3 +1,3 @@
 VERSION_MAJOR = "20.01"
-VERSION_MINOR = "rc1"
+VERSION_MINOR = None
 VERSION = VERSION_MAJOR + ('.' + VERSION_MINOR if VERSION_MINOR else '')

From a974d02b236e104af7089a85f49cd01a2aa03aeb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 27 Feb 2020 21:03:20 +0100
Subject: [PATCH 253/853] Fix newlines in final release notes

---
 doc/source/releases/20.01.rst | 55 -----------------------------------
 1 file changed, 55 deletions(-)

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
index fffe8a32f5e4..1495ff7a09b0 100644
--- a/doc/source/releases/20.01.rst
+++ b/doc/source/releases/20.01.rst
@@ -9,11 +9,6 @@
 Enhancements
 -------------------------------
 
-.. major_feature
-
-
-.. feature
-
 * CLI tools for installing/testing Docker and Singularity containers
   (thanks to `@simonbray <https://github.com/simonbray>`__).
   `Pull Request 7936`_
@@ -37,14 +32,8 @@ Enhancements
 * Remove GenomeSpace tools, OpenID, UI and requirements
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 9363`_
-
-.. enhancement_tag_viz
-
 * Hyphy-vision fixes and updates.
   `Pull Request 9384`_
-
-.. enhancement_tag_datatypes
-
 * Datatypes for MassSpec DIA dlib,elib
   (thanks to `@jj-umn <https://github.com/jj-umn>`__).
   `Pull Request 8657`_
@@ -68,9 +57,6 @@ Enhancements
   `Pull Request 9087`_
 * Add tabular.gz datatype and add embl to uploadable formats
   `Pull Request 9293`_
-
-.. enhancement_tag_tools
-
 * Upgrade askomics interactive tool
   (thanks to `@xgaia <https://github.com/xgaia>`__).
   `Pull Request 8517`_
@@ -86,9 +72,6 @@ Enhancements
   `Pull Request 9003`_
 * Move sam_pileup to GALAXY_LIB_TOOLS_VERSIONED
   `Pull Request 9320`_
-
-.. enhancement_tag_workflows
-
 * Interactive modification of invocation report.
   `Pull Request 8691`_
 * User-facing Workflow Invocation Grid
@@ -107,9 +90,6 @@ Enhancements
   `Pull Request 9099`_
 * add option select_type_workflow_threshold (rebase)
   `Pull Request 9105`_
-
-.. enhancement_tag_ui
-
 * Upgrade eslint (major version), fix compliance with new standard rules.
   `Pull Request 8708`_
 * JobMetrics.vue unit test.
@@ -120,9 +100,6 @@ Enhancements
   `Pull Request 8749`_
 * Added client-side application configs for each target environment
   `Pull Request 8827`_
-
-.. enhancement_tag_jobs
-
 * Small cleanup for job runners kill
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 8523`_
@@ -146,17 +123,11 @@ Enhancements
   `Pull Request 9314`_
 * Allow remote jobs to configure Interactive Tool entry points.
   `Pull Request 9349`_
-
-.. enhancement_tag_admin
-
 * Add Tool Manager Component for Admin Panel
   `Pull Request 8601`_
 * Add process ID to worker_process table
   (thanks to `@selten <https://github.com/selten>`__).
   `Pull Request 8972`_
-
-.. enhancement
-
 * Use official "login with" buttons for OIDC
   (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 8107`_, `Pull Request 9102`_
@@ -308,9 +279,6 @@ Enhancements
   `Pull Request 9233`_
 * Fixes for IGV GEDA handling of genomes
   `Pull Request 9413`_
-
-.. small_enhancement
-
 * Factor out yaml read/write from config_manage.py
   `Pull Request 8509`_
 * Implementation of the workflow list as vue component
@@ -412,11 +380,6 @@ Enhancements
 Fixes
 -------------------------------
 
-.. major_bug
-
-
-.. bug_tag_viz
-
 * Wrap SQL statement in a text() function as required by sqlalchemy
   (thanks to `@kaukrise <https://github.com/kaukrise>`__).
   `Pull Request 9216`_
@@ -425,17 +388,11 @@ Fixes
   `Pull Request 9217`_
 * Various python 3 fixes from sentry
   `Pull Request 9337`_
-
-.. bug_tag_datatypes
-
 * Fix cool sniffing on python3
   `Pull Request 9153`_
 * Fix `SearchGuiArchive.set_meta()`
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 9437`_
-
-.. bug_tag_tools
-
 * grouping: strip newlines
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 8953`_
@@ -448,9 +405,6 @@ Fixes
   `Pull Request 9354`_
 * Fix maf tools
   `Pull Request 9393`_
-
-.. bug_tag_workflows
-
 * Exports reports with workflows (if configured).
   `Pull Request 9055`_
 * Rev gxformat2 dependency to fix various export issues.
@@ -459,9 +413,6 @@ Fixes
   `Pull Request 9315`_
 * Various fixes and enhancements to reports
   `Pull Request 9316`_
-
-.. bug_tag_jobs
-
 * Small fixes for k8s.
   `Pull Request 8759`_
 * Fix output.file_path writing to read-only path on Docker
@@ -496,9 +447,6 @@ Fixes
   `Pull Request 9406`_
 * Strip unicode null characters from traceback and job_messages
   `Pull Request 9430`_
-
-.. bug_tag_admin
-
 * Encode lines in filter_file_fields
   (thanks to `@selten <https://github.com/selten>`__).
   `Pull Request 8652`_
@@ -511,9 +459,6 @@ Fixes
   `Pull Request 9193`_
 * Always add shed_tool_config file to tool_configs
   `Pull Request 9364`_
-
-.. bug
-
 * Documentation update
   (thanks to `@selten <https://github.com/selten>`__).
   `Pull Request 8508`_

From 138fab513815939661c36e1fecd0ee354d1d090b Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 27 Feb 2020 15:08:31 -0500
Subject: [PATCH 254/853] Added the first unit test for iRODS. Some code
 cleanup from previous code review comments.

---
 .../dependencies/pipfiles/default/Pipfile     |  1 +
 .../default/pinned-dev-requirements.txt       |  2 +
 .../pipfiles/default/pinned-requirements.txt  |  1 +
 lib/galaxy/objectstore/irods.py               | 70 +++++++++++--------
 .../objectstore/irods_object_store_conf.xml   | 10 +++
 .../irods_object_store_conf_no_auth.xml       | 10 +++
 .../irods_object_store_conf_no_extra_dir.xml  | 10 +++
 test/unit/objectstore/test_irods.py           | 48 +++++++++++++
 8 files changed, 121 insertions(+), 31 deletions(-)
 create mode 100644 test/unit/objectstore/irods_object_store_conf.xml
 create mode 100644 test/unit/objectstore/irods_object_store_conf_no_auth.xml
 create mode 100644 test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml

diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/lib/galaxy/dependencies/pipfiles/default/Pipfile
index 48114734ccca..12a7b1398ff2 100644
--- a/lib/galaxy/dependencies/pipfiles/default/Pipfile
+++ b/lib/galaxy/dependencies/pipfiles/default/Pipfile
@@ -27,6 +27,7 @@ sphinx_rtd_theme = "*"
 testfixtures = "*"
 twill = {version = "==0.9.1", markers = "python_version < '3'"}
 watchdog = "*"
+python-irodsclient = "*"
 
 [packages]
 numpy = "*"
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index facffd36b33a..8d31cd3884af 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -32,6 +32,7 @@ pathlib2==2.3.5 ; python_version < '3.6'
 pathtools==0.1.2
 pluggy==0.13.1
 port-for==0.4
+prettytable==0.7.2
 psutil==5.6.7
 py==1.8.1
 pygithub3==0.5.1 ; python_version < '3'
@@ -62,4 +63,5 @@ typing==3.7.4.1 ; python_version < '3.5'
 urllib3==1.25.7 ; python_version == '2.7'
 watchdog==0.9.0
 wcwidth==0.1.8 ; sys_platform != 'win32'
+xmlrunner==1.7.7
 zipp==0.6.0
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index ace88d26b5c1..8aa633b8b83a 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -58,6 +58,7 @@ enum34==1.1.6 ; python_version < '3.4'
 fabric3==1.14.post1
 funcsigs==1.0.2 ; python_version < '3.3'
 functools32==3.2.3.post2 ; python_version < '3.2'
+future==0.18.2
 futures==3.3.0 ; python_version == '2.6' or python_version == '2.7'
 galaxy-sequence-utils==1.1.3
 google-api-python-client==1.7.8
diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index a0d8085ffe22..ba4156d26cc1 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -40,38 +40,46 @@
 
 log = logging.getLogger(__name__)
 
+def _parse_error(tag):
+    msg = 'No {tag} element in XML tree'.format(tag=tag)
+    log.error(msg)
+    raise Exception(msg)
+
 def parse_config_xml(config_xml):
     try:
-        a_xml = config_xml.findall('auth')[0]
-        username = a_xml.get('username')
-        password = a_xml.get('password')
-
-        b_xml = config_xml.findall('resource')[0]
-        resource_name = b_xml.get('name')
-
-        b_xml = config_xml.findall('zone')[0]
-        zone_name = b_xml.get('name')
-
-        cn_xml = config_xml.findall('connection')
-        if not cn_xml:
-            cn_xml = {}
-        else:
-            cn_xml = cn_xml[0]
-
-        host = cn_xml.get('host', None)
-        port = int(cn_xml.get('port', 0))
-
-        c_xml = config_xml.findall('cache')[0]
-        cache_size = float(c_xml.get('size', -1))
-        staging_path = c_xml.get('path', None)
-
-        tag, attrs = 'extra_dir', ('type', 'path')
-        extra_dirs = config_xml.findall(tag)
-        if not extra_dirs:
-            msg = 'No {tag} element in XML tree'.format(tag=tag)
-            log.error(msg)
-            raise Exception(msg)
-        extra_dirs = [dict(((k, e.get(k)) for k in attrs)) for e in extra_dirs]
+        a_xml = config_xml.findall('auth')
+        if not a_xml:
+            _parse_error('auth')
+        username = a_xml[0].get('username')
+        password = a_xml[0].get('password')
+
+        r_xml = config_xml.findall('resource')
+        if not r_xml:
+            _parse_error('resource')
+        resource_name = r_xml[0].get('name')
+
+        z_xml = config_xml.findall('zone')
+        if not z_xml:
+            _parse_error('zone')
+        zone_name = z_xml[0].get('name')
+
+        c_xml = config_xml.findall('connection')
+        if not c_xml:
+            _parse_error('connection')
+        host = c_xml[0].get('host', None)
+        port = int(c_xml[0].get('port', 0))
+
+        c_xml = config_xml.findall('cache')
+        if not c_xml:
+            _parse_error('cache')
+        cache_size = float(c_xml[0].get('size', -1))
+        staging_path = c_xml[0].get('path', None)
+
+        attrs = ('type', 'path')
+        e_xml = config_xml.findall('extra_dir')
+        if not e_xml:
+            _parse_error('extra_dir')
+        extra_dirs = [dict(((k, e.get(k)) for k in attrs)) for e in e_xml]
 
         return {
             'auth': {
@@ -96,7 +104,7 @@ def parse_config_xml(config_xml):
         }
     except Exception:
         # Toss it back up after logging, we can't continue loading at this point.
-        log.exception("Malformed iRODS ObjectStore Configuration XML -- unable to continue")
+        log.exception("Malformed iRODS ObjectStore Configuration XML -- unable to continue.")
         raise
 
 class CloudConfigMixin(object):
diff --git a/test/unit/objectstore/irods_object_store_conf.xml b/test/unit/objectstore/irods_object_store_conf.xml
new file mode 100644
index 000000000000..778b42f4083e
--- /dev/null
+++ b/test/unit/objectstore/irods_object_store_conf.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<object_store type="irods"> 
+    <auth username="rods" password="rods" />
+    <resource name="demoResc" />
+    <zone name="tempZone" />
+    <connection host="localhost" port="1247"/>
+    <cache path="database/object_store_cache" size="1000" />
+    <extra_dir type="job_work" path="database/job_working_directory_irods"/>
+    <extra_dir type="temp" path="database/tmp_irods"/>
+</object_store>
diff --git a/test/unit/objectstore/irods_object_store_conf_no_auth.xml b/test/unit/objectstore/irods_object_store_conf_no_auth.xml
new file mode 100644
index 000000000000..7388b11fe358
--- /dev/null
+++ b/test/unit/objectstore/irods_object_store_conf_no_auth.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<object_store type="irods"> 
+    <!--<auth username="rods" password="rods" />-->
+    <resource name="demoResc" />
+    <zone name="tempZone" />
+    <connection host="localhost" port="1247"/>
+    <cache path="database/object_store_cache" size="1000" />
+    <extra_dir type="job_work" path="database/job_working_directory_irods"/>
+    <extra_dir type="temp" path="database/tmp_irods"/>
+</object_store>
diff --git a/test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml b/test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml
new file mode 100644
index 000000000000..d2c07a428ac0
--- /dev/null
+++ b/test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<object_store type="irods"> 
+    <auth username="rods" password="rods" />
+    <resource name="demoResc" />
+    <zone name="tempZone" />
+    <connection host="localhost" port="1247"/>
+    <cache path="database/object_store_cache" size="1000" />
+    <!--<extra_dir type="job_work" path="database/job_working_directory_irods"/>-->
+    <!--<extra_dir type="temp" path="database/tmp_irods"/>-->
+</object_store>
diff --git a/test/unit/objectstore/test_irods.py b/test/unit/objectstore/test_irods.py
index e69de29bb2d1..43cc604b90f1 100644
--- a/test/unit/objectstore/test_irods.py
+++ b/test/unit/objectstore/test_irods.py
@@ -0,0 +1,48 @@
+import os
+import xml.etree.ElementTree as ET
+
+import pytest
+
+from galaxy.objectstore.irods import parse_config_xml
+from galaxy.objectstore.irods import IRODSObjectStore
+
+SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
+
+CONFIG_FILE_NAME = 'irods_object_store_conf.xml'
+CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME)
+
+CONFIG_FILE_NAME_NO_EXTRA_DIR = 'irods_object_store_conf_no_extra_dir.xml'
+CONFIG_FILE_NO_EXTRA_DIR = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME_NO_EXTRA_DIR)
+
+CONFIG_FILE_NAME_NO_AUTH = 'irods_object_store_conf_no_auth.xml'
+CONFIG_FILE_NO_AUTH = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME_NO_AUTH)
+
+def test_parse_valid_config_xml():
+    tree = ET.parse(CONFIG_FILE)
+    root = tree.getroot()
+    config = parse_config_xml(root)
+
+    assert config['auth']['username'] == 'rods'
+    assert config['auth']['password'] == 'rods'
+    assert config['resource']['name'] == 'demoResc'
+    assert config['zone']['name'] == 'tempZone'
+    assert config['connection']['host'] == 'localhost'
+    assert config['connection']['port'] == 1247
+    assert config['cache']['path'] == 'database/object_store_cache'
+    assert config['cache']['size'] == 1000
+    assert config['extra_dirs'][0]['type'] == 'job_work'
+    assert config['extra_dirs'][0]['path'] == 'database/job_working_directory_irods'
+    assert config['extra_dirs'][1]['type'] == 'temp'
+    assert config['extra_dirs'][1]['path'] == 'database/tmp_irods'
+
+def test_parse_config_xml_no_extra_dir():
+    tree = ET.parse(CONFIG_FILE_NO_EXTRA_DIR)
+    root = tree.getroot()
+    with pytest.raises(Exception, match='No extra_dir element in XML tree'): 
+        parse_config_xml(root)
+
+def test_parse_config_xml_no_auth():
+    tree = ET.parse(CONFIG_FILE_NO_AUTH)
+    root = tree.getroot()
+    with pytest.raises(Exception, match='No auth element in XML tree'): 
+        parse_config_xml(root)
\ No newline at end of file

From 8340dda9206a2e14b333a923079f65d3e7034eaf Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 27 Feb 2020 22:32:45 +0100
Subject: [PATCH 255/853] restore imports to be on separate lines

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 27 +++++++++++++++++-----
 1 file changed, 21 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index a9cb1f469e27..c058bbd9eb66 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -18,18 +18,33 @@
 from sqlalchemy import desc, false, or_, true
 from sqlalchemy.orm import joinedload
 
-from galaxy import exceptions, model, util
-from galaxy.managers import histories, workflows
+from galaxy import (
+    exceptions,
+    model,
+    util
+)
+from galaxy.managers import (
+    histories,
+    workflows
+)
 from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
 from galaxy.tools.parameters import populate_state
 from galaxy.tools.parameters.basic import workflow_building_modes
 from galaxy.util.sanitize_html import sanitize_html
-from galaxy.web import (expose_api, expose_api_anonymous_and_sessionless,
-                        expose_api_raw, format_return_as_json)
-from galaxy.webapps.base.controller import (BaseAPIController, SharableMixin,
-                                            url_for, UsesStoredWorkflowMixin)
+from galaxy.web import (
+    expose_api,
+    expose_api_anonymous_and_sessionless,
+    expose_api_raw,
+    format_return_as_json,
+)
+from galaxy.webapps.base.controller import (
+    BaseAPIController,
+    SharableMixin,
+    url_for,
+    UsesStoredWorkflowMixin
+)
 from galaxy.workflow.extract import extract_workflow
 from galaxy.workflow.modules import module_factory
 from galaxy.workflow.reports import generate_report

From 7c8ae9b85b32cec8a2d0d6b53388b228add6d67c Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 27 Feb 2020 22:33:53 +0100
Subject: [PATCH 256/853] R

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index c058bbd9eb66..d79fdae9b454 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -51,7 +51,6 @@
 from galaxy.workflow.run import invoke, queue_invoke
 from galaxy.workflow.run_request import build_workflow_run_configs
 
-
 log = logging.getLogger(__name__)
 
 

From 2f4f567e4b0fae68d0160d2e4f1a3a137540047d Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 27 Feb 2020 23:26:15 +0100
Subject: [PATCH 257/853] Add keras and tensorflow as conditional requirements

---
 lib/galaxy/dependencies/__init__.py                         | 6 ++++++
 lib/galaxy/dependencies/conditional-requirements.txt        | 4 ++++
 .../dependencies/pipfiles/default/pinned-requirements.txt   | 2 --
 lib/galaxy/webapps/galaxy/api/workflows.py                  | 4 +++-
 4 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index 4d398f0f2308..328e553cb73a 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -194,6 +194,12 @@ def check_pygithub(self):
     def check_influxdb(self):
         return 'influxdb' in self.error_report_modules
 
+    def check_keras(self):
+        return asbool(self.config["enable_tool_recommendations"])
+
+    def check_tensorflow(self):
+        return asbool(self.config["enable_tool_recommendations"])
+
 
 def optional(config_file=None):
     if not config_file:
diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index b57b56bfcbb1..239441722983 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -28,3 +28,7 @@ watchdog
 python-gitlab
 pygithub
 influxdb
+
+# Deep learning packages for tool recommendation
+keras==2.2.4
+tensorflow==1.15.0
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index dc64eec6383d..61ceec85d97a 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -78,7 +78,6 @@ jmespath==0.9.4
 jsonpatch==1.25
 jsonpointer==2.0
 jsonschema==3.2.0
-keras==2.2.4
 keystoneauth1==3.18.0
 kombu==4.6.7
 lockfile==0.12.2
@@ -181,7 +180,6 @@ subprocess32==3.5.4 ; python_version < '3.0'
 svgwrite==1.3.1
 tempita==0.5.2
 tenacity==4.12.0
-tensorflow==1.15.0
 typing-extensions==3.7.4.1
 typing==3.7.4.1 ; python_version < '3.5'
 tzlocal==2.0.0
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index d79fdae9b454..3a477020cbb4 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -13,7 +13,6 @@
 import requests
 import yaml
 from gxformat2._yaml import ordered_dump
-from keras.models import model_from_json
 from markupsafe import escape
 from sqlalchemy import desc, false, or_, true
 from sqlalchemy.orm import joinedload
@@ -675,6 +674,9 @@ def __set_model(self, trans, remote_model_url):
         Create model and associated dictionaries for recommendations
         """
         if not self.tool_recommendation_model_path:
+            # import moves from the top of file: in case the tool recommendation feature is disabled,
+            # keras is not downloaded because of conditional requirement and Galaxy does not build
+            from keras.models import model_from_json
             self.tool_recommendation_model_path = self.__download_model(remote_model_url)
             self.all_tools = dict()
             model_weights = list()

From 8ffd6d76a99261f3c542b4d0105af25ff61a4a53 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 28 Feb 2020 01:55:46 +0000
Subject: [PATCH 258/853] Fix `test_run_simple()` test broken on Python 2 by
 virtualenv 20.0.5

xref. https://github.com/pypa/virtualenv/issues/1670
---
 .circleci/config.yml                  | 4 +++-
 test/unit/jobs/test_expression_run.py | 5 ++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index a87c6269b746..6dd34eb5be25 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -95,7 +95,9 @@ jobs:
     <<: *set_workdir
     steps:
       - *restore_repo_cache
-      - *install_tox
+      # Temporary virtualenv pin added due to https://github.com/pypa/virtualenv/issues/1670
+      #- *install_tox
+      - run: sudo pip install tox virtualenv==20.0.4
       - run: tox -e py27-unit
   py35_docstring:
     docker:
diff --git a/test/unit/jobs/test_expression_run.py b/test/unit/jobs/test_expression_run.py
index c23455d6e07d..3a4e0709943f 100644
--- a/test/unit/jobs/test_expression_run.py
+++ b/test/unit/jobs/test_expression_run.py
@@ -32,15 +32,14 @@ def test_run_simple():
         if "PYTHONPATH" in new_env:
             new_env['PYTHONPATH'] = "%s:%s" % (LIB_DIRECTORY, new_env["PYTHONPATH"])
         else:
-            new_env['PYTHONPATH'] = "%s" % (LIB_DIRECTORY)
+            new_env['PYTHONPATH'] = LIB_DIRECTORY
         new_env['GALAXY_EXPRESSION_INPUTS'] = environment_path
-        p = subprocess.Popen(
+        subprocess.check_call(
             args=expressions.EXPRESSION_SCRIPT_CALL,
             shell=True,
             cwd=test_directory,
             env=new_env,
         )
-        assert p.wait() == 0
         with open(os.path.join(test_directory, 'moo')) as f:
             out_content = f.read()
         assert out_content == '7', out_content

From 7b5a1d99dc04dfbb3ae0b7b8d0001490b62fae9a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 28 Feb 2020 11:19:06 +0100
Subject: [PATCH 259/853] Use browser locale over global default

Not 100% sure this is correct, but it seems logical to me.
Should fix https://github.com/galaxyproject/galaxy/issues/9459.
---
 client/galaxy/scripts/app/galaxy.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/app/galaxy.js b/client/galaxy/scripts/app/galaxy.js
index 8431bd1cb5f0..584a7608c7de 100644
--- a/client/galaxy/scripts/app/galaxy.js
+++ b/client/galaxy/scripts/app/galaxy.js
@@ -209,7 +209,7 @@ GalaxyApp.prototype._initUserLocale = function _initUserLocale(options) {
             ? "__root"
             : (navigator.language || navigator.userLanguage || "__root").toLowerCase();
 
-    const locale = user_locale || global_locale || nav_locale;
+    const locale = user_locale || nav_locale || global_locale;
 
     sessionStorage.setItem("currentLocale", locale);
 };

From 34ca9c3167918325aa7c60d2ac78e4ddcedf4c0d Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 28 Feb 2020 11:31:14 -0500
Subject: [PATCH 260/853] Fix handling of default locale as 'auto'

---
 client/galaxy/scripts/app/galaxy.js | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/app/galaxy.js b/client/galaxy/scripts/app/galaxy.js
index 584a7608c7de..1c1d2f484ee4 100644
--- a/client/galaxy/scripts/app/galaxy.js
+++ b/client/galaxy/scripts/app/galaxy.js
@@ -188,7 +188,10 @@ GalaxyApp.prototype._initLocale = function _initLocale(options) {
 /** add the localize fn to this object and the window namespace (as '_l') */
 GalaxyApp.prototype._initUserLocale = function _initUserLocale(options) {
     // Choose best locale
-    const global_locale = this.config.default_locale ? this.config.default_locale.toLowerCase() : false;
+    const global_locale =
+        this.config.default_locale && this.config.default_locale != "auto"
+            ? this.config.default_locale.toLowerCase()
+            : false;
 
     let extra_user_preferences = {};
     if (this.user && this.user.attributes.preferences && "extra_user_preferences" in this.user.attributes.preferences) {

From 8ffa43fbdf3f68fd6915614824f3669bfbc2da9a Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Thu, 27 Feb 2020 13:18:45 -0500
Subject: [PATCH 261/853] Move sanitize_whitelist into mutable_config_dir

---
 lib/galaxy/config/__init__.py               | 2 +-
 lib/galaxy/webapps/galaxy/config_schema.yml | 4 +++-
 test/integration/test_config_defaults.py    | 2 +-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 3fdc7f9af3a1..70df631b7411 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -485,7 +485,7 @@ def _process_config(self, kwargs):
         self.pbs_dataset_server = kwargs.get('pbs_dataset_server', "")
         self.pbs_dataset_path = kwargs.get('pbs_dataset_path', "")
         self.pbs_stage_path = kwargs.get('pbs_stage_path', "")
-        self.sanitize_whitelist_file = os.path.join(self.root, self.sanitize_whitelist_file)
+        self.sanitize_whitelist_file = self._in_mutable_config_dir(self.sanitize_whitelist_file)
         self.allowed_origin_hostnames = self._parse_allowed_origin_hostnames(kwargs)
         if "trust_jupyter_notebook_conversion" not in kwargs:
             # if option not set, check IPython-named alternative, falling back to schema default if not set either
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 692a0e4a3b46..ea9487f31e1a 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -1579,7 +1579,7 @@ mapping:
 
       sanitize_whitelist_file:
         type: str
-        default: config/sanitize_whitelist.txt
+        default: sanitize_whitelist.txt
         required: false
         desc: |
           Whitelist sanitization file.
@@ -1587,6 +1587,8 @@ mapping:
           their HTML sanitized on display.  This can be manually edited or manipulated
           through the Admin control panel -- see "Manage Display Whitelist"
 
+          The value of this option will be resolved with respect to <mutable_config_dir>.
+
       serve_xss_vulnerable_mimetypes:
         type: bool
         default: false
diff --git a/test/integration/test_config_defaults.py b/test/integration/test_config_defaults.py
index c8d2ff5f26e9..2ac152c57c25 100644
--- a/test/integration/test_config_defaults.py
+++ b/test/integration/test_config_defaults.py
@@ -115,7 +115,7 @@
     'object_store_config_file': 'config_dir',
     'oidc_backends_config_file': 'config_dir',
     'oidc_config_file': 'config_dir',
-    'sanitize_whitelist_file': 'root_dir',
+    'sanitize_whitelist_file': 'managed_config_dir',
     'shed_data_manager_config_file': 'managed_config_dir',
     'shed_tool_config_file': 'managed_config_dir',
     'shed_tool_data_path': 'tool_data_path',

From b31d63e92fb14f84128f3ee6794967d5a1213ae2 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Thu, 27 Feb 2020 13:23:43 -0500
Subject: [PATCH 262/853] Run make config-rebuild

---
 doc/source/admin/galaxy_options.rst        | 4 +++-
 lib/galaxy/config/sample/galaxy.yml.sample | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index ac2f2193d4bc..7dbbc2c61774 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -2150,7 +2150,9 @@
     this file are trusted and will not have their HTML sanitized on
     display.  This can be manually edited or manipulated through the
     Admin control panel -- see "Manage Display Whitelist"
-:Default: ``config/sanitize_whitelist.txt``
+    The value of this option will be resolved with respect to
+    <mutable_config_dir>.
+:Default: ``sanitize_whitelist.txt``
 :Type: str
 
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index d83688671589..86d5bde7ec1b 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1085,7 +1085,9 @@ galaxy:
   # this file are trusted and will not have their HTML sanitized on
   # display.  This can be manually edited or manipulated through the
   # Admin control panel -- see "Manage Display Whitelist"
-  #sanitize_whitelist_file: config/sanitize_whitelist.txt
+  # The value of this option will be resolved with respect to
+  # <mutable_config_dir>.
+  #sanitize_whitelist_file: sanitize_whitelist.txt
 
   # By default Galaxy will serve non-HTML tool output that may
   # potentially contain browser executable JavaScript content as plain

From a65c773cb4bd39603d1fb1e3563908121f08796e Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 28 Feb 2020 11:37:13 -0500
Subject: [PATCH 263/853] Check for old default value + rebase

Not to break existing installations. Log a warning message if old file
exists.
---
 lib/galaxy/config/__init__.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 70df631b7411..100b64e57733 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -485,7 +485,17 @@ def _process_config(self, kwargs):
         self.pbs_dataset_server = kwargs.get('pbs_dataset_server', "")
         self.pbs_dataset_path = kwargs.get('pbs_dataset_path', "")
         self.pbs_stage_path = kwargs.get('pbs_stage_path', "")
-        self.sanitize_whitelist_file = self._in_mutable_config_dir(self.sanitize_whitelist_file)
+
+        _sanitize_whitelist_path = self._in_managed_config_dir(self.sanitize_whitelist_file)
+        if not os.path.isfile(_sanitize_whitelist_path):  # then check old default location
+            deprecated = os.path.join(self.root, 'config/sanitize_whitelist.txt')
+            if os.path.isfile(deprecated):
+                log.warning("The path '%s' for the 'sanitize_whitelist_file' config option is "
+                    "deprecated and will be no longer checked in a future release. Please consult "
+                    "the latest version of the sample configuration file." % deprecated)
+                _sanitize_whitelist_path = deprecated
+        self.sanitize_whitelist_file = _sanitize_whitelist_path
+
         self.allowed_origin_hostnames = self._parse_allowed_origin_hostnames(kwargs)
         if "trust_jupyter_notebook_conversion" not in kwargs:
             # if option not set, check IPython-named alternative, falling back to schema default if not set either

From 13f906738a11c8ee7122e15cb4871445a01a580b Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 28 Feb 2020 15:44:59 -0500
Subject: [PATCH 264/853] Added some input validation. Added first integration
 test.

---
 lib/galaxy/objectstore/irods.py            |  68 +++++--
 test/integration/objectstore/test_irods.py | 221 ++++++---------------
 2 files changed, 107 insertions(+), 182 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index ba4156d26cc1..a9ec524cfb11 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -40,45 +40,48 @@
 
 log = logging.getLogger(__name__)
 
-def _parse_error(tag):
-    msg = 'No {tag} element in XML tree'.format(tag=tag)
-    log.error(msg)
+def _config_xml_error(tag):
+    msg = 'No {tag} element in config XML tree'.format(tag=tag)
+    raise Exception(msg)
+
+def _config_dict_error(key):
+    msg = 'No {key} key in config dictionary'.forma(key=key)
     raise Exception(msg)
 
 def parse_config_xml(config_xml):
     try:
         a_xml = config_xml.findall('auth')
         if not a_xml:
-            _parse_error('auth')
+            _config_xml_error('auth')
         username = a_xml[0].get('username')
         password = a_xml[0].get('password')
 
         r_xml = config_xml.findall('resource')
         if not r_xml:
-            _parse_error('resource')
+            _config_xml_error('resource')
         resource_name = r_xml[0].get('name')
 
         z_xml = config_xml.findall('zone')
         if not z_xml:
-            _parse_error('zone')
+            _config_xml_error('zone')
         zone_name = z_xml[0].get('name')
 
         c_xml = config_xml.findall('connection')
         if not c_xml:
-            _parse_error('connection')
+            _config_xml_error('connection')
         host = c_xml[0].get('host', None)
         port = int(c_xml[0].get('port', 0))
 
         c_xml = config_xml.findall('cache')
         if not c_xml:
-            _parse_error('cache')
+            _config_xml_error('cache')
         cache_size = float(c_xml[0].get('size', -1))
         staging_path = c_xml[0].get('path', None)
 
         attrs = ('type', 'path')
         e_xml = config_xml.findall('extra_dir')
         if not e_xml:
-            _parse_error('extra_dir')
+            _config_xml_error('extra_dir')
         extra_dirs = [dict(((k, e.get(k)) for k in attrs)) for e in e_xml]
 
         return {
@@ -139,36 +142,59 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
     
     store_type = 'irods'
     
-    #def _get_bucket(self, bucket_name):
-    #def _key_exists(self, rel_path):
-
     def __init__(self, config, config_dict):
         super(IRODSObjectStore, self).__init__(config, config_dict)
 
-        auth_dict = config_dict['auth']
+        auth_dict = config_dict.get('auth')
+        if auth_dict is None:
+            _config_dict_error('auth')
+
         self.username = auth_dict.get('username')
+        if self.username is None:
+            _config_dict_error('auth->username')
         self.password = auth_dict.get('password')
+        if self.password is None:
+            _config_dict_error('auth->password')
 
         resource_dict = config_dict['resource']
+        if resource_dict is None:
+            _config_dict_error('resource')
         self.resource = resource_dict.get('name')
+        if self.resource is None:
+            _config_dict_error('resource->name')
 
         zone_dict = config_dict['zone']
+        if zone_dict is None:
+            _config_dict_error('zone')
         self.zone = zone_dict.get('name')
+        if self.zone is None:
+            _config_dict_error('zone->name')
 
         connection_dict = config_dict['connection']
+        if connection_dict is None:
+            _config_dict_error('connection')
         self.host = connection_dict.get('host')
+        if self.host is None:
+            _config_dict_error('connection->host')
         self.port = connection_dict.get('port')
+        if self.port is None:
+            _config_dict_error('connection->port')
 
         cache_dict = config_dict['cache']
+        if cache_dict is None:
+            _config_dict_error('cache')
         self.cache_size = cache_dict.get('size', -1)
+        if self.cache_size is None:
+            _config_dict_error('cache->size')
         self.staging_path = cache_dict.get('path') or self.config.object_store_cache_path
+        if self.staging_path is None:
+            _config_dict_error('cache->path')
 
         extra_dirs = dict((e['type'], e['path']) for e in config_dict.get('extra_dirs', []))
+        if not extra_dirs:
+            _config_dict_error('extra_dirs')
         self.extra_dirs.update(extra_dirs)
 
-        log.debug("Object cache dir: %s", self.staging_path)
-        log.debug("Job work dir: %s", self.extra_dirs['job_work'])
-
         self._initialize()
         
     def __del__(self):
@@ -193,8 +219,12 @@ def _initialize(self):
 
     def _configure_connection(self, host='localhost', port='1247', user='rods', password='rods', zone='tempZone'):
         with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
-            # Throws NetworkException if connection fails  
-            session.pool.get_connection()
+            # Throws NetworkException if connection fails
+            try:  
+                session.pool.get_connection()
+            except NetworkException as e:
+                log.error('Could not create iRODS session: ' + str(e))
+                raise
             return session
 
     @classmethod
@@ -207,7 +237,7 @@ def to_dict(self):
         return as_dict
 
     def __cache_monitor(self):
-        time.sleep(2)  # Wait for things to load before starting the monitor
+        time.sleep(5)  # Wait for things to load before starting the monitor
         while self.running:
             total_size = 0
             # Is this going to be too expensive of an operation to be done frequently?
diff --git a/test/integration/objectstore/test_irods.py b/test/integration/objectstore/test_irods.py
index 19bf3a388e24..f70f036630c6 100644
--- a/test/integration/objectstore/test_irods.py
+++ b/test/integration/objectstore/test_irods.py
@@ -9,169 +9,64 @@
 from irods.exception import DataObjectDoesNotExist
 from irods.session import iRODSSession
 
-from galaxy_test.driver import integration_util
+from galaxy.config import GalaxyAppConfiguration
+from galaxy.objectstore.irods import IRODSObjectStore
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 
-class IrodsObjectStoreIntegrationTestCase(integration_util.IntegrationTestCase):
-
-    container_name = "irods_server"
-
-    @classmethod
-    def handle_galaxy_config_kwds(cls, config):
-        config["object_store_config_file"] = "object_store_conf.xml" 
-
-    @classmethod
-    def setUpClass(cls):
-        super(IrodsObjectStoreIntegrationTestCase, cls).setUpClass()
-        IrodsObjectStoreIntegrationTestCase.start_irods_server(container_name=IrodsObjectStoreIntegrationTestCase.container_name)
-
-        # Let the server start before running the test
-        time.sleep(10)
-
-    @classmethod
-    def tearDownClass(cls): 
-        super(IrodsObjectStoreIntegrationTestCase, cls).tearDownClass()
-        IrodsObjectStoreIntegrationTestCase.stop_irods_server(container_name=IrodsObjectStoreIntegrationTestCase.container_name)       
-
-    @classmethod
-    def start_irods_server(cls, container_name, irods_port=1247, docker_image='kxk302/irods-server:0.1'):
-        start_server = ['docker', 'run', '-h', 'localhost', '-p', '{port}:1247'.format(port=irods_port), '-d', '--name', container_name, docker_image]
-        subprocess.check_call(start_server) 
-        
-    @classmethod
-    def stop_irods_server(cls, container_name):
-        subprocess.check_call(['docker', 'rm', '-f', container_name])
-
-    def test_get_existing_collection(self):
-        with iRODSSession(host='localhost', 
-            port='1247', 
-            user='rods',  
-            password='rods', 
-            zone='tempZone') as session:
-
-            zone='tempZone'
-            user='rods'
-        
-            aCollection = "/" + zone + "/home/" + user
-
-            coll = session.collections.get(aCollection)
-            assert coll.path == aCollection, "Error! Got wrong collection path"
-            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
-            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!"
-
-    def test_create_delete_new_collection(self):
-        with iRODSSession(host='localhost', 
-            port='1247', 
-            user='rods',  
-            password='rods', 
-            zone='tempZone') as session:
-
-            zone='tempZone'
-            user='rods'
-
-            newCollection = "/" + zone + "/home/" + user + "/testdir"
-    
-            coll = session.collections.create(newCollection)
-            assert coll.path == newCollection, "Error! Got wrong collection path"
-            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
-            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!" 
-
-            coll.remove(recurse=True, force=True)
-
-            with pytest.raises(CollectionDoesNotExist):
-                coll = session.collections.get(newCollection)
-
-    def test_create_delete_new_data_object(self):
-        with iRODSSession(host='localhost', 
-            port='1247', 
-            user='rods',  
-            password='rods', 
-            zone='tempZone') as session:
-
-            zone='tempZone'
-            user='rods'
-     
-            newCollection = "/" + zone + "/home/" + user + "/testdir"
-            newDataObject = newCollection + "/testDataObject"
-
-            # Create new collection
-            coll = session.collections.create(newCollection)
-            assert coll.path == newCollection, "Error! Got wrong collection path"
-            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
-            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!"
-
-            # Create data object
-            obj = session.data_objects.create(newDataObject)
-            assert obj.name == "testDataObject", "Error! Got wrong data object"
-
-            # Delete data object
-            obj.unlink(force=True)
-
-            # Get data object
-            with pytest.raises(DataObjectDoesNotExist):
-                obj = session.data_objects.get(newDataObject)
-
-            # Delete collection
-            coll.remove(recurse=True, force=True)
-
-            with pytest.raises(CollectionDoesNotExist):
-                coll = session.collections.get(newCollection)
- 
-    def test_populate_fetch_new_data_object(self):
-        with iRODSSession(host='localhost', 
-            port='1247', 
-            user='rods',  
-            password='rods', 
-            zone='tempZone') as session:
-
-            zone='tempZone'
-            user='rods'
-
-            newCollection = "/" + zone + "/home/" + user + "/testdir"
-            fileName = "irods_beginner_training_2016.pdf"
-            fileNamePath = os.path.join(SCRIPT_DIRECTORY, fileName)
-            backupFileName = "irods_beginner_training_2016_backup.pdf"
-            backupFileNamePath = os.path.join(SCRIPT_DIRECTORY, backupFileName)
- 
-            # Copy file from backup
-            shutil.copyfile(fileNamePath, backupFileNamePath)
-
-            # Create new collection 
-            coll = session.collections.create(newCollection)
-            assert coll.path == newCollection, "Error! Got wrong collection path"
-            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
-            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!" 
-
-            # Create new data object
-            session.data_objects.put(backupFileNamePath, newCollection + "/" + backupFileName)
-    
-            # Delete local file
-            os.remove(backupFileNamePath)         
-    
-            # Get the data object back
-            obj = session.data_objects.get(newCollection + "/" + backupFileName)
-    
-            # Write the data object to the file system
-            with obj.open("r") as f_in, open(backupFileNamePath, "wb") as f_out:
-                f_out.write(f_in.read())
-    
-            # Assert the size of file fetched from iRODS matches the local backup copy
-            assert os.path.getsize(fileNamePath) == os.path.getsize(backupFileNamePath), "Error! Size of file fetched from iRODS does not match the size of the original file" 
-    
-            # Delete local file
-            os.remove(backupFileNamePath)         
-    
-            # Delete data object
-            obj.unlink(force=True)
-    
-            # Get data object
-            with pytest.raises(DataObjectDoesNotExist):
-                obj = session.data_objects.get(newCollection + "/" + backupFileName)
-    
-            # Delete collection
-            coll.remove(recurse=True, force=True)
-    
-            # Get collection
-            with pytest.raises(CollectionDoesNotExist):
-                coll = session.collections.get(newCollection)
+CONFIG_DICT = {
+    'auth': {
+        'username': 'rods',
+        'password': 'rods'
+    },
+    'resource': {
+        'name': 'demoResc'
+    },
+    'zone': {
+        'name': 'tempZone'
+    },
+    'connection': {
+        'host': 'localhost',
+        'port': '1247'
+    },
+    'cache': {
+        'size': 1000.0, 
+        'path': 'database/object_store_cache'
+    },
+    'extra_dirs': [{'type': 'job_work', 'path': 'database/job_working_directory_irods'}, {'type': 'temp', 'path': 'database/tmp_irods'}]
+}
+
+#class IrodsObjectStoreIntegrationTestCase(object):
+
+#config = None 
+#config_dict = None
+#irods_os = None
+
+@pytest.fixture(scope='module')
+def setup_module():
+    config = GalaxyAppConfiguration()
+
+    config.object_store_cache_path = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/object_store_cache'
+    config.file_path = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/objects'
+    config.object_store_store_by = 'uuid'
+    config.object_store_check_old_style = False
+    config.jobs_directory = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/job_working_directory_k5dk3021'
+    config.new_file_path = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/new_files_path_sej_tqh7'
+
+    config_dict = CONFIG_DICT
+
+    irods_os = IRODSObjectStore(config, CONFIG_DICT)
+    return irods_os
+
+#    @classmethod
+#def teardown_module(module):
+#     del irods_os
+#     del config_dict
+#     del config
+
+def test_instantiate_irods(setup_module):
+    print('**********************')
+    print('setup_module.to_dict()')
+    print(setup_module.to_dict())
+    print('**********************')
+    assert 1 == 1

From 0aafc6e1592c9a4769507c07d3098484bd9ba079 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 28 Feb 2020 16:17:13 -0500
Subject: [PATCH 265/853] Login is its own entrypoint and we don't want it
 shoved into an iframe anymore.

---
 client/galaxy/scripts/layout/menu.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/galaxy/scripts/layout/menu.js b/client/galaxy/scripts/layout/menu.js
index 46c1ead9f75c..ff5c15ec4488 100644
--- a/client/galaxy/scripts/layout/menu.js
+++ b/client/galaxy/scripts/layout/menu.js
@@ -253,7 +253,6 @@ const Collection = Backbone.Collection.extend({
                     cls: "loggedout-only",
                     tooltip: _l("Login"),
                     url: "login",
-                    target: "galaxy_main",
                     noscratchbook: true
                 };
             }

From 088653e2cb40717382bc5e60a6bad730ad6606f9 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sat, 29 Feb 2020 01:53:29 +0000
Subject: [PATCH 266/853] Add missing pygithub dev-requirement

Follow-up to https://github.com/galaxyproject/galaxy/pull/9271

Also move GitHub client initialisation and check for `requests` closer to where they
are used to prevent error messages when running `make`.
---
 .../dependencies/pipfiles/default/Pipfile     |  1 +
 .../default/pinned-dev-requirements.txt       |  3 +++
 scripts/bootstrap_history.py                  | 24 +++++++++----------
 3 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/lib/galaxy/dependencies/pipfiles/default/Pipfile
index 67964f856123..5cf77f61560c 100644
--- a/lib/galaxy/dependencies/pipfiles/default/Pipfile
+++ b/lib/galaxy/dependencies/pipfiles/default/Pipfile
@@ -13,6 +13,7 @@ gunicorn = "*"
 lxml = "!=4.2.2"
 mock = "*"
 NoseHTML = "*"
+pygithub = "*"
 pytest = "*"
 pytest-cov = "*"
 pytest-html = "*"
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index cbf02baf09f8..1b53e2b2826f 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -11,6 +11,7 @@ commonmark==0.9.1
 configparser==4.0.2 ; python_version < '3.2'
 contextlib2==0.6.0.post1 ; python_version < '3.5'
 coverage==4.5.4
+deprecated==1.2.7
 docutils==0.15.2
 funcsigs==1.0.2 ; python_version < '3.3'
 future==0.18.2
@@ -34,7 +35,9 @@ pluggy==0.13.1
 port-for==0.4
 psutil==5.6.7
 py==1.8.0
+pygithub==1.45
 pygments==2.5.2
+pyjwt==1.7.1
 pyparsing==2.4.5
 pytest-cov==2.8.1
 pytest-html==1.22.1
diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index 87c471a42896..ce753d653a7c 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -400,10 +400,9 @@ def do_release(argv):
 
 
 def check_release(argv):
-    github = _github_client()
     release_name = argv[2]
     for pr in _get_prs(release_name):
-        _text_target(github, pr, labels=_pr_to_labels(pr))
+        _text_target(pr, labels=_pr_to_labels(pr))
 
 
 def check_blocking_prs(argv):
@@ -501,9 +500,6 @@ def _get_prs(release_name, state="closed", pr_cache=[]):
 
 
 def main(argv):
-    if requests is None:
-        raise Exception("Requests library not found, please pip install requests")
-    github = _github_client()
     newest_release = None
 
     if argv[1] == "--print-next-minor-version":
@@ -558,6 +554,8 @@ def extend_target(target, line, source=history):
 
     ident = argv[1]
 
+    if requests is None:
+        raise Exception("Requests library not found, please pip install requests")
     message = ""
     if len(argv) > 2:
         message = argv[2]
@@ -568,13 +566,13 @@ def extend_target(target, line, source=history):
         commit = req["commit"]
         message = commit["message"]
         message = get_first_sentence(message)
-    elif requests is not None and ident.startswith("pr"):
+    elif ident.startswith("pr"):
         pull_request = ident[len("pr"):]
         api_url = urljoin(PROJECT_API, "pulls/%s" % pull_request)
         if req is None:
             req = requests.get(api_url).json()
         message = req["title"]
-    elif requests is not None and ident.startswith("issue"):
+    elif ident.startswith("issue"):
         issue = ident[len("issue"):]
         api_url = urljoin(PROJECT_API, "issues/%s" % issue)
         if req is None:
@@ -600,11 +598,10 @@ def extend_target(target, line, source=history):
                 owner, owner,
             )
         to_doc += "\n`Pull Request {0}`_".format(pull_request)
-        if github:
-            labels = None
-            if req and 'labels' in req:
-                labels = req['labels']
-            text_target = _text_target(github, pull_request, labels=labels)
+        labels = None
+        if req and 'labels' in req:
+            labels = req['labels']
+        text_target = _text_target(pull_request, labels=labels)
     elif ident.startswith("issue"):
         issue = ident[len("issue"):]
         text = ".. _Issue {0}: {1}/issues/{0}".format(issue, PROJECT_URL)
@@ -642,7 +639,7 @@ def _write_file(path, contents):
         f.write(contents)
 
 
-def _text_target(github, pull_request, labels=None):
+def _text_target(pull_request, labels=None):
     pr_number = None
     if isinstance(pull_request, string_types):
         pr_number = pull_request
@@ -652,6 +649,7 @@ def _text_target(github, pull_request, labels=None):
     if labels is None:
         labels = []
         try:
+            github = _github_client()
             labels = github.issues.labels.list_by_issue(int(pr_number), user=PROJECT_OWNER, repo=PROJECT_NAME)
             labels = [l.name.lower() for l in labels]
         except Exception as e:

From 4f79ca43d6c3098b45900b0bb17bbcfa962b03e0 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sat, 29 Feb 2020 10:05:34 -0500
Subject: [PATCH 267/853] Run make update-dependencies

---
 .../pipfiles/default/pinned-dev-requirements.txt     |  3 ++-
 .../pipfiles/default/pinned-requirements.txt         | 12 ++++++------
 .../pipfiles/flake8/pinned-requirements.txt          |  2 +-
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index 6319e533bef3..8dffa3ebf0e9 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -55,10 +55,11 @@ sphinx-markdown-tables==0.0.12
 sphinx-rtd-theme==0.4.3
 sphinx==1.8.5
 sphinxcontrib-websupport==1.1.2
-testfixtures==6.13.0
+testfixtures==6.14.0
 twill==0.9.1 ; python_version < '3'
 typing==3.7.4.1 ; python_version < '3.5'
 urllib3==1.25.8
 watchdog==0.10.2
 wcwidth==0.1.8
+wrapt==1.12.0
 zipp==1.2.0
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 61ceec85d97a..ba7a2f14df95 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -46,7 +46,7 @@ contextlib2==0.6.0.post1 ; python_version < '3.5'
 cryptography==2.8
 cwltool==1.0.20191225192155
 debtcollector==1.22.0
-decorator==4.4.1
+decorator==4.4.2
 deprecated==1.2.7
 deprecation==2.0.7
 dictobj==0.4
@@ -54,7 +54,7 @@ docopt==0.6.2
 docutils==0.15.2
 dogpile.cache==0.9.0
 ecdsa==0.15
-enum34==1.1.6 ; python_version < '3.4'
+enum34==1.1.9 ; python_version < '3.4'
 fabric3==1.14.post1
 funcsigs==1.0.2 ; python_version < '3.3'
 functools32==3.2.3.post2 ; python_version < '3.2'
@@ -64,7 +64,7 @@ galaxy-sequence-utils==1.1.5
 google-api-python-client==1.7.8
 google-auth-httplib2==0.0.3
 google-auth==1.11.2
-gxformat2==0.10.1
+gxformat2==0.11.1
 h5py==2.10.0
 httplib2==0.17.0
 humanfriendly==7.1.1
@@ -74,7 +74,7 @@ ipaddress==1.0.23 ; python_version < '3.3'
 isa-rwval==0.10.7
 iso8601==0.1.12
 isodate==0.6.0
-jmespath==0.9.4
+jmespath==0.9.5
 jsonpatch==1.25
 jsonpointer==2.0
 jsonschema==3.2.0
@@ -126,7 +126,7 @@ pulsar-galaxy-lib==0.14.0.dev1
 pyasn1-modules==0.2.8
 pyasn1==0.4.8
 pycparser==2.19
-pycryptodome==3.9.6
+pycryptodome==3.9.7
 pyeventsystem==0.1.0
 pyinotify==0.9.6 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
 pyjwt==1.7.1
@@ -174,7 +174,7 @@ social-auth-core[openidconnect]==3.1.0+gx0
 sqlalchemy-migrate==0.13.0
 sqlalchemy-utils==0.36.1
 sqlalchemy==1.3.13
-sqlparse==0.3.0
+sqlparse==0.3.1
 stevedore==1.32.0
 subprocess32==3.5.4 ; python_version < '3.0'
 svgwrite==1.3.1
diff --git a/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
index 822a359dfae7..0a1aafdbde5a 100644
--- a/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
@@ -1,7 +1,7 @@
 -i https://pypi.python.org/simple
 configparser==4.0.2 ; python_version < '3.2'
 entrypoints==0.3
-enum34==1.1.6 ; python_version < '3.4'
+enum34==1.1.9 ; python_version < '3.4'
 flake8-import-order==0.18.1
 flake8==3.7.9
 functools32==3.2.3.post2 ; python_version < '3.2'

From a8cbd36d9049f4cd8c86bf12cb1790a16d2304a4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 29 Feb 2020 17:09:26 +0100
Subject: [PATCH 268/853] Drop manage_dependency_relationships altogether

Probably didn't work for some time and seems unnecessary.

Fixes
```
galaxy.tool_shed.galaxy_install.installed_repository_manager DEBUG 2020-02-28 10:57:01,109 [p:94029,w:0,m:0] [MainThread] Adding an entry for version 2.2.4 of package bowtie2 to runtime_tool_dependencies_of_installed_tool_dependencies.
Traceback (most recent call last):
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 48, in app_factory
    app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs)
  File "lib/galaxy/app.py", line 95, in __init__
    self.installed_repository_manager = InstalledRepositoryManager(self)
  File "lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py", line 84, in __init__
    self.load_dependency_relationships()
  File "lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py", line 734, in load_dependency_relationships
    self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
  File "lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py", line 218, in add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies
    status=None)
  File "lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py", line 604, in get_runtime_dependent_tool_dependency_tuples
    required_env_shell_file_path = tool_dependency.get_env_shell_file_path(self.app)
  File "lib/galaxy/model/tool_shed_install/__init__.py", line 522, in get_env_shell_file_path
    installation_directory = self.installation_directory(app)
  File "lib/galaxy/model/tool_shed_install/__init__.py", line 534, in installation_directory
    return os.path.join(app.tool_dependency_dir,
  File "lib/galaxy/config/__init__.py", line 1186, in tool_dependency_dir
    return self.toolbox.dependency_manager.default_base_path
AttributeError: 'UniverseApplication' object has no attribute 'toolbox'
```
reported by @scholtalbers
---
 doc/source/admin/galaxy_options.rst           | 13 ---
 lib/galaxy/app.py                             |  2 -
 lib/galaxy/config/sample/galaxy.yml.sample    |  6 --
 .../galaxy_install/install_manager.py         |  8 --
 .../installed_repository_manager.py           | 91 -------------------
 lib/galaxy/webapps/galaxy/config_schema.yml   |  9 --
 6 files changed, 129 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index f4948b3c19e4..619dd9b285f5 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -697,19 +697,6 @@
 :Type: int
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``manage_dependency_relationships``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    Enable use of an in-memory registry with bi-directional
-    relationships between repositories (i.e., in addition to lists of
-    dependencies for a repository, keep an in-memory registry of
-    dependent items for each repository.
-:Default: ``false``
-:Type: bool
-
-
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``tool_data_table_config_path``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 7cc31f01f086..5b13f02a54ba 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -91,9 +91,7 @@ def __init__(self, **kwargs):
         check_migrate_tools = self.config.check_migrate_tools
         self._configure_models(check_migrate_databases=self.config.check_migrate_databases, check_migrate_tools=check_migrate_tools, config_file=config_file)
 
-        # Manage installed tool shed repositories.
         self.installed_repository_manager = InstalledRepositoryManager(self)
-
         self._configure_datatypes_registry(self.installed_repository_manager)
         galaxy.model.set_datatypes_registry(self.datatypes_registry)
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 1263f0d1b1f1..acd9c1bd0a06 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -447,12 +447,6 @@ galaxy:
   # between 1 and 24.
   #hours_between_check: 12
 
-  # Enable use of an in-memory registry with bi-directional
-  # relationships between repositories (i.e., in addition to lists of
-  # dependencies for a repository, keep an in-memory registry of
-  # dependent items for each repository.
-  #manage_dependency_relationships: false
-
   # XML config file that contains data table entries for the
   # ToolDataTableManager.  This file is manually # maintained by the
   # Galaxy administrator (.sample used if default does not exist).
diff --git a/lib/galaxy/tool_shed/galaxy_install/install_manager.py b/lib/galaxy/tool_shed/galaxy_install/install_manager.py
index 3a2b2bedfc2b..687aa9bf9645 100644
--- a/lib/galaxy/tool_shed/galaxy_install/install_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/install_manager.py
@@ -215,10 +215,6 @@ def install_specified_tool_dependencies(self, tool_shed_repository, tool_depende
                         if tool_dependency and tool_dependency.status in [self.install_model.ToolDependency.installation_status.INSTALLED,
                                                                           self.install_model.ToolDependency.installation_status.ERROR]:
                             installed_packages.append(tool_dependency)
-                            if self.app.config.manage_dependency_relationships:
-                                # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager.
-                                self.app.installed_repository_manager.handle_tool_dependency_install(tool_shed_repository,
-                                                                                                     tool_dependency)
         return installed_packages
 
     def install_via_fabric(self, tool_shed_repository, tool_dependency, install_dir, package_name=None, custom_fabfile_path=None,
@@ -946,10 +942,6 @@ def install_tool_shed_repository(self, tool_shed_repository, repo_info_dict, too
                 basic_util.remove_dir(work_dir)
             self.update_tool_shed_repository_status(tool_shed_repository,
                                                     self.install_model.ToolShedRepository.installation_status.INSTALLED)
-            if self.app.config.manage_dependency_relationships:
-                # Add the installed repository and any tool dependencies to the in-memory dictionaries
-                # in the installed_repository_manager.
-                self.app.installed_repository_manager.handle_repository_install(tool_shed_repository)
         else:
             # An error occurred while cloning the repository, so reset everything necessary to enable another attempt.
             repository_util.set_repository_attributes(self.app,
diff --git a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
index 58f3ba686d6a..3ccd62febb74 100644
--- a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
@@ -79,9 +79,6 @@ def __init__(self, app):
         # whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key
         # at runtime.  The value defines the entire tool dependency tree.
         self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {}
-        if app.config.manage_dependency_relationships:
-            # Load defined dependency relationships for installed tool shed repositories and their contents.
-            self.load_dependency_relationships()
 
     def activate_repository(self, repository):
         """Activate an installed tool shed repository that has been marked as deactivated."""
@@ -651,90 +648,6 @@ def handle_existing_tool_dependencies_that_changed_in_update(self, repository, o
                     deleted_tool_dependency_names.append(original_dependency_val_dict['name'])
         return updated_tool_dependency_names, deleted_tool_dependency_names
 
-    def handle_repository_install(self, repository):
-        """Load the dependency relationships for a repository that was just installed or reinstalled."""
-        # Populate self.repository_dependencies_of_installed_repositories.
-        self.add_entry_to_repository_dependencies_of_installed_repositories(repository)
-        # Populate self.installed_repository_dependencies_of_installed_repositories.
-        self.add_entry_to_installed_repository_dependencies_of_installed_repositories(repository)
-        # Populate self.tool_dependencies_of_installed_repositories.
-        self.add_entry_to_tool_dependencies_of_installed_repositories(repository)
-        # Populate self.installed_tool_dependencies_of_installed_repositories.
-        self.add_entry_to_installed_tool_dependencies_of_installed_repositories(repository)
-        for tool_dependency in repository.tool_dependencies:
-            # Populate self.runtime_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-            # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-
-    def handle_repository_uninstall(self, repository):
-        """Remove the dependency relationships for a repository that was just uninstalled."""
-        for tool_dependency in repository.tool_dependencies:
-            tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
-            # Remove this tool_dependency from all values in
-            # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies
-            altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {}
-            for (td_tup, installed_runtime_dependent_tool_dependency_tups) in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.items():
-                if tool_dependency_tup in installed_runtime_dependent_tool_dependency_tups:
-                    # Remove the tool_dependency from the list.
-                    installed_runtime_dependent_tool_dependency_tups.remove(tool_dependency_tup)
-                # Add the possibly altered list to the altered dictionary.
-                altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[td_tup] = \
-                    installed_runtime_dependent_tool_dependency_tups
-            self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = \
-                altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies
-            # Remove the entry for this tool_dependency from self.runtime_tool_dependencies_of_installed_tool_dependencies.
-            self.remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-            # Remove the entry for this tool_dependency from
-            # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
-            self.remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-        # Remove this repository's entry from self.installed_tool_dependencies_of_installed_repositories.
-        self.remove_entry_from_installed_tool_dependencies_of_installed_repositories(repository)
-        # Remove this repository's entry from self.tool_dependencies_of_installed_repositories
-        self.remove_entry_from_tool_dependencies_of_installed_repositories(repository)
-        # Remove this repository's entry from self.installed_repository_dependencies_of_installed_repositories.
-        self.remove_entry_from_installed_repository_dependencies_of_installed_repositories(repository)
-        # Remove this repository's entry from self.repository_dependencies_of_installed_repositories.
-        self.remove_entry_from_repository_dependencies_of_installed_repositories(repository)
-
-    def handle_tool_dependency_install(self, repository, tool_dependency):
-        """Load the dependency relationships for a tool dependency that was just installed independently of its containing repository."""
-        # The received repository must have a status of 'Installed'.  The value of tool_dependency.status will either be
-        # 'Installed' or 'Error', but we only need to change the in-memory dictionaries if it is 'Installed'.
-        if tool_dependency.is_installed:
-            # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-            # Populate self.installed_tool_dependencies_of_installed_repositories.
-            repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
-            tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
-            if repository_tup in self.installed_tool_dependencies_of_installed_repositories:
-                self.installed_tool_dependencies_of_installed_repositories[repository_tup].append(tool_dependency_tup)
-            else:
-                self.installed_tool_dependencies_of_installed_repositories[repository_tup] = [tool_dependency_tup]
-
-    def load_dependency_relationships(self):
-        """Load relationships for all installed repositories and tool dependencies into in-memnory dictionaries."""
-        # Get the list of installed tool shed repositories.
-        for repository in self.context.query(self.app.install_model.ToolShedRepository) \
-                                      .filter(self.app.install_model.ToolShedRepository.table.c.status ==
-                                              self.app.install_model.ToolShedRepository.installation_status.INSTALLED):
-            # Populate self.repository_dependencies_of_installed_repositories.
-            self.add_entry_to_repository_dependencies_of_installed_repositories(repository)
-            # Populate self.installed_repository_dependencies_of_installed_repositories.
-            self.add_entry_to_installed_repository_dependencies_of_installed_repositories(repository)
-            # Populate self.tool_dependencies_of_installed_repositories.
-            self.add_entry_to_tool_dependencies_of_installed_repositories(repository)
-            # Populate self.installed_tool_dependencies_of_installed_repositories.
-            self.add_entry_to_installed_tool_dependencies_of_installed_repositories(repository)
-        # Get the list of installed tool dependencies.
-        for tool_dependency in self.context.query(self.app.install_model.ToolDependency) \
-                                           .filter(self.app.install_model.ToolDependency.table.c.status ==
-                                                   self.app.install_model.ToolDependency.installation_status.INSTALLED):
-            # Populate self.runtime_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-            # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-
     def load_proprietary_datatypes(self):
         cdl = custom_datatype_manager.CustomDatatypeLoader(self.app)
         for tool_shed_repository in self.context.query(self.install_model.ToolShedRepository) \
@@ -814,10 +727,6 @@ def uninstall_repository(self, repository, remove_from_disk=True):
         if remove_from_disk:
             repository.status = self.app.install_model.ToolShedRepository.installation_status.UNINSTALLED
             repository.error_message = None
-            if self.app.config.manage_dependency_relationships:
-                # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the
-                # installed_repository_manager.
-                self.handle_repository_uninstall(repository)
         else:
             repository.status = self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED
         self.app.install_model.context.current.add(repository)
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index a723a9aec954..d8101b9a342a 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -528,15 +528,6 @@ mapping:
           server process should be able to check for repository updates.  The
           setting for hours_between_check should be an integer between 1 and 24.
 
-      manage_dependency_relationships:
-        type: bool
-        default: false
-        required: false
-        desc: |
-          Enable use of an in-memory registry with bi-directional relationships between
-          repositories (i.e., in addition to lists of dependencies for a repository,
-          keep an in-memory registry of dependent items for each repository.
-
       tool_data_table_config_path:
         type: str
         default: config/tool_data_table_conf.xml

From add9e565aa151b41eb4e7e6e8d0a548c0a9095fc Mon Sep 17 00:00:00 2001
From: Matthias Bernt <bernt@informatik.uni-leipzig.de>
Date: Sun, 1 Mar 2020 00:23:07 +0100
Subject: [PATCH 269/853] fix options_filter_attribute: needs to be str

since in the tool xml the values can only be specified as str
also the attribute needs to be a str. currently, for instance,
filtering for non-str (e.g. int) metadata values does not work.

for instance this does not worked so far

```
    <param ... type="data" format="fasta">
      <options options_filter_attribute="metadata.sequences">
        <filter type="add_value" value="1"/>
      </options>
    </param>
```
---
 lib/galaxy/tools/parameters/basic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index a6f830e746ae..8f64a80c050c 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1913,7 +1913,7 @@ def get_options_filter_attribute(self, value):
             ref = getattr(ref, attribute)
         if call_attribute:
             ref = ref()
-        return ref
+        return str(ref)
 
     def to_dict(self, trans, other_values={}):
         # create dictionary and fill default parameters

From 1ec079b5d045a9b6c13ee17b222278092203968d Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@gmail.com>
Date: Sun, 1 Mar 2020 11:16:06 +0000
Subject: [PATCH 270/853] Restore gxformat2 pin to 0.10.1

It seems 0.11.1 breaks Galaxy at the moment.
---
 .../dependencies/pipfiles/default/pinned-requirements.txt       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index ba7a2f14df95..0d47bdffdc26 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -64,7 +64,7 @@ galaxy-sequence-utils==1.1.5
 google-api-python-client==1.7.8
 google-auth-httplib2==0.0.3
 google-auth==1.11.2
-gxformat2==0.11.1
+gxformat2==0.10.1
 h5py==2.10.0
 httplib2==0.17.0
 humanfriendly==7.1.1

From 666eb07bfbc06d45a8a2726cb90eeff954b72d22 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 29 Feb 2020 21:00:48 -0500
Subject: [PATCH 271/853] Render d3 instead of canvas as workflow noodle

---
 .../mvc/workflow/workflow-connector.js        | 88 +++++++++----------
 .../scripts/mvc/workflow/workflow-manager.js  |  6 +-
 .../mvc/workflow/workflow-view-terminals.js   |  8 +-
 client/galaxy/style/scss/workflow.scss        |  3 -
 4 files changed, 50 insertions(+), 55 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-connector.js b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
index 7201d9162e27..3671b9c3f504 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-connector.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
@@ -1,16 +1,17 @@
 import $ from "jquery";
-
+import * as d3 from "d3";
 import { Toast } from "ui/toast";
 
-function Connector(manager, handle1, handle2) {
+function Connector(manager) {
     this.manager = manager;
-    this.canvas = null;
     this.dragging = false;
     this.inner_color = "#FFFFFF";
     this.outer_color = "#25537b";
-    if (handle1 && handle2) {
-        this.connect(handle1, handle2);
-    }
+    this.canvas = document.createElement("div");
+    this.canvas.style.position = "absolute";
+    const container = document.getElementById("canvas-container");
+    container.appendChild(this.canvas);
+    this.svg = d3.select(this.canvas).append("svg");
 }
 $.extend(Connector.prototype, {
     connect: function(t1, t2) {
@@ -30,7 +31,7 @@ $.extend(Connector.prototype, {
         if (this.handle2) {
             this.handle2.disconnect(this);
         }
-        $(this.canvas).remove();
+        this.canvas.remove();
     },
     destroyIfInvalid: function(warn) {
         if (this.handle1 && this.handle2 && !this.handle2.attachable(this.handle1).canAccept) {
@@ -48,12 +49,8 @@ $.extend(Connector.prototype, {
         const canvasClass = `${startRibbon ? "start-ribbon" : ""} ${endRibbon ? "end-ribbon" : ""}`;
         var canvas_container = $("#canvas-container");
         var canvasZoom = this.manager.canvasZoom;
-        if (!this.canvas) {
-            this.canvas = document.createElement("canvas");
-            canvas_container.append($(this.canvas));
-            if (this.dragging) {
-                this.canvas.style.zIndex = "300";
-            }
+        if (this.dragging) {
+            this.canvas.style.zIndex = 1000;
         }
         this.canvas.setAttribute(
             "handle1-id",
@@ -73,6 +70,7 @@ $.extend(Connector.prototype, {
         var start_y = relativeTop(handle1.element) + 5;
         var end_x = relativeLeft(handle2.element) + 5;
         var end_y = relativeTop(handle2.element) + 5;
+
         // Calculate canvas area
         var canvas_extra = 100;
         var canvas_min_x = Math.min(start_x, end_x);
@@ -84,20 +82,32 @@ $.extend(Connector.prototype, {
         var canvas_top = canvas_min_y - canvas_extra;
         var canvas_width = canvas_max_x - canvas_min_x + 2 * canvas_extra;
         var canvas_height = canvas_max_y - canvas_min_y + 2 * canvas_extra;
+
         // Place the canvas
         this.canvas.style.left = `${canvas_left}px`;
         this.canvas.style.top = `${canvas_top}px`;
-        this.canvas.setAttribute("width", canvas_width);
-        this.canvas.setAttribute("height", canvas_height);
+        this.svg.style("width", `${canvas_width}px`);
+        this.svg.style("height", `${canvas_height}px`);
         this.canvas.setAttribute("class", canvasClass);
+
         // Adjust points to be relative to the canvas
         start_x -= canvas_left;
         start_y -= canvas_top;
         end_x -= canvas_left;
         end_y -= canvas_top;
 
-        // Draw the line
+        this.draw_outlined_curve(
+            start_x,
+            start_y,
+            end_x,
+            end_y,
+            0,
+            0,
+            0,
+            0
+        );
 
+        /*/ Draw the line
         var start_offsets = null;
         var end_offsets = null;
         var num_offsets = 1;
@@ -133,7 +143,7 @@ $.extend(Connector.prototype, {
                 start_offsets[i % start_offsets.length],
                 end_offsets[i % end_offsets.length]
             );
-        }
+        }*/
     },
     draw_outlined_curve: function(
         start_x,
@@ -146,37 +156,23 @@ $.extend(Connector.prototype, {
         offset_start,
         offset_end
     ) {
-        var c = this.canvas.getContext("2d");
         offset_start = offset_start || 0;
         offset_end = offset_end || 0;
-        c.lineCap = "round";
-        c.strokeStyle = this.outer_color;
-        c.lineWidth = outer_width;
-        c.beginPath();
-        c.moveTo(start_x, start_y + offset_start);
-        c.bezierCurveTo(
-            start_x + cp_shift,
-            start_y + offset_start,
-            end_x - cp_shift,
-            end_y + offset_end,
-            end_x,
-            end_y + offset_end
-        );
-        c.stroke();
-        // Inner line
-        c.strokeStyle = this.inner_color;
-        c.lineWidth = inner_width;
-        c.beginPath();
-        c.moveTo(start_x, start_y + offset_start);
-        c.bezierCurveTo(
-            start_x + cp_shift,
-            start_y + offset_start,
-            end_x - cp_shift,
-            end_y + offset_end,
-            end_x,
-            end_y + offset_end
-        );
-        c.stroke();
+        var lineData = [
+            { x: start_x, y: start_y + offset_start },
+            //{ x: start_x + cp_shift,   y: start_y + offset_start},
+            //{ x: end_x - cp_shift,  y: end_y + offset_end },
+            { x: end_x,  y: end_y + offset_end } ];
+        var lineFunction = d3.svg.line()
+                            .x(function(d) { return d.x; })
+                            .y(function(d) { return d.y; })
+                            .interpolate("linear");
+        // The line SVG Path we draw
+        this.svg.selectAll("*").remove();
+        this.svg.append("path")
+                .attr("d", lineFunction(lineData))
+                .attr("stroke", "blue")
+                .attr("stroke-width", 2);
     }
 });
 export default Connector;
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index cc8f7cf83ac6..ada79e2c2458 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -380,15 +380,15 @@ class Workflow extends EventEmitter {
         wf.id_counter = max_id + 1;
         // Second pass, connections
         $.each(data.steps, (id, step) => {
-            var node = wf.nodes[parseInt(id) + offset];
+            const node = wf.nodes[parseInt(id) + offset];
             $.each(step.input_connections, (k, v) => {
                 if (v) {
                     if (!$.isArray(v)) {
                         v = [v];
                     }
                     $.each(v, (l, x) => {
-                        var other_node = wf.nodes[parseInt(x.id) + offset];
-                        var c = new Connector(this.canvas_manager);
+                        const other_node = wf.nodes[parseInt(x.id) + offset];
+                        const c = new Connector(this.canvas_manager);
                         c.connect(other_node.output_terminals[x.output_name], node.input_terminals[k]);
                         c.redraw();
                     });
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index 546fead94979..a6c4886f11e0 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -114,7 +114,9 @@ class BaseInputTerminalView extends TerminalView {
         d.proxy.dropTooltip = "";
         if (this.$el.hasClass("can-accept")) {
             const terminal = this.el.terminal;
-            new Connector(this.app.canvas_manager, d.drag.terminal, terminal).redraw();
+            const c = new Connector(this.app.canvas_manager);
+            c.connect(d.drag.terminal, terminal);
+            c.redraw();
         }
     }
     onHover() {
@@ -251,7 +253,7 @@ export class BaseOutputTerminalView extends TerminalView {
                     break;
                 case 32: // Space
                     removeMenu();
-                    new Connector(this.app.canvas_manager, this.el.terminal, inputTerminal).redraw();
+                    new Connector(this.app.canvas_manager).connect(this.el.terminal, inputTerminal).redraw();
                     ariaAlert("Node connected");
 
                     if (inputTerminal.connectors.length > 0) {
@@ -357,7 +359,7 @@ export class BaseOutputTerminalView extends TerminalView {
             }
         });
         h.terminal = new Terminals.OutputTerminal({ element: h });
-        var c = new Connector(this.app.canvas_manager);
+        const c = new Connector(this.app.canvas_manager);
         c.dragging = true;
         c.connect(this.el.terminal, h.terminal);
         return h;
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 5061dc8b904e..4227ff58d0bb 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -23,9 +23,6 @@
                 @extend .px-2;
                 cursor: move;
                 background: $brand-secondary;
-                .header {
-                    width: 7rem;
-                }
             }
             .node-body {
                 @extend .card-body;

From 1a07617403ef568d2c4bf6ba0ef5d9e803f2d17a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 2 Mar 2020 12:58:39 +0100
Subject: [PATCH 272/853] Fix workflow list filtering dropdown

Not sure if this is the right fix but `computed` sounds like would
be less statuc and it does solve
https://github.com/galaxyproject/galaxy/issues/9467 for me.
---
 .../components/Workflow/WorkflowDropdown.vue  | 28 +++++++++++--------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/WorkflowDropdown.vue b/client/galaxy/scripts/components/Workflow/WorkflowDropdown.vue
index 29f5c7a7616e..67f895f0a0c6 100644
--- a/client/galaxy/scripts/components/Workflow/WorkflowDropdown.vue
+++ b/client/galaxy/scripts/components/Workflow/WorkflowDropdown.vue
@@ -31,18 +31,24 @@ import { getAppRoot } from "onload/loadConfig";
 import { Services } from "./services.js";
 export default {
     props: ["workflow"],
-    data() {
-        return {
-            urlEdit: `${getAppRoot()}workflow/editor?id=${this.workflow.id}`,
-            urlDownload: `${getAppRoot()}api/workflows/${this.workflow.id}/download?format=json-download`,
-            urlShare: `${getAppRoot()}workflow/sharing?id=${this.workflow.id}`,
-            urlView: `${getAppRoot()}workflow/display_by_id?id=${this.workflow.id}`,
-            urlViewShared: `${getAppRoot()}workflow/display_by_username_and_slug?username=${this.workflow.owner}&slug=${
-                this.workflow.slug
-            }`
-        };
-    },
     computed: {
+        urlEdit() {
+            return `${getAppRoot()}workflow/editor?id=${this.workflow.id}`;
+        },
+        urlDownload() {
+            return `${getAppRoot()}api/workflows/${this.workflow.id}/download?format=json-download`;
+        },
+        urlShare() {
+            return `${getAppRoot()}workflow/sharing?id=${this.workflow.id}`;
+        },
+        urlView() {
+            return `${getAppRoot()}workflow/display_by_id?id=${this.workflow.id}`;
+        },
+        urlViewShared() {
+            return `${getAppRoot()}workflow/display_by_username_and_slug?username=${this.workflow.owner}&slug=${
+                this.workflow.slug
+            }`;
+        },
         icon() {
             if (this.workflow.shared) {
                 return "fa fa-share-alt";

From 6bd8cf091005133be6cdd22e65185f842616bc14 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 2 Mar 2020 10:12:46 -0500
Subject: [PATCH 273/853] Swap url building to computed properties in
 HistoryDropdown

---
 .../components/History/HistoryDropdown.vue     | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/client/galaxy/scripts/components/History/HistoryDropdown.vue b/client/galaxy/scripts/components/History/HistoryDropdown.vue
index c0137cceba6e..7e6bc186ca2b 100644
--- a/client/galaxy/scripts/components/History/HistoryDropdown.vue
+++ b/client/galaxy/scripts/components/History/HistoryDropdown.vue
@@ -23,16 +23,20 @@ import { getGalaxyInstance } from "app";
 
 export default {
     props: ["history"],
-    data() {
-        return {
-            urlView: `${getAppRoot()}histories/view?id=${this.history.id}`,
-            urlShowStructure: `${getAppRoot()}histories/show_structure?id=${this.history.id}`,
-            urlSharing: `${getAppRoot()}histories/sharing?id=${this.history.id}`
-        };
-    },
     created() {
         this.root = getAppRoot();
     },
+    computed: {
+        urlView() {
+            return `${getAppRoot()}histories/view?id=${this.history.id}`;
+        },
+        urlShowStructure() {
+            return `${getAppRoot()}histories/show_structure?id=${this.history.id}`;
+        },
+        urlSharing() {
+            return `${getAppRoot()}histories/sharing?id=${this.history.id}`;
+        }
+    },
     methods: {
         onSwitch: function() {
             const Galaxy = getGalaxyInstance();

From f8d1b4f9541c03ac82c905d96fa048335f676941 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 2 Mar 2020 10:21:47 -0500
Subject: [PATCH 274/853] Use method definition shorthand

---
 client/galaxy/scripts/components/History/HistoryDropdown.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/History/HistoryDropdown.vue b/client/galaxy/scripts/components/History/HistoryDropdown.vue
index 7e6bc186ca2b..becdb4169f60 100644
--- a/client/galaxy/scripts/components/History/HistoryDropdown.vue
+++ b/client/galaxy/scripts/components/History/HistoryDropdown.vue
@@ -38,7 +38,7 @@ export default {
         }
     },
     methods: {
-        onSwitch: function() {
+        onSwitch() {
             const Galaxy = getGalaxyInstance();
             Galaxy.currHistoryPanel.switchToHistory(this.history.id);
         }

From 078e50c6e7ab858580d1323e35ef1b0fdaf6d4ba Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 2 Mar 2020 11:39:25 -0500
Subject: [PATCH 275/853] Use const/let in connector, restore curve loop, use
 d3

---
 .../mvc/workflow/workflow-connector.js        | 93 +++++++++----------
 1 file changed, 44 insertions(+), 49 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-connector.js b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
index 3671b9c3f504..23b390ae78dc 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-connector.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
@@ -46,9 +46,8 @@ $.extend(Connector.prototype, {
         const handle2 = this.handle2;
         const startRibbon = handle1 && handle1.isMappedOver();
         const endRibbon = handle2 && handle2.isMappedOver();
-        const canvasClass = `${startRibbon ? "start-ribbon" : ""} ${endRibbon ? "end-ribbon" : ""}`;
-        var canvas_container = $("#canvas-container");
-        var canvasZoom = this.manager.canvasZoom;
+        const canvas_container = $("#canvas-container");
+        const canvasZoom = this.manager.canvasZoom;
         if (this.dragging) {
             this.canvas.style.zIndex = 1000;
         }
@@ -60,35 +59,33 @@ $.extend(Connector.prototype, {
             "handle2-id",
             handle2 && handle2.element.getAttribute ? handle2.element.getAttribute("id") : ""
         );
-        var relativeLeft = e => ($(e).offset().left - canvas_container.offset().left) / canvasZoom;
-        var relativeTop = e => ($(e).offset().top - canvas_container.offset().top) / canvasZoom;
+        const relativeLeft = e => ($(e).offset().left - canvas_container.offset().left) / canvasZoom;
+        const relativeTop = e => ($(e).offset().top - canvas_container.offset().top) / canvasZoom;
         if (!handle1 || !handle2) {
             return;
         }
         // Find the position of each handle
-        var start_x = relativeLeft(handle1.element) + 5;
-        var start_y = relativeTop(handle1.element) + 5;
-        var end_x = relativeLeft(handle2.element) + 5;
-        var end_y = relativeTop(handle2.element) + 5;
+        let start_x = relativeLeft(handle1.element) + 5;
+        let start_y = relativeTop(handle1.element) + 5;
+        let end_x = relativeLeft(handle2.element) + 5;
+        let end_y = relativeTop(handle2.element) + 5;
 
         // Calculate canvas area
-        var canvas_extra = 100;
-        var canvas_min_x = Math.min(start_x, end_x);
-        var canvas_max_x = Math.max(start_x, end_x);
-        var canvas_min_y = Math.min(start_y, end_y);
-        var canvas_max_y = Math.max(start_y, end_y);
-        var cp_shift = Math.min(Math.max(Math.abs(canvas_max_y - canvas_min_y) / 2, 100), 300);
-        var canvas_left = canvas_min_x - canvas_extra;
-        var canvas_top = canvas_min_y - canvas_extra;
-        var canvas_width = canvas_max_x - canvas_min_x + 2 * canvas_extra;
-        var canvas_height = canvas_max_y - canvas_min_y + 2 * canvas_extra;
+        const canvas_extra = 100;
+        const canvas_min_x = Math.min(start_x, end_x);
+        const canvas_max_x = Math.max(start_x, end_x);
+        const canvas_min_y = Math.min(start_y, end_y);
+        const canvas_max_y = Math.max(start_y, end_y);
+        const canvas_left = canvas_min_x - canvas_extra;
+        const canvas_top = canvas_min_y - canvas_extra;
+        const canvas_width = canvas_max_x - canvas_min_x + 2 * canvas_extra;
+        const canvas_height = canvas_max_y - canvas_min_y + 2 * canvas_extra;
 
         // Place the canvas
         this.canvas.style.left = `${canvas_left}px`;
         this.canvas.style.top = `${canvas_top}px`;
         this.svg.style("width", `${canvas_width}px`);
         this.svg.style("height", `${canvas_height}px`);
-        this.canvas.setAttribute("class", canvasClass);
 
         // Adjust points to be relative to the canvas
         start_x -= canvas_left;
@@ -96,21 +93,14 @@ $.extend(Connector.prototype, {
         end_x -= canvas_left;
         end_y -= canvas_top;
 
-        this.draw_outlined_curve(
-            start_x,
-            start_y,
-            end_x,
-            end_y,
-            0,
-            0,
-            0,
-            0
-        );
+        // Determine line shift
+        const cp_factor = 10;
+        const cp_shift = Math.min(Math.max(Math.abs(canvas_max_y - canvas_min_y) / 2, cp_factor), 300 / cp_factor);
 
-        /*/ Draw the line
-        var start_offsets = null;
-        var end_offsets = null;
-        var num_offsets = 1;
+        // Draw the line
+        let start_offsets = null;
+        let end_offsets = null;
+        let num_offsets = 1;
         if (startRibbon) {
             start_offsets = [-6, -3, 0, 3, 6];
             num_offsets = 5;
@@ -123,16 +113,15 @@ $.extend(Connector.prototype, {
         } else {
             end_offsets = [0];
         }
-        var connector = this;
-        for (var i = 0; i < num_offsets; i++) {
-            var inner_width = 5;
-            var outer_width = 7;
+        for (let i = 0; i < num_offsets; i++) {
+            let inner_width = 5;
+            let outer_width = 7;
             if (start_offsets.length > 1 || end_offsets.length > 1) {
                 // We have a multi-run, using many lines, make them small.
                 inner_width = 1;
                 outer_width = 3;
             }
-            connector.draw_outlined_curve(
+            this.draw_outlined_curve(
                 start_x,
                 start_y,
                 end_x,
@@ -143,7 +132,7 @@ $.extend(Connector.prototype, {
                 start_offsets[i % start_offsets.length],
                 end_offsets[i % end_offsets.length]
             );
-        }*/
+        }
     },
     draw_outlined_curve: function(
         start_x,
@@ -158,21 +147,27 @@ $.extend(Connector.prototype, {
     ) {
         offset_start = offset_start || 0;
         offset_end = offset_end || 0;
-        var lineData = [
+        const lineData = [
             { x: start_x, y: start_y + offset_start },
-            //{ x: start_x + cp_shift,   y: start_y + offset_start},
-            //{ x: end_x - cp_shift,  y: end_y + offset_end },
+            { x: start_x + cp_shift,   y: start_y + offset_start},
+            { x: end_x - cp_shift,  y: end_y + offset_end },
             { x: end_x,  y: end_y + offset_end } ];
-        var lineFunction = d3.svg.line()
-                            .x(function(d) { return d.x; })
-                            .y(function(d) { return d.y; })
-                            .interpolate("linear");
+        const lineFunction = d3.svg.line()
+                                   .x(function(d) { return d.x; })
+                                   .y(function(d) { return d.y; })
+                                   .interpolate("basis");
         // The line SVG Path we draw
         this.svg.selectAll("*").remove();
         this.svg.append("path")
                 .attr("d", lineFunction(lineData))
-                .attr("stroke", "blue")
-                .attr("stroke-width", 2);
+                .attr("stroke", this.inner_color)
+                .attr("stroke-width", inner_width)
+                .attr("fill", "none");
+        this.svg.append("path")
+                .attr("d", lineFunction(lineData))
+                .attr("stroke", this.outer_color)
+                .attr("stroke-width", outer_width)
+                .attr("fill", "none");
     }
 });
 export default Connector;

From 47f590c929e6dcb4b0b9b99ab798006498f1dd81 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 2 Mar 2020 11:41:37 -0500
Subject: [PATCH 276/853] Switch connector to es6 class

---
 .../mvc/workflow/workflow-connector.js        | 44 +++++++++----------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-connector.js b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
index 23b390ae78dc..7e777c4ae256 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-connector.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
@@ -2,19 +2,19 @@ import $ from "jquery";
 import * as d3 from "d3";
 import { Toast } from "ui/toast";
 
-function Connector(manager) {
-    this.manager = manager;
-    this.dragging = false;
-    this.inner_color = "#FFFFFF";
-    this.outer_color = "#25537b";
-    this.canvas = document.createElement("div");
-    this.canvas.style.position = "absolute";
-    const container = document.getElementById("canvas-container");
-    container.appendChild(this.canvas);
-    this.svg = d3.select(this.canvas).append("svg");
-}
-$.extend(Connector.prototype, {
-    connect: function(t1, t2) {
+class Connector {
+    constructor(manager) {
+        this.manager = manager;
+        this.dragging = false;
+        this.inner_color = "#FFFFFF";
+        this.outer_color = "#25537b";
+        this.canvas = document.createElement("div");
+        this.canvas.style.position = "absolute";
+        const container = document.getElementById("canvas-container");
+        container.appendChild(this.canvas);
+        this.svg = d3.select(this.canvas).append("svg");
+    }
+    connect(t1, t2) {
         this.handle1 = t1;
         if (this.handle1) {
             this.handle1.connect(this);
@@ -23,8 +23,8 @@ $.extend(Connector.prototype, {
         if (this.handle2) {
             this.handle2.connect(this);
         }
-    },
-    destroy: function() {
+    }
+    destroy() {
         if (this.handle1) {
             this.handle1.disconnect(this);
         }
@@ -32,16 +32,16 @@ $.extend(Connector.prototype, {
             this.handle2.disconnect(this);
         }
         this.canvas.remove();
-    },
-    destroyIfInvalid: function(warn) {
+    }
+    destroyIfInvalid(warn) {
         if (this.handle1 && this.handle2 && !this.handle2.attachable(this.handle1).canAccept) {
             if (warn) {
                 Toast.warning("Destroying a connection because collection type has changed.");
             }
             this.destroy();
         }
-    },
-    redraw: function() {
+    }
+    redraw() {
         const handle1 = this.handle1;
         const handle2 = this.handle2;
         const startRibbon = handle1 && handle1.isMappedOver();
@@ -133,8 +133,8 @@ $.extend(Connector.prototype, {
                 end_offsets[i % end_offsets.length]
             );
         }
-    },
-    draw_outlined_curve: function(
+    }
+    draw_outlined_curve(
         start_x,
         start_y,
         end_x,
@@ -169,5 +169,5 @@ $.extend(Connector.prototype, {
                 .attr("stroke-width", outer_width)
                 .attr("fill", "none");
     }
-});
+}
 export default Connector;

From 76455e9fc46f9ca9946467ba45a1472b6b96cc5e Mon Sep 17 00:00:00 2001
From: Ralf Weber <RJMW@users.noreply.github.com>
Date: Mon, 2 Mar 2020 17:18:21 +0000
Subject: [PATCH 277/853] Add datatypes for xcms and camera

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index b5301b9a4274..8a92bd8e970f 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -563,6 +563,14 @@
     <datatype extension="gal" type="galaxy.datatypes.microarrays:Gal" display_in_upload="true"/>
     <datatype extension="rdata" type="galaxy.datatypes.binary:RData" display_in_upload="true" description="Stored data from an R session"/>
     <datatype extension="rdata.sce" type="galaxy.datatypes.binary:RData" description="Stored RDS from a SingleCellObject" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.msnbase.raw" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
+    <datatype extension="rdata.xcms.findchrompeaks" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
+    <datatype extension="rdata.xcms.group" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
+    <datatype extension="rdata.xcms.retcor" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
+    <datatype extension="rdata.xcms.fillpeaks" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
+    <datatype extension="rdata.camera.positive" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
+    <datatype extension="rdata.camera.negative" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
+    <datatype extension="rdata.camera.quick" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
     <datatype extension="rdock_as" type="galaxy.datatypes.binary:Binary" description="rDock active site format" subclass="true" display_in_upload="true"/>
     <datatype extension="oxlicg" type="galaxy.datatypes.binary:OxliCountGraph" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="oxling" type="galaxy.datatypes.binary:OxliNodeGraph" mimetype="application/octet-stream" display_in_upload="true"/>

From 37dfd4292a69e4f76dcec785361649956eb1c8ca Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Fri, 1 Feb 2019 18:45:52 +0100
Subject: [PATCH 278/853] Fix?

---
 lib/galaxy/objectstore/s3.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index a2577e8464e1..09e78626e24d 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -378,8 +378,6 @@ def _key_exists(self, rel_path):
         except S3ResponseError:
             log.exception("Trouble checking existence of S3 key '%s'", rel_path)
             return False
-        if rel_path[0] == '/':
-            raise
         return exists
 
     def _in_cache(self, rel_path):

From 98cbc672b8dc1da48dcd85811db4e1da992bcd5c Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 2 Mar 2020 13:18:01 -0500
Subject: [PATCH 279/853] Remove static ribbon colors, assign brand colors in
 css instead

---
 .../mvc/workflow/workflow-connector.js        | 147 ++++++++++--------
 .../mvc/workflow/workflow-view-terminals.js   |   6 +-
 client/galaxy/style/scss/workflow.scss        |  14 ++
 3 files changed, 102 insertions(+), 65 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-connector.js b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
index 7e777c4ae256..02cb0ce3a678 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-connector.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
@@ -2,17 +2,29 @@ import $ from "jquery";
 import * as d3 from "d3";
 import { Toast } from "ui/toast";
 
+// Rendering parameters
+const zIndex = 1000;
+const cpFactor = 10;
+const canvasExtra = 100;
+const handleMarginX = 8;
+const handleMarginY = 5;
+const ribbonMargin = 4;
+const ribbonInnerSingle = 4;
+const ribbonOuterSingle = 6;
+const ribbonInnerMultiple = 1;
+const ribbonOuterMultiple = 3;
+
 class Connector {
     constructor(manager) {
         this.manager = manager;
         this.dragging = false;
-        this.inner_color = "#FFFFFF";
-        this.outer_color = "#25537b";
+        this.innerClass = "ribbon-inner";
         this.canvas = document.createElement("div");
         this.canvas.style.position = "absolute";
         const container = document.getElementById("canvas-container");
         container.appendChild(this.canvas);
         this.svg = d3.select(this.canvas).append("svg");
+        this.svg.attr("class", "ribbon");
     }
     connect(t1, t2) {
         this.handle1 = t1;
@@ -41,15 +53,24 @@ class Connector {
             this.destroy();
         }
     }
+    dropStart(canAccept) {
+        if (canAccept) {
+            this.innerClass = "ribbon-inner-valid";
+        } else {
+            this.innerClass = "ribbon-inner-invalid";
+        }
+    }
+    dropEnd() {
+        this.innerClass = "ribbon-inner";
+    }
     redraw() {
+        // Identify handles
         const handle1 = this.handle1;
         const handle2 = this.handle2;
-        const startRibbon = handle1 && handle1.isMappedOver();
-        const endRibbon = handle2 && handle2.isMappedOver();
         const canvas_container = $("#canvas-container");
         const canvasZoom = this.manager.canvasZoom;
         if (this.dragging) {
-            this.canvas.style.zIndex = 1000;
+            this.canvas.style.zIndex = zIndex;
         }
         this.canvas.setAttribute(
             "handle1-id",
@@ -64,26 +85,28 @@ class Connector {
         if (!handle1 || !handle2) {
             return;
         }
+
         // Find the position of each handle
-        let start_x = relativeLeft(handle1.element) + 5;
-        let start_y = relativeTop(handle1.element) + 5;
-        let end_x = relativeLeft(handle2.element) + 5;
-        let end_y = relativeTop(handle2.element) + 5;
+        let start_x = relativeLeft(handle1.element) + handleMarginX;
+        let start_y = relativeTop(handle1.element) + handleMarginY;
+        let end_x = relativeLeft(handle2.element) + handleMarginX;
+        let end_y = relativeTop(handle2.element) + handleMarginY;
 
         // Calculate canvas area
-        const canvas_extra = 100;
         const canvas_min_x = Math.min(start_x, end_x);
         const canvas_max_x = Math.max(start_x, end_x);
         const canvas_min_y = Math.min(start_y, end_y);
         const canvas_max_y = Math.max(start_y, end_y);
-        const canvas_left = canvas_min_x - canvas_extra;
-        const canvas_top = canvas_min_y - canvas_extra;
-        const canvas_width = canvas_max_x - canvas_min_x + 2 * canvas_extra;
-        const canvas_height = canvas_max_y - canvas_min_y + 2 * canvas_extra;
+        const canvas_left = canvas_min_x - canvasExtra;
+        const canvas_top = canvas_min_y - canvasExtra;
+        const canvas_width = canvas_max_x - canvas_min_x + 2 * canvasExtra;
+        const canvas_height = canvas_max_y - canvas_min_y + 2 * canvasExtra;
 
         // Place the canvas
         this.canvas.style.left = `${canvas_left}px`;
         this.canvas.style.top = `${canvas_top}px`;
+
+        // Resize the svg
         this.svg.style("width", `${canvas_width}px`);
         this.svg.style("height", `${canvas_height}px`);
 
@@ -94,34 +117,38 @@ class Connector {
         end_y -= canvas_top;
 
         // Determine line shift
-        const cp_factor = 10;
-        const cp_shift = Math.min(Math.max(Math.abs(canvas_max_y - canvas_min_y) / 2, cp_factor), 300 / cp_factor);
+        const cp_shift = Math.min(Math.max(Math.abs(canvas_max_y - canvas_min_y) / 2, cpFactor), 300 / cpFactor);
+
+        // Draw ribbons
+        this.drawRibbon(handle1, handle2, cp_shift, start_x, start_y, end_x, end_y);
+    }
+    drawRibbon(handle1, handle2, cp_shift, start_x, start_y, end_x, end_y) {
+        // Check ribbon type
+        const startRibbon = handle1 && handle1.isMappedOver();
+        const endRibbon = handle2 && handle2.isMappedOver();
 
         // Draw the line
-        let start_offsets = null;
-        let end_offsets = null;
+        let start_offsets = [0];
+        let end_offsets = [0];
+        const offsets = [-2 * ribbonMargin, -ribbonMargin, 0, ribbonMargin, 2 * ribbonMargin];
         let num_offsets = 1;
         if (startRibbon) {
-            start_offsets = [-6, -3, 0, 3, 6];
-            num_offsets = 5;
-        } else {
-            start_offsets = [0];
+            start_offsets = offsets;
+            num_offsets = offsets.length;
         }
         if (endRibbon) {
-            end_offsets = [-6, -3, 0, 3, 6];
-            num_offsets = 5;
-        } else {
-            end_offsets = [0];
+            end_offsets = offsets;
+            num_offsets = offsets.length;
         }
+        this.svg.selectAll("*").remove();
         for (let i = 0; i < num_offsets; i++) {
-            let inner_width = 5;
-            let outer_width = 7;
+            let inner_width = ribbonInnerSingle;
+            let outer_width = ribbonOuterSingle;
             if (start_offsets.length > 1 || end_offsets.length > 1) {
-                // We have a multi-run, using many lines, make them small.
-                inner_width = 1;
-                outer_width = 3;
+                inner_width = ribbonInnerMultiple;
+                outer_width = ribbonOuterMultiple;
             }
-            this.draw_outlined_curve(
+            this.drawCurve(
                 start_x,
                 start_y,
                 end_x,
@@ -134,40 +161,36 @@ class Connector {
             );
         }
     }
-    draw_outlined_curve(
-        start_x,
-        start_y,
-        end_x,
-        end_y,
-        cp_shift,
-        inner_width,
-        outer_width,
-        offset_start,
-        offset_end
-    ) {
+    drawCurve(start_x, start_y, end_x, end_y, cp_shift, inner_width, outer_width, offset_start, offset_end) {
         offset_start = offset_start || 0;
         offset_end = offset_end || 0;
         const lineData = [
             { x: start_x, y: start_y + offset_start },
-            { x: start_x + cp_shift,   y: start_y + offset_start},
-            { x: end_x - cp_shift,  y: end_y + offset_end },
-            { x: end_x,  y: end_y + offset_end } ];
-        const lineFunction = d3.svg.line()
-                                   .x(function(d) { return d.x; })
-                                   .y(function(d) { return d.y; })
-                                   .interpolate("basis");
-        // The line SVG Path we draw
-        this.svg.selectAll("*").remove();
-        this.svg.append("path")
-                .attr("d", lineFunction(lineData))
-                .attr("stroke", this.inner_color)
-                .attr("stroke-width", inner_width)
-                .attr("fill", "none");
-        this.svg.append("path")
-                .attr("d", lineFunction(lineData))
-                .attr("stroke", this.outer_color)
-                .attr("stroke-width", outer_width)
-                .attr("fill", "none");
+            { x: start_x + cp_shift, y: start_y + offset_start },
+            { x: end_x - cp_shift, y: end_y + offset_end },
+            { x: end_x, y: end_y + offset_end }
+        ];
+        const lineFunction = d3.svg
+            .line()
+            .x(function(d) {
+                return d.x;
+            })
+            .y(function(d) {
+                return d.y;
+            })
+            .interpolate("basis");
+        this.svg
+            .append("path")
+            .attr("class", "ribbon-outer")
+            .attr("d", lineFunction(lineData))
+            .attr("stroke-width", outer_width)
+            .attr("fill", "none");
+        this.svg
+            .append("path")
+            .attr("class", this.innerClass)
+            .attr("d", lineFunction(lineData))
+            .attr("stroke-width", inner_width)
+            .attr("fill", "none");
     }
 }
 export default Connector;
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index a6c4886f11e0..f52c9eb33f7f 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -91,10 +91,10 @@ class BaseInputTerminalView extends TerminalView {
     onDropStart(e, d = {}) {
         if (d.proxy.terminal) {
             if (this.$el.hasClass("can-accept")) {
-                d.proxy.terminal.connectors[0].inner_color = "#BBFFBB";
+                d.proxy.terminal.connectors[0].dropStart(true);
                 d.proxy.dropTooltip = "";
             } else {
-                d.proxy.terminal.connectors[0].inner_color = "#fe7f02";
+                d.proxy.terminal.connectors[0].dropStart(false);
                 if (this.reason) {
                     d.proxy.dropTooltip = this.reason;
                     $(d.proxy).tooltip("show");
@@ -107,7 +107,7 @@ class BaseInputTerminalView extends TerminalView {
     onDropEnd(e, d = {}) {
         d.proxy.dropTooltip = "";
         if (d.proxy.terminal) {
-            d.proxy.terminal.connectors[0].inner_color = "#FFFFFF";
+            d.proxy.terminal.connectors[0].dropEnd();
         }
     }
     onDrop(e, d = {}) {
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 4227ff58d0bb..de03e0c8d3bd 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -55,6 +55,20 @@
                 position: relative;
                 overflow: hidden;
             }
+            .ribbon {
+                .ribbon-outer {
+                    stroke: $brand-primary;
+                }
+                .ribbon-inner {
+                    stroke: $white;
+                }
+                .ribbon-inner-valid {
+                    stroke: $brand-success;
+                }
+                .ribbon-inner-invalid {
+                    stroke: $brand-warning;
+                }
+            }
             .base-terminal {
                 @extend .fa;
                 @extend .fa-circle;

From fc503789451cffafd73e979043601e70bf4ef888 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 2 Mar 2020 15:03:17 -0500
Subject: [PATCH 280/853] Fix qunit workflow test cases

---
 .../mvc/workflow/workflow-connector.js        |  5 +++-
 .../mvc/workflow/workflow-view-terminals.js   |  5 ++--
 .../qunit/tests/workflow_editor_tests.js      | 23 ++++++++-----------
 3 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-connector.js b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
index 02cb0ce3a678..9f107e011993 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-connector.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
@@ -15,7 +15,7 @@ const ribbonInnerMultiple = 1;
 const ribbonOuterMultiple = 3;
 
 class Connector {
-    constructor(manager) {
+    constructor(manager = {}, handle1 = null, handle2 = null) {
         this.manager = manager;
         this.dragging = false;
         this.innerClass = "ribbon-inner";
@@ -25,6 +25,9 @@ class Connector {
         container.appendChild(this.canvas);
         this.svg = d3.select(this.canvas).append("svg");
         this.svg.attr("class", "ribbon");
+        if (handle1 && handle2) {
+            this.connect(handle1, handle2);
+        }
     }
     connect(t1, t2) {
         this.handle1 = t1;
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index f52c9eb33f7f..c481940b653d 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -114,8 +114,7 @@ class BaseInputTerminalView extends TerminalView {
         d.proxy.dropTooltip = "";
         if (this.$el.hasClass("can-accept")) {
             const terminal = this.el.terminal;
-            const c = new Connector(this.app.canvas_manager);
-            c.connect(d.drag.terminal, terminal);
+            const c = new Connector(this.app.canvas_manager, d.drag.terminal, terminal);
             c.redraw();
         }
     }
@@ -253,7 +252,7 @@ export class BaseOutputTerminalView extends TerminalView {
                     break;
                 case 32: // Space
                     removeMenu();
-                    new Connector(this.app.canvas_manager).connect(this.el.terminal, inputTerminal).redraw();
+                    new Connector(this.app.canvas_manager, this.el.terminal, inputTerminal).redraw();
                     ariaAlert("Node connected");
 
                     if (inputTerminal.connectors.length > 0) {
diff --git a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
index 116ecb708d20..643564797f8d 100644
--- a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
+++ b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
@@ -242,9 +242,7 @@ QUnit.test("default attributes", function(assert) {
     const output = { connect: sinon.spy() };
     const connector = new Connector({}, input, output);
     assert.equal(connector.dragging, false);
-    assert.equal(connector.canvas, null);
-    assert.equal(connector.inner_color, "#FFFFFF");
-    assert.equal(connector.outer_color, "#25537b");
+    assert.equal(connector.svg.attr("class"), "ribbon");
 });
 
 QUnit.test("destroy", function(assert) {
@@ -271,13 +269,12 @@ QUnit.test("initial redraw", function(assert) {
             return false;
         }
     };
+    const n = $("#canvas-container").find("svg").length;
     const connector = new Connector({}, input, output);
-    const n = $("#canvas-container").find("canvas").length;
-    connector.redraw();
     // Ensure canvas gets set
     assert.ok(connector.canvas);
     // Ensure it got added to canvas container
-    assert.equal(n + 1, $("#canvas-container").find("canvas").length);
+    assert.equal(n + 1, $("#canvas-container").find("svg").length);
 });
 
 QUnit.module("Input collection terminal model test", {
@@ -366,9 +363,9 @@ QUnit.module("Node unit test", {
 });
 
 QUnit.test("make active", function(assert) {
-    assert.ok(!this.element.hasClass("toolForm-active"));
+    assert.ok(!this.element.hasClass("node-active"));
     this.node.make_active();
-    assert.ok(this.element.hasClass("toolForm-active"));
+    assert.ok(this.element.hasClass("node-active"));
 });
 
 QUnit.test("destroy", function(assert) {
@@ -384,7 +381,7 @@ QUnit.test("error", function(assert) {
     var test = this;
     this.expect_workflow_node_changed(assert, function() {
         test.node.error("TOOL ERROR");
-        assert.equal($(test.$(".toolFormBody").children()[0]).html(), "TOOL ERROR");
+        assert.equal($(test.$(".node-body").children()[0]).html(), "TOOL ERROR");
     });
 });
 
@@ -428,10 +425,10 @@ QUnit.test("init_field_data data", function(assert) {
         assert.equal(this.$(".output-terminal").length, 1);
         assert.equal(this.$(".input-terminal").length, 1);
         assert.equal(this.$(".rule").length, 1);
-        assert.equal(this.$(".toolFormBody").children().length, 3);
+        assert.equal(this.$(".node-body").children().length, 3);
         assert.equal(this.$(".node-title").text(), "newnode");
         assert.ok(
-            this.$(".toolFormTitle")
+            this.$(".node-header")
                 .find("i")
                 .hasClass("fa-wrench")
         );
@@ -607,10 +604,10 @@ QUnit.module("Node view ", {
 QUnit.test("tool error styling", function(assert) {
     this.set_for_node({ errors: false });
     this.view.render();
-    assert.ok(!this.view.$el.hasClass("tool-node-error"));
+    assert.ok(!this.view.$el.hasClass("node-error"));
     this.set_for_node({ errors: true });
     this.view.render();
-    assert.ok(this.view.$el.hasClass("tool-node-error"));
+    assert.ok(this.view.$el.hasClass("node-error"));
 });
 
 QUnit.test("rendering correct width", function(assert) {

From 2be3b473f694c841681d14bdf9da7729ca497537 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 2 Mar 2020 15:43:52 -0500
Subject: [PATCH 281/853] Fix error handling, display error message in node
 body

---
 .../scripts/mvc/workflow/workflow-node.js     | 12 ++-------
 .../mvc/workflow/workflow-view-node.js        | 25 +++++++++++--------
 .../qunit/tests/workflow_editor_tests.js      |  6 ++---
 3 files changed, 20 insertions(+), 23 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js
index 72ca51e2754b..94938aff0f2b 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js
@@ -10,7 +10,7 @@ export class Node {
         this.element = attr.element;
         this.input_terminals = {};
         this.output_terminals = {};
-        this.errors = {};
+        this.errors = null;
         this.workflow_outputs = [];
     }
     getWorkflowOutput(outputName) {
@@ -309,7 +309,7 @@ export class Node {
             var pja_in = data.post_job_actions;
             this.post_job_actions = pja_in ? pja_in : {};
         }
-        node.nodeView.renderToolErrors();
+        node.nodeView.renderErrors();
         // Update input rows
         var old_body = nodeView.$el.find("div.inputs");
         var new_body = nodeView.newInputsDiv();
@@ -340,14 +340,6 @@ export class Node {
         this.markChanged();
         this.redraw();
     }
-    error(text) {
-        var b = $(this.element).find(".node-body");
-        b.find("div").remove();
-        var tmp = `<div style='color: red; text-style: italic;'>${text}</div>`;
-        this.config_form = tmp;
-        b.html(tmp);
-        this.app.node_changed(this);
-    }
     markChanged() {
         this.app.node_changed(this);
     }
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
index 2b16458a0ff7..0686f57ff94a 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
@@ -9,26 +9,31 @@ export class NodeView {
         this.$el = options.$el;
         this.node = options.node;
         this.output_width = Math.max(150, this.$el.width());
-        this.tool_body = this.$el.find(".node-body");
-        this.tool_body.find("div").remove();
-        this.newInputsDiv().appendTo(this.tool_body);
+        this.node_body = this.$el.find(".node-body");
+        this.node_body.find("div").remove();
+        this.newInputsDiv().appendTo(this.node_body);
         this.terminalViews = {};
         this.outputViews = {};
     }
 
     render() {
-        this.renderToolLabel();
-        this.renderToolErrors();
+        this.renderLabel();
+        this.renderErrors();
         this.$el.css("width", Math.min(250, Math.max(this.$el.width(), this.output_width)));
     }
 
-    renderToolLabel() {
+    renderLabel() {
         this.$el.find(".node-title").text(this.node.label || this.node.name);
         this.$el.attr("node-label", this.node.label);
     }
 
-    renderToolErrors() {
-        this.node.errors ? this.$el.addClass("node-error") : this.$el.removeClass("node-error");
+    renderErrors() {
+        if (this.node.errors) {
+            this.$el.addClass("node-error");
+            this.node_body.text(this.node.errors);
+        } else {
+            this.$el.removeClass("node-error");
+        }
     }
 
     newInputsDiv() {
@@ -40,7 +45,7 @@ export class NodeView {
     }
 
     addRule() {
-        this.tool_body.append($("<div/>").addClass("rule"));
+        this.node_body.append($("<div/>").addClass("rule"));
     }
 
     addDataInput(input, body) {
@@ -111,7 +116,7 @@ export class NodeView {
         const terminalView = this.terminalViewForOutput(output);
         const outputView = this.outputViewforOutput(output, terminalView);
         this.outputViews[output.name] = outputView;
-        this.tool_body.append(outputView.$el.append(terminalView.terminalElements()));
+        this.node_body.append(outputView.$el.append(terminalView.terminalElements()));
     }
 
     redrawWorkflowOutputs() {
diff --git a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
index 643564797f8d..449ab1704096 100644
--- a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
+++ b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
@@ -377,11 +377,11 @@ QUnit.test("destroy", function(assert) {
 });
 
 QUnit.test("error", function(assert) {
-    // Test body of toolFormBody div updated and workflow notified of change.
+    // Test body of div updated and workflow notified of change.
     var test = this;
     this.expect_workflow_node_changed(assert, function() {
-        test.node.error("TOOL ERROR");
-        assert.equal($(test.$(".node-body").children()[0]).html(), "TOOL ERROR");
+        test.node.init_field_data({ errors: "NODE ERROR", inputs: [], outputs: [] });
+        assert.equal(test.$(".node-body").html(), "NODE ERROR");
     });
 });
 

From 9155c6806f4fab637b3a68e01c789c30e5399643 Mon Sep 17 00:00:00 2001
From: Dannon <dannon.baker@gmail.com>
Date: Tue, 28 Jan 2020 19:56:02 -0500
Subject: [PATCH 282/853] Merge pull request #9162 from machristie/idp-logout

Add support for logging out of OIDC Identity Provider
---
 client/galaxy/scripts/layout/menu.js          | 26 ++++++++++---
 lib/galaxy/authnz/__init__.py                 | 13 +++++++
 lib/galaxy/authnz/custos_authnz.py            | 13 +++++++
 lib/galaxy/authnz/managers.py                 | 37 +++++++++++++++++--
 .../sample/oidc_backends_config.xml.sample    |  2 +
 lib/galaxy/webapps/galaxy/buildapp.py         |  3 ++
 .../webapps/galaxy/controllers/authnz.py      | 21 +++++++++++
 test/unit/authnz/test_custos_authnz.py        | 12 +++++-
 8 files changed, 116 insertions(+), 11 deletions(-)

diff --git a/client/galaxy/scripts/layout/menu.js b/client/galaxy/scripts/layout/menu.js
index 46c1ead9f75c..305e54776159 100644
--- a/client/galaxy/scripts/layout/menu.js
+++ b/client/galaxy/scripts/layout/menu.js
@@ -14,12 +14,26 @@ function logoutClick() {
     const galaxy = getGalaxyInstance();
     const session_csrf_token = galaxy.session_csrf_token;
     const url = `${galaxy.root}user/logout?session_csrf_token=${session_csrf_token}`;
-    axios.get(url).then(() => {
-        if (galaxy.user) {
-            galaxy.user.clearSessionStorage();
-        }
-        window.top.location.href = `${galaxy.root}root/login?is_logout_redirect=true`;
-    });
+    axios
+        .get(url)
+        .then(() => {
+            if (galaxy.user) {
+                galaxy.user.clearSessionStorage();
+            }
+            // Check if we need to logout of OIDC IDP
+            if (galaxy.config.enable_oidc) {
+                return axios.get(`${galaxy.root}authnz/logout`);
+            } else {
+                return {};
+            }
+        })
+        .then(response => {
+            if (response.data && response.data.redirect_uri) {
+                window.top.location.href = response.data.redirect_uri;
+            } else {
+                window.top.location.href = `${galaxy.root}root/login?is_logout_redirect=true`;
+            }
+        });
 }
 
 const Collection = Backbone.Collection.extend({
diff --git a/lib/galaxy/authnz/__init__.py b/lib/galaxy/authnz/__init__.py
index 6db25196df65..4b70484bc037 100644
--- a/lib/galaxy/authnz/__init__.py
+++ b/lib/galaxy/authnz/__init__.py
@@ -70,3 +70,16 @@ def callback(self, state_token, authz_code, trans, login_redirect_url):
 
     def disconnect(self, provider, trans, disconnect_redirect_url=None):
         raise NotImplementedError()
+
+    def logout(self, trans, post_logout_redirect_url=None):
+        """
+        Return a URL that will log the user out of the IDP. In OIDC this is
+        called the 'end_session_endpoint'.
+
+        :type trans: GalaxyWebTransaction
+        :param trans: Galaxy web transaction.
+
+        :type trans: string
+        :param trans: Optional URL to redirect to after logging out of IDP.
+        """
+        raise NotImplementedError()
diff --git a/lib/galaxy/authnz/custos_authnz.py b/lib/galaxy/authnz/custos_authnz.py
index 1d5b5b17bc0e..165f6a5615a1 100644
--- a/lib/galaxy/authnz/custos_authnz.py
+++ b/lib/galaxy/authnz/custos_authnz.py
@@ -9,6 +9,7 @@
 import requests
 from oauthlib.common import generate_nonce
 from requests_oauthlib import OAuth2Session
+from six.moves.urllib.parse import quote
 
 from galaxy import util
 from galaxy.model import CustosAuthnzToken, User
@@ -39,6 +40,7 @@ def __init__(self, provider, oidc_config, oidc_backend_config):
             self.config['authorization_endpoint'] = well_known_oidc_config['authorization_endpoint']
             self.config['token_endpoint'] = well_known_oidc_config['token_endpoint']
             self.config['userinfo_endpoint'] = well_known_oidc_config['userinfo_endpoint']
+            self.config['end_session_endpoint'] = well_known_oidc_config['end_session_endpoint']
         else:
             realm = oidc_backend_config['realm']
             self._load_config_for_provider_and_realm(self.config['provider'], realm)
@@ -142,6 +144,16 @@ def disconnect(self, provider, trans, disconnect_redirect_url=None):
         except Exception as e:
             return False, "Failed to disconnect provider {}: {}".format(provider, util.unicodify(e)), None
 
+    def logout(self, trans, post_logout_redirect_url=None):
+        try:
+            redirect_url = self.config['end_session_endpoint']
+            if post_logout_redirect_url is not None:
+                redirect_url += "?redirect_uri={}".format(quote(post_logout_redirect_url))
+            return redirect_url
+        except Exception as e:
+            log.error("Failed to generate logout redirect_url", exc_info=e)
+            return None
+
     def _create_oauth2_session(self, state=None, scope=None):
         client_id = self.config['client_id']
         redirect_uri = self.config['redirect_uri']
@@ -191,6 +203,7 @@ def _load_config_for_provider_and_realm(self, provider, realm):
         self.config['authorization_endpoint'] = well_known_oidc_config['authorization_endpoint']
         self.config['token_endpoint'] = well_known_oidc_config['token_endpoint']
         self.config['userinfo_endpoint'] = well_known_oidc_config['userinfo_endpoint']
+        self.config['end_session_endpoint'] = well_known_oidc_config['end_session_endpoint']
 
     def _get_well_known_uri_for_provider_and_realm(self, provider, realm):
         # TODO: Look up this URL from a Python library
diff --git a/lib/galaxy/authnz/managers.py b/lib/galaxy/authnz/managers.py
index b2bcbd94953b..1876bdb82bd0 100644
--- a/lib/galaxy/authnz/managers.py
+++ b/lib/galaxy/authnz/managers.py
@@ -16,7 +16,7 @@
 
 from galaxy import exceptions
 from galaxy import model
-from galaxy.util import string_as_bool
+from galaxy.util import asbool, string_as_bool
 from galaxy.util import unicodify
 from .custos_authnz import CustosAuthnz
 from .psa_authnz import (
@@ -117,7 +117,8 @@ def _parse_idp_config(self, config_xml):
         rtv = {
             'client_id': config_xml.find('client_id').text,
             'client_secret': config_xml.find('client_secret').text,
-            'redirect_uri': config_xml.find('redirect_uri').text}
+            'redirect_uri': config_xml.find('redirect_uri').text,
+            'enable_idp_logout': asbool(config_xml.findtext('enable_idp_logout', 'false'))}
         if config_xml.find('prompt') is not None:
             rtv['prompt'] = config_xml.find('prompt').text
         return rtv
@@ -128,7 +129,8 @@ def _parse_custos_config(self, config_xml):
             'client_id': config_xml.find('client_id').text,
             'client_secret': config_xml.find('client_secret').text,
             'redirect_uri': config_xml.find('redirect_uri').text,
-            'realm': config_xml.find('realm').text}
+            'realm': config_xml.find('realm').text,
+            'enable_idp_logout': asbool(config_xml.findtext('enable_idp_logout', 'false'))}
         if config_xml.find('well_known_oidc_config_uri') is not None:
             rtv['well_known_oidc_config_uri'] = config_xml.find('well_known_oidc_config_uri').text
         if config_xml.find('idphint') is not None:
@@ -262,6 +264,35 @@ def callback(self, provider, state_token, authz_code, trans, login_redirect_url)
             log.exception(msg)
             return False, msg, (None, None)
 
+    def logout(self, provider, trans, post_logout_redirect_url=None):
+        """
+        Log the user out of the identity provider.
+
+        :type provider: string
+        :param provider: set the name of the identity provider.
+        :type trans: GalaxyWebTransaction
+        :param trans: Galaxy web transaction.
+        :type post_logout_redirect_url: string
+        :param post_logout_redirect_url: (Optional) URL for identity provider
+            to redirect to after logging user out.
+        :return: a tuple (success boolean, message, redirect URI)
+        """
+        try:
+            # check if logout is enabled for this idp and return false if not
+            unified_provider_name = self._unify_provider_name(provider)
+            if self.oidc_backends_config[unified_provider_name]['enable_idp_logout'] is False:
+                return False, "IDP logout is not enabled for {}".format(provider), None
+
+            success, message, backend = self._get_authnz_backend(provider)
+            if success is False:
+                return False, message, None
+            return True, message, backend.logout(trans, post_logout_redirect_url)
+        except Exception as e:
+            msg = 'The following error occurred when logging out from `{}` identity provider: ' \
+                  '{}'.format(provider, e.message)
+            log.exception(msg)
+            return False, msg, None
+
     def disconnect(self, provider, trans, disconnect_redirect_url=None):
         try:
             success, message, backend = self._get_authnz_backend(provider)
diff --git a/lib/galaxy/config/sample/oidc_backends_config.xml.sample b/lib/galaxy/config/sample/oidc_backends_config.xml.sample
index 90b157b16320..6cb60e611936 100644
--- a/lib/galaxy/config/sample/oidc_backends_config.xml.sample
+++ b/lib/galaxy/config/sample/oidc_backends_config.xml.sample
@@ -99,6 +99,8 @@ Please mind `http` and `https`.
         <!-- <well_known_oidc_config_uri>https://.../.well-known/openid-configuration</well_known_oidc_config_uri> -->
         <!-- (Optional) Override the default idp hint -->
         <!-- <idphint>cilogon</idphint> -->
+        <!-- (Optional) Enable logging out of the IDP when user logs out of Galaxy -->
+        <!-- <enable_idp_logout>true</enable_idp_logout> -->
     </provider>
     <!-- Documentation: https://galaxyproject.org/authnz/config/oidc/idps/elixir-aai  -->
     <provider name="Elixir">
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 76705a46079d..7db22fe0fe1d 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -72,6 +72,9 @@ def app_factory(global_conf, load_app_kwds={}, **kwargs):
     webapp.add_route('/authnz/{provider}/login', controller='authnz', action='login', provider=None)
     webapp.add_route('/authnz/{provider}/callback', controller='authnz', action='callback', provider=None)
     webapp.add_route('/authnz/{provider}/disconnect', controller='authnz', action='disconnect', provider=None)
+    webapp.add_route('/authnz/{provider}/logout', controller='authnz', action='logout', provider=None)
+    # Returns the provider specific logout url for currently logged in provider
+    webapp.add_route('/authnz/logout', controller='authnz', action='get_logout_url')
 
     # These two routes handle our simple needs at the moment
     webapp.add_route('/async/{tool_id}/{data_id}/{data_secret}', controller='async', action='index', tool_id=None, data_id=None, data_secret=None)
diff --git a/lib/galaxy/webapps/galaxy/controllers/authnz.py b/lib/galaxy/webapps/galaxy/controllers/authnz.py
index 70e68d4098a4..ad4f34435f52 100644
--- a/lib/galaxy/webapps/galaxy/controllers/authnz.py
+++ b/lib/galaxy/webapps/galaxy/controllers/authnz.py
@@ -13,6 +13,8 @@
 
 log = logging.getLogger(__name__)
 
+PROVIDER_COOKIE_NAME = 'oidc-provider'
+
 
 class OIDC(JSAppLauncher):
 
@@ -79,6 +81,8 @@ def callback(self, trans, provider, **kwargs):
                                             "identity provider. Please try again, and if the problem persists, "
                                             "contact the Galaxy instance admin.".format(provider))
         trans.handle_user_login(user)
+        # Record which idp provider was logged into, so we can logout of it later
+        trans.set_cookie(value=provider, name=PROVIDER_COOKIE_NAME)
         return trans.response.send_redirect(url_for('/'))
 
     @web.expose
@@ -95,3 +99,20 @@ def disconnect(self, trans, provider, **kwargs):
         if redirect_url is None:
             redirect_url = url_for('/')
         return trans.response.send_redirect(redirect_url)
+
+    @web.json
+    def logout(self, trans, provider, **kwargs):
+        post_logout_redirect_url = trans.request.base + url_for('/') + 'root/login?is_logout_redirect=true'
+        success, message, redirect_uri = trans.app.authnz_manager.logout(provider,
+                                                                         trans,
+                                                                         post_logout_redirect_url=post_logout_redirect_url)
+        if success:
+            return {'redirect_uri': redirect_uri}
+        else:
+            return {'message': message}
+
+    @web.expose
+    def get_logout_url(self, trans, **kwargs):
+        idp_provider = trans.get_cookie(name=PROVIDER_COOKIE_NAME)
+        if idp_provider:
+            return trans.response.send_redirect(url_for(controller='authnz', action='logout', provider=idp_provider))
diff --git a/test/unit/authnz/test_custos_authnz.py b/test/unit/authnz/test_custos_authnz.py
index 2166a86ed224..6d3d8cfc26d5 100644
--- a/test/unit/authnz/test_custos_authnz.py
+++ b/test/unit/authnz/test_custos_authnz.py
@@ -6,7 +6,7 @@
 
 import jwt
 import requests
-from six.moves.urllib.parse import parse_qs, urlparse
+from six.moves.urllib.parse import parse_qs, quote, urlparse
 
 from galaxy.authnz import custos_authnz
 from galaxy.model import CustosAuthnzToken, User
@@ -33,7 +33,8 @@ def setUp(self):
         requests.get = self.mockRequest(self._get_idp_url(), {
             "authorization_endpoint": "https://test-auth-endpoint",
             "token_endpoint": "https://test-token-endpoint",
-            "userinfo_endpoint": "https://test-userinfo-endpoint"
+            "userinfo_endpoint": "https://test-userinfo-endpoint",
+            "end_session_endpoint": "https://test-end-session-endpoint"
         })
         self.custos_authnz = custos_authnz.CustosAuthnz('Custos', {
             'VERIFY_SSL': True
@@ -476,3 +477,10 @@ def test_disconnect_when_more_than_one_associated_token_for_provider(self):
         self.assertFalse(success)
         self.assertNotEqual("", message)
         self.assertIsNone(redirect_uri)
+
+    def test_logout_with_redirect(self):
+
+        logout_redirect_url = "http://localhost:8080/post-logout"
+        redirect_url = self.custos_authnz.logout(self.trans, logout_redirect_url)
+
+        self.assertEqual(redirect_url, "https://test-end-session-endpoint?redirect_uri=" + quote(logout_redirect_url))

From c631d1f7061267ed9916dbeb952da53695f2da46 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Thu, 13 Feb 2020 01:56:06 -0500
Subject: [PATCH 283/853] Move schema loading/validating code out of config

Add integration test; update several unit tests
---
 lib/galaxy/config/__init__.py          | 64 ++++---------------------
 lib/galaxy/config/schema.py            | 66 +++++++++++++++++++++++++-
 test/integration/test_config_schema.py |  9 ++++
 test/unit/config/test_load_config.py   | 54 ++++++++++++++++-----
 test/unit/config/test_reload_config.py |  6 ++-
 test/unit/config/test_schema.py        | 53 +++++++++++++++++----
 6 files changed, 177 insertions(+), 75 deletions(-)
 create mode 100644 test/integration/test_config_schema.py

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 3fdc7f9af3a1..8bfcb6918467 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -217,9 +217,11 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
     deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
 
     def __init__(self, **kwargs):
-        self._load_schema()  # Load schema from schema definition file
-        self._load_config_from_schema()  # Load default propery values from schema
-        self._validate_schema_paths()  # check that paths can be resolved
+        self.schema = self._load_schema()  # Load schema from schema definition file
+        self.appschema = self.schema.app_schema
+        self._raw_config = self.schema.defaults.copy()  # keeps track of startup values (kwargs or schema default)
+
+        self._load_schema()
         self._update_raw_config_from_kwargs(kwargs)  # Overwrite default values passed as kwargs
         self._create_attributes_from_raw_config()  # Create attributes for LOADED properties
 
@@ -227,57 +229,11 @@ def __init__(self, **kwargs):
         self.root = find_root(kwargs)
         self._set_config_base(kwargs)  # must be called prior to _resolve_paths()
 
-        self._resolve_paths(kwargs)  # Overwrite attributes (not _raw_config) w/resolved paths
+        self._resolve_paths(self.schema.paths_to_resolve)  # Overwrite attributes (not _raw_config) w/resolved paths
         self._process_config(kwargs)  # Finish processing configuration
 
     def _load_schema(self):
-        self.schema = AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
-        self.appschema = self.schema.app_schema
-
-    def _load_config_from_schema(self):
-        self._raw_config = {}  # keeps track of startup values (kwargs or schema default)
-        self.reloadable_options = set()  # config options we can reload at runtime
-        self._paths_to_resolve = {}  # {config option: referenced config option}
-        for key, data in self.appschema.items():
-            self._raw_config[key] = data.get('default')
-            if data.get('reloadable'):
-                self.reloadable_options.add(key)
-            if data.get('path_resolves_to'):
-                self._paths_to_resolve[key] = data.get('path_resolves_to')
-
-    def _validate_schema_paths(self):
-
-        def check_exists(option, key):
-            if not option:
-                message = "Invalid schema: property '{}' listed as path resolution target " \
-                    "for '{}' does not exist".format(resolves_to, key)
-                raise_error(message)
-
-        def check_type_is_str(option, key):
-            if option.get('type') != 'str':
-                message = "Invalid schema: property '{}' should have type 'str'".format(key)
-                raise_error(message)
-
-        def check_is_dag():
-            visited = set()
-            for key in self._paths_to_resolve:
-                visited.clear()
-                while key:
-                    visited.add(key)
-                    key = self.appschema[key].get('path_resolves_to')
-                    if key and key in visited:
-                        raise_error('Invalid schema: cycle detected')
-
-        def raise_error(message):
-            log.error(message)
-            raise ConfigurationError(message)
-
-        for key, resolves_to in self._paths_to_resolve.items():
-            parent = self.appschema.get(resolves_to)
-            check_exists(parent, key)
-            check_type_is_str(parent, key)
-            check_type_is_str(self.appschema[key], key)
-        check_is_dag()  # must be called last: walks entire graph
+        return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
 
     def _update_raw_config_from_kwargs(self, kwargs):
 
@@ -316,7 +272,7 @@ def _create_attributes_from_raw_config(self):
                 raise ConfigurationError("Attempting to override existing attribute '%s'" % key)
             setattr(self, key, value)
 
-    def _resolve_paths(self, kwargs):
+    def _resolve_paths(self, paths_to_resolve):
 
         def resolve(key):
             if key in _cache:  # resolve each path only once
@@ -337,7 +293,7 @@ def resolve(key):
             return path
 
         _cache = {}
-        for key in self._paths_to_resolve:
+        for key in paths_to_resolve:
             resolve(key)
 
     def _process_config(self, kwargs):
@@ -897,7 +853,7 @@ def parse(string):
 def reload_config_options(current_config):
     """ Reload modified reloadable config options """
     modified_config = read_properties_from_file(current_config.config_file)
-    for option in current_config.reloadable_options:
+    for option in current_config.schema.reloadable_options:
         if option in modified_config:
             # compare to raw value, as that one is set only on load and reload
             if current_config._raw_config[option] != modified_config[option]:
diff --git a/lib/galaxy/config/schema.py b/lib/galaxy/config/schema.py
index 780f6763ac51..9ce919775580 100644
--- a/lib/galaxy/config/schema.py
+++ b/lib/galaxy/config/schema.py
@@ -1,8 +1,12 @@
+import logging
+
+from galaxy.exceptions import ConfigurationError
 from galaxy.util.yaml_util import (
     OPTION_DEFAULTS,
     ordered_load,
 )
 
+log = logging.getLogger(__name__)
 
 UNKNOWN_OPTION = {
     "type": "str",
@@ -33,8 +37,68 @@ def __init__(self, schema_path, app_name):
         self.raw_schema = self._read_schema(schema_path)
         self.description = self.raw_schema.get("desc", None)
         app_schema = self.raw_schema['mapping'][app_name]['mapping']
-        super(AppSchema, self).__init__(app_schema)
+        self._preprocess(app_schema)
+        super().__init__(app_schema)
 
     def _read_schema(self, path):
         with open(path, "r") as f:
             return ordered_load(f)
+
+    def _preprocess(self, app_schema):
+        self._defaults = {}  # {config option: default value or null}
+        self._reloadable_options = set()  # config options we can reload at runtime
+        self._paths_to_resolve = {}  # {config option: referenced config option}
+        for key, data in app_schema.items():
+            self._defaults[key] = data.get('default')
+            if data.get('reloadable'):
+                self._reloadable_options.add(key)
+            if data.get('path_resolves_to'):
+                self._paths_to_resolve[key] = data.get('path_resolves_to')
+
+    @property
+    def defaults(self):
+        return self._defaults
+
+    @property
+    def paths_to_resolve(self):
+        return self._paths_to_resolve
+
+    @property
+    def reloadable_options(self):
+        return self._reloadable_options
+
+    def validate_path_resolution_graph(self):
+        # This method is for tests only: we SHOULD validate the schema's path resolution graph
+        # as part of automated testing; but we should NOT validate it at runtime.
+        def check_exists(option, key):
+            if not option:
+                message = "Invalid schema: property '{}' listed as path resolution target " \
+                    "for '{}' does not exist".format(resolves_to, key)
+                raise_error(message)
+
+        def check_type_is_str(option, key):
+            if option.get('type') != 'str':
+                message = "Invalid schema: property '{}' should have type 'str'".format(key)
+                raise_error(message)
+
+        def check_is_dag():
+            visited = set()
+            for key in self.paths_to_resolve:
+                visited.clear()
+                while key:
+                    visited.add(key)
+                    key = self.app_schema[key].get('path_resolves_to')
+                    if key and key in visited:
+                        raise_error('Invalid schema: cycle detected')
+
+        def raise_error(message):
+            log.error(message)
+            raise ConfigurationError(message)
+
+        for key, resolves_to in self.paths_to_resolve.items():
+            print(key)
+            parent = self.app_schema.get(resolves_to)
+            check_exists(parent, key)
+            check_type_is_str(parent, key)
+            check_type_is_str(self.app_schema[key], key)
+        check_is_dag()  # must be called last: walks entire graph
diff --git a/test/integration/test_config_schema.py b/test/integration/test_config_schema.py
new file mode 100644
index 000000000000..8766c91f660d
--- /dev/null
+++ b/test/integration/test_config_schema.py
@@ -0,0 +1,9 @@
+from galaxy_test.driver import integration_util
+
+
+class ConfigSchemaTestCase(integration_util.IntegrationTestCase):
+
+    def test_schema_path_resolution_graph(self):
+        # Run schema's validation method; throws error if schema invalid
+        schema = self._app.config.schema
+        schema.validate_path_resolution_graph()
diff --git a/test/unit/config/test_load_config.py b/test/unit/config/test_load_config.py
index e6c9f36a3701..86c14e573172 100644
--- a/test/unit/config/test_load_config.py
+++ b/test/unit/config/test_load_config.py
@@ -1,27 +1,59 @@
 import pytest
 
 from galaxy.config import GalaxyAppConfiguration
-
-
-MOCK_PROPERTIES = {
-    'property1': {'default': 'a', 'type': 'str'},  # str
-    'property2': {'default': 1, 'type': 'int'},  # int
-    'property3': {'default': 1.0, 'type': 'float'},  # float
-    'property4': {'default': True, 'type': 'bool'},  # bool
-    'property5': {'something_else': 'b', 'type': 'invalid'},
-    'property6': {'something_else': 'b'},  # no type
-}
+from galaxy.config.schema import AppSchema
+from galaxy.util.yaml_util import (
+    ordered_load,
+    OrderedLoader,
+)
+
+
+MOCK_YAML = '''
+    type: map
+    desc: mocked schema
+    mapping:
+      mockgalaxy:
+        type: map
+        mapping:
+          property1:
+            default: a
+            type: str
+          property2:
+            default: 1
+            type: int
+            reloadable: true
+          property3:
+            default: 1.0
+            type: float
+            reloadable: true
+          property4:
+            default: true
+            type: bool
+          property5:
+            something_else: b
+            type: invalid
+          property6:
+            something_else: b
+    '''
 
 
 @pytest.fixture
 def mock_init(monkeypatch):
 
+    def mock_read_schema(self, path):
+        return ordered_load(MOCK_YAML)
+
+    def mock_init(self, stream):
+        super(OrderedLoader, self).__init__(stream)
+
     def mock_load_schema(self):
-        self.appschema = MOCK_PROPERTIES
+        return AppSchema('no path', 'mockgalaxy')
 
     def mock_process_config(self, kwargs):
         pass
 
+    monkeypatch.setattr(AppSchema, '_read_schema', mock_read_schema)
+    monkeypatch.setattr(OrderedLoader, '__init__', mock_init)
     monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', mock_process_config)
 
diff --git a/test/unit/config/test_reload_config.py b/test/unit/config/test_reload_config.py
index e63cdcbce0a2..2bb5f72b74f0 100644
--- a/test/unit/config/test_reload_config.py
+++ b/test/unit/config/test_reload_config.py
@@ -6,9 +6,13 @@
 
 
 class MockGalaxyAppConfiguration():
+
+    class MockSchema():
+        reloadable_options = {R1, R2}
+
     def __init__(self, properties):
         self.config_file = None
-        self.reloadable_options = {R1, R2}
+        self.schema = self.MockSchema
         self._raw_config = {}
         for key, value in properties.items():
             setattr(self, key, value)
diff --git a/test/unit/config/test_schema.py b/test/unit/config/test_schema.py
index 6569627f2e2b..c727d0e4a006 100644
--- a/test/unit/config/test_schema.py
+++ b/test/unit/config/test_schema.py
@@ -12,9 +12,27 @@
       mockgalaxy:
         type: map
         mapping:
-          option:
-            attr1: a
-            attr2: b
+          property1:
+            default: a
+            type: str
+            path_resolves_to: foo
+          property2:
+            default: 1
+            type: int
+            reloadable: true
+          property3:
+            default: 1.0
+            type: float
+            reloadable: true
+          property4:
+            default: true
+            type: bool
+            path_resolves_to: foo
+          property5:
+            something_else: b
+            type: invalid
+          property6:
+            something_else: b
     '''
 
 
@@ -29,10 +47,29 @@ def mock_init(self, stream):
     monkeypatch.setattr(AppSchema, '_read_schema', mock_read_schema)
     monkeypatch.setattr(OrderedLoader, '__init__', mock_init)
 
-    loaded_schema = AppSchema('no path', 'mockgalaxy')
+    schema = AppSchema('no path', 'mockgalaxy')
     data = ordered_load(MOCK_YAML)
 
-    assert loaded_schema.description == data['desc']
-    assert loaded_schema.raw_schema['foo'] == 'bar'
-    assert loaded_schema.app_schema['option']['attr1'] == 'a'
-    assert loaded_schema.get_app_option('option')['attr2'] == 'b'
+    assert schema.description == data['desc']
+    assert schema.raw_schema['foo'] == 'bar'
+
+    assert len(schema.defaults) == 6
+    assert schema.defaults['property1'] == 'a'
+    assert schema.defaults['property2'] == 1
+    assert schema.defaults['property3'] == 1.0
+    assert schema.defaults['property4'] is True
+    assert schema.defaults['property5'] is None
+    assert schema.defaults['property6'] is None
+
+    assert type(schema.defaults['property1']) is str
+    assert type(schema.defaults['property2']) is int
+    assert type(schema.defaults['property3']) is float
+    assert type(schema.defaults['property4']) is bool
+
+    assert len(schema.reloadable_options) == 2
+    assert 'property2' in schema.reloadable_options
+    assert 'property3' in schema.reloadable_options
+
+    assert len(schema.paths_to_resolve) == 2
+    assert 'property1' in schema.paths_to_resolve
+    assert 'property4' in schema.paths_to_resolve

From f292f4dd80b9db59a2c2dce1bd971848d7889247 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 14 Feb 2020 02:03:54 -0500
Subject: [PATCH 284/853] Make schema module python2-compatible; cleanup
 comments

---
 lib/galaxy/config/schema.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/config/schema.py b/lib/galaxy/config/schema.py
index 9ce919775580..34491906e26d 100644
--- a/lib/galaxy/config/schema.py
+++ b/lib/galaxy/config/schema.py
@@ -38,13 +38,14 @@ def __init__(self, schema_path, app_name):
         self.description = self.raw_schema.get("desc", None)
         app_schema = self.raw_schema['mapping'][app_name]['mapping']
         self._preprocess(app_schema)
-        super().__init__(app_schema)
+        super(AppSchema, self).__init__(app_schema)
 
     def _read_schema(self, path):
         with open(path, "r") as f:
             return ordered_load(f)
 
     def _preprocess(self, app_schema):
+        """Populate schema collections used for app configuration."""
         self._defaults = {}  # {config option: default value or null}
         self._reloadable_options = set()  # config options we can reload at runtime
         self._paths_to_resolve = {}  # {config option: referenced config option}
@@ -68,8 +69,9 @@ def reloadable_options(self):
         return self._reloadable_options
 
     def validate_path_resolution_graph(self):
-        # This method is for tests only: we SHOULD validate the schema's path resolution graph
-        # as part of automated testing; but we should NOT validate it at runtime.
+        """This method is for tests only: we SHOULD validate the schema's path resolution graph
+           as part of automated testing; but we should NOT validate it at runtime.
+        """
         def check_exists(option, key):
             if not option:
                 message = "Invalid schema: property '{}' listed as path resolution target " \

From 70f227da246502c2467418f9bfc8fd56635e196f Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 14 Feb 2020 02:08:38 -0500
Subject: [PATCH 285/853] Refactor config unit tests

1. Modify test setup code to adjust to edits in previous commit. Do NOT
   change the tests.

2. Simplify tests; get rid of mocking where possible (use real objects).
---
 test/unit/config/test_load_config.py      | 62 +++++----------------
 test/unit/config/test_path_graph.py       | 66 ++++++++---------------
 test/unit/config/test_path_resolves_to.py | 30 ++++-------
 test/unit/config/test_reload_config.py    | 56 +++++++++----------
 4 files changed, 74 insertions(+), 140 deletions(-)

diff --git a/test/unit/config/test_load_config.py b/test/unit/config/test_load_config.py
index 86c14e573172..f7deb4a49cf8 100644
--- a/test/unit/config/test_load_config.py
+++ b/test/unit/config/test_load_config.py
@@ -2,60 +2,26 @@
 
 from galaxy.config import GalaxyAppConfiguration
 from galaxy.config.schema import AppSchema
-from galaxy.util.yaml_util import (
-    ordered_load,
-    OrderedLoader,
-)
-
-
-MOCK_YAML = '''
-    type: map
-    desc: mocked schema
-    mapping:
-      mockgalaxy:
-        type: map
-        mapping:
-          property1:
-            default: a
-            type: str
-          property2:
-            default: 1
-            type: int
-            reloadable: true
-          property3:
-            default: 1.0
-            type: float
-            reloadable: true
-          property4:
-            default: true
-            type: bool
-          property5:
-            something_else: b
-            type: invalid
-          property6:
-            something_else: b
-    '''
 
 
-@pytest.fixture
-def mock_init(monkeypatch):
-
-    def mock_read_schema(self, path):
-        return ordered_load(MOCK_YAML)
+MOCK_SCHEMA = {
+    'property1': {'default': 'a', 'type': 'str'},  # str
+    'property2': {'default': 1, 'type': 'int'},  # int
+    'property3': {'default': 1.0, 'type': 'float'},  # float
+    'property4': {'default': True, 'type': 'bool'},  # bool
+    'property5': {'something_else': 'b', 'type': 'invalid'},
+    'property6': {'something_else': 'b'},  # no type
+}
 
-    def mock_init(self, stream):
-        super(OrderedLoader, self).__init__(stream)
 
-    def mock_load_schema(self):
-        return AppSchema('no path', 'mockgalaxy')
+def get_schema(app_mapping):
+    return {'mapping': {'galaxy': {'mapping': app_mapping}}}
 
-    def mock_process_config(self, kwargs):
-        pass
 
-    monkeypatch.setattr(AppSchema, '_read_schema', mock_read_schema)
-    monkeypatch.setattr(OrderedLoader, '__init__', mock_init)
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
-    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', mock_process_config)
+@pytest.fixture
+def mock_init(monkeypatch):
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
+    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
 
 
 def test_load_config_from_schema(mock_init):
diff --git a/test/unit/config/test_path_graph.py b/test/unit/config/test_path_graph.py
index 7d3a3626653b..73c719594ea1 100644
--- a/test/unit/config/test_path_graph.py
+++ b/test/unit/config/test_path_graph.py
@@ -1,6 +1,7 @@
 import pytest
 
 from galaxy.config import GalaxyAppConfiguration
+from galaxy.config.schema import AppSchema
 from galaxy.exceptions import ConfigurationError
 
 
@@ -15,14 +16,11 @@
 # whereas an invalid configuration raises an error.
 
 
-@pytest.fixture
-def mock_config(monkeypatch):
-    def mock_process_config(self, kwargs):
-        pass
-    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', mock_process_config)
+def get_schema(app_mapping):
+    return {'mapping': {'galaxy': {'mapping': app_mapping}}}
 
 
-def test_basecase(mock_config, monkeypatch):
+def test_basecase(monkeypatch):
     # Check that a valid graph is loaded correctly (this graph has 2 components)
     mock_schema = {
         'component1_path0': {
@@ -48,12 +46,9 @@ def test_basecase(mock_config, monkeypatch):
             'default': 'value4',
             'path_resolves_to': 'component2_path0',
         },
-
     }
-
-    def mock_load_schema(self):
-        self.appschema = mock_schema
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
+    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
     assert config.component1_path0 == 'value0'
@@ -63,7 +58,7 @@ def mock_load_schema(self):
     assert config.component2_path1 == 'value3/value4'
 
 
-def test_resolves_to_invalid_property(mock_config, monkeypatch):
+def test_resolves_to_invalid_property(monkeypatch):
     # 'path_resolves_to' should point to an existing property in the schema
     mock_schema = {
         'path0': {
@@ -76,17 +71,13 @@ def test_resolves_to_invalid_property(mock_config, monkeypatch):
             'path_resolves_to': 'invalid',  # invalid
         },
     }
-
-    def mock_load_schema(self):
-        self.appschema = mock_schema
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
 
     with pytest.raises(ConfigurationError):
-        GalaxyAppConfiguration()
+        AppSchema(None, 'galaxy').validate_path_resolution_graph()
 
 
-def test_path_resolution_cycle(mock_config, monkeypatch):
+def test_path_resolution_cycle(monkeypatch):
     # Must be a DAG, but this one has a cycle
     mock_schema = {
         'path0': {
@@ -105,17 +96,13 @@ def test_path_resolution_cycle(mock_config, monkeypatch):
             'path_resolves_to': 'path1',
         },
     }
-
-    def mock_load_schema(self):
-        self.appschema = mock_schema
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
 
     with pytest.raises(ConfigurationError):
-        GalaxyAppConfiguration()
+        AppSchema(None, 'galaxy').validate_path_resolution_graph()
 
 
-def test_path_invalid_type(mock_config, monkeypatch):
+def test_path_invalid_type(monkeypatch):
     # Paths should be strings
     mock_schema = {
         'path0': {
@@ -128,17 +115,13 @@ def test_path_invalid_type(mock_config, monkeypatch):
             'path_resolves_to': 'path0',
         },
     }
-
-    def mock_load_schema(self):
-        self.appschema = mock_schema
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
 
     with pytest.raises(ConfigurationError):
-        GalaxyAppConfiguration()
+        AppSchema(None, 'galaxy').validate_path_resolution_graph()
 
 
-def test_resolves_to_invalid_type(mock_config, monkeypatch):
+def test_resolves_to_invalid_type(monkeypatch):
     # Paths should be strings
     mock_schema = {
         'path0': {
@@ -151,17 +134,13 @@ def test_resolves_to_invalid_type(mock_config, monkeypatch):
             'path_resolves_to': 'path0',
         },
     }
-
-    def mock_load_schema(self):
-        self.appschema = mock_schema
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
 
     with pytest.raises(ConfigurationError):
-        GalaxyAppConfiguration()
+        AppSchema(None, 'galaxy').validate_path_resolution_graph()
 
 
-def test_resolves_with_empty_component(mock_config, monkeypatch):
+def test_resolves_with_empty_component(monkeypatch):
     # A path can be None (root path is never None; may be asigned elsewhere)
     mock_schema = {
         'path0': {
@@ -178,11 +157,8 @@ def test_resolves_with_empty_component(mock_config, monkeypatch):
             'path_resolves_to': 'path1',
         },
     }
-
-    def mock_load_schema(self):
-        self.appschema = mock_schema
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
+    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
     assert config.path0 == 'value0'
diff --git a/test/unit/config/test_path_resolves_to.py b/test/unit/config/test_path_resolves_to.py
index 83b5c3198d17..439d2c6c0017 100644
--- a/test/unit/config/test_path_resolves_to.py
+++ b/test/unit/config/test_path_resolves_to.py
@@ -1,6 +1,7 @@
 import pytest
 
 from galaxy.config import GalaxyAppConfiguration
+from galaxy.config.schema import AppSchema
 
 
 MOCK_DEPRECATED_DIRS = {
@@ -35,34 +36,23 @@
 }
 
 
-def test_deprecated_prefixes_set_correctly(monkeypatch):
-    # Before we mock them, check that correct values are assigned
-    def mock_load_schema(self):
-        self.appschema = {}
+def get_schema(app_mapping):
+    return {'mapping': {'galaxy': {'mapping': app_mapping}}}
 
-    def mock_process_config(self, kwargs):
-        pass
 
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
-    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', mock_process_config)
+def test_deprecated_prefixes_set_correctly(monkeypatch):
+    # Before we mock them, check that correct values are assigned
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
+    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
-    expected_deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
-
-    assert config.deprecated_dirs == expected_deprecated_dirs
+    assert config.deprecated_dirs == {'config_dir': 'config', 'data_dir': 'database'}
 
 
 @pytest.fixture
 def mock_init(monkeypatch):
-
-    def mock_load_schema(self):
-        self.appschema = MOCK_SCHEMA
-
-    def mock_process_config(self, kwargs):
-        pass  # because we're done before this is called
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
-    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', mock_process_config)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
+    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
     monkeypatch.setattr(GalaxyAppConfiguration, 'deprecated_dirs', MOCK_DEPRECATED_DIRS)
 
 
diff --git a/test/unit/config/test_reload_config.py b/test/unit/config/test_reload_config.py
index 2bb5f72b74f0..3064b0475adf 100644
--- a/test/unit/config/test_reload_config.py
+++ b/test/unit/config/test_reload_config.py
@@ -1,37 +1,41 @@
+import pytest
+
 from galaxy import config
+from galaxy.config import GalaxyAppConfiguration
 from galaxy.config import reload_config_options
+from galaxy.config.schema import AppSchema
 
 
 R1, R2, N1, N2 = 'reloadable1', 'reloadable2', 'nonrelodable1', 'nonreloadable2'  # config options
 
+MOCK_SCHEMA = {
+    R1: {'reloadable': True, 'default': 1},
+    R2: {'reloadable': True, 'default': 2},
+    N1: {'default': 3},
+    N2: {'default': 4},
+}
+
 
-class MockGalaxyAppConfiguration():
+def get_schema(app_mapping):
+    return {'mapping': {'galaxy': {'mapping': app_mapping}}}
 
-    class MockSchema():
-        reloadable_options = {R1, R2}
 
-    def __init__(self, properties):
-        self.config_file = None
-        self.schema = self.MockSchema
-        self._raw_config = {}
-        for key, value in properties.items():
-            setattr(self, key, value)
-            self._raw_config[key] = value
+@pytest.fixture
+def mock_init(monkeypatch):
 
-    def update_reloadable_property(self, key, value):
-        setattr(self, key, value)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
+    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
 
 
-def test_update_property(monkeypatch):
+def test_update_property(mock_init, monkeypatch):
     # This also covers adding a property. When a config file does not set a property,
     # that property is set to its default value. Thus, if we add a reloadable property
     # to the config file, it's the same as modifying that property's value.
-    appconfig = MockGalaxyAppConfiguration({R1: 1, R2: 2, N1: 3})
 
-    def mock_read_properties_from_file(values):
-        return {R1: 1, R2: 42, N1: 99}  # edits: R2, N1 modified
+    # edits to config file: R2, N1 modified
+    monkeypatch.setattr(config, 'read_properties_from_file', lambda _: {R1: 1, R2: 42, N1: 99})
 
-    monkeypatch.setattr(config, 'read_properties_from_file', mock_read_properties_from_file)
+    appconfig = GalaxyAppConfiguration()
 
     assert getattr(appconfig, R1) == 1
     assert getattr(appconfig, R2) == 2
@@ -44,7 +48,7 @@ def mock_read_properties_from_file(values):
     assert getattr(appconfig, N1) == 3  # no change: option modified but is non-relodable
 
 
-def test_overwrite_reloadable_attribute(monkeypatch):
+def test_overwrite_reloadable_attribute(mock_init, monkeypatch):
     # This is similar to test_update_property, but here we overwrite the attribute before reloading.
     # This can happen if a config property is modified AFTER it has been loaded from schema or kwargs.
     # For example: load `foo` (from schema or kwargs), but then, in a # subsequent step while initializing
@@ -52,12 +56,11 @@ def test_overwrite_reloadable_attribute(monkeypatch):
     # is not what was initially loaded, and if `foo` is reloadable, it will be reset to its default as soon
     # as the config file is modified. To prevent this, we compare the values read from the modified file
     # to the `_raw_config` dict. This test ensures this works correctly.
-    appconfig = MockGalaxyAppConfiguration({R1: 1, R2: 2, N1: 3})
 
-    def mock_read_properties_from_file(values):
-        return {R1: 1, R2: 42}  # edits: R2 modified
+    # edits to config file: R2 modified
+    monkeypatch.setattr(config, 'read_properties_from_file', lambda _: {R1: 1, R2: 42})
 
-    monkeypatch.setattr(config, 'read_properties_from_file', mock_read_properties_from_file)
+    appconfig = GalaxyAppConfiguration()
 
     assert getattr(appconfig, R1) == 1
     assert getattr(appconfig, R2) == 2
@@ -71,16 +74,15 @@ def mock_read_properties_from_file(values):
     assert getattr(appconfig, R2) == 42  # change: reloadable option modified
 
 
-def test_cant_delete_property(monkeypatch):
+def test_cant_delete_property(mock_init, monkeypatch):
     # A property should not be deleted: we don't know whether it was initially
     # set to a default, loaded from a config file, env var, etc. Therefore, if a property
     # is removed from the config file, it will not be modified or deleted.
-    appconfig = MockGalaxyAppConfiguration({R1: 1, R2: 2, N1: 3, N2: 4})
 
-    def mock_read_properties_from_file(values):
-        return {R1: 1, N1: 3}  # edits: R2, N2 deleted
+    # edits to config file: R2, N2 deleted
+    monkeypatch.setattr(config, 'read_properties_from_file', lambda _: {R1: 1, N1: 3})
 
-    monkeypatch.setattr(config, 'read_properties_from_file', mock_read_properties_from_file)
+    appconfig = GalaxyAppConfiguration()
 
     assert getattr(appconfig, R1) == 1
     assert getattr(appconfig, R2) == 2

From 8d40b7441a2ff0bda5375ee2bd4c74fbcb8e70a4 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 14 Feb 2020 20:27:59 -0500
Subject: [PATCH 286/853] Move OPTION_DEFAULTS to Schema

Rationale: group related items together. Constants OPTION_DEFAULTS and
UNKNOWN_OPTION are closely related and are used in the same context.

OPTION_DEFAULTS is only used in `schema.py` and `config_manage.py`; the
latter imports items from `schema.py`. Thus, it is reasonable to place
both constants in the same module.

(cherry-picked from closed #9307)
---
 lib/galaxy/config/config_manage.py |  2 +-
 lib/galaxy/config/schema.py        | 12 ++++++++----
 lib/galaxy/util/yaml_util.py       |  7 -------
 3 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/config/config_manage.py b/lib/galaxy/config/config_manage.py
index 8ae4035bc63b..9588d2d9c15f 100644
--- a/lib/galaxy/config/config_manage.py
+++ b/lib/galaxy/config/config_manage.py
@@ -30,12 +30,12 @@
 from galaxy.config import GALAXY_CONFIG_SCHEMA_PATH
 from galaxy.config.schema import (
     AppSchema,
+    OPTION_DEFAULTS,
     Schema,
 )
 from galaxy.util import safe_makedirs
 from galaxy.util.properties import nice_config_parser
 from galaxy.util.yaml_util import (
-    OPTION_DEFAULTS,
     ordered_dump,
     ordered_load,
 )
diff --git a/lib/galaxy/config/schema.py b/lib/galaxy/config/schema.py
index 34491906e26d..66e3905881fd 100644
--- a/lib/galaxy/config/schema.py
+++ b/lib/galaxy/config/schema.py
@@ -1,13 +1,17 @@
 import logging
 
 from galaxy.exceptions import ConfigurationError
-from galaxy.util.yaml_util import (
-    OPTION_DEFAULTS,
-    ordered_load,
-)
+from galaxy.util.yaml_util import ordered_load
 
 log = logging.getLogger(__name__)
 
+OPTION_DEFAULTS = {
+    "type": "str",
+    "unknown_option": False,
+    "default": None,
+    "desc": None,
+}
+
 UNKNOWN_OPTION = {
     "type": "str",
     "required": False,
diff --git a/lib/galaxy/util/yaml_util.py b/lib/galaxy/util/yaml_util.py
index 70f4683359db..bb466a96981d 100644
--- a/lib/galaxy/util/yaml_util.py
+++ b/lib/galaxy/util/yaml_util.py
@@ -10,13 +10,6 @@
 
 log = logging.getLogger(__name__)
 
-OPTION_DEFAULTS = {
-    "type": "str",
-    "unknown_option": False,
-    "default": None,
-    "desc": None,
-}
-
 
 class OrderedLoader(yaml.SafeLoader):
     # This class was pulled out of ordered_load() for the sake of

From 230e292db56311104bf23aa2dfb4dd40055d22d1 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 14 Feb 2020 21:51:51 -0500
Subject: [PATCH 287/853] Log message instead of raising an exception

This commit drops the exception that guarded against accidental
overwriting of existing attributes, and instead ignores the setattr
call, logging a debug message (which was initialy proposed in #8728).

Rationale: with the previous version, base configuration properties
(config_dir, data_dir, etc.) had to be set *after* this method was
called (otherwise an exeption was raised), but *before* any path
resolving code (because these properties are used for path
resolution). As a result, config loading required a rigid sequence of steps:
1: load defaults and kwargs, create all config attributes.
2: set base configuration properties [CANNOT MOVE THIS]
3: resolve paths, do the rest: load individual properties, etc.

However, setting base configuration properties is a special case that is
*independent of schema loading*, is handled separately (in
set_config_base), and takes precendence over schema loading procedures.

This modification makes config loading more flexible, and logical:
1. set base configuration properties
2. do the rest (now any refactoring can go here)

(cherry-picked from closed #9307)
---
 lib/galaxy/config/__init__.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 8bfcb6918467..344b9a2a395f 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -268,9 +268,10 @@ def strip_deprecated_dir(key, value):
 
     def _create_attributes_from_raw_config(self):
         for key, value in self._raw_config.items():
-            if hasattr(self, key):
-                raise ConfigurationError("Attempting to override existing attribute '%s'" % key)
-            setattr(self, key, value)
+            if not hasattr(self, key):
+                setattr(self, key, value)
+            else:
+                log.debug("Attribute '%s' is set and cannot be overwritten with value '%s'" % (key, value))
 
     def _resolve_paths(self, paths_to_resolve):
 

From 5c07b65f8b961f9d730f939817d03d14fb414812 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 14 Feb 2020 22:33:17 -0500
Subject: [PATCH 288/853] Remove appconfig instance var; simplify code

GalaxyAppConfiguration has a reference to an AppSchema object (`schema`
instance variable), which provides access to relevant schema data. So we
can simplify:
`self.appschema[key].get('path_resolves_to')` >> `self.schema.paths_to_resolve.get(key)`

Accessing the application schema mapping directly is straightforward:
`self.schema.app_schema`
---
 lib/galaxy/config/__init__.py            | 11 +++++------
 lib/galaxy/tools/toolbox/base.py         |  2 +-
 test/integration/test_config_defaults.py |  2 +-
 3 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 344b9a2a395f..c98dfe9800fc 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -218,7 +218,6 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
 
     def __init__(self, **kwargs):
         self.schema = self._load_schema()  # Load schema from schema definition file
-        self.appschema = self.schema.app_schema
         self._raw_config = self.schema.defaults.copy()  # keeps track of startup values (kwargs or schema default)
 
         self._load_schema()
@@ -238,14 +237,14 @@ def _load_schema(self):
     def _update_raw_config_from_kwargs(self, kwargs):
 
         def convert_datatype(key, value):
-            datatype = self.appschema[key].get('type')
+            datatype = self.schema.app_schema[key].get('type')
             # check for `not None` explicitly (value can be falsy)
             if value is not None and datatype in type_converters:
                 return type_converters[datatype](value)
             return value
 
         def strip_deprecated_dir(key, value):
-            resolves_to = self.appschema[key].get('path_resolves_to')
+            resolves_to = self.schema.paths_to_resolve.get(key)
             if resolves_to:  # value is a path that will be resolved
                 first_dir = value.split(os.sep)[0]  # get first directory component
                 if first_dir == self.deprecated_dirs[resolves_to]:  # first_dir is deprecated for this option
@@ -260,7 +259,7 @@ def strip_deprecated_dir(key, value):
         type_converters = {'bool': string_as_bool, 'int': int, 'float': float, 'str': str}
 
         for key, value in kwargs.items():
-            if key in self.appschema:
+            if key in self.schema.app_schema:
                 value = convert_datatype(key, value)
                 if value:
                     value = strip_deprecated_dir(key, value)
@@ -280,7 +279,7 @@ def resolve(key):
                 return _cache[key]
 
             path = getattr(self, key)  # path prior to being resolved
-            parent = self.appschema[key].get('path_resolves_to')
+            parent = paths_to_resolve.get(key)
             if not parent:  # base case: nothing else needs resolving
                 return path
             parent_path = resolve(parent)  # recursively resolve parent path
@@ -483,7 +482,7 @@ def _process_config(self, kwargs):
         if self.tool_dependency_dir and self.tool_dependency_dir.lower() == 'none':
             self.tool_dependency_dir = None
         if self.involucro_path is None:
-            target_dir = self.tool_dependency_dir or self.appschema['tool_dependency_dir'].get('default')
+            target_dir = self.tool_dependency_dir or self.schema.defaults['tool_dependency_dir']
             self.involucro_path = os.path.join(self.data_dir, target_dir, "involucro")
         self.involucro_path = os.path.join(self.root, self.involucro_path)
         if self.mulled_channels:
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 129dd3909b2a..03c1cc968727 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -1217,7 +1217,7 @@ def _init_dependency_manager(self):
             return
         app_config_dict = self.app.config.config_dict
         conf_file = app_config_dict.get("dependency_resolvers_config_file")
-        default_tool_dependency_dir = os.path.join(self.app.config.data_dir, self.app.config.appschema['tool_dependency_dir'].get('default'))
+        default_tool_dependency_dir = os.path.join(self.app.config.data_dir, self.app.config.schema.defaults['tool_dependency_dir'])
         self.dependency_manager = build_dependency_manager(app_config_dict=app_config_dict, conf_file=conf_file,
                                                            default_tool_dependency_dir=default_tool_dependency_dir)
 
diff --git a/test/integration/test_config_defaults.py b/test/integration/test_config_defaults.py
index c8d2ff5f26e9..1087fe5b4f06 100644
--- a/test/integration/test_config_defaults.py
+++ b/test/integration/test_config_defaults.py
@@ -253,7 +253,7 @@ def get_expected(key, data, parent_dirs):
 
     create_driver()  # create + setup DRIVER
     parent_dirs = load_parent_dirs()  # called after DRIVER is setup
-    items = ((k, v) for k, v in DRIVER.app.config.appschema.items() if k not in DO_NOT_TEST)
+    items = ((k, v) for k, v in DRIVER.app.config.schema.app_schema.items() if k not in DO_NOT_TEST)
     for key, data in items:
         expected_value = get_expected(key, data, parent_dirs)
         loaded_value = getattr(DRIVER.app.config, key)

From 6f53e68e18c2d2955e256f40a6e4cbfef9a57341 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Sat, 15 Feb 2020 21:49:50 -0500
Subject: [PATCH 289/853] Fix mock + related code

Add schema var to galaxy mock as a MockSchema stub object
---
 lib/galaxy/tools/toolbox/base.py        | 7 ++++---
 test/unit/tools/test_toolbox.py         | 2 +-
 test/unit/unittest_utils/galaxy_mock.py | 4 ++++
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 03c1cc968727..08a4697564af 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -1217,9 +1217,10 @@ def _init_dependency_manager(self):
             return
         app_config_dict = self.app.config.config_dict
         conf_file = app_config_dict.get("dependency_resolvers_config_file")
-        default_tool_dependency_dir = os.path.join(self.app.config.data_dir, self.app.config.schema.defaults['tool_dependency_dir'])
-        self.dependency_manager = build_dependency_manager(app_config_dict=app_config_dict, conf_file=conf_file,
-                                                           default_tool_dependency_dir=default_tool_dependency_dir)
+        default_tool_dependency_dir = os.path.join(
+            self.app.config.data_dir, self.app.config.schema.app_schema['tool_dependency_dir'].get('default'))
+        self.dependency_manager = build_dependency_manager(
+            app_config_dict=app_config_dict, conf_file=conf_file, default_tool_dependency_dir=default_tool_dependency_dir)
 
     def reload_dependency_manager(self):
         self._init_dependency_manager()
diff --git a/test/unit/tools/test_toolbox.py b/test/unit/tools/test_toolbox.py
index c5695c4ef78a..d2bfc6caaabf 100644
--- a/test/unit/tools/test_toolbox.py
+++ b/test/unit/tools/test_toolbox.py
@@ -564,7 +564,7 @@ def __init__(self, test_case):
         app.tool_cache = ToolCache() if not hasattr(app, 'tool_cache') else app.tool_cache
         app.job_config.get_tool_resource_parameters = lambda tool_id: None
         app.config.update_integrated_tool_panel = True
-        app.config.appschema = {
+        app.config.schema.app_schema = {
             'tool_dependency_dir': {
                 'default': 'dependencies',
             }
diff --git a/test/unit/unittest_utils/galaxy_mock.py b/test/unit/unittest_utils/galaxy_mock.py
index 5b9d06978fce..3cde0eaa3e3d 100644
--- a/test/unit/unittest_utils/galaxy_mock.py
+++ b/test/unit/unittest_utils/galaxy_mock.py
@@ -111,6 +111,9 @@ def __exit__(self, type, value, traceback):
 
 class MockAppConfig(Bunch):
 
+    class MockSchema(Bunch):
+        pass
+
     def __init__(self, root=None, **kwargs):
         Bunch.__init__(self, **kwargs)
         if not root:
@@ -118,6 +121,7 @@ def __init__(self, root=None, **kwargs):
             self._remove_root = True
         else:
             self._remove_root = False
+        self.schema = self.MockSchema()
         self.security = idencoding.IdEncodingHelper(id_secret='6e46ed6483a833c100e68cc3f1d0dd76')
         self.database_connection = kwargs.get('database_connection', "sqlite:///:memory:")
         self.use_remote_user = kwargs.get('use_remote_user', False)

From 9a3400fa0c5129bfd62cb4d303097dfe7d6c16e8 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Sat, 15 Feb 2020 23:40:35 -0500
Subject: [PATCH 290/853] Move a lot of code from config into base class

Provide stub methods for TS config implementation as a temporary
measure. No refactoring of TS config in this commit.
---
 lib/galaxy/config/__init__.py  | 154 +++++++++++++++++----------------
 lib/tool_shed/webapp/config.py |  16 ++++
 2 files changed, 95 insertions(+), 75 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index c98dfe9800fc..0cc90edb6d9c 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -105,6 +105,83 @@ def find_root(kwargs):
 
 
 class BaseAppConfiguration(object):
+
+    def __init__(self, **kwargs):
+        self.schema = self._load_schema()  # Load schema from schema definition file
+        self._raw_config = self.schema.defaults.copy()  # keeps track of startup values (kwargs or schema default)
+        self._load_schema()
+        self._update_raw_config_from_kwargs(kwargs)  # Overwrite default values passed as kwargs
+        self._create_attributes_from_raw_config()  # Create attributes for LOADED properties
+        self.config_dict = kwargs
+        self.root = find_root(kwargs)
+        self._set_config_base(kwargs)  # must be called prior to _resolve_paths()
+        self._resolve_paths(self.schema.paths_to_resolve)  # Overwrite attributes (not _raw_config) w/resolved paths
+
+    def _load_schema(self):
+        raise Exception('Not implemented')
+
+    def _update_raw_config_from_kwargs(self, kwargs):
+
+        def convert_datatype(key, value):
+            datatype = self.schema.app_schema[key].get('type')
+            # check for `not None` explicitly (value can be falsy)
+            if value is not None and datatype in type_converters:
+                return type_converters[datatype](value)
+            return value
+
+        def strip_deprecated_dir(key, value):
+            resolves_to = self.schema.paths_to_resolve.get(key)
+            if resolves_to:  # value is a path that will be resolved
+                first_dir = value.split(os.sep)[0]  # get first directory component
+                if first_dir == self.deprecated_dirs[resolves_to]:  # first_dir is deprecated for this option
+                    ignore = first_dir + os.sep
+                    log.warning(
+                        "Paths for the '%s' option are now relative to '%s', remove the leading '%s' "
+                        "to suppress this warning: %s", key, resolves_to, ignore, value
+                    )
+                    return value[len(ignore):]
+            return value
+
+        type_converters = {'bool': string_as_bool, 'int': int, 'float': float, 'str': str}
+
+        for key, value in kwargs.items():
+            if key in self.schema.app_schema:
+                value = convert_datatype(key, value)
+                if value:
+                    value = strip_deprecated_dir(key, value)
+                self._raw_config[key] = value
+
+    def _create_attributes_from_raw_config(self):
+        for key, value in self._raw_config.items():
+            if not hasattr(self, key):
+                setattr(self, key, value)
+            else:
+                log.debug("Attribute '%s' is set and cannot be overwritten with value '%s'" % (key, value))
+
+    def _resolve_paths(self, paths_to_resolve):
+
+        def resolve(key):
+            if key in _cache:  # resolve each path only once
+                return _cache[key]
+
+            path = getattr(self, key)  # path prior to being resolved
+            parent = paths_to_resolve.get(key)
+            if not parent:  # base case: nothing else needs resolving
+                return path
+            parent_path = resolve(parent)  # recursively resolve parent path
+            if path is not None:
+                path = os.path.join(parent_path, path)  # resolve path
+            else:
+                path = parent_path  # or use parent path
+
+            setattr(self, key, path)  # update property
+            _cache[key] = path  # cache it!
+            return path
+
+        _cache = {}
+        for key in paths_to_resolve:
+            resolve(key)
+
     def _set_config_base(self, config_kwargs):
 
         def _set_global_conf():
@@ -217,85 +294,12 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
     deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
 
     def __init__(self, **kwargs):
-        self.schema = self._load_schema()  # Load schema from schema definition file
-        self._raw_config = self.schema.defaults.copy()  # keeps track of startup values (kwargs or schema default)
-
-        self._load_schema()
-        self._update_raw_config_from_kwargs(kwargs)  # Overwrite default values passed as kwargs
-        self._create_attributes_from_raw_config()  # Create attributes for LOADED properties
-
-        self.config_dict = kwargs
-        self.root = find_root(kwargs)
-        self._set_config_base(kwargs)  # must be called prior to _resolve_paths()
-
-        self._resolve_paths(self.schema.paths_to_resolve)  # Overwrite attributes (not _raw_config) w/resolved paths
-        self._process_config(kwargs)  # Finish processing configuration
+        super(GalaxyAppConfiguration, self).__init__(**kwargs)
+        self._process_config(kwargs)
 
     def _load_schema(self):
         return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
 
-    def _update_raw_config_from_kwargs(self, kwargs):
-
-        def convert_datatype(key, value):
-            datatype = self.schema.app_schema[key].get('type')
-            # check for `not None` explicitly (value can be falsy)
-            if value is not None and datatype in type_converters:
-                return type_converters[datatype](value)
-            return value
-
-        def strip_deprecated_dir(key, value):
-            resolves_to = self.schema.paths_to_resolve.get(key)
-            if resolves_to:  # value is a path that will be resolved
-                first_dir = value.split(os.sep)[0]  # get first directory component
-                if first_dir == self.deprecated_dirs[resolves_to]:  # first_dir is deprecated for this option
-                    ignore = first_dir + os.sep
-                    log.warning(
-                        "Paths for the '%s' option are now relative to '%s', remove the leading '%s' "
-                        "to suppress this warning: %s", key, resolves_to, ignore, value
-                    )
-                    return value[len(ignore):]
-            return value
-
-        type_converters = {'bool': string_as_bool, 'int': int, 'float': float, 'str': str}
-
-        for key, value in kwargs.items():
-            if key in self.schema.app_schema:
-                value = convert_datatype(key, value)
-                if value:
-                    value = strip_deprecated_dir(key, value)
-                self._raw_config[key] = value
-
-    def _create_attributes_from_raw_config(self):
-        for key, value in self._raw_config.items():
-            if not hasattr(self, key):
-                setattr(self, key, value)
-            else:
-                log.debug("Attribute '%s' is set and cannot be overwritten with value '%s'" % (key, value))
-
-    def _resolve_paths(self, paths_to_resolve):
-
-        def resolve(key):
-            if key in _cache:  # resolve each path only once
-                return _cache[key]
-
-            path = getattr(self, key)  # path prior to being resolved
-            parent = paths_to_resolve.get(key)
-            if not parent:  # base case: nothing else needs resolving
-                return path
-            parent_path = resolve(parent)  # recursively resolve parent path
-            if path is not None:
-                path = os.path.join(parent_path, path)  # resolve path
-            else:
-                path = parent_path  # or use parent path
-
-            setattr(self, key, path)  # update property
-            _cache[key] = path  # cache it!
-            return path
-
-        _cache = {}
-        for key in paths_to_resolve:
-            resolve(key)
-
     def _process_config(self, kwargs):
         # Resolve paths of other config files
         self.parse_config_file_options(kwargs)
diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index 424207d353f4..fa7cd14da2e5 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -10,6 +10,7 @@
 from six.moves import configparser
 
 from galaxy.config import BaseAppConfiguration
+from galaxy.config.schema import AppSchema
 from galaxy.util import string_as_bool
 from galaxy.version import VERSION, VERSION_MAJOR
 from galaxy.web.formatting import expand_pretty_datetime_format
@@ -19,6 +20,9 @@
 ts_webapp_path = os.path.abspath(os.path.dirname(__file__))
 templates_path = os.path.join(ts_webapp_path, "templates")
 
+TOOLSHED_APP_NAME = 'tool_shed'
+TOOLSHED_CONFIG_SCHEMA_PATH = 'lib/tool_shed/webapp/config_schema.yml'
+
 
 def resolve_path(path, root):
     """If 'path' is relative make absolute by prepending 'root'"""
@@ -34,6 +38,18 @@ class ConfigurationError(Exception):
 class ToolShedAppConfiguration(BaseAppConfiguration):
     default_config_file_name = 'tool_shed.yml'
 
+    def _load_schema():
+        return AppSchema(TOOLSHED_CONFIG_SCHEMA_PATH, TOOLSHED_APP_NAME)
+
+    def _update_raw_config_from_kwargs(self, kwargs):
+        pass  # Intentionally does nothing. Remove to enable.
+
+    def _create_attributes_from_raw_config(self):
+        pass  # Intentionally does nothing. Remove to enable.
+
+    def _resolve_paths(self, paths_to_resolve):
+        pass  # Intentionally does nothing. Remove to enable.
+
     def __init__(self, **kwargs):
         self.config_dict = kwargs
         self.root = kwargs.get('root_dir', '.')

From bd99a3a734d835a1c60b10955e874f33fc2b9ba8 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Sun, 16 Feb 2020 00:56:51 -0500
Subject: [PATCH 291/853] Change handling of deprecated_dirs

This will prevent an error in TS if the base config class
`_update_raw_config_from_kwargs()` method is invoked.
---
 lib/galaxy/config/__init__.py             | 17 ++++++++++++-----
 test/unit/config/test_path_resolves_to.py |  4 ++--
 2 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 0cc90edb6d9c..f6cd1fa03409 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -118,8 +118,15 @@ def __init__(self, **kwargs):
         self._resolve_paths(self.schema.paths_to_resolve)  # Overwrite attributes (not _raw_config) w/resolved paths
 
     def _load_schema(self):
+        # Override in subclasses
         raise Exception('Not implemented')
 
+    def _deprecated_dirs():
+        # Override in subclasses (optional)
+        # {KEY: config option, VALUE: deprecated directory name}
+        # If VALUE == first directory in a user path that resolves to KEY, it will be stripped from the path
+        return None
+
     def _update_raw_config_from_kwargs(self, kwargs):
 
         def convert_datatype(key, value):
@@ -133,7 +140,7 @@ def strip_deprecated_dir(key, value):
             resolves_to = self.schema.paths_to_resolve.get(key)
             if resolves_to:  # value is a path that will be resolved
                 first_dir = value.split(os.sep)[0]  # get first directory component
-                if first_dir == self.deprecated_dirs[resolves_to]:  # first_dir is deprecated for this option
+                if first_dir == self._deprecated_dirs().get(resolves_to):  # first_dir is deprecated for this option
                     ignore = first_dir + os.sep
                     log.warning(
                         "Paths for the '%s' option are now relative to '%s', remove the leading '%s' "
@@ -147,7 +154,7 @@ def strip_deprecated_dir(key, value):
         for key, value in kwargs.items():
             if key in self.schema.app_schema:
                 value = convert_datatype(key, value)
-                if value:
+                if value and self._deprecated_dirs():
                     value = strip_deprecated_dir(key, value)
                 self._raw_config[key] = value
 
@@ -289,9 +296,6 @@ def _parse_config_file_options(self, defaults, listify_defaults, config_kwargs):
 class GalaxyAppConfiguration(BaseAppConfiguration):
     deprecated_options = ('database_file', 'track_jobs_in_database')
     default_config_file_name = 'galaxy.yml'
-    # {key: config option, value: deprecated directory name}
-    # If value == first dir in a user path that resolves to key, it will be stripped from the path
-    deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
 
     def __init__(self, **kwargs):
         super(GalaxyAppConfiguration, self).__init__(**kwargs)
@@ -300,6 +304,9 @@ def __init__(self, **kwargs):
     def _load_schema(self):
         return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
 
+    def _deprecated_dirs(self):
+        return {'config_dir': 'config', 'data_dir': 'database'}
+
     def _process_config(self, kwargs):
         # Resolve paths of other config files
         self.parse_config_file_options(kwargs)
diff --git a/test/unit/config/test_path_resolves_to.py b/test/unit/config/test_path_resolves_to.py
index 439d2c6c0017..b700a87d86a7 100644
--- a/test/unit/config/test_path_resolves_to.py
+++ b/test/unit/config/test_path_resolves_to.py
@@ -46,14 +46,14 @@ def test_deprecated_prefixes_set_correctly(monkeypatch):
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
-    assert config.deprecated_dirs == {'config_dir': 'config', 'data_dir': 'database'}
+    assert config._deprecated_dirs() == {'config_dir': 'config', 'data_dir': 'database'}
 
 
 @pytest.fixture
 def mock_init(monkeypatch):
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
-    monkeypatch.setattr(GalaxyAppConfiguration, 'deprecated_dirs', MOCK_DEPRECATED_DIRS)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_deprecated_dirs', lambda a: MOCK_DEPRECATED_DIRS)
 
 
 def test_mock_schema_is_loaded(mock_init):

From f0bfcaf0cee5f2674aa8bef8b893e869529274c8 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Sun, 16 Feb 2020 11:05:05 -0500
Subject: [PATCH 292/853] Reorder base config code, edit comments

---
 lib/galaxy/config/__init__.py | 132 +++++++++++++++++-----------------
 1 file changed, 65 insertions(+), 67 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index f6cd1fa03409..b3728b55acd4 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -100,22 +100,78 @@
 
 
 def find_root(kwargs):
-    root = os.path.abspath(kwargs.get('root_dir', '.'))
-    return root
+    return os.path.abspath(kwargs.get('root_dir', '.'))
 
 
 class BaseAppConfiguration(object):
 
     def __init__(self, **kwargs):
-        self.schema = self._load_schema()  # Load schema from schema definition file
-        self._raw_config = self.schema.defaults.copy()  # keeps track of startup values (kwargs or schema default)
-        self._load_schema()
-        self._update_raw_config_from_kwargs(kwargs)  # Overwrite default values passed as kwargs
-        self._create_attributes_from_raw_config()  # Create attributes for LOADED properties
         self.config_dict = kwargs
         self.root = find_root(kwargs)
-        self._set_config_base(kwargs)  # must be called prior to _resolve_paths()
-        self._resolve_paths(self.schema.paths_to_resolve)  # Overwrite attributes (not _raw_config) w/resolved paths
+        self._set_config_base(kwargs)
+        self.schema = self._load_schema()  # Load schema from schema definition file
+        self._raw_config = self.schema.defaults.copy()  # Save schema defaults as initial config values (raw_config)
+        self._update_raw_config_from_kwargs(kwargs)  # Overwrite raw_config with values passed in kwargs
+        self._create_attributes_from_raw_config()  # Create attributes based on raw_config
+        self._resolve_paths(self.schema.paths_to_resolve)  # Overwrite attribute values with resolved paths
+
+    def _set_config_base(self, config_kwargs):
+
+        def _set_global_conf():
+            self.config_file = find_config_file('galaxy')
+            self.global_conf = config_kwargs.get('global_conf')
+            self.global_conf_parser = configparser.ConfigParser()
+            if not self.config_file and self.global_conf and "__file__" in self.global_conf:
+                self.config_file = os.path.join(self.root, self.global_conf['__file__'])
+
+            if self.config_file is None:
+                log.warning("No Galaxy config file found, running from current working directory: %s", os.getcwd())
+            else:
+                try:
+                    self.global_conf_parser.read(self.config_file)
+                except (IOError, OSError):
+                    raise
+                except Exception:
+                    pass  # Not an INI file
+
+        def _set_config_directories():
+            # Set config_dir to value from kwargs OR dirname of config_file OR None
+            _config_dir = os.path.dirname(self.config_file) if self.config_file else None
+            self.config_dir = config_kwargs.get('config_dir', _config_dir)
+            # Make path absolute before using it as base for other paths
+            if self.config_dir:
+                self.config_dir = os.path.abspath(self.config_dir)
+
+            self.data_dir = config_kwargs.get('data_dir')
+            self.sample_config_dir = os.path.join(os.path.dirname(__file__), 'sample')
+            self.managed_config_dir = config_kwargs.get('managed_config_dir')
+            if self.managed_config_dir:
+                self.managed_config_dir = os.path.abspath(self.managed_config_dir)
+
+            if running_from_source:
+                if not self.config_dir:
+                    self.config_dir = os.path.join(self.root, 'config')
+                if not self.data_dir:
+                    self.data_dir = os.path.join(self.root, 'database')
+                if not self.managed_config_dir:
+                    self.managed_config_dir = self.config_dir
+            else:
+                if not self.config_dir:
+                    self.config_dir = os.getcwd()
+                if not self.data_dir:
+                    self.data_dir = self._in_config_dir('data')
+                if not self.managed_config_dir:
+                    self.managed_config_dir = self._in_data_dir('config')
+
+            # TODO: do we still need to support ../shed_tools when running_from_source?
+            self.shed_tools_dir = self._in_data_dir('shed_tools')
+
+            log.debug("Configuration directory is %s", self.config_dir)
+            log.debug("Data directory is %s", self.data_dir)
+            log.debug("Managed config directory is %s", self.managed_config_dir)
+
+        _set_global_conf()
+        _set_config_directories()
 
     def _load_schema(self):
         # Override in subclasses
@@ -189,64 +245,6 @@ def resolve(key):
         for key in paths_to_resolve:
             resolve(key)
 
-    def _set_config_base(self, config_kwargs):
-
-        def _set_global_conf():
-            self.config_file = find_config_file('galaxy')
-            self.global_conf = config_kwargs.get('global_conf')
-            self.global_conf_parser = configparser.ConfigParser()
-            if not self.config_file and self.global_conf and "__file__" in self.global_conf:
-                self.config_file = os.path.join(self.root, self.global_conf['__file__'])
-
-            if self.config_file is None:
-                log.warning("No Galaxy config file found, running from current working directory: %s", os.getcwd())
-            else:
-                try:
-                    self.global_conf_parser.read(self.config_file)
-                except (IOError, OSError):
-                    raise
-                except Exception:
-                    pass  # Not an INI file
-
-        def _set_config_directories():
-            # Set config_dir to value from kwargs OR dirname of config_file OR None
-            _config_dir = os.path.dirname(self.config_file) if self.config_file else None
-            self.config_dir = config_kwargs.get('config_dir', _config_dir)
-            # Make path absolute before using it as base for other paths
-            if self.config_dir:
-                self.config_dir = os.path.abspath(self.config_dir)
-
-            self.data_dir = config_kwargs.get('data_dir')
-            self.sample_config_dir = os.path.join(os.path.dirname(__file__), 'sample')
-            self.managed_config_dir = config_kwargs.get('managed_config_dir')
-            if self.managed_config_dir:
-                self.managed_config_dir = os.path.abspath(self.managed_config_dir)
-
-            if running_from_source:
-                if not self.config_dir:
-                    self.config_dir = os.path.join(self.root, 'config')
-                if not self.data_dir:
-                    self.data_dir = os.path.join(self.root, 'database')
-                if not self.managed_config_dir:
-                    self.managed_config_dir = self.config_dir
-            else:
-                if not self.config_dir:
-                    self.config_dir = os.getcwd()
-                if not self.data_dir:
-                    self.data_dir = self._in_config_dir('data')
-                if not self.managed_config_dir:
-                    self.managed_config_dir = self._in_data_dir('config')
-
-            # TODO: do we still need to support ../shed_tools when running_from_source?
-            self.shed_tools_dir = self._in_data_dir('shed_tools')
-
-            log.debug("Configuration directory is %s", self.config_dir)
-            log.debug("Data directory is %s", self.data_dir)
-            log.debug("Managed config directory is %s", self.managed_config_dir)
-
-        _set_global_conf()
-        _set_config_directories()
-
     def _in_managed_config_dir(self, path):
         return os.path.join(self.managed_config_dir, path)
 

From d9041a76ebe4d1835eb2c0f264c5b2a2d50a7109 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 17 Feb 2020 00:28:46 -0500
Subject: [PATCH 293/853] Correct _load_schema method signature; edit comments

Following the principle of least surprise.
The stub methods are not invoked because the parent's __init__() method
is not called. They can be safely removed. However, if a future commit adds
a call to parent's __init__, without these stub methods the parent's
methods will be called, which may result in a surprise (e.g., attributes
would be created for all schema properties).
---
 lib/tool_shed/webapp/config.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index fa7cd14da2e5..df627d916435 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -38,17 +38,17 @@ class ConfigurationError(Exception):
 class ToolShedAppConfiguration(BaseAppConfiguration):
     default_config_file_name = 'tool_shed.yml'
 
-    def _load_schema():
+    def _load_schema(self):
         return AppSchema(TOOLSHED_CONFIG_SCHEMA_PATH, TOOLSHED_APP_NAME)
 
     def _update_raw_config_from_kwargs(self, kwargs):
-        pass  # Intentionally does nothing. Remove to enable.
+        pass  # Intentionally does nothing. To enable, remove + call base __init__().
 
     def _create_attributes_from_raw_config(self):
-        pass  # Intentionally does nothing. Remove to enable.
+        pass  # Intentionally does nothing. To enable, remove + call base __init__().
 
     def _resolve_paths(self, paths_to_resolve):
-        pass  # Intentionally does nothing. Remove to enable.
+        pass  # Intentionally does nothing. To enable, remove + call base __init__().
 
     def __init__(self, **kwargs):
         self.config_dict = kwargs

From d8f98b227c5db0cce0c8159fa399bc273f9bf15a Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 17 Feb 2020 00:55:02 -0500
Subject: [PATCH 294/853] Fix _deprecated_dirs method signature

---
 lib/galaxy/config/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index b3728b55acd4..9b77cbdde5ed 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -177,7 +177,7 @@ def _load_schema(self):
         # Override in subclasses
         raise Exception('Not implemented')
 
-    def _deprecated_dirs():
+    def _deprecated_dirs(self):
         # Override in subclasses (optional)
         # {KEY: config option, VALUE: deprecated directory name}
         # If VALUE == first directory in a user path that resolves to KEY, it will be stripped from the path

From 163ba59bb189cbb3bc42c7f7404ee075a6da8aeb Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 17 Feb 2020 17:27:24 -0500
Subject: [PATCH 295/853] Cleanup (address items from code review)

---
 lib/galaxy/config/__init__.py             | 25 +++++++++--------------
 test/unit/config/test_path_resolves_to.py |  4 ++--
 2 files changed, 12 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 9b77cbdde5ed..982fa59666cd 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -104,6 +104,9 @@ def find_root(kwargs):
 
 
 class BaseAppConfiguration(object):
+    # Override in subclasses (optional): {KEY: config option, VALUE: deprecated directory name}
+    # If VALUE == first directory in a user-supplied path that resolves to KEY, it will be stripped from that path
+    deprecated_dirs = None
 
     def __init__(self, **kwargs):
         self.config_dict = kwargs
@@ -113,7 +116,7 @@ def __init__(self, **kwargs):
         self._raw_config = self.schema.defaults.copy()  # Save schema defaults as initial config values (raw_config)
         self._update_raw_config_from_kwargs(kwargs)  # Overwrite raw_config with values passed in kwargs
         self._create_attributes_from_raw_config()  # Create attributes based on raw_config
-        self._resolve_paths(self.schema.paths_to_resolve)  # Overwrite attribute values with resolved paths
+        self._resolve_paths()  # Overwrite attribute values with resolved paths
 
     def _set_config_base(self, config_kwargs):
 
@@ -177,12 +180,6 @@ def _load_schema(self):
         # Override in subclasses
         raise Exception('Not implemented')
 
-    def _deprecated_dirs(self):
-        # Override in subclasses (optional)
-        # {KEY: config option, VALUE: deprecated directory name}
-        # If VALUE == first directory in a user path that resolves to KEY, it will be stripped from the path
-        return None
-
     def _update_raw_config_from_kwargs(self, kwargs):
 
         def convert_datatype(key, value):
@@ -196,7 +193,7 @@ def strip_deprecated_dir(key, value):
             resolves_to = self.schema.paths_to_resolve.get(key)
             if resolves_to:  # value is a path that will be resolved
                 first_dir = value.split(os.sep)[0]  # get first directory component
-                if first_dir == self._deprecated_dirs().get(resolves_to):  # first_dir is deprecated for this option
+                if first_dir == self.deprecated_dirs.get(resolves_to):  # first_dir is deprecated for this option
                     ignore = first_dir + os.sep
                     log.warning(
                         "Paths for the '%s' option are now relative to '%s', remove the leading '%s' "
@@ -210,7 +207,7 @@ def strip_deprecated_dir(key, value):
         for key, value in kwargs.items():
             if key in self.schema.app_schema:
                 value = convert_datatype(key, value)
-                if value and self._deprecated_dirs():
+                if value and self.deprecated_dirs:
                     value = strip_deprecated_dir(key, value)
                 self._raw_config[key] = value
 
@@ -221,14 +218,14 @@ def _create_attributes_from_raw_config(self):
             else:
                 log.debug("Attribute '%s' is set and cannot be overwritten with value '%s'" % (key, value))
 
-    def _resolve_paths(self, paths_to_resolve):
+    def _resolve_paths(self):
 
         def resolve(key):
             if key in _cache:  # resolve each path only once
                 return _cache[key]
 
             path = getattr(self, key)  # path prior to being resolved
-            parent = paths_to_resolve.get(key)
+            parent = self.schema.paths_to_resolve.get(key)
             if not parent:  # base case: nothing else needs resolving
                 return path
             parent_path = resolve(parent)  # recursively resolve parent path
@@ -242,7 +239,7 @@ def resolve(key):
             return path
 
         _cache = {}
-        for key in paths_to_resolve:
+        for key in self.schema.paths_to_resolve:
             resolve(key)
 
     def _in_managed_config_dir(self, path):
@@ -294,6 +291,7 @@ def _parse_config_file_options(self, defaults, listify_defaults, config_kwargs):
 class GalaxyAppConfiguration(BaseAppConfiguration):
     deprecated_options = ('database_file', 'track_jobs_in_database')
     default_config_file_name = 'galaxy.yml'
+    deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
 
     def __init__(self, **kwargs):
         super(GalaxyAppConfiguration, self).__init__(**kwargs)
@@ -302,9 +300,6 @@ def __init__(self, **kwargs):
     def _load_schema(self):
         return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
 
-    def _deprecated_dirs(self):
-        return {'config_dir': 'config', 'data_dir': 'database'}
-
     def _process_config(self, kwargs):
         # Resolve paths of other config files
         self.parse_config_file_options(kwargs)
diff --git a/test/unit/config/test_path_resolves_to.py b/test/unit/config/test_path_resolves_to.py
index b700a87d86a7..439d2c6c0017 100644
--- a/test/unit/config/test_path_resolves_to.py
+++ b/test/unit/config/test_path_resolves_to.py
@@ -46,14 +46,14 @@ def test_deprecated_prefixes_set_correctly(monkeypatch):
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
-    assert config._deprecated_dirs() == {'config_dir': 'config', 'data_dir': 'database'}
+    assert config.deprecated_dirs == {'config_dir': 'config', 'data_dir': 'database'}
 
 
 @pytest.fixture
 def mock_init(monkeypatch):
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
-    monkeypatch.setattr(GalaxyAppConfiguration, '_deprecated_dirs', lambda a: MOCK_DEPRECATED_DIRS)
+    monkeypatch.setattr(GalaxyAppConfiguration, 'deprecated_dirs', MOCK_DEPRECATED_DIRS)
 
 
 def test_mock_schema_is_loaded(mock_init):

From 49803eeb033cdfa5c41b7699cf851500c6791f07 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 2 Mar 2020 15:58:55 -0500
Subject: [PATCH 296/853] Fix workflow ribbon shift calculation

---
 client/galaxy/scripts/mvc/workflow/workflow-connector.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-connector.js b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
index 9f107e011993..eeb2735d7de3 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-connector.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
@@ -120,7 +120,7 @@ class Connector {
         end_y -= canvas_top;
 
         // Determine line shift
-        const cp_shift = Math.min(Math.max(Math.abs(canvas_max_y - canvas_min_y) / 2, cpFactor), 300 / cpFactor);
+        const cp_shift = Math.min(Math.max(Math.abs(canvas_max_y - canvas_min_y) / 2, cpFactor), 3 * cpFactor);
 
         // Draw ribbons
         this.drawRibbon(handle1, handle2, cp_shift, start_x, start_y, end_x, end_y);

From 6f1c548ec21b828270652d98e0cf7e807e18612f Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 2 Mar 2020 16:22:48 -0500
Subject: [PATCH 297/853] Improve header button alignment

---
 client/galaxy/style/scss/workflow.scss | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index de03e0c8d3bd..260b3f312ba2 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -23,6 +23,9 @@
                 @extend .px-2;
                 cursor: move;
                 background: $brand-secondary;
+                .header {
+                    width: $worfklow-node-width - 2rem;
+                }
             }
             .node-body {
                 @extend .card-body;

From 9dca223525ddf67aef696d1a066613dfd5480638 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 01:06:11 -0500
Subject: [PATCH 298/853] Fix css selector for workflow node connection canvas
 to svg, use brand primary for node headers

---
 client/galaxy/style/scss/theme/blue.scss | 2 +-
 client/galaxy/style/scss/workflow.scss   | 7 ++++++-
 lib/galaxy/selenium/navigation.yml       | 2 +-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/style/scss/theme/blue.scss b/client/galaxy/style/scss/theme/blue.scss
index 1f463801fb2b..49961495ceb6 100644
--- a/client/galaxy/style/scss/theme/blue.scss
+++ b/client/galaxy/style/scss/theme/blue.scss
@@ -152,7 +152,7 @@ $state-running-border: $border-color;
 // Workflow editor
 $workflow-editor-bg: $white;
 $workflow-editor-grid-size: 0.7rem;
-$workflow-editor-grid-color: lighten($brand-primary, 60%);
+$workflow-editor-grid-color: lighten($brand-primary, 65%);
 $workflow-overview-bg: $panel-bg-color;
 $worfklow-node-width: 10rem;
 
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 260b3f312ba2..039600e7c71a 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -15,6 +15,7 @@
             border: solid $brand-primary 1px;
             &.node-active {
                 z-index: 1001;
+                border: solid $white 1px;
                 box-shadow: 0 0 0 2px $brand-primary;
             }
             .node-header {
@@ -22,10 +23,14 @@
                 @extend .py-1;
                 @extend .px-2;
                 cursor: move;
-                background: $brand-secondary;
+                background: $brand-primary;
+                color: $white;
                 .header {
                     width: $worfklow-node-width - 2rem;
                 }
+                .button {
+                    color: $white;
+                }
             }
             .node-body {
                 @extend .card-body;
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index ae2678deb0f4..4b8851ab78c1 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -294,7 +294,7 @@ workflow_editor:
     label_input: "[tour_id='__label'] input"
     annotation_input: "[tour_id='__annotation'] textarea"
 
-    connector_for: "canvas[handle1-id='${source_id}'][handle2-id='${sink_id}']"
+    connector_for: "div[handle1-id='${source_id}'][handle2-id='${sink_id}']"
 
     connector_destroy_callout: '.delete-terminal'
 

From 61705a054a30bff06d935477396e6c2a84d232c5 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 02:53:56 -0500
Subject: [PATCH 299/853] Restore default workflow node styles

---
 client/galaxy/style/scss/theme/blue.scss | 2 +-
 client/galaxy/style/scss/workflow.scss   | 6 +-----
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/client/galaxy/style/scss/theme/blue.scss b/client/galaxy/style/scss/theme/blue.scss
index 49961495ceb6..1f463801fb2b 100644
--- a/client/galaxy/style/scss/theme/blue.scss
+++ b/client/galaxy/style/scss/theme/blue.scss
@@ -152,7 +152,7 @@ $state-running-border: $border-color;
 // Workflow editor
 $workflow-editor-bg: $white;
 $workflow-editor-grid-size: 0.7rem;
-$workflow-editor-grid-color: lighten($brand-primary, 65%);
+$workflow-editor-grid-color: lighten($brand-primary, 60%);
 $workflow-overview-bg: $panel-bg-color;
 $worfklow-node-width: 10rem;
 
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 039600e7c71a..b34decf2b3be 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -23,14 +23,10 @@
                 @extend .py-1;
                 @extend .px-2;
                 cursor: move;
-                background: $brand-primary;
-                color: $white;
+                background: $brand-secondary;
                 .header {
                     width: $worfklow-node-width - 2rem;
                 }
-                .button {
-                    color: $white;
-                }
             }
             .node-body {
                 @extend .card-body;

From 20aaca36b1ed14487daedaea131a64e51f6bad66 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Mar 2020 12:37:05 +0100
Subject: [PATCH 300/853] Add an integration test case for swift/s3

---
 .../objectstore/test_swift_objectstore.py     | 79 +++++++++++++++++++
 1 file changed, 79 insertions(+)
 create mode 100644 test/integration/objectstore/test_swift_objectstore.py

diff --git a/test/integration/objectstore/test_swift_objectstore.py b/test/integration/objectstore/test_swift_objectstore.py
new file mode 100644
index 000000000000..91b778d263b3
--- /dev/null
+++ b/test/integration/objectstore/test_swift_objectstore.py
@@ -0,0 +1,79 @@
+
+import os
+import string
+
+from galaxy_test.driver import integration_util
+
+OBJECT_STORE_HOST = os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_HOST', '127.0.0.1')
+OBJECT_STORE_PORT = int(os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_PORT', 9000))
+OBJECT_STORE_ACCESS_KEY = os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_ACCESS_KEY', 'minioadmin')
+OBJECT_STORE_SECRET_KEY = os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_SECRET_KEY', 'minioadmin')
+OBJECT_STORE_CONFIG = string.Template("""
+<object_store type="hierarchical" id="primary">
+    <backends>
+        <object_store id="swifty" type="swift" weight="1" order="0">
+            <auth access_key="${access_key}" secret_key="${secret_key}" />
+            <bucket name="galaxy" use_reduced_redundancy="False" max_chunk_size="250"/>
+            <connection host="${host}" port="${port}" is_secure="False" conn_path="" multipart="True"/>
+            <cache path="${temp_directory}/object_store_cache" size="1000" />
+            <extra_dir type="job_work" path="${temp_directory}/job_working_directory_swift"/>
+            <extra_dir type="temp" path="${temp_directory}/tmp_swift"/>
+        </object_store>
+    </backends>
+</object_store>
+""")
+TEST_TOOL_IDS = [
+    "multi_output",
+    "multi_output_configured",
+    "multi_output_assign_primary",
+    "multi_output_recurse",
+    "tool_provided_metadata_1",
+    "tool_provided_metadata_2",
+    "tool_provided_metadata_3",
+    "tool_provided_metadata_4",
+    "tool_provided_metadata_5",
+    "tool_provided_metadata_6",
+    "tool_provided_metadata_7",
+    "tool_provided_metadata_8",
+    "tool_provided_metadata_9",
+    "tool_provided_metadata_10",
+    "tool_provided_metadata_11",
+    "tool_provided_metadata_12",
+    "composite_output",
+    "composite_output_tests",
+    "metadata",
+    "metadata_bam",
+    "output_format",
+    "output_auto_format",
+]
+
+
+class SwiftObjectStoreIntegrationTestCase(integration_util.IntegrationTestCase):
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        temp_directory = cls._test_driver.mkdtemp()
+        cls.object_stores_parent = temp_directory
+        config_path = os.path.join(temp_directory, "object_store_conf.xml")
+        config["object_store_store_by"] = "uuid"
+        config["metadata_strategy"] = "extended"
+        config["outpus_to_working_dir"] = True
+        config["retry_metadata_internally"] = False
+        with open(config_path, "w") as f:
+            f.write(
+                OBJECT_STORE_CONFIG.safe_substitute(
+                    {
+                        "temp_directory": temp_directory,
+                        "host": OBJECT_STORE_HOST,
+                        "port": OBJECT_STORE_PORT,
+                        "access_key": OBJECT_STORE_ACCESS_KEY,
+                        "secret_key": OBJECT_STORE_SECRET_KEY,
+                    }
+                )
+            )
+        config["object_store_config_file"] = config_path
+
+
+instance = integration_util.integration_module_instance(SwiftObjectStoreIntegrationTestCase)
+
+test_tools = integration_util.integration_tool_runner(TEST_TOOL_IDS)
\ No newline at end of file

From 8fef712a5d67e8f6fafef91816cae5b6e0e1722c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Mar 2020 12:57:40 +0100
Subject: [PATCH 301/853] Don't use mutable default argument

---
 lib/galaxy/objectstore/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index ce8f2a579b51..d0dc0d6ac486 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -82,7 +82,7 @@ class ObjectStore(object):
         000/obj.id)
     """
 
-    def __init__(self, config, config_dict={}, **kwargs):
+    def __init__(self, config, config_dict=None, **kwargs):
         """
         :type config: object
         :param config: An object, most likely populated from
@@ -95,6 +95,8 @@ def __init__(self, config, config_dict={}, **kwargs):
               parent directory those directories will be created.
             * new_file_path -- Used to set the 'temp' extra_dir.
         """
+        if config_dict is None:
+            config_dict = {}
         self.running = True
         self.config = config
         self.check_old_style = config.object_store_check_old_style

From 6a56f3a5deb51dd1fafa8c588f32b14e67d10245 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Mar 2020 12:58:48 +0100
Subject: [PATCH 302/853] Disable cleanup thread in set_metadata.py

---
 lib/galaxy/objectstore/s3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index 09e78626e24d..2da1d12b5755 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -123,7 +123,7 @@ def _config_to_dict(self):
                 'conn_path': self.conn_path,
             },
             'cache': {
-                'size': self.cache_size,
+                'size': -1,  # disable cache cleaning when starting an exported object store in set_metadata.py
                 'path': self.staging_path,
             }
         }

From 57e84e78a38fda472067895e30b75d92c13084b6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Mar 2020 13:00:37 +0100
Subject: [PATCH 303/853] Fix store_by_uuid and extended metadata collection
 for s3 obejct stores

---
 lib/galaxy/objectstore/s3.py | 36 +++++++++++++++++++-----------------
 1 file changed, 19 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index 2da1d12b5755..992c7fb968b4 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -138,7 +138,7 @@ class S3ObjectStore(ObjectStore, CloudConfigMixin):
     store_type = 's3'
 
     def __init__(self, config, config_dict):
-        super(S3ObjectStore, self).__init__(config)
+        super(S3ObjectStore, self).__init__(config, config_dict)
 
         self.transfer_progress = 0
 
@@ -162,6 +162,8 @@ def __init__(self, config, config_dict):
 
         self.cache_size = cache_dict.get('size', -1)
         self.staging_path = cache_dict.get('path') or self.config.object_store_cache_path
+        self.store_by = config_dict.get("store_by", None) or getattr(config, "object_store_store_by", "id")
+        assert self.store_by in ["id", "uuid"]
 
         extra_dirs = dict(
             (e['type'], e['path']) for e in config_dict.get('extra_dirs', []))
@@ -187,7 +189,7 @@ def _initialize(self):
                          'conn_path': self.conn_path}
 
         self._configure_connection()
-        self.bucket = self._get_bucket(self.bucket)
+        self.__bucket = self._get_bucket(self.bucket)
         # Clean cache only if value is set in galaxy.ini
         if self.cache_size != -1:
             # Convert GBs to bytes for comparison
@@ -325,7 +327,7 @@ def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, ext
             # alt_name can contain parent directory references, but S3 will not
             # follow them, so if they are valid we normalize them out
             alt_name = os.path.normpath(alt_name)
-        rel_path = os.path.join(*directory_hash_id(obj.id))
+        rel_path = os.path.join(*directory_hash_id(self._get_object_id(obj)))
         if extra_dir is not None:
             if extra_dir_at_root:
                 rel_path = os.path.join(extra_dir, rel_path)
@@ -334,7 +336,7 @@ def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, ext
 
         # for JOB_WORK directory
         if obj_dir:
-            rel_path = os.path.join(rel_path, str(obj.id))
+            rel_path = os.path.join(rel_path, str(self._get_object_id(obj)))
         if base_dir:
             base = self.extra_dirs.get(base_dir)
             return os.path.join(base, rel_path)
@@ -343,7 +345,7 @@ def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, ext
         rel_path = '%s/' % rel_path
 
         if not dir_only:
-            rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
+            rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % self._get_object_id(obj))
         return rel_path
 
     def _get_cache_path(self, rel_path):
@@ -354,7 +356,7 @@ def _get_transfer_progress(self):
 
     def _get_size_in_s3(self, rel_path):
         try:
-            key = self.bucket.get_key(rel_path)
+            key = self.__bucket.get_key(rel_path)
             if key:
                 return key.size
         except S3ResponseError:
@@ -367,13 +369,13 @@ def _key_exists(self, rel_path):
             # A hackish way of testing if the rel_path is a folder vs a file
             is_dir = rel_path[-1] == '/'
             if is_dir:
-                keyresult = self.bucket.get_all_keys(prefix=rel_path)
+                keyresult = self.__bucket.get_all_keys(prefix=rel_path)
                 if len(keyresult) > 0:
                     exists = True
                 else:
                     exists = False
             else:
-                key = Key(self.bucket, rel_path)
+                key = Key(self.__bucket, rel_path)
                 exists = key.exists()
         except S3ResponseError:
             log.exception("Trouble checking existence of S3 key '%s'", rel_path)
@@ -425,7 +427,7 @@ def _transfer_cb(self, complete, total):
     def _download(self, rel_path):
         try:
             log.debug("Pulling key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
-            key = self.bucket.get_key(rel_path)
+            key = self.__bucket.get_key(rel_path)
             # Test if cache is large enough to hold the new file
             if self.cache_size > 0 and key.size > self.cache_size:
                 log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
@@ -444,7 +446,7 @@ def _download(self, rel_path):
                 key.get_contents_to_filename(self._get_cache_path(rel_path), cb=self._transfer_cb, num_cb=10)
                 return True
         except S3ResponseError:
-            log.exception("Problem downloading key '%s' from S3 bucket '%s'", rel_path, self.bucket.name)
+            log.exception("Problem downloading key '%s' from S3 bucket '%s'", rel_path, self.__bucket.name)
         return False
 
     def _push_to_os(self, rel_path, source_file=None, from_string=None):
@@ -458,7 +460,7 @@ def _push_to_os(self, rel_path, source_file=None, from_string=None):
         try:
             source_file = source_file if source_file else self._get_cache_path(rel_path)
             if os.path.exists(source_file):
-                key = Key(self.bucket, rel_path)
+                key = Key(self.__bucket, rel_path)
                 if os.path.getsize(source_file) == 0 and key.exists():
                     log.debug("Wanted to push file '%s' to S3 key '%s' but its size is 0; skipping.", source_file, rel_path)
                     return True
@@ -476,7 +478,7 @@ def _push_to_os(self, rel_path, source_file=None, from_string=None):
                                                        cb=self._transfer_cb,
                                                        num_cb=10)
                     else:
-                        multipart_upload(self.s3server, self.bucket, key.name, source_file, mb_size)
+                        multipart_upload(self.s3server, self.__bucket, key.name, source_file, mb_size)
                     end_time = datetime.now()
                     log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)",
                               source_file, rel_path, os.path.getsize(source_file), end_time - start_time)
@@ -545,7 +547,7 @@ def create(self, obj, **kwargs):
             alt_name = kwargs.get('alt_name', None)
 
             # Construct hashed path
-            rel_path = os.path.join(*directory_hash_id(obj.id))
+            rel_path = os.path.join(*directory_hash_id(self._get_object_id(obj)))
 
             # Optionally append extra_dir
             if extra_dir is not None:
@@ -566,7 +568,7 @@ def create(self, obj, **kwargs):
             # self._push_to_os(s3_dir, from_string='')
             # If instructed, create the dataset in cache & in S3
             if not dir_only:
-                rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
+                rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % self._get_object_id(obj))
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
                 self._push_to_os(rel_path, from_string='')
 
@@ -607,7 +609,7 @@ def delete(self, obj, entire_dir=False, **kwargs):
             # but requires iterating through each individual key in S3 and deleing it.
             if entire_dir and extra_dir:
                 shutil.rmtree(self._get_cache_path(rel_path))
-                results = self.bucket.get_all_keys(prefix=rel_path)
+                results = self.__bucket.get_all_keys(prefix=rel_path)
                 for key in results:
                     log.debug("Deleting key %s", key.name)
                     key.delete()
@@ -617,7 +619,7 @@ def delete(self, obj, entire_dir=False, **kwargs):
                 os.unlink(self._get_cache_path(rel_path))
                 # Delete from S3 as well
                 if self._key_exists(rel_path):
-                    key = Key(self.bucket, rel_path)
+                    key = Key(self.__bucket, rel_path)
                     log.debug("Deleting key %s", key.name)
                     key.delete()
                     return True
@@ -705,7 +707,7 @@ def get_object_url(self, obj, **kwargs):
         if self.exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             try:
-                key = Key(self.bucket, rel_path)
+                key = Key(self.__bucket, rel_path)
                 return key.generate_url(expires_in=86400)  # 24hrs
             except S3ResponseError:
                 log.exception("Trouble generating URL for dataset '%s'", rel_path)

From 0a252ed4f184dd1a5c46b655c4d418173c999cce Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Mar 2020 13:01:13 +0100
Subject: [PATCH 304/853] Manage minio docker container in integration test

---
 .../objectstore/test_swift_objectstore.py     | 36 ++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/test/integration/objectstore/test_swift_objectstore.py b/test/integration/objectstore/test_swift_objectstore.py
index 91b778d263b3..a2efd076d548 100644
--- a/test/integration/objectstore/test_swift_objectstore.py
+++ b/test/integration/objectstore/test_swift_objectstore.py
@@ -1,6 +1,7 @@
 
 import os
 import string
+import subprocess
 
 from galaxy_test.driver import integration_util
 
@@ -48,11 +49,44 @@
 ]
 
 
+def start_minio(container_name):
+    minio_start_args = [
+        'docker',
+        'run',
+        '-p',
+        '{port}:9000'.format(port=OBJECT_STORE_PORT),
+        '-d',
+        '--name',
+        container_name,
+        # '--rm',
+        'minio/minio:latest',
+        'server',
+        '/tmp/data']
+    subprocess.check_call(minio_start_args)
+
+
+def stop_minio(container_name):
+    subprocess.check_call(['docker', 'stop', container_name])
+
+
+@integration_util.skip_unless_docker()
 class SwiftObjectStoreIntegrationTestCase(integration_util.IntegrationTestCase):
 
+    @classmethod
+    def setUpClass(cls):
+        cls.container_name = "%s_container" % cls.__name__
+        start_minio(cls.container_name)
+        super(SwiftObjectStoreIntegrationTestCase, cls).setUpClass()
+
+    @classmethod
+    def tearDownClass(cls):
+        stop_minio(cls.container_name)
+        super(SwiftObjectStoreIntegrationTestCase, cls).tearDownClass()
+
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         temp_directory = cls._test_driver.mkdtemp()
+        cls.container_name = os.path.basename(temp_directory)
         cls.object_stores_parent = temp_directory
         config_path = os.path.join(temp_directory, "object_store_conf.xml")
         config["object_store_store_by"] = "uuid"
@@ -76,4 +110,4 @@ def handle_galaxy_config_kwds(cls, config):
 
 instance = integration_util.integration_module_instance(SwiftObjectStoreIntegrationTestCase)
 
-test_tools = integration_util.integration_tool_runner(TEST_TOOL_IDS)
\ No newline at end of file
+test_tools = integration_util.integration_tool_runner(TEST_TOOL_IDS)

From 110f00495fcfbc199e4737fae63b897f680ed9eb Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Tue, 11 Feb 2020 15:00:40 +0100
Subject: [PATCH 305/853] implement selenium test User->Preferences->Manage
 information workflow

---
 .../components/User/UserPreferences.vue       |   6 +-
 .../components/User/UserPreferencesModel.js   |   9 ++
 lib/galaxy/selenium/navigation.yml            |  16 +++
 .../selenium/test_personal_information.py     | 119 ++++++++++++++++++
 4 files changed, 147 insertions(+), 3 deletions(-)
 create mode 100644 lib/galaxy_test/selenium/test_personal_information.py

diff --git a/client/galaxy/scripts/components/User/UserPreferences.vue b/client/galaxy/scripts/components/User/UserPreferences.vue
index 6bc0e467dd5f..e311ff93023d 100644
--- a/client/galaxy/scripts/components/User/UserPreferences.vue
+++ b/client/galaxy/scripts/components/User/UserPreferences.vue
@@ -5,16 +5,16 @@
             {{ message }}
         </b-alert>
         <p>
-            You are logged in as <strong>{{ email }}</strong
+            You are logged in as <strong id="user-preferences-current-email">{{ email }}</strong
             >.
         </p>
         <b-row class="ml-3 mb-1" v-for="(link, index) in activeLinks" :key="index">
             <i :class="['pref-icon pt-1 fa fa-lg', link.icon]" />
             <div class="pref-content pr-1">
-                <a v-if="link.onclick" @click="link.onclick" href="javascript:void(0)"
+                <a :id="link.id" v-if="link.onclick" @click="link.onclick" href="javascript:void(0)"
                     ><b>{{ link.title }}</b></a
                 >
-                <a v-else :href="`${baseUrl}/${link.action}`"
+                <a :id="link.id" v-else :href="`${baseUrl}/${link.action}`"
                     ><b>{{ link.title }}</b></a
                 >
                 <div class="form-text text-muted">
diff --git a/client/galaxy/scripts/components/User/UserPreferencesModel.js b/client/galaxy/scripts/components/User/UserPreferencesModel.js
index 58660c8549e6..702d038ae394 100644
--- a/client/galaxy/scripts/components/User/UserPreferencesModel.js
+++ b/client/galaxy/scripts/components/User/UserPreferencesModel.js
@@ -7,6 +7,7 @@ export const getUserPreferencesModel = () => {
     return {
         information: {
             title: _l("Manage Information"),
+            id: "edit-preferences-information",
             description: "Edit your email, addresses and custom parameters or change your public name.",
             url: `api/users/${Galaxy.user.id}/information/inputs`,
             icon: "fa-user",
@@ -15,6 +16,7 @@ export const getUserPreferencesModel = () => {
         },
         password: {
             title: _l("Change Password"),
+            id: "edit-preferences-password",
             description: _l("Allows you to change your login credentials."),
             icon: "fa-unlock-alt",
             url: `api/users/${Galaxy.user.id}/password/inputs`,
@@ -24,6 +26,7 @@ export const getUserPreferencesModel = () => {
         },
         communication: {
             title: _l("Change Communication Settings"),
+            id: "edit-preferences-communication",
             description: _l("Enable or disable the communication feature to chat with other users."),
             url: `api/users/${Galaxy.user.id}/communication/inputs`,
             icon: "fa-comments-o",
@@ -32,6 +35,7 @@ export const getUserPreferencesModel = () => {
         },
         permissions: {
             title: _l("Set Dataset Permissions for new Histories"),
+            id: "edit-preferences-permissions",
             description:
                 "Grant others default access to newly created histories. Changes made here will only affect histories created after these settings have been stored.",
             url: `api/users/${Galaxy.user.id}/permissions/inputs`,
@@ -41,11 +45,13 @@ export const getUserPreferencesModel = () => {
         },
         make_data_private: {
             title: _l("Make all Data Private"),
+            id: "edit-preferences-make-data-private",
             description: _l("Click here to make all data private."),
             icon: "fa-lock"
         },
         api_key: {
             title: _l("Manage API Key"),
+            id: "edit-preferences-api-key",
             description: _l("Access your current API key or create a new one."),
             url: `api/users/${Galaxy.user.id}/api_key/inputs`,
             icon: "fa-key",
@@ -53,6 +59,7 @@ export const getUserPreferencesModel = () => {
             submit_icon: "fa-check"
         },
         cloud_auth: {
+            id: "edit-preferences-cloud-auth",
             title: _l("Manage Cloud Authorization"),
             description: _l("Add or modify the configuration that grants Galaxy to access your cloud-based resources."),
             icon: "fa-cloud",
@@ -61,6 +68,7 @@ export const getUserPreferencesModel = () => {
         },
         toolbox_filters: {
             title: _l("Manage Toolbox Filters"),
+            id: "edit-preferences-toolbox-filters",
             description: _l("Customize your Toolbox by displaying or omitting sets of Tools."),
             url: `api/users/${Galaxy.user.id}/toolbox_filters/inputs`,
             icon: "fa-filter",
@@ -75,6 +83,7 @@ export const getUserPreferencesModel = () => {
         },
         logout: {
             title: _l("Sign Out"),
+            id: "edit-preferences-custom-builds",
             description: _l("Click here to sign out of all sessions."),
             icon: "fa-sign-out",
             shouldRender: !!Galaxy.session_csrf_token
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index ae2678deb0f4..2e4ea2fe4b7f 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -60,6 +60,7 @@ masthead:
     # user menu
     logout: 'Logout'
     custom_builds: 'Custom Builds'
+    preferences: 'Preferences'
     histories: 'Histories'
     pages: 'Pages'
 
@@ -67,6 +68,21 @@ masthead:
     libraries: 'Data Libraries'
     published_histories: 'Histories'
 
+preferences:
+  selectors:
+    manage_information: '#edit-preferences-information'
+    current_email: "#user-preferences-current-email"
+
+change_user_email:
+  selectors:
+    submit: '#submit'
+
+change_user_address:
+  selectors:
+    address_button:
+      type: xpath
+      selector: '//span[contains(text(), "Insert Address")]'
+
 history_panel:
   menu:
     labels:
diff --git a/lib/galaxy_test/selenium/test_personal_information.py b/lib/galaxy_test/selenium/test_personal_information.py
new file mode 100644
index 000000000000..d1aef1b7deea
--- /dev/null
+++ b/lib/galaxy_test/selenium/test_personal_information.py
@@ -0,0 +1,119 @@
+from .framework import (
+    selenium_test,
+    SeleniumTestCase,
+)
+
+
+class ManageInformationTestCase(SeleniumTestCase):
+
+    @selenium_test
+    def test_change_email(self):
+        def assert_email(email_to_check):
+            self.assertTrue(email_to_check == self.driver.find_element_by_id("user-preferences-current-email").text)
+
+        email = self._get_random_email()
+        self.register(email)
+        self.navigate_to_user_preferences()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        # rendered email should be equal
+        assert_email(email)
+
+        self.components.preferences.manage_information.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        new_email = self._get_random_email()
+        # new email should be different from initially registered
+        self.assertTrue(email != new_email)
+        email_input_field = self.driver.find_element_by_css_selector("[tour_id='email'] input")
+
+        self.clear_input_field_and_write(email_input_field, new_email)
+        self.components.change_user_email.submit.wait_for_and_click()
+
+        # UX_RENDER time sometimes is not enough
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+
+        # email should be changed
+        assert_email(new_email)
+
+    @selenium_test
+    def test_public_name(self):
+        def get_name_input_field():
+            return self.driver.find_element_by_css_selector("[tour_id='username'] input")
+
+        def assert_public_name(expected_name):
+            self.assertTrue(expected_name == get_name_input_field().get_attribute('value'))
+
+        public_name = "user-public-name"
+        self.register(username=public_name)
+        self.navigate_to_manage_information()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        # make sure that public name is the same as registered
+        assert_public_name(public_name)
+        new_public_name = "new-public-name"
+        # change public name
+        self.clear_input_field_and_write(get_name_input_field(), new_public_name)
+        self.components.change_user_email.submit.wait_for_and_click()
+
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+
+        self.navigate_to_manage_information()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        # public name field should render new public name
+        assert_public_name(new_public_name)
+
+    @selenium_test
+    def test_user_address(self):
+        def get_address_form():
+            return self.driver.find_element_by_css_selector("div.ui-portlet-section > div.portlet-content")
+
+        self.register(self._get_random_email())
+        self.navigate_to_manage_information()
+        self.components.change_user_address.address_button.wait_for_and_click()
+
+        address_field_labels = ["Short address description", "Name", "Institution", "Address", "City",
+                                "State/Province/Region", "Postal Code", "Country", "Phone"]
+
+        address_fields = {}
+        # fill address fields with random data
+        for input_field_label in address_field_labels:
+            input_value = self._get_random_name(prefix=input_field_label)
+            address_fields[input_field_label] = input_value
+            input_field = self.get_address_input_field(get_address_form(), input_field_label)
+            self.clear_input_field_and_write(input_field, input_value)
+        # save new address
+        self.components.change_user_email.submit.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+
+        self.navigate_to_manage_information()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        # check if address was saved correctly
+        for input_field_label in address_fields.keys():
+            input_field = self.get_address_input_field(get_address_form(), input_field_label)
+            self.assertTrue(input_field.get_attribute('value') == address_fields[input_field_label])
+
+    def navigate_to_user_preferences(self):
+        self.home()
+        self.click_masthead_user()
+        self.components.masthead.preferences.wait_for_and_click()
+
+    def navigate_to_manage_information(self):
+        self.navigate_to_user_preferences()
+        self.components.preferences.manage_information.wait_for_and_click()
+
+    def clear_input_field_and_write(self, element, new_input_text):
+        element.clear()
+        element.send_keys(new_input_text)
+
+    # Since ids are not permanent we need to search with xpath
+    def get_address_input_field(self, address_form, input_field_label):
+        # . in the beginning = search only within current element
+        # span[.="variable"] find a span where text equals a variable
+        # //ancestor::div[@class = 'ui-form-title']" get an ancestor of found element with 'ui-form-title' classname
+        parent_element = address_form.find_element_by_xpath(
+            ".//span[.='" + input_field_label + "']//ancestor::div[@class = 'ui-form-title']")
+        # we cannot get to the desired parent directly (@class='ui-form-element section-row'),
+        # because then it will match the entire form. Thus, we need to use '..' to get one element up and get input tag
+        return parent_element.find_element_by_xpath('./..').find_element_by_tag_name('input')

From f2d7948d11633eba4ab79f1dd6bba1e419146ef1 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Mon, 2 Mar 2020 17:24:28 +0100
Subject: [PATCH 306/853] add data-label attribute to address form. Remove
 parent search

---
 client/galaxy/scripts/mvc/form/form-input.js          |  1 +
 lib/galaxy_test/selenium/test_personal_information.py | 10 +---------
 2 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/client/galaxy/scripts/mvc/form/form-input.js b/client/galaxy/scripts/mvc/form/form-input.js
index 89ecd872df1d..2f1c2274e070 100644
--- a/client/galaxy/scripts/mvc/form/form-input.js
+++ b/client/galaxy/scripts/mvc/form/form-input.js
@@ -177,6 +177,7 @@ export default Backbone.View.extend({
             this.$title_text.show().text(this.model.get("label"));
             this.$collapsible.hide();
         }
+        this.$field.attr("data-label", this.model.get("label"));
     },
 
     _template: function() {
diff --git a/lib/galaxy_test/selenium/test_personal_information.py b/lib/galaxy_test/selenium/test_personal_information.py
index d1aef1b7deea..4de0dd03060b 100644
--- a/lib/galaxy_test/selenium/test_personal_information.py
+++ b/lib/galaxy_test/selenium/test_personal_information.py
@@ -107,13 +107,5 @@ def clear_input_field_and_write(self, element, new_input_text):
         element.clear()
         element.send_keys(new_input_text)
 
-    # Since ids are not permanent we need to search with xpath
     def get_address_input_field(self, address_form, input_field_label):
-        # . in the beginning = search only within current element
-        # span[.="variable"] find a span where text equals a variable
-        # //ancestor::div[@class = 'ui-form-title']" get an ancestor of found element with 'ui-form-title' classname
-        parent_element = address_form.find_element_by_xpath(
-            ".//span[.='" + input_field_label + "']//ancestor::div[@class = 'ui-form-title']")
-        # we cannot get to the desired parent directly (@class='ui-form-element section-row'),
-        # because then it will match the entire form. Thus, we need to use '..' to get one element up and get input tag
-        return parent_element.find_element_by_xpath('./..').find_element_by_tag_name('input')
+        return address_form.find_element_by_css_selector("[data-label='" + input_field_label + "'] > input")

From 7a63fd1db202a9993c09cb6f10c0615dc8dc5c99 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Mar 2020 14:16:01 +0100
Subject: [PATCH 307/853] Fix S3 object store shutdown

---
 lib/galaxy/objectstore/s3.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index 992c7fb968b4..71d11b7a1cf4 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -716,6 +716,14 @@ def get_object_url(self, obj, **kwargs):
     def get_store_usage_percent(self):
         return 0.0
 
+    def shutdown(self):
+        self.running = False
+        thread = getattr(self, 'cache_monitor_thread', None)
+        if thread:
+            log.debug("Shutting down thread")
+            self.sleeper.wake()
+            thread.join(5)
+
 
 class SwiftObjectStore(S3ObjectStore):
     """

From b5dd8346fbe8b8bdd88eaf77566a707b9d5b3c94 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Mar 2020 14:18:49 +0100
Subject: [PATCH 308/853] Fix test container shutdown

---
 test/integration/objectstore/test_swift_objectstore.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/test/integration/objectstore/test_swift_objectstore.py b/test/integration/objectstore/test_swift_objectstore.py
index a2efd076d548..0ee10a4b4625 100644
--- a/test/integration/objectstore/test_swift_objectstore.py
+++ b/test/integration/objectstore/test_swift_objectstore.py
@@ -66,7 +66,7 @@ def start_minio(container_name):
 
 
 def stop_minio(container_name):
-    subprocess.check_call(['docker', 'stop', container_name])
+    subprocess.check_call(['docker', 'rm', '-f', container_name])
 
 
 @integration_util.skip_unless_docker()
@@ -86,7 +86,6 @@ def tearDownClass(cls):
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         temp_directory = cls._test_driver.mkdtemp()
-        cls.container_name = os.path.basename(temp_directory)
         cls.object_stores_parent = temp_directory
         config_path = os.path.join(temp_directory, "object_store_conf.xml")
         config["object_store_store_by"] = "uuid"

From 510504075f2c079fe746414b27e2b206dde22652 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Mar 2020 14:22:54 +0100
Subject: [PATCH 309/853] Don't run extended metadata strategy

---
 test/integration/objectstore/test_swift_objectstore.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/integration/objectstore/test_swift_objectstore.py b/test/integration/objectstore/test_swift_objectstore.py
index 0ee10a4b4625..c3e90af15062 100644
--- a/test/integration/objectstore/test_swift_objectstore.py
+++ b/test/integration/objectstore/test_swift_objectstore.py
@@ -89,7 +89,8 @@ def handle_galaxy_config_kwds(cls, config):
         cls.object_stores_parent = temp_directory
         config_path = os.path.join(temp_directory, "object_store_conf.xml")
         config["object_store_store_by"] = "uuid"
-        config["metadata_strategy"] = "extended"
+        # This doesn't quite work yet, fails with extra_files_path
+        # config["metadata_strategy"] = "extended"
         config["outpus_to_working_dir"] = True
         config["retry_metadata_internally"] = False
         with open(config_path, "w") as f:

From 04db689fd0ffc71e491c4404759b27ba9ba0d4b1 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 3 Mar 2020 08:27:21 -0500
Subject: [PATCH 310/853] Fix default quota creation message.

---
 lib/galaxy/actions/admin.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/actions/admin.py b/lib/galaxy/actions/admin.py
index 3879f6b794e9..d2acc040db90 100644
--- a/lib/galaxy/actions/admin.py
+++ b/lib/galaxy/actions/admin.py
@@ -45,7 +45,7 @@ def _create_quota(self, params, decode_id=None):
             # If this is a default quota, create the DefaultQuotaAssociation
             if params.default != 'no':
                 self.app.quota_agent.set_default_quota(params.default, quota)
-                message = "Default quota '%s' has been created."
+                message = "Default quota '%s' has been created." % quota.name
             else:
                 # Create the UserQuotaAssociations
                 in_users = [self.sa_session.query(self.app.model.User).get(decode_id(x) if decode_id else x) for x in util.listify(params.in_users)]

From 46f3af60450098a5a7846edb2f1fec31873cc7d4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Mar 2020 15:20:17 +0100
Subject: [PATCH 311/853] Use single underscore bucket

---
 lib/galaxy/objectstore/s3.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index 71d11b7a1cf4..30d5f1100e14 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -189,7 +189,7 @@ def _initialize(self):
                          'conn_path': self.conn_path}
 
         self._configure_connection()
-        self.__bucket = self._get_bucket(self.bucket)
+        self._bucket = self._get_bucket(self.bucket)
         # Clean cache only if value is set in galaxy.ini
         if self.cache_size != -1:
             # Convert GBs to bytes for comparison
@@ -356,7 +356,7 @@ def _get_transfer_progress(self):
 
     def _get_size_in_s3(self, rel_path):
         try:
-            key = self.__bucket.get_key(rel_path)
+            key = self._bucket.get_key(rel_path)
             if key:
                 return key.size
         except S3ResponseError:
@@ -369,13 +369,13 @@ def _key_exists(self, rel_path):
             # A hackish way of testing if the rel_path is a folder vs a file
             is_dir = rel_path[-1] == '/'
             if is_dir:
-                keyresult = self.__bucket.get_all_keys(prefix=rel_path)
+                keyresult = self._bucket.get_all_keys(prefix=rel_path)
                 if len(keyresult) > 0:
                     exists = True
                 else:
                     exists = False
             else:
-                key = Key(self.__bucket, rel_path)
+                key = Key(self._bucket, rel_path)
                 exists = key.exists()
         except S3ResponseError:
             log.exception("Trouble checking existence of S3 key '%s'", rel_path)
@@ -427,7 +427,7 @@ def _transfer_cb(self, complete, total):
     def _download(self, rel_path):
         try:
             log.debug("Pulling key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
-            key = self.__bucket.get_key(rel_path)
+            key = self._bucket.get_key(rel_path)
             # Test if cache is large enough to hold the new file
             if self.cache_size > 0 and key.size > self.cache_size:
                 log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
@@ -446,7 +446,7 @@ def _download(self, rel_path):
                 key.get_contents_to_filename(self._get_cache_path(rel_path), cb=self._transfer_cb, num_cb=10)
                 return True
         except S3ResponseError:
-            log.exception("Problem downloading key '%s' from S3 bucket '%s'", rel_path, self.__bucket.name)
+            log.exception("Problem downloading key '%s' from S3 bucket '%s'", rel_path, self._bucket.name)
         return False
 
     def _push_to_os(self, rel_path, source_file=None, from_string=None):
@@ -460,7 +460,7 @@ def _push_to_os(self, rel_path, source_file=None, from_string=None):
         try:
             source_file = source_file if source_file else self._get_cache_path(rel_path)
             if os.path.exists(source_file):
-                key = Key(self.__bucket, rel_path)
+                key = Key(self._bucket, rel_path)
                 if os.path.getsize(source_file) == 0 and key.exists():
                     log.debug("Wanted to push file '%s' to S3 key '%s' but its size is 0; skipping.", source_file, rel_path)
                     return True
@@ -478,7 +478,7 @@ def _push_to_os(self, rel_path, source_file=None, from_string=None):
                                                        cb=self._transfer_cb,
                                                        num_cb=10)
                     else:
-                        multipart_upload(self.s3server, self.__bucket, key.name, source_file, mb_size)
+                        multipart_upload(self.s3server, self._bucket, key.name, source_file, mb_size)
                     end_time = datetime.now()
                     log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)",
                               source_file, rel_path, os.path.getsize(source_file), end_time - start_time)
@@ -609,7 +609,7 @@ def delete(self, obj, entire_dir=False, **kwargs):
             # but requires iterating through each individual key in S3 and deleing it.
             if entire_dir and extra_dir:
                 shutil.rmtree(self._get_cache_path(rel_path))
-                results = self.__bucket.get_all_keys(prefix=rel_path)
+                results = self._bucket.get_all_keys(prefix=rel_path)
                 for key in results:
                     log.debug("Deleting key %s", key.name)
                     key.delete()
@@ -619,7 +619,7 @@ def delete(self, obj, entire_dir=False, **kwargs):
                 os.unlink(self._get_cache_path(rel_path))
                 # Delete from S3 as well
                 if self._key_exists(rel_path):
-                    key = Key(self.__bucket, rel_path)
+                    key = Key(self._bucket, rel_path)
                     log.debug("Deleting key %s", key.name)
                     key.delete()
                     return True
@@ -707,7 +707,7 @@ def get_object_url(self, obj, **kwargs):
         if self.exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             try:
-                key = Key(self.__bucket, rel_path)
+                key = Key(self._bucket, rel_path)
                 return key.generate_url(expires_in=86400)  # 24hrs
             except S3ResponseError:
                 log.exception("Trouble generating URL for dataset '%s'", rel_path)

From f54b0e729a5fa8d223df03f824e767ca413b0127 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 3 Mar 2020 10:02:19 -0500
Subject: [PATCH 312/853] Fix data manager table slot usage; this makes the
 header with the name and 'reload' icon display again.  Also refactor a few
 computed props. Should add this to eslint to catch these easier.

---
 .../admin/DataManager/DataManagerTable.vue    | 44 +++++++++++--------
 1 file changed, 26 insertions(+), 18 deletions(-)

diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue b/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
index fa1139df3787..f749b4645144 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
@@ -13,22 +13,24 @@
             <b-row>
                 <b-col>
                     <b-card id="data-table-card" flush>
-                        <b-container v-slot:header>
-                            <b-row align-v="center">
-                                <b-col cols="auto">
-                                    <b-button
-                                        @click="reload()"
-                                        v-b-tooltip.hover
-                                        :title="'Reload ' + this.dataTable['name'] + ' tool data table'"
-                                    >
-                                        <span class="fa fa-refresh" />
-                                    </b-button>
-                                </b-col>
-                                <b-col>
-                                    <b>{{ this.dataTable["name"] }}</b>
-                                </b-col>
-                            </b-row>
-                        </b-container>
+                        <template v-slot:header>
+                            <b-container>
+                                <b-row align-v="center">
+                                    <b-col cols="auto">
+                                        <b-button
+                                            @click="reload()"
+                                            v-b-tooltip.hover
+                                            :title="buttonLabel"
+                                        >
+                                            <span class="fa fa-refresh" />
+                                        </b-button>
+                                    </b-col>
+                                    <b-col>
+                                        <b>{{ dataTableName }}</b>
+                                    </b-col>
+                                </b-row>
+                            </b-container>
+                        </template>
                         <b-table
                             :fields="fields(this.dataTable['columns'])"
                             :items="dataTable['data']"
@@ -68,6 +70,12 @@ export default {
         };
     },
     computed: {
+        dataTableName() {
+            return this.dataTable && this.dataTable.name ? this.dataTable.name : 'null';
+        },
+        buttonLabel() {
+            return `Reload ${this.dataTableName} tool data table`;
+        },
         breadcrumbItems() {
             return [
                 {
@@ -75,7 +83,7 @@ export default {
                     to: "/"
                 },
                 {
-                    text: this.dataTable["name"]
+                    text: this.dataTableName
                 }
             ];
         }
@@ -88,7 +96,7 @@ export default {
         },
         reload() {
             axios
-                .get(`${getAppRoot()}data_manager/reload_tool_data_tables?table_name=${this.dataTable["name"]}`)
+                .get(`${getAppRoot()}data_manager/reload_tool_data_tables?table_name=${this.dataTableName}`)
                 .then(response => {
                     if (response.data.dataTable) {
                         this.dataTable = response.data.dataTable;

From ac9249eb4e4e0f6a5d67b870fa62eccedbe2c7f3 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 3 Mar 2020 10:04:46 -0500
Subject: [PATCH 313/853] Prettier.

---
 .../components/admin/DataManager/DataManagerTable.vue     | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue b/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
index f749b4645144..972612a81160 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
@@ -17,11 +17,7 @@
                             <b-container>
                                 <b-row align-v="center">
                                     <b-col cols="auto">
-                                        <b-button
-                                            @click="reload()"
-                                            v-b-tooltip.hover
-                                            :title="buttonLabel"
-                                        >
+                                        <b-button @click="reload()" v-b-tooltip.hover :title="buttonLabel">
                                             <span class="fa fa-refresh" />
                                         </b-button>
                                     </b-col>
@@ -71,7 +67,7 @@ export default {
     },
     computed: {
         dataTableName() {
-            return this.dataTable && this.dataTable.name ? this.dataTable.name : 'null';
+            return this.dataTable && this.dataTable.name ? this.dataTable.name : "null";
         },
         buttonLabel() {
             return `Reload ${this.dataTableName} tool data table`;

From 6c4deded1a4706fdaed08b9af47b7e9d15b30819 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 3 Mar 2020 10:10:32 -0500
Subject: [PATCH 314/853] Add v-slot linting to check for busted slots

---
 client/.eslintrc.js | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/client/.eslintrc.js b/client/.eslintrc.js
index f5b615f0a69c..619a2dc68605 100644
--- a/client/.eslintrc.js
+++ b/client/.eslintrc.js
@@ -22,6 +22,9 @@ module.exports = {
         "no-unused-vars": ["error", { args: "none" }],
         "prefer-const": "error",
 
+        "vue/valid-v-slot": "error",
+        //"vue/v-slot-style": "error",
+
         // Vue TODO (enable these)
         "vue/require-default-prop": "off",
         "vue/require-prop-types": "off",

From 6f24e88fa7df556141f25dd95c676a52daca2b35 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 3 Mar 2020 10:11:37 -0500
Subject: [PATCH 315/853] Update eslint dependencies to support the v-slot
 rules

---
 client/package.json |   6 +--
 client/yarn.lock    | 124 +++++++++++++++++---------------------------
 2 files changed, 50 insertions(+), 80 deletions(-)

diff --git a/client/package.json b/client/package.json
index 883f7bcbff6e..45f512ff9ded 100644
--- a/client/package.json
+++ b/client/package.json
@@ -87,7 +87,7 @@
     "amdi18n-loader": "^0.9.3",
     "autoprefixer": "^9.7.4",
     "axios-mock-adapter": "^1.17.0",
-    "babel-eslint": "^10.0.3",
+    "babel-eslint": "^10.1.0",
     "babel-loader": "^8.0.6",
     "babel-plugin-rewire": "^1.2.0",
     "babel-plugin-transform-inline-environment-variables": "^0.4.3",
@@ -98,8 +98,8 @@
     "duplicate-package-checker-webpack-plugin": "^3.0.0",
     "eslint": "^6.8.0",
     "eslint-plugin-html": "^6.0.0",
-    "eslint-plugin-import": "^2.20.0",
-    "eslint-plugin-vue": "^6.1.2",
+    "eslint-plugin-import": "^2.20.1",
+    "eslint-plugin-vue": "^6.2.1",
     "expose-loader": "^0.7.5",
     "file-loader": "^5.0.2",
     "gulp": "^4.0.2",
diff --git a/client/yarn.lock b/client/yarn.lock
index 15034d954783..488f2f44eb7f 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -9,13 +9,6 @@
   dependencies:
     "@babel/highlight" "^7.0.0"
 
-"@babel/code-frame@^7.5.5":
-  version "7.5.5"
-  resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.5.5.tgz#bc0782f6d69f7b7d49531219699b988f669a8f9d"
-  integrity sha512-27d4lZoomVyo51VegxI20xZPuSHusqbQag/ztrBC7wegWoQ1nLREPVSKSW8byhTlzTKyNE4ifaTA6lCp7JjpFw==
-  dependencies:
-    "@babel/highlight" "^7.0.0"
-
 "@babel/code-frame@^7.8.3":
   version "7.8.3"
   resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.8.3.tgz#33e25903d7481181534e12ec0a25f16b6fcf419e"
@@ -53,17 +46,6 @@
     semver "^5.4.1"
     source-map "^0.5.0"
 
-"@babel/generator@^7.6.0":
-  version "7.6.0"
-  resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.6.0.tgz#e2c21efbfd3293ad819a2359b448f002bfdfda56"
-  integrity sha512-Ms8Mo7YBdMMn1BYuNtKuP/z0TgEIhbcyB8HVR6PPNYp4P61lMsABiS4A3VG1qznjXVCf3r+fVHhm4efTYVsySA==
-  dependencies:
-    "@babel/types" "^7.6.0"
-    jsesc "^2.5.1"
-    lodash "^4.17.13"
-    source-map "^0.5.0"
-    trim-right "^1.0.1"
-
 "@babel/generator@^7.8.3":
   version "7.8.3"
   resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.8.3.tgz#0e22c005b0a94c1c74eafe19ef78ce53a4d45c03"
@@ -84,6 +66,16 @@
     lodash "^4.17.13"
     source-map "^0.5.0"
 
+"@babel/generator@^7.8.6":
+  version "7.8.6"
+  resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.8.6.tgz#57adf96d370c9a63c241cd719f9111468578537a"
+  integrity sha512-4bpOR5ZBz+wWcMeVtcf7FbjcFzCp+817z2/gHNncIRcM9MmKzUhtWCYAq27RAfUrAFwb+OCG1s9WEaVxfi6cjg==
+  dependencies:
+    "@babel/types" "^7.8.6"
+    jsesc "^2.5.1"
+    lodash "^4.17.13"
+    source-map "^0.5.0"
+
 "@babel/helper-annotate-as-pure@^7.8.3":
   version "7.8.3"
   resolved "https://registry.yarnpkg.com/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.8.3.tgz#60bc0bc657f63a0924ff9a4b4a0b24a13cf4deee"
@@ -144,15 +136,6 @@
     "@babel/traverse" "^7.8.3"
     "@babel/types" "^7.8.3"
 
-"@babel/helper-function-name@^7.1.0":
-  version "7.1.0"
-  resolved "https://registry.yarnpkg.com/@babel/helper-function-name/-/helper-function-name-7.1.0.tgz#a0ceb01685f73355d4360c1247f582bfafc8ff53"
-  integrity sha512-A95XEoCpb3TO+KZzJ4S/5uW5fNe26DjBGqf1o9ucyLyCmi1dXq/B3c8iaWTfBk3VvetUxl16e8tIrd5teOCfGw==
-  dependencies:
-    "@babel/helper-get-function-arity" "^7.0.0"
-    "@babel/template" "^7.1.0"
-    "@babel/types" "^7.0.0"
-
 "@babel/helper-function-name@^7.8.3":
   version "7.8.3"
   resolved "https://registry.yarnpkg.com/@babel/helper-function-name/-/helper-function-name-7.8.3.tgz#eeeb665a01b1f11068e9fb86ad56a1cb1a824cca"
@@ -162,13 +145,6 @@
     "@babel/template" "^7.8.3"
     "@babel/types" "^7.8.3"
 
-"@babel/helper-get-function-arity@^7.0.0":
-  version "7.0.0"
-  resolved "https://registry.yarnpkg.com/@babel/helper-get-function-arity/-/helper-get-function-arity-7.0.0.tgz#83572d4320e2a4657263734113c42868b64e49c3"
-  integrity sha512-r2DbJeg4svYvt3HOS74U4eWKsUAMRH01Z1ds1zx8KNTPtpTL5JAsdFv8BNyOpVqdFhHkkRDIg5B4AsxmkjAlmQ==
-  dependencies:
-    "@babel/types" "^7.0.0"
-
 "@babel/helper-get-function-arity@^7.8.3":
   version "7.8.3"
   resolved "https://registry.yarnpkg.com/@babel/helper-get-function-arity/-/helper-get-function-arity-7.8.3.tgz#b894b947bd004381ce63ea1db9f08547e920abd5"
@@ -257,13 +233,6 @@
     "@babel/template" "^7.8.3"
     "@babel/types" "^7.8.3"
 
-"@babel/helper-split-export-declaration@^7.4.4":
-  version "7.4.4"
-  resolved "https://registry.yarnpkg.com/@babel/helper-split-export-declaration/-/helper-split-export-declaration-7.4.4.tgz#ff94894a340be78f53f06af038b205c49d993677"
-  integrity sha512-Ro/XkzLf3JFITkW6b+hNxzZ1n5OQ80NvIUdmHspih1XAhtN3vPTuUFT4eQnela+2MaZ5ulH+iyP513KJrxbN7Q==
-  dependencies:
-    "@babel/types" "^7.4.4"
-
 "@babel/helper-split-export-declaration@^7.8.3":
   version "7.8.3"
   resolved "https://registry.yarnpkg.com/@babel/helper-split-export-declaration/-/helper-split-export-declaration-7.8.3.tgz#31a9f30070f91368a7182cf05f831781065fc7a9"
@@ -308,11 +277,6 @@
     esutils "^2.0.2"
     js-tokens "^4.0.0"
 
-"@babel/parser@^7.0.0", "@babel/parser@^7.6.0":
-  version "7.6.0"
-  resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.6.0.tgz#3e05d0647432a8326cb28d0de03895ae5a57f39b"
-  integrity sha512-+o2q111WEx4srBs7L9eJmcwi655eD8sXniLqMB93TBK9GrNzGrxDWSjiqz2hLU0Ha8MTXFIP0yd9fNdP+m43ZQ==
-
 "@babel/parser@^7.1.2", "@babel/parser@^7.1.3":
   version "7.1.3"
   resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.1.3.tgz#2c92469bac2b7fbff810b67fca07bd138b48af77"
@@ -323,6 +287,11 @@
   resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.4.2.tgz#b4521a400cb5a871eab3890787b4bc1326d38d91"
   integrity sha512-9fJTDipQFvlfSVdD/JBtkiY0br9BtfvW2R8wo6CX/Ej2eMuV0gWPk1M67Mt3eggQvBqYW1FCEk8BN7WvGm/g5g==
 
+"@babel/parser@^7.7.0", "@babel/parser@^7.8.6":
+  version "7.8.6"
+  resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.8.6.tgz#ba5c9910cddb77685a008e3c587af8d27b67962c"
+  integrity sha512-trGNYSfwq5s0SgM1BMEB8hX3NDmO7EP2wsDGDexiaKMB92BaRpS+qZfpkMqUBhcsOTBwNy9B/jieo4ad/t/z2g==
+
 "@babel/parser@^7.8.3":
   version "7.8.3"
   resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.8.3.tgz#790874091d2001c9be6ec426c2eed47bc7679081"
@@ -777,7 +746,7 @@
   dependencies:
     regenerator-runtime "^0.12.0"
 
-"@babel/template@^7.0.0-beta.46", "@babel/template@^7.1.0":
+"@babel/template@^7.0.0-beta.46":
   version "7.1.2"
   resolved "https://registry.yarnpkg.com/@babel/template/-/template-7.1.2.tgz#090484a574fef5a2d2d7726a674eceda5c5b5644"
   integrity sha512-SY1MmplssORfFiLDcOETrW7fCLl+PavlwMh92rrGcikQaRq4iWPVH0MpwPpY3etVMx6RnDjXtr6VZYr/IbP/Ag==
@@ -795,17 +764,17 @@
     "@babel/parser" "^7.8.3"
     "@babel/types" "^7.8.3"
 
-"@babel/traverse@^7.0.0":
-  version "7.6.0"
-  resolved "https://registry.yarnpkg.com/@babel/traverse/-/traverse-7.6.0.tgz#389391d510f79be7ce2ddd6717be66d3fed4b516"
-  integrity sha512-93t52SaOBgml/xY74lsmt7xOR4ufYvhb5c5qiM6lu4J/dWGMAfAh6eKw4PjLes6DI6nQgearoxnFJk60YchpvQ==
-  dependencies:
-    "@babel/code-frame" "^7.5.5"
-    "@babel/generator" "^7.6.0"
-    "@babel/helper-function-name" "^7.1.0"
-    "@babel/helper-split-export-declaration" "^7.4.4"
-    "@babel/parser" "^7.6.0"
-    "@babel/types" "^7.6.0"
+"@babel/traverse@^7.7.0":
+  version "7.8.6"
+  resolved "https://registry.yarnpkg.com/@babel/traverse/-/traverse-7.8.6.tgz#acfe0c64e1cd991b3e32eae813a6eb564954b5ff"
+  integrity sha512-2B8l0db/DPi8iinITKuo7cbPznLCEk0kCxDoB9/N6gGNg/gxOXiR/IcymAFPiBwk5w6TtQ27w4wpElgp9btR9A==
+  dependencies:
+    "@babel/code-frame" "^7.8.3"
+    "@babel/generator" "^7.8.6"
+    "@babel/helper-function-name" "^7.8.3"
+    "@babel/helper-split-export-declaration" "^7.8.3"
+    "@babel/parser" "^7.8.6"
+    "@babel/types" "^7.8.6"
     debug "^4.1.0"
     globals "^11.1.0"
     lodash "^4.17.13"
@@ -849,10 +818,10 @@
     lodash "^4.17.10"
     to-fast-properties "^2.0.0"
 
-"@babel/types@^7.4.4", "@babel/types@^7.6.0":
-  version "7.6.1"
-  resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.6.1.tgz#53abf3308add3ac2a2884d539151c57c4b3ac648"
-  integrity sha512-X7gdiuaCmA0uRjCmRtYJNAVCc/q+5xSgsfKJHqMN4iNLILX39677fJE1O40arPMh0TTtS9ItH67yre6c7k6t0g==
+"@babel/types@^7.7.0", "@babel/types@^7.8.6":
+  version "7.8.6"
+  resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.8.6.tgz#629ecc33c2557fcde7126e58053127afdb3e6d01"
+  integrity sha512-wqz7pgWMIrht3gquyEFPVXeXCti72Rm8ep9b5tQKz9Yg9LzJA3HxosF1SB3Kc81KD1A3XBkkVYtJvCKS2Z/QrA==
   dependencies:
     esutils "^2.0.2"
     lodash "^4.17.13"
@@ -2034,15 +2003,15 @@ babel-core@^6.26.0, babel-core@^6.3.21:
     slash "^1.0.0"
     source-map "^0.5.7"
 
-babel-eslint@^10.0.3:
-  version "10.0.3"
-  resolved "https://registry.yarnpkg.com/babel-eslint/-/babel-eslint-10.0.3.tgz#81a2c669be0f205e19462fed2482d33e4687a88a"
-  integrity sha512-z3U7eMY6r/3f3/JB9mTsLjyxrv0Yb1zb8PCWCLpguxfCzBIZUwy23R1t/XKewP+8mEN2Ck8Dtr4q20z6ce6SoA==
+babel-eslint@^10.1.0:
+  version "10.1.0"
+  resolved "https://registry.yarnpkg.com/babel-eslint/-/babel-eslint-10.1.0.tgz#6968e568a910b78fb3779cdd8b6ac2f479943232"
+  integrity sha512-ifWaTHQ0ce+448CYop8AdrQiBsGrnC+bMgfyKFdi6EsPLTAWG+QfyDeM6OH+FmWnKvEq5NnBMLvlBUPKQZoDSg==
   dependencies:
     "@babel/code-frame" "^7.0.0"
-    "@babel/parser" "^7.0.0"
-    "@babel/traverse" "^7.0.0"
-    "@babel/types" "^7.0.0"
+    "@babel/parser" "^7.7.0"
+    "@babel/traverse" "^7.7.0"
+    "@babel/types" "^7.7.0"
     eslint-visitor-keys "^1.0.0"
     resolve "^1.12.0"
 
@@ -5355,10 +5324,10 @@ eslint-plugin-html@^6.0.0:
   dependencies:
     htmlparser2 "^3.10.1"
 
-eslint-plugin-import@^2.20.0:
-  version "2.20.0"
-  resolved "https://registry.yarnpkg.com/eslint-plugin-import/-/eslint-plugin-import-2.20.0.tgz#d749a7263fb6c29980def8e960d380a6aa6aecaa"
-  integrity sha512-NK42oA0mUc8Ngn4kONOPsPB1XhbUvNHqF+g307dPV28aknPoiNnKLFd9em4nkswwepdF5ouieqv5Th/63U7YJQ==
+eslint-plugin-import@^2.20.1:
+  version "2.20.1"
+  resolved "https://registry.yarnpkg.com/eslint-plugin-import/-/eslint-plugin-import-2.20.1.tgz#802423196dcb11d9ce8435a5fc02a6d3b46939b3"
+  integrity sha512-qQHgFOTjguR+LnYRoToeZWT62XM55MBVXObHM6SKFd1VzDcX/vqT1kAz8ssqigh5eMj8qXcRoXXGZpPP6RfdCw==
   dependencies:
     array-includes "^3.0.3"
     array.prototype.flat "^1.2.1"
@@ -5373,11 +5342,12 @@ eslint-plugin-import@^2.20.0:
     read-pkg-up "^2.0.0"
     resolve "^1.12.0"
 
-eslint-plugin-vue@^6.1.2:
-  version "6.1.2"
-  resolved "https://registry.yarnpkg.com/eslint-plugin-vue/-/eslint-plugin-vue-6.1.2.tgz#4b05c28c83c0ec912669b64dbd998bb8bf692ef6"
-  integrity sha512-M75oAB+2a/LNkLKRbeEaS07EjzjIUaV7/hYoHAfRFeeF8ZMmCbahUn8nQLsLP85mkar24+zDU3QW2iT1JRsACw==
+eslint-plugin-vue@^6.2.1:
+  version "6.2.1"
+  resolved "https://registry.yarnpkg.com/eslint-plugin-vue/-/eslint-plugin-vue-6.2.1.tgz#ca802df5c33146aed1e56bb21d250c1abb6120a3"
+  integrity sha512-MiIDOotoWseIfLIfGeDzF6sDvHkVvGd2JgkvjyHtN3q4RoxdAXrAMuI3SXTOKatljgacKwpNAYShmcKZa4yZzw==
   dependencies:
+    natural-compare "^1.4.0"
     semver "^5.6.0"
     vue-eslint-parser "^7.0.0"
 

From df06f925f0ce960fa00cede3970ea4a1386d1190 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 3 Mar 2020 10:16:40 -0500
Subject: [PATCH 316/853] Fix v-slot-style directive; use standard v-slot
 everywhere

---
 client/.eslintrc.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/.eslintrc.js b/client/.eslintrc.js
index 619a2dc68605..1392624c1b3b 100644
--- a/client/.eslintrc.js
+++ b/client/.eslintrc.js
@@ -23,7 +23,7 @@ module.exports = {
         "prefer-const": "error",
 
         "vue/valid-v-slot": "error",
-        //"vue/v-slot-style": "error",
+        "vue/v-slot-style": ["error", {"atComponent": "v-slot", "default": "v-slot", "named": "longform"}],
 
         // Vue TODO (enable these)
         "vue/require-default-prop": "off",

From 9cbb20eb68e64e7351538eb99af14aa4317f6e72 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 3 Mar 2020 10:29:34 -0500
Subject: [PATCH 317/853] Fix eslint-plugin-import to actually lint

---
 client/.eslintrc.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/.eslintrc.js b/client/.eslintrc.js
index 1392624c1b3b..942c0b278304 100644
--- a/client/.eslintrc.js
+++ b/client/.eslintrc.js
@@ -2,6 +2,7 @@ module.exports = {
     extends: [
         "eslint:recommended",
         "plugin:vue/strongly-recommended",
+        "plugin:import/errors"
         //"airbnb-base", eventually
     ],
     env: {

From 004957a66e81dfba7f7ad18d89ee98c94f04f1a7 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 3 Mar 2020 10:30:29 -0500
Subject: [PATCH 318/853] Drop eslint-plugin-import completely; it's not useful
 for us.  Webpack is going to complain if any of this fails anyway.

---
 client/.eslintrc.js |   1 -
 client/package.json |   1 -
 client/yarn.lock    | 195 +++-----------------------------------------
 3 files changed, 12 insertions(+), 185 deletions(-)

diff --git a/client/.eslintrc.js b/client/.eslintrc.js
index 942c0b278304..1392624c1b3b 100644
--- a/client/.eslintrc.js
+++ b/client/.eslintrc.js
@@ -2,7 +2,6 @@ module.exports = {
     extends: [
         "eslint:recommended",
         "plugin:vue/strongly-recommended",
-        "plugin:import/errors"
         //"airbnb-base", eventually
     ],
     env: {
diff --git a/client/package.json b/client/package.json
index 45f512ff9ded..cf0e9425c691 100644
--- a/client/package.json
+++ b/client/package.json
@@ -98,7 +98,6 @@
     "duplicate-package-checker-webpack-plugin": "^3.0.0",
     "eslint": "^6.8.0",
     "eslint-plugin-html": "^6.0.0",
-    "eslint-plugin-import": "^2.20.1",
     "eslint-plugin-vue": "^6.2.1",
     "expose-loader": "^0.7.5",
     "file-loader": "^5.0.2",
diff --git a/client/yarn.lock b/client/yarn.lock
index 488f2f44eb7f..f3a0dfee897e 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -1615,14 +1615,6 @@ array-flatten@^2.1.0:
   resolved "https://registry.yarnpkg.com/array-flatten/-/array-flatten-2.1.1.tgz#426bb9da84090c1838d812c8150af20a8331e296"
   integrity sha1-Qmu52oQJDBg42BLIFQryCoMx4pY=
 
-array-includes@^3.0.3:
-  version "3.1.0"
-  resolved "https://registry.yarnpkg.com/array-includes/-/array-includes-3.1.0.tgz#48a929ef4c6bb1fa6dc4a92c9b023a261b0ca404"
-  integrity sha512-ONOEQoKrvXPKk7Su92Co0YMqYO32FfqJTzkKU9u2UpIXyYZIzLSvpdg4AwvSw4mSUW0czu6inK+zby6Oj6gDjQ==
-  dependencies:
-    define-properties "^1.1.3"
-    es-abstract "^1.17.0-next.0"
-
 array-initial@^1.0.0:
   version "1.1.0"
   resolved "https://registry.yarnpkg.com/array-initial/-/array-initial-1.1.0.tgz#2fa74b26739371c3947bd7a7adc73be334b3d795"
@@ -1689,14 +1681,6 @@ array-unique@^0.3.2:
   resolved "https://registry.yarnpkg.com/array-unique/-/array-unique-0.3.2.tgz#a894b75d4bc4f6cd679ef3244a9fd8f46ae2d428"
   integrity sha1-qJS3XUvE9s1nnvMkSp/Y9Gri1Cg=
 
-array.prototype.flat@^1.2.1:
-  version "1.2.3"
-  resolved "https://registry.yarnpkg.com/array.prototype.flat/-/array.prototype.flat-1.2.3.tgz#0de82b426b0318dbfdb940089e38b043d37f6c7b"
-  integrity sha512-gBlRZV0VSmfPIeWfuuy56XZMvbVfbEUnOXUvt3F/eUUUSyzlgLxhEX4YAEpxNAogRGehPSnfXyPtYyKAhkzQhQ==
-  dependencies:
-    define-properties "^1.1.3"
-    es-abstract "^1.17.0-next.1"
-
 arraybuffer.slice@~0.0.7:
   version "0.0.7"
   resolved "https://registry.yarnpkg.com/arraybuffer.slice/-/arraybuffer.slice-0.0.7.tgz#3bbc4275dd584cc1b10809b89d4e8b63a69e7675"
@@ -4108,11 +4092,6 @@ constants-browserify@^1.0.0:
   resolved "https://registry.yarnpkg.com/constants-browserify/-/constants-browserify-1.0.0.tgz#c20b96d8c617748aaf1c16021760cd27fcb8cb75"
   integrity sha1-wguW2MYXdIqvHBYCF2DNJ/y4y3U=
 
-contains-path@^0.1.0:
-  version "0.1.0"
-  resolved "https://registry.yarnpkg.com/contains-path/-/contains-path-0.1.0.tgz#fe8cf184ff6670b6baef01a9d4861a5cbec4120a"
-  integrity sha1-/ozxhP9mcLa67wGp1IYaXL7EEgo=
-
 content-disposition@0.5.2:
   version "0.5.2"
   resolved "https://registry.yarnpkg.com/content-disposition/-/content-disposition-0.5.2.tgz#0cf68bb9ddf5f2be7961c3a85178cb85dba78cb4"
@@ -4673,7 +4652,7 @@ defaults@^1.0.3:
   dependencies:
     clone "^1.0.2"
 
-define-properties@^1.1.2, define-properties@^1.1.3:
+define-properties@^1.1.2:
   version "1.1.3"
   resolved "https://registry.yarnpkg.com/define-properties/-/define-properties-1.1.3.tgz#cf88da6cbee26fe6db7094f61d870cbd84cee9f1"
   integrity sha512-3MqfYKj2lLzdMSf8ZIZE/V+Zuy+BgD6f164e8K2w7dgnpKArBDerGYpM46IYYcjnkdPNMjPk9A6VFB8+3SKlXQ==
@@ -4868,14 +4847,6 @@ dns-txt@^2.0.2:
   dependencies:
     buffer-indexof "^1.0.0"
 
-doctrine@1.5.0:
-  version "1.5.0"
-  resolved "https://registry.yarnpkg.com/doctrine/-/doctrine-1.5.0.tgz#379dce730f6166f76cefa4e6707a159b02c5a6fa"
-  integrity sha1-N53Ocw9hZvds76TmcHoVmwLFpvo=
-  dependencies:
-    esutils "^2.0.2"
-    isarray "^1.0.0"
-
 doctrine@^2.0.0, doctrine@^2.1.0:
   version "2.1.0"
   resolved "https://registry.yarnpkg.com/doctrine/-/doctrine-2.1.0.tgz#5cd01fc101621b42c4cd7f5d1a66243716d3f39d"
@@ -5163,7 +5134,12 @@ ent@~2.2.0:
   resolved "https://registry.yarnpkg.com/ent/-/ent-2.2.0.tgz#e964219325a21d05f44466a2f686ed6ce5f5dd1d"
   integrity sha1-6WQhkyWiHQX0RGai9obtbOX13R0=
 
-entities@^1.1.1, entities@~1.1.1:
+entities@^1.1.1:
+  version "1.1.2"
+  resolved "https://registry.yarnpkg.com/entities/-/entities-1.1.2.tgz#bdfa735299664dfafd34529ed4f8522a275fea56"
+  integrity sha512-f2LZMYl1Fzu7YSBKg+RoROelpOaNrcGmE9AZubeDfrCEia483oW4MI4VyFd5VNHIgQ/7qm1I0wUHK1eJnn2y2w==
+
+entities@~1.1.1:
   version "1.1.1"
   resolved "https://registry.yarnpkg.com/entities/-/entities-1.1.1.tgz#6e5c2d0a5621b5dadaecef80b90edfb5cd7772f0"
   integrity sha1-blwtClYhtdra7O+AuQ7ftc13cvA=
@@ -5182,23 +5158,6 @@ error-ex@^1.2.0, error-ex@^1.3.1:
   dependencies:
     is-arrayish "^0.2.1"
 
-es-abstract@^1.17.0-next.0, es-abstract@^1.17.0-next.1:
-  version "1.17.0-next.1"
-  resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.17.0-next.1.tgz#94acc93e20b05a6e96dacb5ab2f1cb3a81fc2172"
-  integrity sha512-7MmGr03N7Rnuid6+wyhD9sHNE2n4tFSwExnU2lQl3lIo2ShXWGePY80zYaoMOmILWv57H0amMjZGHNzzGG70Rw==
-  dependencies:
-    es-to-primitive "^1.2.1"
-    function-bind "^1.1.1"
-    has "^1.0.3"
-    has-symbols "^1.0.1"
-    is-callable "^1.1.4"
-    is-regex "^1.0.4"
-    object-inspect "^1.7.0"
-    object-keys "^1.1.1"
-    object.assign "^4.1.0"
-    string.prototype.trimleft "^2.1.0"
-    string.prototype.trimright "^2.1.0"
-
 es-abstract@^1.5.1, es-abstract@^1.6.1:
   version "1.12.0"
   resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.12.0.tgz#9dbbdd27c6856f0001421ca18782d786bf8a6165"
@@ -5219,15 +5178,6 @@ es-to-primitive@^1.1.1:
     is-date-object "^1.0.1"
     is-symbol "^1.0.2"
 
-es-to-primitive@^1.2.1:
-  version "1.2.1"
-  resolved "https://registry.yarnpkg.com/es-to-primitive/-/es-to-primitive-1.2.1.tgz#e55cd4c9cdc188bcefb03b366c736323fc5c898a"
-  integrity sha512-QCOllgZJtaUo9miYBcLChTUaHNjJF3PYs1VidD7AwiEj1kYxKeQTctLAezAOH5ZKRH0g2IgPn6KwB4IT8iRpvA==
-  dependencies:
-    is-callable "^1.1.4"
-    is-date-object "^1.0.1"
-    is-symbol "^1.0.2"
-
 es5-ext@^0.10.14, es5-ext@^0.10.35, es5-ext@^0.10.9, es5-ext@~0.10.14:
   version "0.10.46"
   resolved "https://registry.yarnpkg.com/es5-ext/-/es5-ext-0.10.46.tgz#efd99f67c5a7ec789baa3daa7f79870388f7f572"
@@ -5301,22 +5251,6 @@ escodegen@^1.11.1:
   optionalDependencies:
     source-map "~0.6.1"
 
-eslint-import-resolver-node@^0.3.2:
-  version "0.3.2"
-  resolved "https://registry.yarnpkg.com/eslint-import-resolver-node/-/eslint-import-resolver-node-0.3.2.tgz#58f15fb839b8d0576ca980413476aab2472db66a"
-  integrity sha512-sfmTqJfPSizWu4aymbPr4Iidp5yKm8yDkHp+Ir3YiTHiiDfxh69mOUsmiqW6RZ9zRXFaF64GtYmN7e+8GHBv6Q==
-  dependencies:
-    debug "^2.6.9"
-    resolve "^1.5.0"
-
-eslint-module-utils@^2.4.1:
-  version "2.5.0"
-  resolved "https://registry.yarnpkg.com/eslint-module-utils/-/eslint-module-utils-2.5.0.tgz#cdf0b40d623032274ccd2abd7e64c4e524d6e19c"
-  integrity sha512-kCo8pZaNz2dsAW7nCUjuVoI11EBXXpIzfNxmaoLhXoRDOnqXLC4iSGVRdZPhOitfbdEfMEfKOiENaK6wDPZEGw==
-  dependencies:
-    debug "^2.6.9"
-    pkg-dir "^2.0.0"
-
 eslint-plugin-html@^6.0.0:
   version "6.0.0"
   resolved "https://registry.yarnpkg.com/eslint-plugin-html/-/eslint-plugin-html-6.0.0.tgz#28e5c3e71e6f612e07e73d7c215e469766628c13"
@@ -5324,24 +5258,6 @@ eslint-plugin-html@^6.0.0:
   dependencies:
     htmlparser2 "^3.10.1"
 
-eslint-plugin-import@^2.20.1:
-  version "2.20.1"
-  resolved "https://registry.yarnpkg.com/eslint-plugin-import/-/eslint-plugin-import-2.20.1.tgz#802423196dcb11d9ce8435a5fc02a6d3b46939b3"
-  integrity sha512-qQHgFOTjguR+LnYRoToeZWT62XM55MBVXObHM6SKFd1VzDcX/vqT1kAz8ssqigh5eMj8qXcRoXXGZpPP6RfdCw==
-  dependencies:
-    array-includes "^3.0.3"
-    array.prototype.flat "^1.2.1"
-    contains-path "^0.1.0"
-    debug "^2.6.9"
-    doctrine "1.5.0"
-    eslint-import-resolver-node "^0.3.2"
-    eslint-module-utils "^2.4.1"
-    has "^1.0.3"
-    minimatch "^3.0.4"
-    object.values "^1.1.0"
-    read-pkg-up "^2.0.0"
-    resolve "^1.12.0"
-
 eslint-plugin-vue@^6.2.1:
   version "6.2.1"
   resolved "https://registry.yarnpkg.com/eslint-plugin-vue/-/eslint-plugin-vue-6.2.1.tgz#ca802df5c33146aed1e56bb21d250c1abb6120a3"
@@ -6011,7 +5927,7 @@ find-up@^1.0.0:
     path-exists "^2.0.0"
     pinkie-promise "^2.0.0"
 
-find-up@^2.0.0, find-up@^2.1.0:
+find-up@^2.1.0:
   version "2.1.0"
   resolved "https://registry.yarnpkg.com/find-up/-/find-up-2.1.0.tgz#45d1b7e506c717ddd482775a2b77920a3c0c57a7"
   integrity sha1-RdG35QbHF93UgndaK3eSCjwMV6c=
@@ -6788,11 +6704,6 @@ has-symbols@^1.0.0:
   resolved "https://registry.yarnpkg.com/has-symbols/-/has-symbols-1.0.0.tgz#ba1a8f1af2a0fc39650f5c850367704122063b44"
   integrity sha1-uhqPGvKg/DllD1yFA2dwQSIGO0Q=
 
-has-symbols@^1.0.1:
-  version "1.0.1"
-  resolved "https://registry.yarnpkg.com/has-symbols/-/has-symbols-1.0.1.tgz#9f5214758a44196c406d9bd76cebf81ec2dd31e8"
-  integrity sha512-PLcsoqu++dmEIZB+6totNFKq/7Do+Z0u4oT0zKOJNl3lYK6vGwwu2hjHs+68OEZbTjiUE9bgOABXbP/GvrS0Kg==
-
 has-unicode@^2.0.0:
   version "2.0.1"
   resolved "https://registry.yarnpkg.com/has-unicode/-/has-unicode-2.0.1.tgz#e0e6fe6a28cf51138855e086d1691e771de2a8b9"
@@ -6829,7 +6740,7 @@ has-values@^1.0.0:
     is-number "^3.0.0"
     kind-of "^4.0.0"
 
-has@^1.0.0, has@^1.0.1, has@^1.0.3:
+has@^1.0.0, has@^1.0.1:
   version "1.0.3"
   resolved "https://registry.yarnpkg.com/has/-/has-1.0.3.tgz#722d7cbfc1f6aa8241f16dd814e011e1f41e8796"
   integrity sha512-f2dvO0VU6Oej7RkWJGrehjbzMAjFp5/VKPp5tTpWIV4JHHZK1/BxbFRtf/siA2SWTe09caDmVtYYzWEIbBS4zw==
@@ -8449,16 +8360,6 @@ load-json-file@^1.0.0, load-json-file@^1.1.0:
     pinkie-promise "^2.0.0"
     strip-bom "^2.0.0"
 
-load-json-file@^2.0.0:
-  version "2.0.0"
-  resolved "https://registry.yarnpkg.com/load-json-file/-/load-json-file-2.0.0.tgz#7947e42149af80d696cbf797bcaabcfe1fe29ca8"
-  integrity sha1-eUfkIUmvgNaWy/eXvKq8/h/inKg=
-  dependencies:
-    graceful-fs "^4.1.2"
-    parse-json "^2.2.0"
-    pify "^2.0.0"
-    strip-bom "^3.0.0"
-
 loader-runner@^2.3.0:
   version "2.3.1"
   resolved "https://registry.yarnpkg.com/loader-runner/-/loader-runner-2.3.1.tgz#026f12fe7c3115992896ac02ba022ba92971b979"
@@ -9605,11 +9506,6 @@ object-copy@^0.1.0:
     define-property "^0.2.5"
     kind-of "^3.0.3"
 
-object-inspect@^1.7.0:
-  version "1.7.0"
-  resolved "https://registry.yarnpkg.com/object-inspect/-/object-inspect-1.7.0.tgz#f4f6bd181ad77f006b5ece60bd0b6f398ff74a67"
-  integrity sha512-a7pEHdh1xKIAgTySUGgLMx/xwDZskN1Ud6egYYN3EdRW4ZMPNEDUTF+hwy2LUC+Bl+SyLXANnwz/jyh/qutKUw==
-
 object-keys@^1.0.11:
   version "1.1.0"
   resolved "https://registry.yarnpkg.com/object-keys/-/object-keys-1.1.0.tgz#11bd22348dd2e096a045ab06f6c85bcc340fa032"
@@ -9620,11 +9516,6 @@ object-keys@^1.0.12:
   resolved "https://registry.yarnpkg.com/object-keys/-/object-keys-1.0.12.tgz#09c53855377575310cca62f55bb334abff7b3ed2"
   integrity sha512-FTMyFUm2wBcGHnH2eXmz7tC6IwlqQZ6mVZ+6dm6vZ4IQIHjs6FdNsQBuKGPuUUUY6NfJw2PshC08Tn6LzLDOag==
 
-object-keys@^1.1.1:
-  version "1.1.1"
-  resolved "https://registry.yarnpkg.com/object-keys/-/object-keys-1.1.1.tgz#1c47f272df277f3b1daf061677d9c82e2322c60e"
-  integrity sha512-NuAESUOUMrlIXOfHKzD6bpPu3tYt3xvjNdRIQ+FeT0lNb4K8WR70CaDxhuNguS2XG+GjkyMwOzsN5ZktImfhLA==
-
 object-visit@^1.0.0:
   version "1.0.1"
   resolved "https://registry.yarnpkg.com/object-visit/-/object-visit-1.0.1.tgz#f79c4493af0c5377b59fe39d395e41042dd045bb"
@@ -9701,16 +9592,6 @@ object.values@^1.0.4:
     function-bind "^1.1.0"
     has "^1.0.1"
 
-object.values@^1.1.0:
-  version "1.1.1"
-  resolved "https://registry.yarnpkg.com/object.values/-/object.values-1.1.1.tgz#68a99ecde356b7e9295a3c5e0ce31dc8c953de5e"
-  integrity sha512-WTa54g2K8iu0kmS/us18jEmdv1a4Wi//BZ/DTVYEcH0XhLM5NYdpDHja3gt57VrZLcNAO2WGA+KpWsDBaHt6eA==
-  dependencies:
-    define-properties "^1.1.3"
-    es-abstract "^1.17.0-next.1"
-    function-bind "^1.1.1"
-    has "^1.0.3"
-
 observable-to-promise@^0.4.0:
   version "0.4.0"
   resolved "https://registry.yarnpkg.com/observable-to-promise/-/observable-to-promise-0.4.0.tgz#28afe71645308f2d41d71f47ad3fece1a377e52b"
@@ -10220,13 +10101,6 @@ path-type@^1.0.0:
     pify "^2.0.0"
     pinkie-promise "^2.0.0"
 
-path-type@^2.0.0:
-  version "2.0.0"
-  resolved "https://registry.yarnpkg.com/path-type/-/path-type-2.0.0.tgz#f012ccb8415b7096fc2daa1054c3d72389594c73"
-  integrity sha1-8BLMuEFbcJb8LaoQVMPXI4lZTHM=
-  dependencies:
-    pify "^2.0.0"
-
 path-type@^3.0.0:
   version "3.0.0"
   resolved "https://registry.yarnpkg.com/path-type/-/path-type-3.0.0.tgz#cef31dc8e0a1a3bb0d105c0cd97cf3bf47f4e36f"
@@ -11631,14 +11505,6 @@ read-pkg-up@^1.0.1:
     find-up "^1.0.0"
     read-pkg "^1.0.0"
 
-read-pkg-up@^2.0.0:
-  version "2.0.0"
-  resolved "https://registry.yarnpkg.com/read-pkg-up/-/read-pkg-up-2.0.0.tgz#6b72a8048984e0c41e79510fd5e9fa99b3b549be"
-  integrity sha1-a3KoBImE4MQeeVEP1en6mbO1Sb4=
-  dependencies:
-    find-up "^2.0.0"
-    read-pkg "^2.0.0"
-
 read-pkg@^1.0.0:
   version "1.1.0"
   resolved "https://registry.yarnpkg.com/read-pkg/-/read-pkg-1.1.0.tgz#f5ffaa5ecd29cb31c0474bca7d756b6bb29e3f28"
@@ -11648,15 +11514,6 @@ read-pkg@^1.0.0:
     normalize-package-data "^2.3.2"
     path-type "^1.0.0"
 
-read-pkg@^2.0.0:
-  version "2.0.0"
-  resolved "https://registry.yarnpkg.com/read-pkg/-/read-pkg-2.0.0.tgz#8ef1c0623c6a6db0dc6713c4bfac46332b2368f8"
-  integrity sha1-jvHAYjxqbbDcZxPEv6xGMysjaPg=
-  dependencies:
-    load-json-file "^2.0.0"
-    normalize-package-data "^2.3.2"
-    path-type "^2.0.0"
-
 "readable-stream@1 || 2", readable-stream@^2.0.0, readable-stream@^2.0.1, readable-stream@^2.0.2, readable-stream@^2.0.4, readable-stream@^2.0.5, readable-stream@^2.0.6, readable-stream@^2.1.5, readable-stream@^2.2.2, readable-stream@^2.3.3, readable-stream@^2.3.5, readable-stream@^2.3.6, readable-stream@~2.3.6:
   version "2.3.6"
   resolved "https://registry.yarnpkg.com/readable-stream/-/readable-stream-2.3.6.tgz#b11c27d88b8ff1fbe070643cf94b0c79ae1b0aaf"
@@ -11680,9 +11537,9 @@ readable-stream@^3.0.6:
     util-deprecate "^1.0.1"
 
 readable-stream@^3.1.1:
-  version "3.4.0"
-  resolved "https://registry.yarnpkg.com/readable-stream/-/readable-stream-3.4.0.tgz#a51c26754658e0a3c21dbf59163bd45ba6f447fc"
-  integrity sha512-jItXPLmrSR8jmTRmRWJXCnGJsfy85mB3Wd/uINMXA65yrnFo0cPClFIUWzo2najVNSl+mx7/4W8ttlLWJe99pQ==
+  version "3.6.0"
+  resolved "https://registry.yarnpkg.com/readable-stream/-/readable-stream-3.6.0.tgz#337bbda3adc0706bd3e024426a286d4b4b2c9198"
+  integrity sha512-BViHy7LKeTz4oNnkcLJ+lVSL6vpiFeX6/d3oSH8zCW7UxP2onchk+vTGB143xuFjHS3deTgkKoXXymXqymiIdA==
   dependencies:
     inherits "^2.0.3"
     string_decoder "^1.1.1"
@@ -12169,13 +12026,6 @@ resolve@^1.4.0:
   dependencies:
     path-parse "^1.0.6"
 
-resolve@^1.5.0:
-  version "1.13.1"
-  resolved "https://registry.yarnpkg.com/resolve/-/resolve-1.13.1.tgz#be0aa4c06acd53083505abb35f4d66932ab35d16"
-  integrity sha512-CxqObCX8K8YtAhOBRg+lrcdn+LK+WYOS8tSjqSFbjtrI5PnS63QPhZl4+yKfrU9tdsbMu9Anr/amegT87M9Z6w==
-  dependencies:
-    path-parse "^1.0.6"
-
 restore-cursor@^1.0.1:
   version "1.0.1"
   resolved "https://registry.yarnpkg.com/restore-cursor/-/restore-cursor-1.0.1.tgz#34661f46886327fed2991479152252df92daa541"
@@ -13146,22 +12996,6 @@ string-width@^4.1.0:
     is-fullwidth-code-point "^3.0.0"
     strip-ansi "^6.0.0"
 
-string.prototype.trimleft@^2.1.0:
-  version "2.1.0"
-  resolved "https://registry.yarnpkg.com/string.prototype.trimleft/-/string.prototype.trimleft-2.1.0.tgz#6cc47f0d7eb8d62b0f3701611715a3954591d634"
-  integrity sha512-FJ6b7EgdKxxbDxc79cOlok6Afd++TTs5szo+zJTUyow3ycrRfJVE2pq3vcN53XexvKZu/DJMDfeI/qMiZTrjTw==
-  dependencies:
-    define-properties "^1.1.3"
-    function-bind "^1.1.1"
-
-string.prototype.trimright@^2.1.0:
-  version "2.1.0"
-  resolved "https://registry.yarnpkg.com/string.prototype.trimright/-/string.prototype.trimright-2.1.0.tgz#669d164be9df9b6f7559fa8e89945b168a5a6c58"
-  integrity sha512-fXZTSV55dNBwv16uw+hh5jkghxSnc5oHq+5K/gXgizHwAvMetdAJlHqqoFC1FSDVPYWLkAKl2cxpUT41sV7nSg==
-  dependencies:
-    define-properties "^1.1.3"
-    function-bind "^1.1.1"
-
 string_decoder@^1.0.0, string_decoder@~1.1.1:
   version "1.1.1"
   resolved "https://registry.yarnpkg.com/string_decoder/-/string_decoder-1.1.1.tgz#9cf1611ba62685d7030ae9e4ba34149c3af03fc8"
@@ -13258,11 +13092,6 @@ strip-bom@^2.0.0:
   dependencies:
     is-utf8 "^0.2.0"
 
-strip-bom@^3.0.0:
-  version "3.0.0"
-  resolved "https://registry.yarnpkg.com/strip-bom/-/strip-bom-3.0.0.tgz#2334c18e9c759f7bdd56fdef7e9ae3d588e68ed3"
-  integrity sha1-IzTBjpx1n3vdVv3vfprj1YjmjtM=
-
 strip-eof@^1.0.0:
   version "1.0.0"
   resolved "https://registry.yarnpkg.com/strip-eof/-/strip-eof-1.0.0.tgz#bb43ff5598a6eb05d89b59fcd129c983313606bf"

From c5fba2b66a74ec4cbb6a36ad40c8e3fcf1bd029f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 3 Mar 2020 10:31:36 -0500
Subject: [PATCH 319/853] Drop (loaded but unused) eslint-plugin-html

---
 client/.eslintrc.js |  1 -
 client/package.json |  1 -
 client/yarn.lock    | 47 +--------------------------------------------
 3 files changed, 1 insertion(+), 48 deletions(-)

diff --git a/client/.eslintrc.js b/client/.eslintrc.js
index 1392624c1b3b..cec6fe2aa21c 100644
--- a/client/.eslintrc.js
+++ b/client/.eslintrc.js
@@ -15,7 +15,6 @@ module.exports = {
         parser: "babel-eslint",
         sourceType: "module"
     },
-    plugins: ["html"],
     rules: {
         // Standard rules
         "no-console": "off",
diff --git a/client/package.json b/client/package.json
index cf0e9425c691..11b40d63bd09 100644
--- a/client/package.json
+++ b/client/package.json
@@ -97,7 +97,6 @@
     "del": "^5.1.0",
     "duplicate-package-checker-webpack-plugin": "^3.0.0",
     "eslint": "^6.8.0",
-    "eslint-plugin-html": "^6.0.0",
     "eslint-plugin-vue": "^6.2.1",
     "expose-loader": "^0.7.5",
     "file-loader": "^5.0.2",
diff --git a/client/yarn.lock b/client/yarn.lock
index f3a0dfee897e..84da73abfb14 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -4899,24 +4899,12 @@ domelementtype@1:
   resolved "https://registry.yarnpkg.com/domelementtype/-/domelementtype-1.3.0.tgz#b17aed82e8ab59e52dd9c19b1756e0fc187204c2"
   integrity sha1-sXrtguirWeUt2cGbF1bg/BhyBMI=
 
-domelementtype@^1.3.1:
-  version "1.3.1"
-  resolved "https://registry.yarnpkg.com/domelementtype/-/domelementtype-1.3.1.tgz#d048c44b37b0d10a7f2a3d5fee3f4333d790481f"
-  integrity sha512-BSKB+TSpMpFI/HOxCNr1O8aMOTZ8hT3pM3GQ0w/mWRmkhEDSFJkkyzz4XQsBV44BChwGkrDfMyjVD0eA2aFV3w==
-
 domelementtype@~1.1.1:
   version "1.1.3"
   resolved "https://registry.yarnpkg.com/domelementtype/-/domelementtype-1.1.3.tgz#bd28773e2642881aec51544924299c5cd822185b"
   integrity sha1-vSh3PiZCiBrsUVRJJCmcXNgiGFs=
 
-domhandler@^2.3.0:
-  version "2.4.2"
-  resolved "https://registry.yarnpkg.com/domhandler/-/domhandler-2.4.2.tgz#8805097e933d65e85546f726d60f5eb88b44f803"
-  integrity sha512-JiK04h0Ht5u/80fdLMCEmV4zkNh2BcoMFBmZ/91WtYZ8qVXSKjiw7fXMgFPnHcSZgOo3XdinHvmnDUeMf5R4wA==
-  dependencies:
-    domelementtype "1"
-
-domutils@^1.5.1, domutils@^1.7.0:
+domutils@^1.7.0:
   version "1.7.0"
   resolved "https://registry.yarnpkg.com/domutils/-/domutils-1.7.0.tgz#56ea341e834e06e6748af7a1cb25da67ea9f8c2a"
   integrity sha512-Lgd2XcJ/NjEw+7tFvfKxOzCYKZsdct5lczQ2ZaQY8Djz7pfAD3Gbp8ySJWtreII/vDlMVmxwa6pHmdxIYgttDg==
@@ -5134,11 +5122,6 @@ ent@~2.2.0:
   resolved "https://registry.yarnpkg.com/ent/-/ent-2.2.0.tgz#e964219325a21d05f44466a2f686ed6ce5f5dd1d"
   integrity sha1-6WQhkyWiHQX0RGai9obtbOX13R0=
 
-entities@^1.1.1:
-  version "1.1.2"
-  resolved "https://registry.yarnpkg.com/entities/-/entities-1.1.2.tgz#bdfa735299664dfafd34529ed4f8522a275fea56"
-  integrity sha512-f2LZMYl1Fzu7YSBKg+RoROelpOaNrcGmE9AZubeDfrCEia483oW4MI4VyFd5VNHIgQ/7qm1I0wUHK1eJnn2y2w==
-
 entities@~1.1.1:
   version "1.1.1"
   resolved "https://registry.yarnpkg.com/entities/-/entities-1.1.1.tgz#6e5c2d0a5621b5dadaecef80b90edfb5cd7772f0"
@@ -5251,13 +5234,6 @@ escodegen@^1.11.1:
   optionalDependencies:
     source-map "~0.6.1"
 
-eslint-plugin-html@^6.0.0:
-  version "6.0.0"
-  resolved "https://registry.yarnpkg.com/eslint-plugin-html/-/eslint-plugin-html-6.0.0.tgz#28e5c3e71e6f612e07e73d7c215e469766628c13"
-  integrity sha512-PQcGippOHS+HTbQCStmH5MY1BF2MaU8qW/+Mvo/8xTa/ioeMXdSP+IiaBw2+nh0KEMfYQKuTz1Zo+vHynjwhbg==
-  dependencies:
-    htmlparser2 "^3.10.1"
-
 eslint-plugin-vue@^6.2.1:
   version "6.2.1"
   resolved "https://registry.yarnpkg.com/eslint-plugin-vue/-/eslint-plugin-vue-6.2.1.tgz#ca802df5c33146aed1e56bb21d250c1abb6120a3"
@@ -6850,18 +6826,6 @@ html-entities@^1.2.0, html-entities@^1.2.1:
   resolved "https://registry.yarnpkg.com/html-entities/-/html-entities-1.2.1.tgz#0df29351f0721163515dfb9e5543e5f6eed5162f"
   integrity sha1-DfKTUfByEWNRXfueVUPl9u7VFi8=
 
-htmlparser2@^3.10.1:
-  version "3.10.1"
-  resolved "https://registry.yarnpkg.com/htmlparser2/-/htmlparser2-3.10.1.tgz#bd679dc3f59897b6a34bb10749c855bb53a9392f"
-  integrity sha512-IgieNijUMbkDovyoKObU1DUhm1iwNYE/fuifEoEHfd1oZKZDaONBSkal7Y01shxsM49R4XaMdGez3WnF9UfiCQ==
-  dependencies:
-    domelementtype "^1.3.1"
-    domhandler "^2.3.0"
-    domutils "^1.5.1"
-    entities "^1.1.1"
-    inherits "^2.0.1"
-    readable-stream "^3.1.1"
-
 http-deceiver@^1.2.7:
   version "1.2.7"
   resolved "https://registry.yarnpkg.com/http-deceiver/-/http-deceiver-1.2.7.tgz#fa7168944ab9a519d337cb0bec7284dc3e723d87"
@@ -11536,15 +11500,6 @@ readable-stream@^3.0.6:
     string_decoder "^1.1.1"
     util-deprecate "^1.0.1"
 
-readable-stream@^3.1.1:
-  version "3.6.0"
-  resolved "https://registry.yarnpkg.com/readable-stream/-/readable-stream-3.6.0.tgz#337bbda3adc0706bd3e024426a286d4b4b2c9198"
-  integrity sha512-BViHy7LKeTz4oNnkcLJ+lVSL6vpiFeX6/d3oSH8zCW7UxP2onchk+vTGB143xuFjHS3deTgkKoXXymXqymiIdA==
-  dependencies:
-    inherits "^2.0.3"
-    string_decoder "^1.1.1"
-    util-deprecate "^1.0.1"
-
 readdirp@^2.0.0, readdirp@^2.2.1:
   version "2.2.1"
   resolved "https://registry.yarnpkg.com/readdirp/-/readdirp-2.2.1.tgz#0e87622a3325aa33e892285caf8b4e846529a525"

From 98d6229b880173992750c159a59aa7def0aee307 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 3 Mar 2020 10:34:43 -0500
Subject: [PATCH 320/853] Swap three rules we do want to work towards to 'warn'
 instead of 'off'

---
 client/.eslintrc.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/.eslintrc.js b/client/.eslintrc.js
index cec6fe2aa21c..392057590fdb 100644
--- a/client/.eslintrc.js
+++ b/client/.eslintrc.js
@@ -25,9 +25,9 @@ module.exports = {
         "vue/v-slot-style": ["error", {"atComponent": "v-slot", "default": "v-slot", "named": "longform"}],
 
         // Vue TODO (enable these)
-        "vue/require-default-prop": "off",
-        "vue/require-prop-types": "off",
-        "vue/prop-name-casing": "off",
+        "vue/require-default-prop": "warn",
+        "vue/require-prop-types": "warn",
+        "vue/prop-name-casing": "warn",
 
         // Prettier compromises/workarounds -- mostly #wontfix?
         "vue/html-indent": "off",

From 09bfa57ab93657a08ed2035e2f8b6f0c5f334444 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Tue, 3 Mar 2020 17:26:02 +0100
Subject: [PATCH 321/853] rebuild

---
 doc/source/admin/galaxy_options.rst         | 15 +++++++++++++--
 lib/galaxy/config/sample/galaxy.yml.sample  |  6 +++++-
 lib/galaxy/webapps/galaxy/config_schema.yml | 11 +++++++++--
 3 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index ac2f2193d4bc..10beabbb6ff8 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -3271,6 +3271,17 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``job_metrics_config_file``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    XML config file that contains the job metric collection
+    configuration.
+:Default: ``config/job_metrics_conf.xml``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``expose_potentially_sensitive_job_metrics``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -3673,7 +3684,7 @@
 
 :Description:
     CSS file to apply to "Galaxy Page" exports to PDF. Generally
-    prefer  markdown_export_css, but this is here for deployments that
+    prefer markdown_export_css, but this is here for deployments that
     would like to tailor different kinds of exports.
 :Default: ``markdown_export_pages.css``
 :Type: str
@@ -3685,7 +3696,7 @@
 
 :Description:
     CSS file to apply to invocation report exports to PDF. Generally
-    prefer  markdown_export_css, but this is here for deployments that
+    prefer markdown_export_css, but this is here for deployments that
     would like to tailor different kinds of exports.
 :Default: ``markdown_export_invocation_reports.css``
 :Type: str
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index d83688671589..19721ae13b9c 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1611,6 +1611,10 @@ galaxy:
   # see dataset paths.
   #expose_dataset_path: false
 
+  # XML config file that contains the job metric collection
+  # configuration.
+  #job_metrics_config_file: config/job_metrics_conf.xml
+
   # This option allows users to see the job metrics (except for
   # environment variables).
   #expose_potentially_sensitive_job_metrics: false
@@ -1815,7 +1819,7 @@ galaxy:
   #markdown_export_css_pages: markdown_export_pages.css
 
   # CSS file to apply to invocation report exports to PDF. Generally
-  # prefer  markdown_export_css, but this is here for deployments that
+  # prefer markdown_export_css, but this is here for deployments that
   # would like to tailor different kinds of exports.
   #markdown_export_css_invocation_reports: markdown_export_invocation_reports.css
 
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 692a0e4a3b46..72db2811e085 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2417,6 +2417,13 @@ mapping:
           Details" option in the history. This option also exposes the command line to
           non-administrative users. Administrators can always see dataset paths.
 
+      job_metrics_config_file:
+        type: str
+        default: config/job_metrics_conf.xml
+        required: false
+        desc: |
+          XML config file that contains the job metric collection configuration.
+
       expose_potentially_sensitive_job_metrics:
         type: bool
         default: false
@@ -2728,7 +2735,7 @@ mapping:
         default: markdown_export_pages.css
         required: false
         desc: |
-          CSS file to apply to "Galaxy Page" exports to PDF. Generally prefer 
+          CSS file to apply to "Galaxy Page" exports to PDF. Generally prefer
           markdown_export_css, but this is here for deployments that
           would like to tailor different kinds of exports.
 
@@ -2737,7 +2744,7 @@ mapping:
         default: markdown_export_invocation_reports.css
         required: false
         desc: |
-          CSS file to apply to invocation report exports to PDF. Generally prefer 
+          CSS file to apply to invocation report exports to PDF. Generally prefer
           markdown_export_css, but this is here for deployments that
           would like to tailor different kinds of exports.
 

From 494c15cb9d622c3c75bbcf72b880ee386cbe01f5 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Mar 2020 18:31:06 +0100
Subject: [PATCH 322/853] Be more explcit about starting cache monitor thread

---
 lib/galaxy/objectstore/s3.py | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index 30d5f1100e14..c6049441a03d 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -123,9 +123,10 @@ def _config_to_dict(self):
                 'conn_path': self.conn_path,
             },
             'cache': {
-                'size': -1,  # disable cache cleaning when starting an exported object store in set_metadata.py
+                'size': self.cache_size,
                 'path': self.staging_path,
-            }
+            },
+            'enable_cache_monitor': False,
         }
 
 
@@ -146,6 +147,7 @@ def __init__(self, config, config_dict):
         bucket_dict = config_dict['bucket']
         connection_dict = config_dict.get('connection', {})
         cache_dict = config_dict['cache']
+        self.enable_cache_monitor = config_dict.get('enable_cache_monitor', True)
 
         self.access_key = auth_dict.get('access_key')
         self.secret_key = auth_dict.get('secret_key')
@@ -190,8 +192,16 @@ def _initialize(self):
 
         self._configure_connection()
         self._bucket = self._get_bucket(self.bucket)
+        self.start_cache_monitor()
+        # Test if 'axel' is available for parallel download and pull the key into cache
+        if which('axel'):
+            self.use_axel = True
+        else:
+            self.use_axel = False
+
+    def start_cache_monitor(self):
         # Clean cache only if value is set in galaxy.ini
-        if self.cache_size != -1:
+        if self.cache_size != -1 and self.enable_cache_monitor:
             # Convert GBs to bytes for comparison
             self.cache_size = self.cache_size * 1073741824
             # Helper for interruptable sleep
@@ -199,11 +209,6 @@ def _initialize(self):
             self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
             self.cache_monitor_thread.start()
             log.info("Cache cleaner manager started")
-        # Test if 'axel' is available for parallel download and pull the key into cache
-        if which('axel'):
-            self.use_axel = True
-        else:
-            self.use_axel = False
 
     def _configure_connection(self):
         log.debug("Configuring S3 Connection")

From 6d2e2ef10bde3812dfe292ae1074b08fd501033d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Mar 2020 18:31:58 +0100
Subject: [PATCH 323/853] Drop redundant store_by attribute

---
 lib/galaxy/objectstore/s3.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index c6049441a03d..9c53c0aed295 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -164,8 +164,6 @@ def __init__(self, config, config_dict):
 
         self.cache_size = cache_dict.get('size', -1)
         self.staging_path = cache_dict.get('path') or self.config.object_store_cache_path
-        self.store_by = config_dict.get("store_by", None) or getattr(config, "object_store_store_by", "id")
-        assert self.store_by in ["id", "uuid"]
 
         extra_dirs = dict(
             (e['type'], e['path']) for e in config_dict.get('extra_dirs', []))

From 3623f226f1474cb233e74bf6ae7e42a71012d300 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Mar 2020 18:32:10 +0100
Subject: [PATCH 324/853] Drop badly formatted logging

---
 lib/galaxy/objectstore/s3.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index 9c53c0aed295..327988be7bed 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -169,9 +169,6 @@ def __init__(self, config, config_dict):
             (e['type'], e['path']) for e in config_dict.get('extra_dirs', []))
         self.extra_dirs.update(extra_dirs)
 
-        log.debug("Object cache dir:    %s", self.staging_path)
-        log.debug("       job work dir: %s", self.extra_dirs['job_work'])
-
         self._initialize()
 
     def _initialize(self):

From 12f8c78e344a948be6bb1b52bd56add610e7a8b9 Mon Sep 17 00:00:00 2001
From: Ralf Weber <RJMW@users.noreply.github.com>
Date: Tue, 3 Mar 2020 21:09:16 +0000
Subject: [PATCH 325/853] Add rdata.xcms.raw for older versions of XCMS

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 8a92bd8e970f..43a5f031d740 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -563,6 +563,7 @@
     <datatype extension="gal" type="galaxy.datatypes.microarrays:Gal" display_in_upload="true"/>
     <datatype extension="rdata" type="galaxy.datatypes.binary:RData" display_in_upload="true" description="Stored data from an R session"/>
     <datatype extension="rdata.sce" type="galaxy.datatypes.binary:RData" description="Stored RDS from a SingleCellObject" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.xcms.raw" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
     <datatype extension="rdata.msnbase.raw" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
     <datatype extension="rdata.xcms.findchrompeaks" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
     <datatype extension="rdata.xcms.group" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />

From 33c963487b7e0d320081773ac6f8dcfe22ac8721 Mon Sep 17 00:00:00 2001
From: Ralf Weber <RJMW@users.noreply.github.com>
Date: Tue, 3 Mar 2020 21:29:15 +0000
Subject: [PATCH 326/853] Add missing mimetype and remove spaces

---
 .../config/sample/datatypes_conf.xml.sample   | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 43a5f031d740..433b799404be 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -561,17 +561,17 @@
     <datatype extension="cel" type="galaxy.datatypes.microarrays:Cel" display_in_upload="true"/>
     <datatype extension="gpr" type="galaxy.datatypes.microarrays:Gpr" display_in_upload="true"/>
     <datatype extension="gal" type="galaxy.datatypes.microarrays:Gal" display_in_upload="true"/>
-    <datatype extension="rdata" type="galaxy.datatypes.binary:RData" display_in_upload="true" description="Stored data from an R session"/>
-    <datatype extension="rdata.sce" type="galaxy.datatypes.binary:RData" description="Stored RDS from a SingleCellObject" subclass="true" display_in_upload="true"/>
-    <datatype extension="rdata.xcms.raw" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
-    <datatype extension="rdata.msnbase.raw" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
-    <datatype extension="rdata.xcms.findchrompeaks" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
-    <datatype extension="rdata.xcms.group" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
-    <datatype extension="rdata.xcms.retcor" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
-    <datatype extension="rdata.xcms.fillpeaks" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
-    <datatype extension="rdata.camera.positive" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
-    <datatype extension="rdata.camera.negative" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
-    <datatype extension="rdata.camera.quick" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" />
+    <datatype extension="rdata" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" display_in_upload="true" description="Stored data from an R session"/>
+    <datatype extension="rdata.sce" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" description="Stored RDS from a SingleCellObject"/>
+    <datatype extension="rdata.xcms.raw" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.msnbase.raw" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.xcms.findchrompeaks" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.xcms.group" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.xcms.retcor" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.xcms.fillpeaks" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.camera.positive" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.camera.negative" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.camera.quick" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
     <datatype extension="rdock_as" type="galaxy.datatypes.binary:Binary" description="rDock active site format" subclass="true" display_in_upload="true"/>
     <datatype extension="oxlicg" type="galaxy.datatypes.binary:OxliCountGraph" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="oxling" type="galaxy.datatypes.binary:OxliNodeGraph" mimetype="application/octet-stream" display_in_upload="true"/>

From ae5e3ea54d10891de362601ac223fa25fb76bd8d Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Wed, 4 Mar 2020 08:57:42 +0100
Subject: [PATCH 327/853] Update lib/galaxy/webapps/galaxy/config_schema.yml

Co-Authored-By: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
---
 lib/galaxy/webapps/galaxy/config_schema.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 72db2811e085..bd62b5d10727 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2419,7 +2419,7 @@ mapping:
 
       job_metrics_config_file:
         type: str
-        default: config/job_metrics_conf.xml
+        default: job_metrics_conf.xml
         required: false
         desc: |
           XML config file that contains the job metric collection configuration.

From 787620dc24fafa4e6b480466f444effa4223131b Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Wed, 4 Mar 2020 08:57:50 +0100
Subject: [PATCH 328/853] Update lib/galaxy/webapps/galaxy/config_schema.yml

Co-Authored-By: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
---
 lib/galaxy/webapps/galaxy/config_schema.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index bd62b5d10727..dc974f0ae1d1 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2423,6 +2423,8 @@ mapping:
         required: false
         desc: |
           XML config file that contains the job metric collection configuration.
+          
+          The value of this option will be resolved with respect to <config_dir>.
 
       expose_potentially_sensitive_job_metrics:
         type: bool

From 97cc7e4370bd5b08a9bccd822be6b673457e392f Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Thu, 20 Feb 2020 18:38:08 +0100
Subject: [PATCH 329/853] Vuefy interactive tools

---
 .../InteractiveTools/InteractiveTools.vue     | 156 ++++++++++++++++++
 .../components/InteractiveTools/services.js   |  32 ++++
 .../scripts/entry/analysis/AnalysisRouter.js  |   8 +-
 lib/galaxy/model/__init__.py                  |   4 +-
 .../galaxy/controllers/interactivetool.py     |  48 +-----
 5 files changed, 193 insertions(+), 55 deletions(-)
 create mode 100644 client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue
 create mode 100644 client/galaxy/scripts/components/InteractiveTools/services.js

diff --git a/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue
new file mode 100644
index 000000000000..df685a17a5e4
--- /dev/null
+++ b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue
@@ -0,0 +1,156 @@
+<template>
+    <div>
+        <b-alert :variant="messageVariant" :show="showMessage">{{ message }}</b-alert>
+        <h2>Active Interactive Tools</h2>
+        <b-row class="mb-3">
+            <b-col cols="6">
+                <b-input
+                    id="workflow-search"
+                    class="m-1"
+                    name="query"
+                    placeholder="Search Interactive Tool"
+                    autocomplete="off"
+                    type="text"
+                    v-model="filter"
+                />
+            </b-col>
+        </b-row>
+        <b-table
+            id="workflow-table"
+            striped
+            :fields="fields"
+            :items="activeInteractiveTools"
+            :filter="filter"
+            @filtered="filtered"
+        >
+            <template v-slot:cell(checkbox)="row">
+                <b-form-checkbox v-model="row.item.marked" />
+            </template>
+            <template v-slot:cell(name)="row">
+                <a :index="row.index" :href="row.item.target" target="_blank" :name="row.item.name">{{
+                    row.item.name
+                }}</a>
+            </template>
+            <template v-slot:cell(job_info)="row">
+                <label v-if="row.item.active">
+                    running
+                </label>
+                <label v-else>
+                    stopped
+                </label>
+            </template>
+            <template v-slot:cell(created_time)="row">
+                <UtcDate :date="row.item.created_time" mode="elapsed" />
+            </template>
+            <template v-slot:cell(last_updated)="row">
+                <UtcDate :date="row.item.modified_time" mode="elapsed" />
+            </template>
+        </b-table>
+        <label v-if="isActiveToolsListEmpty">You do not have active interactive tools yet </label>
+        <div v-if="showNotFound">
+            No matching entries found for: <span class="font-weight-bold">{{ this.filter }}</span
+            >.
+        </div>
+        <b-button
+            v-if="isCheckboxMarked"
+            v-b-tooltip.hover.bottom
+            title="Terminate selected tools"
+            @click.stop="stopInteractiveToolSession()"
+            >Stop
+        </b-button>
+    </div>
+</template>
+
+<script>
+import { Services } from "./services";
+import { getAppRoot } from "onload/loadConfig";
+import UtcDate from "components/UtcDate";
+
+export default {
+    components: {
+        UtcDate
+    },
+    data() {
+        return {
+            error: null,
+            fields: [
+                {
+                    label: "",
+                    key: "checkbox",
+                    sortable: true
+                },
+                {
+                    label: "Name",
+                    key: "name",
+                    sortable: true
+                },
+                {
+                    label: "Job Info",
+                    key: "job_info",
+                    sortable: true
+                },
+                {
+                    label: "Created",
+                    key: "created_time",
+                    sortable: true
+                },
+                {
+                    label: "Last Updated",
+                    key: "last_updated",
+                    sortable: true
+                }
+            ],
+            filter: "",
+            message: null,
+            messageVariant: null,
+            nInteractiveTools: 0,
+            activeInteractiveTools: []
+        };
+    },
+    computed: {
+        showNotFound() {
+            return this.nInteractiveTools === 0 && this.filter && !this.isActiveToolsListEmpty;
+        },
+        isCheckboxMarked() {
+            return this.activeInteractiveTools.some(tool => tool.marked);
+        },
+        isActiveToolsListEmpty() {
+            return this.activeInteractiveTools.length === 0;
+        },
+        showMessage() {
+            return !!this.message;
+        }
+    },
+    created() {
+        this.root = getAppRoot();
+        this.services = new Services({ root: this.root });
+        this.load();
+    },
+    methods: {
+        load() {
+            this.loading = true;
+            this.filter = "";
+            this.services
+                .getActiveInteractiveTools()
+                .then(activeInteractiveTools => {
+                    this.activeInteractiveTools = activeInteractiveTools;
+                })
+                .catch(error => {
+                    this.error = error;
+                });
+        },
+        filtered: function(items) {
+            this.nInteractiveTools = items.length;
+        },
+        stopInteractiveToolSession() {
+            const idsToStop = this.activeInteractiveTools.filter(tool => tool.marked).map(tool => tool.id);
+            this.services.stopInteractiveTool(idsToStop).then(response => {
+                if (response.status === "ok") this.messageVariant = "success";
+                else this.messageVariant = "danger";
+                this.message = response.message;
+                this.activeInteractiveTools = this.activeInteractiveTools.filter(tool => !tool.marked);
+            });
+        }
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/InteractiveTools/services.js b/client/galaxy/scripts/components/InteractiveTools/services.js
new file mode 100644
index 000000000000..556fac68b808
--- /dev/null
+++ b/client/galaxy/scripts/components/InteractiveTools/services.js
@@ -0,0 +1,32 @@
+import axios from "axios";
+import { rethrowSimple } from "utils/simple-error";
+import { getAppRoot } from "onload/loadConfig";
+
+export class Services {
+    constructor(options = {}) {
+        this.root = options.root || getAppRoot();
+    }
+
+    async getActiveInteractiveTools() {
+        const url = `${this.root}api/entry_points?running=true`;
+        try {
+            const response = await axios.get(url);
+            const activeInteractiveTools = response.data;
+            return activeInteractiveTools;
+        } catch (e) {
+            rethrowSimple(e);
+        }
+    }
+
+    async stopInteractiveTool(ids) {
+        const url = `${this.root}interactivetool/list`;
+        const formData = new FormData();
+        formData.append("operation", "stop");
+        ids.forEach(id => formData.append("id", id));
+        const response = await axios.post(url, formData);
+        return response.data;
+    }
+    catch(e) {
+        rethrowSimple(e);
+    }
+}
diff --git a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
index c7bb042d06f3..7b4724cc6859 100644
--- a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
+++ b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
@@ -27,6 +27,7 @@ import GridView from "mvc/grid/grid-view";
 import EntryPointGridView from "mvc/entrypoints/view";
 import GridShared from "mvc/grid/grid-shared";
 import WorkflowImport from "components/Workflow/WorkflowImport.vue";
+import InteractiveTools from "components/InteractiveTools/InteractiveTools.vue";
 import WorkflowList from "components/Workflow/WorkflowList.vue";
 import HistoryImport from "components/HistoryImport.vue";
 import HistoryView from "components/HistoryView.vue";
@@ -126,12 +127,7 @@ export const getAnalysisRouter = Galaxy =>
         },
 
         show_interactivetool_list: function() {
-            this.page.display(
-                new EntryPointGridView({
-                    url_base: `${getAppRoot()}interactivetool/list`,
-                    active_tab: "analysis"
-                })
-            );
+            this._display_vue_helper(InteractiveTools);
         },
 
         show_cloud_auth: function() {
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index c97363eedf00..720dd3a83143 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1491,8 +1491,8 @@ def __init__(self, job=None, container_type=None, container_name=None, container
 
 
 class InteractiveToolEntryPoint(Dictifiable, RepresentById):
-    dict_collection_visible_keys = ['id', 'name', 'active']
-    dict_element_visible_keys = ['id', 'name', 'active']
+    dict_collection_visible_keys = ['id', 'name', 'active', 'created_time', 'modified_time']
+    dict_element_visible_keys = ['id', 'name', 'active', 'created_time', 'modified_time']
 
     def __init__(self, job=None, name=None, token=None, tool_port=None, host=None, port=None, protocol=None,
                  entry_url=None, info=None, configured=False, deleted=False):
diff --git a/lib/galaxy/webapps/galaxy/controllers/interactivetool.py b/lib/galaxy/webapps/galaxy/controllers/interactivetool.py
index d71962cfe104..bacf14f4cb11 100644
--- a/lib/galaxy/webapps/galaxy/controllers/interactivetool.py
+++ b/lib/galaxy/webapps/galaxy/controllers/interactivetool.py
@@ -4,13 +4,8 @@
 import logging
 
 from galaxy import (
-    model,
     web
 )
-from galaxy.web.framework.helpers import (
-    grids,
-    time_ago,
-)
 from galaxy.webapps.base.controller import (
     BaseUIController,
 )
@@ -18,48 +13,7 @@
 log = logging.getLogger(__name__)
 
 
-class JobStatusColumn(grids.StateColumn):
-    def get_value(self, trans, grid, item):
-        return super(JobStatusColumn, self).get_value(trans, grid, item.job)
-
-
-class EntryPointLinkColumn(grids.GridColumn):
-    def get_value(self, trans, grid, item):
-        return '<a class="entry-point-link" entry_point_id="%s">%s</a>' % (trans.security.encode_id(item.id), item.name)
-
-
-class InteractiveToolEntryPointListGrid(grids.Grid):
-
-    use_panels = True
-    title = "Available InteractiveTools"
-    model_class = model.InteractiveToolEntryPoint
-    default_filter = {"name": "All"}
-    default_sort_key = "-update_time"
-    columns = [
-        EntryPointLinkColumn("Name", filterable="advanced"),
-        JobStatusColumn("Job Info", key="job_state", model_class=model.Job),
-        grids.GridColumn("Created", key="created_time", format=time_ago),
-        grids.GridColumn("Last Updated", key="modified_time", format=time_ago),
-    ]
-    columns.append(
-        grids.MulticolFilterColumn(
-            "Search",
-            cols_to_filter=[columns[0]],
-            key="free-text-search", visible=False, filterable="standard"
-        )
-    )
-    operations = [
-        grids.GridOperation("Stop", condition=(lambda item: item.active), async_compatible=False),
-    ]
-
-    def build_initial_query(self, trans, **kwargs):
-        # Get list of user's active InteractiveTools
-        return trans.app.interactivetool_manager.get_nonterminal_for_user_by_trans(trans)
-
-
 class InteractiveTool(BaseUIController):
-    entry_point_grid = InteractiveToolEntryPointListGrid()
-
     @web.expose_api_anonymous
     def list(self, trans, **kwargs):
         """List all available interactivetools"""
@@ -103,4 +57,4 @@ def list(self, trans, **kwargs):
         if message and status:
             kwargs['message'] = message
             kwargs['status'] = status
-        return self.entry_point_grid(trans, **kwargs)
+        return kwargs

From 5ec3a9da14f8f7ce8672979988c28f2e5b372650 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Fri, 21 Feb 2020 16:16:17 +0100
Subject: [PATCH 330/853] delete unused import

---
 client/galaxy/scripts/entry/analysis/AnalysisRouter.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
index 7b4724cc6859..647b60fc74af 100644
--- a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
+++ b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
@@ -24,7 +24,6 @@ import { getUserPreferencesModel } from "components/User/UserPreferencesModel";
 import CustomBuilds from "components/User/CustomBuilds.vue";
 import Tours from "mvc/tours";
 import GridView from "mvc/grid/grid-view";
-import EntryPointGridView from "mvc/entrypoints/view";
 import GridShared from "mvc/grid/grid-shared";
 import WorkflowImport from "components/Workflow/WorkflowImport.vue";
 import InteractiveTools from "components/InteractiveTools/InteractiveTools.vue";

From 14a771f918a497d5a0aea2513dc3788c1c13616f Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Tue, 3 Mar 2020 18:10:48 +0100
Subject: [PATCH 331/853] Vue testing

---
 .../InteractiveTools/InteractiveTools.test.js | 64 +++++++++++++++++++
 .../InteractiveTools/InteractiveTools.vue     | 27 +++++---
 .../components/InteractiveTools/services.js   |  3 +-
 .../testInteractiveToolsResponse.json         | 20 ++++++
 4 files changed, 104 insertions(+), 10 deletions(-)
 create mode 100644 client/galaxy/scripts/components/InteractiveTools/InteractiveTools.test.js
 create mode 100644 client/galaxy/scripts/components/InteractiveTools/testData/testInteractiveToolsResponse.json

diff --git a/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.test.js b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.test.js
new file mode 100644
index 000000000000..483b61a01ccd
--- /dev/null
+++ b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.test.js
@@ -0,0 +1,64 @@
+import InteractiveTools from "./InteractiveTools";
+import { mount, createLocalVue } from "@vue/test-utils";
+import _l from "utils/localization";
+import Vue from "vue";
+import testInteractiveToolsResponse from "./testData/testInteractiveToolsResponse";
+
+import MockAdapter from "axios-mock-adapter";
+import axios from "axios";
+
+describe("ToolsView/ToolsView.vue", () => {
+    const localVue = createLocalVue();
+    localVue.filter("localize", value => _l(value));
+    let wrapper, emitted, axiosMock;
+
+    beforeEach(async () => {
+        axiosMock = new MockAdapter(axios);
+        wrapper = mount(InteractiveTools);
+        emitted = wrapper.emitted();
+        axiosMock.onGet("/api/entry_points?running=true").reply(200, testInteractiveToolsResponse);
+        axiosMock.onPost("/interactivetool/list").reply(200, { status: "ok", message: "ok" });
+        await Vue.nextTick();
+        await Vue.nextTick();
+        await Vue.nextTick();
+    });
+
+    afterEach(() => {
+        axiosMock.restore();
+    });
+
+    it("table should exist", async () => {
+        const table = wrapper.find("#workflow-table");
+        assert(table.exists() === true, "Interactive Tools table doesn't exist!");
+    });
+
+    it("selected tool should disappear after stop button pressed", async () => {
+        function checkIfExists(tag, toolId) {
+            return wrapper.find(tag + toolId).exists();
+        }
+        const toolId = testInteractiveToolsResponse[0].id;
+        const tool = wrapper.vm.activeInteractiveTools.find(tool => tool.id === toolId);
+
+        assert(checkIfExists("#link-", toolId) === true, "tool is not rendered!");
+        // ensure that the tool is not marked
+        assert(tool.marked === undefined || false, "tool was marked before click!");
+        // mark & delete tool
+        const checkbox = wrapper.find("#checkbox-" + toolId);
+        checkbox.trigger("click");
+        await Vue.nextTick();
+        // ensure that the tool is marked
+        assert(tool.marked === true, "clicking on checkbox did not mark corresponding tool!");
+
+        const stopBtn = wrapper.find("#stopInteractiveTool");
+        stopBtn.trigger("click");
+
+        await Vue.nextTick();
+        await Vue.nextTick();
+        await Vue.nextTick();
+
+        const toolExists = wrapper.vm.activeInteractiveTools.includes(tool => tool.id === toolId);
+        // ensure that the tool was deleted from the list
+        assert(toolExists === false, "tool was not deleted from the list!");
+        assert(checkIfExists("#link-", toolId) === false, "tool is rendered after deletion!");
+    });
+});
diff --git a/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue
index df685a17a5e4..70dcb05a980b 100644
--- a/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue
+++ b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <b-alert :variant="messageVariant" :show="showMessage">{{ message }}</b-alert>
+        <b-alert :name="message" :variant="messageVariant" :show="showMessage">{{ message }}</b-alert>
         <h2>Active Interactive Tools</h2>
         <b-row class="mb-3">
             <b-col cols="6">
@@ -24,12 +24,17 @@
             @filtered="filtered"
         >
             <template v-slot:cell(checkbox)="row">
-                <b-form-checkbox v-model="row.item.marked" />
+                <b-form-checkbox :id="createId('checkbox', row.item.id)" v-model="row.item.marked" />
             </template>
             <template v-slot:cell(name)="row">
-                <a :index="row.index" :href="row.item.target" target="_blank" :name="row.item.name">{{
-                    row.item.name
-                }}</a>
+                <a
+                    :index="row.index"
+                    :id="createId('link', row.item.id)"
+                    :href="row.item.target"
+                    target="_blank"
+                    :name="row.item.name"
+                    >{{ row.item.name }}</a
+                >
             </template>
             <template v-slot:cell(job_info)="row">
                 <label v-if="row.item.active">
@@ -52,6 +57,7 @@
             >.
         </div>
         <b-button
+            id="stopInteractiveTool"
             v-if="isCheckboxMarked"
             v-b-tooltip.hover.bottom
             title="Terminate selected tools"
@@ -63,8 +69,12 @@
 
 <script>
 import { Services } from "./services";
+import Vue from "vue";
 import { getAppRoot } from "onload/loadConfig";
 import UtcDate from "components/UtcDate";
+import BootstrapVue from "bootstrap-vue";
+
+Vue.use(BootstrapVue);
 
 export default {
     components: {
@@ -76,8 +86,7 @@ export default {
             fields: [
                 {
                     label: "",
-                    key: "checkbox",
-                    sortable: true
+                    key: "checkbox"
                 },
                 {
                     label: "Name",
@@ -128,7 +137,6 @@ export default {
     },
     methods: {
         load() {
-            this.loading = true;
             this.filter = "";
             this.services
                 .getActiveInteractiveTools()
@@ -150,6 +158,9 @@ export default {
                 this.message = response.message;
                 this.activeInteractiveTools = this.activeInteractiveTools.filter(tool => !tool.marked);
             });
+        },
+        createId(tagLabel, id) {
+            return tagLabel + "-" + id;
         }
     }
 };
diff --git a/client/galaxy/scripts/components/InteractiveTools/services.js b/client/galaxy/scripts/components/InteractiveTools/services.js
index 556fac68b808..9003754f871d 100644
--- a/client/galaxy/scripts/components/InteractiveTools/services.js
+++ b/client/galaxy/scripts/components/InteractiveTools/services.js
@@ -11,8 +11,7 @@ export class Services {
         const url = `${this.root}api/entry_points?running=true`;
         try {
             const response = await axios.get(url);
-            const activeInteractiveTools = response.data;
-            return activeInteractiveTools;
+            return response.data;
         } catch (e) {
             rethrowSimple(e);
         }
diff --git a/client/galaxy/scripts/components/InteractiveTools/testData/testInteractiveToolsResponse.json b/client/galaxy/scripts/components/InteractiveTools/testData/testInteractiveToolsResponse.json
new file mode 100644
index 000000000000..8fbfcaf225df
--- /dev/null
+++ b/client/galaxy/scripts/components/InteractiveTools/testData/testInteractiveToolsResponse.json
@@ -0,0 +1,20 @@
+[
+  {
+    "model_class": "InteractiveToolEntryPoint",
+    "id": "52e496b945151ee8",
+    "name": "Jupyter Interactive Tool",
+    "active": true,
+    "created_time": "2020-02-24T15:59:18.122103",
+    "modified_time": "2020-02-24T15:59:20.428594",
+    "target": "http://52e496b945151ee8-be8a5bee5d5849a5b4e035b51305256e.interactivetoolentrypoint.interactivetool.localhost:8080/ipython/lab"
+  },
+  {
+    "model_class": "InteractiveToolEntryPoint",
+    "id": "b887d74393f85b6d",
+    "name": "AskOmics instance on None",
+    "active": true,
+    "created_time": "2020-01-24T15:59:22.406480",
+    "modified_time": "2020-02-24T15:59:24.757453",
+    "target": "http://b887d74393f85b6d-b1fd3f42331a49c1b3d8a4d1b27240b8.interactivetoolentrypoint.interactivetool.localhost:8080/loginapikey/oleg"
+  }
+]
\ No newline at end of file

From 5b15a8fa9999c869deb73ee3e431f8ac509b991d Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 4 Mar 2020 14:51:24 +0100
Subject: [PATCH 332/853] Fix failing test

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 19 +++++++++++----
 lib/galaxy_test/api/test_workflows.py      | 27 +++++++++++++---------
 2 files changed, 30 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 6ccfa3f3c1ff..2fe44a58dc16 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -653,13 +653,17 @@ def get_tool_predictions(self, trans, payload, **kwd):
             remote_model_url = trans.app.config.tool_recommendation_model_path
         if 'tool_sequence' not in payload or remote_model_url is None:
             return
-        tool_sequence = payload.get('tool_sequence', "")
+        isModelSet = True
+        recommended_tools = dict()
+        tool_sequence = ""
         # collect tool recommendation preferences if set by admin
         self.__collect_admin_preferences(trans.app.config.admin_tool_recommendations_path)
         # recreate the neural network model to be used for prediction
-        self.__set_model(trans, remote_model_url)
-        # get the recommended tools for a tool sequence
-        recommended_tools = self.__compute_tool_prediction(trans, tool_sequence)
+        isModelSet = self.__set_model(trans, remote_model_url)
+        if isModelSet is True:
+            # get the recommended tools for a tool sequence
+            tool_sequence = payload.get('tool_sequence', "")
+            recommended_tools = self.__compute_tool_prediction(trans, tool_sequence)
         return {
             "current_tool": tool_sequence,
             "predicted_data": recommended_tools
@@ -676,7 +680,11 @@ def __set_model(self, trans, remote_model_url):
         if not self.tool_recommendation_model_path:
             # import moves from the top of file: in case the tool recommendation feature is disabled,
             # keras is not downloaded because of conditional requirement and Galaxy does not build
-            from keras.models import model_from_json
+            try:
+                from keras.models import model_from_json
+            except Exception as e:
+                trans.response.status = 400
+                return False
             self.tool_recommendation_model_path = self.__download_model(remote_model_url)
             self.all_tools = dict()
             model_weights = list()
@@ -711,6 +719,7 @@ def __set_model(self, trans, remote_model_url):
                     counter_layer_weights += 1
             # set the model weights
             self.loaded_model.set_weights(model_weights)
+        return True
 
     def __collect_admin_preferences(self, admin_path):
         """
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index 5e957cec22ce..45eb96e26463 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -337,17 +337,22 @@ def test_get_tool_predictions(self):
         route = "workflows/get_tool_predictions"
         response = self._post(route, data=request)
         recommendation_response = response.json()
-        # check Ok response from the API
-        self._assert_status_code_is(response, 200)
-        # check the input tool sequence
-        assert recommendation_response["current_tool"] == request["tool_sequence"]
-        # check non-empty predictions list
-        predicted_tools = recommendation_response["predicted_data"]["children"]
-        assert len(predicted_tools) > 0
-        # check for the correct predictions
-        for tool in predicted_tools:
-            assert tool["tool_id"] in actual_recommendations
-            break
+        is_empty = bool(recommendation_response["current_tool"])
+        if is_empty is False:
+            self._assert_status_code_is(response, 400)
+        else:
+            # check Ok response from the API
+            self._assert_status_code_is(response, 200)
+            recommendation_response = response.json()
+            # check the input tool sequence
+            assert recommendation_response["current_tool"] == request["tool_sequence"]
+            # check non-empty predictions list
+            predicted_tools = recommendation_response["predicted_data"]["children"]
+            assert len(predicted_tools) > 0
+            # check for the correct predictions
+            for tool in predicted_tools:
+                assert tool["tool_id"] in actual_recommendations
+                break
 
     def test_update(self):
         original_workflow = self.workflow_populator.load_workflow(name="test_import")

From e69d70cad319ebc21cad27b892feeb035d886bdb Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 4 Mar 2020 15:18:57 +0100
Subject: [PATCH 333/853] Fix var

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 2fe44a58dc16..63ab76a70580 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -682,7 +682,7 @@ def __set_model(self, trans, remote_model_url):
             # keras is not downloaded because of conditional requirement and Galaxy does not build
             try:
                 from keras.models import model_from_json
-            except Exception as e:
+            except Exception:
                 trans.response.status = 400
                 return False
             self.tool_recommendation_model_path = self.__download_model(remote_model_url)

From 89b8e62f1f5009c047f39d0a091148db4232f525 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 4 Mar 2020 09:23:39 -0500
Subject: [PATCH 334/853] Do not test defaults for job_metrics_config_file

---
 test/integration/test_config_defaults.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/integration/test_config_defaults.py b/test/integration/test_config_defaults.py
index c8d2ff5f26e9..be1f15ea9475 100644
--- a/test/integration/test_config_defaults.py
+++ b/test/integration/test_config_defaults.py
@@ -178,6 +178,7 @@ def expected_default_config_dir(value):
     'id_secret',  # broken: default overridden
     'job_config',  # no obvious testable defaults
     'job_config_file',  # broken: remove 'config/' prefix from schema
+    'job_metrics_config_file',
     'job_working_directory',  # broken; may or may not be able to test
     'library_import_dir',  # broken: default overridden
     'logging',  # mapping loaded in config/

From ecfb7922be5b9abb9e125af55b482c6e9c96f046 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Wed, 4 Mar 2020 16:29:05 +0100
Subject: [PATCH 335/853] hide interactive tool from history after deletion

---
 .../InteractiveTools/InteractiveTools.test.js         | 11 ++++++++++-
 .../components/InteractiveTools/InteractiveTools.vue  |  5 +++++
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.test.js b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.test.js
index 483b61a01ccd..e904c8030d9f 100644
--- a/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.test.js
+++ b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.test.js
@@ -14,7 +14,15 @@ describe("ToolsView/ToolsView.vue", () => {
 
     beforeEach(async () => {
         axiosMock = new MockAdapter(axios);
-        wrapper = mount(InteractiveTools);
+        wrapper = mount(InteractiveTools, {
+            computed: {
+                currentHistory() {
+                    return {
+                        loadCurrentHistory() {}
+                    };
+                }
+            }
+        });
         emitted = wrapper.emitted();
         axiosMock.onGet("/api/entry_points?running=true").reply(200, testInteractiveToolsResponse);
         axiosMock.onPost("/interactivetool/list").reply(200, { status: "ok", message: "ok" });
@@ -36,6 +44,7 @@ describe("ToolsView/ToolsView.vue", () => {
         function checkIfExists(tag, toolId) {
             return wrapper.find(tag + toolId).exists();
         }
+
         const toolId = testInteractiveToolsResponse[0].id;
         const tool = wrapper.vm.activeInteractiveTools.find(tool => tool.id === toolId);
 
diff --git a/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue
index 70dcb05a980b..fb5ee6b0b1be 100644
--- a/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue
+++ b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue
@@ -72,6 +72,7 @@ import { Services } from "./services";
 import Vue from "vue";
 import { getAppRoot } from "onload/loadConfig";
 import UtcDate from "components/UtcDate";
+import { getGalaxyInstance } from "app";
 import BootstrapVue from "bootstrap-vue";
 
 Vue.use(BootstrapVue);
@@ -128,6 +129,9 @@ export default {
         },
         showMessage() {
             return !!this.message;
+        },
+        currentHistory() {
+            return getGalaxyInstance().currHistoryPanel;
         }
     },
     created() {
@@ -157,6 +161,7 @@ export default {
                 else this.messageVariant = "danger";
                 this.message = response.message;
                 this.activeInteractiveTools = this.activeInteractiveTools.filter(tool => !tool.marked);
+                this.currentHistory.loadCurrentHistory();
             });
         },
         createId(tagLabel, id) {

From 39ac5dbd7a439bd62f2ff7fec65a1db5c5f05089 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 5 Mar 2020 12:36:10 +0100
Subject: [PATCH 336/853] Skip migration if uninitialzed database exists

As we do when Galaxy created the database. This is useful if the
database was pre-created because the Galaxy user doesn't have
permissions to create new databases.
---
 lib/galaxy/model/migrate/check.py | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/model/migrate/check.py b/lib/galaxy/model/migrate/check.py
index 0feaaefa789e..a5c9388dd543 100644
--- a/lib/galaxy/model/migrate/check.py
+++ b/lib/galaxy/model/migrate/check.py
@@ -61,8 +61,7 @@ def migrate():
         # Apply all scripts to get to current version
         migrate_to_current_version(engine, db_schema)
 
-    meta = MetaData(bind=engine)
-    if new_database:
+    def migrate_from_scratch():
         log.info("Creating new database from scratch, skipping migrations")
         current_version = migrate_repository.version().version
         mapping.init(file_path='/tmp', url=url, map_install_models=map_install_models, create_tables=True)
@@ -70,6 +69,13 @@ def migrate():
         db_schema = schema.ControlledSchema(engine, migrate_repository)
         assert db_schema.version == current_version
         migrate()
+        if app:
+            # skips the tool migration process.
+            app.new_installation = True
+
+    meta = MetaData(bind=engine)
+    if new_database:
+        migrate_from_scratch()
         return
     elif app and getattr(app.config, 'database_auto_migrate', False):
         migrate()
@@ -79,12 +85,9 @@ def migrate():
     try:
         Table("dataset", meta, autoload=True)
     except NoSuchTableError:
-        # No 'dataset' table means a completely uninitialized database.  If we have an app, we'll
-        # set its new_installation setting to True so the tool migration process will be skipped.
-        if app:
-            app.new_installation = True
+        # No 'dataset' table means a completely uninitialized database.
         log.info("No database, initializing")
-        migrate()
+        migrate_from_scratch()
         return
     try:
         hda_table = Table("history_dataset_association", meta, autoload=True)

From a17bf9e8b411903471f2e10471c9fbcbc293a003 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 5 Mar 2020 12:19:01 +0100
Subject: [PATCH 337/853] Clearer exception message

---
 lib/galaxy/util/properties.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/util/properties.py b/lib/galaxy/util/properties.py
index 000344fe1320..7252f425a912 100644
--- a/lib/galaxy/util/properties.py
+++ b/lib/galaxy/util/properties.py
@@ -117,7 +117,7 @@ def read_properties_from_file(config_file, config_section=None):
         else:
             properties.update(parser.defaults())
     else:
-        raise InvalidFileFormatError()
+        raise InvalidFileFormatError("File '%s' doesn't have a supported extension" % config_file)
     return properties
 
 

From 56450de8a9fde036e13d19c283c6fe49cb8d8cb7 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 5 Mar 2020 12:17:41 +0100
Subject: [PATCH 338/853] Print help if no action is selected

---
 scripts/cleanup_datasets/pgcleanup.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py
index a0d012efb713..6bf7ae21cf27 100755
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -1052,6 +1052,8 @@ def __parse_args(self):
         self.args.sequence = [x.strip() for x in self.args.sequence.split(',')]
         if self.args.sequence != ['']:
             self.args.actions.extend(self.args.sequence)
+        if not self.args.actions:
+            parser.error("Please specify one or more actions")
 
     def __setup_logging(self):
         logging.basicConfig(

From efb6710f064427ce7dea5ff3135a4f6f022175cb Mon Sep 17 00:00:00 2001
From: Ignacio Eguinoa <igegu@psb.ugent.be>
Date: Thu, 5 Mar 2020 17:31:27 +0100
Subject: [PATCH 339/853] unicodify message

---
 lib/galaxy/jobs/runners/util/condor/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/jobs/runners/util/condor/__init__.py b/lib/galaxy/jobs/runners/util/condor/__init__.py
index c71f79bb5bb3..c3c10450e4c9 100644
--- a/lib/galaxy/jobs/runners/util/condor/__init__.py
+++ b/lib/galaxy/jobs/runners/util/condor/__init__.py
@@ -78,6 +78,7 @@ def condor_submit(submit_file):
     try:
         submit = Popen(('condor_submit', submit_file), stdout=PIPE, stderr=STDOUT)
         message, _ = submit.communicate()
+        message=unicodify(message)
         if submit.returncode == 0:
             external_id = parse_external_id(message, type='condor')
         else:

From 064433756d22663e3501e4c5cc25551d957d7cd4 Mon Sep 17 00:00:00 2001
From: Ignacio Eguinoa <ignacio.eguinoa@gmail.com>
Date: Thu, 5 Mar 2020 18:02:34 +0100
Subject: [PATCH 340/853] Update
 lib/galaxy/jobs/runners/util/condor/__init__.py

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/jobs/runners/util/condor/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/runners/util/condor/__init__.py b/lib/galaxy/jobs/runners/util/condor/__init__.py
index c3c10450e4c9..2bb31001fca7 100644
--- a/lib/galaxy/jobs/runners/util/condor/__init__.py
+++ b/lib/galaxy/jobs/runners/util/condor/__init__.py
@@ -78,7 +78,7 @@ def condor_submit(submit_file):
     try:
         submit = Popen(('condor_submit', submit_file), stdout=PIPE, stderr=STDOUT)
         message, _ = submit.communicate()
-        message=unicodify(message)
+        message = unicodify(message)
         if submit.returncode == 0:
             external_id = parse_external_id(message, type='condor')
         else:

From 656639c7460dd24e45774f3fb9a02e52ccae6f99 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Fri, 6 Mar 2020 09:22:58 +0100
Subject: [PATCH 341/853] document maxpctfull

---
 lib/galaxy/config/sample/object_store_conf.xml.sample | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/config/sample/object_store_conf.xml.sample b/lib/galaxy/config/sample/object_store_conf.xml.sample
index 12dbf9aef5b3..d5bd58b181c8 100644
--- a/lib/galaxy/config/sample/object_store_conf.xml.sample
+++ b/lib/galaxy/config/sample/object_store_conf.xml.sample
@@ -1,7 +1,14 @@
 <?xml version="1.0"?>
 <object_store type="hierarchical">
     <backends>
-        <object_store type="distributed" id="primary" order="0">
+        <!-- In distributed and hierarchical world, you can choose that some
+             backends are automatically unused whenever they become too full.
+             Setting the maxpctfull attribute (on top level object_store it
+             behaves as a global default), or it can be applied to individual
+             backends to override a global setting. This only applies to disk
+             based backends and not remote object stores.
+             -->
+        <object_store type="distributed" id="primary" order="0" maxpctfull="90">
             <backends>
                 <backend id="files1" type="disk" weight="1">
                     <files_dir path="database/files1"/>

From 0488972359ffb66d1ac11be5e93649fd79e5be2e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 6 Mar 2020 10:48:28 +0100
Subject: [PATCH 342/853] Set status code even if creating a html message body

That makes it way easier to understand that for instance an exported
history has not been shared and so the archive can't be downloaded.
---
 lib/galaxy/web/framework/webapp.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py
index 273eb40cc69f..d77b230a2752 100644
--- a/lib/galaxy/web/framework/webapp.py
+++ b/lib/galaxy/web/framework/webapp.py
@@ -106,6 +106,7 @@ def handle_controller_exception(self, e, trans, **kwargs):
         if isinstance(e, MessageException):
             # In the case of a controller exception, sanitize to make sure
             # unsafe html input isn't reflected back to the user
+            trans.response.status = e.status_code
             return trans.show_message(sanitize_html(e.err_msg), e.type)
 
     def make_body_iterable(self, trans, body):

From 2d8ab3bc6b6da44535bb9faaf63efd2d1cdfe2d3 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 6 Mar 2020 10:51:15 +0100
Subject: [PATCH 343/853] Use exit to determine failure, let exceptions bubble
 up

---
 .../imp_exp/imp_history_from_archive.xml      |  5 ++-
 .../tools/imp_exp/unpack_tar_gz_archive.py    | 35 ++++++++-----------
 2 files changed, 18 insertions(+), 22 deletions(-)

diff --git a/lib/galaxy/tools/imp_exp/imp_history_from_archive.xml b/lib/galaxy/tools/imp_exp/imp_history_from_archive.xml
index 94e165c7d5ad..c749b6115f6a 100644
--- a/lib/galaxy/tools/imp_exp/imp_history_from_archive.xml
+++ b/lib/galaxy/tools/imp_exp/imp_history_from_archive.xml
@@ -1,6 +1,9 @@
-<tool id="__IMPORT_HISTORY__" name="Import History" version="0.1" tool_type="import_history">
+<tool id="__IMPORT_HISTORY__" name="Import History" version="0.1" tool_type="import_history" profile="16.04">
   <type class="ImportHistoryTool" module="galaxy.tools"/>
   <action module="galaxy.tools.actions.history_imp_exp" class="ImportHistoryToolAction"/>
+  <requirements>
+    <requirement type="package" version="2.23.0">requests</requirement>
+  </requirements>
   <command>#from base64 import b64encode#
 python '$__tool_directory__/unpack_tar_gz_archive.py'
 '${ b64encode(str($__ARCHIVE_SOURCE__).encode('utf-8')).decode('utf-8')}'
diff --git a/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
index f1a8d1daf4b2..5611fe6d2bed 100644
--- a/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
+++ b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
@@ -10,7 +10,6 @@
 import math
 import optparse
 import os
-import sys
 import tarfile
 import tempfile
 from base64 import b64decode
@@ -26,22 +25,19 @@ def url_to_file(url, dest_file):
     """
     Transfer a file from a remote URL to a temporary file.
     """
-    try:
-        url_reader = requests.get(url, stream=True)
-        CHUNK = 10 * 1024  # 10k
-        total = 0
-        fp = open(dest_file, 'wb')
-        for chunk in url_reader.iter_content(chunk_size=CHUNK):
-            if chunk:
-                fp.write(chunk)
-                total += CHUNK
-                if total > MAX_SIZE:
-                    break
-        fp.close()
-        return dest_file
-    except Exception as e:
-        print("Exception getting file from URL: %s" % e, file=sys.stderr)
-        return None
+    url_reader = requests.get(url, stream=True)
+    assert url_reader.ok, "History import failed, server returned '%s'" % url_reader.reason
+    CHUNK = 10 * 1024  # 10k
+    total = 0
+    fp = open(dest_file, 'wb')
+    for chunk in url_reader.iter_content(chunk_size=CHUNK):
+        if chunk:
+            fp.write(chunk)
+            total += CHUNK
+            if total > MAX_SIZE:
+                break
+    fp.close()
+    return dest_file
 
 
 def check_archive(archive_file, dest_dir):
@@ -96,7 +92,4 @@ def main(options, args):
     parser.add_option('-F', '--file', dest='is_file', action="store_true", help='Source is a file.')
     parser.add_option('-e', '--encoded', dest='is_b64encoded', action="store_true", default=False, help='Source and destination dir values are base64 encoded.')
     (options, args) = parser.parse_args()
-    try:
-        main(options, args)
-    except Exception as e:
-        print("Error unpacking tar/gz archive: %s" % e, file=sys.stderr)
+    main(options, args)

From 3d5ec396db64cc895185a483093f3925c3acfe88 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 6 Mar 2020 11:01:34 +0100
Subject: [PATCH 344/853] Fix history export for outputs_to_working_directory

---
 lib/galaxy/jobs/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index f485b52e88bb..71dd60e7852e 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1939,7 +1939,7 @@ def compute_outputs(self):
         self.output_paths = [t[2] for t in results]
         self.output_hdas_and_paths = dict([(t[0], t[1:]) for t in results])
         if special:
-            false_path = dataset_path_rewriter.rewrite_dataset_path(special.dataset, 'output')
+            false_path = dataset_path_rewriter.rewrite_dataset_path(special, 'output')
             dsp = DatasetPath(special.dataset.id, special.dataset.file_name, false_path)
             self.output_paths.append(dsp)
         return self.output_paths

From fde103db24063ac01cc12d7f24c85950c65ca0a2 Mon Sep 17 00:00:00 2001
From: MiguelJulia <migueljuliamolina@gmail.com>
Date: Fri, 6 Mar 2020 16:07:37 +0100
Subject: [PATCH 345/853] Added whitelisting option for user registration

---
 lib/galaxy/config/__init__.py              | 10 ++++++++++
 lib/galaxy/security/validate_user_input.py |  7 +++++++
 lib/tool_shed/webapp/config_schema.yml     | 10 ++++++++++
 3 files changed, 27 insertions(+)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 3fdc7f9af3a1..021e7a7d710c 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -465,6 +465,16 @@ def _process_config(self, kwargs):
             except IOError:
                 log.error("CONFIGURATION ERROR: Can't open supplied blacklist file from path: %s", self.blacklist_file)
 
+        #  Create whitelist file to accept only certain email domains
+        self.whitelist_content = None
+        if self.whitelist_file:
+            self.whitelist_file = os.path.join(self.root, self.whitelist_file)
+            try:
+                with open(self.whitelist_file) as f:
+                    self.whitelist_content = [line.rstrip() for line in f]
+            except IOError:
+                log.error("CONFIGURATION ERROR: Can't open supplied whitelist file from path: %s", self.whitelist_file)
+
         self.persistent_communication_rooms = listify(self.persistent_communication_rooms, do_strip=True)
         # The transfer manager and deferred job queue
         self.enable_beta_job_managers = string_as_bool(kwargs.get('enable_beta_job_managers', 'False'))
diff --git a/lib/galaxy/security/validate_user_input.py b/lib/galaxy/security/validate_user_input.py
index ae5dc840910e..12bba4c06f55 100644
--- a/lib/galaxy/security/validate_user_input.py
+++ b/lib/galaxy/security/validate_user_input.py
@@ -46,6 +46,13 @@ def validate_email(trans, email, user=None, check_dup=True, allow_empty=False):
             domain = ('.').join(domain.split('.')[-2:])
         if domain in trans.app.config.blacklist_content:
             message = "Please enter your permanent email address."
+    #  If the whitelist is not empty filter out any domain not in the list.
+    elif trans.app.config.whitelist_content is not None:
+        domain = email.split('@')[1]
+        if len(domain.split('.')) > 2:
+            domain = ('.').join(domain.split('.')[-2:])
+        if domain not in trans.app.config.whitelist_content:
+            message = "Please enter an allowed domain email address for this server."
     return message
 
 
diff --git a/lib/tool_shed/webapp/config_schema.yml b/lib/tool_shed/webapp/config_schema.yml
index cc014e2c6302..3a6b836292ea 100644
--- a/lib/tool_shed/webapp/config_schema.yml
+++ b/lib/tool_shed/webapp/config_schema.yml
@@ -482,6 +482,16 @@ mapping:
           disposable email address during the registration.  If their address domain
           matches any domain in the blacklist, they are refused the registration.
 
+      whitelist_file:
+        type: str
+        default: config/disposable_email_whitelist.conf
+        required: false
+        desc: |
+          E-mail domains whitelist is used for filtering out users that are using
+          email address not belonging to the instition/company domains during the
+          registration. If their address domain matches any domain in the whitelist,
+          they are refused the registration.
+
       brand:
         type: str
         default: null

From 7538b3eb5c7d6deb532ae1f00bf2bb323b093251 Mon Sep 17 00:00:00 2001
From: MiguelJulia <migueljuliamolina@gmail.com>
Date: Fri, 6 Mar 2020 16:37:26 +0100
Subject: [PATCH 346/853] Move to correct configuration

---
 lib/galaxy/webapps/galaxy/config_schema.yml | 12 +++++++++++-
 lib/tool_shed/webapp/config_schema.yml      | 10 ----------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index a312531459fb..1a8a688d6603 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -902,6 +902,16 @@ mapping:
 
           Example value 'config/disposable_email_blacklist.conf'
 
+      whitelist_file:
+        type: str
+        default: config/disposable_email_whitelist.conf
+        required: false
+        desc: |
+          E-mail domains whitelist is used for filtering out users that are using
+          email address not belonging to the instition/company domains during the
+          registration. If their address domain matches any domain in the whitelist,
+          they are refused the registration.
+
       registration_warning_message:
         type: str
         default: >-
@@ -2414,7 +2424,7 @@ mapping:
         required: false
         desc: |
           XML config file that contains the job metric collection configuration.
-          
+
           The value of this option will be resolved with respect to <config_dir>.
 
       expose_potentially_sensitive_job_metrics:
diff --git a/lib/tool_shed/webapp/config_schema.yml b/lib/tool_shed/webapp/config_schema.yml
index 3a6b836292ea..cc014e2c6302 100644
--- a/lib/tool_shed/webapp/config_schema.yml
+++ b/lib/tool_shed/webapp/config_schema.yml
@@ -482,16 +482,6 @@ mapping:
           disposable email address during the registration.  If their address domain
           matches any domain in the blacklist, they are refused the registration.
 
-      whitelist_file:
-        type: str
-        default: config/disposable_email_whitelist.conf
-        required: false
-        desc: |
-          E-mail domains whitelist is used for filtering out users that are using
-          email address not belonging to the instition/company domains during the
-          registration. If their address domain matches any domain in the whitelist,
-          they are refused the registration.
-
       brand:
         type: str
         default: null

From 75d26ab896cde9b92077e1994ac33530e60879d5 Mon Sep 17 00:00:00 2001
From: MiguelJulia <migueljuliamolina@gmail.com>
Date: Fri, 6 Mar 2020 16:39:26 +0100
Subject: [PATCH 347/853] Explanation about whitelist/blacklist priority

---
 lib/galaxy/webapps/galaxy/config_schema.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 1a8a688d6603..a0e5f760d4b2 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -910,7 +910,9 @@ mapping:
           E-mail domains whitelist is used for filtering out users that are using
           email address not belonging to the instition/company domains during the
           registration. If their address domain matches any domain in the whitelist,
-          they are refused the registration.
+          they are refused the registration. This is a more restrictive option than
+          blacklist, and therefore, in case the previous one is defined this one
+          will be ignored.
 
       registration_warning_message:
         type: str

From e7f086c33431e463f02c2e3089fc7e2b23553e34 Mon Sep 17 00:00:00 2001
From: MiguelJulia <migueljuliamolina@gmail.com>
Date: Fri, 6 Mar 2020 16:45:35 +0100
Subject: [PATCH 348/853] Added documentation generated with make

---
 doc/source/admin/galaxy_options.rst        | 19 ++++++++++++++++++-
 lib/galaxy/config/sample/galaxy.yml.sample | 12 +++++++++++-
 2 files changed, 29 insertions(+), 2 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 1c78cc612b54..3f8728d28f19 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -1221,6 +1221,21 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~
+``whitelist_file``
+~~~~~~~~~~~~~~~~~~
+
+:Description:
+    E-mail domains whitelist is used for filtering out users that are
+    using email address not belonging to the instition/company domains
+    during the registration. If their address domain matches any
+    domain in the whitelist, they are refused the registration. This
+    is a more restrictive option than blacklist, and therefore, in
+    case the previous one is defined this one will be ignored.
+:Default: ``config/disposable_email_whitelist.conf``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``registration_warning_message``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -3265,7 +3280,9 @@
 :Description:
     XML config file that contains the job metric collection
     configuration.
-:Default: ``config/job_metrics_conf.xml``
+    The value of this option will be resolved with respect to
+    <config_dir>.
+:Default: ``job_metrics_conf.xml``
 :Type: str
 
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index dea2580aeb78..9054cf7f2d7c 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -687,6 +687,14 @@ galaxy:
   # Example value 'config/disposable_email_blacklist.conf'
   #blacklist_file: null
 
+  # E-mail domains whitelist is used for filtering out users that are
+  # using email address not belonging to the instition/company domains
+  # during the registration. If their address domain matches any domain
+  # in the whitelist, they are refused the registration. This is a more
+  # restrictive option than blacklist, and therefore, in case the
+  # previous one is defined this one will be ignored.
+  #whitelist_file: config/disposable_email_whitelist.conf
+
   # Registration warning message is used to discourage people from
   # registering multiple accounts.  Applies mostly for the main Galaxy
   # instance. If no message specified the warning box will not be shown.
@@ -1607,7 +1615,9 @@ galaxy:
 
   # XML config file that contains the job metric collection
   # configuration.
-  #job_metrics_config_file: config/job_metrics_conf.xml
+  # The value of this option will be resolved with respect to
+  # <config_dir>.
+  #job_metrics_config_file: job_metrics_conf.xml
 
   # This option allows users to see the job metrics (except for
   # environment variables).

From d4e6ebe9f722709e1d47b949205878e8b969ae67 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 6 Mar 2020 16:46:47 +0100
Subject: [PATCH 349/853] Use with statement

---
 lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
index 5611fe6d2bed..f3fad8681695 100644
--- a/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
+++ b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
@@ -29,14 +29,13 @@ def url_to_file(url, dest_file):
     assert url_reader.ok, "History import failed, server returned '%s'" % url_reader.reason
     CHUNK = 10 * 1024  # 10k
     total = 0
-    fp = open(dest_file, 'wb')
-    for chunk in url_reader.iter_content(chunk_size=CHUNK):
-        if chunk:
-            fp.write(chunk)
-            total += CHUNK
-            if total > MAX_SIZE:
-                break
-    fp.close()
+    with open(dest_file, 'wb') as fp:
+        for chunk in url_reader.iter_content(chunk_size=CHUNK):
+            if chunk:
+                fp.write(chunk)
+                total += CHUNK
+                if total > MAX_SIZE:
+                    break
     return dest_file
 
 

From a16bd19f685f481b06661dcaa7364587fd393630 Mon Sep 17 00:00:00 2001
From: MiguelJulia <migueljuliamolina@gmail.com>
Date: Fri, 6 Mar 2020 18:18:09 +0100
Subject: [PATCH 350/853] Reworded documentation as suggested by ic4f

---
 lib/galaxy/webapps/galaxy/config_schema.yml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index a0e5f760d4b2..375fdf5e2754 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -907,12 +907,11 @@ mapping:
         default: config/disposable_email_whitelist.conf
         required: false
         desc: |
-          E-mail domains whitelist is used for filtering out users that are using
-          email address not belonging to the instition/company domains during the
-          registration. If their address domain matches any domain in the whitelist,
-          they are refused the registration. This is a more restrictive option than
-          blacklist, and therefore, in case the previous one is defined this one
-          will be ignored.
+          E-mail domains whitelist is used to specify allowed email address domains.
+          If the list is non-empty and a user attempts registration using an email
+          address belonging to a domain that is not on the list, registration will be
+          enied. This is a more restrictive option than <blacklist_file>, and therefore,
+          in case <blacklist_file> is defined, <whitelist_file> will be ignored.
 
       registration_warning_message:
         type: str

From 2eeb542b79653f465370a541614240959252080c Mon Sep 17 00:00:00 2001
From: MiguelJulia <migueljuliamolina@gmail.com>
Date: Fri, 6 Mar 2020 18:31:21 +0100
Subject: [PATCH 351/853] removed hardcoded path

---
 lib/galaxy/webapps/galaxy/config_schema.yml |  3 ++-
 lib/tool_shed/webapp/config_schema.yml      | 12 ++++++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 375fdf5e2754..4733fd2b23e9 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -904,7 +904,8 @@ mapping:
 
       whitelist_file:
         type: str
-        default: config/disposable_email_whitelist.conf
+        default: disposable_email_whitelist.conf
+        path_resolves_to: config_dir
         required: false
         desc: |
           E-mail domains whitelist is used to specify allowed email address domains.
diff --git a/lib/tool_shed/webapp/config_schema.yml b/lib/tool_shed/webapp/config_schema.yml
index cc014e2c6302..79fb569a79e9 100644
--- a/lib/tool_shed/webapp/config_schema.yml
+++ b/lib/tool_shed/webapp/config_schema.yml
@@ -482,6 +482,18 @@ mapping:
           disposable email address during the registration.  If their address domain
           matches any domain in the blacklist, they are refused the registration.
 
+      whitelist_file:
+        type: str
+        default: disposable_email_whitelist.conf
+        path_resolves_to: config_dir
+        required: false
+        desc: |
+          E-mail domains whitelist is used to specify allowed email address domains.
+          If the list is non-empty and a user attempts registration using an email
+          address belonging to a domain that is not on the list, registration will be
+          enied. This is a more restrictive option than <blacklist_file>, and therefore,
+          in case <blacklist_file> is defined, <whitelist_file> will be ignored.
+
       brand:
         type: str
         default: null

From d2c0ddddfbe12b19ad49afa4e35ed8b375ea3990 Mon Sep 17 00:00:00 2001
From: MiguelJulia <migueljuliamolina@gmail.com>
Date: Fri, 6 Mar 2020 18:33:44 +0100
Subject: [PATCH 352/853] removed line unnecessary 471 for whitelist_file
 location

---
 lib/galaxy/config/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 021e7a7d710c..3a8c60a35e52 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -468,7 +468,6 @@ def _process_config(self, kwargs):
         #  Create whitelist file to accept only certain email domains
         self.whitelist_content = None
         if self.whitelist_file:
-            self.whitelist_file = os.path.join(self.root, self.whitelist_file)
             try:
                 with open(self.whitelist_file) as f:
                     self.whitelist_content = [line.rstrip() for line in f]

From 70f0a4dc896543b4672f9dd0c248ec8aa530b6d7 Mon Sep 17 00:00:00 2001
From: MiguelJulia <migueljuliamolina@gmail.com>
Date: Fri, 6 Mar 2020 18:37:23 +0100
Subject: [PATCH 353/853] make config-rebuild

---
 doc/source/admin/galaxy_options.rst           | 14 +++++++-------
 lib/galaxy/config/sample/galaxy.yml.sample    | 14 +++++++-------
 lib/galaxy/config/sample/tool_shed.yml.sample |  8 ++++++++
 3 files changed, 22 insertions(+), 14 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 3f8728d28f19..ed7c6319cacd 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -1226,13 +1226,13 @@
 ~~~~~~~~~~~~~~~~~~
 
 :Description:
-    E-mail domains whitelist is used for filtering out users that are
-    using email address not belonging to the instition/company domains
-    during the registration. If their address domain matches any
-    domain in the whitelist, they are refused the registration. This
-    is a more restrictive option than blacklist, and therefore, in
-    case the previous one is defined this one will be ignored.
-:Default: ``config/disposable_email_whitelist.conf``
+    E-mail domains whitelist is used to specify allowed email address
+    domains. If the list is non-empty and a user attempts registration
+    using an email address belonging to a domain that is not on the
+    list, registration will be enied. This is a more restrictive
+    option than <blacklist_file>, and therefore, in case
+    <blacklist_file> is defined, <whitelist_file> will be ignored.
+:Default: ``disposable_email_whitelist.conf``
 :Type: str
 
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 9054cf7f2d7c..e1e71076dfb3 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -687,13 +687,13 @@ galaxy:
   # Example value 'config/disposable_email_blacklist.conf'
   #blacklist_file: null
 
-  # E-mail domains whitelist is used for filtering out users that are
-  # using email address not belonging to the instition/company domains
-  # during the registration. If their address domain matches any domain
-  # in the whitelist, they are refused the registration. This is a more
-  # restrictive option than blacklist, and therefore, in case the
-  # previous one is defined this one will be ignored.
-  #whitelist_file: config/disposable_email_whitelist.conf
+  # E-mail domains whitelist is used to specify allowed email address
+  # domains. If the list is non-empty and a user attempts registration
+  # using an email address belonging to a domain that is not on the
+  # list, registration will be enied. This is a more restrictive option
+  # than <blacklist_file>, and therefore, in case <blacklist_file> is
+  # defined, <whitelist_file> will be ignored.
+  #whitelist_file: disposable_email_whitelist.conf
 
   # Registration warning message is used to discourage people from
   # registering multiple accounts.  Applies mostly for the main Galaxy
diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample
index 2e1934d55fad..52d6994638e2 100644
--- a/lib/galaxy/config/sample/tool_shed.yml.sample
+++ b/lib/galaxy/config/sample/tool_shed.yml.sample
@@ -344,6 +344,14 @@ tool_shed:
   # the registration.
   #blacklist_file: config/disposable_email_blacklist.conf
 
+  # E-mail domains whitelist is used to specify allowed email address
+  # domains. If the list is non-empty and a user attempts registration
+  # using an email address belonging to a domain that is not on the
+  # list, registration will be enied. This is a more restrictive option
+  # than <blacklist_file>, and therefore, in case <blacklist_file> is
+  # defined, <whitelist_file> will be ignored.
+  #whitelist_file: disposable_email_whitelist.conf
+
   # Append "/{brand}" to the "Galaxy" text in the masthead.
   #brand: null
 

From 6a0eb4d746faf13bcb8e2bb11ca7576ac2df6f26 Mon Sep 17 00:00:00 2001
From: MiguelJulia <migueljuliamolina@gmail.com>
Date: Fri, 6 Mar 2020 19:57:41 +0100
Subject: [PATCH 354/853] changed priority: ignoring blacklist when whitelist
 exists

---
 lib/galaxy/security/validate_user_input.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/security/validate_user_input.py b/lib/galaxy/security/validate_user_input.py
index 12bba4c06f55..d81f7ef53983 100644
--- a/lib/galaxy/security/validate_user_input.py
+++ b/lib/galaxy/security/validate_user_input.py
@@ -39,6 +39,13 @@ def validate_email(trans, email, user=None, check_dup=True, allow_empty=False):
         message = "Email address cannot be more than %d characters in length." % EMAIL_MAX_LEN
     elif check_dup and trans.sa_session.query(trans.app.model.User).filter(func.lower(trans.app.model.User.table.c.email) == email.lower()).first():
         message = "User with email '%s' already exists." % email
+    #  If the whitelist is not empty filter out any domain not in the list and ignore blacklist.
+    elif trans.app.config.whitelist_content is not None:
+        domain = email.split('@')[1]
+        if len(domain.split('.')) > 2:
+            domain = ('.').join(domain.split('.')[-2:])
+        if domain not in trans.app.config.whitelist_content:
+            message = "Please enter an allowed domain email address for this server."
     #  If the blacklist is not empty filter out the disposable domains.
     elif trans.app.config.blacklist_content is not None:
         domain = email.split('@')[1]
@@ -46,13 +53,6 @@ def validate_email(trans, email, user=None, check_dup=True, allow_empty=False):
             domain = ('.').join(domain.split('.')[-2:])
         if domain in trans.app.config.blacklist_content:
             message = "Please enter your permanent email address."
-    #  If the whitelist is not empty filter out any domain not in the list.
-    elif trans.app.config.whitelist_content is not None:
-        domain = email.split('@')[1]
-        if len(domain.split('.')) > 2:
-            domain = ('.').join(domain.split('.')[-2:])
-        if domain not in trans.app.config.whitelist_content:
-            message = "Please enter an allowed domain email address for this server."
     return message
 
 

From 64e4cfe19e7fd8efa54350c259629ddeb0c4628f Mon Sep 17 00:00:00 2001
From: MiguelJulia <migueljuliamolina@gmail.com>
Date: Fri, 6 Mar 2020 21:21:34 +0100
Subject: [PATCH 355/853] updated documentation with new priority over lists

---
 doc/source/admin/galaxy_options.rst           | 2 +-
 lib/galaxy/config/sample/galaxy.yml.sample    | 4 ++--
 lib/galaxy/config/sample/tool_shed.yml.sample | 4 ++--
 lib/galaxy/webapps/galaxy/config_schema.yml   | 2 +-
 lib/tool_shed/webapp/config_schema.yml        | 2 +-
 5 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index ed7c6319cacd..41abe433853d 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -1231,7 +1231,7 @@
     using an email address belonging to a domain that is not on the
     list, registration will be enied. This is a more restrictive
     option than <blacklist_file>, and therefore, in case
-    <blacklist_file> is defined, <whitelist_file> will be ignored.
+    <whitelist_file> is defined, <blacklist_file> will be ignored.
 :Default: ``disposable_email_whitelist.conf``
 :Type: str
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index e1e71076dfb3..dc1e81c10edf 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -691,8 +691,8 @@ galaxy:
   # domains. If the list is non-empty and a user attempts registration
   # using an email address belonging to a domain that is not on the
   # list, registration will be enied. This is a more restrictive option
-  # than <blacklist_file>, and therefore, in case <blacklist_file> is
-  # defined, <whitelist_file> will be ignored.
+  # than <blacklist_file>, and therefore, in case <whitelist_file> is
+  # defined, <blacklist_file> will be ignored.
   #whitelist_file: disposable_email_whitelist.conf
 
   # Registration warning message is used to discourage people from
diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample
index 52d6994638e2..0c4c9907021e 100644
--- a/lib/galaxy/config/sample/tool_shed.yml.sample
+++ b/lib/galaxy/config/sample/tool_shed.yml.sample
@@ -348,8 +348,8 @@ tool_shed:
   # domains. If the list is non-empty and a user attempts registration
   # using an email address belonging to a domain that is not on the
   # list, registration will be enied. This is a more restrictive option
-  # than <blacklist_file>, and therefore, in case <blacklist_file> is
-  # defined, <whitelist_file> will be ignored.
+  # than <blacklist_file>, and therefore, in case <whitelist_file> is
+  # defined, <blacklist_file> will be ignored.
   #whitelist_file: disposable_email_whitelist.conf
 
   # Append "/{brand}" to the "Galaxy" text in the masthead.
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 4733fd2b23e9..d8529ef43fda 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -912,7 +912,7 @@ mapping:
           If the list is non-empty and a user attempts registration using an email
           address belonging to a domain that is not on the list, registration will be
           enied. This is a more restrictive option than <blacklist_file>, and therefore,
-          in case <blacklist_file> is defined, <whitelist_file> will be ignored.
+          in case <whitelist_file> is defined, <blacklist_file> will be ignored.
 
       registration_warning_message:
         type: str
diff --git a/lib/tool_shed/webapp/config_schema.yml b/lib/tool_shed/webapp/config_schema.yml
index 79fb569a79e9..9de65d6ef686 100644
--- a/lib/tool_shed/webapp/config_schema.yml
+++ b/lib/tool_shed/webapp/config_schema.yml
@@ -492,7 +492,7 @@ mapping:
           If the list is non-empty and a user attempts registration using an email
           address belonging to a domain that is not on the list, registration will be
           enied. This is a more restrictive option than <blacklist_file>, and therefore,
-          in case <blacklist_file> is defined, <whitelist_file> will be ignored.
+          in case <whitelist_file> is defined, <blacklist_file> will be ignored.
 
       brand:
         type: str

From 486d633cdef61a976a53a79cfb0080fe186d6619 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Fri, 6 Mar 2020 16:46:05 -0500
Subject: [PATCH 356/853] run make config-rebuild

---
 doc/source/admin/galaxy_options.rst        | 4 +++-
 lib/galaxy/config/sample/galaxy.yml.sample | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 1c78cc612b54..b7a8d9d6ad33 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -3265,7 +3265,9 @@
 :Description:
     XML config file that contains the job metric collection
     configuration.
-:Default: ``config/job_metrics_conf.xml``
+    The value of this option will be resolved with respect to
+    <config_dir>.
+:Default: ``job_metrics_conf.xml``
 :Type: str
 
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index dea2580aeb78..a2818be4173a 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1607,7 +1607,9 @@ galaxy:
 
   # XML config file that contains the job metric collection
   # configuration.
-  #job_metrics_config_file: config/job_metrics_conf.xml
+  # The value of this option will be resolved with respect to
+  # <config_dir>.
+  #job_metrics_config_file: job_metrics_conf.xml
 
   # This option allows users to see the job metrics (except for
   # environment variables).

From 3a51247e8b235a0ea2dd53e1673c06002e7ce9bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Mon, 9 Mar 2020 08:52:41 +0100
Subject: [PATCH 357/853] Delete interactivetool_hicbrowser.xml

---
 interactivetool_hicbrowser.xml | 33 ---------------------------------
 1 file changed, 33 deletions(-)
 delete mode 100644 interactivetool_hicbrowser.xml

diff --git a/interactivetool_hicbrowser.xml b/interactivetool_hicbrowser.xml
deleted file mode 100644
index 7aaa8a3e8e7b..000000000000
--- a/interactivetool_hicbrowser.xml
+++ /dev/null
@@ -1,33 +0,0 @@
-<tool id="interactive_tool_hicbrowser" tool_type="interactive" name="HiCBrowser" version="0.1">
-    <requirements>
-        <container type="docker">bgruening/hicbrowser</container>
-    </requirements>
-    <entry_points>
-        <entry_point name="HiCBrowser on $infile.display_name" requires_domain="True">
-            <port>80</port>
-        </entry_point>
-    </entry_points>
-    <command><![CDATA[
-        #set $PROXY_PREFIX = ""
-        sed -i "s|PROXY_PREFIX|${PROXY_PREFIX}|" /etc/nginx/conf.d/nginx.conf &&
-        rm /data/* -rf &&
-        cp '$infile' /data/data_pack.zip &&
-        cd /data &&
-        unzip data_pack.zip &&
-        supervisord &&
-        tail -f /var/log/supervisor/*
-
-    ]]>
-    </command>
-    <inputs>
-        <param name="infile" type="data" format="zip" label="HiCExplorer archive"/>
-    </inputs>
-    <outputs>
-        <data name="outfile" format="txt" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-        Visualising HiC data with HiCBrowser.
-    </help>
-</tool>

From 715d05f79441748f5a4a34f057354f312b2d152a Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Mon, 9 Mar 2020 14:56:07 +0100
Subject: [PATCH 358/853] switching, copying, deleting, purging, creating new

---
 .../galaxy/scripts/mvc/history/multi-panel.js |   8 +-
 lib/galaxy/selenium/navigation.yml            |  21 +++
 .../selenium/test_history_multi_view.py       | 124 +++++++++++++++---
 3 files changed, 134 insertions(+), 19 deletions(-)

diff --git a/client/galaxy/scripts/mvc/history/multi-panel.js b/client/galaxy/scripts/mvc/history/multi-panel.js
index a2d003b4ef4b..e7d9d47770bd 100644
--- a/client/galaxy/scripts/mvc/history/multi-panel.js
+++ b/client/galaxy/scripts/mvc/history/multi-panel.js
@@ -212,10 +212,14 @@ var HistoryViewColumn = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         `<div class="text-right col-4">
             <% if( !data.history.purged ){ %>
                 <div class="panel-menu btn-group">
-                    <button type="button" class="btn btn-secondary dropdown-toggle" data-toggle="dropdown">
+                    <button 
+                    history-dropdown-btn="<%= data.history.id %>" 
+                    type="button"
+                    class="btn btn-secondary dropdown-toggle"
+                    data-toggle="dropdown">
                         <span class="caret"></span>
                     </button>
-                    <div class="dropdown-menu" role="menu">
+                    <div history-dropdown-menu="<%= data.history.id %>"  class="dropdown-menu" role="menu">
                         <% if( !data.history.deleted ){ %>
                             <a class="dropdown-item copy-history" href="javascript:void(0);">
                                 ${_l("Copy")}
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index ae2678deb0f4..193ca4aa42bb 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -172,9 +172,30 @@ multi_history_view:
 
   selectors:
     _: '.multi-panel-history'
+    histories: '.middle .history-column'
     current_label: '.current-label'
     create_new_button: '.create-new'
     drag_drop_help: '.history-drop-target-help'
+    switch_history: '.switch-to'
+    history_dropdown_btn: '[history-dropdown-btn="${history_id}"]'
+    copy: '.copy-history'
+    delete: '.copy-history'
+    current_history_check: '#history-column-${history_id} .current-label'
+    empty_message_check: '.empty-message'
+
+
+  history_dropdown_menu:
+    selectors:
+      _: '[history-dropdown-menu="${history_id}"]'
+      delete:  '[history-dropdown-menu="${history_id}"] > .delete-history'
+      purge:  '[history-dropdown-menu="${history_id}"] > .purge-history'
+  copy_history_modal:
+    selectors:
+      _: '.modal-dialog'
+      copy_btn:
+        type: xpath
+        selector: '//button[contains(text(), "Copy")]'
+
 
 history_copy_elements:
 
diff --git a/lib/galaxy_test/selenium/test_history_multi_view.py b/lib/galaxy_test/selenium/test_history_multi_view.py
index 195558f789d5..74498b3b6b59 100644
--- a/lib/galaxy_test/selenium/test_history_multi_view.py
+++ b/lib/galaxy_test/selenium/test_history_multi_view.py
@@ -2,6 +2,8 @@
     selenium_test,
     SeleniumTestCase
 )
+from selenium.common.exceptions import NoSuchElementException
+
 
 
 class HistoryMultiViewTestCase(SeleniumTestCase):
@@ -27,15 +29,8 @@ def test_create_new_old_slides_next(self):
     @selenium_test
     def test_list_list_display(self):
         history_id = self.current_history_id()
-        collection = self.dataset_collection_populator.create_list_of_list_in_history(history_id).json()
-        collection_hid = collection["hid"]
-
-        self.home()
-
-        self.components.history_panel.multi_view_button.wait_for_and_click()
-
-        selector = self.history_panel_wait_for_hid_state(collection_hid, "ok")
-        self.click(selector)
+        method = self.dataset_collection_populator.create_list_of_list_in_history(history_id).json
+        selector = self.prepare_multi_history_view(method)
         first_level_element_selector = selector.descendant(".dataset-collection-element")
         self.wait_for_and_click(first_level_element_selector)
         dataset_selector = first_level_element_selector.descendant(".dataset")
@@ -47,15 +42,9 @@ def test_list_list_display(self):
     @selenium_test
     def test_list_list_list_display(self):
         history_id = self.current_history_id()
-        collection = self.dataset_collection_populator.create_nested_collection(history_id, collection_type="list:list:list").json()
-        collection_hid = collection["hid"]
-
-        self.home()
-
-        self.components.history_panel.multi_view_button.wait_for_and_click()
+        method = self.dataset_collection_populator.create_nested_collection(history_id, collection_type="list:list:list").json
+        selector = self.prepare_multi_history_view(method)
 
-        selector = self.history_panel_wait_for_hid_state(collection_hid, "ok")
-        self.click(selector)
         first_level_element_selector = selector.descendant(".dataset-collection-element")
         self.wait_for_and_click(first_level_element_selector)
         second_level_element_selector = first_level_element_selector.descendant(".dataset-collection-element")
@@ -65,3 +54,104 @@ def test_list_list_list_display(self):
 
         self.sleep_for(self.wait_types.UX_TRANSITION)
         self.screenshot("multi_history_list_list_list")
+
+    @selenium_test
+    def test_copy_history(self):
+        history_id = self.current_history_id()
+        method = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json
+
+        self.prepare_multi_history_view(method)
+        self.copy_history(history_id)
+        self.assert_history(history_id, histories_number=2)
+
+
+    @selenium_test
+    def test_delete_history(self):
+        history_id = self.current_history_id()
+        method = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json
+
+        self.prepare_multi_history_view(method)
+        self.copy_history(history_id)
+        self.components.multi_history_view.history_dropdown_btn(history_id=history_id).wait_for_and_click()
+        # click on delete button with corresponding history_id
+        self.components.multi_history_view.history_dropdown_menu.delete(history_id=history_id).wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        self.assert_history(history_id, should_exist=False)
+
+
+    @selenium_test
+    def test_purge_history(self):
+        history_id = self.current_history_id()
+        method = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json
+
+        self.prepare_multi_history_view(method)
+        self.copy_history(history_id)
+        self.components.multi_history_view.history_dropdown_btn(history_id=history_id).wait_for_and_click()
+        # click on purge button with corresponding history_id
+        self.components.multi_history_view.history_dropdown_menu.purge(history_id=history_id).wait_for_and_click()
+
+        self.driver.switch_to_alert().accept()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        self.assert_history(history_id, should_exist=False)
+
+    @selenium_test
+    def test_switching_history(self):
+        history_id = self.current_history_id()
+        method = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json
+
+        self.prepare_multi_history_view(method)
+        self.copy_history(history_id)
+        self.components.multi_history_view.switch_history.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.assert_history(history_id, histories_number=2)
+        # assert that id of current history equals history_id
+        assert self.components.multi_history_view.current_history_check(history_id=history_id).is_displayed
+        self.components.multi_history_view.switch_history.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        # assert that 'history_id' is not current history
+        self.assertRaises(NoSuchElementException, lambda:
+                          self.components.multi_history_view.current_history_check(history_id=history_id).is_displayed)
+
+    @selenium_test
+    def test_create_new_history(self):
+        history_id = self.current_history_id()
+        method = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json
+
+        self.prepare_multi_history_view(method)
+        # assert that empty history is not created in advance
+        self.components.multi_history_view.empty_message_check.assert_absent_or_hidden()
+
+        self.components.multi_history_view.create_new_button.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        self.assert_history(history_id, histories_number=2)
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        # assert that empty history is present
+        self.components.multi_history_view.empty_message_check.wait_for_present()
+
+
+    def assert_history(self, history_id, histories_number=1, should_exist=True):
+        histories = self.components.multi_history_view.histories.all()
+        assert len(histories) == histories_number
+        # search for history with history_id
+        assert should_exist == any(history.get_attribute("id") == "history-column-" + history_id for history in histories)
+
+    def copy_history(self, history_id):
+        self.components.multi_history_view.history_dropdown_btn(history_id=history_id).wait_for_and_click()
+        self.components.multi_history_view.copy.wait_for_and_click()
+        self.components.multi_history_view.copy_history_modal.copy_btn.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+    def prepare_multi_history_view(self, collection_populator_method):
+        collection = collection_populator_method()
+        collection_hid = collection["hid"]
+
+        self.home()
+        self.components.history_panel.multi_view_button.wait_for_and_click()
+
+        selector = self.history_panel_wait_for_hid_state(collection_hid, "ok")
+        self.click(selector)
+        return selector

From c9683cd3ce82414179e5d80f4dfb70d824b2cd03 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Mon, 9 Mar 2020 16:06:57 +0100
Subject: [PATCH 359/853] fix python lint

---
 lib/galaxy_test/selenium/test_history_multi_view.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy_test/selenium/test_history_multi_view.py b/lib/galaxy_test/selenium/test_history_multi_view.py
index 74498b3b6b59..6aee96691987 100644
--- a/lib/galaxy_test/selenium/test_history_multi_view.py
+++ b/lib/galaxy_test/selenium/test_history_multi_view.py
@@ -1,9 +1,9 @@
+from selenium.common.exceptions import NoSuchElementException
+
 from .framework import (
     selenium_test,
     SeleniumTestCase
 )
-from selenium.common.exceptions import NoSuchElementException
-
 
 
 class HistoryMultiViewTestCase(SeleniumTestCase):
@@ -64,7 +64,6 @@ def test_copy_history(self):
         self.copy_history(history_id)
         self.assert_history(history_id, histories_number=2)
 
-
     @selenium_test
     def test_delete_history(self):
         history_id = self.current_history_id()
@@ -79,7 +78,6 @@ def test_delete_history(self):
 
         self.assert_history(history_id, should_exist=False)
 
-
     @selenium_test
     def test_purge_history(self):
         history_id = self.current_history_id()
@@ -132,7 +130,6 @@ def test_create_new_history(self):
         # assert that empty history is present
         self.components.multi_history_view.empty_message_check.wait_for_present()
 
-
     def assert_history(self, history_id, histories_number=1, should_exist=True):
         histories = self.components.multi_history_view.histories.all()
         assert len(histories) == histories_number

From 397d9609d78af602b2cbb788c71f8b9fb10315ab Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Mon, 9 Mar 2020 13:41:28 -0400
Subject: [PATCH 360/853] fix for python3 and GEDA, was getting "Connection
 closed at byte 0"

---
 lib/galaxy/webapps/galaxy/controllers/dataset.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 708423f3a3b2..10d1d26ee32f 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -701,7 +701,7 @@ def display_application(self, trans, dataset_id=None, user_id=None, app_name=Non
                                 else:
                                     file_name = value.file_name
                                 content_length = os.path.getsize(file_name)
-                                rval = open(file_name)
+                                rval = open(file_name, 'rb')
                             except OSError as e:
                                 log.debug("Unable to access requested file in display application: %s", e)
                                 return paste.httpexceptions.HTTPNotFound("This file is no longer available.")

From d0acfaf0a1384941fcc56dc41a9f2f2e9d702c7e Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Mon, 9 Mar 2020 13:53:14 -0400
Subject: [PATCH 361/853] fix for igv fasta having name=name=

---
 display_applications/igv/genome_fasta.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/display_applications/igv/genome_fasta.xml b/display_applications/igv/genome_fasta.xml
index 1dbb9d203e01..9f5295a3a355 100644
--- a/display_applications/igv/genome_fasta.xml
+++ b/display_applications/igv/genome_fasta.xml
@@ -70,10 +70,10 @@
 </jnlp>
 ]]>
         </param>
-        <param type="data" name="fai_file" dataset="fasta_file" url="galaxy_${DATASET_HASH}.fasta.fai" format="fai" />
+        <param type="data" name="fai_file" dataset="fasta_file" url="galaxy_${DATASET_HASH}.${fasta_file.ext}.fai" format="fai" />
         <param type="template" name="redirect_url" strip="True" >
             #if $site_id.startswith( 'local_' )
-                ${site_link}?genome=${fasta_file.qp}&amp;merge=true&amp;name=name=${qp( ( $fasta_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?genome=${fasta_file.qp}&amp;merge=true&amp;name=${qp( ( $fasta_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #elif $site_id.startswith( 'web_link_' ):
 ${site_link}?sessionURL=${fasta_file.qp}&amp;genome=${fasta_file.qp}&amp;merge=true&amp;name=${qp( ( $fasta_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #else:

From f01d409f4a5b1db17463ec3a10feb2401828bf3f Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 9 Mar 2020 17:47:09 -0400
Subject: [PATCH 362/853] Revise dataset error reporting page, remove email
 option, remove long help text

---
 .../scripts/mvc/dataset/dataset-error.js      | 81 +++++--------------
 1 file changed, 21 insertions(+), 60 deletions(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-error.js b/client/galaxy/scripts/mvc/dataset/dataset-error.js
index efb2af6a8579..63d2caffbe43 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-error.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-error.js
@@ -23,7 +23,6 @@ var View = Backbone.View.extend({
     // Fetch data for the selected dataset and
     render: function() {
         var data_url = `${getAppRoot()}api/datasets/${this.model.get("dataset_id")}`;
-
         Utils.get({
             url: data_url,
             success: dataset => {
@@ -34,7 +33,7 @@ var View = Backbone.View.extend({
                         this.render_error_page(dataset, job);
                         this.find_common_problems(job);
                     },
-                    error: response => {
+                    error: () => {
                         var error_response = {
                             status: "error",
                             message: "Error occurred while loading the job.",
@@ -45,7 +44,7 @@ var View = Backbone.View.extend({
                     }
                 });
             },
-            error: response => {
+            error: () => {
                 var error_response = {
                     status: "error",
                     message: "Error occurred while loading the dataset.",
@@ -62,7 +61,7 @@ var View = Backbone.View.extend({
         Utils.get({
             url: job_url,
             success: common_problems => {
-                this.render_common_problems(job, common_problems);
+                this.render_common_problems(common_problems);
             },
             error: response => {
                 console.log("error");
@@ -72,7 +71,7 @@ var View = Backbone.View.extend({
         return;
     },
 
-    render_common_problems: function(job, common_problems) {
+    render_common_problems: function(common_problems) {
         const has_duplicate_inputs = common_problems.has_duplicate_inputs;
         const has_empty_inputs = common_problems.has_empty_inputs;
         if (has_duplicate_inputs || has_empty_inputs) {
@@ -99,10 +98,10 @@ var View = Backbone.View.extend({
     render_error_page: function(dataset, job) {
         this.$el.empty().append(`
             ${this._templateHeader()}
-            <h2>Dataset Error</h2>
+            <h2>Dataset Error Report</h2>
             <p>An error occurred while running the tool <b>${job.tool_id}</b>.</p>
             ${this.job_summary(job)}
-            <h3>Troubleshoot This Error</h3>
+            <h3>Troubleshooting</h3>
             <p>
                 There are a number of help resources to self diagnose and
                 correct problems.
@@ -110,15 +109,7 @@ var View = Backbone.View.extend({
                 href="https://galaxyproject.org/support/tool-error/"
                 target="_blank"> My job ended with an error. What can I do?</a>
             </p>
-
-            <h3>Report This Error</h3>
-            <p>
-                Usually the local Galaxy administrators regularly review errors
-                that occur on the server However, if you would like to provide
-                additional information (such as what you were trying to do when
-                the error occurred) and a contact e-mail address, we will be
-                better able to investigate your problem and get back to you.
-            </p>`);
+            <h3>Issue Report</h3>`);
         this.$el.append(this._getBugFormTemplate(dataset, job));
     },
 
@@ -129,7 +120,7 @@ var View = Backbone.View.extend({
         if (!tool_stderr && !job_stderr && !job_messages) {
             return '<h3 class="common_problems"></h3>';
         }
-        var message = "<h3>Error Details</h3>";
+        var message = "<h3>Details</h3>";
         if (job_messages) {
             message += "<p>Execution resulted in the following messages:</p>";
             for (const job_message of job_messages) {
@@ -138,7 +129,7 @@ var View = Backbone.View.extend({
         }
         if (tool_stderr) {
             message += "<p>Tool generated the following standard error:</p>";
-            message += `<pre class="code">${_.escape(tool_stderr)}</pre>`;
+            message += `<pre class="rounded code">${_.escape(tool_stderr)}</pre>`;
         }
         if (job_stderr) {
             message += "<p>Galaxy job runner generated the following standard error:</p>";
@@ -172,51 +163,21 @@ var View = Backbone.View.extend({
 
     /** Convert tab template */
     _getBugFormTemplate: function(dataset, job) {
-        const Galaxy = getGalaxyInstance();
-        var inputs = [
-            {
-                help: _l("Your email address"),
-                options: [],
-                type: "text",
-                name: "email",
-                label: "Your email",
-                value: Galaxy.user.get("email")
-            },
-            {
-                help: _l(
-                    "Any additional comments you can provide regarding what you were doing at the time of the bug."
-                ),
-                options: [],
-                type: "text",
-                area: true,
-                name: "message",
-                label: "Message"
-            }
-        ];
-
-        // TODO
-        /*
-        if (false && response.any_public) {
-            inputs.push({
-                name: "public_consent",
-                label: "Public Disclosure Consent",
-                help:
-                    "This Galaxy is configured to report to one or more error reporting backends that public to the world. By selecting 'yes', you acknowledge that this bug report will be made public.",
-                value: String(Boolean(false)),
-                options: [],
-                type: "boolean"
-            });
-        }
-        */
-
-        var form = new Form({
-            title: _l("Error Report"),
-            inputs: inputs,
+        const form = new Form({
+            inputs: [
+                {
+                    options: [],
+                    type: "text",
+                    area: true,
+                    name: "message",
+                    label: "Please provide detailed information on the activities leading to this issue:"
+                }
+            ],
             buttons: {
                 save: new Ui.Button({
                     icon: "fa-bug",
                     title: _l("Report"),
-                    cls: "ui-button btn btn-primary",
+                    cls: "btn btn-primary",
                     floating: "clear",
                     onclick: () => {
                         var form_data = form.data.create();
@@ -254,7 +215,7 @@ var View = Backbone.View.extend({
                     );
                 });
             },
-            error: response => {
+            error: () => {
                 var error_response = {
                     status: "error",
                     message: "Error occurred while saving. Please fill all the required fields and try again.",

From 92df119804bd5be6c0220fdc3415358704859cd7 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 9 Mar 2020 18:08:19 -0400
Subject: [PATCH 363/853] Disable error reporting for anonymous users, refer to
 public resources instead

---
 client/galaxy/scripts/mvc/dataset/dataset-error.js | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-error.js b/client/galaxy/scripts/mvc/dataset/dataset-error.js
index 63d2caffbe43..e6d73a606d3a 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-error.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-error.js
@@ -108,9 +108,11 @@ var View = Backbone.View.extend({
                 Start here: <a
                 href="https://galaxyproject.org/support/tool-error/"
                 target="_blank"> My job ended with an error. What can I do?</a>
-            </p>
-            <h3>Issue Report</h3>`);
-        this.$el.append(this._getBugFormTemplate(dataset, job));
+            </p>`);
+        const Galaxy = getGalaxyInstance();
+        if (Galaxy.user.id) {
+            this.$el.append("<h3>Issue Report</h3>").append(this._getBugFormTemplate(dataset, job));
+        }
     },
 
     job_summary: function(job) {

From 6af2eb432c63575347041bb1d2af82ea803cddc5 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 9 Mar 2020 18:12:44 -0400
Subject: [PATCH 364/853] Highlight public help resources link in dataset error
 report

---
 client/galaxy/scripts/mvc/dataset/dataset-error.js | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-error.js b/client/galaxy/scripts/mvc/dataset/dataset-error.js
index e6d73a606d3a..9c8169730e46 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-error.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-error.js
@@ -103,11 +103,15 @@ var View = Backbone.View.extend({
             ${this.job_summary(job)}
             <h3>Troubleshooting</h3>
             <p>
-                There are a number of help resources to self diagnose and
+                There are a number of helpful resources to self diagnose and
                 correct problems.
-                Start here: <a
-                href="https://galaxyproject.org/support/tool-error/"
-                target="_blank"> My job ended with an error. What can I do?</a>
+                <br>
+                Start here:
+                <b>
+                    <a href="https://galaxyproject.org/support/tool-error/" target="_blank">
+                        My job ended with an error. What can I do?
+                    </a>
+                </b>
             </p>`);
         const Galaxy = getGalaxyInstance();
         if (Galaxy.user.id) {

From 89ba43f8472550cddf5e77c934eff0434a88d9fe Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 9 Mar 2020 19:27:35 -0400
Subject: [PATCH 365/853] Raise exception when trying to overwrite existing
 attr

Except base config attributes set in `_set_config_base()`
---
 lib/galaxy/config/__init__.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 982fa59666cd..c3a8bf5af599 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -212,11 +212,14 @@ def strip_deprecated_dir(key, value):
                 self._raw_config[key] = value
 
     def _create_attributes_from_raw_config(self):
+        # `base_configs` are a special case: these attributes have been created and will be ignored
+        # by the code below. Trying to overwrite any other existing attributes will raise an error.
+        base_configs = {'config_dir', 'data_dir', 'managed_config_dir'}
         for key, value in self._raw_config.items():
             if not hasattr(self, key):
                 setattr(self, key, value)
-            else:
-                log.debug("Attribute '%s' is set and cannot be overwritten with value '%s'" % (key, value))
+            elif key not in base_configs:
+                raise ConfigurationError("Attempting to override existing attribute '%s'" % key)
 
     def _resolve_paths(self):
 

From 49da637f7158d3f69a8680a868e9d324e40e9d6b Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 9 Mar 2020 19:37:58 -0400
Subject: [PATCH 366/853] Explicitly specify user email on client as hidden
 field for dataset error reporting

---
 client/galaxy/scripts/mvc/dataset/dataset-error.js | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-error.js b/client/galaxy/scripts/mvc/dataset/dataset-error.js
index 9c8169730e46..6bf8d2ead990 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-error.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-error.js
@@ -169,10 +169,16 @@ var View = Backbone.View.extend({
 
     /** Convert tab template */
     _getBugFormTemplate: function(dataset, job) {
+        const Galaxy = getGalaxyInstance();
         const form = new Form({
             inputs: [
                 {
-                    options: [],
+                    type: "text",
+                    hidden: true,
+                    name: "email",
+                    value: Galaxy.user.email
+                },
+                {
                     type: "text",
                     area: true,
                     name: "message",

From 7ac4d8301000939048cb6648b6d32471098d661b Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 9 Mar 2020 19:45:36 -0400
Subject: [PATCH 367/853] Use new schema.defaults property

Instead of app_schema['foo'].get('default') - as per code review
---
 lib/galaxy/tools/toolbox/base.py | 2 +-
 test/unit/tools/test_toolbox.py  | 6 +-----
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 08a4697564af..070791cf08f4 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -1218,7 +1218,7 @@ def _init_dependency_manager(self):
         app_config_dict = self.app.config.config_dict
         conf_file = app_config_dict.get("dependency_resolvers_config_file")
         default_tool_dependency_dir = os.path.join(
-            self.app.config.data_dir, self.app.config.schema.app_schema['tool_dependency_dir'].get('default'))
+            self.app.config.data_dir, self.app.config.schema.defaults['tool_dependency_dir'])
         self.dependency_manager = build_dependency_manager(
             app_config_dict=app_config_dict, conf_file=conf_file, default_tool_dependency_dir=default_tool_dependency_dir)
 
diff --git a/test/unit/tools/test_toolbox.py b/test/unit/tools/test_toolbox.py
index d2bfc6caaabf..974b30bfb419 100644
--- a/test/unit/tools/test_toolbox.py
+++ b/test/unit/tools/test_toolbox.py
@@ -564,11 +564,7 @@ def __init__(self, test_case):
         app.tool_cache = ToolCache() if not hasattr(app, 'tool_cache') else app.tool_cache
         app.job_config.get_tool_resource_parameters = lambda tool_id: None
         app.config.update_integrated_tool_panel = True
-        app.config.schema.app_schema = {
-            'tool_dependency_dir': {
-                'default': 'dependencies',
-            }
-        }
+        app.config.schema.defaults = {'tool_dependency_dir': 'dependencies'}
         config_files = test_case.config_files
         tool_root_dir = test_case.test_directory
         super(SimplifiedToolBox, self).__init__(

From 9ab7a94aacfc94e6fc90a0e90565b59f5b7eb4aa Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 9 Mar 2020 20:20:24 -0400
Subject: [PATCH 368/853] Retrieve user email through model get helper in
 dataset issue report form

---
 client/galaxy/scripts/mvc/dataset/dataset-error.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-error.js b/client/galaxy/scripts/mvc/dataset/dataset-error.js
index 6bf8d2ead990..32533a206258 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-error.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-error.js
@@ -176,7 +176,7 @@ var View = Backbone.View.extend({
                     type: "text",
                     hidden: true,
                     name: "email",
-                    value: Galaxy.user.email
+                    value: Galaxy.user.get("email")
                 },
                 {
                     type: "text",

From 76d52f40cd871a70894272cb1fa780ee964afc23 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 10 Mar 2020 04:18:41 +0000
Subject: [PATCH 369/853] Use auto_create functionality of
 `get_private_user_role()`

Address https://github.com/galaxyproject/galaxy/pull/9168/files#r361814891
---
 lib/galaxy/model/security.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index ec728dc6143a..a73e4967f51a 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -658,8 +658,7 @@ def associate_action_dataset_role(self, action, dataset, role):
 
     def create_user_role(self, user, app):
         # Create private user role if necessary
-        if not self.get_private_user_role(user):
-            self.create_private_user_role(user)
+        self.get_private_user_role(user, auto_create=True)
         # Create default user permissions if necessary
         if not user.default_permissions:
             if hasattr(app.config, "new_user_dataset_access_role_default_private"):

From 92987e38e5067a25d6cd54db15bb1dc945bb3940 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 10 Mar 2020 01:22:19 -0400
Subject: [PATCH 370/853] Allow anonymous users to report dataset errors

---
 client/galaxy/scripts/mvc/dataset/dataset-error.js | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-error.js b/client/galaxy/scripts/mvc/dataset/dataset-error.js
index 32533a206258..175934dec525 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-error.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-error.js
@@ -113,10 +113,7 @@ var View = Backbone.View.extend({
                     </a>
                 </b>
             </p>`);
-        const Galaxy = getGalaxyInstance();
-        if (Galaxy.user.id) {
-            this.$el.append("<h3>Issue Report</h3>").append(this._getBugFormTemplate(dataset, job));
-        }
+        this.$el.append("<h3>Issue Report</h3>").append(this._getBugFormTemplate(dataset, job));
     },
 
     job_summary: function(job) {
@@ -170,13 +167,15 @@ var View = Backbone.View.extend({
     /** Convert tab template */
     _getBugFormTemplate: function(dataset, job) {
         const Galaxy = getGalaxyInstance();
+        const userEmail = Galaxy.user.get("email");
         const form = new Form({
             inputs: [
                 {
                     type: "text",
-                    hidden: true,
+                    hidden: !!userEmail,
                     name: "email",
-                    value: Galaxy.user.get("email")
+                    value: userEmail,
+                    label: "Please provide your email:"
                 },
                 {
                     type: "text",

From 42abe1660e70717edaa3c4eb69dc9bbff7a15bae Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Tue, 10 Mar 2020 13:28:51 +0100
Subject: [PATCH 371/853] Migrate to VueJS from Backbone

---
 .../scripts/components/ToolRecommendation.vue | 286 ++++++++++++++++++
 .../galaxy/scripts/mvc/tool-recommendation.js | 237 ---------------
 client/galaxy/scripts/mvc/tool/tool-form.js   |  15 +-
 client/galaxy/style/scss/base.scss            |  20 --
 4 files changed, 296 insertions(+), 262 deletions(-)
 create mode 100644 client/galaxy/scripts/components/ToolRecommendation.vue
 delete mode 100644 client/galaxy/scripts/mvc/tool-recommendation.js

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
new file mode 100644
index 000000000000..28886ab8bcd5
--- /dev/null
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -0,0 +1,286 @@
+<template>
+    <div id="tool-recommendation-view">
+        <div v-if="deprecated == false" class='infomessagelarge'>
+            You have used {{ getToolId }} tool. For further analysis, you could try using the following/recommended tools. The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to open its definition.
+        </div>   
+        <div v-if="deprecated == true" class='warningmessagelarge'>
+            You have used {{ getToolId }} tool. {{deprecatedMessage}}
+        </div>
+    </div>
+</template>
+
+<script>
+import Utils from "utils/utils";
+import * as d3 from "d3";
+import { getAppRoot } from "onload/loadConfig";
+import $ from "jquery";
+
+export default {
+    props: {
+        toolId: {
+            type: String,
+            required: true
+        }
+    },
+    data() {
+        return {
+            deprecated: null,
+            deprecatedMessage: ""
+        };
+    },
+    created: function() {
+        this.loadRecommendations();
+    },
+    computed: {
+        getToolId: function() {
+            let toolId = this.toolId || "";
+            if (toolId.indexOf("/") > 0) {
+                const toolIdSlash = toolId.split("/");
+                toolId = toolIdSlash[toolIdSlash.length - 2];
+            }
+            return toolId;
+        }
+    },
+    methods: {
+        loadRecommendations: function() {
+            const self = this;
+            let toolId = this.getToolId;
+            Utils.request({
+                type: "POST",
+                url: `${getAppRoot()}api/workflows/get_tool_predictions`,
+                data: {tool_sequence: toolId},
+                success: data => {
+                    // get datatypes mapping
+                    const datatypes_mapping = JSON.parse(
+                        $.ajax({
+                            url: `${getAppRoot()}api/datatypes/mapping`,
+                            async: false
+                        }).responseText
+                    ),
+                    extToType = datatypes_mapping.ext_to_class_name,
+                    typeToType = datatypes_mapping.class_to_classes,
+                    predData = data.predicted_data;
+                    this.deprecated = predData["is_deprecated"];
+                    if (data !== null && predData.children.length > 0) {
+                        const filteredData = {},
+                        compatibleTools = {},
+                        filteredChildren = [],
+                        outputDatatypes = predData["o_extensions"],
+                        children = predData.children;
+                        for (const nameObj of children.entries()) {
+                            const inputDatatypes = nameObj[1]["i_extensions"];
+                            for (const out_t of outputDatatypes.entries()) {
+                                for (const in_t of inputDatatypes.entries()) {
+                                    const child = extToType[out_t[1]],
+                                    parent = extToType[in_t[1]];
+                                    if (
+                                        (typeToType[child] && parent in typeToType[child]) === true ||
+                                        out_t[1] === "input" ||
+                                        out_t[1] === "_sniff_" ||
+                                        out_t[1] === "input_collection"
+                                    ) {
+                                        compatibleTools[nameObj[1]["tool_id"]] = nameObj[1]["name"];
+                                        break;
+                                    }
+                                }
+                            }
+                        }
+                        for (const id in compatibleTools) {
+                            for (const nameObj of children.entries()) {
+                                if (nameObj[1]["tool_id"] === id) {
+                                    filteredChildren.push(nameObj[1]);
+                                    break;
+                                }
+                            }
+                        }
+                        filteredData["o_extensions"] = predData["o_extensions"];
+                        filteredData["name"] = predData["name"];
+                        filteredData["children"] = filteredChildren;
+                        if (filteredChildren.length > 0 && this.deprecated === false) {
+                            self.renderD3Tree(filteredData);
+                        }
+                        else if (this.deprecated === true) {
+                            this.deprecatedMessage = predData["message"];
+                        }
+                    }
+                }
+            });
+        },
+        renderD3Tree: function(predictedTools) {
+            const margin = { top: 20, right: 30, bottom: 20, left: 250 },
+            width = 900 - margin.right - margin.left,
+            height = 300 - margin.top - margin.bottom,
+            duration = 750;
+            const tree = d3.layout.tree().size([height, width]);
+            const diagonal = d3.svg.diagonal().projection(d => {
+                return [d.y, d.x];
+            });
+            const svg = d3
+                .select("#tool-recommendation-view")
+                .append("svg")
+                .attr("class", "tree-size")
+                .append("g")
+                .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+            let i = 0,
+            root = null;
+            function update(source) {
+                // Compute the new tree layout.
+                const nodes = tree.nodes(root).reverse(),
+                links = tree.links(nodes);
+                // Normalize for fixed-depth.
+                nodes.forEach(d => {
+                    d.y = d.depth * 180;
+                });
+                // Update the nodes…
+                const node = svg.selectAll("g.node").data(nodes, d => {
+                    return d.id || (d.id = ++i);
+                });
+                // Enter any new nodes at the parent's previous position.
+                const nodeEnter = node
+                    .enter()
+                    .append("g")
+                    .attr("class", "node")
+                    .attr("transform", d => {
+                        return "translate(" + source.y0 + "," + source.x0 + ")";
+                    })
+                    .on("click", click);
+                nodeEnter
+                    .append("circle")
+                    .attr("r", 1e-6)
+                nodeEnter
+                    .append("text")
+                    .attr("x", d => {
+                        return d.children || d._children ? -10 : 10;
+                    })
+                    .attr("dy", ".35em")
+                    .attr("text-anchor", d => {
+                        return d.children || d._children ? "end" : "start";
+                    })
+                    .text(d => {
+                        return d.name;
+                    })
+                    .attr("class", "node-enter");
+                nodeEnter.append("title").text(d => {
+                    return d.children || d._children ? "Click to collapse" : "Click to open tool definition";
+                });
+                // Transition nodes to their new position.
+                const nodeUpdate = node
+                    .transition()
+                    .duration(duration)
+                    .attr("transform", d => {
+                        return "translate(" + d.y + "," + d.x + ")";
+                    });
+                nodeUpdate
+                    .select("circle")
+                    .attr("r", 4.5)
+                nodeUpdate.select("text")
+                    .attr("class", "node-update")
+                // Transition exiting nodes to the parent's new position.
+                const nodeExit = node
+                    .exit()
+                    .transition()
+                    .duration(duration)
+                    .attr("transform", d => {
+                        return "translate(" + source.y + "," + source.x + ")";
+                    })
+                    .remove();
+                nodeExit.select("circle")
+                    .attr("r", 1e-6);
+                nodeExit.select("text")
+                    .attr("class", "node-enter");
+                // Update the links
+                const link = svg.selectAll("path.link").data(links, d => {
+                    return d.target.id;
+                });
+                // Enter any new links at the parent's previous position.
+                link.enter()
+                    .insert("path", "g")
+                    .attr("class", "link")
+                    .attr("d", d => {
+                        const o = {x: source.x0, y: source.y0};
+                        return diagonal({source: o, target: o});
+                    });
+                // Transition links to their new position.
+                link.transition()
+                    .duration(duration)
+                    .attr("d", diagonal);
+                // Transition exiting nodes to the parent's new position.
+                link.exit()
+                    .transition()
+                    .duration(duration)
+                    .attr("d", d => {
+                        const o = { x: source.x, y: source.y };
+                        return diagonal({ source: o, target: o });
+                    })
+                    .remove();
+                // Stash the old positions for transition.
+                nodes.forEach(d => {
+                    d.x0 = d.x;
+                    d.y0 = d.y;
+                });
+            }
+            // Toggle children on click.
+            function click(d) {
+                if (d.children) {
+                    d._children = d.children;
+                    d.children = null;
+                } else {
+                    d.children = d._children;
+                    d._children = null;
+                }
+                update(d);
+                if (d.tool_id !== undefined && d.tool_id !== "undefined" && d.tool_id !== null && d.tool_id !== "") {
+                    document.location.href = `${getAppRoot()}` + "tool_runner?tool_id=" + d.tool_id;
+                }
+            }
+            function collapse(d) {
+                if (d.children) {
+                    d._children = d.children;
+                    d._children.forEach(collapse);
+                    d.children = null;
+                }
+            }
+            root = predictedTools;
+            root.x0 = height / 2;
+            root.y0 = 0;
+            root.children.forEach(collapse);
+            update(root);
+        }
+    }
+};
+</script>
+
+<style>
+.node {
+    cursor: pointer;
+}
+
+.node circle {
+    fill: #000;
+    stroke: #c2ebc2;
+    stroke-width: 0.3rem;
+}
+
+.node text {
+    font: 0.75rem sans-serif;
+}
+
+.node-enter {
+    fill-opacity: 1e-6;
+}
+
+.node-update {
+    fill-opacity: 1;
+}
+
+.tree-size {
+    width: 100%;
+    height: 450px;
+}
+
+.link {
+    fill: none;
+    stroke: #c2ebc2;
+    stroke-width: 0.3rem;
+}
+</style>
diff --git a/client/galaxy/scripts/mvc/tool-recommendation.js b/client/galaxy/scripts/mvc/tool-recommendation.js
deleted file mode 100644
index 09e9a29812f3..000000000000
--- a/client/galaxy/scripts/mvc/tool-recommendation.js
+++ /dev/null
@@ -1,237 +0,0 @@
-import Backbone from "backbone";
-import Utils from "utils/utils";
-import * as d3 from "d3";
-import { getAppRoot } from "onload/loadConfig";
-import $ from "jquery";
-
-var ToolRecommendationView = Backbone.View.extend({
-    el: "#tool-recommendation-view",
-
-    initialize: function(options) {
-        let toolId = options.toolId || "";
-        const self = this;
-        if (toolId.indexOf("/") > 0) {
-            const toolIdSlash = toolId.split("/");
-            toolId = toolIdSlash[toolIdSlash.length - 2];
-        }
-        Utils.request({
-            type: "POST",
-            url: `${getAppRoot()}api/workflows/get_tool_predictions`,
-            data: { tool_sequence: toolId },
-            success: data => {
-                // get datatypes mapping
-                const datatypes_mapping = JSON.parse(
-                        $.ajax({
-                            url: `${getAppRoot()}api/datatypes/mapping`,
-                            async: false
-                        }).responseText
-                    ),
-                    extToType = datatypes_mapping.ext_to_class_name,
-                    typeToType = datatypes_mapping.class_to_classes,
-                    predData = data.predicted_data;
-                if (data !== null && predData.children.length > 0) {
-                    const filteredData = {},
-                        compatibleTools = {},
-                        filteredChildren = [],
-                        outputDatatypes = predData["o_extensions"],
-                        children = predData.children;
-                    for (const nameObj of children.entries()) {
-                        const inputDatatypes = nameObj[1]["i_extensions"];
-                        for (const out_t of outputDatatypes.entries()) {
-                            for (const in_t of inputDatatypes.entries()) {
-                                const child = extToType[out_t[1]],
-                                    parent = extToType[in_t[1]];
-                                if (
-                                    (typeToType[child] && parent in typeToType[child]) === true ||
-                                    out_t[1] === "input" ||
-                                    out_t[1] === "_sniff_" ||
-                                    out_t[1] === "input_collection"
-                                ) {
-                                    compatibleTools[nameObj[1]["tool_id"]] = nameObj[1]["name"];
-                                    break;
-                                }
-                            }
-                        }
-                    }
-                    for (const id in compatibleTools) {
-                        for (const nameObj of children.entries()) {
-                            if (nameObj[1]["tool_id"] === id) {
-                                filteredChildren.push(nameObj[1]);
-                                break;
-                            }
-                        }
-                    }
-                    filteredData["o_extensions"] = predData["o_extensions"];
-                    filteredData["name"] = predData["name"];
-                    filteredData["children"] = filteredChildren;
-                    if (filteredChildren.length > 0 && predData["is_deprecated"] === false) {
-                        self.$el.append(
-                            "<div class='infomessagelarge'>You have used " +
-                                filteredData.name +
-                                " tool. For further analysis, you could try using the following/recommended tools. The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to open its definition. </div>"
-                        );
-                        self.render_tree(filteredData);
-                    } else if (predData["is_deprecated"] === true) {
-                        self.$el.append(
-                            "<div class='warningmessagelarge'>You have used " +
-                                predData.name +
-                                " tool. " +
-                                predData["message"] +
-                                ". </div>"
-                        );
-                    }
-                }
-            }
-        });
-    },
-
-    render_tree: function(predicted_data) {
-        const margin = { top: 20, right: 30, bottom: 20, left: 250 },
-            width = 900 - margin.right - margin.left,
-            height = 300 - margin.top - margin.bottom,
-            duration = 750;
-        const tree = d3.layout.tree().size([height, width]);
-        const diagonal = d3.svg.diagonal().projection(d => {
-            return [d.y, d.x];
-        });
-        const svg = d3
-            .select("#tool-recommendation-view")
-            .append("svg")
-            .attr("width", width + margin.right + margin.left)
-            .attr("height", height + margin.top + margin.bottom)
-            .append("g")
-            .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
-        let i = 0,
-            root = null;
-        function update(source) {
-            // Compute the new tree layout.
-            const nodes = tree.nodes(root).reverse(),
-                links = tree.links(nodes);
-            // Normalize for fixed-depth.
-            nodes.forEach(d => {
-                d.y = d.depth * 180;
-            });
-            // Update the nodes…
-            const node = svg.selectAll("g.node").data(nodes, d => {
-                return d.id || (d.id = ++i);
-            });
-            // Enter any new nodes at the parent's previous position.
-            const nodeEnter = node
-                .enter()
-                .append("g")
-                .attr("class", "node")
-                .attr("transform", d => {
-                    return "translate(" + source.y0 + "," + source.x0 + ")";
-                })
-                .on("click", click);
-            nodeEnter
-                .append("circle")
-                .attr("r", 1e-6)
-                .style("fill", d => {
-                    return d._children ? "lightsteelblue" : "#fff";
-                });
-            nodeEnter
-                .append("text")
-                .attr("x", d => {
-                    return d.children || d._children ? -10 : 10;
-                })
-                .attr("dy", ".35em")
-                .attr("text-anchor", d => {
-                    return d.children || d._children ? "end" : "start";
-                })
-                .text(d => {
-                    return d.name;
-                })
-                .style("fill-opacity", 1e-6);
-            nodeEnter.append("title").text(d => {
-                return d.children || d._children ? "Click to collapse" : "Click to open tool definition";
-            });
-            // Transition nodes to their new position.
-            const nodeUpdate = node
-                .transition()
-                .duration(duration)
-                .attr("transform", d => {
-                    return "translate(" + d.y + "," + d.x + ")";
-                });
-            nodeUpdate
-                .select("circle")
-                .attr("r", 4.5)
-                .style("fill", d => {
-                    return d._children ? "lightsteelblue" : "#fff";
-                });
-            nodeUpdate.select("text").style("fill-opacity", 1);
-            // Transition exiting nodes to the parent's new position.
-            const nodeExit = node
-                .exit()
-                .transition()
-                .duration(duration)
-                .attr("transform", d => {
-                    return "translate(" + source.y + "," + source.x + ")";
-                })
-                .remove();
-            nodeExit.select("circle").attr("r", 1e-6);
-            nodeExit.select("text").style("fill-opacity", 1e-6);
-            // Update the links…
-            const link = svg.selectAll("path.link").data(links, d => {
-                return d.target.id;
-            });
-            // Enter any new links at the parent's previous position.
-            link.enter()
-                .insert("path", "g")
-                .attr("class", "link")
-                .attr("d", d => {
-                    const o = { x: source.x0, y: source.y0 };
-                    return diagonal({ source: o, target: o });
-                });
-            // Transition links to their new position.
-            link.transition()
-                .duration(duration)
-                .attr("d", diagonal);
-            // Transition exiting nodes to the parent's new position.
-            link.exit()
-                .transition()
-                .duration(duration)
-                .attr("d", d => {
-                    const o = { x: source.x, y: source.y };
-                    return diagonal({ source: o, target: o });
-                })
-                .remove();
-            // Stash the old positions for transition.
-            nodes.forEach(d => {
-                d.x0 = d.x;
-                d.y0 = d.y;
-            });
-        }
-        // Toggle children on click.
-        function click(d) {
-            if (d.children) {
-                d._children = d.children;
-                d.children = null;
-            } else {
-                d.children = d._children;
-                d._children = null;
-            }
-            update(d);
-            if (d.tool_id !== undefined && d.tool_id !== "undefined" && d.tool_id !== null && d.tool_id !== "") {
-                document.location.href = `${getAppRoot()}` + "tool_runner?tool_id=" + d.tool_id;
-            }
-        }
-        function collapse(d) {
-            if (d.children) {
-                d._children = d.children;
-                d._children.forEach(collapse);
-                d.children = null;
-            }
-        }
-        d3.select(self.frameElement).style("height", "400px");
-        root = predicted_data;
-        root.x0 = height / 2;
-        root.y0 = 0;
-        root.children.forEach(collapse);
-        update(root);
-    }
-});
-
-export default {
-    ToolRecommendationView: ToolRecommendationView
-};
diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index f973f10b2880..10386c03008f 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -13,7 +13,7 @@ import ToolFormBase from "mvc/tool/tool-form-base";
 import Webhooks from "mvc/webhooks";
 import Vue from "vue";
 import ToolEntryPoints from "components/ToolEntryPoints/ToolEntryPoints";
-import ToolRecommendation from "mvc/tool-recommendation";
+import ToolRecommendation from "components/ToolRecommendation";
 
 const View = Backbone.View.extend({
     initialize: function(options) {
@@ -271,10 +271,15 @@ const View = Backbone.View.extend({
                 const enable_tool_recommendations = window.Galaxy.config.enable_tool_recommendations;
                 if (enable_tool_recommendations === true || enable_tool_recommendations === "true") {
                     // show tool recommendations
-                    this.$el.append($("<div/>", { id: "tool-recommendation-view" }));
-                    new ToolRecommendation.ToolRecommendationView({
-                        toolId: job_def.tool_id
-                    });
+                    const ToolRecommendationInstance = Vue.extend(ToolRecommendation);
+                        const vm = document.createElement("div");
+                        this.$el.append(vm);
+                        const instance = new ToolRecommendationInstance({
+                            propsData: {
+                                toolId: job_def.tool_id
+                            }
+                        });
+                        instance.$mount(vm);
                 }
                 this.$el.parent().scrollTop(0);
                 // Show Webhook if job is running
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index c6b0e3f2e19d..ed488b4f892e 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1650,23 +1650,3 @@ body.reports {
     bottom: 0;
     background: url(../../images/largespinner.gif) no-repeat center center fixed;
 }
-
-/* For collapsible D3 tree */
-
-.node {
-    cursor: pointer;
-}
-.node circle {
-    fill: #000;
-    stroke: #c2ebc2;
-    stroke-width: 0.3rem;
-}
-.node text {
-    font: 0.75rem sans-serif;
-}
-
-.link {
-    fill: none;
-    stroke: #c2ebc2;
-    stroke-width: 0.3rem;
-}

From 2c723457086875854273c6bb69f697681ac53e1f Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Tue, 10 Mar 2020 15:03:46 +0100
Subject: [PATCH 372/853] Fix linting error

---
 client/galaxy/scripts/components/ToolRecommendation.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 28886ab8bcd5..85c08679e5d9 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -44,7 +44,7 @@ export default {
     methods: {
         loadRecommendations: function() {
             const self = this;
-            let toolId = this.getToolId;
+            const toolId = this.getToolId;
             Utils.request({
                 type: "POST",
                 url: `${getAppRoot()}api/workflows/get_tool_predictions`,

From b797b0fb4689e801b473e7b2d702175ecb18504e Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Tue, 10 Mar 2020 15:06:39 +0100
Subject: [PATCH 373/853] Fix indentation

---
 client/galaxy/scripts/mvc/tool/tool-form.js | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index 10386c03008f..212134fc247c 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -272,14 +272,14 @@ const View = Backbone.View.extend({
                 if (enable_tool_recommendations === true || enable_tool_recommendations === "true") {
                     // show tool recommendations
                     const ToolRecommendationInstance = Vue.extend(ToolRecommendation);
-                        const vm = document.createElement("div");
-                        this.$el.append(vm);
-                        const instance = new ToolRecommendationInstance({
-                            propsData: {
-                                toolId: job_def.tool_id
-                            }
-                        });
-                        instance.$mount(vm);
+                    const vm = document.createElement("div");
+                    this.$el.append(vm);
+                    const instance = new ToolRecommendationInstance({
+                        propsData: {
+                            toolId: job_def.tool_id
+                        }
+                    });
+                    instance.$mount(vm);
                 }
                 this.$el.parent().scrollTop(0);
                 // Show Webhook if job is running

From b6051585b82caeaf51f054fb4e96d5e339408f52 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Tue, 10 Mar 2020 16:42:46 +0100
Subject: [PATCH 374/853] Fix prettier

---
 .../scripts/components/ToolRecommendation.vue | 76 +++++++++----------
 1 file changed, 36 insertions(+), 40 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 85c08679e5d9..6abcf09b319f 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -1,10 +1,14 @@
 <template>
     <div id="tool-recommendation-view">
-        <div v-if="deprecated == false" class='infomessagelarge'>
-            You have used {{ getToolId }} tool. For further analysis, you could try using the following/recommended tools. The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to open its definition.
-        </div>   
-        <div v-if="deprecated == true" class='warningmessagelarge'>
-            You have used {{ getToolId }} tool. {{deprecatedMessage}}
+        <div v-if="deprecated == false" class="infomessagelarge">
+            You have used {{ getToolId }} tool. For further analysis, you could try using the following/recommended
+            tools. The recommended tools are shown in the decreasing order of their scores predicted using machine
+            learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following
+            tool than a tool with a lower score. Please click on one of the following/recommended tools to open its
+            definition.
+        </div>
+        <div v-if="deprecated == true" class="warningmessagelarge">
+            You have used {{ getToolId }} tool. {{ deprecatedMessage }}
         </div>
     </div>
 </template>
@@ -48,31 +52,31 @@ export default {
             Utils.request({
                 type: "POST",
                 url: `${getAppRoot()}api/workflows/get_tool_predictions`,
-                data: {tool_sequence: toolId},
+                data: { tool_sequence: toolId },
                 success: data => {
                     // get datatypes mapping
                     const datatypes_mapping = JSON.parse(
-                        $.ajax({
-                            url: `${getAppRoot()}api/datatypes/mapping`,
-                            async: false
-                        }).responseText
-                    ),
-                    extToType = datatypes_mapping.ext_to_class_name,
-                    typeToType = datatypes_mapping.class_to_classes,
-                    predData = data.predicted_data;
+                            $.ajax({
+                                url: `${getAppRoot()}api/datatypes/mapping`,
+                                async: false
+                            }).responseText
+                        ),
+                        extToType = datatypes_mapping.ext_to_class_name,
+                        typeToType = datatypes_mapping.class_to_classes,
+                        predData = data.predicted_data;
                     this.deprecated = predData["is_deprecated"];
                     if (data !== null && predData.children.length > 0) {
                         const filteredData = {},
-                        compatibleTools = {},
-                        filteredChildren = [],
-                        outputDatatypes = predData["o_extensions"],
-                        children = predData.children;
+                            compatibleTools = {},
+                            filteredChildren = [],
+                            outputDatatypes = predData["o_extensions"],
+                            children = predData.children;
                         for (const nameObj of children.entries()) {
                             const inputDatatypes = nameObj[1]["i_extensions"];
                             for (const out_t of outputDatatypes.entries()) {
                                 for (const in_t of inputDatatypes.entries()) {
                                     const child = extToType[out_t[1]],
-                                    parent = extToType[in_t[1]];
+                                        parent = extToType[in_t[1]];
                                     if (
                                         (typeToType[child] && parent in typeToType[child]) === true ||
                                         out_t[1] === "input" ||
@@ -98,8 +102,7 @@ export default {
                         filteredData["children"] = filteredChildren;
                         if (filteredChildren.length > 0 && this.deprecated === false) {
                             self.renderD3Tree(filteredData);
-                        }
-                        else if (this.deprecated === true) {
+                        } else if (this.deprecated === true) {
                             this.deprecatedMessage = predData["message"];
                         }
                     }
@@ -108,9 +111,9 @@ export default {
         },
         renderD3Tree: function(predictedTools) {
             const margin = { top: 20, right: 30, bottom: 20, left: 250 },
-            width = 900 - margin.right - margin.left,
-            height = 300 - margin.top - margin.bottom,
-            duration = 750;
+                width = 900 - margin.right - margin.left,
+                height = 300 - margin.top - margin.bottom,
+                duration = 750;
             const tree = d3.layout.tree().size([height, width]);
             const diagonal = d3.svg.diagonal().projection(d => {
                 return [d.y, d.x];
@@ -122,11 +125,11 @@ export default {
                 .append("g")
                 .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
             let i = 0,
-            root = null;
+                root = null;
             function update(source) {
                 // Compute the new tree layout.
                 const nodes = tree.nodes(root).reverse(),
-                links = tree.links(nodes);
+                    links = tree.links(nodes);
                 // Normalize for fixed-depth.
                 nodes.forEach(d => {
                     d.y = d.depth * 180;
@@ -144,9 +147,7 @@ export default {
                         return "translate(" + source.y0 + "," + source.x0 + ")";
                     })
                     .on("click", click);
-                nodeEnter
-                    .append("circle")
-                    .attr("r", 1e-6)
+                nodeEnter.append("circle").attr("r", 1e-6);
                 nodeEnter
                     .append("text")
                     .attr("x", d => {
@@ -170,11 +171,8 @@ export default {
                     .attr("transform", d => {
                         return "translate(" + d.y + "," + d.x + ")";
                     });
-                nodeUpdate
-                    .select("circle")
-                    .attr("r", 4.5)
-                nodeUpdate.select("text")
-                    .attr("class", "node-update")
+                nodeUpdate.select("circle").attr("r", 4.5);
+                nodeUpdate.select("text").attr("class", "node-update");
                 // Transition exiting nodes to the parent's new position.
                 const nodeExit = node
                     .exit()
@@ -184,10 +182,8 @@ export default {
                         return "translate(" + source.y + "," + source.x + ")";
                     })
                     .remove();
-                nodeExit.select("circle")
-                    .attr("r", 1e-6);
-                nodeExit.select("text")
-                    .attr("class", "node-enter");
+                nodeExit.select("circle").attr("r", 1e-6);
+                nodeExit.select("text").attr("class", "node-enter");
                 // Update the links
                 const link = svg.selectAll("path.link").data(links, d => {
                     return d.target.id;
@@ -197,8 +193,8 @@ export default {
                     .insert("path", "g")
                     .attr("class", "link")
                     .attr("d", d => {
-                        const o = {x: source.x0, y: source.y0};
-                        return diagonal({source: o, target: o});
+                        const o = { x: source.x0, y: source.y0 };
+                        return diagonal({ source: o, target: o });
                     });
                 // Transition links to their new position.
                 link.transition()

From 09a0e4696e999b362ba581e1810d42eed111cce9 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 10 Mar 2020 12:36:10 -0400
Subject: [PATCH 375/853] Update charts entrypoint inclusion of dist artifacts

---
 .../common/templates/chart_entry_point.mako          | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/config/plugins/visualizations/common/templates/chart_entry_point.mako b/config/plugins/visualizations/common/templates/chart_entry_point.mako
index 2ec6e28303ef..4b67cf76a33c 100644
--- a/config/plugins/visualizations/common/templates/chart_entry_point.mako
+++ b/config/plugins/visualizations/common/templates/chart_entry_point.mako
@@ -1,19 +1,17 @@
 # -*- coding: utf-8 -*-
 <%inherit file="visualization_base.mako"/>
 <%def name="stylesheets()">
-    ${h.css('jquery-ui/smoothness/jquery-ui')}
-    ${h.css('base')}
+    ${h.dist_css('base')}
     <%css_path = script_attributes.get("css") %>
     %if css_path is not None:
         <link rel="stylesheet" href="${static_url}${css_path}">
     %endif
 </%def>
 <%def name="javascripts()">
-    ${h.js('libs/jquery/jquery',
-           'libs/jquery/jquery-ui',
-           'bundled/libs.chunk',
-           'bundled/base.chunk',
-           'bundled/generic.bundled')}
+    ${h.dist_js(
+           'libs.chunk',
+           'base.chunk',
+           'generic.bundled')}
     <%src_path = script_attributes.get("src") %>
     <script type="text/javascript" src="${static_url}${src_path}"></script>
     <script type="text/javascript">

From 39a8c0ca6342e2ceba8721244a222b5ef266aecd Mon Sep 17 00:00:00 2001
From: Alex Ostrovsky <40246333+astrovsky01@users.noreply.github.com>
Date: Tue, 10 Mar 2020 12:52:13 -0400
Subject: [PATCH 376/853] Fixed tool locations

---
 doc/source/admin/special_topics/interactivetools.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/source/admin/special_topics/interactivetools.rst b/doc/source/admin/special_topics/interactivetools.rst
index d08e4d7a968b..2b5a4111cfe0 100644
--- a/doc/source/admin/special_topics/interactivetools.rst
+++ b/doc/source/admin/special_topics/interactivetools.rst
@@ -115,7 +115,7 @@ Some **example test InteractiveTools** have been defined, and can be added to th
 
 .. code-block:: xml
 
-        <tool file="../test/functional/tools/interactive_juypter_notebook.xml" />
-        <tool file="../test/functional/tools/interactive_cellxgene.xml" />
+        <tool file="interactive/interactive_juypter_notebook.xml" />
+        <tool file="interactive/interactive_cellxgene.xml" />
 
 

From 3b7c307de9d2ded4b9b647c8633a31677a2d21d3 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 10 Mar 2020 16:31:37 -0400
Subject: [PATCH 377/853] Clean up a few (unused, broken, and also duplicated)
 jquery/migrate imports in viz base.

---
 .../common/templates/visualization_base.mako              | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/config/plugins/visualizations/common/templates/visualization_base.mako b/config/plugins/visualizations/common/templates/visualization_base.mako
index 80bab0bfe463..3fd2b5a8b8f4 100644
--- a/config/plugins/visualizations/common/templates/visualization_base.mako
+++ b/config/plugins/visualizations/common/templates/visualization_base.mako
@@ -44,10 +44,6 @@ ${h.css('base')}
 
 ## Default javascripts
 <%def name="javascripts()">
-${h.js(
-    "libs/jquery/jquery",
-    "libs/jquery/jquery.migrate"
-)}
 ## connect to Galaxy here
 
 <script type="text/javascript">
@@ -70,8 +66,4 @@ ${h.js(
 
 ## Default javascripts
 <%def name="late_javascripts()">
-${h.js(
-    "libs/jquery/jquery",
-    "libs/jquery/jquery.migrate"
-)}
 </%def>

From cbecde300f102e33f1c842b57d7c940f42dc562f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 10 Mar 2020 17:11:52 -0400
Subject: [PATCH 378/853] Fix IT wrapper filenames.

---
 doc/source/admin/special_topics/interactivetools.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/source/admin/special_topics/interactivetools.rst b/doc/source/admin/special_topics/interactivetools.rst
index 2b5a4111cfe0..5238281943fd 100644
--- a/doc/source/admin/special_topics/interactivetools.rst
+++ b/doc/source/admin/special_topics/interactivetools.rst
@@ -115,7 +115,7 @@ Some **example test InteractiveTools** have been defined, and can be added to th
 
 .. code-block:: xml
 
-        <tool file="interactive/interactive_juypter_notebook.xml" />
-        <tool file="interactive/interactive_cellxgene.xml" />
+        <tool file="interactive/interactivetool_juypter_notebook.xml" />
+        <tool file="interactive/interactivetool_cellxgene.xml" />
 
 

From 302df392d7749748e193aa7b7febd46bdbb7893c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 10 Mar 2020 17:13:24 -0400
Subject: [PATCH 379/853] typo: juypter/jupyter

---
 doc/source/admin/special_topics/interactivetools.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/admin/special_topics/interactivetools.rst b/doc/source/admin/special_topics/interactivetools.rst
index 5238281943fd..d0f89719f4d8 100644
--- a/doc/source/admin/special_topics/interactivetools.rst
+++ b/doc/source/admin/special_topics/interactivetools.rst
@@ -115,7 +115,7 @@ Some **example test InteractiveTools** have been defined, and can be added to th
 
 .. code-block:: xml
 
-        <tool file="interactive/interactivetool_juypter_notebook.xml" />
+        <tool file="interactive/interactivetool_jupyter_notebook.xml" />
         <tool file="interactive/interactivetool_cellxgene.xml" />
 
 

From ec7f59a033091ea4650aec5214c1ba0ae9798fe3 Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Fri, 6 Mar 2020 14:15:03 -0500
Subject: [PATCH 380/853] Update the current_history method.

In this method, it was assumed that the first returned history
from the API endpoint would be the currently active history,
but that list is returned in create-time descending order. The
`/history/current_history_json` is an existing way to retrieve
the data the `current_history` method needs to return.
---
 lib/galaxy/selenium/navigates_galaxy.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index c607395bd1a1..d4421873c610 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -208,8 +208,9 @@ def history_panel_name(self):
         return self.history_panel_name_element().text
 
     def current_history(self):
-        history = self.api_get("histories")[0]
-        return history
+        full_url = self.build_url("history/current_history_json", for_selenium=False)
+        response = requests.get(full_url, cookies=self.selenium_to_requests_cookies())
+        return response.json()
 
     def current_history_id(self):
         return self.current_history()["id"]

From 7074ffd15c104f8e6ecc7917bc260e64a70e0259 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 12 Mar 2020 15:09:29 +0100
Subject: [PATCH 381/853] Fix toolshed tests

---
 lib/tool_shed/webapp/config.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index df627d916435..2d421012b676 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -112,6 +112,8 @@ def __init__(self, **kwargs):
         self.terms_url = kwargs.get('terms_url', None)
         self.blacklist_location = kwargs.get('blacklist_file', None)
         self.blacklist_content = None
+        self.whitelist_location = kwargs.get('blacklist_file', None)
+        self.whitelist_content = None
         self.remote_user_maildomain = kwargs.get("remote_user_maildomain", None)
         self.remote_user_header = kwargs.get("remote_user_header", 'HTTP_REMOTE_USER')
         self.remote_user_logout_href = kwargs.get("remote_user_logout_href", None)

From 1587bb604fcdbc3694e4b587a7d0dfad63acce36 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Thu, 12 Mar 2020 18:28:05 +0100
Subject: [PATCH 382/853] Get the right file ...

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/tool_shed/webapp/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index 2d421012b676..dc4292c0a7ef 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -112,7 +112,7 @@ def __init__(self, **kwargs):
         self.terms_url = kwargs.get('terms_url', None)
         self.blacklist_location = kwargs.get('blacklist_file', None)
         self.blacklist_content = None
-        self.whitelist_location = kwargs.get('blacklist_file', None)
+        self.whitelist_location = kwargs.get('whitelist_file', None)
         self.whitelist_content = None
         self.remote_user_maildomain = kwargs.get("remote_user_maildomain", None)
         self.remote_user_header = kwargs.get("remote_user_header", 'HTTP_REMOTE_USER')

From 8c30410f9eb40f3f65c8cb5ec4572b61d919b965 Mon Sep 17 00:00:00 2001
From: Juan David Mendez Solano <mendezj@tf.uni-freiburg.de>
Date: Fri, 13 Mar 2020 14:07:36 +0100
Subject: [PATCH 383/853] Tests for the change password webpage

---
 lib/galaxy/selenium/navigation.yml            |  5 +
 .../selenium/test_change_password.py          | 91 +++++++++++++++++++
 2 files changed, 96 insertions(+)
 create mode 100644 lib/galaxy_test/selenium/test_change_password.py

diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index c6160ba379d3..b9a6d0ccdae3 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -70,6 +70,7 @@ masthead:
 
 preferences:
   selectors:
+    change_password: "#edit-preferences-password"
     manage_information: '#edit-preferences-information'
     current_email: "#user-preferences-current-email"
 
@@ -77,6 +78,10 @@ change_user_email:
   selectors:
     submit: '#submit'
 
+change_user_password:
+  selectors:
+    submit: '#submit'
+
 change_user_address:
   selectors:
     address_button:
diff --git a/lib/galaxy_test/selenium/test_change_password.py b/lib/galaxy_test/selenium/test_change_password.py
new file mode 100644
index 000000000000..759ae672292e
--- /dev/null
+++ b/lib/galaxy_test/selenium/test_change_password.py
@@ -0,0 +1,91 @@
+import time
+from .framework import (
+    selenium_test,
+    SeleniumTestCase
+)
+
+class ChangePasswordTestCase(SeleniumTestCase):
+    @selenium_test
+    def test_change_password(self):
+        self.home()
+        email = self._get_random_email()
+        password = self.default_password
+        confirm = password
+        username = email.split("@")[0]
+        self.register(email, password, username, confirm)
+        self.navigate_to_password()
+        self.fill_input_fields(password, "123123", "123123")        
+        self.logout_if_needed()
+        self.submit_login(email, "123123")
+
+    @selenium_test
+    def test_new_password_password(self):
+        self.home()
+        email = self._get_random_email()
+        password = self.default_password
+        confirm = password
+        username = email.split("@")[0]
+        self.register(email, password, username, confirm)
+        self.navigate_to_password()
+        self.fill_input_fields(password, "", "123123")
+        self.assert_error_message(contains='Please provide a new password.')
+
+    @selenium_test
+    def test_no_password_confirmation(self):
+        self.home()
+        email = self._get_random_email()
+        password = self.default_password
+        confirm = password
+        username = email.split("@")[0]
+        self.register(email, password, username, confirm)
+        self.navigate_to_password()
+        self.fill_input_fields(password, "123123", "")
+        self.assert_error_message(contains='Passwords do not match.')
+
+    @selenium_test
+    def test_currect_password_incorrect(self):
+        self.home()
+        email = self._get_random_email()
+        password = self.default_password
+        confirm = password
+        username = email.split("@")[0]
+        self.register(email, password, username, confirm)
+        self.navigate_to_password()
+        time.sleep(5)
+        self.fill_input_fields("4444444", "123123", "123123")
+        self.assert_error_message(contains='Invalid current password.')
+
+    @selenium_test
+    def test_new_password_short(self):
+        self.home()
+        email = self._get_random_email()
+        password = self.default_password
+        confirm = password
+        username = email.split("@")[0]
+        self.register(email, password, username, confirm)
+        self.navigate_to_password()
+        self.fill_input_fields(password, "123", "123")
+        self.assert_error_message(contains='Use a password of at least 6 characters.')
+
+    @selenium_test
+    def test_new_password_same_password(self):
+        self.home()
+        email = self._get_random_email()
+        password = self.default_password
+        confirm = password
+        username = email.split("@")[0]
+        self.register(email, password, username, confirm)
+        self.navigate_to_password()
+        self.fill_input_fields(password, password, password)
+
+    def navigate_to_password(self):
+        self.click_masthead_user()
+        self.components.masthead.preferences.wait_for_and_click()
+        self.components.preferences.change_password.wait_for_and_click()
+
+    def fill_input_fields(self, password, new_password, password_confirm):
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+        self.driver.find_element_by_id('field-uid-5').send_keys(password)
+        self.driver.find_element_by_id('field-uid-6').send_keys(new_password)
+        self.driver.find_element_by_id('field-uid-7').send_keys(password_confirm)
+        self.components.change_user_password.submit.wait_for_and_click()
\ No newline at end of file

From 766bd0fcc1451587633067354ea1e5631e43c091 Mon Sep 17 00:00:00 2001
From: Juan David Mendez Solano <mendezj@tf.uni-freiburg.de>
Date: Fri, 13 Mar 2020 14:46:15 +0100
Subject: [PATCH 384/853] Change to use tour_id instead of id

---
 lib/galaxy_test/selenium/test_change_password.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy_test/selenium/test_change_password.py b/lib/galaxy_test/selenium/test_change_password.py
index 759ae672292e..39b6751a267e 100644
--- a/lib/galaxy_test/selenium/test_change_password.py
+++ b/lib/galaxy_test/selenium/test_change_password.py
@@ -83,9 +83,9 @@ def navigate_to_password(self):
         self.components.masthead.preferences.wait_for_and_click()
         self.components.preferences.change_password.wait_for_and_click()
 
-    def fill_input_fields(self, password, new_password, password_confirm):
+    def fill_input_fields(self, current, password, confirm):
         self.sleep_for(self.wait_types.UX_TRANSITION)
-        self.driver.find_element_by_id('field-uid-5').send_keys(password)
-        self.driver.find_element_by_id('field-uid-6').send_keys(new_password)
-        self.driver.find_element_by_id('field-uid-7').send_keys(password_confirm)
+        self.driver.find_element_by_css_selector("[tour_id='current'] input").send_keys(current)
+        self.driver.find_element_by_css_selector("[tour_id='password'] input").send_keys(password)
+        self.driver.find_element_by_css_selector("[tour_id='confirm'] input").send_keys(confirm)
         self.components.change_user_password.submit.wait_for_and_click()
\ No newline at end of file

From 4bcaf8a0110403e7a92c52929f7fd9fb59b84692 Mon Sep 17 00:00:00 2001
From: Juan David Mendez Solano <mendezj@tf.uni-freiburg.de>
Date: Fri, 13 Mar 2020 14:55:16 +0100
Subject: [PATCH 385/853] Remove one unneeded  import

---
 lib/galaxy_test/selenium/test_change_password.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/lib/galaxy_test/selenium/test_change_password.py b/lib/galaxy_test/selenium/test_change_password.py
index 39b6751a267e..e7ba3bc4020f 100644
--- a/lib/galaxy_test/selenium/test_change_password.py
+++ b/lib/galaxy_test/selenium/test_change_password.py
@@ -1,4 +1,3 @@
-import time
 from .framework import (
     selenium_test,
     SeleniumTestCase
@@ -51,7 +50,6 @@ def test_currect_password_incorrect(self):
         username = email.split("@")[0]
         self.register(email, password, username, confirm)
         self.navigate_to_password()
-        time.sleep(5)
         self.fill_input_fields("4444444", "123123", "123123")
         self.assert_error_message(contains='Invalid current password.')
 

From 4b1b7b62b24d540d32c046be4afa67de977bcc25 Mon Sep 17 00:00:00 2001
From: Juan David Mendez Solano <mendezj@tf.uni-freiburg.de>
Date: Fri, 13 Mar 2020 15:29:12 +0100
Subject: [PATCH 386/853] Fix lint rules violations

---
 lib/galaxy_test/selenium/test_change_password.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy_test/selenium/test_change_password.py b/lib/galaxy_test/selenium/test_change_password.py
index e7ba3bc4020f..a51adb555a07 100644
--- a/lib/galaxy_test/selenium/test_change_password.py
+++ b/lib/galaxy_test/selenium/test_change_password.py
@@ -3,6 +3,7 @@
     SeleniumTestCase
 )
 
+
 class ChangePasswordTestCase(SeleniumTestCase):
     @selenium_test
     def test_change_password(self):
@@ -13,7 +14,7 @@ def test_change_password(self):
         username = email.split("@")[0]
         self.register(email, password, username, confirm)
         self.navigate_to_password()
-        self.fill_input_fields(password, "123123", "123123")        
+        self.fill_input_fields(password, "123123", "123123")
         self.logout_if_needed()
         self.submit_login(email, "123123")
 
@@ -86,4 +87,4 @@ def fill_input_fields(self, current, password, confirm):
         self.driver.find_element_by_css_selector("[tour_id='current'] input").send_keys(current)
         self.driver.find_element_by_css_selector("[tour_id='password'] input").send_keys(password)
         self.driver.find_element_by_css_selector("[tour_id='confirm'] input").send_keys(confirm)
-        self.components.change_user_password.submit.wait_for_and_click()
\ No newline at end of file
+        self.components.change_user_password.submit.wait_for_and_click()

From 40be7e409959d4317643c33142e33e62e0e39387 Mon Sep 17 00:00:00 2001
From: Juan David Mendez Solano <mendezj@tf.uni-freiburg.de>
Date: Fri, 13 Mar 2020 17:30:09 +0100
Subject: [PATCH 387/853] Condense the code

---
 .../selenium/test_change_password.py          | 60 +++++--------------
 1 file changed, 16 insertions(+), 44 deletions(-)

diff --git a/lib/galaxy_test/selenium/test_change_password.py b/lib/galaxy_test/selenium/test_change_password.py
index a51adb555a07..f088b992b6e0 100644
--- a/lib/galaxy_test/selenium/test_change_password.py
+++ b/lib/galaxy_test/selenium/test_change_password.py
@@ -9,75 +9,47 @@ class ChangePasswordTestCase(SeleniumTestCase):
     def test_change_password(self):
         self.home()
         email = self._get_random_email()
-        password = self.default_password
-        confirm = password
-        username = email.split("@")[0]
-        self.register(email, password, username, confirm)
-        self.navigate_to_password()
-        self.fill_input_fields(password, "123123", "123123")
+        self.register(email)
+        self.click_masthead_user()
+        self.components.masthead.preferences.wait_for_and_click()
+        self.components.preferences.change_password.wait_for_and_click()
+        self.fill_input_fields(self.default_password, "123123", "123123")
         self.logout_if_needed()
         self.submit_login(email, "123123")
 
     @selenium_test
     def test_new_password_password(self):
-        self.home()
-        email = self._get_random_email()
-        password = self.default_password
-        confirm = password
-        username = email.split("@")[0]
-        self.register(email, password, username, confirm)
-        self.navigate_to_password()
-        self.fill_input_fields(password, "", "123123")
+        self.register_and_change_password()
+        self.fill_input_fields(self.default_password, "", "123123")
         self.assert_error_message(contains='Please provide a new password.')
 
     @selenium_test
     def test_no_password_confirmation(self):
-        self.home()
-        email = self._get_random_email()
-        password = self.default_password
-        confirm = password
-        username = email.split("@")[0]
-        self.register(email, password, username, confirm)
-        self.navigate_to_password()
-        self.fill_input_fields(password, "123123", "")
+        self.register_and_change_password()
+        self.fill_input_fields(self.default_password, "123123", "5444484")
         self.assert_error_message(contains='Passwords do not match.')
 
     @selenium_test
     def test_currect_password_incorrect(self):
-        self.home()
-        email = self._get_random_email()
-        password = self.default_password
-        confirm = password
-        username = email.split("@")[0]
-        self.register(email, password, username, confirm)
-        self.navigate_to_password()
+        self.register_and_change_password()
         self.fill_input_fields("4444444", "123123", "123123")
         self.assert_error_message(contains='Invalid current password.')
 
     @selenium_test
     def test_new_password_short(self):
-        self.home()
-        email = self._get_random_email()
-        password = self.default_password
-        confirm = password
-        username = email.split("@")[0]
-        self.register(email, password, username, confirm)
-        self.navigate_to_password()
-        self.fill_input_fields(password, "123", "123")
+        self.register_and_change_password()
+        self.fill_input_fields(self.default_password, "123", "123")
         self.assert_error_message(contains='Use a password of at least 6 characters.')
 
     @selenium_test
     def test_new_password_same_password(self):
-        self.home()
-        email = self._get_random_email()
+        self.register_and_change_password()
         password = self.default_password
-        confirm = password
-        username = email.split("@")[0]
-        self.register(email, password, username, confirm)
-        self.navigate_to_password()
         self.fill_input_fields(password, password, password)
 
-    def navigate_to_password(self):
+    def register_and_change_password(self):
+        self.home()
+        self.register()
         self.click_masthead_user()
         self.components.masthead.preferences.wait_for_and_click()
         self.components.preferences.change_password.wait_for_and_click()

From 5612524a741c77ae357d68d9198824fa3a8cec9f Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 02:04:19 -0500
Subject: [PATCH 388/853] Use labeled dropdown options for workflow node
 operations

---
 .../components/Workflow/Editor/Node.vue       | 22 ++++++++++++-------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 5de4895e8177..b2a854bde841 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -5,23 +5,29 @@
                 <i :class="iconClass" />
                 <span class="node-title">{{ title }}</span>
             </div>
-            <div class="buttons float-right">
-                <a
+            <b-dropdown right class="float-right" toggle-class="py-0" offset="50" variant="primary" size="sm">
+                <b-dropdown-item
                     v-if="canClone"
-                    class="fa-icon-button fa fa-files-o node-clone"
                     aria-label="clone node"
                     role="button"
                     href="#"
+                    class="node-clone"
                     @click="onClone"
-                />
-                <a
-                    class="fa-icon-button fa fa-times node-destroy"
+                >
+                    <span class="fa-icon-button fa fa-files-o" />
+                    Duplicate
+                </b-dropdown-item>
+                <b-dropdown-item
                     aria-label="destroy node"
                     role="button"
                     href="#"
+                    class="node-destroy"
                     @click="onDestroy"
-                />
-            </div>
+                >
+                    <span class="fa-icon-button fa fa-fw fa-trash" />
+                    Remove
+                </b-dropdown-item>
+            </b-dropdown>
         </div>
         <div class="node-body">
             <div>

From 6739a1b5386c13ba269578dc68a8a4488396bfd2 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 02:13:48 -0500
Subject: [PATCH 389/853] Fix workflow terminal z-index to avoid overlap with
 node dropdown options menu

---
 client/galaxy/style/scss/workflow.scss | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index b34decf2b3be..078f50725c38 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -79,7 +79,7 @@
                 @extend .mt-1;
                 color: $brand-light;
                 position: absolute;
-                z-index: 1500;
+                z-index: 101;
                 > icon {
                     @extend .fa;
                     @extend .fa-chevron-circle-right;
@@ -111,7 +111,7 @@
                 @extend .fa-circle;
                 color: $brand-success;
                 position: absolute;
-                z-index: 1500;
+                z-index: 101;
             }
             .mark-terminal {
                 cursor: pointer;

From 602b8208652ab96db052fbe377fabc2dde7b2a8a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 02:19:38 -0500
Subject: [PATCH 390/853] Increase width of active workflow node border

---
 client/galaxy/style/scss/workflow.scss | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 078f50725c38..397c61f18162 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -16,7 +16,7 @@
             &.node-active {
                 z-index: 1001;
                 border: solid $white 1px;
-                box-shadow: 0 0 0 2px $brand-primary;
+                box-shadow: 0 0 0 3px $brand-primary;
             }
             .node-header {
                 @extend .card-header;

From 6277c9c97e3e4d2174b00d043c391c88f837a0ce Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 02:33:08 -0500
Subject: [PATCH 391/853] Fix consolidate workflow node icon with options menu
 caret

---
 .../galaxy/scripts/components/Workflow/Editor/Node.vue | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index b2a854bde841..9448ae1879ae 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -1,11 +1,11 @@
 <template>
     <div>
         <div class="node-header unselectable clearfix">
-            <div class="header float-left">
-                <i :class="iconClass" />
-                <span class="node-title">{{ title }}</span>
-            </div>
-            <b-dropdown right class="float-right" toggle-class="py-0" offset="50" variant="primary" size="sm">
+            <span class="node-title">{{ title }}</span>
+            <b-dropdown right no-caret class="float-right" toggle-class="py-0" offset="50" variant="info" size="sm">
+                <template v-slot:button-content>
+                    <i :class="iconClass" />
+                </template>
                 <b-dropdown-item
                     v-if="canClone"
                     aria-label="clone node"

From a47acbf3fdfe09ecf5d0abe43ec3fa5fe4610f16 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 03:21:26 -0500
Subject: [PATCH 392/853] Remove unused workflow node styles

---
 client/galaxy/scripts/components/Workflow/Editor/Node.vue | 4 ++--
 client/galaxy/style/scss/workflow.scss                    | 6 ++----
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 9448ae1879ae..43a4e4908530 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -14,7 +14,7 @@
                     class="node-clone"
                     @click="onClone"
                 >
-                    <span class="fa-icon-button fa fa-files-o" />
+                    <span class="fa fa-fw fa-files-o" />
                     Duplicate
                 </b-dropdown-item>
                 <b-dropdown-item
@@ -24,7 +24,7 @@
                     class="node-destroy"
                     @click="onDestroy"
                 >
-                    <span class="fa-icon-button fa fa-fw fa-trash" />
+                    <span class="fa fa-fw fa-trash" />
                     Remove
                 </b-dropdown-item>
             </b-dropdown>
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 397c61f18162..823e711905b1 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -23,10 +23,8 @@
                 @extend .py-1;
                 @extend .px-2;
                 cursor: move;
-                background: $brand-secondary;
-                .header {
-                    width: $worfklow-node-width - 2rem;
-                }
+                background: $brand-primary;
+                color: $white;
             }
             .node-body {
                 @extend .card-body;

From 3aa15a670aa62acf16dad7b6c354fa1e0447a943 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 11:31:56 -0500
Subject: [PATCH 393/853] Fix workflow node header dom element order,
 priorities node operations for upper right corner

---
 client/galaxy/scripts/components/Workflow/Editor/Node.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 43a4e4908530..58898f84e1d0 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -1,7 +1,6 @@
 <template>
     <div>
         <div class="node-header unselectable clearfix">
-            <span class="node-title">{{ title }}</span>
             <b-dropdown right no-caret class="float-right" toggle-class="py-0" offset="50" variant="info" size="sm">
                 <template v-slot:button-content>
                     <i :class="iconClass" />
@@ -28,6 +27,7 @@
                     Remove
                 </b-dropdown-item>
             </b-dropdown>
+            <span class="node-title">{{ title }}</span>
         </div>
         <div class="node-body">
             <div>

From d10063d150551e5d319ebec0055af4f6776e3741 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 12:11:38 -0500
Subject: [PATCH 394/853] Fix workflow node output asterisk highlighting

---
 client/galaxy/scripts/mvc/workflow/workflow-view-data.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
index 27bb09975587..4d28a4a2139f 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
@@ -127,12 +127,12 @@ export class OutputCalloutView {
         this.output = options.output;
         const view = this;
         const node = this.node;
+        const outputName = view.output.name;
         this.$el
-            .attr("class", `callout-terminal ${this.label}`)
+            .attr("class", `callout-terminal ${outputName}`)
             .css({ display: "none" })
             .append(
-                $("<icon class='mark-terminal fa fa-asterisk'/>").click(() => {
-                    const outputName = view.output.name;
+                $("<icon />").addClass("mark-terminal fa fa-asterisk").click(() => {
                     if (node.isWorkflowOutput(outputName)) {
                         node.removeWorkflowOutput(outputName);
                         view.$el.find("icon").removeClass("mark-terminal-active");

From 35eef69206510920a4457411a20748bfb4b0dce7 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 13:15:29 -0500
Subject: [PATCH 395/853] Remove folder icon from multi-run views

---
 client/galaxy/scripts/mvc/workflow/workflow-view-node.js      | 4 ++--
 client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js | 3 ---
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
index 0686f57ff94a..eadfae646943 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
@@ -86,7 +86,7 @@ export class NodeView {
             skipResize: skipResize
         });
         var ib = inputView.$el;
-        body.append(ib.prepend(terminalView.terminalElements()));
+        body.append(ib.prepend(terminalView.el));
         return terminalView;
     }
 
@@ -116,7 +116,7 @@ export class NodeView {
         const terminalView = this.terminalViewForOutput(output);
         const outputView = this.outputViewforOutput(output, terminalView);
         this.outputViews[output.name] = outputView;
-        this.node_body.append(outputView.$el.append(terminalView.terminalElements()));
+        this.node_body.append(outputView.$el.append(terminalView.el));
     }
 
     redrawWorkflowOutputs() {
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index c481940b653d..1354366f6de1 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -34,9 +34,6 @@ class TerminalView {
         terminal.terminalMappingView = terminalMappingView;
         this.terminalMappingView = terminalMappingView;
     }
-    terminalElements() {
-        return [this.terminalMappingView.$el, this.el];
-    }
 }
 
 class BaseInputTerminalView extends TerminalView {

From b846a9a4a06ae64bb6af5c4a4b3d4c7920303d1f Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 14:07:21 -0500
Subject: [PATCH 396/853] Strip terminal mapping view from workflow client

---
 .../mvc/workflow/workflow-view-terminals.js   | 61 +++++--------------
 1 file changed, 16 insertions(+), 45 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index 1354366f6de1..3679955d06f4 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -5,40 +5,8 @@ import ariaAlert from "utils/ariaAlert";
 
 var NODEINDEX = 0;
 
-class TerminalMappingView {
-    constructor(options = {}) {
-        this.$el = $("<div class='fa-icon-button fa fa-folder-o' />");
-        var mapText = "Run tool in parallel over collection";
-        this.$el.tooltip({ delay: 500, title: mapText });
-        this.model = options.model;
-        this.model.on("change", this.render.bind(this));
-    }
-    render() {
-        if (this.model.mapOver && this.model.mapOver.isCollection) {
-            this.$el.show();
-        } else {
-            this.$el.hide();
-        }
-    }
-}
-
-class TerminalView {
-    setupMappingView(terminalMappingClass, terminal) {
-        var terminalMapping = new terminalMappingClass({
-            terminal: terminal
-        });
-        var terminalMappingView = new TerminalMappingView({
-            model: terminalMapping
-        });
-        terminalMappingView.render();
-        terminal.terminalMappingView = terminalMappingView;
-        this.terminalMappingView = terminalMappingView;
-    }
-}
-
-class BaseInputTerminalView extends TerminalView {
-    constructor(app, options = {}, terminalMappingClass = null) {
-        super();
+class BaseInputTerminalView {
+    constructor(app, options = {}) {
         this.app = app;
         this.el = document.createElement("div");
         this.el.className = "terminal input-terminal";
@@ -49,7 +17,9 @@ class BaseInputTerminalView extends TerminalView {
         node.cid = NODEINDEX++;
         const id = `node-${node.cid}-input-${name}`;
         const terminal = this.terminalForInput(input);
-        this.setupMappingView(terminalMappingClass, terminal);
+        new Terminals.TerminalMapping({
+            terminal: terminal
+        });
         this.el.terminal = terminal;
         this.$el.attr("input-name", name);
         this.$el.attr("id", id);
@@ -142,7 +112,7 @@ class BaseInputTerminalView extends TerminalView {
 
 export class InputTerminalView extends BaseInputTerminalView {
     constructor(app, options = {}) {
-        super(app, options, Terminals.TerminalMapping);
+        super(app, options);
     }
     terminalForInput(input) {
         return new Terminals.InputTerminal({
@@ -155,7 +125,7 @@ export class InputTerminalView extends BaseInputTerminalView {
 
 export class InputParameterTerminalView extends BaseInputTerminalView {
     constructor(app, options = {}) {
-        super(app, options, Terminals.TerminalMapping);
+        super(app, options);
     }
     terminalForInput(input) {
         return new Terminals.InputParameterTerminal({
@@ -168,7 +138,7 @@ export class InputParameterTerminalView extends BaseInputTerminalView {
 
 export class InputCollectionTerminalView extends BaseInputTerminalView {
     constructor(app, options = {}) {
-        super(app, options, Terminals.TerminalMapping);
+        super(app, options);
     }
     terminalForInput(input = {}) {
         return new Terminals.InputCollectionTerminal({
@@ -179,9 +149,8 @@ export class InputCollectionTerminalView extends BaseInputTerminalView {
     }
 }
 
-export class BaseOutputTerminalView extends TerminalView {
-    constructor(app, options, terminalMappingClass = null) {
-        super();
+export class BaseOutputTerminalView {
+    constructor(app, options) {
         this.app = app;
         this.el = document.createElement("div");
         this.el.className = "terminal output-terminal";
@@ -192,7 +161,9 @@ export class BaseOutputTerminalView extends TerminalView {
         node.cid = NODEINDEX++;
         const id = `node-${node.cid}-output-${name}`;
         const terminal = this.terminalForOutput(output);
-        this.setupMappingView(terminalMappingClass, terminal);
+        new Terminals.TerminalMapping({
+            terminal: terminal
+        });
         this.el.terminal = terminal;
         this.$el.attr(
             "aria-label",
@@ -376,7 +347,7 @@ export class BaseOutputTerminalView extends TerminalView {
 
 export class OutputTerminalView extends BaseOutputTerminalView {
     constructor(app, options = {}) {
-        super(app, options, Terminals.TerminalMapping);
+        super(app, options);
     }
     terminalForOutput(output) {
         var type = output.extensions;
@@ -391,7 +362,7 @@ export class OutputTerminalView extends BaseOutputTerminalView {
 
 export class OutputCollectionTerminalView extends BaseOutputTerminalView {
     constructor(app, options = {}) {
-        super(app, options, Terminals.TerminalMapping);
+        super(app, options);
     }
     terminalForOutput(output) {
         var collection_type = output.collection_type;
@@ -409,7 +380,7 @@ export class OutputCollectionTerminalView extends BaseOutputTerminalView {
 
 export class OutputParameterTerminalView extends BaseOutputTerminalView {
     constructor(app, options = {}) {
-        super(app, options, Terminals.TerminalMapping);
+        super(app, options);
     }
     terminalForOutput(output) {
         return new Terminals.OutputParameterTerminal({

From 3dd8b978e61b08a8d60326ba10db0e3a87ba6571 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 14:37:41 -0500
Subject: [PATCH 397/853] Consolidate terminal and terminal mapping class in
 workflow client

---
 .../mvc/workflow/workflow-terminals.js        | 41 +++++--------------
 .../mvc/workflow/workflow-view-terminals.js   |  6 ---
 2 files changed, 11 insertions(+), 36 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
index 9cd90cfd6536..ead3ceec8cb9 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
@@ -103,25 +103,11 @@ $.extend(CollectionTypeDescription.prototype, {
     }
 });
 
-class TerminalMapping extends EventEmitter {
+class Terminal extends EventEmitter {
     constructor(attr) {
         super();
-        this.mapOver = attr.mapOver || NULL_COLLECTION_TYPE_DESCRIPTION;
-        this.terminal = attr.terminal;
-        this.terminal.terminalMapping = this;
-    }
-    disableMapOver() {
-        this.setMapOver(NULL_COLLECTION_TYPE_DESCRIPTION);
-    }
-    setMapOver(collectionTypeDescription) {
-        this.mapOver = collectionTypeDescription;
-        this.emit("change");
-    }
-}
-
-class Terminal {
-    constructor(attr) {
         this.element = attr.element;
+        this.mapList = attr.mapList || NULL_COLLECTION_TYPE_DESCRIPTION;
         this.attributes = attr;
         this.connectors = [];
     }
@@ -169,26 +155,22 @@ class Terminal {
             }
             output_val = val.effectiveMapOver ? val.effectiveMapOver(description) : val;
         }
-
         if (!this.mapOver().equal(val)) {
-            this.terminalMapping.setMapOver(val);
+            this.mapList = val;
             _.each(this.node.output_terminals, outputTerminal => {
                 outputTerminal.setMapOver(output_val);
             });
         }
+        this.emit("change");
     }
     mapOver() {
-        if (!this.terminalMapping) {
-            return NULL_COLLECTION_TYPE_DESCRIPTION;
-        } else {
-            return this.terminalMapping.mapOver;
-        }
+        return this.mapList;
     }
     isMappedOver() {
-        return this.terminalMapping && this.terminalMapping.mapOver.isCollection;
+        return this.mapList.isCollection;
     }
     resetMapping() {
-        this.terminalMapping.disableMapOver();
+        this.mapList = NULL_COLLECTION_TYPE_DESCRIPTION;
     }
     resetCollectionTypeSource() {
         const node = this.node;
@@ -233,7 +215,7 @@ class OutputTerminal extends Terminal {
         }
     }
     resetMapping() {
-        this.terminalMapping.disableMapOver();
+        super.resetMapping();
         _.each(this.connectors, connector => {
             var connectedInput = connector.handle2;
             if (connectedInput) {
@@ -277,7 +259,7 @@ class BaseInputTerminal extends Terminal {
         }
     }
     resetMapping() {
-        this.terminalMapping.disableMapOver();
+        super.resetMapping();
         if (!this.node.hasMappedOverInputTerminals()) {
             _.each(this.node.output_terminals, terminal => {
                 // This shouldn't be called if there are mapped over
@@ -514,11 +496,11 @@ class InputCollectionTerminal extends BaseInputTerminal {
                 if (output_terminal.attributes.collection_type_source && !connector.dragging) {
                     if (other.isMappedOver()) {
                         if (other.isCollection) {
-                            output_terminal.attributes.collection_type = other.terminalMapping.mapOver.append(
+                            output_terminal.attributes.collection_type = other.mapList.append(
                                 other.collectionType
                             ).collectionType;
                         } else {
-                            output_terminal.attributes.collection_type = other.terminalMapping.mapOver.collectionType;
+                            output_terminal.attributes.collection_type = other.mapList.collectionType;
                         }
                     } else {
                         output_terminal.attributes.collection_type = other.attributes.collection_type;
@@ -661,7 +643,6 @@ export default {
     OutputParameterTerminal: OutputParameterTerminal,
     InputCollectionTerminal: InputCollectionTerminal,
     OutputCollectionTerminal: OutputCollectionTerminal,
-    TerminalMapping: TerminalMapping,
 
     // test export
     CollectionTypeDescription: CollectionTypeDescription,
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index 3679955d06f4..c5b6f92a5ce9 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -17,9 +17,6 @@ class BaseInputTerminalView {
         node.cid = NODEINDEX++;
         const id = `node-${node.cid}-input-${name}`;
         const terminal = this.terminalForInput(input);
-        new Terminals.TerminalMapping({
-            terminal: terminal
-        });
         this.el.terminal = terminal;
         this.$el.attr("input-name", name);
         this.$el.attr("id", id);
@@ -161,9 +158,6 @@ export class BaseOutputTerminalView {
         node.cid = NODEINDEX++;
         const id = `node-${node.cid}-output-${name}`;
         const terminal = this.terminalForOutput(output);
-        new Terminals.TerminalMapping({
-            terminal: terminal
-        });
         this.el.terminal = terminal;
         this.$el.attr(
             "aria-label",

From 12cd30ec1500b2f38b138a5f587254ab4f126041 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 14:43:13 -0500
Subject: [PATCH 398/853] Use mapover consistently as parameter name in
 workflow client terminals

---
 .../scripts/mvc/workflow/workflow-node.js     |  6 +--
 .../mvc/workflow/workflow-terminals.js        | 43 +++++++++----------
 2 files changed, 23 insertions(+), 26 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js
index 94938aff0f2b..e9e0b935046e 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js
@@ -116,7 +116,7 @@ export class Node {
     _connectedMappedTerminals(terminals) {
         var mapped_outputs = [];
         $.each(terminals, (_, t) => {
-            var mapOver = t.mapOver();
+            var mapOver = t.mapOver;
             if (mapOver.isCollection) {
                 if (t.connectors.length > 0) {
                     mapped_outputs.push(t);
@@ -131,7 +131,7 @@ export class Node {
     _mappedTerminals(terminals) {
         var mappedTerminals = [];
         $.each(terminals, (_, t) => {
-            var mapOver = t.mapOver();
+            var mapOver = t.mapOver;
             if (mapOver.isCollection) {
                 mappedTerminals.push(t);
             }
@@ -141,7 +141,7 @@ export class Node {
     hasMappedOverInputTerminals() {
         var found = false;
         _.each(this.input_terminals, t => {
-            var mapOver = t.mapOver();
+            var mapOver = t.mapOver;
             if (mapOver.isCollection) {
                 found = true;
             }
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
index ead3ceec8cb9..da00fa9471b2 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
@@ -107,7 +107,7 @@ class Terminal extends EventEmitter {
     constructor(attr) {
         super();
         this.element = attr.element;
-        this.mapList = attr.mapList || NULL_COLLECTION_TYPE_DESCRIPTION;
+        this.mapOver = attr.mapOver || NULL_COLLECTION_TYPE_DESCRIPTION;
         this.attributes = attr;
         this.connectors = [];
     }
@@ -155,22 +155,19 @@ class Terminal extends EventEmitter {
             }
             output_val = val.effectiveMapOver ? val.effectiveMapOver(description) : val;
         }
-        if (!this.mapOver().equal(val)) {
-            this.mapList = val;
+        if (!this.mapOver.equal(val)) {
+            this.mapOver = val;
             _.each(this.node.output_terminals, outputTerminal => {
                 outputTerminal.setMapOver(output_val);
             });
         }
         this.emit("change");
     }
-    mapOver() {
-        return this.mapList;
-    }
     isMappedOver() {
-        return this.mapList.isCollection;
+        return this.mapOver.isCollection;
     }
     resetMapping() {
-        this.mapList = NULL_COLLECTION_TYPE_DESCRIPTION;
+        this.mapOver = NULL_COLLECTION_TYPE_DESCRIPTION;
     }
     resetCollectionTypeSource() {
         const node = this.node;
@@ -246,7 +243,7 @@ class BaseInputTerminal extends Terminal {
         }
     }
     resetMappingIfNeeded() {
-        var mapOver = this.mapOver();
+        var mapOver = this.mapOver;
         if (!mapOver.isCollection) {
             return;
         }
@@ -312,7 +309,7 @@ class BaseInputTerminal extends Terminal {
         if (!this.node) {
             return []; // No node - completely unconstrained
         }
-        var mapOver = this.mapOver();
+        var mapOver = this.mapOver;
         if (mapOver.isCollection) {
             return [mapOver];
         }
@@ -320,11 +317,11 @@ class BaseInputTerminal extends Terminal {
         var constraints = [];
         if (!this.node.hasConnectedOutputTerminals()) {
             _.each(this.node.connectedMappedInputTerminals(), inputTerminal => {
-                constraints.push(inputTerminal.mapOver());
+                constraints.push(inputTerminal.mapOver);
             });
         } else {
             // All outputs should have same mapOver status - least specific.
-            constraints.push(_.first(_.values(this.node.output_terminals)).mapOver());
+            constraints.push(_.first(_.values(this.node.output_terminals)).mapOver);
         }
         return constraints;
     }
@@ -366,7 +363,7 @@ class BaseInputTerminal extends Terminal {
         if (other.isCollection) {
             otherCollectionType = other.collectionType;
         }
-        var otherMapOver = other.mapOver();
+        var otherMapOver = other.mapOver;
         if (otherMapOver.isCollection) {
             otherCollectionType = otherMapOver.append(otherCollectionType);
         }
@@ -394,7 +391,7 @@ class InputTerminal extends BaseInputTerminal {
     }
     attachable(other) {
         var otherCollectionType = this._otherCollectionType(other);
-        var thisMapOver = this.mapOver();
+        var mapOver = this.mapOver;
         if (otherCollectionType.isCollection) {
             if (this.multiple) {
                 if (this.connected() && !this._collectionAttached()) {
@@ -410,7 +407,7 @@ class InputTerminal extends BaseInputTerminal {
                     );
                 }
             }
-            if (thisMapOver.isCollection && thisMapOver.canMatch(otherCollectionType)) {
+            if (mapOver.isCollection && mapOver.canMatch(otherCollectionType)) {
                 return this._producesAcceptableDatatypeAndOptionalness(other);
             } else if (this.multiple && new CollectionTypeDescription("list").canMatch(otherCollectionType)) {
                 // This handles the special case of a list input being connected to a multiple="true" data input.
@@ -422,7 +419,7 @@ class InputTerminal extends BaseInputTerminal {
                 if (mappingConstraints.every(_.bind(otherCollectionType.canMatch, otherCollectionType))) {
                     return this._producesAcceptableDatatypeAndOptionalness(other);
                 } else {
-                    if (thisMapOver.isCollection) {
+                    if (mapOver.isCollection) {
                         // incompatible collection type attached
                         if (this.node.hasConnectedMappedInputTerminals()) {
                             return new ConnectionAcceptable(
@@ -443,7 +440,7 @@ class InputTerminal extends BaseInputTerminal {
                     }
                 }
             }
-        } else if (thisMapOver.isCollection) {
+        } else if (mapOver.isCollection) {
             return new ConnectionAcceptable(
                 false,
                 "Cannot attach non-collection outputs to mapped over inputs, consider disconnecting inputs and outputs to reset this input's mapping."
@@ -496,11 +493,11 @@ class InputCollectionTerminal extends BaseInputTerminal {
                 if (output_terminal.attributes.collection_type_source && !connector.dragging) {
                     if (other.isMappedOver()) {
                         if (other.isCollection) {
-                            output_terminal.attributes.collection_type = other.mapList.append(
+                            output_terminal.attributes.collection_type = other.mapOver.append(
                                 other.collectionType
                             ).collectionType;
                         } else {
-                            output_terminal.attributes.collection_type = other.mapList.collectionType;
+                            output_terminal.attributes.collection_type = other.mapOver.collectionType;
                         }
                     } else {
                         output_terminal.attributes.collection_type = other.attributes.collection_type;
@@ -532,14 +529,14 @@ class InputCollectionTerminal extends BaseInputTerminal {
         return NULL_COLLECTION_TYPE_DESCRIPTION;
     }
     _effectiveCollectionTypes() {
-        var thisMapOver = this.mapOver();
-        return _.map(this.collectionTypes, t => thisMapOver.append(t));
+        var mapOver = this.mapOver;
+        return _.map(this.collectionTypes, t => mapOver.append(t));
     }
     attachable(other) {
         var otherCollectionType = this._otherCollectionType(other);
         if (otherCollectionType.isCollection) {
             var effectiveCollectionTypes = this._effectiveCollectionTypes();
-            var thisMapOver = this.mapOver();
+            var mapOver = this.mapOver;
             var canMatch = _.some(effectiveCollectionTypes, effectiveCollectionType =>
                 effectiveCollectionType.canMatch(otherCollectionType)
             );
@@ -547,7 +544,7 @@ class InputCollectionTerminal extends BaseInputTerminal {
                 // Only way a direct match...
                 return this._producesAcceptableDatatypeAndOptionalness(other);
                 // Otherwise we need to mapOver
-            } else if (thisMapOver.isCollection) {
+            } else if (mapOver.isCollection) {
                 // In this case, mapOver already set and we didn't match skipping...
                 if (this.node.hasConnectedMappedInputTerminals()) {
                     return new ConnectionAcceptable(

From 4db4de2fc51e48e9ff813c1046e2b2d2aa42981e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 17:18:31 -0500
Subject: [PATCH 399/853] Sync workflow input and output terminal creation,
 avoid usage of dom attached terminal

---
 .../components/Workflow/Editor/services.js    |  1 +
 .../scripts/mvc/workflow/workflow-node.js     |  2 +-
 .../mvc/workflow/workflow-view-data.js        | 24 ++++---
 .../mvc/workflow/workflow-view-node.js        |  4 +-
 .../mvc/workflow/workflow-view-terminals.js   | 72 ++++++++++---------
 client/galaxy/style/scss/workflow.scss        | 13 ++++
 6 files changed, 68 insertions(+), 48 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/services.js b/client/galaxy/scripts/components/Workflow/Editor/services.js
index 74ff7a21a78c..aeea83c9762e 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/services.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/services.js
@@ -45,6 +45,7 @@ export async function loadWorkflow(workflow, id, version) {
         workflow.canvas_manager.draw_overview();
         return data;
     } catch (e) {
+        console.debug(e);
         rethrowSimple(e);
     }
 }
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js
index e9e0b935046e..1eb79015fbaa 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js
@@ -319,7 +319,7 @@ export class Node {
         });
         // Cleanup any leftover terminals
         _.each(_.difference(_.values(nodeView.terminalViews), _.values(newTerminalViews)), unusedView => {
-            unusedView.el.terminal.destroy();
+            unusedView.terminal.destroy();
         });
         nodeView.terminalViews = newTerminalViews;
         node.nodeView.render();
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
index 4d28a4a2139f..e89b88d4f94d 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
@@ -132,17 +132,19 @@ export class OutputCalloutView {
             .attr("class", `callout-terminal ${outputName}`)
             .css({ display: "none" })
             .append(
-                $("<icon />").addClass("mark-terminal fa fa-asterisk").click(() => {
-                    if (node.isWorkflowOutput(outputName)) {
-                        node.removeWorkflowOutput(outputName);
-                        view.$el.find("icon").removeClass("mark-terminal-active");
-                    } else {
-                        node.addWorkflowOutput(outputName);
-                        view.$el.find("icon").addClass("mark-terminal-active");
-                    }
-                    app.has_changes = true;
-                    app.canvas_manager.draw_overview();
-                })
+                $("<icon />")
+                    .addClass("mark-terminal fa fa-asterisk")
+                    .click(() => {
+                        if (node.isWorkflowOutput(outputName)) {
+                            node.removeWorkflowOutput(outputName);
+                            view.$el.find("icon").removeClass("mark-terminal-active");
+                        } else {
+                            node.addWorkflowOutput(outputName);
+                            view.$el.find("icon").addClass("mark-terminal-active");
+                        }
+                        app.has_changes = true;
+                        app.canvas_manager.draw_overview();
+                    })
             )
             .tooltip({
                 delay: 500,
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
index eadfae646943..01e38c6787bf 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
@@ -64,7 +64,7 @@ export class NodeView {
             terminalViewClass = TerminalViews.InputParameterTerminalView;
         }
         if (terminalView && !(terminalView instanceof terminalViewClass)) {
-            terminalView.el.terminal.destroy();
+            terminalView.terminal.destroy();
             terminalView = null;
         }
         if (!terminalView) {
@@ -73,7 +73,7 @@ export class NodeView {
                 input: input
             });
         } else {
-            var terminal = terminalView.el.terminal;
+            var terminal = terminalView.terminal;
             terminal.update(input);
             terminal.destroyInvalidConnections();
         }
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index c5b6f92a5ce9..127c0eafa8a6 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -10,33 +10,39 @@ class BaseInputTerminalView {
         this.app = app;
         this.el = document.createElement("div");
         this.el.className = "terminal input-terminal";
-        this.$el = $(this.el);
         const node = options.node;
         const input = options.input;
         const name = input.name;
-        node.cid = NODEINDEX++;
-        const id = `node-${node.cid}-input-${name}`;
-        const terminal = this.terminalForInput(input);
-        this.el.terminal = terminal;
+        const nodeIndex = NODEINDEX++;
+        this.id = `node-${nodeIndex}-input-${name}`;
+        this.terminal = this.terminalForInput(input);
+        this.terminal.node = node;
+        this.terminal.name = name;
+        this.terminal.label = input.label;
+        node.input_terminals[name] = this.terminal;
+        this.el.terminal = this.terminal;
+        this.$el = $(this.el);
         this.$el.attr("input-name", name);
-        this.$el.attr("id", id);
+        this.$el.attr("id", this.id);
         this.$el.append($("<icon/>"));
-        this.id = id;
-
-        terminal.node = node;
-        terminal.name = name;
-        terminal.label = input.label;
-        node.input_terminals[name] = terminal;
-
         const self = this;
         this.$el.on("dropinit", (e, d) => self.onDropInit(e, d));
         this.$el.on("dropstart", (e, d) => self.onDropStart(e, d));
         this.$el.on("dropend", (e, d) => self.onDropEnd(e, d));
         this.$el.on("drop", (e, d) => self.onDrop(e, d));
         this.$el.on("hover", () => self.onHover());
+        //this.terminal.on("change", this.render.bind(this));
+    }
+    render() {
+        console.log("here");
+        /*if (this.terminal.mapOver && this.terminal.mapOver.isCollection) {
+             this.$el.addClass("multiple");
+         } else {
+             this.$el.removeClass("multiple");
+         }*/
     }
     onDropInit(e, d = {}) {
-        var terminal = this.el.terminal;
+        var terminal = this.terminal;
         // Accept a dragable if it is an output terminal and has a
         // compatible type
         var connectionAcceptable = $(d.drag).hasClass("output-terminal") && terminal.canAccept(d.drag.terminal);
@@ -77,14 +83,13 @@ class BaseInputTerminalView {
     onDrop(e, d = {}) {
         d.proxy.dropTooltip = "";
         if (this.$el.hasClass("can-accept")) {
-            const terminal = this.el.terminal;
+            const terminal = this.terminal;
             const c = new Connector(this.app.canvas_manager, d.drag.terminal, terminal);
             c.redraw();
         }
     }
     onHover() {
-        const element = this.el;
-        const terminal = element.terminal;
+        const terminal = this.terminal;
         // If connected, create a popup to allow disconnection
         if (terminal.connectors.length > 0) {
             const t = $("<div/>")
@@ -100,7 +105,7 @@ class BaseInputTerminalView {
                 .on("mouseleave", () => {
                     t.remove();
                 });
-            $(element)
+            $(this.el)
                 .parent()
                 .append(t);
         }
@@ -151,28 +156,27 @@ export class BaseOutputTerminalView {
         this.app = app;
         this.el = document.createElement("div");
         this.el.className = "terminal output-terminal";
-        this.$el = $(this.el);
         const node = options.node;
         const output = options.output;
         const name = output.name;
-        node.cid = NODEINDEX++;
-        const id = `node-${node.cid}-output-${name}`;
-        const terminal = this.terminalForOutput(output);
-        this.el.terminal = terminal;
+        const nodeIndex = NODEINDEX++;
+        this.id = `node-${nodeIndex}-output-${name}`;
+        this.terminal = this.terminalForOutput(output);
+        this.terminal.node = node;
+        this.terminal.name = name;
+        this.terminal.label = output.label;
+        node.output_terminals[name] = this.terminal;
+        this.el.terminal = this.terminal;
+        this.$el = $(this.el);
+        this.$el.attr("output-name", name);
+        this.$el.attr("id", this.id);
+        this.$el.append($("<icon/>"));
         this.$el.attr(
             "aria-label",
             `connect output ${name} from ${node.name} to input. Press space to see a list of available inputs`
         );
-        this.$el.attr("output-name", name);
-        this.$el.attr("id", id);
         this.$el.attr("tabindex", "0");
         this.$el.attr("aria-grabbed", "false");
-        this.$el.append($("<icon/>"));
-        terminal.node = node;
-        terminal.name = name;
-        terminal.label = output.label;
-        node.output_terminals[name] = terminal;
-
         const self = this;
         this.$el.on("drag", (d, e) => self.onDrag(d, e));
         this.$el.on("dragstart", (d, e) => self.onDragStart(d, e));
@@ -214,7 +218,7 @@ export class BaseOutputTerminalView {
                     break;
                 case 32: // Space
                     removeMenu();
-                    new Connector(this.app.canvas_manager, this.el.terminal, inputTerminal).redraw();
+                    new Connector(this.app.canvas_manager, this.terminal, inputTerminal).redraw();
                     ariaAlert("Node connected");
 
                     if (inputTerminal.connectors.length > 0) {
@@ -259,7 +263,7 @@ export class BaseOutputTerminalView {
             $(".input-terminal").each((i, el) => {
                 const input = $(el);
                 const inputTerminal = input.context.terminal;
-                const connectionAcceptable = inputTerminal.canAccept(this.el.terminal);
+                const connectionAcceptable = inputTerminal.canAccept(this.terminal);
                 if (connectionAcceptable.canAccept) {
                     const inputChoiceItem = document.createElement("li");
                     inputChoiceItem.textContent = `${inputTerminal.name} in ${inputTerminal.node.name} node`;
@@ -322,7 +326,7 @@ export class BaseOutputTerminalView {
         h.terminal = new Terminals.OutputTerminal({ element: h });
         const c = new Connector(this.app.canvas_manager);
         c.dragging = true;
-        c.connect(this.el.terminal, h.terminal);
+        c.connect(this.terminal, h.terminal);
         return h;
     }
     onDragEnd(e, d = {}) {
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 823e711905b1..dd362bf2b34a 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -86,6 +86,19 @@
                     left: 0px;
                     top: 0px;
                 }
+                > icon.multiple {
+                    @extend .fa;
+                    @extend .fa-chevron-circle-right;
+                    @extend .btn;
+                    @extend .btn-sm;
+                    @extend .btn-primary;
+                    @extend .p-1;
+                    @extend .mt-1;
+                    color: $white;
+                    position: absolute;
+                    left: -8px;
+                    top: -8px;
+                }
             }
             .input-terminal {
                 @extend .base-terminal;

From 54089a6976d987dcbf19bc9a4b21e748f4da7437 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 17:38:29 -0500
Subject: [PATCH 400/853] Add support to change the workflow connector icon

---
 .../mvc/workflow/workflow-view-terminals.js   | 21 ++++++++++++-------
 client/galaxy/style/scss/workflow.scss        | 16 ++++++--------
 2 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index 127c0eafa8a6..ca7c0d13c42b 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -31,15 +31,14 @@ class BaseInputTerminalView {
         this.$el.on("dropend", (e, d) => self.onDropEnd(e, d));
         this.$el.on("drop", (e, d) => self.onDrop(e, d));
         this.$el.on("hover", () => self.onHover());
-        //this.terminal.on("change", this.render.bind(this));
+        this.terminal.on("change", this.render.bind(this));
     }
     render() {
-        console.log("here");
-        /*if (this.terminal.mapOver && this.terminal.mapOver.isCollection) {
-             this.$el.addClass("multiple");
-         } else {
-             this.$el.removeClass("multiple");
-         }*/
+        if (this.terminal.mapOver && this.terminal.mapOver.isCollection) {
+            this.$el.find("icon").addClass("multiple");
+        } else {
+            this.$el.find("icon").removeClass("multiple");
+        }
     }
     onDropInit(e, d = {}) {
         var terminal = this.terminal;
@@ -182,6 +181,14 @@ export class BaseOutputTerminalView {
         this.$el.on("dragstart", (d, e) => self.onDragStart(d, e));
         this.$el.on("dragend", (d, e) => self.onDragEnd(d, e));
         this.$el.on("keydown", e => self.screenReaderSelectOutputNode(e));
+        this.terminal.on("change", this.render.bind(this));
+    }
+    render() {
+        if (this.terminal.mapOver && this.terminal.mapOver.isCollection) {
+            this.$el.find("icon").addClass("multiple");
+        } else {
+            this.$el.find("icon").removeClass("multiple");
+        }
     }
     screenReaderSelectOutputNode(e) {
         const inputChoiceKeyDown = e => {
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index dd362bf2b34a..3276df83c89c 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -78,7 +78,7 @@
                 color: $brand-light;
                 position: absolute;
                 z-index: 101;
-                > icon {
+                icon {
                     @extend .fa;
                     @extend .fa-chevron-circle-right;
                     color: $brand-primary;
@@ -86,18 +86,14 @@
                     left: 0px;
                     top: 0px;
                 }
-                > icon.multiple {
+                icon.multiple {
                     @extend .fa;
                     @extend .fa-chevron-circle-right;
-                    @extend .btn;
-                    @extend .btn-sm;
-                    @extend .btn-primary;
-                    @extend .p-1;
-                    @extend .mt-1;
-                    color: $white;
+                    color: $brand-primary;
                     position: absolute;
-                    left: -8px;
-                    top: -8px;
+                    font-size: 1.2rem;
+                    left: -5px;
+                    top: -5px;
                 }
             }
             .input-terminal {

From 493d7d5709d5b11400d191dcf1be77be20439235 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 18:24:25 -0500
Subject: [PATCH 401/853] Emit terminal change event on terminal disconnection

---
 .../mvc/workflow/workflow-terminals.js        |  1 +
 .../mvc/workflow/workflow-view-terminals.js   |  8 +++----
 client/galaxy/style/scss/workflow.scss        | 21 ++++++++++---------
 3 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
index da00fa9471b2..ddc1a3769beb 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
@@ -126,6 +126,7 @@ class Terminal extends EventEmitter {
                 connector.handle2.resetCollectionTypeSource();
             }
         }
+        this.emit("change");
     }
     redraw() {
         $.each(this.connectors, (_, c) => {
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index ca7c0d13c42b..516e60dc9b19 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -35,9 +35,9 @@ class BaseInputTerminalView {
     }
     render() {
         if (this.terminal.mapOver && this.terminal.mapOver.isCollection) {
-            this.$el.find("icon").addClass("multiple");
+            this.$el.addClass("multiple");
         } else {
-            this.$el.find("icon").removeClass("multiple");
+            this.$el.removeClass("multiple");
         }
     }
     onDropInit(e, d = {}) {
@@ -185,9 +185,9 @@ export class BaseOutputTerminalView {
     }
     render() {
         if (this.terminal.mapOver && this.terminal.mapOver.isCollection) {
-            this.$el.find("icon").addClass("multiple");
+            this.$el.addClass("multiple");
         } else {
-            this.$el.find("icon").removeClass("multiple");
+            this.$el.removeClass("multiple");
         }
     }
     screenReaderSelectOutputNode(e) {
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 3276df83c89c..c37c9458a3e4 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -86,15 +86,6 @@
                     left: 0px;
                     top: 0px;
                 }
-                icon.multiple {
-                    @extend .fa;
-                    @extend .fa-chevron-circle-right;
-                    color: $brand-primary;
-                    position: absolute;
-                    font-size: 1.2rem;
-                    left: -5px;
-                    top: -5px;
-                }
             }
             .input-terminal {
                 @extend .base-terminal;
@@ -107,6 +98,16 @@
                     color: $brand-success;
                 }
             }
+            .input-terminal.multiple {
+                font-size: 1.2rem;
+                left: -12px;
+                top: 2px;
+            }
+            .output-terminal.multiple {
+                font-size: 1.2rem;
+                right: -12px;
+                top: 2px;
+            }
             .input-terminal-active.can-accept > icon {
                 color: $brand-success;
             }
@@ -130,7 +131,7 @@
             .delete-terminal {
                 @extend .btn;
                 @extend .btn-sm;
-                @extend .btn-primary;
+                @extend .btn-info;
                 @extend .fa;
                 @extend .fa-minus-circle;
                 @extend .p-1;

From 6e2873e913319e046261e372680701759959b6c8 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 18:39:41 -0500
Subject: [PATCH 402/853] Augment workflow connector to allow for different
 sized terminal icons

---
 client/galaxy/scripts/mvc/workflow/workflow-connector.js | 5 ++---
 client/galaxy/scripts/mvc/workflow/workflow-terminals.js | 2 ++
 client/galaxy/style/scss/workflow.scss                   | 4 ++--
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-connector.js b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
index eeb2735d7de3..728eebd1cafa 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-connector.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
@@ -7,7 +7,6 @@ const zIndex = 1000;
 const cpFactor = 10;
 const canvasExtra = 100;
 const handleMarginX = 8;
-const handleMarginY = 5;
 const ribbonMargin = 4;
 const ribbonInnerSingle = 4;
 const ribbonOuterSingle = 6;
@@ -91,9 +90,9 @@ class Connector {
 
         // Find the position of each handle
         let start_x = relativeLeft(handle1.element) + handleMarginX;
-        let start_y = relativeTop(handle1.element) + handleMarginY;
+        let start_y = relativeTop(handle1.element) + 0.5 * $(handle1.element).height();
         let end_x = relativeLeft(handle2.element) + handleMarginX;
-        let end_y = relativeTop(handle2.element) + handleMarginY;
+        let end_y = relativeTop(handle2.element) + 0.5 * $(handle2.element).height();
 
         // Calculate canvas area
         const canvas_min_x = Math.min(start_x, end_x);
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
index ddc1a3769beb..24669c20c280 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
@@ -137,6 +137,7 @@ class Terminal extends EventEmitter {
         $.each(this.connectors.slice(), (_, c) => {
             c.destroy();
         });
+        this.emit("change");
     }
     destroyInvalidConnections() {
         _.each(this.connectors, connector => {
@@ -144,6 +145,7 @@ class Terminal extends EventEmitter {
                 connector.destroyIfInvalid();
             }
         });
+        this.emit("change");
     }
     setMapOver(val) {
         let output_val = val;
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index c37c9458a3e4..90a2cf750d5a 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -100,12 +100,12 @@
             }
             .input-terminal.multiple {
                 font-size: 1.2rem;
-                left: -12px;
+                left: -11px;
                 top: 2px;
             }
             .output-terminal.multiple {
                 font-size: 1.2rem;
-                right: -12px;
+                right: -11px;
                 top: 2px;
             }
             .input-terminal-active.can-accept > icon {

From 0186f1088d5719ccab7d35680d4fb4e0965fcdc6 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 18:54:00 -0500
Subject: [PATCH 403/853] Align terminal icons in workflow nodes, show delete
 button in danger variant

---
 client/galaxy/style/scss/workflow.scss | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 90a2cf750d5a..d0634069e234 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -89,23 +89,23 @@
             }
             .input-terminal {
                 @extend .base-terminal;
-                left: -9px;
+                left: -0.65rem;
             }
             .output-terminal {
                 @extend .base-terminal;
-                right: -9px;
+                right: -0.65rem;
                 &:hover > icon {
                     color: $brand-success;
                 }
             }
             .input-terminal.multiple {
                 font-size: 1.2rem;
-                left: -11px;
+                left: -0.8rem;
                 top: 2px;
             }
             .output-terminal.multiple {
                 font-size: 1.2rem;
-                right: -11px;
+                right: -0.8rem;
                 top: 2px;
             }
             .input-terminal-active.can-accept > icon {
@@ -131,15 +131,15 @@
             .delete-terminal {
                 @extend .btn;
                 @extend .btn-sm;
-                @extend .btn-info;
+                @extend .btn-danger;
                 @extend .fa;
                 @extend .fa-minus-circle;
                 @extend .p-1;
                 @extend .mt-1;
                 position: absolute;
                 z-index: 2500;
-                top: 0px;
-                left: -15px;
+                top: 2px;
+                left: -0.8rem;
             }
             .callout-terminal {
                 position: absolute;

From c12274e045695db60be24e5f8440549c68491f24 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 3 Mar 2020 18:55:39 -0500
Subject: [PATCH 404/853] Fix cursor on delete in workflow node client

---
 client/galaxy/style/scss/workflow.scss | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index d0634069e234..7834c8dbe0f2 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -136,6 +136,7 @@
                 @extend .fa-minus-circle;
                 @extend .p-1;
                 @extend .mt-1;
+                cursor: pointer;
                 position: absolute;
                 z-index: 2500;
                 top: 2px;

From 6e13145b5990de83a6ad6a3d53997f679d305999 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Mar 2020 12:05:12 -0500
Subject: [PATCH 405/853] Increase workflow editor grid transparency

---
 client/galaxy/scripts/components/Workflow/Editor/Node.vue | 2 +-
 client/galaxy/style/scss/theme/blue.scss                  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 58898f84e1d0..4977bb13c5c7 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -65,7 +65,7 @@ export default {
         iconClass() {
             const iconType = WorkflowIcons[this.type];
             if (iconType) {
-                return `icon fa ${iconType}`;
+                return `icon fa fa-fw ${iconType}`;
             }
             return null;
         },
diff --git a/client/galaxy/style/scss/theme/blue.scss b/client/galaxy/style/scss/theme/blue.scss
index 1f463801fb2b..49961495ceb6 100644
--- a/client/galaxy/style/scss/theme/blue.scss
+++ b/client/galaxy/style/scss/theme/blue.scss
@@ -152,7 +152,7 @@ $state-running-border: $border-color;
 // Workflow editor
 $workflow-editor-bg: $white;
 $workflow-editor-grid-size: 0.7rem;
-$workflow-editor-grid-color: lighten($brand-primary, 60%);
+$workflow-editor-grid-color: lighten($brand-primary, 65%);
 $workflow-overview-bg: $panel-bg-color;
 $worfklow-node-width: 10rem;
 

From 700c40470b34bf61899ae2a6373d0e11e283f486 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 5 Mar 2020 18:19:08 -0500
Subject: [PATCH 406/853] Remove unused terminal output handling methods

---
 client/galaxy/scripts/mvc/workflow/workflow-manager.js | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index ada79e2c2458..c988e72796de 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -1,5 +1,4 @@
 import $ from "jquery";
-import { getGalaxyInstance } from "app";
 import Connector from "mvc/workflow/workflow-connector";
 import { Toast } from "ui/toast";
 import { Node } from "mvc/workflow/workflow-node";
@@ -48,18 +47,10 @@ class Workflow extends EventEmitter {
         };
     }
     set_node(node, data) {
-        const Galaxy = getGalaxyInstance();
         node.init_field_data(data);
         node.update_field_data(data);
-        // Post init/update, for new modules we want to default to
-        // nodes being outputs
-        // TODO: Overhaul the handling of all this when we modernize
-        // the editor, replace callout image manipulation with a simple
-        // class toggle, etc.
         $.each(node.output_terminals, (ot_id, ot) => {
             node.addWorkflowOutput(ot.name);
-            var callout = $(node.element).find(`.callout.${ot.name.replace(/(?=[()])/g, "\\")}`);
-            callout.find("img").attr("src", `${Galaxy.root}static/images/fugue/asterisk-small.png`);
         });
         this.activate_node(node);
     }
@@ -102,7 +93,6 @@ class Workflow extends EventEmitter {
     attemptUpdateOutputLabel(node, outputName, label) {
         if (this.canLabelOutputWith(label)) {
             node.labelWorkflowOutput(outputName, label);
-            node.nodeView.redrawWorkflowOutputs();
             return true;
         } else {
             return false;

From e713a0b6c3aa3e1b395067766067dc6988f17d0c Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Mar 2020 19:56:55 -0400
Subject: [PATCH 407/853] Replace asterisk with checkbox in workflow node, with
 left aligned checkbox

---
 .../mvc/workflow/workflow-view-data.js        | 33 ++++++++-----------
 .../mvc/workflow/workflow-view-terminals.js   |  5 ---
 client/galaxy/style/scss/workflow.scss        |  8 +++--
 3 files changed, 19 insertions(+), 27 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
index e89b88d4f94d..35818af99280 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
@@ -5,7 +5,7 @@ export class DataInputView {
         this.input = options.input;
         this.nodeView = options.nodeView;
         this.terminalElement = options.terminalElement;
-        this.$el = $("<div class='form-row dataRow input-data-row'/>");
+        this.$el = $(`<div class="form-row dataRow input-data-row"/>`);
         this.$el.attr("name", this.input.name).html(this.input.label || this.input.name);
         if (!options.skipResize) {
             this.$el.css({
@@ -29,7 +29,7 @@ export class DataInputView {
 
 export class DataOutputView {
     constructor(app, options = {}) {
-        this.$el = $("<div class='form-row dataRow'/>");
+        this.$el = $(`<div class="form-row dataRow"/>`);
         this.output = options.output;
         this.terminalElement = options.terminalElement;
         this.nodeView = options.nodeView;
@@ -37,8 +37,9 @@ export class DataOutputView {
         let label = output.label || output.name;
         const node = this.nodeView.node;
         const isInput = output.extensions.indexOf("input") >= 0;
+        const datatype = output.force_datatype || output.extensions.join(", ");
         if (!isInput) {
-            label = `${label} (${output.force_datatype || output.extensions.join(", ")})`;
+            label = `${label} (${datatype})`;
         }
         this.$el.html(label);
         this.calloutView = null;
@@ -49,7 +50,7 @@ export class DataOutputView {
                 node: node
             });
             this.calloutView = calloutView;
-            this.$el.append(calloutView.$el);
+            this.$el.prepend(calloutView.$el);
         }
         this.$el.css({
             position: "absolute",
@@ -70,14 +71,14 @@ export class DataOutputView {
     }
     redrawWorkflowOutput() {
         if (this.calloutView) {
-            this.calloutView.resetImage();
+            this.calloutView.render();
         }
     }
 }
 
 export class ParameterOutputView {
     constructor(app, options = {}) {
-        this.$el = $("<div class='form-row dataRow'/>");
+        this.$el = $(`<div class="form-row dataRow"/>`);
         this.output = options.output;
         this.terminalElement = options.terminalElement;
         this.nodeView = options.nodeView;
@@ -114,7 +115,7 @@ export class ParameterOutputView {
     }
     redrawWorkflowOutput() {
         if (this.calloutView) {
-            this.calloutView.resetImage();
+            this.calloutView.render();
         }
     }
 }
@@ -130,18 +131,17 @@ export class OutputCalloutView {
         const outputName = view.output.name;
         this.$el
             .attr("class", `callout-terminal ${outputName}`)
-            .css({ display: "none" })
             .append(
                 $("<icon />")
-                    .addClass("mark-terminal fa fa-asterisk")
+                    .addClass("mark-terminal")
                     .click(() => {
+                        this.render();
                         if (node.isWorkflowOutput(outputName)) {
                             node.removeWorkflowOutput(outputName);
-                            view.$el.find("icon").removeClass("mark-terminal-active");
                         } else {
                             node.addWorkflowOutput(outputName);
-                            view.$el.find("icon").addClass("mark-terminal-active");
                         }
+                        this.render();
                         app.has_changes = true;
                         app.canvas_manager.draw_overview();
                     })
@@ -150,16 +150,9 @@ export class OutputCalloutView {
                 delay: 500,
                 title: "Mark dataset as a workflow output. All unmarked datasets will be hidden."
             });
-
-        this.$el.css({
-            top: "50%",
-            margin: "-8px 0px 0px 0px",
-            right: 8
-        });
-        this.$el.show();
-        this.resetImage();
+        this.render();
     }
-    resetImage() {
+    render() {
         if (!this.node.isWorkflowOutput(this.output.name)) {
             this.$el.find("icon").removeClass("mark-terminal-active");
         } else {
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index 516e60dc9b19..5697fc976f0c 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -227,7 +227,6 @@ export class BaseOutputTerminalView {
                     removeMenu();
                     new Connector(this.app.canvas_manager, this.terminal, inputTerminal).redraw();
                     ariaAlert("Node connected");
-
                     if (inputTerminal.connectors.length > 0) {
                         const t = $("<div/>")
                             .addClass("delete-terminal")
@@ -266,7 +265,6 @@ export class BaseOutputTerminalView {
             inputChoicesMenu.setAttribute("role", "menu");
             this.$el.attr("aria-grabbed", "true");
             this.$el.attr("aria-owns", "input-choices-menu");
-
             $(".input-terminal").each((i, el) => {
                 const input = $(el);
                 const inputTerminal = input.context.terminal;
@@ -290,7 +288,6 @@ export class BaseOutputTerminalView {
                 ariaAlert("There are no available inputs for this selected output");
             }
         };
-
         if (e.keyCode === 32) {
             //Space
             ariaAlert("Node selected");
@@ -321,9 +318,7 @@ export class BaseOutputTerminalView {
         var h = $("<div class='drag-terminal'/>")
             .appendTo("#canvas-container")
             .get(0);
-
         h.dropTooltip = "";
-
         // Terminal and connection to display noodle while dragging
         $(h).tooltip({
             title: function() {
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 7834c8dbe0f2..e3461a4895f5 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -122,9 +122,12 @@
                 z-index: 101;
             }
             .mark-terminal {
-                cursor: pointer;
+                @extend .far;
+                @extend .fa-square;
                 color: $text-muted;
+                cursor: pointer;
                 &.mark-terminal-active {
+                    @extend .fa-check-square;
                     color: $brand-success;
                 }
             }
@@ -143,7 +146,8 @@
                 left: -0.8rem;
             }
             .callout-terminal {
-                position: absolute;
+                @extend .float-left;
+                @extend .mr-1;
             }
             .workflow-overview {
                 border-top-left-radius: 0.3rem;

From d920801ac362881a6d1ab58a51729181f6bd54e2 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Mar 2020 20:04:57 -0400
Subject: [PATCH 408/853] Add vue import to workflow node component

---
 client/galaxy/scripts/components/Workflow/Editor/Node.vue | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 4977bb13c5c7..dbdc78c89d84 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -38,9 +38,13 @@
 </template>
 
 <script>
+import Vue from "vue";
+import BootstrapVue from "bootstrap-vue";
 import WorkflowIcons from "components/Workflow/icons";
 import LoadingSpan from "components/LoadingSpan";
 
+Vue.use(BootstrapVue);
+
 export default {
     components: {
         LoadingSpan

From ac367d04ec403cb246bc7eebd21de5599e6ba04d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Mar 2020 22:50:19 -0400
Subject: [PATCH 409/853] Fix terminal mapping class missing qunit test cases

---
 .../qunit/tests/workflow_editor_tests.js      | 64 +++++++++----------
 1 file changed, 29 insertions(+), 35 deletions(-)

diff --git a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
index 449ab1704096..524a9e7b5abb 100644
--- a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
+++ b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
@@ -526,7 +526,7 @@ QUnit.module("Node view ", {
             markChanged: function() {},
             hasConnectedOutputTerminals: function() {},
             connectedMappedInputTerminals: function() {},
-            terminalMapping: { disableMapOver: function() {} }
+            disableMapOver: function() {}
         });
     },
     afterEach: function() {
@@ -540,7 +540,12 @@ QUnit.module("Node view ", {
         this.view.addDataInput({ name: "TestName", extensions: [inputType] });
         var terminal = this.view.node.input_terminals["TestName"];
 
-        var outputTerminal = new Terminals.OutputTerminal({ name: "TestOuptut", datatypes: [outputType] });
+        var outputTerminal = new Terminals.OutputTerminal({
+            name: "TestOuptut",
+            datatypes: [outputType],
+            disableMapOver: function() {},
+            mapOver: Terminals.NULL_COLLECTION_TYPE_DESCRIPTION
+        });
         outputTerminal.node = {
             markChanged: function() {},
             post_job_actions: [],
@@ -551,17 +556,18 @@ QUnit.module("Node view ", {
                 return true;
             }
         };
-        outputTerminal.terminalMapping = {
-            disableMapOver: function() {},
-            mapOver: Terminals.NULL_COLLECTION_TYPE_DESCRIPTION
-        };
         return new Connector({}, outputTerminal, terminal);
     },
     connectAttachedMultiInputTerminal: function(inputType, outputType) {
         this.view.addDataInput({ name: "TestName", extensions: [inputType], multiple: true });
         var terminal = this.view.node.input_terminals["TestName"];
 
-        var outputTerminal = new Terminals.OutputTerminal({ name: "TestOuptut", datatypes: ["txt"] });
+        var outputTerminal = new Terminals.OutputTerminal({
+            name: "TestOuptut",
+            datatypes: ["txt"],
+            disableMapOver: function() {},
+            mapOver: new Terminals.CollectionTypeDescription("list")
+        });
         outputTerminal.node = {
             markChanged: function() {},
             post_job_actions: [],
@@ -572,17 +578,18 @@ QUnit.module("Node view ", {
                 return true;
             }
         };
-        outputTerminal.terminalMapping = {
-            disableMapOver: function() {},
-            mapOver: new Terminals.CollectionTypeDescription("list")
-        };
         return new Connector({}, outputTerminal, terminal);
     },
     connectAttachedMappedOutput: function() {
         this.view.addDataInput({ name: "TestName", extensions: ["txt"], input_type: "dataset_collection" });
         var terminal = this.view.node.input_terminals["TestName"];
 
-        var outputTerminal = new Terminals.OutputTerminal({ name: "TestOuptut", datatypes: ["txt"] });
+        var outputTerminal = new Terminals.OutputTerminal({
+            name: "TestOuptut",
+            datatypes: ["txt"],
+            disableMapOver: function() {},
+            mapOver: new Terminals.CollectionTypeDescription("list")
+        });
         outputTerminal.node = {
             markChanged: function() {},
             post_job_actions: [],
@@ -593,10 +600,6 @@ QUnit.module("Node view ", {
                 return true;
             }
         };
-        outputTerminal.terminalMapping = {
-            disableMapOver: function() {},
-            mapOver: new Terminals.CollectionTypeDescription("list")
-        };
         return new Connector({}, outputTerminal, terminal);
     }
 });
@@ -799,31 +802,26 @@ QUnit.test("equal", function(assert) {
 });
 
 QUnit.test("default constructor", function(assert) {
-    var terminal = {};
-    var mapping = new Terminals.TerminalMapping({ terminal: terminal });
-    assert.ok(terminal.terminalMapping === mapping);
-    assert.ok(mapping.mapOver === Terminals.NULL_COLLECTION_TYPE_DESCRIPTION);
+    var terminal = new Terminals({});
+    assert.ok(terminal.mapOver === Terminals.NULL_COLLECTION_TYPE_DESCRIPTION);
 });
 
 QUnit.test("constructing with mapOver", function(assert) {
-    var terminal = {};
-    var mapping = new Terminals.TerminalMapping({
-        terminal: terminal,
+    var terminal = new Terminals({
         mapOver: new Terminals.CollectionTypeDescription("list")
     });
-    assert.ok(mapping.mapOver.collectionType == "list");
+    assert.ok(terminal.mapOver.collectionType == "list");
 });
 
 QUnit.test("disableMapOver", function(assert) {
-    var terminal = {};
-    var mapping = new Terminals.TerminalMapping({
+    var terminal = new Terminals({
         terminal: terminal,
         mapOver: new Terminals.CollectionTypeDescription("list")
     });
     var changeSpy = sinon.spy();
-    mapping.on("change", changeSpy);
-    mapping.disableMapOver();
-    assert.ok(mapping.mapOver === Terminals.NULL_COLLECTION_TYPE_DESCRIPTION);
+    terminal.on("change", changeSpy);
+    terminal.disableMapOver();
+    assert.ok(terminal.mapOver === Terminals.NULL_COLLECTION_TYPE_DESCRIPTION);
     assert.ok(changeSpy.called);
 });
 
@@ -837,7 +835,6 @@ QUnit.module("terminal mapping logic", {
         var inputEl = $("<div>")[0];
         const app = create_app();
         var inputTerminal = new Terminals.InputTerminal({ app: app, element: inputEl, input: input });
-        new Terminals.TerminalMapping({ terminal: inputTerminal });
         inputTerminal.node = node;
         if (mapOver) {
             inputTerminal.setMapOver(new Terminals.CollectionTypeDescription(mapOver));
@@ -857,7 +854,6 @@ QUnit.module("terminal mapping logic", {
             element: inputEl,
             input: input
         });
-        new Terminals.TerminalMapping({ terminal: inputTerminal });
         inputTerminal.node = node;
         return inputTerminal;
     },
@@ -869,7 +865,6 @@ QUnit.module("terminal mapping logic", {
         }
         const outputEl = $("<div>")[0];
         const outputTerminal = new Terminals.OutputTerminal({ element: outputEl, datatypes: output.extensions });
-        new Terminals.TerminalMapping({ terminal: outputTerminal });
         outputTerminal.node = node;
         if (mapOver) {
             outputTerminal.setMapOver(new Terminals.CollectionTypeDescription(mapOver));
@@ -889,7 +884,6 @@ QUnit.module("terminal mapping logic", {
             datatypes: output.extensions,
             collection_type: collectionType
         });
-        new Terminals.TerminalMapping({ terminal: outputTerminal });
         outputTerminal.node = node;
         if (mapOver) {
             outputTerminal.setMapOver(new Terminals.CollectionTypeDescription(mapOver));
@@ -973,10 +967,10 @@ QUnit.module("terminal mapping logic", {
         assert.ok(!inputTerminal.attachable(outputTerminal).canAccept);
     },
     verifyMappedOver: function(assert, terminal) {
-        assert.ok(terminal.terminalMapping.mapOver.isCollection);
+        assert.ok(terminal.mapOver.isCollection);
     },
     verifyNotMappedOver: function(assert, terminal) {
-        assert.ok(!terminal.terminalMapping.mapOver.isCollection);
+        assert.ok(!terminal.mapOver.isCollection);
     }
 });
 

From 290f0f84758311904847524de8cc01a03152da70 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 8 Mar 2020 23:01:51 -0400
Subject: [PATCH 410/853] Fix resetmapover test cases

---
 .../mvc/workflow/workflow-terminals.js        |  3 ++-
 .../qunit/tests/workflow_editor_tests.js      | 20 +++++++++----------
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
index 24669c20c280..a91dee984c51 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
@@ -171,6 +171,7 @@ class Terminal extends EventEmitter {
     }
     resetMapping() {
         this.mapOver = NULL_COLLECTION_TYPE_DESCRIPTION;
+        this.emit("change");
     }
     resetCollectionTypeSource() {
         const node = this.node;
@@ -375,7 +376,7 @@ class BaseInputTerminal extends Terminal {
 }
 
 class InputTerminal extends BaseInputTerminal {
-    update(input) {
+    update(input = {}) {
         this.datatypes = input.extensions;
         this.multiple = input.multiple;
         this.optional = input.optional;
diff --git a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
index 524a9e7b5abb..369515bb3356 100644
--- a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
+++ b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
@@ -184,7 +184,6 @@ QUnit.test("can accept already connected inputs if input is multiple", function(
 
 QUnit.test("cannot accept already connected inputs if input is multiple but datatypes don't match", function(assert) {
     var other = { node: {}, datatypes: ["binary"] }; // binary is not txt
-
     this.multiple();
     this.with_test_connector(() => {
         assert.ok(!this.test_accept(other));
@@ -525,8 +524,7 @@ QUnit.module("Node view ", {
             output_terminals: {},
             markChanged: function() {},
             hasConnectedOutputTerminals: function() {},
-            connectedMappedInputTerminals: function() {},
-            disableMapOver: function() {}
+            connectedMappedInputTerminals: function() {}
         });
     },
     afterEach: function() {
@@ -543,7 +541,6 @@ QUnit.module("Node view ", {
         var outputTerminal = new Terminals.OutputTerminal({
             name: "TestOuptut",
             datatypes: [outputType],
-            disableMapOver: function() {},
             mapOver: Terminals.NULL_COLLECTION_TYPE_DESCRIPTION
         });
         outputTerminal.node = {
@@ -565,7 +562,6 @@ QUnit.module("Node view ", {
         var outputTerminal = new Terminals.OutputTerminal({
             name: "TestOuptut",
             datatypes: ["txt"],
-            disableMapOver: function() {},
             mapOver: new Terminals.CollectionTypeDescription("list")
         });
         outputTerminal.node = {
@@ -587,7 +583,6 @@ QUnit.module("Node view ", {
         var outputTerminal = new Terminals.OutputTerminal({
             name: "TestOuptut",
             datatypes: ["txt"],
-            disableMapOver: function() {},
             mapOver: new Terminals.CollectionTypeDescription("list")
         });
         outputTerminal.node = {
@@ -802,25 +797,28 @@ QUnit.test("equal", function(assert) {
 });
 
 QUnit.test("default constructor", function(assert) {
-    var terminal = new Terminals({});
+    var terminal = new Terminals.InputTerminal({});
     assert.ok(terminal.mapOver === Terminals.NULL_COLLECTION_TYPE_DESCRIPTION);
 });
 
 QUnit.test("constructing with mapOver", function(assert) {
-    var terminal = new Terminals({
+    var terminal = new Terminals.InputTerminal({
         mapOver: new Terminals.CollectionTypeDescription("list")
     });
     assert.ok(terminal.mapOver.collectionType == "list");
 });
 
-QUnit.test("disableMapOver", function(assert) {
-    var terminal = new Terminals({
+QUnit.test("resetMapping", function(assert) {
+    var terminal = new Terminals.InputTerminal({
         terminal: terminal,
         mapOver: new Terminals.CollectionTypeDescription("list")
     });
+    terminal.node = {
+        hasMappedOverInputTerminals: () => true
+    };
     var changeSpy = sinon.spy();
     terminal.on("change", changeSpy);
-    terminal.disableMapOver();
+    terminal.resetMapping();
     assert.ok(terminal.mapOver === Terminals.NULL_COLLECTION_TYPE_DESCRIPTION);
     assert.ok(changeSpy.called);
 });

From 4ff6e71679ba811787a2cc5c6124d1c11dbdaf4a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 9 Mar 2020 00:22:29 -0400
Subject: [PATCH 411/853] Fix qunit test cases for workflow client

---
 .../galaxy/scripts/qunit/tests/workflow_editor_tests.js   | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
index 369515bb3356..6e49e2bbfad0 100644
--- a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
+++ b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
@@ -199,9 +199,7 @@ QUnit.test("can accept list collection for empty multiple inputs", function(asse
     var other = {
         node: {},
         datatypes: ["tabular"],
-        mapOver: function() {
-            return new Terminals.CollectionTypeDescription("list");
-        }
+        mapOver: new Terminals.CollectionTypeDescription("list")
     };
     this.multiple();
     assert.ok(this.test_accept(other));
@@ -211,9 +209,7 @@ QUnit.test("cannot accept list collection for multiple input if collection alrea
     var other = {
         node: {},
         datatypes: ["tabular"],
-        mapOver: function() {
-            return new Terminals.CollectionTypeDescription("list");
-        }
+        mapOver: new Terminals.CollectionTypeDescription("list")
     };
     this.multiple();
     this.with_test_connector(() => {

From 022c00960c125bbe98b476e4b365fd2ec599adf1 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 9 Mar 2020 10:52:22 -0400
Subject: [PATCH 412/853] Fix selenium test cases for workflow editor nodes

---
 client/galaxy/scripts/components/Workflow/Editor/Node.vue | 2 +-
 lib/galaxy/selenium/navigation.yml                        | 3 ++-
 lib/galaxy_test/selenium/test_workflow_editor.py          | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index dbdc78c89d84..43815e2cedc3 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -1,7 +1,7 @@
 <template>
     <div>
         <div class="node-header unselectable clearfix">
-            <b-dropdown right no-caret class="float-right" toggle-class="py-0" offset="50" variant="info" size="sm">
+            <b-dropdown right no-caret class="node-dropdown float-right" toggle-class="py-0" offset="50" variant="info" size="sm">
                 <template v-slot:button-content>
                     <i :class="iconClass" />
                 </template>
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index c6160ba379d3..3069bb2a6691 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -308,13 +308,14 @@ workflow_editor:
       _: "[node-label='${label}']"
 
       title: '${_} .node-title'
+      dropdown: '${_} .node-dropdown'
       destroy: '${_} .node-destroy'
       clone: '${_} .node-clone'
 
       output_terminal: "${_} [output-name='${name}']"
       input_terminal: "${_} [input-name='${name}']"
 
-      input_mapping_icon: "${_} [name='${name}'] .fa-folder-o"
+      input_mapping_icon: "${_} [name='${name}'] .multiple"
 
   selectors:
     canvas_body: '#workflow-canvas'
diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index 73216201b388..0392019b4056 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -76,7 +76,7 @@ def test_data_input(self):
         assert label == "input1", label
         # should work but Galaxy is broken.
         # assert editor.annotation_input.wait_for_value() == "my cool annotation"
-
+        data_input_node.dropdown.wait_for_and_click();
         data_input_node.destroy.wait_for_and_click()
         data_input_node.wait_for_absent()
         self.screenshot("workflow_editor_data_input_deleted")

From 822f6e7f7e3fb594440d7fcd2a622d8c5ef2d438 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 9 Mar 2020 10:55:09 -0400
Subject: [PATCH 413/853] Format client, fix remaining selenium tests for
 workflow node

---
 .../galaxy/scripts/components/Workflow/Editor/Node.vue | 10 +++++++++-
 lib/galaxy_test/selenium/test_workflow_editor.py       |  6 +++---
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 43815e2cedc3..c29e6f618696 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -1,7 +1,15 @@
 <template>
     <div>
         <div class="node-header unselectable clearfix">
-            <b-dropdown right no-caret class="node-dropdown float-right" toggle-class="py-0" offset="50" variant="info" size="sm">
+            <b-dropdown
+                right
+                no-caret
+                class="node-dropdown float-right"
+                toggle-class="py-0"
+                offset="50"
+                variant="info"
+                size="sm"
+            >
                 <template v-slot:button-content>
                     <i :class="iconClass" />
                 </template>
diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index 0392019b4056..658174f0c7da 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -76,7 +76,7 @@ def test_data_input(self):
         assert label == "input1", label
         # should work but Galaxy is broken.
         # assert editor.annotation_input.wait_for_value() == "my cool annotation"
-        data_input_node.dropdown.wait_for_and_click();
+        data_input_node.dropdown.wait_for_and_click()
         data_input_node.destroy.wait_for_and_click()
         data_input_node.wait_for_absent()
         self.screenshot("workflow_editor_data_input_deleted")
@@ -102,7 +102,7 @@ def test_collection_input(self):
         assert label == "input1", label
         # should work but Galaxy is broken.
         # assert editor.annotation_input.wait_for_value() == "my cool annotation"
-
+        data_input_node.dropdown.wait_for_and_click()
         data_input_node.destroy.wait_for_and_click()
         data_input_node.wait_for_absent()
         self.screenshot("workflow_editor_data_collection_input_deleted")
@@ -129,7 +129,7 @@ def test_integer_input(self):
         assert label == "input1", label
         # should work but Galaxy is broken.
         # assert editor.annotation_input.wait_for_value() == "my cool annotation"
-
+        data_input_node.dropdown.wait_for_and_click()
         data_input_node.destroy.wait_for_and_click()
         data_input_node.wait_for_absent()
         self.screenshot("workflow_editor_parameter_input_deleted")

From 007c1f087567bb3110a4d50735801ec95d6747e2 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 9 Mar 2020 14:02:17 -0400
Subject: [PATCH 414/853] Fix workflow node tooltip for workflow outputs

---
 client/galaxy/scripts/mvc/workflow/workflow-view-data.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
index 35818af99280..143d24f71da2 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
@@ -148,7 +148,7 @@ export class OutputCalloutView {
             )
             .tooltip({
                 delay: 500,
-                title: "Mark dataset as a workflow output. All unmarked datasets will be hidden."
+                title: "Check dataset as output, unchecked datasets will be hidden."
             });
         this.render();
     }

From b0a1962f1b865f5c4bcde43052bc79d8afa364c7 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 9 Mar 2020 14:33:02 -0400
Subject: [PATCH 415/853] Remove duplicate render call from workflow view data
 click handler

---
 client/galaxy/scripts/mvc/workflow/workflow-view-data.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
index 143d24f71da2..c1404f1bab6e 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
@@ -135,7 +135,6 @@ export class OutputCalloutView {
                 $("<icon />")
                     .addClass("mark-terminal")
                     .click(() => {
-                        this.render();
                         if (node.isWorkflowOutput(outputName)) {
                             node.removeWorkflowOutput(outputName);
                         } else {

From f7329b3b8e9cd6fdbddf582cd7f9ad9c0fcfcdb1 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 9 Mar 2020 23:25:16 -0400
Subject: [PATCH 416/853] Unify workflow node colors, use primary colors
 instead of info and success brand colors

---
 client/galaxy/scripts/components/Workflow/Editor/Node.vue | 2 +-
 client/galaxy/style/scss/workflow.scss                    | 8 ++++++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index c29e6f618696..d21e12dd9ec5 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -7,7 +7,7 @@
                 class="node-dropdown float-right"
                 toggle-class="py-0"
                 offset="50"
-                variant="info"
+                variant="primary"
                 size="sm"
             >
                 <template v-slot:button-content>
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index e3461a4895f5..7575cdac821e 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -25,6 +25,10 @@
                 cursor: move;
                 background: $brand-primary;
                 color: $white;
+                .node-dropdown {
+                    @extend .rounded;
+                    border: solid $border-color 1px;
+                }
             }
             .node-body {
                 @extend .card-body;
@@ -124,11 +128,11 @@
             .mark-terminal {
                 @extend .far;
                 @extend .fa-square;
-                color: $text-muted;
+                color: $brand-primary;
                 cursor: pointer;
                 &.mark-terminal-active {
+                    @extend .fa;
                     @extend .fa-check-square;
-                    color: $brand-success;
                 }
             }
             .delete-terminal {

From 79f0be1b2cd56db707fab0f7956a28962db74fe0 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 9 Mar 2020 23:55:04 -0400
Subject: [PATCH 417/853] Remove unused local variable in workflow data node
 handler, revise tooltip for destroy option

---
 client/galaxy/scripts/mvc/workflow/workflow-view-data.js | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
index c1404f1bab6e..8dca75014b21 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
@@ -126,9 +126,8 @@ export class OutputCalloutView {
         this.label = options.label;
         this.node = options.node;
         this.output = options.output;
-        const view = this;
         const node = this.node;
-        const outputName = view.output.name;
+        const outputName = this.output.name;
         this.$el
             .attr("class", `callout-terminal ${outputName}`)
             .append(
@@ -147,7 +146,7 @@ export class OutputCalloutView {
             )
             .tooltip({
                 delay: 500,
-                title: "Check dataset as output, unchecked datasets will be hidden."
+                title: "Unchecked output datasets will be hidden."
             });
         this.render();
     }

From 1589e4a852821d37485a391e6861f0072d298b25 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 10 Mar 2020 00:00:29 -0400
Subject: [PATCH 418/853] Properly highlight initial workflow output state when
 adding new nodes

---
 client/galaxy/scripts/mvc/workflow/workflow-manager.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index c988e72796de..490d92bbae89 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -51,6 +51,7 @@ class Workflow extends EventEmitter {
         node.update_field_data(data);
         $.each(node.output_terminals, (ot_id, ot) => {
             node.addWorkflowOutput(ot.name);
+            node.markWorkflowOutput(ot.name);
         });
         this.activate_node(node);
     }

From 25dc9a6023d7d10959e24618f4b7d8e11303a9a1 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 10 Mar 2020 20:08:04 -0400
Subject: [PATCH 419/853] Restore 3-button workflow node header

---
 .../components/Workflow/Editor/Node.vue       | 48 +++++++------------
 client/galaxy/style/scss/workflow.scss        |  4 --
 lib/galaxy/selenium/navigation.yml            |  1 -
 .../selenium/test_workflow_editor.py          |  3 --
 4 files changed, 17 insertions(+), 39 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index d21e12dd9ec5..93070869e0a7 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -1,40 +1,26 @@
 <template>
     <div>
         <div class="node-header unselectable clearfix">
-            <b-dropdown
-                right
-                no-caret
-                class="node-dropdown float-right"
-                toggle-class="py-0"
-                offset="50"
+            <b-button
+                class="node-destroy py-0 float-right"
                 variant="primary"
                 size="sm"
+                aria-label="clone node"
+                @click="onDestroy"
             >
-                <template v-slot:button-content>
-                    <i :class="iconClass" />
-                </template>
-                <b-dropdown-item
-                    v-if="canClone"
-                    aria-label="clone node"
-                    role="button"
-                    href="#"
-                    class="node-clone"
-                    @click="onClone"
-                >
-                    <span class="fa fa-fw fa-files-o" />
-                    Duplicate
-                </b-dropdown-item>
-                <b-dropdown-item
-                    aria-label="destroy node"
-                    role="button"
-                    href="#"
-                    class="node-destroy"
-                    @click="onDestroy"
-                >
-                    <span class="fa fa-fw fa-trash" />
-                    Remove
-                </b-dropdown-item>
-            </b-dropdown>
+                <i class="fa fa-times" />
+            </b-button>
+            <b-button
+                v-if="canClone"
+                class="node-clone py-0 float-right"
+                variant="primary"
+                size="sm"
+                aria-label="clone node"
+                @click="onClone"
+            >
+                <i class="fa fa-files-o" />
+            </b-button>
+            <i :class="iconClass" />
             <span class="node-title">{{ title }}</span>
         </div>
         <div class="node-body">
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 7575cdac821e..b89ca0bc69e7 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -25,10 +25,6 @@
                 cursor: move;
                 background: $brand-primary;
                 color: $white;
-                .node-dropdown {
-                    @extend .rounded;
-                    border: solid $border-color 1px;
-                }
             }
             .node-body {
                 @extend .card-body;
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index 3069bb2a6691..bbf6aad52d00 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -308,7 +308,6 @@ workflow_editor:
       _: "[node-label='${label}']"
 
       title: '${_} .node-title'
-      dropdown: '${_} .node-dropdown'
       destroy: '${_} .node-destroy'
       clone: '${_} .node-clone'
 
diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index 658174f0c7da..d55e3b860e37 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -76,7 +76,6 @@ def test_data_input(self):
         assert label == "input1", label
         # should work but Galaxy is broken.
         # assert editor.annotation_input.wait_for_value() == "my cool annotation"
-        data_input_node.dropdown.wait_for_and_click()
         data_input_node.destroy.wait_for_and_click()
         data_input_node.wait_for_absent()
         self.screenshot("workflow_editor_data_input_deleted")
@@ -102,7 +101,6 @@ def test_collection_input(self):
         assert label == "input1", label
         # should work but Galaxy is broken.
         # assert editor.annotation_input.wait_for_value() == "my cool annotation"
-        data_input_node.dropdown.wait_for_and_click()
         data_input_node.destroy.wait_for_and_click()
         data_input_node.wait_for_absent()
         self.screenshot("workflow_editor_data_collection_input_deleted")
@@ -129,7 +127,6 @@ def test_integer_input(self):
         assert label == "input1", label
         # should work but Galaxy is broken.
         # assert editor.annotation_input.wait_for_value() == "my cool annotation"
-        data_input_node.dropdown.wait_for_and_click()
         data_input_node.destroy.wait_for_and_click()
         data_input_node.wait_for_absent()
         self.screenshot("workflow_editor_parameter_input_deleted")

From cbd22e4242f6f9cb28427d1b5211eb657f381e97 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 11 Mar 2020 10:41:20 -0400
Subject: [PATCH 420/853] Fix workflow node component test

---
 .../components/Workflow/Editor/Node.test.js        | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.test.js b/client/galaxy/scripts/components/Workflow/Editor/Node.test.js
index 16b6bf92014e..c0599c340441 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.test.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.test.js
@@ -11,15 +11,15 @@ describe("Node", () => {
                 type: "tool"
             }
         });
-        const icon = wrapper.find("i");
-        expect(icon.classes()).to.contain("fa-wrench");
-        const toolLinks = wrapper.findAll("a");
-        expect(toolLinks.length).to.equal(2);
+        const icon = wrapper.findAll("i");
+        expect(icon.at(2).classes()).to.contain("fa-wrench");
+        const toolLinks = wrapper.findAll("i");
+        expect(toolLinks.length).to.equal(3);
         wrapper.setProps({ type: "subworkflow" });
         await Vue.nextTick();
-        expect(icon.classes()).to.contain("fa-sitemap");
-        const subworkflowLinks = wrapper.findAll("a");
-        expect(subworkflowLinks.length).to.equal(1);
+        expect(icon.at(2).classes()).to.contain("fa-sitemap");
+        const subworkflowLinks = wrapper.findAll("i");
+        expect(subworkflowLinks.length).to.equal(2);
         const workflowTitle = wrapper.find(".node-title");
         expect(workflowTitle.text()).to.equal("node-title");
     });

From a50878613d134d23e27364a3c779cb6fe81eefb5 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 14 Mar 2020 09:27:33 -0400
Subject: [PATCH 421/853] Prep release for tool-util 20.5.0.dev0

---
 packages/tool_util/HISTORY.rst                        | 8 +++++++-
 packages/tool_util/galaxy/project_galaxy_tool_util.py | 2 +-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst
index f08ef0fed61a..d2be3810139c 100644
--- a/packages/tool_util/HISTORY.rst
+++ b/packages/tool_util/HISTORY.rst
@@ -5,11 +5,17 @@ History
 
 .. to_doc
 
+---------------------
+20.5.0.dev0
+---------------------
+
+* First release from the 20.05 branch of Galaxy.
+
 ---------------------
 20.1.0.dev0
 ---------------------
 
-* First release from 20.01 branch of Galaxy.
+* First release from the 20.01 branch of Galaxy.
 
 ---------------------
 19.9.1 (2019-12-28)
diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py
index 7c43e5164826..c644d9692d67 100644
--- a/packages/tool_util/galaxy/project_galaxy_tool_util.py
+++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.1.0.dev6'
+__version__ = '20.5.0.dev1'
 
 PROJECT_NAME = "galaxy-tool-util"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From df6c6047742efc8fb8e820bf51b5f3e2b32e19a1 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 14 Mar 2020 09:34:02 -0400
Subject: [PATCH 422/853] Starting work on tool-util 20.5.0.dev2

---
 packages/tool_util/galaxy/project_galaxy_tool_util.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py
index c644d9692d67..7d009b8f20bf 100644
--- a/packages/tool_util/galaxy/project_galaxy_tool_util.py
+++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev1'
+__version__ = '20.5.0.dev2'
 
 PROJECT_NAME = "galaxy-tool-util"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 82e6cd0874f6f43c1be8e0304849806f919b9db7 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 16 Mar 2020 12:57:14 +0100
Subject: [PATCH 423/853] Remove jquery and add axios

---
 .../scripts/components/ToolRecommendation.vue | 111 +++++++++---------
 1 file changed, 54 insertions(+), 57 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 6abcf09b319f..6d3dfbf5a190 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -17,7 +17,7 @@
 import Utils from "utils/utils";
 import * as d3 from "d3";
 import { getAppRoot } from "onload/loadConfig";
-import $ from "jquery";
+import axios from "axios";
 
 export default {
     props: {
@@ -47,67 +47,64 @@ export default {
     },
     methods: {
         loadRecommendations: function() {
-            const self = this;
-            const toolId = this.getToolId;
-            Utils.request({
-                type: "POST",
-                url: `${getAppRoot()}api/workflows/get_tool_predictions`,
-                data: { tool_sequence: toolId },
-                success: data => {
-                    // get datatypes mapping
-                    const datatypes_mapping = JSON.parse(
-                            $.ajax({
-                                url: `${getAppRoot()}api/datatypes/mapping`,
-                                async: false
-                            }).responseText
-                        ),
-                        extToType = datatypes_mapping.ext_to_class_name,
-                        typeToType = datatypes_mapping.class_to_classes,
-                        predData = data.predicted_data;
-                    this.deprecated = predData["is_deprecated"];
-                    if (data !== null && predData.children.length > 0) {
-                        const filteredData = {},
-                            compatibleTools = {},
-                            filteredChildren = [],
-                            outputDatatypes = predData["o_extensions"],
-                            children = predData.children;
-                        for (const nameObj of children.entries()) {
-                            const inputDatatypes = nameObj[1]["i_extensions"];
-                            for (const out_t of outputDatatypes.entries()) {
-                                for (const in_t of inputDatatypes.entries()) {
-                                    const child = extToType[out_t[1]],
-                                        parent = extToType[in_t[1]];
-                                    if (
-                                        (typeToType[child] && parent in typeToType[child]) === true ||
-                                        out_t[1] === "input" ||
-                                        out_t[1] === "_sniff_" ||
-                                        out_t[1] === "input_collection"
-                                    ) {
-                                        compatibleTools[nameObj[1]["tool_id"]] = nameObj[1]["name"];
-                                        break;
+            const self = this,
+                toolId = this.getToolId,
+                url = getAppRoot() + "api/workflows/get_tool_predictions";
+            axios
+                .post(url, {
+                    tool_sequence: toolId
+                })
+                .then(response => {
+                    axios.get(getAppRoot() + "api/datatypes/mapping").then(responseMapping => {
+                        const predData = response.data.predicted_data,
+                            datatypesMapping = responseMapping.data,
+                            extToType = datatypesMapping.ext_to_class_name,
+                            typeToType = datatypesMapping.class_to_classes;
+                        self.deprecated = predData.is_deprecated;
+
+                        if (response.data !== null && predData.children.length > 0) {
+                            const filteredData = {},
+                                compatibleTools = {},
+                                filteredChildren = [],
+                                outputDatatypes = predData.o_extensions,
+                                children = predData.children;
+                            for (const nameObj of children.entries()) {
+                                const inputDatatypes = nameObj[1].i_extensions;
+                                for (const out_t of outputDatatypes.entries()) {
+                                    for (const in_t of inputDatatypes.entries()) {
+                                        const child = extToType[out_t[1]],
+                                            parent = extToType[in_t[1]];
+                                        if (
+                                            (typeToType[child] && parent in typeToType[child]) === true ||
+                                            out_t[1] === "input" ||
+                                            out_t[1] === "_sniff_" ||
+                                            out_t[1] === "input_collection"
+                                        ) {
+                                            compatibleTools[nameObj[1]["tool_id"]] = nameObj[1]["name"];
+                                            break;
+                                        }
                                     }
                                 }
                             }
-                        }
-                        for (const id in compatibleTools) {
-                            for (const nameObj of children.entries()) {
-                                if (nameObj[1]["tool_id"] === id) {
-                                    filteredChildren.push(nameObj[1]);
-                                    break;
+                            for (const id in compatibleTools) {
+                                for (const nameObj of children.entries()) {
+                                    if (nameObj[1]["tool_id"] === id) {
+                                        filteredChildren.push(nameObj[1]);
+                                        break;
+                                    }
                                 }
                             }
+                            filteredData["o_extensions"] = predData.o_extensions;
+                            filteredData["name"] = predData.name;
+                            filteredData["children"] = filteredChildren;
+                            if (filteredChildren.length > 0 && self.deprecated === false) {
+                                self.renderD3Tree(filteredData);
+                            } else if (self.deprecated === true) {
+                                self.deprecatedMessage = predData.message;
+                            }
                         }
-                        filteredData["o_extensions"] = predData["o_extensions"];
-                        filteredData["name"] = predData["name"];
-                        filteredData["children"] = filteredChildren;
-                        if (filteredChildren.length > 0 && this.deprecated === false) {
-                            self.renderD3Tree(filteredData);
-                        } else if (this.deprecated === true) {
-                            this.deprecatedMessage = predData["message"];
-                        }
-                    }
-                }
-            });
+                    });
+                });
         },
         renderD3Tree: function(predictedTools) {
             const margin = { top: 20, right: 30, bottom: 20, left: 250 },
@@ -226,7 +223,7 @@ export default {
                 }
                 update(d);
                 if (d.tool_id !== undefined && d.tool_id !== "undefined" && d.tool_id !== null && d.tool_id !== "") {
-                    document.location.href = `${getAppRoot()}` + "tool_runner?tool_id=" + d.tool_id;
+                    document.location.href = getAppRoot() + "tool_runner?tool_id=" + d.tool_id;
                 }
             }
             function collapse(d) {

From 6174c232a50371d4deae7c115cf6b5b556b56944 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 16 Mar 2020 12:58:26 +0100
Subject: [PATCH 424/853] Remove utils

---
 client/galaxy/scripts/components/ToolRecommendation.vue | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 6d3dfbf5a190..88d0eaa4f4ab 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -14,7 +14,6 @@
 </template>
 
 <script>
-import Utils from "utils/utils";
 import * as d3 from "d3";
 import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";

From 13ccc54750ad967a0e00ea5720451a888a37bba7 Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Mon, 16 Mar 2020 10:09:17 -0400
Subject: [PATCH 425/853] Rename and modify current_history_contents method

I think the current functionality will be useful in the future,
when we want to retrieve or compare history contents or history
datasets from the API with what is displayed.
---
 lib/galaxy/selenium/navigates_galaxy.py       | 19 +++++++++++++------
 lib/galaxy_test/selenium/test_anon_history.py |  2 +-
 lib/galaxy_test/selenium/test_uploads.py      |  8 ++++----
 3 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index d4421873c610..6cc481fbcda0 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -207,6 +207,18 @@ def history_panel_name_element(self):
     def history_panel_name(self):
         return self.history_panel_name_element().text
 
+    def history_contents(self, history_id=None, view='summary', datasets_only=True):
+        if history_id is None:
+            history_id = self.current_history_id()
+        histories = self.api_get('histories?keys=id')
+        if history_id not in [h['id'] for h in histories]:
+            return {}
+        if datasets_only:
+            endpoint = 'histories/%s/contents?view=%s' % (history_id, view)
+        else:
+            endpoint = 'histories/%s?view=%s' % (history_id, view)
+        return self.api_get(endpoint)
+
     def current_history(self):
         full_url = self.build_url("history/current_history_json", for_selenium=False)
         response = requests.get(full_url, cookies=self.selenium_to_requests_cookies())
@@ -215,13 +227,8 @@ def current_history(self):
     def current_history_id(self):
         return self.current_history()["id"]
 
-    def current_history_contents(self):
-        current_history_id = self.current_history_id()
-        history_contents = self.api_get("histories/%s/contents" % current_history_id)
-        return history_contents
-
     def latest_history_item(self):
-        history_contents = self.current_history_contents()
+        history_contents = self.history_contents()
         assert len(history_contents) > 0
         return history_contents[-1]
 
diff --git a/lib/galaxy_test/selenium/test_anon_history.py b/lib/galaxy_test/selenium/test_anon_history.py
index 95caafb10fe5..5c29ecaa9701 100644
--- a/lib/galaxy_test/selenium/test_anon_history.py
+++ b/lib/galaxy_test/selenium/test_anon_history.py
@@ -48,7 +48,7 @@ def test_clean_anon_history_after_logout(self):
         # anonymous user. Make sure this new history is empty.
         self.home()
         self.history_panel_wait_for_history_loaded()
-        history_contents = self.current_history_contents()
+        history_contents = self.history_contents()
         assert len(history_contents) == 0
 
     def _upload_file_anonymous_then_register_user(self):
diff --git a/lib/galaxy_test/selenium/test_uploads.py b/lib/galaxy_test/selenium/test_uploads.py
index ed0c8fa1d044..7606f0c1dfdf 100644
--- a/lib/galaxy_test/selenium/test_uploads.py
+++ b/lib/galaxy_test/selenium/test_uploads.py
@@ -16,7 +16,7 @@ def test_upload_simplest(self):
         self.perform_upload(self.get_filename("1.sam"))
 
         self.history_panel_wait_for_hid_ok(1)
-        history_contents = self.current_history_contents()
+        history_contents = self.history_contents()
         history_count = len(history_contents)
         assert history_count == 1, "Incorrect number of items in history - expected 1, found %d" % history_count
 
@@ -31,7 +31,7 @@ def test_upload_simplest(self):
     def test_upload_specify_ext(self):
         self.perform_upload(self.get_filename("1.sam"), ext="txt")
         self.history_panel_wait_for_hid_ok(1)
-        history_contents = self.current_history_contents()
+        history_contents = self.history_contents()
         hda = history_contents[0]
         assert hda["name"] == '1.sam'
         assert hda["extension"] == "txt", hda
@@ -48,7 +48,7 @@ def test_upload_specify_genome(self):
     def test_upload_specify_ext_all(self):
         self.perform_upload(self.get_filename("1.sam"), ext_all="txt")
         self.history_panel_wait_for_hid_ok(1)
-        history_contents = self.current_history_contents()
+        history_contents = self.history_contents()
         hda = history_contents[0]
         assert hda["name"] == '1.sam'
         assert hda["extension"] == "txt", hda
@@ -92,7 +92,7 @@ def test_upload_pair_specify_extension(self):
         self.history_panel_wait_for_hid_ok(3)
         self.history_panel_wait_for_hid_ok(1)
 
-        history_contents = self.current_history_contents()
+        history_contents = self.history_contents()
         hda = history_contents[0]
         assert hda["name"] == '1.tabular'
         assert hda["extension"] == "txt", hda

From b1c5879854fb8781e3e98e6fbc9edcae71b26322 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 16 Mar 2020 17:03:43 +0100
Subject: [PATCH 426/853] Refactor API

---
 lib/galaxy/tools/tool_recommendations.py   | 219 +++++++++++++++++++++
 lib/galaxy/webapps/galaxy/api/workflows.py | 217 +-------------------
 2 files changed, 226 insertions(+), 210 deletions(-)
 create mode 100644 lib/galaxy/tools/tool_recommendations.py

diff --git a/lib/galaxy/tools/tool_recommendations.py b/lib/galaxy/tools/tool_recommendations.py
new file mode 100644
index 000000000000..c8df15f36a76
--- /dev/null
+++ b/lib/galaxy/tools/tool_recommendations.py
@@ -0,0 +1,219 @@
+""" Compute tool recommendations """
+
+import json
+import logging
+import os
+
+import h5py
+import numpy as np
+import requests
+import yaml
+
+from galaxy.tools.parameters import populate_state
+from galaxy.tools.parameters.basic import workflow_building_modes
+from galaxy.workflow.modules import module_factory
+
+log = logging.getLogger(__name__)
+
+
+class ToolRecommendations():
+
+    def __init__(self):
+        self.tool_recommendation_model_path = None
+        self.admin_tool_recommendations_path = None
+        self.deprecated_tools = dict()
+        self.admin_recommendations = dict()
+
+    def set_model(self, trans, remote_model_url):
+        """
+        Create model and associated dictionaries for recommendations
+        """
+        if not self.tool_recommendation_model_path:
+            # import moves from the top of file: in case the tool recommendation feature is disabled,
+            # keras is not downloaded because of conditional requirement and Galaxy does not build
+            try:
+                from keras.models import model_from_json
+            except Exception:
+                trans.response.status = 400
+                return False
+            self.tool_recommendation_model_path = self.download_model(remote_model_url)
+            self.all_tools = dict()
+            model_weights = list()
+            counter_layer_weights = 0
+            # collect ids and names of all the installed tools
+            for tool_id, tool in trans.app.toolbox.tools():
+                t_id_renamed = tool_id
+                if t_id_renamed.find("/") > -1:
+                    t_id_renamed = t_id_renamed.split("/")[-2]
+                self.all_tools[t_id_renamed] = (tool_id, tool.name)
+            # read the hdf5 attributes
+            trained_model = h5py.File(self.tool_recommendation_model_path, 'r')
+            model_config = json.loads(trained_model['model_config'][()])
+            self.loaded_model = model_from_json(model_config)
+            # set the dictionary of tools
+            self.model_data_dictionary = json.loads(trained_model['data_dictionary'][()])
+            self.reverse_dictionary = dict((v, k) for k, v in self.model_data_dictionary.items())
+            # set the list of compatible tools
+            self.compatible_tools = json.loads(trained_model['compatible_tools'][()])
+            self.tool_weights = json.loads(trained_model['class_weights'][()])
+            self.tool_weights_sorted = dict()
+            # sort the tools' usage dictionary
+            tool_pos_sorted = [int(key) for key in self.tool_weights.keys()]
+            for k in tool_pos_sorted:
+                self.tool_weights_sorted[k] = self.tool_weights[str(k)]
+            # iterate through all the attributes of the model to find weights of neural network layers
+            for item in trained_model.keys():
+                if "weight_" in item:
+                    d_key = "weight_" + str(counter_layer_weights)
+                    weights = trained_model[d_key][()]
+                    model_weights.append(weights)
+                    counter_layer_weights += 1
+            # set the model weights
+            self.loaded_model.set_weights(model_weights)
+        return True
+
+    def collect_admin_preferences(self, admin_path):
+        """
+        Collect preferences for recommendations of tools
+        set by admins as dictionaries of deprecated tools and
+        additional recommendations
+        """
+        if not self.admin_tool_recommendations_path and admin_path is not None:
+            self.admin_tool_recommendations_path = os.path.join(os.getcwd(), admin_path)
+            if os.path.exists(self.admin_tool_recommendations_path):
+                with open(self.admin_tool_recommendations_path) as admin_recommendations:
+                    admin_recommendation_preferences = yaml.safe_load(admin_recommendations)
+                    if admin_recommendation_preferences:
+                        for tool_id in admin_recommendation_preferences:
+                            tool_info = admin_recommendation_preferences[tool_id]
+                            if 'is_deprecated' in tool_info[0]:
+                                self.deprecated_tools[tool_id] = tool_info[0]["text_message"]
+                            else:
+                                if tool_id not in self.admin_recommendations:
+                                    self.admin_recommendations[tool_id] = tool_info
+
+    def download_model(self, model_url, download_local='database/'):
+        """
+        Download the model from remote server
+        """
+        local_dir = os.path.join(os.getcwd(), download_local, 'tool_recommendation_model.hdf5')
+        # read model from remote
+        model_binary = requests.get(model_url)
+        # save model to a local directory
+        with open(local_dir, 'wb') as model_file:
+            model_file.write(model_binary.content)
+            return local_dir
+
+    def get_tool_extensions(self, trans, tool_id):
+        """
+        Get the input and output extensions of a tool
+        """
+        payload = {'type': 'tool', 'tool_id': tool_id, '_': 'true'}
+        inputs = payload.get('inputs', {})
+        trans.workflow_building_mode = workflow_building_modes.ENABLED
+        module = module_factory.from_dict(trans, payload)
+        if 'tool_state' not in payload:
+            module_state = {}
+            populate_state(trans, module.get_inputs(), inputs, module_state, check=False)
+            module.recover_state(module_state)
+        inputs = module.get_all_inputs(connectable_only=True)
+        outputs = module.get_all_outputs()
+        input_extensions = list()
+        output_extensions = list()
+        for i_ext in inputs:
+            input_extensions.extend(i_ext['extensions'])
+        for o_ext in outputs:
+            output_extensions.extend(o_ext['extensions'])
+        return input_extensions, output_extensions
+
+    def filter_tool_predictions(self, trans, prediction_data, tool_ids, tool_scores, last_tool_name):
+        """
+        Filter tool predictions based on datatype compatibility and tool connections.
+        Add admin preferences to recommendations.
+        """
+        last_compatible_tools = list()
+        if last_tool_name in self.compatible_tools:
+            last_compatible_tools = self.compatible_tools[last_tool_name].split(",")
+        prediction_data["is_deprecated"] = False
+        t_ids_scores = zip(tool_ids, tool_scores)
+        # form the payload of the predicted tools to be shown
+        for child, score in t_ids_scores:
+            c_dict = dict()
+            for t_id in self.all_tools:
+                # select the name and tool id if it is installed in Galaxy
+                if t_id == child and score > 0.0 and child in last_compatible_tools and child not in self.deprecated_tools:
+                    full_tool_id = self.all_tools[t_id][0]
+                    pred_input_extensions, _ = self.get_tool_extensions(trans, full_tool_id)
+                    c_dict["name"] = self.all_tools[t_id][1] + " (" + str(score) + "%)"
+                    c_dict["tool_id"] = full_tool_id
+                    c_dict["i_extensions"] = list(set(pred_input_extensions))
+                    prediction_data["children"].append(c_dict)
+                    break
+        # incorporate preferences set by admins
+        if self.admin_tool_recommendations_path:
+            # filter out deprecated tools
+            t_ids_scores = [(tid, score) for tid, score in zip(tool_ids, tool_scores) if tid not in self.deprecated_tools]
+            # set the property if the last tool of the sequence is deprecated
+            if last_tool_name in self.deprecated_tools:
+                prediction_data["is_deprecated"] = True
+                prediction_data["message"] = self.deprecated_tools[last_tool_name]
+            # add the recommendations given by admins
+            for tool_id in self.admin_recommendations:
+                if last_tool_name == tool_id:
+                    admin_recommendations = self.admin_recommendations[tool_id]
+                    if trans.app.config.overwrite_model_recommendations is True:
+                        prediction_data["children"] = admin_recommendations
+                    else:
+                        prediction_data["children"].extend(admin_recommendations)
+                    break
+        # get the root name for displaying after tool run
+        for t_id in self.all_tools:
+            if t_id == last_tool_name:
+                prediction_data["name"] = self.all_tools[t_id][1]
+                break
+        return prediction_data
+
+    def compute_tool_prediction(self, trans, tool_sequence):
+        """
+        Compute the predicted tools for a tool sequences
+        Return a payload with the tool sequences and recommended tools
+        Return an empty payload with just the tool sequence if anything goes wrong within the try block
+        """
+        max_seq_len = 25
+        topk = trans.app.config.topk_recommendations
+        prediction_data = dict()
+        tool_sequence = tool_sequence.split(",")[::-1]
+        prediction_data["name"] = ",".join(tool_sequence)
+        prediction_data["children"] = list()
+        last_tool_name = tool_sequence[-1]
+        # do prediction only if the last is present in the collections of tools
+        if last_tool_name in self.model_data_dictionary:
+            sample = np.zeros(max_seq_len)
+            # get the list of datatype extensions of the last tool of the tool sequence
+            _, last_output_extensions = self.get_tool_extensions(trans, self.all_tools[last_tool_name][0])
+            prediction_data["o_extensions"] = list(set(last_output_extensions))
+            # get tool names without slashes and create a sequence vector
+            for idx, tool_name in enumerate(tool_sequence):
+                if tool_name.find("/") > -1:
+                    tool_name = tool_name.split("/")[-2]
+                sample[idx] = int(self.model_data_dictionary[tool_name])
+            sample = np.reshape(sample, (1, max_seq_len))
+            # predict next tools for a test path
+            prediction = self.loaded_model.predict(sample, verbose=0)
+            prediction = np.reshape(prediction, (prediction.shape[1],))
+            # boost the predicted scores using tools' usage
+            weight_values = list(self.tool_weights_sorted.values())
+            prediction = prediction * weight_values
+            # normalize the predicted scores with max and sort the predictions
+            max_prediction = float(np.max(prediction))
+            if max_prediction == 0.0:
+                max_prediction = 1.0
+            prediction = prediction / max_prediction
+            prediction_pos = np.argsort(prediction, axis=-1)
+            # get topk prediction
+            topk_prediction_pos = prediction_pos[-topk:]
+            # read tool names using reverse dictionary
+            pred_tool_ids = [self.reverse_dictionary[int(tool_pos)] for tool_pos in topk_prediction_pos]
+            predicted_scores = [int(prediction[pos] * 100) for pos in topk_prediction_pos]
+            prediction_data = self.filter_tool_predictions(trans, prediction_data, pred_tool_ids[::-1], predicted_scores[::-1], last_tool_name)
+        return prediction_data
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 63ab76a70580..664224751fe2 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -8,10 +8,7 @@
 import logging
 import os
 
-import h5py
-import numpy as np
 import requests
-import yaml
 from gxformat2._yaml import ordered_dump
 from markupsafe import escape
 from sqlalchemy import desc, false, or_, true
@@ -49,6 +46,7 @@
 from galaxy.workflow.reports import generate_report
 from galaxy.workflow.run import invoke, queue_invoke
 from galaxy.workflow.run_request import build_workflow_run_configs
+from galaxy.tools import tool_recommendations
 
 log = logging.getLogger(__name__)
 
@@ -60,10 +58,7 @@ def __init__(self, app):
         self.history_manager = histories.HistoryManager(app)
         self.workflow_manager = workflows.WorkflowsManager(app)
         self.workflow_contents_manager = workflows.WorkflowContentsManager(app)
-        self.tool_recommendation_model_path = None
-        self.admin_tool_recommendations_path = None
-        self.deprecated_tools = dict()
-        self.admin_recommendations = dict()
+        self.tool_recommendations = tool_recommendations.ToolRecommendations()
 
     def __get_full_shed_url(self, url):
         for name, shed_url in self.app.tool_shed_registry.tool_sheds.items():
@@ -653,220 +648,22 @@ def get_tool_predictions(self, trans, payload, **kwd):
             remote_model_url = trans.app.config.tool_recommendation_model_path
         if 'tool_sequence' not in payload or remote_model_url is None:
             return
-        isModelSet = True
+        is_model_set = True
         recommended_tools = dict()
         tool_sequence = ""
         # collect tool recommendation preferences if set by admin
-        self.__collect_admin_preferences(trans.app.config.admin_tool_recommendations_path)
+        self.tool_recommendations.collect_admin_preferences(trans.app.config.admin_tool_recommendations_path)
         # recreate the neural network model to be used for prediction
-        isModelSet = self.__set_model(trans, remote_model_url)
-        if isModelSet is True:
+        is_model_set = self.tool_recommendations.set_model(trans, remote_model_url)
+        if is_model_set is True:
             # get the recommended tools for a tool sequence
             tool_sequence = payload.get('tool_sequence', "")
-            recommended_tools = self.__compute_tool_prediction(trans, tool_sequence)
+            recommended_tools = self.tool_recommendations.compute_tool_prediction(trans, tool_sequence)
         return {
             "current_tool": tool_sequence,
             "predicted_data": recommended_tools
         }
 
-    #
-    # -- Helper methods --
-    #
-
-    def __set_model(self, trans, remote_model_url):
-        """
-        Create model and associated dictionaries for recommendations
-        """
-        if not self.tool_recommendation_model_path:
-            # import moves from the top of file: in case the tool recommendation feature is disabled,
-            # keras is not downloaded because of conditional requirement and Galaxy does not build
-            try:
-                from keras.models import model_from_json
-            except Exception:
-                trans.response.status = 400
-                return False
-            self.tool_recommendation_model_path = self.__download_model(remote_model_url)
-            self.all_tools = dict()
-            model_weights = list()
-            counter_layer_weights = 0
-            # collect ids and names of all the installed tools
-            for tool_id, tool in trans.app.toolbox.tools():
-                t_id_renamed = tool_id
-                if t_id_renamed.find("/") > -1:
-                    t_id_renamed = t_id_renamed.split("/")[-2]
-                self.all_tools[t_id_renamed] = (tool_id, tool.name)
-            # read the hdf5 attributes
-            trained_model = h5py.File(self.tool_recommendation_model_path, 'r')
-            model_config = json.loads(trained_model['model_config'][()])
-            self.loaded_model = model_from_json(model_config)
-            # set the dictionary of tools
-            self.model_data_dictionary = json.loads(trained_model['data_dictionary'][()])
-            self.reverse_dictionary = dict((v, k) for k, v in self.model_data_dictionary.items())
-            # set the list of compatible tools
-            self.compatible_tools = json.loads(trained_model['compatible_tools'][()])
-            self.tool_weights = json.loads(trained_model['class_weights'][()])
-            self.tool_weights_sorted = dict()
-            # sort the tools' usage dictionary
-            tool_pos_sorted = [int(key) for key in self.tool_weights.keys()]
-            for k in tool_pos_sorted:
-                self.tool_weights_sorted[k] = self.tool_weights[str(k)]
-            # iterate through all the attributes of the model to find weights of neural network layers
-            for item in trained_model.keys():
-                if "weight_" in item:
-                    d_key = "weight_" + str(counter_layer_weights)
-                    weights = trained_model[d_key][()]
-                    model_weights.append(weights)
-                    counter_layer_weights += 1
-            # set the model weights
-            self.loaded_model.set_weights(model_weights)
-        return True
-
-    def __collect_admin_preferences(self, admin_path):
-        """
-        Collect preferences for recommendations of tools
-        set by admins as dictionaries of deprecated tools and
-        additional recommendations
-        """
-        if not self.admin_tool_recommendations_path and admin_path is not None:
-            self.admin_tool_recommendations_path = os.path.join(os.getcwd(), admin_path)
-            if os.path.exists(self.admin_tool_recommendations_path):
-                with open(self.admin_tool_recommendations_path) as admin_recommendations:
-                    admin_recommendation_preferences = yaml.safe_load(admin_recommendations)
-                    if admin_recommendation_preferences:
-                        for tool_id in admin_recommendation_preferences:
-                            tool_info = admin_recommendation_preferences[tool_id]
-                            if 'is_deprecated' in tool_info[0]:
-                                self.deprecated_tools[tool_id] = tool_info[0]["text_message"]
-                            else:
-                                if tool_id not in self.admin_recommendations:
-                                    self.admin_recommendations[tool_id] = tool_info
-
-    def __download_model(self, model_url, download_local='database/'):
-        """
-        Download the model from remote server
-        """
-        local_dir = os.path.join(os.getcwd(), download_local, 'tool_recommendation_model.hdf5')
-        # read model from remote
-        model_binary = requests.get(model_url)
-        # save model to a local directory
-        with open(local_dir, 'wb') as model_file:
-            model_file.write(model_binary.content)
-            return local_dir
-
-    def __get_tool_extensions(self, trans, tool_id):
-        """
-        Get the input and output extensions of a tool
-        """
-        payload = {'type': 'tool', 'tool_id': tool_id, '_': 'true'}
-        inputs = payload.get('inputs', {})
-        trans.workflow_building_mode = workflow_building_modes.ENABLED
-        module = module_factory.from_dict(trans, payload)
-        if 'tool_state' not in payload:
-            module_state = {}
-            populate_state(trans, module.get_inputs(), inputs, module_state, check=False)
-            module.recover_state(module_state)
-        inputs = module.get_all_inputs(connectable_only=True)
-        outputs = module.get_all_outputs()
-        input_extensions = list()
-        output_extensions = list()
-        for i_ext in inputs:
-            input_extensions.extend(i_ext['extensions'])
-        for o_ext in outputs:
-            output_extensions.extend(o_ext['extensions'])
-        return input_extensions, output_extensions
-
-    def __filter_tool_predictions(self, trans, prediction_data, tool_ids, tool_scores, last_tool_name):
-        """
-        Filter tool predictions based on datatype compatibility and tool connections.
-        Add admin preferences to recommendations.
-        """
-        last_compatible_tools = list()
-        if last_tool_name in self.compatible_tools:
-            last_compatible_tools = self.compatible_tools[last_tool_name].split(",")
-        prediction_data["is_deprecated"] = False
-        t_ids_scores = zip(tool_ids, tool_scores)
-        # form the payload of the predicted tools to be shown
-        for child, score in t_ids_scores:
-            c_dict = dict()
-            for t_id in self.all_tools:
-                # select the name and tool id if it is installed in Galaxy
-                if t_id == child and score > 0.0 and child in last_compatible_tools and child not in self.deprecated_tools:
-                    full_tool_id = self.all_tools[t_id][0]
-                    pred_input_extensions, _ = self.__get_tool_extensions(trans, full_tool_id)
-                    c_dict["name"] = self.all_tools[t_id][1] + " (" + str(score) + "%)"
-                    c_dict["tool_id"] = full_tool_id
-                    c_dict["i_extensions"] = list(set(pred_input_extensions))
-                    prediction_data["children"].append(c_dict)
-                    break
-        # incorporate preferences set by admins
-        if self.admin_tool_recommendations_path:
-            # filter out deprecated tools
-            t_ids_scores = [(tid, score) for tid, score in zip(tool_ids, tool_scores) if tid not in self.deprecated_tools]
-            # set the property if the last tool of the sequence is deprecated
-            if last_tool_name in self.deprecated_tools:
-                prediction_data["is_deprecated"] = True
-                prediction_data["message"] = self.deprecated_tools[last_tool_name]
-            # add the recommendations given by admins
-            for tool_id in self.admin_recommendations:
-                if last_tool_name == tool_id:
-                    admin_recommendations = self.admin_recommendations[tool_id]
-                    if trans.app.config.overwrite_model_recommendations is True:
-                        prediction_data["children"] = admin_recommendations
-                    else:
-                        prediction_data["children"].extend(admin_recommendations)
-                    break
-        # get the root name for displaying after tool run
-        for t_id in self.all_tools:
-            if t_id == last_tool_name:
-                prediction_data["name"] = self.all_tools[t_id][1]
-                break
-        return prediction_data
-
-    def __compute_tool_prediction(self, trans, tool_sequence):
-        """
-        Compute the predicted tools for a tool sequences
-        Return a payload with the tool sequences and recommended tools
-        Return an empty payload with just the tool sequence if anything goes wrong within the try block
-        """
-        max_seq_len = 25
-        topk = trans.app.config.topk_recommendations
-        prediction_data = dict()
-        tool_sequence = tool_sequence.split(",")[::-1]
-        prediction_data["name"] = ",".join(tool_sequence)
-        prediction_data["children"] = list()
-        last_tool_name = tool_sequence[-1]
-        # do prediction only if the last is present in the collections of tools
-        if last_tool_name in self.model_data_dictionary:
-            sample = np.zeros(max_seq_len)
-            # get the list of datatype extensions of the last tool of the tool sequence
-            _, last_output_extensions = self.__get_tool_extensions(trans, self.all_tools[last_tool_name][0])
-            prediction_data["o_extensions"] = list(set(last_output_extensions))
-            # get tool names without slashes and create a sequence vector
-            for idx, tool_name in enumerate(tool_sequence):
-                if tool_name.find("/") > -1:
-                    tool_name = tool_name.split("/")[-2]
-                sample[idx] = int(self.model_data_dictionary[tool_name])
-            sample = np.reshape(sample, (1, max_seq_len))
-            # predict next tools for a test path
-            prediction = self.loaded_model.predict(sample, verbose=0)
-            prediction = np.reshape(prediction, (prediction.shape[1],))
-            # boost the predicted scores using tools' usage
-            weight_values = list(self.tool_weights_sorted.values())
-            prediction = prediction * weight_values
-            # normalize the predicted scores with max and sort the predictions
-            max_prediction = float(np.max(prediction))
-            if max_prediction == 0.0:
-                max_prediction = 1.0
-            prediction = prediction / max_prediction
-            prediction_pos = np.argsort(prediction, axis=-1)
-            # get topk prediction
-            topk_prediction_pos = prediction_pos[-topk:]
-            # read tool names using reverse dictionary
-            pred_tool_ids = [self.reverse_dictionary[int(tool_pos)] for tool_pos in topk_prediction_pos]
-            predicted_scores = [int(prediction[pos] * 100) for pos in topk_prediction_pos]
-            prediction_data = self.__filter_tool_predictions(trans, prediction_data, pred_tool_ids[::-1], predicted_scores[::-1], last_tool_name)
-        return prediction_data
-
     #
     # -- Helper methods --
     #

From 47a1c793a2b027f8fd4f5485e2a15dd8541abea5 Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Mon, 16 Mar 2020 12:08:33 -0400
Subject: [PATCH 427/853] Combine tests for creating and switching histories.

Since creating a new history automatically activates it, I think it's
sufficient to test switching *back* to the original history after
creating a new one.

This also adds a way to select the individual history columns in the
multi-view and the switch-to button for each history.
---
 lib/galaxy/selenium/navigation.yml            |  5 ++
 .../selenium/test_history_multi_view.py       | 56 +++++++++----------
 2 files changed, 30 insertions(+), 31 deletions(-)

diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index c6160ba379d3..a3f326283c9a 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -213,6 +213,11 @@ multi_history_view:
         selector: '//button[contains(text(), "Copy")]'
 
 
+multiple_histories:
+  selectors:
+    _: '#history-column-${history_id}'
+    switch_button: '${_} button.switch-to'
+
 history_copy_elements:
 
   selectors:
diff --git a/lib/galaxy_test/selenium/test_history_multi_view.py b/lib/galaxy_test/selenium/test_history_multi_view.py
index 6aee96691987..a1d2cda8bcfd 100644
--- a/lib/galaxy_test/selenium/test_history_multi_view.py
+++ b/lib/galaxy_test/selenium/test_history_multi_view.py
@@ -95,40 +95,34 @@ def test_purge_history(self):
         self.assert_history(history_id, should_exist=False)
 
     @selenium_test
-    def test_switching_history(self):
-        history_id = self.current_history_id()
-        method = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json
-
-        self.prepare_multi_history_view(method)
-        self.copy_history(history_id)
-        self.components.multi_history_view.switch_history.wait_for_and_click()
-        self.sleep_for(self.wait_types.UX_RENDER)
-        self.assert_history(history_id, histories_number=2)
-        # assert that id of current history equals history_id
-        assert self.components.multi_history_view.current_history_check(history_id=history_id).is_displayed
-        self.components.multi_history_view.switch_history.wait_for_and_click()
-        self.sleep_for(self.wait_types.UX_RENDER)
-        # assert that 'history_id' is not current history
-        self.assertRaises(NoSuchElementException, lambda:
-                          self.components.multi_history_view.current_history_check(history_id=history_id).is_displayed)
-
-    @selenium_test
-    def test_create_new_history(self):
-        history_id = self.current_history_id()
-        method = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json
-
-        self.prepare_multi_history_view(method)
-        # assert that empty history is not created in advance
-        self.components.multi_history_view.empty_message_check.assert_absent_or_hidden()
-
+    def test_switch_history(self):
+        '''
+        1. Load the multi history view. There should be a selector for the button
+           to create a new history.
+        2. Create a new history. This *should* automatically switch to the newly
+           created history.
+        3. Switch back to the original history. A button should appear on the old,
+           previously created history that allows switching back to that one, and
+           the history ID should now match the ID of the history with which we
+           started.
+        '''
+        self.home()
+        original_history_id = self.current_history_id()
+        # Load the multi-view
+        self.components.history_panel.multi_view_button.wait_for_and_click()
+        # Creating a new history should automatically switch to it
         self.components.multi_history_view.create_new_button.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
-
-        self.assert_history(history_id, histories_number=2)
+        new_history_id = self.current_history_id()
+        # Otherwise this assertion would fail
+        self.screenshot("multi_history_switch_created_history")
+        self.assertNotEqual(original_history_id, new_history_id)
+        # Switch back to the original history
+        switch_button = self.components.multiple_histories._(history_id=original_history_id).switch_button
+        switch_button.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
-
-        # assert that empty history is present
-        self.components.multi_history_view.empty_message_check.wait_for_present()
+        self.screenshot("multi_history_switch_changed_history")
+        self.assertEqual(original_history_id, self.current_history_id())
 
     def assert_history(self, history_id, histories_number=1, should_exist=True):
         histories = self.components.multi_history_view.histories.all()

From 4d8ce116c9544d6b54863d1df30da9e9e6e51580 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 16 Mar 2020 18:00:46 +0100
Subject: [PATCH 428/853] Fix import order

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 664224751fe2..c2a055e2946e 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -23,6 +23,7 @@
     histories,
     workflows
 )
+from galaxy.tools import tool_recommendations
 from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
@@ -46,7 +47,6 @@
 from galaxy.workflow.reports import generate_report
 from galaxy.workflow.run import invoke, queue_invoke
 from galaxy.workflow.run_request import build_workflow_run_configs
-from galaxy.tools import tool_recommendations
 
 log = logging.getLogger(__name__)
 

From 49ab57d979686ed3be7761681044e78a51084a93 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 16 Mar 2020 18:42:12 +0100
Subject: [PATCH 429/853] Fix css

---
 .../scripts/components/ToolRecommendation.vue | 40 ++-----------------
 client/galaxy/style/scss/base.scss            | 33 +++++++++++++++
 2 files changed, 36 insertions(+), 37 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 88d0eaa4f4ab..ff46367d6418 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -18,6 +18,8 @@ import * as d3 from "d3";
 import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 
+const margin = { top: 20, right: 30, bottom: 20, left: 250 };
+
 export default {
     props: {
         toolId: {
@@ -106,8 +108,7 @@ export default {
                 });
         },
         renderD3Tree: function(predictedTools) {
-            const margin = { top: 20, right: 30, bottom: 20, left: 250 },
-                width = 900 - margin.right - margin.left,
+            const width = 900 - margin.right - margin.left,
                 height = 300 - margin.top - margin.bottom,
                 duration = 750;
             const tree = d3.layout.tree().size([height, width]);
@@ -241,38 +242,3 @@ export default {
     }
 };
 </script>
-
-<style>
-.node {
-    cursor: pointer;
-}
-
-.node circle {
-    fill: #000;
-    stroke: #c2ebc2;
-    stroke-width: 0.3rem;
-}
-
-.node text {
-    font: 0.75rem sans-serif;
-}
-
-.node-enter {
-    fill-opacity: 1e-6;
-}
-
-.node-update {
-    fill-opacity: 1;
-}
-
-.tree-size {
-    width: 100%;
-    height: 450px;
-}
-
-.link {
-    fill: none;
-    stroke: #c2ebc2;
-    stroke-width: 0.3rem;
-}
-</style>
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index ed488b4f892e..c8ec6e2aee78 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1650,3 +1650,36 @@ body.reports {
     bottom: 0;
     background: url(../../images/largespinner.gif) no-repeat center center fixed;
 }
+
+/* Used for tree in tool recommendations */
+.node {
+    cursor: pointer;
+    circle {
+        fill: rgb(0, 0, 0);
+        stroke: rgb(194, 235, 194);
+        stroke-width: 0.3rem;
+    }
+    text {
+        font: 0.75rem sans-serif;
+    }
+}
+
+.node-enter {
+    fill-opacity: 1e-6;
+}
+
+.node-update {
+    fill-opacity: 1;
+}
+
+.tree-size {
+    width: 100%;
+    height: 100%;
+    position: fixed;
+}
+
+.link {
+    fill: none;
+    stroke: rgb(194, 235, 194);
+    stroke-width: 0.3rem;
+}

From db51c95c82f3e0c6bcc197e70e3587fd872fad33 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 16 Mar 2020 23:57:50 +0100
Subject: [PATCH 430/853] Fix import order

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index c2a055e2946e..1dee03f7000e 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -23,10 +23,10 @@
     histories,
     workflows
 )
-from galaxy.tools import tool_recommendations
 from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
+from galaxy.tools import tool_recommendations
 from galaxy.tools.parameters import populate_state
 from galaxy.tools.parameters.basic import workflow_building_modes
 from galaxy.util.sanitize_html import sanitize_html

From cbc606023032c94aed76fbfdd75392cbaacfcd18 Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Tue, 17 Mar 2020 13:00:23 -0400
Subject: [PATCH 431/853] Cleaner selectors for switch history button.

---
 lib/galaxy/selenium/navigation.yml                  | 7 +------
 lib/galaxy_test/selenium/test_history_multi_view.py | 2 +-
 2 files changed, 2 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index a3f326283c9a..1ec1f72e80bf 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -198,7 +198,7 @@ multi_history_view:
     delete: '.copy-history'
     current_history_check: '#history-column-${history_id} .current-label'
     empty_message_check: '.empty-message'
-
+    switch_button: '#history-column-${history_id} .switch-to'
 
   history_dropdown_menu:
     selectors:
@@ -213,11 +213,6 @@ multi_history_view:
         selector: '//button[contains(text(), "Copy")]'
 
 
-multiple_histories:
-  selectors:
-    _: '#history-column-${history_id}'
-    switch_button: '${_} button.switch-to'
-
 history_copy_elements:
 
   selectors:
diff --git a/lib/galaxy_test/selenium/test_history_multi_view.py b/lib/galaxy_test/selenium/test_history_multi_view.py
index a1d2cda8bcfd..65123c244172 100644
--- a/lib/galaxy_test/selenium/test_history_multi_view.py
+++ b/lib/galaxy_test/selenium/test_history_multi_view.py
@@ -118,7 +118,7 @@ def test_switch_history(self):
         self.screenshot("multi_history_switch_created_history")
         self.assertNotEqual(original_history_id, new_history_id)
         # Switch back to the original history
-        switch_button = self.components.multiple_histories._(history_id=original_history_id).switch_button
+        switch_button = self.components.multi_history_view.switch_button(history_id=original_history_id)
         switch_button.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
         self.screenshot("multi_history_switch_changed_history")

From d703eed26f7d14041c0fd704cc9c8487e6097dfc Mon Sep 17 00:00:00 2001
From: Sebastian Kapust <sebastian@kapust.org>
Date: Tue, 1 Oct 2019 07:04:12 +0200
Subject: [PATCH 432/853] Add inf. scroll, collapsible citations, info modal

---
 .../galaxy/scripts/components/Citations.vue   |  20 ++-
 .../galaxy/scripts/components/ToolsView.vue   | 169 ++++++++++++++++++
 .../scripts/entry/analysis/AnalysisRouter.js  |   6 +-
 client/package.json                           |   3 +-
 client/yarn.lock                              |   5 +
 5 files changed, 200 insertions(+), 3 deletions(-)
 create mode 100644 client/galaxy/scripts/components/ToolsView.vue

diff --git a/client/galaxy/scripts/components/Citations.vue b/client/galaxy/scripts/components/Citations.vue
index 75906671f882..8402cd04d6e1 100644
--- a/client/galaxy/scripts/components/Citations.vue
+++ b/client/galaxy/scripts/components/Citations.vue
@@ -1,4 +1,5 @@
 <template>
+    <div>
     <b-card>
         <template v-slot:header>
             <h4 class="mb-0">
@@ -28,6 +29,22 @@
             </code>
         </pre>
     </b-card>
+
+    <div v-else-if="citations.length">
+      <b-btn
+        v-b-toggle="id"
+        variant="primary"
+      >Citations</b-btn>
+      <b-collapse
+        :id="id"
+        class="mt-2"
+      >
+        <b-card>
+          <p v-html="formattedReferences"></p>
+        </b-card>
+      </b-collapse>
+    </div>
+  </div>
 </template>
 <script>
 import _ from "underscore";
@@ -61,7 +78,8 @@ export default {
         return {
             citations: [],
             content: "",
-            errors: []
+            errors: [],
+            showCollapse: false
         };
     },
     computed: {
diff --git a/client/galaxy/scripts/components/ToolsView.vue b/client/galaxy/scripts/components/ToolsView.vue
new file mode 100644
index 000000000000..f5d17c74d88f
--- /dev/null
+++ b/client/galaxy/scripts/components/ToolsView.vue
@@ -0,0 +1,169 @@
+<template>
+  <div
+    v-infinite-scroll="loadMore"
+    infinite-scroll-disabled="busy"
+  >
+    <h2 class="mb-3">
+      <span id="tools-view">Tools View</span>
+    </h2>
+    <div v-if="!loading">
+      <b-container
+        fluid
+        class="mb-4"
+      >
+        <b-row>
+          <b-col md="6">
+            <b-form-group description="Search for strings or regular expressions">
+              <b-input-group>
+                <b-form-input
+                  v-model="filter"
+                  placeholder="Type to Search"
+                  @keyup.esc.native="filter = ''"
+                />
+                <b-input-group-append>
+                  <b-btn
+                    :disabled="!filter"
+                    @click="filter = ''"
+                  >Clear (esc)</b-btn>
+                </b-input-group-append>
+              </b-input-group>
+            </b-form-group>
+          </b-col>
+        </b-row>
+      </b-container>
+      <b-card-group
+        v-for="(deck, dindex) in bufferView"
+        :key="dindex"
+        deck
+        class="mb-4"
+      >
+        <b-card
+          v-for="(info, index) in deck"
+          :key="index"
+        >
+          <div slot="header">
+            <b-link
+              :href="info['url']"
+              target="_blank"
+            >
+              <h4>{{ info['name'] }}</h4>
+            </b-link>
+            <b-badge>
+              {{ info['section'] }}
+            </b-badge>
+          </div>
+          <p class="card-text">
+            {{ info["description"] }}
+          </p>
+          <p class="card-text">
+            <b-btn v-b-modal="'modal-' + dindex + '-' + index">Info</b-btn>
+            <b-modal
+              :id="'modal-' + dindex + '-' + index"
+              centered
+              :title="info['name']"
+            >
+              <b>{{ info['version'] + ' / ' + info['id'] }}</b>
+              <p>{{ info['description'] }}</p>
+            </b-modal>
+          </p>
+          <Citations
+            simple
+            source="tools"
+            :id="info['id']"
+          />
+        </b-card>
+      </b-card-group>
+    </div>
+  </div>
+</template>
+
+<script>
+import { getAppRoot } from "onload/loadConfig";
+import infiniteScroll from "vue-infinite-scroll";
+import axios from "axios";
+import Citations from "components/Citations.vue";
+
+export default {
+    components: {
+        Citations
+    },
+    directives: { infiniteScroll },
+    data() {
+        return {
+            tools: [],
+            buffer: [],
+            filter: "",
+            busy: false,
+            loading: true
+        };
+    },
+    computed: {
+        bufferView() {
+            let a = [];
+            let b = this.bufferFiltered.slice(0);
+            while (b.length) a.push(b.splice(0, 3));
+            return a;
+        },
+        bufferFiltered() {
+            let f = [];
+            let filter = this.filter;
+            if (!this.loading) {
+                f = this.buffer.filter(x => {
+                    let re = new RegExp(filter, "i");
+                    return x["name"].match(re) || x["description"].match(re);
+                });
+            }
+            return f;
+        }
+    },
+    methods: {
+        toolsExtracted(tools) {
+            function extractSections(acc, section) {
+                function extractTools(_acc, tool) {
+                    return tool["name"]
+                        ? [
+                              ..._acc,
+                              {
+                                  id: tool["id"],
+                                  name: tool["name"],
+                                  section: section["name"],
+                                  description: tool["description"],
+                                  url: getAppRoot() + String(tool["link"]).substring(1),
+                                  version: tool["version"]
+                              }
+                          ]
+                        : _acc;
+                }
+                return acc.concat(section["elems"].reduce(extractTools, []));
+            }
+            return tools
+                .reduce(extractSections, [])
+                .map(a => [Math.random(), a])
+                .sort((a, b) => a[0] - b[0])
+                .map(a => a[1]);
+        },
+        loadMore: function() {
+            this.busy = true;
+
+            setTimeout(() => {
+                const start = this.buffer.length;
+                const end = start + 20;
+                this.buffer = this.buffer.concat(this.tools.slice(start, end));
+                this.busy = false;
+            }, 1000);
+        }
+    },
+    created() {
+        axios
+            .get(`${getAppRoot()}api/tools`)
+            .then(response => {
+                this.tools = this.toolsExtracted(response.data);
+                this.buffer = this.tools.slice(0, 20);
+                this.loading = false;
+            })
+            .catch(error => {
+                console.error(error);
+            });
+    }
+};
+</script>
\ No newline at end of file
diff --git a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
index 647b60fc74af..db4e56409762 100644
--- a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
+++ b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
@@ -241,7 +241,11 @@ export const getAnalysisRouter = Galaxy =>
         show_histories_import: function() {
             this._display_vue_helper(HistoryImport);
         },
-
+        show_tools_view: function() {
+            this.page.panels.left.hide();
+            this.page.panels.right.hide();
+            this._display_vue_helper(ToolsView);
+        },
         show_histories_permissions: function() {
             this.page.display(
                 new FormWrapper.View({
diff --git a/client/package.json b/client/package.json
index 11b40d63bd09..29648030c0ca 100644
--- a/client/package.json
+++ b/client/package.json
@@ -54,7 +54,8 @@
     "vue-router": "^3.1.5",
     "vue-rx": "^6.2.0",
     "vuex": "^3.1.2",
-    "vuex-cache": "^3.1.0"
+    "vuex-cache": "^3.1.0",
+    "vue-infinite-scroll": "^2.0.2"
   },
   "scripts": {
     "watch": "gulp && yarn run save-build-hash && yarn run webpack-watch",
diff --git a/client/yarn.lock b/client/yarn.lock
index 84da73abfb14..f2f1f72a1f63 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -14116,6 +14116,11 @@ vue-hot-reload-api@^2.3.0:
   resolved "https://registry.yarnpkg.com/vue-hot-reload-api/-/vue-hot-reload-api-2.3.1.tgz#b2d3d95402a811602380783ea4f566eb875569a2"
   integrity sha512-AA86yKZ5uOKz87/q1UpngEXhbRkaYg1b7HMMVRobNV1IVKqZe8oLIzo6iMocVwZXnYitlGwf2k4ZRLOZlS8oPQ==
 
+vue-infinite-scroll@^2.0.2:
+  version "2.0.2"
+  resolved "https://registry.yarnpkg.com/vue-infinite-scroll/-/vue-infinite-scroll-2.0.2.tgz#ca37a91fe92ee0ad3b74acf8682c00917144b711"
+  integrity sha512-n+YghR059YmciANGJh9SsNWRi1YZEBVlODtmnb/12zI+4R72QZSWd+EuZ5mW6auEo/yaJXgxzwsuhvALVnm73A==
+
 vue-loader@^15.8.3:
   version "15.8.3"
   resolved "https://registry.yarnpkg.com/vue-loader/-/vue-loader-15.8.3.tgz#857cb9e30eb5fc25e66db48dce7e4f768602a23c"

From 104e5ff8f2ac7ee5a214e7fbe617c9ea744d9a19 Mon Sep 17 00:00:00 2001
From: Sebastian Kapust <sebastian@kapust.org>
Date: Tue, 1 Oct 2019 07:04:12 +0200
Subject: [PATCH 433/853] Include help text summary in tools view cards

---
 .../galaxy/scripts/components/ToolsView.vue   | 143 ++++++++----------
 lib/galaxy/tools/__init__.py                  |   6 +
 2 files changed, 71 insertions(+), 78 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolsView.vue b/client/galaxy/scripts/components/ToolsView.vue
index f5d17c74d88f..38d7e188e73b 100644
--- a/client/galaxy/scripts/components/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView.vue
@@ -1,80 +1,49 @@
 <template>
-  <div
-    v-infinite-scroll="loadMore"
-    infinite-scroll-disabled="busy"
-  >
-    <h2 class="mb-3">
-      <span id="tools-view">Tools View</span>
-    </h2>
-    <div v-if="!loading">
-      <b-container
-        fluid
-        class="mb-4"
-      >
-        <b-row>
-          <b-col md="6">
-            <b-form-group description="Search for strings or regular expressions">
-              <b-input-group>
-                <b-form-input
-                  v-model="filter"
-                  placeholder="Type to Search"
-                  @keyup.esc.native="filter = ''"
-                />
-                <b-input-group-append>
-                  <b-btn
-                    :disabled="!filter"
-                    @click="filter = ''"
-                  >Clear (esc)</b-btn>
-                </b-input-group-append>
-              </b-input-group>
-            </b-form-group>
-          </b-col>
-        </b-row>
-      </b-container>
-      <b-card-group
-        v-for="(deck, dindex) in bufferView"
-        :key="dindex"
-        deck
-        class="mb-4"
-      >
-        <b-card
-          v-for="(info, index) in deck"
-          :key="index"
-        >
-          <div slot="header">
-            <b-link
-              :href="info['url']"
-              target="_blank"
-            >
-              <h4>{{ info['name'] }}</h4>
-            </b-link>
-            <b-badge>
-              {{ info['section'] }}
-            </b-badge>
-          </div>
-          <p class="card-text">
-            {{ info["description"] }}
-          </p>
-          <p class="card-text">
-            <b-btn v-b-modal="'modal-' + dindex + '-' + index">Info</b-btn>
-            <b-modal
-              :id="'modal-' + dindex + '-' + index"
-              centered
-              :title="info['name']"
-            >
-              <b>{{ info['version'] + ' / ' + info['id'] }}</b>
-              <p>{{ info['description'] }}</p>
-            </b-modal>
-          </p>
-          <Citations
-            simple
-            source="tools"
-            :id="info['id']"
-          />
-        </b-card>
-      </b-card-group>
+    <div v-infinite-scroll="loadMore" infinite-scroll-disabled="busy">
+        <h2 class="mb-3">
+            <span id="tools-view">Tools View</span>
+        </h2>
+        <div v-if="!loading">
+            <b-container fluid class="mb-4">
+                <b-row>
+                    <b-col md="6">
+                        <b-form-group description="Search for strings or regular expressions">
+                            <b-input-group>
+                                <b-form-input
+                                    v-model="filter"
+                                    placeholder="Type to Search"
+                                    @keyup.esc.native="filter = ''"
+                                />
+                                <b-input-group-append>
+                                    <b-btn :disabled="!filter" @click="filter = ''">Clear (esc)</b-btn>
+                                </b-input-group-append>
+                            </b-input-group>
+                        </b-form-group>
+                    </b-col>
+                </b-row>
+            </b-container>
+            <b-card-group v-for="(deck, dindex) in bufferView" :key="dindex" deck class="mb-4">
+                <b-card v-for="(info, index) in deck" :key="index">
+                    <div slot="header">
+                        <b-link :href="info['url']" target="_blank">
+                            <h4>{{ info["name"] }}</h4>
+                        </b-link>
+                        <b-badge>{{ info["section"] }}</b-badge>
+                    </div>
+                    <p class="card-text" v-html="helpSummary(info['help']) || info['description']" />
+                    <p class="card-text">
+                        <b-btn v-b-modal="'modal-' + dindex + '-' + index">Info</b-btn>
+                        <b-modal :id="'modal-' + dindex + '-' + index" centered :title="info['name']">
+                            <b>{{ info["version"] + " / " + info["id"] }}</b>
+                            <p>{{ info["description"] }}</p>
+                            <p v-html="info['help']"></p>
+                        </b-modal>
+                    </p>
+                    <Citations simple source="tools" :id="info['id']" />
+                </b-card>
+            </b-card-group>
+        </div>
     </div>
-  </div>
 </template>
 
 <script>
@@ -129,7 +98,8 @@ export default {
                                   section: section["name"],
                                   description: tool["description"],
                                   url: getAppRoot() + String(tool["link"]).substring(1),
-                                  version: tool["version"]
+                                  version: tool["version"],
+                                  help: tool["help"]
                               }
                           ]
                         : _acc;
@@ -142,7 +112,7 @@ export default {
                 .sort((a, b) => a[0] - b[0])
                 .map(a => a[1]);
         },
-        loadMore: function() {
+        loadMore() {
             this.busy = true;
 
             setTimeout(() => {
@@ -151,6 +121,23 @@ export default {
                 this.buffer = this.buffer.concat(this.tools.slice(start, end));
                 this.busy = false;
             }, 1000);
+        },
+        helpSummary(help) {
+            const parser = new DOMParser();
+            const helpDoc = parser.parseFromString(help, "text/html");
+            const xpath = "//strong[text()='What it does']/../following-sibling::*";
+            const match = helpDoc.evaluate(xpath, helpDoc, null, XPathResult.FIRST_ORDERED_NODE_TYPE, null)
+                .singleNodeValue;
+            if (match) {
+                return match.innerHTML;
+            } else {
+                const helpText = helpDoc.documentElement.textContent;
+                if (helpText) {
+                    return helpText.substring(0, helpText.indexOf("\n\n"));
+                } else {
+                    return null;
+                }
+            }
         }
     },
     created() {
@@ -166,4 +153,4 @@ export default {
             });
     }
 };
-</script>
\ No newline at end of file
+</script>
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 5aa4ee7b9a52..86757e416cf1 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1969,6 +1969,12 @@ def to_dict(self, trans, link_details=False, io_details=False):
         # FIXME: the Tool class should declare directly, instead of ad hoc inspection
         regular_form = tool_class == Tool or isinstance(self, (DatabaseOperationTool, InteractiveTool))
         tool_dict["form_style"] = "regular" if regular_form else "special"
+        # create tool help
+        tool_help = ''
+        if self.help:
+            tool_help = self.help.render(static_path=self.app.url_for('/static'), host_url=self.app.url_for('/', qualified=True))
+            tool_help = unicodify(tool_help, 'utf-8')
+        tool_dict["help"] = tool_help
 
         return tool_dict
 

From 1a8440fe9eef480e1bc160bfd9dea102deea37d7 Mon Sep 17 00:00:00 2001
From: Sebastian Kapust <sebastian@kapust.org>
Date: Tue, 1 Oct 2019 07:04:12 +0200
Subject: [PATCH 434/853] Add tool_help option to api/tools

---
 .../galaxy/scripts/components/ToolsView.vue   |  2 +-
 lib/galaxy/tools/__init__.py                  | 15 +++++------
 lib/galaxy/tools/toolbox/base.py              | 25 +++++++++++--------
 lib/galaxy/tools/toolbox/panel.py             |  7 +++---
 lib/galaxy/webapps/galaxy/api/tools.py        |  3 ++-
 5 files changed, 30 insertions(+), 22 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolsView.vue b/client/galaxy/scripts/components/ToolsView.vue
index 38d7e188e73b..422850995d27 100644
--- a/client/galaxy/scripts/components/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView.vue
@@ -142,7 +142,7 @@ export default {
     },
     created() {
         axios
-            .get(`${getAppRoot()}api/tools`)
+            .get(`${getAppRoot()}api/tools?tool_help=True`)
             .then(response => {
                 this.tools = this.toolsExtracted(response.data);
                 this.buffer = this.tools.slice(0, 20);
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 86757e416cf1..531f81358cde 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1919,7 +1919,7 @@ def to_archive(self):
             os.remove(temp_file)
         return tarball_archive
 
-    def to_dict(self, trans, link_details=False, io_details=False):
+    def to_dict(self, trans, link_details=False, io_details=False, tool_help=False):
         """ Returns dict of tool. """
 
         # Basic information
@@ -1969,12 +1969,13 @@ def to_dict(self, trans, link_details=False, io_details=False):
         # FIXME: the Tool class should declare directly, instead of ad hoc inspection
         regular_form = tool_class == Tool or isinstance(self, (DatabaseOperationTool, InteractiveTool))
         tool_dict["form_style"] = "regular" if regular_form else "special"
-        # create tool help
-        tool_help = ''
-        if self.help:
-            tool_help = self.help.render(static_path=self.app.url_for('/static'), host_url=self.app.url_for('/', qualified=True))
-            tool_help = unicodify(tool_help, 'utf-8')
-        tool_dict["help"] = tool_help
+        if tool_help:
+            # create tool help
+            help_txt = ''
+            if self.help:
+                help_txt = self.help.render(static_path=self.app.url_for('/static'), host_url=self.app.url_for('/', qualified=True))
+                help_txt = unicodify(help_txt, 'utf-8')
+            tool_dict['help'] = help_txt
 
         return tool_dict
 
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 070791cf08f4..c69027fe33a3 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -1050,24 +1050,29 @@ def tool_panel_contents(self, trans, **kwds):
             if elt:
                 yield elt
 
-    def get_tool_to_dict(self, trans, tool):
+    def get_tool_to_dict(self, trans, tool, tool_help=False):
         """Return tool's to_dict.
         Use cache if present, store to cache otherwise.
         Note: The cached tool's to_dict is specific to the calls from toolbox.
         """
+        to_dict = None
         if not trans.user_is_admin:
-            to_dict = self._tool_to_dict_cache.get(tool.id, None)
+            if not tool_help:
+                to_dict = self._tool_to_dict_cache.get(tool.id, None)
             if not to_dict:
-                to_dict = tool.to_dict(trans, link_details=True)
-                self._tool_to_dict_cache[tool.id] = to_dict
+                to_dict = tool.to_dict(trans, link_details=True, tool_help=tool_help)
+                if not tool_help:
+                    self._tool_to_dict_cache[tool.id] = to_dict
         else:
-            to_dict = self._tool_to_dict_cache_admin.get(tool.id, None)
+            if not tool_help:
+                to_dict = self._tool_to_dict_cache_admin.get(tool.id, None)
             if not to_dict:
-                to_dict = tool.to_dict(trans, link_details=True)
-                self._tool_to_dict_cache_admin[tool.id] = to_dict
+                to_dict = tool.to_dict(trans, link_details=True, tool_help=tool_help)
+                if not tool_help:
+                    self._tool_to_dict_cache_admin[tool.id] = to_dict
         return to_dict
 
-    def to_dict(self, trans, in_panel=True, **kwds):
+    def to_dict(self, trans, in_panel=True, tool_help=False, **kwds):
         """
         Create a dictionary representation of the toolbox.
         Uses primitive cache for toolbox-specific tool 'to_dict's.
@@ -1078,9 +1083,9 @@ def to_dict(self, trans, in_panel=True, **kwds):
             for elt in panel_elts:
                 # Only use cache for objects that are Tools.
                 if hasattr(elt, "tool_type"):
-                    rval.append(self.get_tool_to_dict(trans, elt))
+                    rval.append(self.get_tool_to_dict(trans, elt, tool_help=tool_help))
                 else:
-                    kwargs = dict(trans=trans, link_details=True, toolbox=self)
+                    kwargs = dict(trans=trans, link_details=True, tool_help=tool_help, toolbox=self)
                     rval.append(elt.to_dict(**kwargs))
         else:
             filter_method = self._build_filter_method(trans)
diff --git a/lib/galaxy/tools/toolbox/panel.py b/lib/galaxy/tools/toolbox/panel.py
index 891feaf4255f..e325cd922ab2 100644
--- a/lib/galaxy/tools/toolbox/panel.py
+++ b/lib/galaxy/tools/toolbox/panel.py
@@ -69,18 +69,19 @@ def copy(self):
         copy.elems = self.elems.copy()
         return copy
 
-    def to_dict(self, trans, link_details=False, toolbox=None):
+    def to_dict(self, trans, link_details=False, tool_help=False, toolbox=None):
         """ Return a dict that includes section's attributes. """
 
         section_dict = super(ToolSection, self).to_dict()
         section_elts = []
         kwargs = dict(
             trans=trans,
-            link_details=link_details
+            link_details=link_details,
+            tool_help=tool_help
         )
         for elt in self.elems.values():
             if hasattr(elt, "tool_type") and toolbox:
-                section_elts.append(toolbox.get_tool_to_dict(trans, elt))
+                section_elts.append(toolbox.get_tool_to_dict(trans, elt, tool_help=tool_help))
             else:
                 section_elts.append(elt.to_dict(**kwargs))
         section_dict['elems'] = section_elts
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index b2fe46e52a3d..360682a8afd9 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -57,6 +57,7 @@ def index(self, trans, **kwds):
         trackster = util.string_as_bool(kwds.get('trackster', 'False'))
         q = kwds.get('q', '')
         tool_id = kwds.get('tool_id', '')
+        tool_help = util.string_as_bool(kwds.get('tool_help', 'False'))
 
         # Find whether to search.
         if q:
@@ -88,7 +89,7 @@ def index(self, trans, **kwds):
 
         # Return everything.
         try:
-            return self.app.toolbox.to_dict(trans, in_panel=in_panel, trackster=trackster)
+            return self.app.toolbox.to_dict(trans, in_panel=in_panel, trackster=trackster, tool_help=tool_help)
         except Exception:
             raise exceptions.InternalServerError("Error: Could not convert toolbox to dictionary")
 

From d40bfd1ab228fef6d2490a00fe03fd9a436837a8 Mon Sep 17 00:00:00 2001
From: Sebastian Kapust <sebastian@kapust.org>
Date: Tue, 1 Oct 2019 07:04:12 +0200
Subject: [PATCH 435/853] Add minimal bioschemas annotations for the tools

---
 client/galaxy/scripts/components/ToolsView.vue | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolsView.vue b/client/galaxy/scripts/components/ToolsView.vue
index 422850995d27..5a0ecc02529e 100644
--- a/client/galaxy/scripts/components/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView.vue
@@ -23,23 +23,25 @@
                 </b-row>
             </b-container>
             <b-card-group v-for="(deck, dindex) in bufferView" :key="dindex" deck class="mb-4">
-                <b-card v-for="(info, index) in deck" :key="index">
+                <b-card v-for="(info, index) in deck" :key="index" itemscope itemtype="http://schema.org/SoftwareApplication">
+                    <meta itemprop="operatingSystem" content="Any">
+                    <meta itemprop="applicationCategory" content="Web application">
                     <div slot="header">
-                        <b-link :href="info['url']" target="_blank">
-                            <h4>{{ info["name"] }}</h4>
+                        <b-link :href="info['url']" target="_blank" itemprop="url">
+                            <h4 itemprop="name">{{ info["name"] }}</h4>
                         </b-link>
                         <b-badge>{{ info["section"] }}</b-badge>
                     </div>
-                    <p class="card-text" v-html="helpSummary(info['help']) || info['description']" />
+                    <p class="card-text" v-html="helpSummary(info['help']) || info['description']" itemprop="description"/>
                     <p class="card-text">
                         <b-btn v-b-modal="'modal-' + dindex + '-' + index">Info</b-btn>
                         <b-modal :id="'modal-' + dindex + '-' + index" centered :title="info['name']">
-                            <b>{{ info["version"] + " / " + info["id"] }}</b>
+                            <b itemprop="softwareVersion">{{ info["version"] + " / " + info["id"] }}</b>
                             <p>{{ info["description"] }}</p>
                             <p v-html="info['help']"></p>
                         </b-modal>
                     </p>
-                    <Citations simple source="tools" :id="info['id']" />
+                    <Citations simple source="tools" :id="info['id']" itemprop="citation"/>
                 </b-card>
             </b-card-group>
         </div>

From fc782ac09227f99a7277a6c6e40646964bc840fb Mon Sep 17 00:00:00 2001
From: Sebastian Kapust <sebastian@kapust.org>
Date: Tue, 1 Oct 2019 07:04:12 +0200
Subject: [PATCH 436/853] Add masonry layout

---
 .../galaxy/scripts/components/ToolsView.vue   | 113 +++++++++++-------
 client/package.json                           |   6 +-
 client/yarn.lock                              |  60 +++++++++-
 3 files changed, 135 insertions(+), 44 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolsView.vue b/client/galaxy/scripts/components/ToolsView.vue
index 5a0ecc02529e..020487cf4f79 100644
--- a/client/galaxy/scripts/components/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView.vue
@@ -10,9 +10,10 @@
                         <b-form-group description="Search for strings or regular expressions">
                             <b-input-group>
                                 <b-form-input
-                                    v-model="filter"
+                                    v-model="filterText"
                                     placeholder="Type to Search"
-                                    @keyup.esc.native="filter = ''"
+                                    @keyup.native="filter('filterByText')"
+                                    @keyup.esc.native="filterText = ''"
                                 />
                                 <b-input-group-append>
                                     <b-btn :disabled="!filter" @click="filter = ''">Clear (esc)</b-btn>
@@ -22,28 +23,45 @@
                     </b-col>
                 </b-row>
             </b-container>
-            <b-card-group v-for="(deck, dindex) in bufferView" :key="dindex" deck class="mb-4">
-                <b-card v-for="(info, index) in deck" :key="index" itemscope itemtype="http://schema.org/SoftwareApplication">
-                    <meta itemprop="operatingSystem" content="Any">
-                    <meta itemprop="applicationCategory" content="Web application">
+            <isotope
+                ref="iso"
+                :options="isoOptions"
+                @filter="filterOption = arguments[2]"
+                :list="buffer"
+                style="margin: 0 auto;"
+            >
+                <b-card
+                    v-for="(info, index) in buffer"
+                    :key="index"
+                    class="m-2"
+                    style="width: 23rem;"
+                    itemscope
+                    itemtype="http://schema.org/SoftwareApplication"
+                >
+                    <meta itemprop="operatingSystem" content="Any" />
+                    <meta itemprop="applicationCategory" content="Web application" />
                     <div slot="header">
                         <b-link :href="info['url']" target="_blank" itemprop="url">
-                            <h4 itemprop="name">{{ info["name"] }}</h4>
+                            <h4 class="tools-view-name" itemprop="name">{{ info["name"] }}</h4>
                         </b-link>
-                        <b-badge>{{ info["section"] }}</b-badge>
+                        <b-badge class="tools-view-section">{{ info["section"] }}</b-badge>
                     </div>
-                    <p class="card-text" v-html="helpSummary(info['help']) || info['description']" itemprop="description"/>
+                    <p
+                        class="card-text"
+                        v-html="helpSummary(info['help']) || info['description']"
+                        itemprop="description"
+                    />
                     <p class="card-text">
-                        <b-btn v-b-modal="'modal-' + dindex + '-' + index">Info</b-btn>
-                        <b-modal :id="'modal-' + dindex + '-' + index" centered :title="info['name']">
+                        <b-btn v-b-modal="'modal-' + '-' + index">Info</b-btn>
+                        <b-modal :id="'modal-' + '-' + index" centered :title="info['name']">
                             <b itemprop="softwareVersion">{{ info["version"] + " / " + info["id"] }}</b>
                             <p>{{ info["description"] }}</p>
                             <p v-html="info['help']"></p>
                         </b-modal>
                     </p>
-                    <Citations simple source="tools" :id="info['id']" itemprop="citation"/>
+                    <Citations simple source="tools" @click.native="updateLayout()" :id="info['id']" />
                 </b-card>
-            </b-card-group>
+            </isotope>
         </div>
     </div>
 </template>
@@ -51,43 +69,50 @@
 <script>
 import { getAppRoot } from "onload/loadConfig";
 import infiniteScroll from "vue-infinite-scroll";
+import isotope from "vueisotope";
+import Isotope from "isotope-layout";
 import axios from "axios";
 import Citations from "components/Citations.vue";
+import { setTimeout } from "timers";
 
 export default {
     components: {
-        Citations
+        Citations,
+        isotope
     },
     directives: { infiniteScroll },
     data() {
         return {
             tools: [],
             buffer: [],
-            filter: "",
+            isoOptions: {
+                masonry: {
+                    fitWidth: true
+                },
+                getFilterData: {
+                    filterByText: el => {
+                        const re = new RegExp(this.filterText, "i");
+                        console.log(this.filterText);
+                        return el["name"].match(re) || el["description"].match(re) || el["help"].match(re);
+                    }
+                }
+            },
+            filterOption: null,
+            filterText: "",
             busy: false,
             loading: true
         };
     },
-    computed: {
-        bufferView() {
-            let a = [];
-            let b = this.bufferFiltered.slice(0);
-            while (b.length) a.push(b.splice(0, 3));
-            return a;
-        },
-        bufferFiltered() {
-            let f = [];
-            let filter = this.filter;
-            if (!this.loading) {
-                f = this.buffer.filter(x => {
-                    let re = new RegExp(filter, "i");
-                    return x["name"].match(re) || x["description"].match(re);
-                });
-            }
-            return f;
-        }
-    },
     methods: {
+        updateLayout() {
+            setTimeout(() => {
+                this.$refs.iso.layout();
+            }, 500);
+        },
+        filter(key) {
+            console.log("filter here with key: ", key);
+            this.$refs.iso.filter(key);
+        },
         toolsExtracted(tools) {
             function extractSections(acc, section) {
                 function extractTools(_acc, tool) {
@@ -115,14 +140,18 @@ export default {
                 .map(a => a[1]);
         },
         loadMore() {
-            this.busy = true;
+            if (this.buffer.length < this.tools.length) {
+                this.busy = true;
 
-            setTimeout(() => {
-                const start = this.buffer.length;
-                const end = start + 20;
-                this.buffer = this.buffer.concat(this.tools.slice(start, end));
-                this.busy = false;
-            }, 1000);
+                setTimeout(() => {
+                    const start = this.buffer.length;
+                    const end = start + 10;
+                    const newItems = this.tools.slice(start, end);
+                    this.buffer = this.buffer.concat(newItems);
+
+                    this.busy = false;
+                }, 100);
+            }
         },
         helpSummary(help) {
             const parser = new DOMParser();
@@ -149,6 +178,8 @@ export default {
                 this.tools = this.toolsExtracted(response.data);
                 this.buffer = this.tools.slice(0, 20);
                 this.loading = false;
+
+                this.updateLayout();
             })
             .catch(error => {
                 console.error(error);
diff --git a/client/package.json b/client/package.json
index 29648030c0ca..2f6982dfe5f6 100644
--- a/client/package.json
+++ b/client/package.json
@@ -31,6 +31,7 @@
     "glob": "^7.1.4",
     "handsontable": "^2.0.0",
     "imask": "^4.1.5",
+    "isotope-layout": "^3.0.6",
     "jquery": "2",
     "jquery-migrate": "~1.4",
     "jquery-mousewheel": "^3.1.13",
@@ -50,12 +51,13 @@
     "toastr": "^2.1.4",
     "underscore": "^1.9.2",
     "vue": "^2.6.11",
+    "vue-infinite-scroll": "^2.0.2",
     "vue-multiselect": "^2.1.0",
     "vue-router": "^3.1.5",
     "vue-rx": "^6.2.0",
+    "vueisotope": "^3.1.2",
     "vuex": "^3.1.2",
-    "vuex-cache": "^3.1.0",
-    "vue-infinite-scroll": "^2.0.2"
+    "vuex-cache": "^3.1.0"
   },
   "scripts": {
     "watch": "gulp && yarn run save-build-hash && yarn run webpack-watch",
diff --git a/client/yarn.lock b/client/yarn.lock
index f2f1f72a1f63..3bc8e50d224d 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -4748,6 +4748,11 @@ des.js@^1.0.0:
     inherits "^2.0.1"
     minimalistic-assert "^1.0.0"
 
+desandro-matches-selector@^2.0.0:
+  version "2.0.2"
+  resolved "https://registry.yarnpkg.com/desandro-matches-selector/-/desandro-matches-selector-2.0.2.tgz#717beed4dc13e7d8f3762f707a6d58a6774218e1"
+  integrity sha1-cXvu1NwT59jzdi9wem1YpndCGOE=
+
 destroy@~1.0.4:
   version "1.0.4"
   resolved "https://registry.yarnpkg.com/destroy/-/destroy-1.0.4.tgz#978857442c44749e4206613e37946205826abd80"
@@ -5397,6 +5402,11 @@ etag@~1.8.1:
   resolved "https://registry.yarnpkg.com/etag/-/etag-1.8.1.tgz#41ae2eeb65efa62268aebfea83ac7d79299b0887"
   integrity sha1-Qa4u62XvpiJorr/qg6x9eSmbCIc=
 
+ev-emitter@^1.0.0:
+  version "1.1.1"
+  resolved "https://registry.yarnpkg.com/ev-emitter/-/ev-emitter-1.1.1.tgz#8f18b0ce5c76a5d18017f71c0a795c65b9138f2a"
+  integrity sha512-ipiDYhdQSCZ4hSbX4rMW+XzNKMD1prg/sTvoVmSLkuQ1MVlwjJQQA+sW8tMYR3BLUr9KjodFV4pvzunvRhd33Q==
+
 eventemitter3@^3.0.0:
   version "3.1.0"
   resolved "https://registry.yarnpkg.com/eventemitter3/-/eventemitter3-3.1.0.tgz#090b4d6cdbd645ed10bf750d4b5407942d7ba163"
@@ -5949,6 +5959,13 @@ fined@^1.0.1:
     object.pick "^1.2.0"
     parse-filepath "^1.0.1"
 
+fizzy-ui-utils@^2.0.0, fizzy-ui-utils@^2.0.4:
+  version "2.0.7"
+  resolved "https://registry.yarnpkg.com/fizzy-ui-utils/-/fizzy-ui-utils-2.0.7.tgz#7df45dcc4eb374a08b65d39bb9a4beedf7330505"
+  integrity sha512-CZXDVXQ1If3/r8s0T+v+qVeMshhfcuq0rqIFgJnrtd+Bu8GmDmqMjntjUePypVtjHXKJ6V4sw9zeyox34n9aCg==
+  dependencies:
+    desandro-matches-selector "^2.0.0"
+
 flagged-respawn@^1.0.0:
   version "1.0.0"
   resolved "https://registry.yarnpkg.com/flagged-respawn/-/flagged-respawn-1.0.0.tgz#4e79ae9b2eb38bf86b3bb56bf3e0a56aa5fcabd7"
@@ -6213,6 +6230,11 @@ get-own-enumerable-property-symbols@^3.0.0:
   resolved "https://registry.yarnpkg.com/get-own-enumerable-property-symbols/-/get-own-enumerable-property-symbols-3.0.0.tgz#b877b49a5c16aefac3655f2ed2ea5b684df8d203"
   integrity sha512-CIJYJC4GGF06TakLg8z4GQKvDsx9EMspVxOYih7LerEL/WosUnFIww45CGfxfeKHqlg3twgUrYRT1O3WQqjGCg==
 
+get-size@^2.0.0, get-size@^2.0.2:
+  version "2.0.3"
+  resolved "https://registry.yarnpkg.com/get-size/-/get-size-2.0.3.tgz#54a1d0256b20ea7ac646516756202769941ad2ef"
+  integrity sha512-lXNzT/h/dTjTxRbm9BXb+SGxxzkm97h/PCIKtlN/CBCxxmkkIVV21udumMS93MuVTDX583gqc94v3RjuHmI+2Q==
+
 get-stdin@^4.0.1:
   version "4.0.1"
   resolved "https://registry.yarnpkg.com/get-stdin/-/get-stdin-4.0.1.tgz#b968c6b0a04384324902e8bf1a5df32579a450fe"
@@ -7770,6 +7792,17 @@ isobject@^3.0.0, isobject@^3.0.1:
   resolved "https://registry.yarnpkg.com/isobject/-/isobject-3.0.1.tgz#4e431e92b11a9731636aa1f9c8d1ccbcfdab78df"
   integrity sha1-TkMekrEalzFjaqH5yNHMvP2reN8=
 
+isotope-layout@^3.0.1, isotope-layout@^3.0.6:
+  version "3.0.6"
+  resolved "https://registry.yarnpkg.com/isotope-layout/-/isotope-layout-3.0.6.tgz#d5636ec74d68e7e88fa5166fe6396858db00f432"
+  integrity sha512-z2ZKablhocXhoNyWwzJPFd7u7FWbYbVJA51Nvsqsod8jH2ExGc1SwDsSWKE54e3PhXzqf2yZPhFSq/c2MR1arw==
+  dependencies:
+    desandro-matches-selector "^2.0.0"
+    fizzy-ui-utils "^2.0.4"
+    get-size "^2.0.0"
+    masonry-layout "^4.1.0"
+    outlayer "^2.1.0"
+
 isstream@~0.1.2:
   version "0.1.2"
   resolved "https://registry.yarnpkg.com/isstream/-/isstream-0.1.2.tgz#47e63f7af55afa6f92e1500e690eb8b8529c099a"
@@ -8388,7 +8421,7 @@ lodash.uniq@^4.5.0:
   resolved "https://registry.yarnpkg.com/lodash.uniq/-/lodash.uniq-4.5.0.tgz#d0225373aeb652adc1bc82e4945339a842754773"
   integrity sha1-0CJTc662Uq3BvILklFM5qEJ1R3M=
 
-lodash@^4.0.0, lodash@^4.0.1, lodash@^4.17.10, lodash@^4.17.11, lodash@^4.17.4, lodash@^4.17.5, lodash@~4.17.10:
+lodash@^4.0.0, lodash@^4.0.1, lodash@^4.13.1, lodash@^4.17.10, lodash@^4.17.11, lodash@^4.17.4, lodash@^4.17.5, lodash@~4.17.10:
   version "4.17.11"
   resolved "https://registry.yarnpkg.com/lodash/-/lodash-4.17.11.tgz#b39ea6229ef607ecd89e2c8df12536891cac9b8d"
   integrity sha512-cQKh8igo5QUhZ7lg38DYWAxMvjSAKG0A8wGSVimP07SIUEK2UO+arSRKbRZWtelMtN5V0Hkwh5ryOto/SshYIg==
@@ -8588,6 +8621,14 @@ markdown-to-jsx@^6.9.1:
     prop-types "^15.6.2"
     unquote "^1.1.0"
 
+masonry-layout@^4.1.0:
+  version "4.2.2"
+  resolved "https://registry.yarnpkg.com/masonry-layout/-/masonry-layout-4.2.2.tgz#d57b44af13e601bfcdc423f1dd8348b5524de348"
+  integrity sha512-iGtAlrpHNyxaR19CvKC3npnEcAwszXoyJiI8ARV2ePi7fmYhIud25MHK8Zx4P0LCC4d3TNO9+rFa1KoK1OEOaA==
+  dependencies:
+    get-size "^2.0.2"
+    outlayer "^2.1.0"
+
 matchdep@^2.0.0:
   version "2.0.0"
   resolved "https://registry.yarnpkg.com/matchdep/-/matchdep-2.0.0.tgz#c6f34834a0d8dbc3b37c27ee8bbcb27c7775582e"
@@ -9759,6 +9800,15 @@ osenv@0, osenv@^0.1.0, osenv@^0.1.4:
     os-homedir "^1.0.0"
     os-tmpdir "^1.0.0"
 
+outlayer@^2.1.0:
+  version "2.1.1"
+  resolved "https://registry.yarnpkg.com/outlayer/-/outlayer-2.1.1.tgz#29863b6de10ea5dadfffcadfa0d728907387e9a2"
+  integrity sha1-KYY7beEOpdrf/8rfoNcokHOH6aI=
+  dependencies:
+    ev-emitter "^1.0.0"
+    fizzy-ui-utils "^2.0.0"
+    get-size "^2.0.2"
+
 p-defer@^1.0.0:
   version "1.0.0"
   resolved "https://registry.yarnpkg.com/p-defer/-/p-defer-1.0.0.tgz#9f6eb182f6c9aa8cd743004a7d4f96b196b0fb0c"
@@ -14263,6 +14313,14 @@ vue@^2.6.9:
   resolved "https://registry.yarnpkg.com/vue/-/vue-2.6.10.tgz#a72b1a42a4d82a721ea438d1b6bf55e66195c637"
   integrity sha512-ImThpeNU9HbdZL3utgMCq0oiMzAkt1mcgy3/E6zWC/G6AaQoeuFdsl9nDhTDU3X1R6FK7nsIUuRACVcjI+A2GQ==
 
+vueisotope@^3.1.2:
+  version "3.1.2"
+  resolved "https://registry.yarnpkg.com/vueisotope/-/vueisotope-3.1.2.tgz#df9d3e32d9770ff97a409d6baca68ec830f03ae7"
+  integrity sha512-mPlHr+YT1kaXXPLzAEwLxgE8Q3gauqj7hfs1U0ww2oeO9cYCdI8sWbJL1iNRDZTSd6p7Lks+6el+FwWcnXLHvQ==
+  dependencies:
+    isotope-layout "^3.0.1"
+    lodash "^4.13.1"
+
 vuex-cache@^3.1.0:
   version "3.1.0"
   resolved "https://registry.yarnpkg.com/vuex-cache/-/vuex-cache-3.1.0.tgz#aad576cfb39b325cc7a43ea9a42414e356374c4b"

From 7270e7e57f2832b9175a9ed8f2a9851f5fc17ab8 Mon Sep 17 00:00:00 2001
From: Sebastian Kapust <sebastian@kapust.org>
Date: Tue, 1 Oct 2019 07:04:12 +0200
Subject: [PATCH 437/853] Add tools/json page which serves json-ld data

---
 .../galaxy/scripts/components/ToolsJson.vue   | 52 +++++++++++++++++++
 .../scripts/entry/analysis/AnalysisRouter.js  | 15 ++++++
 lib/galaxy/webapps/galaxy/buildapp.py         |  2 +
 3 files changed, 69 insertions(+)
 create mode 100644 client/galaxy/scripts/components/ToolsJson.vue

diff --git a/client/galaxy/scripts/components/ToolsJson.vue b/client/galaxy/scripts/components/ToolsJson.vue
new file mode 100644
index 000000000000..dac788bb7844
--- /dev/null
+++ b/client/galaxy/scripts/components/ToolsJson.vue
@@ -0,0 +1,52 @@
+<script>
+import { getAppRoot } from "onload/loadConfig";
+import axios from "axios";
+
+export default {
+    data() {
+        return { toolsJsonLD: {} };
+    },
+    methods: {
+        createToolsJson(tools) {
+            function extractSections(acc, section) {
+                function extractTools(_acc, tool) {
+                    return tool["name"]
+                        ? [
+                              ..._acc,
+                              {
+                                  "@type": "SoftwareApplication",
+                                  operatingSystem: "Any",
+                                  applicationCategory: "Web application",
+                                  name: tool["name"],
+                                  description: tool["help"] || tool["description"],
+                                  softwareVersion: tool["version"],
+                                  url: getAppRoot() + String(tool["link"]).substring(1)
+                              }
+                          ]
+                        : _acc;
+                }
+                return acc.concat(section["elems"].reduce(extractTools, []));
+            }
+            return {
+                "@context": "http://schema.org",
+                "@graph": tools.reduce(extractSections, [])
+            };
+        }
+    },
+    created() {
+        axios
+            .get(`${getAppRoot()}api/tools?tool_help=True`)
+            .then(response => {
+                this.toolsJsonLD = this.createToolsJson(response.data);
+
+                const el = document.createElement("script");
+                el.type = "application/ld+json";
+                el.text = JSON.stringify(this.toolsJsonLD);
+                document.head.appendChild(el);
+            })
+            .catch(error => {
+                console.error(error);
+            });
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
index db4e56409762..039828d5fc95 100644
--- a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
+++ b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
@@ -33,6 +33,11 @@ import HistoryView from "components/HistoryView.vue";
 import WorkflowInvocationReport from "components/WorkflowInvocationReport.vue";
 import WorkflowRun from "components/Workflow/Run/WorkflowRun.vue";
 import RecentInvocations from "components/User/RecentInvocations.vue";
+<<<<<<< HEAD
+=======
+import ToolsView from "components/ToolsView.vue";
+import ToolsJson from "components/ToolsJson.vue";
+>>>>>>> 669a685171... Add tools/json page which serves json-ld data
 import HistoryList from "mvc/history/history-list";
 import PluginList from "components/PluginList.vue";
 import QueryStringParsing from "utils/query-string-parsing";
@@ -51,6 +56,11 @@ export const getAnalysisRouter = Galaxy =>
         routes: {
             "(/)(#)(_=_)": "home",
             "(/)root*": "home",
+<<<<<<< HEAD
+=======
+            "(/)tools/view": "show_tools_view",
+            "(/)tools/json": "show_tools_json",
+>>>>>>> 669a685171... Add tools/json page which serves json-ld data
             "(/)tours(/)(:tour_id)": "show_tours",
             "(/)user(/)": "show_user",
             "(/)user(/)cloud_auth": "show_cloud_auth",
@@ -241,11 +251,16 @@ export const getAnalysisRouter = Galaxy =>
         show_histories_import: function() {
             this._display_vue_helper(HistoryImport);
         },
+
         show_tools_view: function() {
             this.page.panels.left.hide();
             this.page.panels.right.hide();
             this._display_vue_helper(ToolsView);
         },
+
+        show_tools_json: function() {
+            this._display_vue_helper(ToolsJson);
+        },
         show_histories_permissions: function() {
             this.page.display(
                 new FormWrapper.View({
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 7281d8240af3..f998ca73765d 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -123,6 +123,8 @@ def app_factory(global_conf, load_app_kwds={}, **kwargs):
     webapp.add_client_route('/admin/quotas', 'admin')
     webapp.add_client_route('/admin/form/{form_id}', 'admin')
     webapp.add_client_route('/admin/api_keys', 'admin')
+    webapp.add_client_route('/tools/view')
+    webapp.add_client_route('/tools/json')
     webapp.add_client_route('/tours')
     webapp.add_client_route('/tours/{tour_id}')
     webapp.add_client_route('/user')

From 772f7b9fac78bd6854d3093873c54af34ce14fa1 Mon Sep 17 00:00:00 2001
From: Sebastian Kapust <sebastian@kapust.org>
Date: Tue, 1 Oct 2019 07:04:12 +0200
Subject: [PATCH 438/853] Remove microdata tags

---
 client/galaxy/scripts/components/ToolsView.vue | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolsView.vue b/client/galaxy/scripts/components/ToolsView.vue
index 020487cf4f79..16269529f6ce 100644
--- a/client/galaxy/scripts/components/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView.vue
@@ -35,26 +35,21 @@
                     :key="index"
                     class="m-2"
                     style="width: 23rem;"
-                    itemscope
-                    itemtype="http://schema.org/SoftwareApplication"
                 >
-                    <meta itemprop="operatingSystem" content="Any" />
-                    <meta itemprop="applicationCategory" content="Web application" />
                     <div slot="header">
-                        <b-link :href="info['url']" target="_blank" itemprop="url">
-                            <h4 class="tools-view-name" itemprop="name">{{ info["name"] }}</h4>
+                        <b-link :href="info['url']" target="_blank">
+                            <h4 class="tools-view-name">{{ info["name"] }}</h4>
                         </b-link>
                         <b-badge class="tools-view-section">{{ info["section"] }}</b-badge>
                     </div>
                     <p
                         class="card-text"
                         v-html="helpSummary(info['help']) || info['description']"
-                        itemprop="description"
                     />
                     <p class="card-text">
                         <b-btn v-b-modal="'modal-' + '-' + index">Info</b-btn>
                         <b-modal :id="'modal-' + '-' + index" centered :title="info['name']">
-                            <b itemprop="softwareVersion">{{ info["version"] + " / " + info["id"] }}</b>
+                            <b>{{ info["version"] + " / " + info["id"] }}</b>
                             <p>{{ info["description"] }}</p>
                             <p v-html="info['help']"></p>
                         </b-modal>

From b335a2f641c1ae2a7d7cb0c4f4f610abfa37d8b8 Mon Sep 17 00:00:00 2001
From: Sebastian Kapust <sebastian@kapust.org>
Date: Tue, 1 Oct 2019 07:04:12 +0200
Subject: [PATCH 439/853] Fixes

* Handle empty tool panel data
* Robust collapse/layout animation transitions
---
 .../galaxy/scripts/components/Citations.vue   |  7 ++++
 .../galaxy/scripts/components/ToolsJson.vue   |  6 ++-
 .../galaxy/scripts/components/ToolsView.vue   | 37 +++++++++----------
 3 files changed, 29 insertions(+), 21 deletions(-)

diff --git a/client/galaxy/scripts/components/Citations.vue b/client/galaxy/scripts/components/Citations.vue
index 8402cd04d6e1..fd6acfa2e72d 100644
--- a/client/galaxy/scripts/components/Citations.vue
+++ b/client/galaxy/scripts/components/Citations.vue
@@ -38,6 +38,8 @@
       <b-collapse
         :id="id"
         class="mt-2"
+        @shown='$emit("shown")'
+        @hidden='$emit("hidden")'
       >
         <b-card>
           <p v-html="formattedReferences"></p>
@@ -90,6 +92,11 @@ export default {
             );
         }
     },
+    updated: function() {
+        this.$nextTick(function() {
+            this.$emit("rendered");
+        });
+    },
     created: function() {
         axios
             .get(`${getAppRoot()}api/${this.source}/${this.id}/citations`)
diff --git a/client/galaxy/scripts/components/ToolsJson.vue b/client/galaxy/scripts/components/ToolsJson.vue
index dac788bb7844..0772b80d2435 100644
--- a/client/galaxy/scripts/components/ToolsJson.vue
+++ b/client/galaxy/scripts/components/ToolsJson.vue
@@ -25,7 +25,11 @@ export default {
                           ]
                         : _acc;
                 }
-                return acc.concat(section["elems"].reduce(extractTools, []));
+                if ("elems" in section) {
+                    return acc.concat(section["elems"].reduce(extractTools, []));
+                } else {
+                    return acc;
+                }
             }
             return {
                 "@context": "http://schema.org",
diff --git a/client/galaxy/scripts/components/ToolsView.vue b/client/galaxy/scripts/components/ToolsView.vue
index 16269529f6ce..c5fa26211c82 100644
--- a/client/galaxy/scripts/components/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView.vue
@@ -30,22 +30,14 @@
                 :list="buffer"
                 style="margin: 0 auto;"
             >
-                <b-card
-                    v-for="(info, index) in buffer"
-                    :key="index"
-                    class="m-2"
-                    style="width: 23rem;"
-                >
+                <b-card v-for="(info, index) in buffer" :key="index" class="m-2" style="width: 23rem;">
                     <div slot="header">
                         <b-link :href="info['url']" target="_blank">
                             <h4 class="tools-view-name">{{ info["name"] }}</h4>
                         </b-link>
                         <b-badge class="tools-view-section">{{ info["section"] }}</b-badge>
                     </div>
-                    <p
-                        class="card-text"
-                        v-html="helpSummary(info['help']) || info['description']"
-                    />
+                    <p class="card-text" v-html="helpSummary(info['help']) || info['description']" />
                     <p class="card-text">
                         <b-btn v-b-modal="'modal-' + '-' + index">Info</b-btn>
                         <b-modal :id="'modal-' + '-' + index" centered :title="info['name']">
@@ -54,7 +46,14 @@
                             <p v-html="info['help']"></p>
                         </b-modal>
                     </p>
-                    <Citations simple source="tools" @click.native="updateLayout()" :id="info['id']" />
+                    <Citations
+                        simple
+                        source="tools"
+                        @rendered="layout"
+                        @shown="layout"
+                        @hidden="layout"
+                        :id="info['id']"
+                    />
                 </b-card>
             </isotope>
         </div>
@@ -87,7 +86,6 @@ export default {
                 getFilterData: {
                     filterByText: el => {
                         const re = new RegExp(this.filterText, "i");
-                        console.log(this.filterText);
                         return el["name"].match(re) || el["description"].match(re) || el["help"].match(re);
                     }
                 }
@@ -99,13 +97,10 @@ export default {
         };
     },
     methods: {
-        updateLayout() {
-            setTimeout(() => {
-                this.$refs.iso.layout();
-            }, 500);
+        layout() {
+            this.$refs.iso.layout();
         },
         filter(key) {
-            console.log("filter here with key: ", key);
             this.$refs.iso.filter(key);
         },
         toolsExtracted(tools) {
@@ -126,7 +121,11 @@ export default {
                           ]
                         : _acc;
                 }
-                return acc.concat(section["elems"].reduce(extractTools, []));
+                if ("elems" in section) {
+                    return acc.concat(section["elems"].reduce(extractTools, []));
+                } else {
+                    return acc;
+                }
             }
             return tools
                 .reduce(extractSections, [])
@@ -173,8 +172,6 @@ export default {
                 this.tools = this.toolsExtracted(response.data);
                 this.buffer = this.tools.slice(0, 20);
                 this.loading = false;
-
-                this.updateLayout();
             })
             .catch(error => {
                 console.error(error);

From a3bf24dd401967f14b4b3ae00436978ca23b66e2 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Thu, 23 Jan 2020 18:03:44 +0100
Subject: [PATCH 440/853] fix cherry-pick artifacts

---
 client/galaxy/scripts/components/Citations.vue         | 9 ++++++++-
 client/galaxy/scripts/entry/analysis/AnalysisRouter.js | 6 ------
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/client/galaxy/scripts/components/Citations.vue b/client/galaxy/scripts/components/Citations.vue
index fd6acfa2e72d..bbaaabc1fd88 100644
--- a/client/galaxy/scripts/components/Citations.vue
+++ b/client/galaxy/scripts/components/Citations.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-    <b-card>
+    <b-card  v-if="!simple">
         <template v-slot:header>
             <h4 class="mb-0">
                 Citations
@@ -38,7 +38,9 @@
       <b-collapse
         :id="id"
         class="mt-2"
+        @show='$emit("show")'
         @shown='$emit("shown")'
+        @hide='$emit("hide")'
         @hidden='$emit("hidden")'
       >
         <b-card>
@@ -74,6 +76,11 @@ export default {
             type: Boolean,
             requried: false,
             default: true
+        },
+        simple: {
+            type: Boolean,
+            required: false,
+            default: false
         }
     },
     data() {
diff --git a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
index 039828d5fc95..199b4945f516 100644
--- a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
+++ b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
@@ -33,11 +33,8 @@ import HistoryView from "components/HistoryView.vue";
 import WorkflowInvocationReport from "components/WorkflowInvocationReport.vue";
 import WorkflowRun from "components/Workflow/Run/WorkflowRun.vue";
 import RecentInvocations from "components/User/RecentInvocations.vue";
-<<<<<<< HEAD
-=======
 import ToolsView from "components/ToolsView.vue";
 import ToolsJson from "components/ToolsJson.vue";
->>>>>>> 669a685171... Add tools/json page which serves json-ld data
 import HistoryList from "mvc/history/history-list";
 import PluginList from "components/PluginList.vue";
 import QueryStringParsing from "utils/query-string-parsing";
@@ -56,11 +53,8 @@ export const getAnalysisRouter = Galaxy =>
         routes: {
             "(/)(#)(_=_)": "home",
             "(/)root*": "home",
-<<<<<<< HEAD
-=======
             "(/)tools/view": "show_tools_view",
             "(/)tools/json": "show_tools_json",
->>>>>>> 669a685171... Add tools/json page which serves json-ld data
             "(/)tours(/)(:tour_id)": "show_tours",
             "(/)user(/)": "show_user",
             "(/)user(/)cloud_auth": "show_cloud_auth",

From 700901e17bb229a82bb71c3d9332c2d4693d3891 Mon Sep 17 00:00:00 2001
From: Sebastian Kapust <sebastian@kapust.org>
Date: Tue, 1 Oct 2019 07:04:12 +0200
Subject: [PATCH 441/853] Draw expanding card in front until layout is done

Increase the z-index of the expanding citation
card until layout is done. Reset the z-index
afterwards.
---
 .../galaxy/scripts/components/ToolsView.vue   | 49 ++++++++++++++-----
 1 file changed, 36 insertions(+), 13 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolsView.vue b/client/galaxy/scripts/components/ToolsView.vue
index c5fa26211c82..efa6f531cd8a 100644
--- a/client/galaxy/scripts/components/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView.vue
@@ -1,11 +1,11 @@
 <template>
     <div v-infinite-scroll="loadMore" infinite-scroll-disabled="busy">
-        <h2 class="mb-3">
+        <h2 class="mb-3" style="text-align: center">
             <span id="tools-view">Tools View</span>
         </h2>
         <div v-if="!loading">
             <b-container fluid class="mb-4">
-                <b-row>
+                <b-row class="justify-content-center">
                     <b-col md="6">
                         <b-form-group description="Search for strings or regular expressions">
                             <b-input-group>
@@ -30,7 +30,7 @@
                 :list="buffer"
                 style="margin: 0 auto;"
             >
-                <b-card v-for="(info, index) in buffer" :key="index" class="m-2" style="width: 23rem;">
+                <b-card v-for="(info, index) in buffer" :key="index" ref="cards" class="m-2" style="width: 23rem;">
                     <div slot="header">
                         <b-link :href="info['url']" target="_blank">
                             <h4 class="tools-view-name">{{ info["name"] }}</h4>
@@ -50,8 +50,9 @@
                         simple
                         source="tools"
                         @rendered="layout"
-                        @shown="layout"
-                        @hidden="layout"
+                        @show="show(index)"
+                        @shown="shown(index)"
+                        @hidden="hidden(index)"
                         :id="info['id']"
                     />
                 </b-card>
@@ -64,7 +65,6 @@
 import { getAppRoot } from "onload/loadConfig";
 import infiniteScroll from "vue-infinite-scroll";
 import isotope from "vueisotope";
-import Isotope from "isotope-layout";
 import axios from "axios";
 import Citations from "components/Citations.vue";
 import { setTimeout } from "timers";
@@ -75,11 +75,26 @@ export default {
         isotope
     },
     directives: { infiniteScroll },
+    props: {
+        transitionDuration: {
+            type: Number,
+            default: 200
+        }
+    },
     data() {
         return {
             tools: [],
             buffer: [],
-            isoOptions: {
+            filterOption: null,
+            filterText: "",
+            busy: false,
+            loading: true
+        };
+    },
+    computed: {
+        isoOptions() {
+            return {
+                transitionDuration: this.transitionDuration,
                 masonry: {
                     fitWidth: true
                 },
@@ -89,14 +104,22 @@ export default {
                         return el["name"].match(re) || el["description"].match(re) || el["help"].match(re);
                     }
                 }
-            },
-            filterOption: null,
-            filterText: "",
-            busy: false,
-            loading: true
-        };
+            };
+        }
     },
     methods: {
+        show(index) {
+            this.$refs.cards[index].style.zIndex = "1";
+        },
+        shown(index) {
+            this.layout();
+            setTimeout(() => {
+                this.$refs.cards[index].style.zIndex = "auto";
+            }, 200);
+        },
+        hidden(index) {
+            this.layout();
+        },
         layout() {
             this.$refs.iso.layout();
         },

From 05c33aa989e9a9998531c72da763bd215b8bb1be Mon Sep 17 00:00:00 2001
From: Sebastian Kapust <sebastian@kapust.org>
Date: Tue, 1 Oct 2019 07:04:12 +0200
Subject: [PATCH 442/853] Format and lint ToolsView and Citations

Format and lint using eslint+airbnb-base+prettier+vue configuration.
---
 .../galaxy/scripts/components/Citations.vue   | 129 +++++++++---------
 .../galaxy/scripts/components/ToolsView.vue   |  63 ++++-----
 2 files changed, 92 insertions(+), 100 deletions(-)

diff --git a/client/galaxy/scripts/components/Citations.vue b/client/galaxy/scripts/components/Citations.vue
index bbaaabc1fd88..d3ecca0c92e5 100644
--- a/client/galaxy/scripts/components/Citations.vue
+++ b/client/galaxy/scripts/components/Citations.vue
@@ -1,54 +1,50 @@
 <template>
     <div>
-    <b-card  v-if="!simple">
-        <template v-slot:header>
-            <h4 class="mb-0">
+        <b-card v-if="!simple">
+            <h4 slot="header" class="mb-0">
                 Citations
                 <b-button
                     v-if="viewRender"
-                    @click="toggleViewRender"
                     title="Show all in BibTeX format."
                     class="citations-to-bibtex"
+                    @click="toggleViewRender"
                 >
                     <i class="fa fa-pencil-square-o"></i> Show BibTeX
                 </b-button>
-                <b-button v-else @click="toggleViewRender" title="Return to formatted citation list.">
+                <b-button v-else title="Return to formatted citation list." @click="toggleViewRender">
                     <i class="fa fa-times"></i> Hide BibTeX
                 </b-button>
             </h4>
-        </template>
-        <div v-if="source === 'histories'" class="infomessage">
-            When writing up your analysis, remember to include all references that should be cited in order to
-            completely describe your work. Also, please remember to
-            <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.
-        </div>
-        <span v-if="viewRender" class="citations-formatted"> <p v-html="formattedReferences"></p> </span>
-        <pre v-else>
+            <div v-if="source === 'histories'" class="infomessage">
+                When writing up your analysis, remember to include all references that should be cited in order to
+                completely describe your work. Also, please remember to
+                <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.
+            </div>
+            <span v-if="viewRender" class="citations-formatted">
+                <p v-html="formattedReferences"></p>
+            </span>
+            <pre v-else>
             <code class="citations-bibtex">
                 {{ content }}
             </code>
         </pre>
-    </b-card>
-
-    <div v-else-if="citations.length">
-      <b-btn
-        v-b-toggle="id"
-        variant="primary"
-      >Citations</b-btn>
-      <b-collapse
-        :id="id"
-        class="mt-2"
-        @show='$emit("show")'
-        @shown='$emit("shown")'
-        @hide='$emit("hide")'
-        @hidden='$emit("hidden")'
-      >
-        <b-card>
-          <p v-html="formattedReferences"></p>
         </b-card>
-      </b-collapse>
+        <div v-else-if="citations.length">
+            <b-btn v-b-toggle="id" variant="primary">Citations</b-btn>
+            <b-collapse
+                :id="id"
+                class="mt-2"
+                @show="$emit('show')"
+                @shown="$emit('shown')"
+                @hide="$emit('hide')"
+                @hidden="$emit('hidden')"
+            >
+                <b-card>
+                    <p v-html="formattedReferences"></p>
+                </b-card>
+            </b-collapse>
+        </div>
     </div>
-  </div>
 </template>
 <script>
 import _ from "underscore";
@@ -92,24 +88,24 @@ export default {
         };
     },
     computed: {
-        formattedReferences: function() {
+        formattedReferences() {
             return this.citations.reduce(
                 (a, b) => a.concat(`<p class="formatted-reference">${this.formattedReference(b)}</p>`),
                 ""
             );
         }
     },
-    updated: function() {
-        this.$nextTick(function() {
+    updated() {
+        this.$nextTick(() => {
             this.$emit("rendered");
         });
     },
-    created: function() {
+    created() {
         axios
             .get(`${getAppRoot()}api/${this.source}/${this.id}/citations`)
             .then(response => {
                 this.content = "";
-                for (const rawCitation of response.data) {
+                response.data.forEach(rawCitation => {
                     try {
                         const citation = {
                             fields: {},
@@ -119,68 +115,67 @@ export default {
                         if (parsed) {
                             parsed = _.first(parsed);
                             citation.entryType = parsed.entryType || undefined;
-                            for (const key in parsed.entryTags) {
+                            Object.keys(parsed.entryTags).forEach(key => {
                                 citation.fields[key.toLowerCase()] = parsed.entryTags[key];
-                            }
+                            });
                         }
                         this.citations.push(citation);
                         this.content += rawCitation.content;
                     } catch (err) {
-                        console.warn("Error parsing bibtex: " + err);
+                        console.warn(`Error parsing bibtex: ${err}`);
                     }
-                }
+                });
             })
             .catch(e => {
                 console.error(e);
             });
     },
     methods: {
-        formattedReference: function(citation) {
-            const entryType = citation.entryType;
-            const fields = citation.fields;
+        formattedReference(citation) {
+            const { entryType, fields } = citation;
 
             let ref = "";
-            const authorsAndYear = `${this._asSentence(
+            const authorsAndYear = `${this.asSentence(
                 (fields.author ? fields.author : "") + (fields.year ? ` (${fields.year})` : "")
             )} `;
             const title = fields.title || "";
             const pages = fields.pages ? `pp. ${fields.pages}` : "";
-            const address = fields.address;
-            if (entryType == "article") {
+            const { address } = fields;
+            if (entryType === "article") {
                 const volume =
                     (fields.volume ? fields.volume : "") +
                     (fields.number ? ` (${fields.number})` : "") +
                     (pages ? `, ${pages}` : "");
                 ref = `${authorsAndYear +
-                    this._asSentence(title) +
+                    this.asSentence(title) +
                     (fields.journal ? `In <em>${fields.journal}, ` : "") +
-                    this._asSentence(volume) +
-                    this._asSentence(fields.address)}</em>`;
-            } else if (entryType == "inproceedings" || entryType == "proceedings") {
+                    this.asSentence(volume) +
+                    this.asSentence(fields.address)}</em>`;
+            } else if (entryType === "inproceedings" || entryType === "proceedings") {
                 ref = `${authorsAndYear +
-                    this._asSentence(title) +
+                    this.asSentence(title) +
                     (fields.booktitle ? `In <em>${fields.booktitle}, ` : "") +
-                    (pages ? pages : "") +
+                    (pages || "") +
                     (address ? `, ${address}` : "")}.</em>`;
-            } else if (entryType == "mastersthesis" || entryType == "phdthesis") {
+            } else if (entryType === "mastersthesis" || entryType === "phdthesis") {
                 ref =
                     authorsAndYear +
-                    this._asSentence(title) +
+                    this.asSentence(title) +
                     (fields.howpublished ? `${fields.howpublished}. ` : "") +
                     (fields.note ? `${fields.note}.` : "");
-            } else if (entryType == "techreport") {
+            } else if (entryType === "techreport") {
                 ref =
                     authorsAndYear +
-                    this._asSentence(title) +
-                    this._asSentence(fields.institution) +
-                    this._asSentence(fields.number) +
-                    this._asSentence(fields.type);
-            } else if (entryType == "book" || entryType == "inbook" || entryType == "incollection") {
-                ref = `${authorsAndYear} ${this._formatBookInfo(fields)}`;
+                    this.asSentence(title) +
+                    this.asSentence(fields.institution) +
+                    this.asSentence(fields.number) +
+                    this.asSentence(fields.type);
+            } else if (entryType === "book" || entryType === "inbook" || entryType === "incollection") {
+                ref = `${authorsAndYear} ${this.formatBookInfo(fields)}`;
             } else {
-                ref = `${authorsAndYear} ${this._asSentence(title)}${this._asSentence(
+                ref = `${authorsAndYear} ${this.asSentence(title)}${this.asSentence(
                     fields.howpublished
-                )}${this._asSentence(fields.note)}`;
+                )}${this.asSentence(fields.note)}`;
             }
             if (fields.doi) {
                 ref += `[<a href="https://doi.org/${fields.doi}" target="_blank">doi:${fields.doi}</a>]`;
@@ -190,7 +185,7 @@ export default {
             }
             return convertLaTeX({ onError: (error, latex) => `{${stringifyLaTeX(latex)}}` }, ref);
         },
-        _formatBookInfo: function(fields) {
+        formatBookInfo(fields) {
             let info = "";
             if (fields.chapter) {
                 info += `${fields.chapter} in `;
@@ -218,10 +213,10 @@ export default {
             }
             return `${info}.`;
         },
-        _asSentence: function(str) {
+        asSentence(str) {
             return str && str.trim() ? `${str}. ` : "";
         },
-        toggleViewRender: function() {
+        toggleViewRender() {
             this.viewRender = !this.viewRender;
         }
     }
diff --git a/client/galaxy/scripts/components/ToolsView.vue b/client/galaxy/scripts/components/ToolsView.vue
index efa6f531cd8a..950999c93087 100644
--- a/client/galaxy/scripts/components/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView.vue
@@ -26,9 +26,9 @@
             <isotope
                 ref="iso"
                 :options="isoOptions"
-                @filter="filterOption = arguments[2]"
                 :list="buffer"
                 style="margin: 0 auto;"
+                @filter="filterOption = arguments[2]"
             >
                 <b-card v-for="(info, index) in buffer" :key="index" ref="cards" class="m-2" style="width: 23rem;">
                     <div slot="header">
@@ -47,13 +47,13 @@
                         </b-modal>
                     </p>
                     <Citations
+                        :id="info['id']"
                         simple
                         source="tools"
                         @rendered="layout"
                         @show="show(index)"
                         @shown="shown(index)"
                         @hidden="hidden(index)"
-                        :id="info['id']"
                     />
                 </b-card>
             </isotope>
@@ -101,12 +101,24 @@ export default {
                 getFilterData: {
                     filterByText: el => {
                         const re = new RegExp(this.filterText, "i");
-                        return el["name"].match(re) || el["description"].match(re) || el["help"].match(re);
+                        return el.name.match(re) || el.description.match(re) || el.help.match(re);
                     }
                 }
             };
         }
     },
+    created() {
+        axios
+            .get(`${getAppRoot()}api/tools?tool_help=True`)
+            .then(response => {
+                this.tools = this.toolsExtracted(response.data);
+                this.buffer = this.tools.slice(0, 20);
+                this.loading = false;
+            })
+            .catch(error => {
+                console.error(error);
+            });
+    },
     methods: {
         show(index) {
             this.$refs.cards[index].style.zIndex = "1";
@@ -129,26 +141,25 @@ export default {
         toolsExtracted(tools) {
             function extractSections(acc, section) {
                 function extractTools(_acc, tool) {
-                    return tool["name"]
+                    return tool.name
                         ? [
                               ..._acc,
                               {
-                                  id: tool["id"],
-                                  name: tool["name"],
-                                  section: section["name"],
-                                  description: tool["description"],
-                                  url: getAppRoot() + String(tool["link"]).substring(1),
-                                  version: tool["version"],
-                                  help: tool["help"]
+                                  id: tool.id,
+                                  name: tool.name,
+                                  section: section.name,
+                                  description: tool.description,
+                                  url: getAppRoot() + String(tool.link).substring(1),
+                                  version: tool.version,
+                                  help: tool.help
                               }
                           ]
                         : _acc;
                 }
                 if ("elems" in section) {
-                    return acc.concat(section["elems"].reduce(extractTools, []));
-                } else {
-                    return acc;
+                    return acc.concat(section.elems.reduce(extractTools, []));
                 }
+                return acc;
             }
             return tools
                 .reduce(extractSections, [])
@@ -178,27 +189,13 @@ export default {
                 .singleNodeValue;
             if (match) {
                 return match.innerHTML;
-            } else {
-                const helpText = helpDoc.documentElement.textContent;
-                if (helpText) {
-                    return helpText.substring(0, helpText.indexOf("\n\n"));
-                } else {
-                    return null;
-                }
             }
+            const helpText = helpDoc.documentElement.textContent;
+            if (helpText) {
+                return helpText.substring(0, helpText.indexOf("\n\n"));
+            }
+            return null;
         }
-    },
-    created() {
-        axios
-            .get(`${getAppRoot()}api/tools?tool_help=True`)
-            .then(response => {
-                this.tools = this.toolsExtracted(response.data);
-                this.buffer = this.tools.slice(0, 20);
-                this.loading = false;
-            })
-            .catch(error => {
-                console.error(error);
-            });
     }
 };
 </script>

From 6ac30321df94d5db28dee4b3341ac0a36d950413 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Mon, 27 Jan 2020 15:44:51 +0100
Subject: [PATCH 443/853] show number of availabke tools, hide side panel

---
 client/galaxy/scripts/components/Panels/SidePanel.vue  | 8 ++++++++
 client/galaxy/scripts/components/ToolsView.vue         | 5 ++++-
 client/galaxy/scripts/entry/analysis/AnalysisRouter.js | 4 ++--
 3 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/components/Panels/SidePanel.vue b/client/galaxy/scripts/components/Panels/SidePanel.vue
index 4c087659ad4e..85e232d0c932 100644
--- a/client/galaxy/scripts/components/Panels/SidePanel.vue
+++ b/client/galaxy/scripts/components/Panels/SidePanel.vue
@@ -84,6 +84,14 @@ export default {
                     document.getElementById("center").style.transition = "";
                 }, 250);
             }
+        },
+        hide() {
+            this.show = false;
+            document.getElementById("center").style.transition = `${this.side} 200ms linear`;
+            document.getElementById("center").style[this.side] = "0";
+            setTimeout(() => {
+                document.getElementById("center").style.transition = "";
+            }, 250);
         }
     }
 };
diff --git a/client/galaxy/scripts/components/ToolsView.vue b/client/galaxy/scripts/components/ToolsView.vue
index 950999c93087..451482971c8c 100644
--- a/client/galaxy/scripts/components/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView.vue
@@ -1,7 +1,7 @@
 <template>
     <div v-infinite-scroll="loadMore" infinite-scroll-disabled="busy">
         <h2 class="mb-3" style="text-align: center">
-            <span id="tools-view">Tools View</span>
+            <span id="tools-view">Consolidated view of {{tools.length}} available tools.</span>
         </h2>
         <div v-if="!loading">
             <b-container fluid class="mb-4">
@@ -195,6 +195,9 @@ export default {
                 return helpText.substring(0, helpText.indexOf("\n\n"));
             }
             return null;
+        },
+        getToolsNumber(){
+            return this.tools.length;
         }
     }
 };
diff --git a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
index 199b4945f516..56d89ff4c80f 100644
--- a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
+++ b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
@@ -245,9 +245,9 @@ export const getAnalysisRouter = Galaxy =>
         show_histories_import: function() {
             this._display_vue_helper(HistoryImport);
         },
-
+    
         show_tools_view: function() {
-            this.page.panels.left.hide();
+            this.page.toolPanel.getVueComponent().hide();
             this.page.panels.right.hide();
             this._display_vue_helper(ToolsView);
         },

From b631584111e3ffccb848f40c273a0adc7abff989 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Tue, 28 Jan 2020 16:38:13 +0100
Subject: [PATCH 444/853] Fix properties access. replace brackets with dots

---
 client/galaxy/scripts/components/ToolsJson.vue | 12 ++++++------
 client/galaxy/scripts/components/ToolsView.vue | 18 +++++++++---------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolsJson.vue b/client/galaxy/scripts/components/ToolsJson.vue
index 0772b80d2435..5f393fce8ba7 100644
--- a/client/galaxy/scripts/components/ToolsJson.vue
+++ b/client/galaxy/scripts/components/ToolsJson.vue
@@ -10,23 +10,23 @@ export default {
         createToolsJson(tools) {
             function extractSections(acc, section) {
                 function extractTools(_acc, tool) {
-                    return tool["name"]
+                    return tool.name
                         ? [
                               ..._acc,
                               {
                                   "@type": "SoftwareApplication",
                                   operatingSystem: "Any",
                                   applicationCategory: "Web application",
-                                  name: tool["name"],
-                                  description: tool["help"] || tool["description"],
-                                  softwareVersion: tool["version"],
-                                  url: getAppRoot() + String(tool["link"]).substring(1)
+                                  name: tool.name,
+                                  description: tool.help || tool.description,
+                                  softwareVersion: tool.version,
+                                  url: getAppRoot() + String(tool.link).substring(1)
                               }
                           ]
                         : _acc;
                 }
                 if ("elems" in section) {
-                    return acc.concat(section["elems"].reduce(extractTools, []));
+                    return acc.concat(section.elems.reduce(extractTools, []));
                 } else {
                     return acc;
                 }
diff --git a/client/galaxy/scripts/components/ToolsView.vue b/client/galaxy/scripts/components/ToolsView.vue
index 451482971c8c..3e68555a0001 100644
--- a/client/galaxy/scripts/components/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView.vue
@@ -32,22 +32,22 @@
             >
                 <b-card v-for="(info, index) in buffer" :key="index" ref="cards" class="m-2" style="width: 23rem;">
                     <div slot="header">
-                        <b-link :href="info['url']" target="_blank">
-                            <h4 class="tools-view-name">{{ info["name"] }}</h4>
+                        <b-link :href="info.url" target="_blank">
+                            <h4 class="tools-view-name">{{ info.name }}</h4>
                         </b-link>
-                        <b-badge class="tools-view-section">{{ info["section"] }}</b-badge>
+                        <b-badge class="tools-view-section">{{ info.section }}</b-badge>
                     </div>
-                    <p class="card-text" v-html="helpSummary(info['help']) || info['description']" />
+                    <p class="card-text" v-html="helpSummary(info.help) || info.description" />
                     <p class="card-text">
                         <b-btn v-b-modal="'modal-' + '-' + index">Info</b-btn>
-                        <b-modal :id="'modal-' + '-' + index" centered :title="info['name']">
-                            <b>{{ info["version"] + " / " + info["id"] }}</b>
-                            <p>{{ info["description"] }}</p>
-                            <p v-html="info['help']"></p>
+                        <b-modal :id="'modal-' + '-' + index" centered :title="info.name">
+                            <b>{{ info.version + " / " + info.id }}</b>
+                            <p>{{ info.description }}</p>
+                            <p v-html="info.help"></p>
                         </b-modal>
                     </p>
                     <Citations
-                        :id="info['id']"
+                        :id="info.id"
                         simple
                         source="tools"
                         @rendered="layout"

From 12864b10731f43aecbe88ee10ce07e2b3ccd85b5 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Wed, 29 Jan 2020 17:07:26 +0100
Subject: [PATCH 445/853] Move ToolView to a package, create initizalize method
 for easier testing, hide cancel button in info modal

---
 .../components/{ => ToolsView}/ToolsView.vue       | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)
 rename client/galaxy/scripts/components/{ => ToolsView}/ToolsView.vue (96%)

diff --git a/client/galaxy/scripts/components/ToolsView.vue b/client/galaxy/scripts/components/ToolsView/ToolsView.vue
similarity index 96%
rename from client/galaxy/scripts/components/ToolsView.vue
rename to client/galaxy/scripts/components/ToolsView/ToolsView.vue
index 3e68555a0001..8e706ee4db7d 100644
--- a/client/galaxy/scripts/components/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView/ToolsView.vue
@@ -39,8 +39,8 @@
                     </div>
                     <p class="card-text" v-html="helpSummary(info.help) || info.description" />
                     <p class="card-text">
-                        <b-btn v-b-modal="'modal-' + '-' + index">Info</b-btn>
-                        <b-modal :id="'modal-' + '-' + index" centered :title="info.name">
+                        <b-btn v-b-modal="'modal-' + '-' + index" >Info</b-btn>
+                        <b-modal :id="'modal-' + '-' + index" centered ok-only :title="info.name">
                             <b>{{ info.version + " / " + info.id }}</b>
                             <p>{{ info.description }}</p>
                             <p v-html="info.help"></p>
@@ -111,9 +111,8 @@ export default {
         axios
             .get(`${getAppRoot()}api/tools?tool_help=True`)
             .then(response => {
-                this.tools = this.toolsExtracted(response.data);
-                this.buffer = this.tools.slice(0, 20);
-                this.loading = false;
+                this.initialize(response.data);
+
             })
             .catch(error => {
                 console.error(error);
@@ -198,6 +197,11 @@ export default {
         },
         getToolsNumber(){
             return this.tools.length;
+        },
+        initialize(tools){
+            this.tools = this.toolsExtracted(tools);
+            this.buffer = this.tools.slice(0, 20);
+            this.loading = false;
         }
     }
 };

From 8d69237c9faaccc856975672c7f73696731f5471 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Fri, 31 Jan 2020 18:20:08 +0100
Subject: [PATCH 446/853] implement ToolsView.test.js, run prettier, make
 ToolsView.vue a bit more testable

---
 .../SelectionDialog/WorkflowDialog.test.js    |    4 +-
 .../components/ToolsView/ToolsView.test.js    |   59 +
 .../components/ToolsView/ToolsView.vue        |   11 +-
 .../ToolsView/testData/toolsList.json         | 1810 +++++++++++++++++
 .../scripts/entry/analysis/AnalysisRouter.js  |    4 +-
 5 files changed, 1878 insertions(+), 10 deletions(-)
 create mode 100644 client/galaxy/scripts/components/ToolsView/ToolsView.test.js
 create mode 100644 client/galaxy/scripts/components/ToolsView/testData/toolsList.json

diff --git a/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js b/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js
index 556054a438c9..1f1b1a77d4b5 100644
--- a/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js
+++ b/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js
@@ -34,7 +34,7 @@ describe("WorkflowDialog.vue", () => {
 
     it("loads correctly in loading state, shows options when optionsShow becomes true", async () => {
         // Initially in loading state.
-        const workflowsResponse = [{ id: "f2db41e1fa331b3e", name: "Awesome Workflow" }];
+        const workflowsResponse = [{ id: "f2db41e1fa331b3e", name: "Awesom e Workflow" }];
         axiosMock.onGet("/api/workflows").reply(200, workflowsResponse);
 
         expect(wrapper.find(SelectionDialog).is(SelectionDialog)).to.equals(true);
@@ -44,7 +44,7 @@ describe("WorkflowDialog.vue", () => {
         await localVue.nextTick();
         await localVue.nextTick();
 
-        // why not shown?
+        // why not shown?xios-mock-adapter
         expect(wrapper.vm.errorMessage).to.equals(null);
         expect(wrapper.vm.optionsShow).to.equals(true);
     });
diff --git a/client/galaxy/scripts/components/ToolsView/ToolsView.test.js b/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
new file mode 100644
index 000000000000..189ed9831832
--- /dev/null
+++ b/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
@@ -0,0 +1,59 @@
+/* global expect */
+import ToolsView from "./ToolsView";
+import { shallowMount, mount, createLocalVue } from "@vue/test-utils";
+import _l from "utils/localization";
+import Vue from "vue";
+
+// test response
+import testToolsListResponse from "./testData/toolsList";
+import MockAdapter from "axios-mock-adapter";
+import axios from "axios";
+
+describe("ToolsView/ToolsView.vue", () => {
+    const localVue = createLocalVue();
+    localVue.filter("localize", value => _l(value));
+    let wrapper, emitted, axiosMock;
+
+    beforeEach(async () => {
+        axiosMock = new MockAdapter(axios);
+        // using shallow because of inner 'Citation' component
+        wrapper = mount(ToolsView);
+        emitted = wrapper.emitted();
+        axiosMock.onGet("/api/tools?tool_help=True").reply(200, testToolsListResponse);
+        await Vue.nextTick();
+        await Vue.nextTick();
+    });
+
+    afterEach(() => {
+        axiosMock.restore();
+    });
+
+    it("should render infinite scroll div", async () => {
+        expect(wrapper.html()).contain('<div infinite-scroll-disabled="busy">');
+    });
+
+    it("should return defined number of tools", async () => {
+        assert(wrapper.vm.getToolsNumber() === 84, "Tools Get Response is not parsed correctly!");
+    });
+
+    it("should render only specific number of tools, equal to current buffer", async () => {
+        let buttons = wrapper.findAll('[type="button"]').filter(button => button.text() === "Info");
+        // one 'info' button per tool
+        assert(wrapper.vm.buffer.length === buttons.length, "Number of 'info' buttons do not equal the buffer size!");
+    });
+    it("should open modal on button click", async () => {
+        // findAll() returns WrapperArray, thus regular array.find() won't work
+        let infoButton = wrapper
+            .findAll('[type="button"]')
+            .filter(button => button.text() === "Info")
+            .at(0);
+        const modalId = "modal--" + infoButton.attributes().index;
+        const modal = wrapper.find("#" + modalId);
+        assert(modal.isVisible() === false, "modal is visible before the click!");
+
+        infoButton.trigger("click");
+        await Vue.nextTick();
+
+        assert(modal.isVisible(), "'Info' button didn't open a modal!");
+    });
+});
diff --git a/client/galaxy/scripts/components/ToolsView/ToolsView.vue b/client/galaxy/scripts/components/ToolsView/ToolsView.vue
index 8e706ee4db7d..fa3c43fcd4c0 100644
--- a/client/galaxy/scripts/components/ToolsView/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView/ToolsView.vue
@@ -1,7 +1,7 @@
 <template>
     <div v-infinite-scroll="loadMore" infinite-scroll-disabled="busy">
         <h2 class="mb-3" style="text-align: center">
-            <span id="tools-view">Consolidated view of {{tools.length}} available tools.</span>
+            <span id="tools-view">Consolidated view of {{ tools.length }} available tools.</span>
         </h2>
         <div v-if="!loading">
             <b-container fluid class="mb-4">
@@ -39,8 +39,8 @@
                     </div>
                     <p class="card-text" v-html="helpSummary(info.help) || info.description" />
                     <p class="card-text">
-                        <b-btn v-b-modal="'modal-' + '-' + index" >Info</b-btn>
-                        <b-modal :id="'modal-' + '-' + index" centered ok-only :title="info.name">
+                        <b-btn :index="index" v-b-modal="'modal-' + '-' + index">Info</b-btn>
+                        <b-modal :id="'modal-' + '-' + index" centered ok-only :static="true" :title="info.name">
                             <b>{{ info.version + " / " + info.id }}</b>
                             <p>{{ info.description }}</p>
                             <p v-html="info.help"></p>
@@ -112,7 +112,6 @@ export default {
             .get(`${getAppRoot()}api/tools?tool_help=True`)
             .then(response => {
                 this.initialize(response.data);
-
             })
             .catch(error => {
                 console.error(error);
@@ -195,10 +194,10 @@ export default {
             }
             return null;
         },
-        getToolsNumber(){
+        getToolsNumber() {
             return this.tools.length;
         },
-        initialize(tools){
+        initialize(tools) {
             this.tools = this.toolsExtracted(tools);
             this.buffer = this.tools.slice(0, 20);
             this.loading = false;
diff --git a/client/galaxy/scripts/components/ToolsView/testData/toolsList.json b/client/galaxy/scripts/components/ToolsView/testData/toolsList.json
new file mode 100644
index 000000000000..8f644230acd8
--- /dev/null
+++ b/client/galaxy/scripts/components/ToolsView/testData/toolsList.json
@@ -0,0 +1,1810 @@
+[
+  {
+    "elems": [
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "from your computer",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "<p><strong>Auto-detect<\/strong><\/p>\n<p>The system will attempt to detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular, Wiggle, Bed and Interval (Bed with headers) formats. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be.  You can also upload compressed files, which will automatically be decompressed.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Ab1<\/strong><\/p>\n<p>A binary sequence file in 'ab1' format with a '.ab1' file extension.  You must manually select this 'File Format' when uploading the file.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Axt<\/strong><\/p>\n<p>blastz pairwise alignment format.  Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines.  Blocks are separated from one another by blank lines.  The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Bam<\/strong><\/p>\n<p>A binary file compressed in the BGZF format with a '.bam' file extension.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Bed<\/strong><\/p>\n<ul>\n<li><p class=\"first\">Tab delimited format (tabular)<\/p>\n<\/li>\n<li><p class=\"first\">Does not require header line<\/p>\n<\/li>\n<li><p class=\"first\">Contains 3 required fields:<\/p>\n<ul class=\"simple\">\n<li>chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or contig (e.g. ctgY1).<\/li>\n<li>chromStart - The starting position of the feature in the chromosome or contig. The first base in a chromosome is numbered 0.<\/li>\n<li>chromEnd - The ending position of the feature in the chromosome or contig. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.<\/li>\n<\/ul>\n<\/li>\n<li><p class=\"first\">May contain 9 additional optional BED fields:<\/p>\n<ul class=\"simple\">\n<li>name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.<\/li>\n<li>score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray).<\/li>\n<li>strand - Defines the strand - either '+' or '-'.<\/li>\n<li>thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays).<\/li>\n<li>thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).<\/li>\n<li>itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to &quot;On&quot;, this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.<\/li>\n<li>blockCount - The number of blocks (exons) in the BED line.<\/li>\n<li>blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.<\/li>\n<li>blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.<\/li>\n<\/ul>\n<\/li>\n<li><p class=\"first\">Example:<\/p>\n<pre class=\"literal-block\">\nchr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512\nchr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601\n<\/pre>\n<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Fasta<\/strong><\/p>\n<p>A sequence in FASTA format consists of a single-line description, followed by lines of sequence data.  The first character of the description line is a greater-than (&quot;&gt;&quot;) symbol in the first column.  All lines should be shorter than 80 characters:<\/p>\n<pre class=\"literal-block\">\n&gt;sequence1\natgcgtttgcgtgc\ngtcggtttcgttgc\n&gt;sequence2\ntttcgtgcgtatag\ntggcgcggtga\n<\/pre>\n<hr class=\"docutils\" />\n<p><strong>FastqSolexa<\/strong><\/p>\n<p>FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file:<\/p>\n<pre class=\"literal-block\">\n&#64;seq1\nGACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT\n+seq1\nhhhhhhhhhhhhhhhhhhhhhhhhhhPW&#64;hhhhhh\n&#64;seq2\nGCAATGACGGCAGCAATAAACTCAACAGGTGCTGG\n+seq2\nhhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO\n<\/pre>\n<p>Or:<\/p>\n<pre class=\"literal-block\">\n&#64;seq1\nGAATTGATCAGGACATAGGACAACTGTAGGCACCAT\n+seq1\n40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4\n&#64;seq2\nGAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG\n+seq2\n40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9\n<\/pre>\n<hr class=\"docutils\" />\n<p><strong>Gff<\/strong><\/p>\n<p>GFF lines have nine required fields that must be tab-separated.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Gff3<\/strong><\/p>\n<p>The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Interval (Genomic Intervals)<\/strong><\/p>\n<ul>\n<li><p class=\"first\">Tab delimited format (tabular)<\/p>\n<\/li>\n<li><p class=\"first\">File must start with definition line in the following format (columns may be in any order).:<\/p>\n<pre class=\"literal-block\">\n#CHROM START END STRAND\n<\/pre>\n<\/li>\n<li><p class=\"first\">CHROM - The name of the chromosome (e.g. chr3, chrY, chr2_random) or contig (e.g. ctgY1).<\/p>\n<\/li>\n<li><p class=\"first\">START - The starting position of the feature in the chromosome or contig. The first base in a chromosome is numbered 0.<\/p>\n<\/li>\n<li><p class=\"first\">END - The ending position of the feature in the chromosome or contig. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.<\/p>\n<\/li>\n<li><p class=\"first\">STRAND - Defines the strand - either '+' or '-'.<\/p>\n<\/li>\n<li><p class=\"first\">Example:<\/p>\n<pre class=\"literal-block\">\n#CHROM START END   STRAND NAME COMMENT\nchr1   10    100   +      exon myExon\nchrX   1000  10050 -      gene myGene\n<\/pre>\n<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Lav<\/strong><\/p>\n<p>Lav is the primary output format for BLASTZ.  The first line of a .lav file begins with #:lav..<\/p>\n<hr class=\"docutils\" />\n<p><strong>MAF<\/strong><\/p>\n<p>TBA and multiz multiple alignment format.  The first line of a .maf file begins with ##maf. This word is followed by white-space-separated &quot;variable=value&quot; pairs. There should be no white space surrounding the &quot;=&quot;.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Scf<\/strong><\/p>\n<p>A binary sequence file in 'scf' format with a '.scf' file extension.  You must manually select this 'File Format' when uploading the file.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Sff<\/strong><\/p>\n<p>A binary file in 'Standard Flowgram Format' with a '.sff' file extension.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Tabular (tab delimited)<\/strong><\/p>\n<p>Any data in tab delimited format (tabular)<\/p>\n<hr class=\"docutils\" />\n<p><strong>Table (delimiter-separated)<\/strong><\/p>\n<p>Any delimiter-separated tabular data (CSV or TSV).<\/p>\n<hr class=\"docutils\" />\n<p><strong>Wig<\/strong><\/p>\n<p>The wiggle format is line-oriented.  Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Other text type<\/strong><\/p>\n<p>Any text file<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.1.6",
+        "link": "/tool_runner?tool_id=upload1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "upload1",
+        "name": "Upload File"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "table browser",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.0",
+        "link": "/tool_runner/data_source_redirect?tool_id=ucsc_table_direct1",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "ucsc_table_direct1",
+        "name": "UCSC Main"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "table browser",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.0",
+        "link": "/tool_runner/data_source_redirect?tool_id=ucsc_table_direct_archaea1",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "ucsc_table_direct_archaea1",
+        "name": "UCSC Archaea"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "ENA SRA",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.1",
+        "link": "/tool_runner/data_source_redirect?tool_id=ebi_sra_main",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "ebi_sra_main",
+        "name": "EBI SRA"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "server",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.1",
+        "link": "/tool_runner/data_source_redirect?tool_id=modENCODEfly",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "modENCODEfly",
+        "name": "modENCODE fly"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "server",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.0",
+        "link": "/tool_runner/data_source_redirect?tool_id=intermine",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "intermine",
+        "name": "InterMine"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "server",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.0",
+        "link": "/tool_runner/data_source_redirect?tool_id=flymine",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "flymine",
+        "name": "Flymine"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "server",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.0",
+        "link": "/tool_runner/data_source_redirect?tool_id=modmine",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "modmine",
+        "name": "modENCODE modMine"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "server",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.0",
+        "link": "/tool_runner/data_source_redirect?tool_id=mousemine",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "mousemine",
+        "name": "MouseMine"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "server",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.0",
+        "link": "/tool_runner/data_source_redirect?tool_id=ratmine",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "ratmine",
+        "name": "Ratmine"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "server",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.0",
+        "link": "/tool_runner/data_source_redirect?tool_id=yeastmine",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "yeastmine",
+        "name": "YeastMine"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "server",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.1",
+        "link": "/tool_runner/data_source_redirect?tool_id=modENCODEworm",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "modENCODEworm",
+        "name": "modENCODE worm"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "server",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.1",
+        "link": "/tool_runner/data_source_redirect?tool_id=wormbase",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "wormbase",
+        "name": "WormBase"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "server",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.0",
+        "link": "/tool_runner/data_source_redirect?tool_id=zebrafishmine",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "zebrafishmine",
+        "name": "ZebrafishMine"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "server",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "1.0.0",
+        "link": "/tool_runner/data_source_redirect?tool_id=eupathdb",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "eupathdb",
+        "name": "EuPathDB"
+      },
+      {
+        "panel_section_name": "Get Data",
+        "xrefs": [],
+        "description": "Human Hemoglobin Variants and Thalassemias",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "getext",
+        "version": "2.0.0",
+        "link": "/tool_runner/data_source_redirect?tool_id=hbvar",
+        "target": "_top",
+        "min_width": "800",
+        "model_class": "DataSourceTool",
+        "hidden": "",
+        "id": "hbvar",
+        "name": "HbVar"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "getext",
+    "name": "Get Data"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Send Data",
+        "xrefs": [],
+        "description": "",
+        "is_workflow_compatible": false,
+        "labels": [],
+        "help": "<dl class=\"docutils\">\n<dt><strong>What it does<\/strong><\/dt>\n<dd><p class=\"first\">Send dataset(s) from Galaxy to cloud-based storage (e.g., AWS S3).<\/p>\n<p class=\"last\">Supply a name of the target bucket where the data will be sent along\nwith an id for the desired cloud authorization. To get the list of Cloud\nAuthorization IDs available for your account, visit <cite>/api/cloud/authz<\/cite>.<\/p>\n<\/dd>\n<dt><strong>Remarks<\/strong><\/dt>\n<dd><p class=\"first\">This tool leverages OpenID Connect protocol and CloudAuthz (<a class=\"reference external\" href=\"https://github.com/galaxyproject/cloudauthz\">https://github.com/galaxyproject/cloudauthz<\/a>)\nto access cloud-based resources without requiring user credentials.<\/p>\n<p class=\"last\">If selecting multiple datasets, make sure each dataset is named\ndifferently; otherwise, only one copy of the selected datasets will be\ncopied.<\/p>\n<\/dd>\n<\/dl>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "send",
+        "version": "0.1.0",
+        "link": "/tool_runner?tool_id=send_to_cloud",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "send_to_cloud",
+        "name": "Send to cloud"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "send",
+    "name": "Send Data"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p>This tool takes a paired dataset collection and builds two datasets from it. If mapped over a list of paired datasets, this tool will produce two lists of datasets.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>If a collection consists of two forward and two reverse datasets (e.g., forward and reverse reads from a sequencing experiment) this tool will output two collections: one consisting of forward reads and one of reverse reads.<\/p>\n<p class=\"infomark\">This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__UNZIP_COLLECTION__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "UnzipCollectionTool",
+        "hidden": "",
+        "id": "__UNZIP_COLLECTION__",
+        "name": "Unzip Collection"
+      },
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p>This tool takes two datasets and creates a dataset pair from them. Mapping over two lists, this tool can be used to build a list of dataset pairs from two individual lists of datasets.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>If you have one collection containing only forward reads and one containing only reverse, this tools will &quot;zip&quot; them together into a simple paired collection.<\/p>\n<p class=\"infomark\">This tool will create new history datasets for your collection but your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__ZIP_COLLECTION__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "ZipCollectionTool",
+        "hidden": "",
+        "id": "__ZIP_COLLECTION__",
+        "name": "Zip Collection"
+      },
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "datasets from a collection",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p>This tool takes a dataset collection and filters out datasets in the failed state. This is useful for continuing a multi-sample analysis when one of more of the samples fails at some point.<\/p>\n<p class=\"infomark\">This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__FILTER_FAILED_DATASETS__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "FilterFailedDatasetsTool",
+        "hidden": "",
+        "id": "__FILTER_FAILED_DATASETS__",
+        "name": "Filter failed"
+      },
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "datasets from a collection",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p>This tool takes a dataset collection and filters out empty datasets. This is useful for continuing a multi-sample analysis when downstream tools require datasets to have content.<\/p>\n<p class=\"infomark\">This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__FILTER_EMPTY_DATASETS__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "FilterEmptyDatasetsTool",
+        "hidden": "",
+        "id": "__FILTER_EMPTY_DATASETS__",
+        "name": "Filter empty"
+      },
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "into a flat list of datasets",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p>This tool takes nested collections such as a list of lists or a list of dataset pairs - and produces a flat list from the inputs. The collection identifiers are merged together to create new collection identifiers in the flattened result.<\/p>\n<p class=\"infomark\">This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__FLATTEN__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "FlattenTool",
+        "hidden": "",
+        "id": "__FLATTEN__",
+        "name": "Flatten Collection"
+      },
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "into single list of datasets",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p>This tool takes two lists and creates a single unified list.<\/p>\n<p class=\"infomark\">This tool will create new history datasets for your collection but your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__MERGE_COLLECTION__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "MergeCollectionTool",
+        "hidden": "",
+        "id": "__MERGE_COLLECTION__",
+        "name": "Merge Collections"
+      },
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "from contents of a file",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\">This tool will take an input list and a text file with new identifiers\nand build a new list with the same datasets but these new identifiers.\nThe order and number of entries in the text file must match the order\nof the items you want to rename in your dataset collection.<\/p>\n<p class=\"infomark\">Alternatively a tabular file may be supplied, where the first column\nif the current identifier that should be renamed, and the second column\ncontains the new label. This file may contain less entries than items\nin the collection. In that case only matching list identifiers will be\nrelabeled.<\/p>\n<p class=\"infomark\">Valid identifiers must contain only characters (a-z, A-Z), numbers (0-9),\ndash and underscore (-, _). Punctuation or whitespace are not allowed.<\/p>\n<p class=\"infomark\">This tool will create new history datasets from your collection\nbut your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__RELABEL_FROM_FILE__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "RelabelFromFileTool",
+        "hidden": "",
+        "id": "__RELABEL_FROM_FILE__",
+        "name": "Relabel List Identifiers"
+      },
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "from contents of a file",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\">This tool will take an input list and a text file with\nnames (i.e. identifiers). It will split the input list into\ntwo new lists - one filtered to contain only the list members\nwhose names are listed in the text file, and one containing\nall the other elements.<\/p>\n<p class=\"infomark\">This tool will create new history datasets from your collection\nbut your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__FILTER_FROM_FILE__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "FilterFromFileTool",
+        "hidden": "",
+        "id": "__FILTER_FROM_FILE__",
+        "name": "Filter List"
+      },
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "of list of datasets",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p>This tool takes list-type collections - and produces a sorted ist from the inputs. The collection identifiers are sorted either alphabetically or numerically (where the characters other than 0-9 are stripped before sorting).<\/p>\n<p class=\"infomark\">This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__SORTLIST__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "SortTool",
+        "hidden": "",
+        "id": "__SORTLIST__",
+        "name": "Sort Collection"
+      },
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "from contents of a file",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\">This tool will take an input collection and a tabular file,\nwhere the first column indicates an element identifier and the\nremaining columns contains the new tags. This file may contain\nless entries than elements in the collection.\nIn that case only matching list identifiers will be tagged.<\/p>\n<p class=\"infomark\">This tool will create new history datasets from your collection\nbut your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__TAG_FROM_FILE__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "TagFromFileTool",
+        "hidden": "",
+        "id": "__TAG_FROM_FILE__",
+        "name": "Tag elements from file"
+      },
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p>This tool allows one to process an existing Galaxy dataset collection's metadata as tabular data,\napply a series of rules to it, and generate a new collection. When used interactively in the tool\nform, a dynamic preview of the processing will be available in a tabular data viewer but this tool\nmay be used in workflows as well where no such preview can be generated.<\/p>\n<p>This tool is an advanced feature but has a lot of flexibility - it can be used to process collections\nwith arbitrary nesting and can do many kinds of filtering, re-sorting, nesting,\nflattening, and arbitrary combinations thereof not possible with Galaxy's other, more simple\ncollection operation tools.<\/p>\n<p>More information about the rule processor in general can be found <a class=\"reference external\" href=\"https://github.com/jmchilton/training-material/blob/rules/topics/introduction/tutorials/galaxy-intro-rules/tutorial.md\">here<\/a> (this link is to documentation that is pretty rough still).<\/p>\n<p class=\"infomark\">This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__APPLY_RULES__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "ApplyRulesTool",
+        "hidden": "",
+        "id": "__APPLY_RULES__",
+        "name": "Apply Rule to Collection"
+      },
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "from one or more datasets",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\">This tool will create a new collection from your history datasets but your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__BUILD_LIST__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "BuildListCollectionTool",
+        "hidden": "",
+        "id": "__BUILD_LIST__",
+        "name": "Build List"
+      },
+      {
+        "panel_section_name": "Collection Operations",
+        "xrefs": [],
+        "description": "from a list",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\">This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "collection_operations",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=__EXTRACT_DATASET__",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "ExtractDatasetCollectionTool",
+        "hidden": "",
+        "id": "__EXTRACT_DATASET__",
+        "name": "Extract Dataset"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "collection_operations",
+    "name": "Collection Operations"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Expression Tools",
+        "xrefs": [],
+        "description": "from dataset",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "",
+        "edam_operations": [],
+        "form_style": "special",
+        "edam_topics": [],
+        "panel_section_id": "expression_tools",
+        "version": "0.1.0",
+        "link": "/tool_runner?tool_id=param_value_from_file",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "ExpressionTool",
+        "hidden": "",
+        "id": "param_value_from_file",
+        "name": "Parse parameter value"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "expression_tools",
+    "name": "Expression Tools"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Lift-Over",
+        "xrefs": [],
+        "description": "between assemblies and genomes",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"warningmark\">Make sure that the genome build of the input dataset is specified (click the pencil icon in the history item to set it if necessary).<\/p>\n<p class=\"warningmark\">This tool can work with interval, GFF, and GTF datasets. It requires the interval datasets to have chromosome in column 1,\nstart co-ordinate in column 2 and end co-ordinate in column 3. BED comments\nand track and browser lines will be ignored, but if other non-interval lines\nare present the tool will return empty output datasets.<\/p>\n<hr class=\"docutils\" />\n<p class=\"infomark\"><strong>What it does<\/strong><\/p>\n<p>This tool is based on the LiftOver utility and Chain track from <a class=\"reference external\" href=\"http://genome.ucsc.edu/\">the UC Santa Cruz Genome Browser<\/a>.<\/p>\n<p>It converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any.<\/p>\n<blockquote>\n<\/blockquote>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Converting the following hg16 intervals to hg18 intervals:<\/p>\n<pre class=\"literal-block\">\nchrX  85170   112199  AK002185  0  +\nchrX  110458  112199  AK097346  0  +\nchrX  112203  121212  AK074528  0  -\n<\/pre>\n<p>will produce the following hg18 intervals:<\/p>\n<pre class=\"literal-block\">\nchrX  132991  160020  AK002185  0  +\nchrX  158279  160020  AK097346  0  +\nchrX  160024  169033  AK074528  0  -\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "liftOver",
+        "version": "1.0.6",
+        "link": "/tool_runner?tool_id=liftOver1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "liftOver1",
+        "name": "Convert genome coordinates"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "liftOver",
+    "name": "Lift-Over"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "to an existing dataset",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\"><strong>TIP:<\/strong> If your data is not TAB delimited, use <em>Text Manipulation-&gt;Convert<\/em><\/p>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>You can enter any value and it will be added as a new column to your dataset<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>If your original data looks like this:<\/p>\n<pre class=\"literal-block\">\nchr1 10  100 geneA\nchr2 200 300 geneB\nchr2 400 500 geneC\n<\/pre>\n<p>Typing <strong>+<\/strong> in the text box will generate:<\/p>\n<pre class=\"literal-block\">\nchr1 10  100 geneA +\nchr2 200 300 geneB +\nchr2 400 500 geneC +\n<\/pre>\n<p>You can also add line numbers by selecting <strong>Iterate: YES<\/strong>. In this case if you enter <strong>1<\/strong> in the text box you will get:<\/p>\n<pre class=\"literal-block\">\nchr1 10  100 geneA 1\nchr2 200 300 geneB 2\nchr2 400 500 geneC 3\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=addValue",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "addValue",
+        "name": "Add column"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "tail-to-head",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"warningmark\"><strong>WARNING:<\/strong> Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format.<\/p>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>Concatenates datasets<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Concatenating Dataset:<\/p>\n<pre class=\"literal-block\">\nchrX  151087187  151087355  A  0  -\nchrX  151572400  151572481  B  0  +\n<\/pre>\n<p>with Dataset1:<\/p>\n<pre class=\"literal-block\">\nchr1  151242630  151242955  X  0  +\nchr1  151271715  151271999  Y  0  +\nchr1  151278832  151279227  Z  0  -\n<\/pre>\n<p>and with Dataset2:<\/p>\n<pre class=\"literal-block\">\nchr2  100000030  200000955  P  0  +\nchr2  100000015  200000999  Q  0  +\n<\/pre>\n<p>will result in the following:<\/p>\n<pre class=\"literal-block\">\nchrX  151087187  151087355  A  0  -\nchrX  151572400  151572481  B  0  +\nchr1  151242630  151242955  X  0  +\nchr1  151271715  151271999  Y  0  +\nchr1  151278832  151279227  Z  0  -\nchr2  100000030  200000955  P  0  +\nchr2  100000015  200000999  Q  0  +\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=cat1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "cat1",
+        "name": "Concatenate datasets"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "columns from a table",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"warningmark\"><strong>WARNING: This tool breaks column assignments.<\/strong> To re-establish column assignments run the tools and click on the pencil icon in the latest history item.<\/p>\n<p class=\"infomark\">The output of this tool is always in tabular format (e.g., if your original delimiters are commas, they will be replaced with tabs). For example:<\/p>\n<blockquote>\n<p>Cutting columns 1 and 3 from:<\/p>\n<pre class=\"literal-block\">\napple,is,good\nwindows,is,bad\n<\/pre>\n<p>will give:<\/p>\n<pre class=\"literal-block\">\napple   good\nwindows bad\n<\/pre>\n<\/blockquote>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>This tool selects (cuts out) specified columns from the dataset.<\/p>\n<ul class=\"simple\">\n<li>Columns are specified as <strong>c1<\/strong>, <strong>c2<\/strong>, and so on. Column count begins with <strong>1<\/strong><\/li>\n<li>Columns can be specified in any order (e.g., <strong>c2,c1,c6<\/strong>)<\/li>\n<li>If you specify more columns than actually present - empty spaces will be filled with dots<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Input dataset (six columns: c1, c2, c3, c4, c5, and c6):<\/p>\n<pre class=\"literal-block\">\nchr1 10   1000  gene1 0 +\nchr2 100  1500  gene2 0 +\n<\/pre>\n<p><strong>cut<\/strong> on columns &quot;<strong>c1,c4,c6<\/strong>&quot; will return:<\/p>\n<pre class=\"literal-block\">\nchr1 gene1 +\nchr2 gene2 +\n<\/pre>\n<p><strong>cut<\/strong> on columns &quot;<strong>c6,c5,c4,c1<\/strong>&quot; will return:<\/p>\n<pre class=\"literal-block\">\n+ 0 gene1 chr1\n+ 0 gene2 chr2\n<\/pre>\n<p><strong>cut<\/strong> on columns &quot;<strong>c1-c3<\/strong>&quot; will return:<\/p>\n<pre class=\"literal-block\">\nchr1 10   1000\nchr2 100  1500\n<\/pre>\n<p><strong>cut<\/strong> on columns &quot;<strong>c8,c7,c4<\/strong>&quot; will return:<\/p>\n<pre class=\"literal-block\">\n. . gene1\n. . gene2\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "1.0.2",
+        "link": "/tool_runner?tool_id=Cut1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Cut1",
+        "name": "Cut"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "together",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\"><strong>TIP:<\/strong> If your data is not TAB delimited, use <em>Text Manipulation-&gt;Convert<\/em><\/p>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>This tool merges columns together. Any number of valid columns can be merged in any order.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Input dataset (five columns: c1, c2, c3, c4, and c5):<\/p>\n<pre class=\"literal-block\">\n1 10   1000  gene1 chr\n2 100  1500  gene2 chr\n<\/pre>\n<p>merging columns &quot;<strong>c5,c1<\/strong>&quot; will return:<\/p>\n<pre class=\"literal-block\">\n1 10   1000  gene1 chr chr1\n2 100  1500  gene2 chr chr2\n<\/pre>\n<p class=\"warningmark\">Note that all original columns are preserved and the result of merge is added as the rightmost column.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=mergeCols1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "mergeCols1",
+        "name": "Merge Columns"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "delimiters to TAB",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>Converts all delimiters of a specified type into TABs. Consecutive delimiters can be condensed in a single TAB.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<ul>\n<li><p class=\"first\">Input file:<\/p>\n<pre class=\"literal-block\">\nchrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-\nchrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-\nchrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+\nchrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+\n<\/pre>\n<\/li>\n<li><p class=\"first\">Converting all pipe delimiters of the above file to TABs and condensing delimiters will get:<\/p>\n<pre class=\"literal-block\">\nchrX  151283558  151283724  NM_000808_exon_8_0_chrX_151283559_r  0  -\nchrX  151370273  151370486  NM_000808_exon_9_0_chrX_151370274_r  0  -\nchrX  151559494  151559583  NM_018558_exon_1_0_chrX_151559495_f  0  +\nchrX  151564643  151564711  NM_018558_exon_2_0_chrX_151564644_f  0  +\n<\/pre>\n<\/li>\n<\/ul>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=Convert+characters1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Convert characters1",
+        "name": "Convert"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "as a new dataset",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"warningmark\"><strong>TIP<\/strong>. Once your interval appears in history, you must tell Galaxy which genome it belongs to by clicking pencil icon or the &quot;?&quot; link in the history item.<\/p>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>This tool allows you to create a single genomic interval. The resulting history item will be in the BED format.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Typing the following values in the form:<\/p>\n<pre class=\"literal-block\">\nChromosome: chrX\nStart position: 151087187\nEnd position: 151370486\nName: NM_000808\nStrand: minus\n<\/pre>\n<p>will create a single interval:<\/p>\n<pre class=\"literal-block\">\nchrX  151087187  151370486  NM_000808  0  -\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=createInterval",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "createInterval",
+        "name": "Create single interval"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "of selected columns",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"warningmark\"><strong>This tool breaks column assignments.<\/strong> To re-establish column assignments run the tool and click on the pencil icon in the resulting history item.<\/p>\n<p class=\"warningmark\">The format of the resulting dataset from this tool is always tabular.<\/p>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>This tool selects specified columns from a dataset and converts the values of those columns to upper or lower case.<\/p>\n<ul class=\"simple\">\n<li>Columns are specified as <strong>c1<\/strong>, <strong>c2<\/strong>, and so on.<\/li>\n<li>Columns can be specified in any order (e.g., <strong>c2,c1,c6<\/strong>)<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Changing columns 1 and 3 ( delimited by Comma ) to upper case in:<\/p>\n<pre class=\"literal-block\">\napple,is,good\nwindows,is,bad\n<\/pre>\n<p>will result in:<\/p>\n<pre class=\"literal-block\">\nAPPLE is GOOD\nWINDOWS is BAD\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=ChangeCase",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "ChangeCase",
+        "name": "Change Case"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "two files side by side",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\">Paste preserves column assignments of the first dataset.<\/p>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>This tool merges two datasets side by side. If the first (left) dataset contains column assignments such as chromosome, start, end and strand, these will be preserved. However, if you would like to change column assignments, click the pencil icon in the history item.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>First dataset:<\/p>\n<pre class=\"literal-block\">\na 1\na 2\na 3\n<\/pre>\n<p>Second dataset:<\/p>\n<pre class=\"literal-block\">\n20\n30\n40\n<\/pre>\n<p>Pasting them together will produce:<\/p>\n<pre class=\"literal-block\">\na 1 20\na 2 30\na 3 40\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=Paste1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Paste1",
+        "name": "Paste"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "of a file",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool removes a specified number of lines from the beginning of a dataset.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Input File:<\/p>\n<pre class=\"literal-block\">\nchr7  56632  56652   D17003_CTCF_R6  310  +\nchr7  56736  56756   D17003_CTCF_R7  354  +\nchr7  56761  56781   D17003_CTCF_R4  220  +\nchr7  56772  56792   D17003_CTCF_R7  372  +\nchr7  56775  56795   D17003_CTCF_R4  207  +\n<\/pre>\n<p>After removing the first 3 lines the dataset will look like this:<\/p>\n<pre class=\"literal-block\">\nchr7  56772  56792   D17003_CTCF_R7  372  +\nchr7  56775  56795   D17003_CTCF_R4  207  +\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=Remove+beginning1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Remove beginning1",
+        "name": "Remove beginning"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "from a file",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool selects N random lines from a file, with no repeats, and preserving ordering.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Input File:<\/p>\n<pre class=\"literal-block\">\nchr7  56632  56652   D17003_CTCF_R6  310  +\nchr7  56736  56756   D17003_CTCF_R7  354  +\nchr7  56761  56781   D17003_CTCF_R4  220  +\nchr7  56772  56792   D17003_CTCF_R7  372  +\nchr7  56775  56795   D17003_CTCF_R4  207  +\n<\/pre>\n<p>Selecting 2 random lines might return this:<\/p>\n<pre class=\"literal-block\">\nchr7  56736  56756   D17003_CTCF_R7  354  +\nchr7  56775  56795   D17003_CTCF_R4  207  +\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "2.0.2",
+        "link": "/tool_runner?tool_id=random_lines1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "random_lines1",
+        "name": "Select random lines"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "lines from a dataset",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool outputs specified number of lines from the <strong>beginning<\/strong> of a dataset<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Selecting 2 lines from this:<\/p>\n<pre class=\"literal-block\">\nchr7  56632  56652  D17003_CTCF_R6  310  +\nchr7  56736  56756  D17003_CTCF_R7  354  +\nchr7  56761  56781  D17003_CTCF_R4  220  +\nchr7  56772  56792  D17003_CTCF_R7  372  +\nchr7  56775  56795  D17003_CTCF_R4  207  +\n<\/pre>\n<p>will produce:<\/p>\n<pre class=\"literal-block\">\nchr7  56632  56652  D17003_CTCF_R6  310  +\nchr7  56736  56756  D17003_CTCF_R7  354  +\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=Show+beginning1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Show beginning1",
+        "name": "Select first"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "lines from a dataset",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool outputs specified number of lines from the <strong>end<\/strong> of a dataset<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<ul>\n<li><p class=\"first\">Input File:<\/p>\n<pre class=\"literal-block\">\nchr7    57134   57154   D17003_CTCF_R7  356     -\nchr7    57247   57267   D17003_CTCF_R4  207     +\nchr7    57314   57334   D17003_CTCF_R5  269     +\nchr7    57341   57361   D17003_CTCF_R7  375     +\nchr7    57457   57477   D17003_CTCF_R3  188     +\n<\/pre>\n<\/li>\n<li><p class=\"first\">Show last two lines of above file. The result is:<\/p>\n<pre class=\"literal-block\">\nchr7    57341   57361   D17003_CTCF_R7  375     +\nchr7    57457   57477   D17003_CTCF_R3  188     +\n<\/pre>\n<\/li>\n<\/ul>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=Show+tail1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Show tail1",
+        "name": "Select last"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "leading or trailing characters",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>Trims specified number of characters from a dataset or its field (if dataset is tab-delimited).<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example 1<\/strong><\/p>\n<p>Trimming this dataset:<\/p>\n<pre class=\"literal-block\">\n1234567890\nabcdefghijk\n<\/pre>\n<p>by setting <strong>Trim from the beginning up to this position<\/strong> to <em>2<\/em> and <strong>Remove everything from this position to the end<\/strong> to <em>6<\/em> will produce:<\/p>\n<pre class=\"literal-block\">\n23456\nbcdef\n<\/pre>\n<hr class=\"docutils\" />\n<p><strong>Example 2<\/strong><\/p>\n<p>Trimming column 2 of this dataset:<\/p>\n<pre class=\"literal-block\">\nabcde 12345 fghij 67890\nfghij 67890 abcde 12345\n<\/pre>\n<p>by setting <strong>Trim content of this column only<\/strong> to <em>2<\/em>, <strong>Trim from the beginning up to this position<\/strong> to <em>2<\/em>, and <strong>Remove everything from this position to the end<\/strong> to <em>4<\/em> will produce:<\/p>\n<pre class=\"literal-block\">\nabcde  234 fghij 67890\nfghij  789 abcde 12345\n<\/pre>\n<hr class=\"docutils\" />\n<p><strong>Example 3<\/strong><\/p>\n<p>Trimming column 2 of this dataset:<\/p>\n<pre class=\"literal-block\">\nabcde 12345 fghij 67890\nfghij 67890 abcde 12345\n<\/pre>\n<p>by setting <strong>Trim content of this column only<\/strong> to <em>2<\/em>, <strong>Trim from the beginning up to this position<\/strong> to <em>2<\/em>, and <strong>Remove everything from this position to the end<\/strong> to <em>-2<\/em> will produce:<\/p>\n<pre class=\"literal-block\">\nabcde  23 fghij 67890\nfghij  78 abcde 12345\n<\/pre>\n<hr class=\"docutils\" />\n<p><strong>Trimming FASTQ datasets<\/strong><\/p>\n<p>This tool can be used to trim sequences and quality strings in FASTQ datasets. This is done by selected <em>Yes<\/em> from the <strong>Is input dataset in FASTQ format?<\/strong> dropdown. If set to <em>Yes<\/em>, the tool will skip all even numbered lines (see warning below). For example, trimming last 5 bases of this dataset:<\/p>\n<pre class=\"literal-block\">\n&#64;081017-and-081020:1:1:1715:1759\nGGACTCAGATAGTAATCCACGCTCCTTTAAAATATC\n+\nII#IIIIIII$5+.(9IIIIIII$%*$G$A31I&amp;&amp;B\n<\/pre>\n<p>cab done by setting <strong>Remove everything from this position to the end<\/strong> to 31:<\/p>\n<pre class=\"literal-block\">\n&#64;081017-and-081020:1:1:1715:1759\nGGACTCAGATAGTAATCCACGCTCCTTTAAA\n+\nII#IIIIIII$5+.(9IIIIIII$%*$G$A3\n<\/pre>\n<p><strong>Note<\/strong> that headers are skipped.<\/p>\n<p class=\"warningmark\"><strong>WARNING:<\/strong> This tool will only work on properly formatted FASTQ datasets where (1) each read and quality string occupy one line and (2) '&#64;' (read header) and &quot;+&quot; (quality header) lines are evenly numbered like in the above example.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "0.0.1",
+        "link": "/tool_runner?tool_id=trimmer",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "trimmer",
+        "name": "Trim"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "of a dataset",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool outputs counts of specified attributes (lines, words, characters) of a dataset.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example Output<\/strong><\/p>\n<pre class=\"literal-block\">\n#lines  words  characters\n7499    41376  624971\n<\/pre>\n<hr class=\"docutils\" />\n<p><strong>Citation<\/strong><\/p>\n<p>If you use this tool in Galaxy, please cite Blankenberg D, et al. <em>In preparation.<\/em><\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=wc_gnu",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "wc_gnu",
+        "name": "Line/Word/Character count"
+      },
+      {
+        "panel_section_name": "Text Manipulation",
+        "xrefs": [],
+        "description": "on a dataset",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool outputs Secure Hashes / Message Digests of a dataset using the user selected algorithms.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Citation<\/strong><\/p>\n<p>If you use this tool in Galaxy, please cite Blankenberg D, et al. <em>In preparation.<\/em><\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "textutil",
+        "version": "0.0.1",
+        "link": "/tool_runner?tool_id=secure_hash_message_digest",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "secure_hash_message_digest",
+        "name": "Secure Hash / Message Digest"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "textutil",
+    "name": "Text Manipulation"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Convert Formats",
+        "xrefs": [],
+        "description": "converter",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool converts data from BED format to GFF format (scroll down for format description).<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>The following data in BED format:<\/p>\n<pre class=\"literal-block\">\nchr28   346187  388197  BC114771        0       +       346187  388197  0       9       144,81,115,63,155,96,134,105,112,       0,24095,26190,31006,32131,33534,36994,41793,41898,\n<\/pre>\n<p>Will be converted to GFF (<strong>note<\/strong> that the start coordinate is incremented by 1):<\/p>\n<pre class=\"literal-block\">\n\nchr28   bed2gff mRNA    346188  388197  0       +       .       mRNA BC114771;\nchr28   bed2gff exon    346188  346331  0       +       .       exon BC114771;\nchr28   bed2gff exon    370283  370363  0       +       .       exon BC114771;\nchr28   bed2gff exon    372378  372492  0       +       .       exon BC114771;\nchr28   bed2gff exon    377194  377256  0       +       .       exon BC114771;\nchr28   bed2gff exon    378319  378473  0       +       .       exon BC114771;\nchr28   bed2gff exon    379722  379817  0       +       .       exon BC114771;\nchr28   bed2gff exon    383182  383315  0       +       .       exon BC114771;\nchr28   bed2gff exon    387981  388085  0       +       .       exon BC114771;\nchr28   bed2gff exon    388086  388197  0       +       .       exon BC114771;\n<\/pre>\n<hr class=\"docutils\" />\n<p class=\"informark\"><strong>About formats<\/strong><\/p>\n<p><strong>BED format<\/strong> Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:<\/p>\n<p>The first three BED fields (required) are:<\/p>\n<pre class=\"literal-block\">\n1. chrom - The name of the chromosome (e.g. chr1, chrY_random).\n2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)\n3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).\n<\/pre>\n<p>The additional BED fields (optional) are:<\/p>\n<pre class=\"literal-block\">\n 4. name - The name of the BED line.\n 5. score - A score between 0 and 1000.\n 6. strand - Defines the strand - either '+' or '-'.\n 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.\n 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.\n 9. reserved - This should always be set to zero.\n10. blockCount - The number of blocks (exons) in the BED line.\n11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.\n12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.\n13. expCount - The number of experiments.\n14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.\n15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.\n<\/pre>\n<p><strong>GFF format<\/strong> General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields:<\/p>\n<pre class=\"literal-block\">\n1. seqname - Must be a chromosome or scaffold.\n2. source - The program that generated this feature.\n3. feature - The name of this type of feature. Some examples of standard feature types are &quot;CDS&quot;, &quot;start_codon&quot;, &quot;stop_codon&quot;, and &quot;exon&quot;.\n4. start - The starting position of the feature in the sequence. The first base is numbered 1.\n5. end - The ending position of the feature (inclusive).\n6. score - A score between 0 and 1000. If there is no score value, enter &quot;.&quot;.\n7. strand - Valid entries include '+', '-', or '.' (for don't know/care).\n8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.\n9. group - All lines with the same group are linked together into a single item.\n<\/pre>\n",
+        "edam_operations": [
+          "operation_3434"
+        ],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "convert",
+        "version": "2.0.0",
+        "link": "/tool_runner?tool_id=bed2gff1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "bed2gff1",
+        "name": "BED-to-GFF"
+      },
+      {
+        "panel_section_name": "Convert Formats",
+        "xrefs": [],
+        "description": "converter",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool converts data from GFF format to BED format (scroll down for format description).<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>The following data in GFF format:<\/p>\n<pre class=\"literal-block\">\nchr22  GeneA  enhancer  10000000  10001000  500      +   .  TGA\nchr22  GeneA  promoter  10010000  10010100  900      +   .  TGA\n<\/pre>\n<p>Will be converted to BED (<strong>note<\/strong> that 1 is subtracted from the start coordinate):<\/p>\n<pre class=\"literal-block\">\nchr22   9999999  10001000   enhancer   0   +\nchr22  10009999  10010100   promoter   0   +\n<\/pre>\n<hr class=\"docutils\" />\n<p class=\"infomark\"><strong>About formats<\/strong><\/p>\n<p><strong>BED format<\/strong> Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:<\/p>\n<p>The first three BED fields (required) are:<\/p>\n<pre class=\"literal-block\">\n1. chrom - The name of the chromosome (e.g. chr1, chrY_random).\n2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)\n3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).\n<\/pre>\n<p>The additional BED fields (optional) are:<\/p>\n<pre class=\"literal-block\">\n 4. name - The name of the BED line.\n 5. score - A score between 0 and 1000.\n 6. strand - Defines the strand - either '+' or '-'.\n 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.\n 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.\n 9. reserved - This should always be set to zero.\n10. blockCount - The number of blocks (exons) in the BED line.\n11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.\n12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.\n13. expCount - The number of experiments.\n14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.\n15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.\n<\/pre>\n<p><strong>GFF format<\/strong> General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields:<\/p>\n<pre class=\"literal-block\">\n1. seqname - Must be a chromosome or scaffold.\n2. source - The program that generated this feature.\n3. feature - The name of this type of feature. Some examples of standard feature types are &quot;CDS&quot;, &quot;start_codon&quot;, &quot;stop_codon&quot;, and &quot;exon&quot;.\n4. start - The starting position of the feature in the sequence. The first base is numbered 1.\n5. end - The ending position of the feature (inclusive).\n6. score - A score between 0 and 1000. If there is no score value, enter &quot;.&quot;.\n7. strand - Valid entries include '+', '-', or '.' (for don't know/care).\n8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.\n9. group - All lines with the same group are linked together into a single item.\n<\/pre>\n",
+        "edam_operations": [
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+        "edam_topics": [],
+        "panel_section_id": "convert",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=gff2bed1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "gff2bed1",
+        "name": "GFF-to-BED"
+      },
+      {
+        "panel_section_name": "Convert Formats",
+        "xrefs": [],
+        "description": "Converts a MAF formatted file to the BED format",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool converts every MAF block to an interval line (in BED format; scroll down for description of MAF and BED formats) describing position of that alignment block within a corresponding genome.<\/p>\n<p>The interface for this tool contains two pages (steps):<\/p>\n<blockquote>\n<ul class=\"simple\">\n<li><strong>Step 1 of 2<\/strong>. Choose multiple alignments from history to be converted to BED format.<\/li>\n<li><strong>Step 2 of 2<\/strong>. Choose species from the alignment to be included in the output and specify how to deal with alignment blocks that lack one or more species:<ul>\n<li><strong>Choose species<\/strong> - the tool reads the alignment provided during Step 1 and generates a list of species contained within that alignment. Using checkboxes you can specify taxa to be included in the output (only reference genome, shown in <strong>bold<\/strong>, is selected by default). If you select more than one species, then more than one history item will be created.<\/li>\n<li><strong>Choose to include/exclude blocks with missing species<\/strong> - if an alignment block does not contain any one of the species you selected within <strong>Choose species<\/strong> menu and this option is set to <strong>exclude blocks with missing species<\/strong>, then coordinates of such a block <strong>will not<\/strong> be included in the output (see <strong>Example 2<\/strong> below).<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/blockquote>\n<hr class=\"docutils\" />\n<p><strong>Example 1<\/strong>: <strong>Include only reference genome<\/strong> (hg18 in this case) and <strong>include blocks with missing species<\/strong>:<\/p>\n<p>For the following alignment:<\/p>\n<pre class=\"literal-block\">\na score=68686.000000\ns hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------\ns mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------\ns canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C\n\na score=10289.000000\ns hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG\n<\/pre>\n<p>the tool will create <strong>a single<\/strong> history item containing the following (<strong>note<\/strong> that field 4 is added to the output and is numbered iteratively: hg18_0, hg18_1 etc.):<\/p>\n<pre class=\"literal-block\">\nchr20    56827368    56827443   hg18_0   0   +\nchr20    56827443    56827480   hg18_1   0   +\n<\/pre>\n<hr class=\"docutils\" />\n<p><strong>Example 2<\/strong>: <strong>Include hg18 and mm8<\/strong> and <strong>exclude blocks with missing species<\/strong>:<\/p>\n<p>For the following alignment:<\/p>\n<pre class=\"literal-block\">\na score=68686.000000\ns hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------\ns mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------\ns canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C\n\na score=10289.000000\ns hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG\n<\/pre>\n<p>the tool will create <strong>two<\/strong> history items (one for hg18 and one fopr mm8) containing the following (<strong>note<\/strong> that both history items contain only one line describing the first alignment block. The second MAF block is not included in the output because it does not contain mm8):<\/p>\n<p>History item <strong>1<\/strong> (for hg18):<\/p>\n<pre class=\"literal-block\">\nchr20    56827368    56827443   hg18_0   0   +\n<\/pre>\n<p>History item <strong>2<\/strong> (for mm8):<\/p>\n<pre class=\"literal-block\">\nchr2    173910832   173910893    mm8_0   0   +\n<\/pre>\n<hr class=\"docutils\" />\n<p class=\"infomark\"><strong>About formats<\/strong><\/p>\n<p><strong>MAF format<\/strong> multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes.<\/p>\n<blockquote>\n<ul class=\"simple\">\n<li>The .maf format is line-oriented. Each multiple alignment ends with a blank line.<\/li>\n<li>Each sequence in an alignment is on a single line.<\/li>\n<li>Lines starting with # are considered to be comments.<\/li>\n<li>Each multiple alignment is in a separate paragraph that begins with an &quot;a&quot; line and contains an &quot;s&quot; line for each sequence in the multiple alignment.<\/li>\n<li>Some MAF files may contain two optional line types:<ul>\n<li>An &quot;i&quot; line containing information about what is in the aligned species DNA before and after the immediately preceding &quot;s&quot; line;<\/li>\n<li>An &quot;e&quot; line containing information about the size of the gap between the alignments that span the current block.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/blockquote>\n<p><strong>BED format<\/strong> Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and a number of additional optional ones:<\/p>\n<p>The first three BED fields (required) are:<\/p>\n<pre class=\"literal-block\">\n1. chrom - The name of the chromosome (e.g. chr1, chrY_random).\n2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)\n3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).\n<\/pre>\n<p>Additional (optional) fields are:<\/p>\n<pre class=\"literal-block\">\n4. name - The name of the BED line.\n5. score - A score between 0 and 1000.\n6. strand - Defines the strand - either '+' or '-'.\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "convert",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=MAF_To_BED1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "MAF_To_BED1",
+        "name": "MAF to BED"
+      },
+      {
+        "panel_section_name": "Convert Formats",
+        "xrefs": [],
+        "description": "Converts a MAF formatted file to the Interval format",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool converts every MAF block to a set of genomic intervals describing the position of that alignment block within a corresponding genome. Sequences from aligning species are also included in the output.<\/p>\n<p>The interface for this tool contains several options:<\/p>\n<blockquote>\n<ul class=\"simple\">\n<li><strong>MAF file to convert<\/strong>. Choose multiple alignments from history to be converted to BED format.<\/li>\n<li><strong>Choose species<\/strong>. Choose additional species from the alignment to be included in the output<\/li>\n<li><strong>Exclude blocks which have a species missing<\/strong>. if an alignment block does not contain any one of the species found in the alignment set and this option is set to <strong>exclude blocks with missing species<\/strong>, then coordinates of such a block <strong>will not<\/strong> be included in the output (see <strong>Example 2<\/strong> below).<\/li>\n<li><strong>Remove Gap characters from sequences<\/strong>. Gaps can be removed from sequences before they are output.<\/li>\n<\/ul>\n<\/blockquote>\n<hr class=\"docutils\" />\n<p><strong>Example 1<\/strong>: <strong>Include only reference genome<\/strong> (hg18 in this case) and <strong>include blocks with missing species<\/strong>:<\/p>\n<p>For the following alignment:<\/p>\n<pre class=\"literal-block\">\na score=68686.000000\ns hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------\ns mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------\ns canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C\n\na score=10289.000000\ns hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG\n<\/pre>\n<p>the tool will create <strong>a single<\/strong> history item containing the following (<strong>note<\/strong> the name field is numbered iteratively: hg18_0_0, hg18_1_0 etc. where the first number is the block number and the second number is the iteration through the block (if a species appears twice in a block, that interval will be repeated) and sequences for each species are included in the order specified in the header: the field is left empty when no sequence is available for that species):<\/p>\n<pre class=\"literal-block\">\n#chrom        start   end     strand  score   name    canFam2 hg18    mm8     panTro2 rheMac2\nchr20 56827368        56827443        +       68686.0 hg18_0_0        CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C        GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-        AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------        GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-        GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------\nchr20 56827443        56827480        +       10289.0 hg18_1_0                ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG           ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG   ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG\n<\/pre>\n<hr class=\"docutils\" />\n<p><strong>Example 2<\/strong>: <strong>Include hg18 and mm8<\/strong> and <strong>exclude blocks with missing species<\/strong>:<\/p>\n<p>For the following alignment:<\/p>\n<pre class=\"literal-block\">\na score=68686.000000\ns hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------\ns mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------\ns canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C\n\na score=10289.000000\ns hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG\n<\/pre>\n<p>the tool will create <strong>two<\/strong> history items (one for hg18 and one for mm8) containing the following (<strong>note<\/strong> that both history items contain only one line describing the first alignment block. The second MAF block is not included in the output because it does not contain mm8):<\/p>\n<p>History item <strong>1<\/strong> (for hg18):<\/p>\n<pre class=\"literal-block\">\n#chrom       start   end     strand  score   name    canFam2 hg18    mm8     panTro2 rheMac2\nchr20        56827368        56827443        +       68686.0 hg18_0_0        CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C        GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-        AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------        GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-        GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------\n<\/pre>\n<p>History item <strong>2<\/strong> (for mm8):<\/p>\n<pre class=\"literal-block\">\n#chrom       start   end     strand  score   name    canFam2 hg18    mm8     panTro2 rheMac2\nchr2 173910832       173910893       +       68686.0 mm8_0_0 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C        GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-        AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------        GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-        GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------\n<\/pre>\n<hr class=\"docutils\" />\n<p class=\"infomark\"><strong>About formats<\/strong><\/p>\n<p><strong>MAF format<\/strong> multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes.<\/p>\n<blockquote>\n<ul class=\"simple\">\n<li>The .maf format is line-oriented. Each multiple alignment ends with a blank line.<\/li>\n<li>Each sequence in an alignment is on a single line.<\/li>\n<li>Lines starting with # are considered to be comments.<\/li>\n<li>Each multiple alignment is in a separate paragraph that begins with an &quot;a&quot; line and contains an &quot;s&quot; line for each sequence in the multiple alignment.<\/li>\n<li>Some MAF files may contain two optional line types:<ul>\n<li>An &quot;i&quot; line containing information about what is in the aligned species DNA before and after the immediately preceding &quot;s&quot; line;<\/li>\n<li>An &quot;e&quot; line containing information about the size of the gap between the alignments that span the current block.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/blockquote>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "convert",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=MAF_To_Interval1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "MAF_To_Interval1",
+        "name": "MAF to Interval"
+      },
+      {
+        "panel_section_name": "Convert Formats",
+        "xrefs": [],
+        "description": "Converts a MAF formatted file to FASTA format",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>Types of MAF to FASTA conversion<\/strong><\/p>\n<blockquote>\n<ul class=\"simple\">\n<li><strong>Multiple Blocks<\/strong> converts a single MAF block to a single FASTA block. For example, if you have 6 MAF blocks, they will be converted to 6 FASTA blocks.<\/li>\n<li><strong>One Sequence per Species<\/strong> converts MAF blocks to a single aggregated FASTA block. For example, if you have 6 MAF blocks, they will be converted and concatenated into a single FASTA block.<\/li>\n<\/ul>\n<\/blockquote>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>This tool converts MAF blocks to FASTA format and concatenates them into a single FASTA block or outputs multiple FASTA blocks separated by empty lines.<\/p>\n<p>The interface for this tool contains two pages (steps):<\/p>\n<blockquote>\n<ul>\n<li><p class=\"first\"><strong>Step 1 of 2<\/strong>. Choose multiple alignments from history to be converted to FASTA format.<\/p>\n<\/li>\n<li><p class=\"first\"><strong>Step 2 of 2<\/strong>. Choose the type of output as well as the species from the alignment to be included in the output.<\/p>\n<p>Multiple Block output has additional options:<\/p>\n<ul class=\"simple\">\n<li><strong>Choose species<\/strong> - the tool reads the alignment provided during Step 1 and generates a list of species contained within that alignment. Using checkboxes you can specify taxa to be included in the output (all species are selected by default).<\/li>\n<li><strong>Choose to include/exclude blocks with missing species<\/strong> - if an alignment block does not contain any one of the species you selected within <strong>Choose species<\/strong> menu and this option is set to <strong>exclude blocks with missing species<\/strong>, then such a block <strong>will not<\/strong> be included in the output (see <strong>Example 2<\/strong> below).  For example, if you want to extract human, mouse, and rat from a series of alignments and one of the blocks does not contain mouse sequence, then this block will not be converted to FASTA and will not be returned.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/blockquote>\n<hr class=\"docutils\" />\n<p><strong>Example 1<\/strong>:<\/p>\n<p>In the concatenated approach, the following alignment:<\/p>\n<pre class=\"literal-block\">\na score=68686.000000\ns hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------\ns mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------\ns canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C\n\na score=10289.000000\ns hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG\n<\/pre>\n<p>will be converted to (<strong>note<\/strong> that because mm8 (mouse) and canFam2 (dog) are absent from the second block, they are replaced with gaps after concatenation):<\/p>\n<pre class=\"literal-block\">\n&gt;canFam2\nCG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C-------------------------------------\n&gt;hg18\nGACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\n&gt;mm8\nAGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC--------------------------------------------\n&gt;panTro2\nGACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\n&gt;rheMac2\nGACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG\n<\/pre>\n<hr class=\"docutils\" />\n<p><strong>Example 2a<\/strong>: Multiple Block Approach <strong>Include all species<\/strong> and <strong>include blocks with missing species<\/strong>:<\/p>\n<p>The following alignment:<\/p>\n<pre class=\"literal-block\">\na score=68686.000000\ns hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------\ns mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------\ns canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C\n\na score=10289.000000\ns hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG\n<\/pre>\n<p>will be converted to:<\/p>\n<pre class=\"literal-block\">\n&gt;hg18.chr20(+):56827368-56827443|hg18_0\nGACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\n&gt;panTro2.chr20(+):56528685-56528760|panTro2_0\nGACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\n&gt;rheMac2.chr10(-):89144112-89144181|rheMac2_0\nGACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------\n&gt;mm8.chr2(+):173910832-173910893|mm8_0\nAGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------\n&gt;canFam2.chr24(+):46551822-46551889|canFam2_0\nCG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C\n\n&gt;hg18.chr20(+):56827443-56827480|hg18_1\nATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\n&gt;panTro2.chr20(+):56528760-56528797|panTro2_1\nATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\n&gt;rheMac2.chr10(-):89144181-89144218|rheMac2_1\nATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG\n<\/pre>\n<hr class=\"docutils\" />\n<p><strong>Example 2b<\/strong>: Multiple Block Approach <strong>Include hg18 and mm8<\/strong> and <strong>exclude blocks with missing species<\/strong>:<\/p>\n<p>The following alignment:<\/p>\n<pre class=\"literal-block\">\na score=68686.000000\ns hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-\ns rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------\ns mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------\ns canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C\n\na score=10289.000000\ns hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG\ns rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG\n<\/pre>\n<p>will be converted to (<strong>note<\/strong> that the second MAF block, which does not have mm8, is not included in the output):<\/p>\n<pre class=\"literal-block\">\n&gt;hg18.chr20(+):56827368-56827443|hg18_0\nGACAGGGTGCATCTGGGAGGGCCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC\n&gt;mm8.chr2(+):173910832-173910893|mm8_0\nAGAAGGATCCACCT---------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------\n<\/pre>\n<hr class=\"docutils\" />\n<p class=\"infomark\"><strong>About formats<\/strong><\/p>\n<blockquote>\n<p><strong>MAF format<\/strong> multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes.<\/p>\n<ul class=\"simple\">\n<li>The .maf format is line-oriented. Each multiple alignment ends with a blank line.<\/li>\n<li>Each sequence in an alignment is on a single line.<\/li>\n<li>Lines starting with # are considered to be comments.<\/li>\n<li>Each multiple alignment is in a separate paragraph that begins with an &quot;a&quot; line and contains an &quot;s&quot; line for each sequence in the multiple alignment.<\/li>\n<li>Some MAF files may contain two optional line types:<ul>\n<li>An &quot;i&quot; line containing information about what is in the aligned species DNA before and after the immediately preceding &quot;s&quot; line;<\/li>\n<li>An &quot;e&quot; line containing information about the size of the gap between the alignments that span the current block.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/blockquote>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "convert",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=MAF_To_Fasta1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "MAF_To_Fasta1",
+        "name": "MAF to FASTA"
+      },
+      {
+        "panel_section_name": "Convert Formats",
+        "xrefs": [],
+        "description": "",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool extracts data from the 454 Sequencer SFF format and creates three files containing the:\nSequences (FASTA),\nQualities (QUAL) and\nClippings (XML)<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "convert",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=Sff_extractor",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Sff_extractor",
+        "name": "SFF converter"
+      },
+      {
+        "panel_section_name": "Convert Formats",
+        "xrefs": [],
+        "description": "converter",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>Syntax<\/strong><\/p>\n<p>This tool converts bedgraph or wiggle data into bigWig type.<\/p>\n<ul>\n<li><p class=\"first\"><strong>Wiggle format<\/strong>: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line.  Following the track definition line is the track data, which can be entered in three different formats described below.<\/p>\n<ul>\n<li><p class=\"first\"><strong>BED format<\/strong> with no declaration line and four columns of data:<\/p>\n<pre class=\"literal-block\">\nchromA  chromStartA  chromEndA  dataValueA\nchromB  chromStartB  chromEndB  dataValueB\n<\/pre>\n<\/li>\n<li><p class=\"first\"><strong>variableStep<\/strong> two column data; started by a declaration line and followed with chromosome positions and data values:<\/p>\n<pre class=\"literal-block\">\nvariableStep  chrom=chrN  [span=windowSize]\nchromStartA  dataValueA\nchromStartB  dataValueB\n<\/pre>\n<\/li>\n<li><p class=\"first\"><strong>fixedStep<\/strong> single column data; started by a declaration line and followed with data values:<\/p>\n<pre class=\"literal-block\">\nfixedStep  chrom=chrN  start=position  step=stepInterval  [span=windowSize]\ndataValue1\ndataValue2\n<\/pre>\n<\/li>\n<\/ul>\n<\/li>\n<li><p class=\"first\">The <strong>BedGraph format<\/strong> is described in detail at the <a class=\"reference external\" href=\"http://genome.ucsc.edu/goldenPath/help/bedgraph.html\">UCSC Bioinformatics website<\/a><\/p>\n<\/li>\n<\/ul>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "convert",
+        "version": "1.1.1",
+        "link": "/tool_runner?tool_id=wig_to_bigWig",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "wig_to_bigWig",
+        "name": "Wig/BedGraph-to-bigWig"
+      },
+      {
+        "panel_section_name": "Convert Formats",
+        "xrefs": [],
+        "description": "converter",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p>This tool converts a <strong>sorted<\/strong> BED file into a bigBed file.<\/p>\n<p>Currently, the bedFields option to specify the number of non-standard fields is not supported as an AutoSQL file must be provided, which is a format\ncurrently not supported by Galaxy.<\/p>\n",
+        "edam_operations": [
+          "operation_3434"
+        ],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "convert",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=bed_to_bigBed",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "bed_to_bigBed",
+        "name": "BED-to-bigBed"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "convert",
+    "name": "Convert Formats"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Filter and Sort",
+        "xrefs": [],
+        "description": "data on any column using simple expressions",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"warningmark\">Double equal signs, ==, must be used as <em>&quot;equal to&quot;<\/em> (e.g., <strong>c1 == 'chr22'<\/strong>)<\/p>\n<p class=\"infomark\"><strong>TIP:<\/strong> Attempting to apply a filtering condition may throw exceptions if the data type (e.g., string, integer) in every line of the columns being filtered is not appropriate for the condition (e.g., attempting certain numerical calculations on strings).  If an exception is thrown when applying the condition to a line, that line is skipped as invalid for the filter condition.  The number of invalid skipped lines is documented in the resulting history item as a &quot;Condition/data issue&quot;.<\/p>\n<p class=\"infomark\"><strong>TIP:<\/strong> If your data is not TAB delimited, use <em>Text Manipulation-&gt;Convert<\/em><\/p>\n<hr class=\"docutils\" />\n<p><strong>Syntax<\/strong><\/p>\n<p>The filter tool allows you to restrict the dataset using simple conditional statements.<\/p>\n<ul class=\"simple\">\n<li>Columns are referenced with <strong>c<\/strong> and a <strong>number<\/strong>. For example, <strong>c1<\/strong> refers to the first column of a tab-delimited file<\/li>\n<li>Make sure that multi-character operators contain no white space ( e.g., <strong>&lt;=<\/strong> is valid while <strong>&lt; =<\/strong> is not valid )<\/li>\n<li>When using 'equal-to' operator <strong>double equal sign '==' must be used<\/strong> ( e.g., <strong>c1=='chr1'<\/strong> )<\/li>\n<li>Non-numerical values must be included in single or double quotes ( e.g., <strong>c6=='+'<\/strong> )<\/li>\n<li>Filtering condition can include logical operators, but <strong>make sure operators are all lower case<\/strong> ( e.g., <strong>(c1!='chrX' and c1!='chrY') or not c6=='+'<\/strong> )<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<ul class=\"simple\">\n<li><strong>c1=='chr1'<\/strong> selects lines in which the first column is chr1<\/li>\n<li><strong>c3-c2&lt;100*c4<\/strong> selects lines where subtracting column 3 from column 2 is less than the value of column 4 times 100<\/li>\n<li><strong>len(c2.split(',')) &lt; 4<\/strong> will select lines where the second column has less than four comma separated elements<\/li>\n<li><strong>c2&gt;=1<\/strong> selects lines in which the value of column 2 is greater than or equal to 1<\/li>\n<li>Numbers should not contain commas - <strong>c2&lt;=44,554,350<\/strong> will not work, but <strong>c2&lt;=44554350<\/strong> will<\/li>\n<li>Some words in the data can be used, but must be single or double quoted ( e.g., <strong>c3=='exon'<\/strong> )<\/li>\n<\/ul>\n",
+        "edam_operations": [
+          "operation_0335"
+        ],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "filter",
+        "version": "1.1.0",
+        "link": "/tool_runner?tool_id=Filter1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Filter1",
+        "name": "Filter"
+      },
+      {
+        "panel_section_name": "Filter and Sort",
+        "xrefs": [],
+        "description": "data in ascending or descending order",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\"><strong>TIP:<\/strong> If your data is not TAB delimited, use <em>Text Manipulation-&gt;Convert<\/em><\/p>\n<hr class=\"docutils\" />\n<p><strong>Syntax<\/strong><\/p>\n<p>This tool sorts the dataset on any number of columns in either ascending or descending order.<\/p>\n<ul class=\"simple\">\n<li><strong>Numerical sort<\/strong> orders numbers by their magnitude, ignores all characters besides numbers, and evaluates a string of numbers to the value they signify.<\/li>\n<li><strong>General numeric sort<\/strong> orders numbers by their general numerical value. Unlike the numerical sort option, it can handle numbers in scientific notation too.<\/li>\n<li><strong>Alphabetical sort<\/strong> is a phonebook type sort based on the conventional order of letters in an alphabet. Each nth letter is compared with the nth letter of other words in the list, starting at the first letter of each word and advancing to the second, third, fourth, and so on, until the order is established. Therefore, in an alphabetical sort, 2 comes after 100 (1 &lt; 2).<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Examples<\/strong><\/p>\n<p>The list of numbers 4,17,3,5 collates to 3,4,5,17 by numerical sorting, while it collates to 17,3,4,5 by alphabetical sorting.<\/p>\n<p>Sorting the following:<\/p>\n<pre class=\"literal-block\">\nQ     d    7   II    jhu  45\nA     kk   4   I     h    111\nPd    p    1   ktY   WS   113\nA     g    10  H     ZZ   856\nA     edf  4   tw    b    234\nBBB   rt   10  H     ZZ   100\nA     rew  10  d     b    1111\nC     sd   19  YH    aa   10\nHah   c    23  ver   bb   467\nMN    gtr  1   a     X    32\nN     j    9   a     T    205\nBBB   rrf  10  b     Z    134\nodfr  ws   6   Weg   dew  201\nC     f    3   WW    SW   34\nA     jhg  4   I     b    345\nPd    gf   7   Gthe  de   567\nrS    hty  90  YY    LOp  89\nA     g    10  H     h    43\nA     g    4   I     h    500\n<\/pre>\n<p>on columns 1 (alphabetical), 3 (numerical), and 6 (numerical) in ascending order will yield:<\/p>\n<pre class=\"literal-block\">\nA     kk   4   I     h    111\nA     edf  4   tw    b    234\nA     jhg  4   I     b    345\nA     g    4   I     h    500\nA     g    10  H     h    43\nA     g    10  H     ZZ   856\nA     rew  10  d     b    1111\nBBB   rt   10  H     ZZ   100\nBBB   rrf  10  b     Z    134\nC     f    3   WW    SW   34\nC     sd   19  YH    aa   10\nHah   c    23  ver   bb   467\nMN    gtr  1   a     X    32\nN     j    9   a     T    205\nodfr  ws   6   Weg   dew  201\nPd    p    1   ktY   WS   113\nPd    gf   7   Gthe  de   567\nQ     d    7   II    jhu  45\nrS    hty  90  YY    LOp  89\n<\/pre>\n<p>Sorting the following:<\/p>\n<pre class=\"literal-block\">\nchr10  100  200  feature1  100.01   +\nchr20  800  900  feature2  1.1      +\nchr2   500  600  feature3  1000.1   +\nchr1   300  400  feature4  1.1e-05  +\nchr21  300  500  feature5  1.1e2    +\nchr15  700  800  feature6  1.1e4    +\n<\/pre>\n<p>on column 5 (numerical) in ascending order will yield:<\/p>\n<pre class=\"literal-block\">\nchr1   300  400  feature4  1.1e-05  +\nchr15  700  800  feature6  1.1e4    +\nchr20  800  900  feature2  1.1      +\nchr21  300  500  feature5  1.1e2    +\nchr10  100  200  feature1  100.01   +\nchr2   500  600  feature3  1000.1   +\n<\/pre>\n<p>on column 5 (general numeric) in ascending order will yield:<\/p>\n<pre class=\"literal-block\">\nchr1   300  400  feature4  1.1e-05  +\nchr20  800  900  feature2  1.1      +\nchr10  100  200  feature1  100.01   +\nchr21  300  500  feature5  1.1e2    +\nchr2   500  600  feature3  1000.1   +\nchr15  700  800  feature6  1.1e4    +\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "filter",
+        "version": "1.1.0",
+        "link": "/tool_runner?tool_id=sort1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "sort1",
+        "name": "Sort"
+      },
+      {
+        "panel_section_name": "Filter and Sort",
+        "xrefs": [],
+        "description": "lines that match an expression",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\"><strong>TIP:<\/strong> If your data is not TAB delimited, use <em>Text Manipulation-&gt;Convert<\/em><\/p>\n<hr class=\"docutils\" />\n<p><strong>Syntax<\/strong><\/p>\n<p>The select tool searches the data for lines containing or not containing a match to the given pattern. Regular Expression is introduced in this tool. A Regular Expression is a pattern describing a certain amount of text.<\/p>\n<ul class=\"simple\">\n<li><strong>( ) { } [ ] . * ? + ^ $<\/strong> are all special characters. <strong>\\<\/strong> can be used to &quot;escape&quot; a special character, allowing that special character to be searched for.<\/li>\n<li><strong>\\A<\/strong> matches the beginning of a string(but not an internal line).<\/li>\n<li><strong>\\d<\/strong> matches a digit, same as [0-9].<\/li>\n<li><strong>\\D<\/strong> matches a non-digit.<\/li>\n<li><strong>\\s<\/strong> matches a whitespace character.<\/li>\n<li><strong>\\S<\/strong> matches anything BUT a whitespace.<\/li>\n<li><strong>\\t<\/strong> matches a tab.<\/li>\n<li><strong>\\w<\/strong> matches an alphanumeric character.<\/li>\n<li><strong>\\W<\/strong> matches anything but an alphanumeric character.<\/li>\n<li><strong>(<\/strong> .. <strong>)<\/strong> groups a particular pattern.<\/li>\n<li><strong>\\Z<\/strong> matches the end of a string(but not a internal line).<\/li>\n<li><strong>{<\/strong> n or n, or n,m <strong>}<\/strong> specifies an expected number of repetitions of the preceding pattern.<ul>\n<li><strong>{n}<\/strong> The preceding item is matched exactly n times.<\/li>\n<li><strong>{n,}<\/strong> The preceding item is matched n or more times.<\/li>\n<li><strong>{n,m}<\/strong> The preceding item is matched at least n times but not more than m times.<\/li>\n<\/ul>\n<\/li>\n<li><strong>[<\/strong> ... <strong>]<\/strong> creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as <strong>a-z<\/strong>.<\/li>\n<li><strong>.<\/strong> Matches any single character except a newline.<\/li>\n<li><strong>*<\/strong> The preceding item will be matched zero or more times.<\/li>\n<li><strong>?<\/strong> The preceding item is optional and matched at most once.<\/li>\n<li><strong>+<\/strong> The preceding item will be matched one or more times.<\/li>\n<li><strong>^<\/strong> has two meaning:\n- matches the beginning of a line or string.\n- indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.<\/li>\n<li><strong>$<\/strong> matches the end of a line or string.<\/li>\n<li><strong>|<\/strong> Separates alternate possibilities.<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<ul class=\"simple\">\n<li><strong>^chr([0-9A-Za-z])+<\/strong> would match lines that begin with chromosomes, such as lines in a BED format file.<\/li>\n<li><strong>(ACGT){1,5}<\/strong> would match at least 1 &quot;ACGT&quot; and at most 5 &quot;ACGT&quot; consecutively.<\/li>\n<li><strong>([^,][0-9]{1,3})(,[0-9]{3})*<\/strong> would match a large integer that is properly separated with commas such as 23,078,651.<\/li>\n<li><strong>(abc)|(def)<\/strong> would match either &quot;abc&quot; or &quot;def&quot;.<\/li>\n<li><strong>^\\W+#<\/strong> would match any line that is a comment.<\/li>\n<\/ul>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "filter",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=Grep1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Grep1",
+        "name": "Select"
+      },
+      {
+        "model_class": "ToolSectionLabel",
+        "version": "",
+        "id": "gff",
+        "text": "GFF"
+      },
+      {
+        "panel_section_name": "Filter and Sort",
+        "xrefs": [],
+        "description": "from GFF data",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool extracts selected features from GFF data.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Selecting <strong>promoter<\/strong> from the following GFF data:<\/p>\n<pre class=\"literal-block\">\nchr22  GeneA  enhancer  10000000  10001000  500  +  .  TGA\nchr22  GeneA  promoter  10010000  10010100  900  +  .  TGA\nchr22  GeneB  promoter  10020000  10025000  400  -  .  TGB\nchr22  GeneB  CCDS2220  10030000  10065000  800  -  .  TGB\n<\/pre>\n<p>will produce the following output:<\/p>\n<pre class=\"literal-block\">\nchr22  GeneA  promoter  10010000  10010100  900  +  .  TGA\nchr22  GeneB  promoter  10020000  10025000  400  -  .  TGB\n<\/pre>\n<hr class=\"docutils\" />\n<p class=\"infomark\"><strong>About formats<\/strong><\/p>\n<p><strong>GFF format<\/strong> General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields:<\/p>\n<pre class=\"literal-block\">\n1. seqname - Must be a chromosome or scaffold.\n2. source - The program that generated this feature.\n3. feature - The name of this type of feature. Some examples of standard feature types are &quot;CDS&quot;, &quot;start_codon&quot;, &quot;stop_codon&quot;, and &quot;exon&quot;.\n4. start - The starting position of the feature in the sequence. The first base is numbered 1.\n5. end - The ending position of the feature (inclusive).\n6. score - A score between 0 and 1000. If there is no score value, enter &quot;.&quot;.\n7. strand - Valid entries include '+', '-', or '.' (for don't know/care).\n8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.\n9. group - All lines with the same group are linked together into a single item.\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "filter",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=Extract_features1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Extract_features1",
+        "name": "Extract features"
+      },
+      {
+        "panel_section_name": "Filter and Sort",
+        "xrefs": [],
+        "description": "using simple expressions",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"warningmark\">Double equal signs, ==, must be used as <em>&quot;equal to&quot;<\/em> (e.g., <strong>c1 == 'chr22'<\/strong>)<\/p>\n<p class=\"infomark\"><strong>TIP:<\/strong> Attempting to apply a filtering condition may throw exceptions if the data type (e.g., string, integer) in every line of the attribute being filtered is not appropriate for the condition (e.g., attempting certain numerical calculations on strings).  If an exception is thrown when applying the condition to a line, that line is skipped as invalid for the filter condition.  The number of invalid skipped lines is documented in the resulting history item as a &quot;Condition/data issue&quot;.<\/p>\n<p class=\"infomark\"><strong>TIP:<\/strong> If your data is not TAB delimited, use <em>Text Manipulation-&gt;Convert<\/em><\/p>\n<hr class=\"docutils\" />\n<p><strong>Syntax<\/strong><\/p>\n<p>The filter tool allows you to restrict the dataset using simple conditional statements.<\/p>\n<ul class=\"simple\">\n<li>Make sure that multi-character operators contain no white space ( e.g., <strong>&lt;=<\/strong> is valid while <strong>&lt; =<\/strong> is not valid )<\/li>\n<li>When using 'equal-to' operator <strong>double equal sign '==' must be used<\/strong> ( e.g., <strong>attribute_name=='chr1'<\/strong> )<\/li>\n<li>Non-numerical values must be included in single or double quotes ( e.g., <strong>attribute_name=='XX22'<\/strong> )<\/li>\n<li>You can combine multiple conditional statements using <strong>and<\/strong> or <strong>or<\/strong> ( e.g., <strong>attribute_name=='XX22' or attribute_name=='XX21'<\/strong> )<\/li>\n<\/ul>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "filter",
+        "version": "0.2",
+        "link": "/tool_runner?tool_id=gff_filter_by_attribute",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "gff_filter_by_attribute",
+        "name": "Filter GFF data by attribute"
+      },
+      {
+        "panel_section_name": "Filter and Sort",
+        "xrefs": [],
+        "description": "using simple expressions",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\">Valid comparison operators are: &gt; &lt; &gt;=, &lt;=, !=, and ==<\/p>\n<hr class=\"docutils\" />\n<p><strong>Syntax<\/strong><\/p>\n<p>The filter tool allows you to restrict the dataset based on transcripts' feature counts.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "filter",
+        "version": "0.1.1",
+        "link": "/tool_runner?tool_id=gff_filter_by_feature_count",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "gff_filter_by_feature_count",
+        "name": "Filter GFF data by feature count"
+      },
+      {
+        "panel_section_name": "Filter and Sort",
+        "xrefs": [],
+        "description": "",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p>This tool filters a GTF file using a list of attribute values. The attribute values are\ntaken from the first column in the file; additional columns in the file are ignored. An example\nuse of this tool is to filter a GTF file using a list of transcript_ids or gene_ids obtained from Cuffdiff.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "filter",
+        "version": "0.1",
+        "link": "/tool_runner?tool_id=gtf_filter_by_attribute_values_list",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "gtf_filter_by_attribute_values_list",
+        "name": "Filter GTF data by attribute values_list"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "filter",
+    "name": "Filter and Sort"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Join, Subtract and Group",
+        "xrefs": [],
+        "description": "side by side on a specified field",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"warningmark\"><strong>This tool will force the ouput datatype to tabular.<\/strong> To change metadata assignments click on the &quot;edit attributes&quot; link of the history item generated by this tool.<\/p>\n<p class=\"infomark\"><strong>TIP:<\/strong> If your data is not TAB delimited, use <em>Text Manipulation-&gt;Convert<\/em><\/p>\n<hr class=\"docutils\" />\n<p><strong>Syntax<\/strong><\/p>\n<p>This tool joins lines of two datasets on a common field. An empty string (&quot;&quot;) is not a valid identifier.\nYou may choose to include lines of your first input that do not join with your second input.<\/p>\n<ul class=\"simple\">\n<li>Columns are referenced with a <strong>number<\/strong>. For example, <strong>3<\/strong> refers to the 3rd column of a tab-delimited file.<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Dataset1:<\/p>\n<pre class=\"literal-block\">\nchr1 10 20 geneA\nchr1 50 80 geneB\nchr5 10 40 geneL\n<\/pre>\n<p>Dataset2:<\/p>\n<pre class=\"literal-block\">\ngeneA tumor-supressor\ngeneB Foxp2\ngeneC Gnas1\ngeneE INK4a\n<\/pre>\n<p>Joining the 4th column of Dataset1 with the 1st column of Dataset2 will yield:<\/p>\n<pre class=\"literal-block\">\nchr1 10 20 geneA geneA tumor-suppressor\nchr1 50 80 geneB geneB Foxp2\n<\/pre>\n<p>Joining the 4th column of Dataset1 with the 1st column of Dataset2, while keeping all lines from Dataset1, will yield:<\/p>\n<pre class=\"literal-block\">\nchr1 10 20 geneA geneA tumor-suppressor\nchr1 50 80 geneB geneB Foxp2\nchr5 10 40 geneL\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "group",
+        "version": "2.1.2",
+        "link": "/tool_runner?tool_id=join1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "join1",
+        "name": "Join two Datasets"
+      },
+      {
+        "panel_section_name": "Join, Subtract and Group",
+        "xrefs": [],
+        "description": "to find common or distinct rows",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\"><strong>TIP:<\/strong> If your data is not TAB delimited, use <em>Text Manipulation-&gt;Convert<\/em><\/p>\n<hr class=\"docutils\" />\n<p><strong>Syntax<\/strong><\/p>\n<p>This tool finds lines in one dataset that HAVE or DO NOT HAVE a common field with another dataset.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>If this is <strong>First dataset<\/strong>:<\/p>\n<pre class=\"literal-block\">\nchr1 10 20 geneA\nchr1 50 80 geneB\nchr5 10 40 geneL\n<\/pre>\n<p>and this is <strong>Second dataset<\/strong>:<\/p>\n<pre class=\"literal-block\">\ngeneA tumor-suppressor\ngeneB Foxp2\ngeneC Gnas1\ngeneE INK4a\n<\/pre>\n<p>Finding lines of the <strong>First dataset<\/strong> whose 4th column matches the 1st column of the <strong>Second dataset<\/strong> yields:<\/p>\n<pre class=\"literal-block\">\nchr1 10 20 geneA\nchr1 50 80 geneB\n<\/pre>\n<p>Conversely, using option <strong>Non Matching rows of First dataset<\/strong> on the same fields will yield:<\/p>\n<pre class=\"literal-block\">\nchr5 10 40 geneL\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "group",
+        "version": "1.0.2",
+        "link": "/tool_runner?tool_id=comp1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "comp1",
+        "name": "Compare two Datasets"
+      },
+      {
+        "panel_section_name": "Join, Subtract and Group",
+        "xrefs": [],
+        "description": "data by a column and perform aggregate operation on other columns.",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\"><strong>TIP:<\/strong> If your data is not TAB delimited, use <em>Text Manipulation-&gt;Convert<\/em><\/p>\n<hr class=\"docutils\" />\n<p><strong>Syntax<\/strong><\/p>\n<p>This tool allows you to group the input dataset by a particular column and perform aggregate functions: Mean, Median, Mode, Sum, Max, Min, Count, Concatenate, and Randomly pick on any column(s).<\/p>\n<p>The Concatenate function will take, for each group, each item in the specified column and build a comma delimited list. Concatenate Unique will do the same but will build a list of unique items with no repetition.<\/p>\n<p>Count and Count Unique are equivalent to Concatenate and Concatenate Unique, but will only count the number of items and will return an integer.<\/p>\n<ul class=\"simple\">\n<li>If multiple modes are present, all are reported.<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<ul>\n<li><p class=\"first\">For the following input:<\/p>\n<pre class=\"literal-block\">\nchr22  1000  1003  TTT\nchr22  2000  2003  aaa\nchr10  2200  2203  TTT\nchr10  1200  1203  ttt\nchr22  1600  1603  AAA\n<\/pre>\n<\/li>\n<li><p class=\"first\"><strong>Grouping on column 4<\/strong> while ignoring case, and performing operation <strong>Count on column 1<\/strong> will return:<\/p>\n<pre class=\"literal-block\">\nAAA    2\nTTT    3\n<\/pre>\n<\/li>\n<li><p class=\"first\"><strong>Grouping on column 4<\/strong> while not ignoring case, and performing operation <strong>Count on column 1<\/strong> will return:<\/p>\n<pre class=\"literal-block\">\naaa    1\nAAA    1\nttt    1\nTTT    2\n<\/pre>\n<\/li>\n<\/ul>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "group",
+        "version": "2.1.4",
+        "link": "/tool_runner?tool_id=Grouping1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Grouping1",
+        "name": "Group"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "group",
+    "name": "Join, Subtract and Group"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Fetch Alignments/Sequences",
+        "xrefs": [],
+        "description": "by Species",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool examines each MAF block for multiple occurrences of a species in a single block. When this occurs, a block is split into multiple blocks where every combination of one sequence per species per block is represented.<\/p>\n<p>The interface for this tool has two inputs:<\/p>\n<blockquote>\n<ul class=\"simple\">\n<li><strong>MAF file to split<\/strong>. Choose multiple alignments from history to be split by species.<\/li>\n<li><strong>Collapse empty alignment columns<\/strong>. Should alignment columns containing only gaps in the new blocks be removed.<\/li>\n<\/ul>\n<\/blockquote>\n<hr class=\"docutils\" />\n<p><strong>Example 1<\/strong>: <strong>Collapse empty alignment columns is Yes<\/strong>:<\/p>\n<p>For the following alignment:<\/p>\n<pre class=\"literal-block\">\na score=2047408.0\ns species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG\ns species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG\ns species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n<\/pre>\n<p>the tool will create <strong>a single<\/strong> history item containing 12 alignment blocks (notice that no columns contain only gaps):<\/p>\n<pre class=\"literal-block\">\na score=2047408.0\ns species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG\ns species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG\ns species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT-GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT-GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC--GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG\ns species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC-GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG\ns species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC-GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTAG\ns species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGCAG\n\na score=2047408.0\ns species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCAG\ns species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC---AG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC---AG\n<\/pre>\n<hr class=\"docutils\" />\n<p><strong>Example 2<\/strong>: <strong>Collapse empty alignment columns is No<\/strong>:<\/p>\n<p>For the following alignment:<\/p>\n<pre class=\"literal-block\">\na score=2047408.0\ns species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG\ns species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG\ns species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n<\/pre>\n<p>the tool will create <strong>a single<\/strong> history item containing 12 alignment blocks (notice that some columns contain only gaps):<\/p>\n<pre class=\"literal-block\">\na score=2047408.0\ns species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG\ns species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG\ns species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG\ns species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG\ns species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\ns species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG\ns species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n\na score=2047408.0\ns species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG\ns species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG\ns species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n<\/pre>\n<hr class=\"docutils\" />\n<p class=\"infomark\"><strong>About formats<\/strong><\/p>\n<p><strong>MAF format<\/strong> multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes.<\/p>\n<blockquote>\n<ul class=\"simple\">\n<li>The .maf format is line-oriented. Each multiple alignment ends with a blank line.<\/li>\n<li>Each sequence in an alignment is on a single line.<\/li>\n<li>Lines starting with # are considered to be comments.<\/li>\n<li>Each multiple alignment is in a separate paragraph that begins with an &quot;a&quot; line and contains an &quot;s&quot; line for each sequence in the multiple alignment.<\/li>\n<li>Some MAF files may contain two optional line types:<ul>\n<li>An &quot;i&quot; line containing information about what is in the aligned species DNA before and after the immediately preceding &quot;s&quot; line;<\/li>\n<li>An &quot;e&quot; line containing information about the size of the gap between the alignments that span the current block.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/blockquote>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "fetchAlignSeq",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=MAF_split_blocks_by_species1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "MAF_split_blocks_by_species1",
+        "name": "Split MAF blocks"
+      },
+      {
+        "panel_section_name": "Fetch Alignments/Sequences",
+        "xrefs": [],
+        "description": "given a set of coding exon intervals",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>The coding sequence of genes are usually composed of several coding exons. Each of these coding exons is an individual genomic region, which when concatenated with each other constitutes the coding sequence. A single genomic region can be covered by multiple alignment blocks. In many cases it is desirable to stitch these alignment blocks together. This tool accepts a list of gene-based intervals, in the Gene BED format. For every interval it performs the following:<\/p>\n<blockquote>\n<ul class=\"simple\">\n<li>finds all MAF blocks that overlap the coding regions;<\/li>\n<li>sorts MAF blocks by alignment score;<\/li>\n<li>stitches blocks together and resolves overlaps based on alignment score;<\/li>\n<li>outputs alignments in FASTA format.<\/li>\n<\/ul>\n<\/blockquote>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "fetchAlignSeq",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=GeneBed_Maf_Fasta2",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "GeneBed_Maf_Fasta2",
+        "name": "Stitch Gene blocks"
+      },
+      {
+        "panel_section_name": "Fetch Alignments/Sequences",
+        "xrefs": [],
+        "description": "Alignment coverage information",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool takes a MAF file and an interval file and relates coverage information by interval for each species.\nIf a column does not exist in the reference genome, it is not included in the output.<\/p>\n<dl class=\"docutils\">\n<dt>Consider the interval: &quot;chrX 1000 1100 myInterval&quot;<\/dt>\n<dd><p class=\"first\">Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this:<\/p>\n<blockquote>\n<p>chrX 1000 1100 myInterval H XXX YYY<\/p>\n<p>chrX 1000 1100 myInterval M XXX YYY<\/p>\n<p>chrX 1000 1100 myInterval R XXX YYY<\/p>\n<\/blockquote>\n<p>where XXX and YYY are:<\/p>\n<blockquote class=\"last\">\n<p>XXX = number of nucleotides<\/p>\n<p>YYY = number of gaps<\/p>\n<\/blockquote>\n<\/dd>\n<\/dl>\n<hr class=\"docutils\" />\n<p>Alternatively, you can request only summary information for a set of intervals:<\/p>\n<blockquote>\n<table border=\"1\" class=\"docutils\">\n<colgroup>\n<col width=\"30%\" />\n<col width=\"41%\" />\n<col width=\"30%\" />\n<\/colgroup>\n<thead valign=\"bottom\">\n<tr><th class=\"head\">#species<\/th>\n<th class=\"head\">nucleotides<\/th>\n<th class=\"head\">coverage<\/th>\n<\/tr>\n<\/thead>\n<tbody valign=\"top\">\n<tr><td>hg18<\/td>\n<td>30639<\/td>\n<td>0.2372<\/td>\n<\/tr>\n<tr><td>rheMac2<\/td>\n<td>7524<\/td>\n<td>0.0582<\/td>\n<\/tr>\n<tr><td>panTro2<\/td>\n<td>30390<\/td>\n<td>0.2353<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>where <strong>coverage<\/strong> is the number of nucleotides divided by the total length of the provided intervals.<\/p>\n<\/blockquote>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "fetchAlignSeq",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=maf_stats1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "maf_stats1",
+        "name": "MAF Coverage Stats"
+      },
+      {
+        "panel_section_name": "Fetch Alignments/Sequences",
+        "xrefs": [],
+        "description": "by Species",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool allows the user to merge MAF blocks which are adjoining in each specified species from a MAF file. Columns which contain only gaps are removed. Species which are not desired are removed from the output.<\/p>\n<p><strong>Example<\/strong><\/p>\n<p>Specifying the desired species as hg17 and panTro1 with this MAF file:<\/p>\n<pre class=\"literal-block\">\na score=60426.000000\ns hg17.chr7    127471195 331 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA\ns panTro1.chr6 129885076 331 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA\ns mm5.chr6      28904571 357 + 149721531 CTCCACTCTCGTTTGCTGTT----------------CTGTCACCATGGAAACAAA-CGAGGGTGGTCCAGTTACTATCTTGACTGCAGCTGGCAGTCAGTT-GCCACT-----CAGGAATAAGGCTATGCCATT-GATCCACTGAACCGTGATCTGGAAACCTGGCTGTTGTTT-------CAAGCCTTGGGGCCAGTTTGCGGTGTTACTCATGA--CTCTAAGATCGTGTGCTTG----CTGCAGGAAGAGACAGCAAGGGGGTTACATTTAAAAAGCCCCCAGTTTAGCTATAGGCAGGCCAACAGGTGTAAAAATACTCACTAGTAATGGGCTGAACTCATGGAGGTAGCATTAGTGAGACACTGTAACTGTTTTTTTAAAAATCACTAA\ns rn3.chr4      56178191 282 + 187371129 CTTCACTCTCATTTGCTGTT----------------CTGTCACTATGGAGACAAACACAGGCTAGCCCAGTTACTATCTTGATCACAGCAGCT-GTCAGCTAGCTGCCACTCACAGGAATAAGGCCATACCATT-GATCCACTGAACCTTGATCTAGGAATTTGGC----------------------TGGGGCCAGTTTGCGGTGTCACTCATGA--CTCTAAGATTGTGTGTTTG----CTCCAGGAAGAGACGGCAAGAGGATTACCTTTAAAAGGTTC---------------------------------GGAGTCTAGCTGTAGACAGCCCA-----ATG--GGTA-------TAAC-------------------AATACTCACTAA\n\na score=8157.000000\ns hg17.chr7    127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\ns panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\ns mm5.chr6      28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG\n<\/pre>\n<p>results in:<\/p>\n<pre class=\"literal-block\">\na score=0.0\ns hg17.chr7    127471195 389 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\ns panTro1.chr6 129885076 389 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "fetchAlignSeq",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=MAF_Thread_For_Species1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "MAF_Thread_For_Species1",
+        "name": "Join MAF blocks"
+      },
+      {
+        "panel_section_name": "Fetch Alignments/Sequences",
+        "xrefs": [],
+        "description": "by Species",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What It Does<\/strong><\/p>\n<p>This tool allows the user to remove any undesired species from a MAF file. Columns which contain only gaps are removed. The options for this tool are:<\/p>\n<blockquote>\n<ul class=\"simple\">\n<li><strong>Exclude blocks which have missing species<\/strong> - suppose you want to restrict an 8-way alignment to human, mouse, and rat.  The tool will first remove all other species. Next, if this option is set to <strong>YES<\/strong> the tool WILL NOT return MAF blocks, which do not include human, mouse, or rat. This means that all alignment blocks returned by the tool will have exactly three sequences in this example.<\/li>\n<li><strong>Exclude blocks with have only one species<\/strong> - if this option is set to <strong>YES<\/strong> all single sequence alignment blocks WILL NOT be returned.<\/li>\n<\/ul>\n<\/blockquote>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "fetchAlignSeq",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=MAF_Limit_To_Species1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "MAF_Limit_To_Species1",
+        "name": "Filter MAF blocks"
+      },
+      {
+        "panel_section_name": "Fetch Alignments/Sequences",
+        "xrefs": [],
+        "description": "by Size",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool takes a MAF file and a size range and extracts the MAF blocks which fall within the specified range.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "fetchAlignSeq",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=maf_limit_size1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "maf_limit_size1",
+        "name": "Filter MAF blocks"
+      },
+      {
+        "panel_section_name": "Fetch Alignments/Sequences",
+        "xrefs": [],
+        "description": "given a set of block numbers and a MAF file",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool takes a list of block numbers, one per line, and extracts the corresponding MAF blocks from the provided file. Block numbers start at 0.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "fetchAlignSeq",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=maf_by_block_number1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "maf_by_block_number1",
+        "name": "Extract MAF by block number"
+      },
+      {
+        "panel_section_name": "Fetch Alignments/Sequences",
+        "xrefs": [],
+        "description": "a MAF file",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool takes a MAF file and creates a new MAF file, where each block has been reversed complemented.<\/p>\n<p><strong>Example<\/strong><\/p>\n<p>This MAF Block:<\/p>\n<pre class=\"literal-block\">\na score=8157.000000\ns hg17.chr7    127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\ns panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\ns mm5.chr6      28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG\n<\/pre>\n<p>becomes:<\/p>\n<pre class=\"literal-block\">\na score=8157.000000\ns hg17.chr7     31156555 58 - 158628139 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAATGAATAAACCACAAATT\ns panTro1.chr6  31691510 58 - 161576975 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAACGAATAAACCACAAATT\ns mm5.chr6     120816549 54 - 149721531 CCTCTTCCACTGAGGAATTTCTTTTTTTAAATGATGAGCAATCAATGAAACG----TT\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "fetchAlignSeq",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=MAF_Reverse_Complement_1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "MAF_Reverse_Complement_1",
+        "name": "Reverse Complement"
+      },
+      {
+        "panel_section_name": "Fetch Alignments/Sequences",
+        "xrefs": [],
+        "description": "by specified attributes",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p>This tool allows you to build complex filters to be applied to each alignment block of a MAF file. You can define restraints on species based upon chromosome and strand. You can specify comma separated lists of chromosomes where appropriate.<\/p>\n<p class=\"infomark\">For example, this tool is useful to restrict a set of alignments to only those blocks which contain alignments between chromosomes that are considered homologous.<\/p>\n<hr class=\"docutils\" />\n<p class=\"warningmark\">If a species is not found in a particular block, all filters on that species are ignored.<\/p>\n<hr class=\"docutils\" />\n<p>This tool allows the user to remove any undesired species from a MAF file. If no species are specified then all species will be kept. If species are specified, columns which contain only gaps are removed. The options for this are:<\/p>\n<blockquote>\n<ul class=\"simple\">\n<li><strong>Exclude blocks which have missing species<\/strong> - suppose you want to restrict an 8-way alignment to human, mouse, and rat.  The tool will first remove all other species. Next, if this option is set to <strong>YES<\/strong> the tool WILL NOT return MAF blocks, which do not include human, mouse, or rat. This means that all alignment blocks returned by the tool will have exactly three sequences in this example.<\/li>\n<li><strong>Exclude blocks which have only one species<\/strong> - if this option is set to <strong>YES<\/strong> all single sequence alignment blocks WILL NOT be returned.<\/li>\n<\/ul>\n<\/blockquote>\n<hr class=\"docutils\" />\n<p>You can also provide a size range and limit your output to the MAF blocks which fall within the specified range.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "fetchAlignSeq",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=MAF_filter",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "MAF_filter",
+        "name": "Filter MAF"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "fetchAlignSeq",
+    "name": "Fetch Alignments/Sequences"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Operate on Genomic Intervals",
+        "xrefs": [],
+        "description": "converter",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>Syntax<\/strong><\/p>\n<p>This tool converts wiggle data into interval type.<\/p>\n<ul>\n<li><p class=\"first\"><strong>Wiggle format<\/strong>: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line.  Following the track definition line is the track data, which can be entered in three different formats described below.<\/p>\n<ul>\n<li><p class=\"first\"><strong>BED format<\/strong> with no declaration line and four columns of data:<\/p>\n<pre class=\"literal-block\">\nchromA  chromStartA  chromEndA  dataValueA\nchromB  chromStartB  chromEndB  dataValueB\n<\/pre>\n<\/li>\n<li><p class=\"first\"><strong>variableStep<\/strong> two column data; started by a declaration line and followed with chromosome positions and data values:<\/p>\n<pre class=\"literal-block\">\nvariableStep  chrom=chrN  [span=windowSize]\nchromStartA  dataValueA\nchromStartB  dataValueB\n<\/pre>\n<\/li>\n<li><p class=\"first\"><strong>fixedStep<\/strong> single column data; started by a declaration line and followed with data values:<\/p>\n<pre class=\"literal-block\">\nfixedStep  chrom=chrN  start=position  step=stepInterval  [span=windowSize]\ndataValue1\ndataValue2\n<\/pre>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<ul>\n<li><p class=\"first\">input wiggle format file:<\/p>\n<pre class=\"literal-block\">\n#track type=wiggle_0 name=&quot;Bed Format&quot; description=&quot;BED format&quot;\nchr19 59302000 59302300 -1.0\nchr19 59302300 59302600 -0.75\nchr19 59302600 59302900 -0.50\nchr19 59302900 59303200 -0.25\nchr19 59303200 59303500 0.0\n#track type=wiggle_0 name=&quot;variableStep&quot; description=&quot;variableStep format&quot;\nvariableStep chrom=chr19 span=150\n59304701 10.0\n59304901 12.5\n59305401 15.0\n59305601 17.5\n#track type=wiggle_0 name=&quot;fixedStep&quot; description=&quot;fixed step&quot; visibility=full\nfixedStep chrom=chr19 start=59307401 step=300 span=200\n1000\n900\n800\n700\n600\n<\/pre>\n<\/li>\n<li><p class=\"first\">convert the above file to interval file:<\/p>\n<pre class=\"literal-block\">\nchr19       59302000        59302300        +       -1.0\nchr19       59302300        59302600        +       -0.75\nchr19       59302600        59302900        +       -0.5\nchr19       59302900        59303200        +       -0.25\nchr19       59303200        59303500        +       0.0\nchr19       59304701        59304851        +       10.0\nchr19       59304901        59305051        +       12.5\nchr19       59305401        59305551        +       15.0\nchr19       59305601        59305751        +       17.5\nchr19       59307701        59307901        +       1000.0\nchr19       59308001        59308201        +       900.0\nchr19       59308301        59308501        +       800.0\nchr19       59308601        59308801        +       700.0\nchr19       59308901        59309101        +       600.0\n<\/pre>\n<\/li>\n<\/ul>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "bxops",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=wiggle2simple1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "wiggle2simple1",
+        "name": "Wiggle-to-Interval"
+      },
+      {
+        "panel_section_name": "Operate on Genomic Intervals",
+        "xrefs": [],
+        "description": "Appends the average, min, max of datapoints per interval",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"warningmark\">This tool currently only has cached data for genome builds hg16, hg17 and hg18. However, you may use your own data point (wiggle) data, such as those available from UCSC. If you are trying to use your own data point file and it is not appearing as an option, make sure that the builds for your history items are the same.<\/p>\n<p class=\"warningmark\">This tool assumes that the input dataset is in interval format and contains at least a chrom column, a start column and an end column.  These 3 columns can be dispersed throughout any number of other data columns.<\/p>\n<hr class=\"docutils\" />\n<p class=\"infomark\"><strong>TIP:<\/strong> Computing summary information may throw exceptions if the data type (e.g., string, integer) in every line of the columns is not appropriate for the computation (e.g., attempting numerical calculations on strings).  If an exception is thrown when computing summary information for a line, that line is skipped as invalid for the computation.  The number of invalid skipped lines is documented in the resulting history item as a &quot;Data issue&quot;.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Syntax<\/strong><\/p>\n<p>This tool appends columns of summary information for each interval matched against a selected dataset.  For each interval, the average, minimum and maximum for the data falling within the interval is computed.<\/p>\n<ul class=\"simple\">\n<li>Several quantitative scores are provided for the ENCODE regions.<ul>\n<li><dl class=\"first docutils\">\n<dt>Various Scores<\/dt>\n<dd><ul class=\"first last\">\n<li>Regulatory Potential<\/li>\n<li>Neutral rate (Ancestral Repeats)<\/li>\n<li>GC fraction<\/li>\n<\/ul>\n<\/dd>\n<\/dl>\n<\/li>\n<li><dl class=\"first docutils\">\n<dt>Conservation Scores<\/dt>\n<dd><ul class=\"first last\">\n<li>PhastCons<\/li>\n<li>binCons<\/li>\n<li>GERP<\/li>\n<\/ul>\n<\/dd>\n<\/dl>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>If your original data has the following format:<\/p>\n<table border=\"1\" class=\"docutils\">\n<colgroup>\n<col width=\"24%\" />\n<col width=\"20%\" />\n<col width=\"20%\" />\n<col width=\"12%\" />\n<col width=\"24%\" />\n<\/colgroup>\n<tbody valign=\"top\">\n<tr><td>other1<\/td>\n<td>chrom<\/td>\n<td>start<\/td>\n<td>end<\/td>\n<td>other2<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>and you choose to aggregate phastCons scores, your output will look like this:<\/p>\n<table border=\"1\" class=\"docutils\">\n<colgroup>\n<col width=\"18%\" />\n<col width=\"15%\" />\n<col width=\"15%\" />\n<col width=\"9%\" />\n<col width=\"18%\" />\n<col width=\"9%\" />\n<col width=\"9%\" />\n<col width=\"9%\" />\n<\/colgroup>\n<tbody valign=\"top\">\n<tr><td>other1<\/td>\n<td>chrom<\/td>\n<td>start<\/td>\n<td>end<\/td>\n<td>other2<\/td>\n<td>avg<\/td>\n<td>min<\/td>\n<td>max<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>where:<\/p>\n<ul class=\"simple\">\n<li><strong>avg<\/strong> - average phastCons score for each region<\/li>\n<li><strong>min<\/strong> - minimum phastCons score for each region<\/li>\n<li><strong>max<\/strong> - maximum phastCons score for each region<\/li>\n<\/ul>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "bxops",
+        "version": "1.1.3",
+        "link": "/tool_runner?tool_id=aggregate_scores_in_intervals2",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "aggregate_scores_in_intervals2",
+        "name": "Aggregate datapoints"
+      },
+      {
+        "panel_section_name": "Operate on Genomic Intervals",
+        "xrefs": [],
+        "description": "expander",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"warningmark\">This tool works only on a BED file that contains at least 12 fields (see <strong>Example<\/strong> and <strong>About formats<\/strong> below).  The output will be empty if applied to a BED file with 3 or 6 fields.<\/p>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>BED format can be used to represent a single gene in just one line, which contains the information about exons, coding sequence location (CDS), and positions of untranslated regions (UTRs).  This tool <em>unpacks<\/em> this information by converting a single line describing a gene into a collection of lines representing individual exons, introns, UTRs, etc.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Extracting <strong>Coding Exons + UTR Exons<\/strong> from the following two BED lines:<\/p>\n<pre class=\"literal-block\">\nchr7 127475281 127491632 NM_000230 0 + 127486022 127488767 0 3 29,172,3225,    0,10713,13126\nchr7 127486011 127488900 D49487    0 + 127486022 127488767 0 2 155,490,        0,2399\n<\/pre>\n<p>will return:<\/p>\n<pre class=\"literal-block\">\nchr7 127475281 127475310 NM_000230 0 +\nchr7 127485994 127486166 NM_000230 0 +\nchr7 127488407 127491632 NM_000230 0 +\nchr7 127486011 127486166 D49487    0 +\nchr7 127488410 127488900 D49487    0 +\n<\/pre>\n<hr class=\"docutils\" />\n<p class=\"infomark\"><strong>About formats<\/strong><\/p>\n<p><strong>BED format<\/strong> Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and additional optional ones. In the specific case of this tool the following fields must be present:<\/p>\n<pre class=\"literal-block\">\n 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).\n 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)\n 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).\n 4. name - The name of the BED line.\n 5. score - A score between 0 and 1000.\n 6. strand - Defines the strand - either '+' or '-'.\n 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.\n 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.\n 9. reserved - This should always be set to zero.\n10. blockCount - The number of blocks (exons) in the BED line.\n11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.\n12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "bxops",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=gene2exon1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "gene2exon1",
+        "name": "Gene BED To Exon/Intron/Codon BED"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "bxops",
+    "name": "Operate on Genomic Intervals"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Statistics",
+        "xrefs": [],
+        "description": "for any numerical column",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"warningmark\">This tool expects input datasets consisting of tab-delimited columns (blank or comment lines beginning with a # character are automatically skipped).<\/p>\n<p class=\"infomark\"><strong>TIP:<\/strong> If your data is not TAB delimited, use <em>Text Manipulation-&gt;Convert delimiters to TAB<\/em><\/p>\n<p class=\"infomark\"><strong>TIP:<\/strong> Computing summary statistics may throw exceptions if the data value in every line of the columns being summarized is not numerical.  If a line is missing a value or contains a non-numerical value in the column being summarized, that line is skipped and the value is not included in the statistical computation.  The number of invalid skipped lines is documented in the resulting history item.<\/p>\n<p class=\"infomark\"><strong>USING R FUNCTIONS:<\/strong> Most functions (like <em>abs<\/em>) take only a single expression. <em>log<\/em> can take one or two parameters, like <em>log(expression,base)<\/em><\/p>\n<p>Currently, these R functions are supported: <em>abs, sign, sqrt, floor, ceiling, trunc, round, signif, exp, log, cos, sin, tan, acos, asin, atan, cosh, sinh, tanh, acosh, asinh, atanh, lgamma, gamma, gammaCody, digamma, trigamma, cumsum, cumprod, cummax, cummin<\/em><\/p>\n<hr class=\"docutils\" />\n<p><strong>Syntax<\/strong><\/p>\n<p>This tool computes basic summary statistics on a given column, or on a valid expression containing one or more columns.<\/p>\n<ul class=\"simple\">\n<li>Columns are referenced with <strong>c<\/strong> and a <strong>number<\/strong>. For example, <strong>c1<\/strong> refers to the first column of a tab-delimited file.<\/li>\n<li>For example:<ul>\n<li><strong>log(c5)<\/strong> calculates the summary statistics for the natural log of column 5<\/li>\n<li><strong>(c5 + c6 + c7) / 3<\/strong> calculates the summary statistics on the average of columns 5-7<\/li>\n<li><strong>log(c5,10)<\/strong> summary statistics of the base 10 log of column 5<\/li>\n<li><strong>sqrt(c5+c9)<\/strong> summary statistics of the square root of column 5 + column 9<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Examples<\/strong><\/p>\n<ul>\n<li><p class=\"first\">Input Dataset:<\/p>\n<pre class=\"literal-block\">\nc1      c2      c3      c4      c5              c6\n586     chrX    161416  170887  41108_at        16990\n73      chrX    505078  532318  35073_at        1700\n595     chrX    1361578 1388460 33665_s_at      1960\n74      chrX    1420620 1461919 1185_at         8600\n<\/pre>\n<\/li>\n<li><p class=\"first\">Summary Statistics on column c6 of the above input dataset:<\/p>\n<pre class=\"literal-block\">\n#sum       mean      stdev     0%        25%       50%       75%        100%\n29250.000  7312.500  7198.636  1700.000  1895.000  5280.000  10697.500  16990.000\n<\/pre>\n<\/li>\n<\/ul>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [
+          "topic_2269"
+        ],
+        "panel_section_id": "stats",
+        "version": "1.1.2",
+        "link": "/tool_runner?tool_id=Summary_Statistics1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Summary_Statistics1",
+        "name": "Summary Statistics"
+      },
+      {
+        "panel_section_name": "Statistics",
+        "xrefs": [],
+        "description": "occurrences of each record",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p class=\"infomark\"><strong>TIP:<\/strong> If your data is not TAB delimited, use <em>Text Manipulation-&gt;Convert<\/em><\/p>\n<hr class=\"docutils\" />\n<p><strong>Syntax<\/strong><\/p>\n<p>This tool counts occurrences of unique values in selected column(s).<\/p>\n<ul class=\"simple\">\n<li>If multiple columns are selected, counting is performed on each unique group of all values in the selected columns.<\/li>\n<li>The first column of the resulting dataset will be the count of unique values in the selected column(s) and will be followed by each value.<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<ul>\n<li><p class=\"first\">Input file:<\/p>\n<pre class=\"literal-block\">\nchr1   10  100  gene1\nchr1  105  200  gene2\nchr1  205  300  gene3\nchr2   10  100  gene4\nchr2 1000 1900  gene5\nchr3   15 1656  gene6\nchr4   10 1765  gene7\nchr4   10 1765  gene8\n<\/pre>\n<\/li>\n<li><p class=\"first\">Counting unique values in column c1 will result in:<\/p>\n<pre class=\"literal-block\">\n3 chr1\n2 chr2\n1 chr3\n2 chr4\n<\/pre>\n<\/li>\n<li><p class=\"first\">Counting unique values in the grouping of columns c2 and c3 will result in:<\/p>\n<pre class=\"literal-block\">\n2    10    100\n2    10    1765\n1    1000  1900\n1    105   200\n1    15    1656\n1    205   300\n<\/pre>\n<\/li>\n<\/ul>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "stats",
+        "version": "1.0.3",
+        "link": "/tool_runner?tool_id=Count1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "Count1",
+        "name": "Count"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "stats",
+    "name": "Statistics"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Graph/Display Data",
+        "xrefs": [],
+        "description": "for display at UCSC",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>What it does<\/strong><\/p>\n<p>This tool converts a Variant Call Format (VCF) file into a Multiple Alignment Format (MAF) custom track file suitable for display at genome browsers.<\/p>\n<p>This file should be used for display purposes only (e.g as a UCSC Custom Track). Performing an analysis using the output created by this tool as input is not recommended; the source VCF file should be used when performing an analysis.<\/p>\n<p><em>Unknown nucleotides<\/em> are represented as '*' as required to allow the display to draw properly; these include e.g. reference bases which appear before a deletion and are not available without querying the original reference sequence.<\/p>\n<p><strong>Example<\/strong><\/p>\n<p>Starting with a VCF:<\/p>\n<pre class=\"literal-block\">\n#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA00001 NA00002 NA00003\n20  14370   rs6054257   G   A   29  0   NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51  1|0:48:8:51,51  1/1:43:5:-1,-1\n20  17330   .   T   A   3   q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50  0|1:3:5:65,3    0/0:41:3:-1,-1\n20  1110696 rs6040355   A   G,T 67  0   NS=2;DP=10;AF=0.333,0.667;AA=T;DB   GT:GQ:DP:HQ 1|2:21:6:23,27  2|1:2:0:18,2    2/2:35:4:-1,-1\n20  1230237 .   T   .   47  0   NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60  0|0:48:4:51,51  0/0:61:2:-1,-1\n20  1234567 microsat1   G   D4,IGA  50  0   NS=3;DP=9;AA=G  GT:GQ:DP    0/1:35:4    0/2:17:2    1/1:40:3\n<\/pre>\n<p>Under the following conditions: <strong>VCF Source type:<\/strong> <em>Per Population (file)<\/em>, <strong>Name for this population:<\/strong> <em>CHB+JPT<\/em>\nResults in the following MAF custom track:<\/p>\n<pre class=\"literal-block\">\ntrack name=&quot;Galaxy Custom Track&quot; visibility=pack\na score=0\ns hg18.chr20  14369 1 + 14370 G\ns CHB+JPT_1.1     0 1 +     1 A\n\na score=0\ns hg18.chr20  17329 1 + 17330 T\ns CHB+JPT_1.2     0 1 +     1 A\n\na score=0\ns hg18.chr20  1110695 1 + 1110696 A\ns CHB+JPT_1.3       0 1 +       1 G\ns CHB+JPT_2.3       0 1 +       1 T\n\na score=0\ns hg18.chr20  1230236 1 + 1230237 T\ns CHB+JPT_1.4       0 1 +       1 .\n\na score=0\ns hg18.chr20  1234565 5 + 1234572 *G--***\ns CHB+JPT_1.5       0 1 +       1 *------\ns CHB+JPT_2.5       0 7 +       7 *GGA***\n<\/pre>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "plots",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=vcf_to_maf_customtrack1",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "vcf_to_maf_customtrack1",
+        "name": "VCF to MAF Custom Track"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "plots",
+    "name": "Graph/Display Data"
+  },
+  {
+    "elems": [
+      {
+        "panel_section_name": "Phenotype Association",
+        "xrefs": [],
+        "description": "tools for functional profiling of gene lists",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>Dataset formats<\/strong><\/p>\n<p>The input dataset is <a class=\"reference external\" href=\"/static/formatHelp.html#tab\">tabular<\/a> with a column of identifiers.\nThe output dataset is <a class=\"reference external\" href=\"/static/formatHelp.html#html\">html<\/a> with a link to g:Profiler.\n(<a class=\"reference external\" href=\"/static/formatHelp.html\">Dataset missing?<\/a>)<\/p>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>This tool creates a link to the g:GOSt tool (Gene Group Functional\nProfiling), which is part of the g:Profiler site at the University\nof Tartu in Estonia.  g:GOSt retrieves the most significant Gene\nOntology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs\nfor a user-specified group of genes, proteins, or microarray probes.\ng:GOSt also allows analysis of ranked or ordered lists of genes,\nvisual browsing of GO graph structure, interactive visualization of\nretrieved results, and many other features.  Multiple testing\ncorrections are applied to extract only statistically important\nresults.<\/p>\n<p>The g:GOSt form is pre-filled with gene, protein, or microarray probe\nIDs from the selected column of a tabular Galaxy dataset.  Or you\ncan chose to use the genomic coordinates (must be lastest build used by\nEnsembl).  The coordinates don't have to be genes they can be for\nSNPs, and g:GOst will map to the gene ID.  To follow\nthe created link, click on the eye icon when the Galaxy tool has\nfinished running.  Once at the g:Profiler site, scroll down to see\nthe g:GOSt results.  You can also adjust the options in the g:GOSt\nform to your liking, or use the row of links between the form and\nthe results to run other g:Profiler tools using the same list of IDs.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Reference<\/strong><\/p>\n<p>Reimand J, Kull M, Peterson H, Hansen J, Vilo J. (2007) g:Profiler -- a web-based\ntoolset for functional profiling of gene lists from large-scale experiments.\nNucleic Acids Res. 35(Web Server issue):W193-200. Epub 2007 May 3.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "hgv",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=hgv_linkToGProfile",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "hgv_linkToGProfile",
+        "name": "g:Profiler"
+      },
+      {
+        "panel_section_name": "Phenotype Association",
+        "xrefs": [],
+        "description": "functional annotation for a list of genes",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<blockquote>\n<\/blockquote>\n<p class=\"infomark\">The list is limited to 400 IDs.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Dataset formats<\/strong><\/p>\n<p>The input dataset is in <a class=\"reference external\" href=\"/static/formatHelp.html#tab\">tabular<\/a> format.  The output dataset is <a class=\"reference external\" href=\"/static/formatHelp.html#html\">html<\/a> with\na link to the DAVID website as described below.\n(<a class=\"reference external\" href=\"/static/formatHelp.html\">Dataset missing?<\/a>)<\/p>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>This tool creates a link to the Database for Annotation,\nVisualization, and Integrated Discovery (DAVID) website at NIH,\nsending a list of IDs from the selected column of a tabular\nGalaxy dataset.  To follow the created link, click on the\neye icon once the Galaxy tool has finished running.<\/p>\n<p>DAVID provides a comprehensive set of functional annotation tools\nto help investigators discover biological meaning behind large\nlists of genes.<\/p>\n<hr class=\"docutils\" />\n<p><strong>References<\/strong><\/p>\n<p>Huang DW, Sherman BT, Lempicki RA. (2009) Systematic and integrative analysis\nof large gene lists using DAVID bioinformatics resources.\nNat Protoc. 4(1):44-57.<\/p>\n<p>Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. (2003)\nDAVID: database for annotation, visualization, and integrated discovery.\nGenome Biol. 4(5):P3. Epub 2003 Apr 3.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "hgv",
+        "version": "1.0.1",
+        "link": "/tool_runner?tool_id=hgv_david",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "hgv_david",
+        "name": "DAVID"
+      },
+      {
+        "panel_section_name": "Phenotype Association",
+        "xrefs": [],
+        "description": "linkage disequilibrium and tag SNPs",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>Dataset formats<\/strong><\/p>\n<p>The input and output datasets are <a class=\"reference external\" href=\"/static/formatHelp.html#tab\">tabular<\/a>.\n(<a class=\"reference external\" href=\"/static/formatHelp.html\">Dataset missing?<\/a>)<\/p>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>This tool can be used to analyze the patterns of linkage disequilibrium\n(LD) between polymorphic sites in a locus.  SNPs are grouped based on the\nthreshold level of LD as measured by r<sup>2<\/sup> (regardless of genomic\nposition), and a representative &quot;tag SNP&quot; is reported for each group.\nThe other SNPs in the group are in LD with the tag SNP, but not necessarily\nwith each other.<\/p>\n<p>The underlying algorithm is the same as the one used in ldSelect (Carlson\net al. 2004).  However, this tool is implemented to be much faster and more\nefficient than ldSelect.<\/p>\n<p>The input is a tabular file with genotype information for each individual\nat each SNP site, in exactly four columns: site ID, sample ID, and the\ntwo allele nucleotides.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<ul>\n<li><p class=\"first\">input file:<\/p>\n<pre class=\"literal-block\">\nrs2334386  NA20364  G  T\nrs2334386  NA20363  G  G\nrs2334386  NA20360  G  G\nrs2334386  NA20359  G  G\nrs2334386  NA20358  G  G\nrs2334386  NA20356  G  G\nrs2334386  NA20357  G  G\nrs2334386  NA20350  G  G\nrs2334386  NA20349  G  G\nrs2334386  NA20348  G  G\nrs2334386  NA20347  G  G\nrs2334386  NA20346  G  G\nrs2334386  NA20345  G  G\nrs2334386  NA20344  G  G\nrs2334386  NA20342  G  G\netc.\n<\/pre>\n<\/li>\n<li><p class=\"first\">output file:<\/p>\n<pre class=\"literal-block\">\nrs2238748  rs2793064,rs6518516,rs6518517,rs2283641,rs5993533,rs715590,rs2072123,rs2105421,rs2800954,rs1557847,rs807750,rs807753,rs5993488,rs8138035,rs2800980,rs2525079,rs5992353,rs712966,rs2525036,rs807743,rs1034727,rs807744,rs2074003\nrs2871023  rs1210715,rs1210711,rs5748189,rs1210709,rs3788298,rs7284649,rs9306217,rs9604954,rs1210703,rs5748179,rs5746727,rs5748190,rs5993603,rs2238766,rs885981,rs2238763,rs5748165,rs9605996,rs9606001,rs5992398\nrs7292006  rs13447232,rs5993665,rs2073733,rs1057457,rs756658,rs5992395,rs2073760,rs739369,rs9606017,rs739370,rs4493360,rs2073736\nrs2518840  rs1061325,rs2283646,rs362148,rs1340958,rs361956,rs361991,rs2073754,rs2040771,rs2073740,rs2282684\nrs2073775  rs10160,rs2800981,rs807751,rs5993492,rs2189490,rs5747997,rs2238743\nrs5747263  rs12159924,rs2300688,rs4239846,rs3747025,rs3747024,rs3747023,rs2300691\nrs433576   rs9605439,rs1109052,rs400509,rs401099,rs396012,rs410456,rs385105\nrs2106145  rs5748131,rs2013516,rs1210684,rs1210685,rs2238767,rs2277837\nrs2587082  rs2257083,rs2109659,rs2587081,rs5747306,rs2535704,rs2535694\nrs807667   rs2800974,rs756651,rs762523,rs2800973,rs1018764\nrs2518866  rs1206542,rs807467,rs807464,rs807462,rs712950\nrs1110661  rs1110660,rs7286607,rs1110659,rs5992917,rs1110662\nrs759076   rs5748760,rs5748755,rs5748752,rs4819925,rs933461\nrs5746487  rs5992895,rs2034113,rs2075455,rs1867353\nrs5748212  rs5746736,rs4141527,rs5748147,rs5748202\netc.\n<\/pre>\n<\/li>\n<\/ul>\n<hr class=\"docutils\" />\n<p><strong>Reference<\/strong><\/p>\n<p>Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. (2004)\nSelecting a maximally informative set of single-nucleotide polymorphisms for\nassociation analyses using linkage disequilibrium.\nAm J Hum Genet. 74(1):106-20. Epub 2003 Dec 15.<\/p>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "hgv",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=hgv_ldtools",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "hgv_ldtools",
+        "name": "LD"
+      },
+      {
+        "panel_section_name": "Phenotype Association",
+        "xrefs": [],
+        "description": "Convert from MasterVar to pgSnp format",
+        "is_workflow_compatible": true,
+        "labels": [],
+        "help": "<p><strong>Dataset formats<\/strong><\/p>\n<p>The input dataset is in the <a class=\"reference external\" href=\"./static/formatHelp.html#mastervar\">MasterVar<\/a> format provided by the Complete Genomics\nanalysis process (Galaxy considers this to be <a class=\"reference external\" href=\"./static/formatHelp.html#tab\">tabular<\/a>, but it must have the\ncolumns specified for MasterVar).\nThe output dataset is in <a class=\"reference external\" href=\"./static/formatHelp.html#pgSnp\">pgSnp<\/a> format.  (<a class=\"reference external\" href=\"./static/formatHelp.html\">Dataset missing?<\/a>)<\/p>\n<hr class=\"docutils\" />\n<p><strong>What it does<\/strong><\/p>\n<p>This converts a Complete Genomics MasterVar file to pgSnp format,\nso it can be viewed in browsers or used with the phenotype association and\ninterval operations tools.\nPositions homozygous for the reference are skipped.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Examples<\/strong><\/p>\n<ul>\n<li><p class=\"first\">input MasterVar file:<\/p>\n<pre class=\"literal-block\">\n934     2       chr1    41980   41981   hom     snp     A       G       G       76      97                      dbsnp.86:rs806721       425     1       1       1       2       -170                            ERVL-E-int:ERVL:47.4    2       1.17    N\n935     2       chr1    41981   42198   hom     ref     =       =       =                                                                                       -170                                            1.17    N\n1102    2       chr1    53205   53206   het-ref snp     G       C       G       93      127                     dbsnp.100:rs2854676     477     7       30      0       37      -127                                    2       1.17    N\netc.\n<\/pre>\n<\/li>\n<li><p class=\"first\">output:<\/p>\n<pre class=\"literal-block\">\nchr1    41980   41981   G       1       1       76\nchr1    51672   51673   C       1       1       53\nchr1    52237   52238   G       1       7       63\nchr1    53205   53206   C/G     2       7,30    93,127\netc.\n<\/pre>\n<\/li>\n<\/ul>\n",
+        "edam_operations": [],
+        "form_style": "regular",
+        "edam_topics": [],
+        "panel_section_id": "hgv",
+        "version": "1.0.0",
+        "link": "/tool_runner?tool_id=master2pgSnp",
+        "target": "galaxy_main",
+        "min_width": -1,
+        "model_class": "Tool",
+        "hidden": "",
+        "id": "master2pgSnp",
+        "name": "MasterVar to pgSnp"
+      }
+    ],
+    "model_class": "ToolSection",
+    "version": "",
+    "id": "hgv",
+    "name": "Phenotype Association"
+  }
+]
\ No newline at end of file
diff --git a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
index 56d89ff4c80f..e5877d345b0d 100644
--- a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
+++ b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
@@ -33,7 +33,7 @@ import HistoryView from "components/HistoryView.vue";
 import WorkflowInvocationReport from "components/WorkflowInvocationReport.vue";
 import WorkflowRun from "components/Workflow/Run/WorkflowRun.vue";
 import RecentInvocations from "components/User/RecentInvocations.vue";
-import ToolsView from "components/ToolsView.vue";
+import ToolsView from "components/ToolsView/ToolsView.vue";
 import ToolsJson from "components/ToolsJson.vue";
 import HistoryList from "mvc/history/history-list";
 import PluginList from "components/PluginList.vue";
@@ -245,7 +245,7 @@ export const getAnalysisRouter = Galaxy =>
         show_histories_import: function() {
             this._display_vue_helper(HistoryImport);
         },
-    
+
         show_tools_view: function() {
             this.page.toolPanel.getVueComponent().hide();
             this.page.panels.right.hide();

From a9ff13d486eda5030a516864f6f7d6eba906a7b7 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Mon, 3 Feb 2020 18:22:48 +0100
Subject: [PATCH 447/853] implement citation test

---
 .../components/ToolsView/ToolsView.test.js    | 24 +++++++++++++++++++
 .../ToolsView/testData/citation.json          |  1 +
 2 files changed, 25 insertions(+)
 create mode 100644 client/galaxy/scripts/components/ToolsView/testData/citation.json

diff --git a/client/galaxy/scripts/components/ToolsView/ToolsView.test.js b/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
index 189ed9831832..f5829a83305d 100644
--- a/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
+++ b/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
@@ -6,6 +6,7 @@ import Vue from "vue";
 
 // test response
 import testToolsListResponse from "./testData/toolsList";
+import testCitation from "./testData/citation";
 import MockAdapter from "axios-mock-adapter";
 import axios from "axios";
 
@@ -20,6 +21,7 @@ describe("ToolsView/ToolsView.vue", () => {
         wrapper = mount(ToolsView);
         emitted = wrapper.emitted();
         axiosMock.onGet("/api/tools?tool_help=True").reply(200, testToolsListResponse);
+        axiosMock.onGet(new RegExp(`./*/citations`)).reply(200, testCitation);
         await Vue.nextTick();
         await Vue.nextTick();
     });
@@ -41,6 +43,7 @@ describe("ToolsView/ToolsView.vue", () => {
         // one 'info' button per tool
         assert(wrapper.vm.buffer.length === buttons.length, "Number of 'info' buttons do not equal the buffer size!");
     });
+
     it("should open modal on button click", async () => {
         // findAll() returns WrapperArray, thus regular array.find() won't work
         let infoButton = wrapper
@@ -56,4 +59,25 @@ describe("ToolsView/ToolsView.vue", () => {
 
         assert(modal.isVisible(), "'Info' button didn't open a modal!");
     });
+
+    it("citation should open on click", async () => {
+        await Vue.nextTick();
+        await Vue.nextTick();
+        await Vue.nextTick();
+
+        let infoButton = wrapper
+            .findAll('[type="button"]')
+            .filter(button => button.text() === "Citations")
+            .at(0);
+        const citation = wrapper.find("#" + infoButton.attributes("aria-controls"));
+
+        assert(citation.isVisible() === false, "citation is visible before being triggered!");
+        assert(infoButton.attributes("aria-expanded") === "false", "citation is expanded before being triggered!");
+
+        infoButton.trigger("click");
+        await Vue.nextTick();
+
+        assert(infoButton.attributes("aria-expanded") === "true", "citation is expanded before being triggered!");
+        assert(citation.isVisible(), "citation is not visible, after being triggered!");
+    });
 });
diff --git a/client/galaxy/scripts/components/ToolsView/testData/citation.json b/client/galaxy/scripts/components/ToolsView/testData/citation.json
new file mode 100644
index 000000000000..57b0e8214e0b
--- /dev/null
+++ b/client/galaxy/scripts/components/ToolsView/testData/citation.json
@@ -0,0 +1 @@
+[{"content": " @article{Blankenberg_2011, title={Making whole genome multiple alignments usable for biologists}, volume={27}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btr398}, DOI={10.1093/bioinformatics/btr398}, number={17}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Blankenberg, Daniel and Taylor, James and Nekrutenko, Anton}, year={2011}, month={Jul}, pages={2426\u00e2\u0080\u00932428}}\n", "format": "bibtex"}]
\ No newline at end of file

From b48df77624ab7d93d8c48250de9d44afe67d3182 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Tue, 4 Feb 2020 14:28:49 +0100
Subject: [PATCH 448/853] fix typo in toolsview test

---
 client/galaxy/scripts/components/{ => ToolsJson}/ToolsJson.vue | 0
 client/galaxy/scripts/components/ToolsView/ToolsView.test.js   | 3 +--
 2 files changed, 1 insertion(+), 2 deletions(-)
 rename client/galaxy/scripts/components/{ => ToolsJson}/ToolsJson.vue (100%)

diff --git a/client/galaxy/scripts/components/ToolsJson.vue b/client/galaxy/scripts/components/ToolsJson/ToolsJson.vue
similarity index 100%
rename from client/galaxy/scripts/components/ToolsJson.vue
rename to client/galaxy/scripts/components/ToolsJson/ToolsJson.vue
diff --git a/client/galaxy/scripts/components/ToolsView/ToolsView.test.js b/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
index f5829a83305d..f12b524ca8ac 100644
--- a/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
+++ b/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
@@ -17,7 +17,6 @@ describe("ToolsView/ToolsView.vue", () => {
 
     beforeEach(async () => {
         axiosMock = new MockAdapter(axios);
-        // using shallow because of inner 'Citation' component
         wrapper = mount(ToolsView);
         emitted = wrapper.emitted();
         axiosMock.onGet("/api/tools?tool_help=True").reply(200, testToolsListResponse);
@@ -77,7 +76,7 @@ describe("ToolsView/ToolsView.vue", () => {
         infoButton.trigger("click");
         await Vue.nextTick();
 
-        assert(infoButton.attributes("aria-expanded") === "true", "citation is expanded before being triggered!");
+        assert(infoButton.attributes("aria-expanded") === "true", "citation field did not expand!");
         assert(citation.isVisible(), "citation is not visible, after being triggered!");
     });
 });

From 36d5543147cc5df8a502d6058f275b1361216af5 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Tue, 4 Feb 2020 17:57:16 +0100
Subject: [PATCH 449/853] implement Vue test for schema.org component. Call
 unicody with default encoding  in __init__.py, add missing tool_help in
 base.py

---
 .../ToolsSchemaJson/ToolsJson.test.js         | 29 +++++++++++++++++++
 .../ToolsSchemaJson}/ToolsJson.vue            | 10 ++++---
 .../scripts/entry/analysis/AnalysisRouter.js  |  2 +-
 lib/galaxy/tools/__init__.py                  |  2 +-
 lib/galaxy/tools/toolbox/base.py              |  2 +-
 5 files changed, 38 insertions(+), 7 deletions(-)
 create mode 100644 client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.test.js
 rename client/galaxy/scripts/components/{ToolsJson => ToolsView/ToolsSchemaJson}/ToolsJson.vue (87%)

diff --git a/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.test.js b/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.test.js
new file mode 100644
index 000000000000..9b818bdb62bc
--- /dev/null
+++ b/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.test.js
@@ -0,0 +1,29 @@
+import ToolsJson from "./ToolsJson";
+// test response
+import testToolsListResponse from "../testData/toolsList";
+import MockAdapter from "axios-mock-adapter";
+import axios from "axios";
+import Vue from "vue";
+import { mount } from "@vue/test-utils";
+
+describe("ToolsView/ToolsView.vue", () => {
+    let wrapper, axiosMock;
+    const defaultSchemaElementTag = "application/ld+json";
+
+    beforeEach(async () => {
+        axiosMock = new MockAdapter(axios);
+        wrapper = mount(ToolsJson);
+        axiosMock.onGet("/api/tools?tool_help=True").reply(200, testToolsListResponse);
+        await Vue.nextTick();
+    });
+
+    it("schema.org script element is created", async () => {
+        await Vue.nextTick();
+        const tools = wrapper.vm.createToolsJson(testToolsListResponse);
+        const schemaElement = document.getElementById("schema-json");
+        const schemaText = JSON.parse(schemaElement.text);
+        assert(tools["@graph"].length === 84, "tools are not parsed correctly!");
+        assert(schemaText["@graph"].length === 84, "tools are not correctly presented in schema script tag!");
+        assert(schemaElement.type === defaultSchemaElementTag, "element type is not correct!");
+    });
+});
diff --git a/client/galaxy/scripts/components/ToolsJson/ToolsJson.vue b/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.vue
similarity index 87%
rename from client/galaxy/scripts/components/ToolsJson/ToolsJson.vue
rename to client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.vue
index 5f393fce8ba7..3775a91f9a44 100644
--- a/client/galaxy/scripts/components/ToolsJson/ToolsJson.vue
+++ b/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.vue
@@ -1,10 +1,12 @@
+<template />
 <script>
 import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
+import Vue from "vue";
 
 export default {
     data() {
-        return { toolsJsonLD: {} };
+        return { schemaTagObj: {} };
     },
     methods: {
         createToolsJson(tools) {
@@ -41,11 +43,11 @@ export default {
         axios
             .get(`${getAppRoot()}api/tools?tool_help=True`)
             .then(response => {
-                this.toolsJsonLD = this.createToolsJson(response.data);
-
+                this.schemaTagObj = this.createToolsJson(response.data);
                 const el = document.createElement("script");
+                el.id = "schema-json";
                 el.type = "application/ld+json";
-                el.text = JSON.stringify(this.toolsJsonLD);
+                el.text = JSON.stringify(this.schemaTagObj);
                 document.head.appendChild(el);
             })
             .catch(error => {
diff --git a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
index e5877d345b0d..6d5239673bab 100644
--- a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
+++ b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
@@ -34,7 +34,7 @@ import WorkflowInvocationReport from "components/WorkflowInvocationReport.vue";
 import WorkflowRun from "components/Workflow/Run/WorkflowRun.vue";
 import RecentInvocations from "components/User/RecentInvocations.vue";
 import ToolsView from "components/ToolsView/ToolsView.vue";
-import ToolsJson from "components/ToolsJson.vue";
+import ToolsJson from "components/ToolsView/ToolsSchemaJson/ToolsJson.vue";
 import HistoryList from "mvc/history/history-list";
 import PluginList from "components/PluginList.vue";
 import QueryStringParsing from "utils/query-string-parsing";
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 531f81358cde..7665ac7fc7e8 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1974,7 +1974,7 @@ def to_dict(self, trans, link_details=False, io_details=False, tool_help=False):
             help_txt = ''
             if self.help:
                 help_txt = self.help.render(static_path=self.app.url_for('/static'), host_url=self.app.url_for('/', qualified=True))
-                help_txt = unicodify(help_txt, 'utf-8')
+                help_txt = unicodify(help_txt)
             tool_dict['help'] = help_txt
 
         return tool_dict
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index c69027fe33a3..de683796ec77 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -1093,7 +1093,7 @@ def to_dict(self, trans, in_panel=True, tool_help=False, **kwds):
                 tool = filter_method(tool, panel_item_types.TOOL)
                 if not tool:
                     continue
-                rval.append(self.get_tool_to_dict(trans, tool))
+                rval.append(self.get_tool_to_dict(trans, tool, tool_help=tool_help))
         return rval
 
     def _lineage_in_panel(self, panel_dict, tool=None, tool_lineage=None):

From 8abfd6c2073d4ae83389802d8a136cfdd7ce4a56 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Tue, 4 Feb 2020 18:22:57 +0100
Subject: [PATCH 450/853] fix js-lint test

---
 .../components/ToolsView/ToolsSchemaJson/ToolsJson.vue      | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.vue b/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.vue
index 3775a91f9a44..00d933adb075 100644
--- a/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.vue
+++ b/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.vue
@@ -1,8 +1,10 @@
-<template />
+<template>
+    <div />
+</template>
+
 <script>
 import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
-import Vue from "vue";
 
 export default {
     data() {

From 757dbdff1343bbfa14ab274191095779b5e7465c Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Wed, 5 Feb 2020 14:37:33 +0100
Subject: [PATCH 451/853] remove merge artifacts from package.json

---
 .../components/SelectionDialog/WorkflowDialog.test.js       | 4 ++--
 client/yarn.lock                                            | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js b/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js
index 1f1b1a77d4b5..556054a438c9 100644
--- a/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js
+++ b/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js
@@ -34,7 +34,7 @@ describe("WorkflowDialog.vue", () => {
 
     it("loads correctly in loading state, shows options when optionsShow becomes true", async () => {
         // Initially in loading state.
-        const workflowsResponse = [{ id: "f2db41e1fa331b3e", name: "Awesom e Workflow" }];
+        const workflowsResponse = [{ id: "f2db41e1fa331b3e", name: "Awesome Workflow" }];
         axiosMock.onGet("/api/workflows").reply(200, workflowsResponse);
 
         expect(wrapper.find(SelectionDialog).is(SelectionDialog)).to.equals(true);
@@ -44,7 +44,7 @@ describe("WorkflowDialog.vue", () => {
         await localVue.nextTick();
         await localVue.nextTick();
 
-        // why not shown?xios-mock-adapter
+        // why not shown?
         expect(wrapper.vm.errorMessage).to.equals(null);
         expect(wrapper.vm.optionsShow).to.equals(true);
     });
diff --git a/client/yarn.lock b/client/yarn.lock
index 3bc8e50d224d..f54ba943e00c 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -14441,9 +14441,9 @@ webpack-dev-server@^3.1.14:
     yargs "12.0.2"
 
 webpack-dev-server@^3.10.1:
-  version "3.10.1"
-  resolved "https://registry.yarnpkg.com/webpack-dev-server/-/webpack-dev-server-3.10.1.tgz#1ff3e5cccf8e0897aa3f5909c654e623f69b1c0e"
-  integrity sha512-AGG4+XrrXn4rbZUueyNrQgO4KGnol+0wm3MPdqGLmmA+NofZl3blZQKxZ9BND6RDNuvAK9OMYClhjOSnxpWRoA==
+  version "3.10.3"
+  resolved "https://registry.yarnpkg.com/webpack-dev-server/-/webpack-dev-server-3.10.3.tgz#f35945036813e57ef582c2420ef7b470e14d3af0"
+  integrity sha512-e4nWev8YzEVNdOMcNzNeCN947sWJNd43E5XvsJzbAL08kGc2frm1tQ32hTJslRS+H65LCb/AaUCYU7fjHCpDeQ==
   dependencies:
     ansi-html "0.0.7"
     bonjour "^3.5.0"

From 4bcda9633677ded865e00d4bf9f923fe7d555a5e Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 13 Mar 2020 14:02:53 -0400
Subject: [PATCH 452/853] Swap citations.vue back to v-slot syntax, which we
 should use consistently going forward.

---
 .../galaxy/scripts/components/Citations.vue   | 30 ++++++++++---------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/client/galaxy/scripts/components/Citations.vue b/client/galaxy/scripts/components/Citations.vue
index d3ecca0c92e5..e138738d76e7 100644
--- a/client/galaxy/scripts/components/Citations.vue
+++ b/client/galaxy/scripts/components/Citations.vue
@@ -1,20 +1,22 @@
 <template>
     <div>
         <b-card v-if="!simple">
-            <h4 slot="header" class="mb-0">
-                Citations
-                <b-button
-                    v-if="viewRender"
-                    title="Show all in BibTeX format."
-                    class="citations-to-bibtex"
-                    @click="toggleViewRender"
-                >
-                    <i class="fa fa-pencil-square-o"></i> Show BibTeX
-                </b-button>
-                <b-button v-else title="Return to formatted citation list." @click="toggleViewRender">
-                    <i class="fa fa-times"></i> Hide BibTeX
-                </b-button>
-            </h4>
+            <template v-slot:header>
+                <h4 class="mb-0">
+                    Citations
+                    <b-button
+                        v-if="viewRender"
+                        title="Show all in BibTeX format."
+                        class="citations-to-bibtex"
+                        @click="toggleViewRender"
+                    >
+                        <i class="fa fa-pencil-square-o"></i> Show BibTeX
+                    </b-button>
+                    <b-button v-else title="Return to formatted citation list." @click="toggleViewRender">
+                        <i class="fa fa-times"></i> Hide BibTeX
+                    </b-button>
+                </h4>
+            </template>
             <div v-if="source === 'histories'" class="infomessage">
                 When writing up your analysis, remember to include all references that should be cited in order to
                 completely describe your work. Also, please remember to

From 321460a6af60fc15c3b2b6d73929e5a8638fca48 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 13 Mar 2020 14:03:41 -0400
Subject: [PATCH 453/853] Swap toolsview to v-slot syntax.

---
 .../scripts/components/ToolsView/ToolsView.vue     | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolsView/ToolsView.vue b/client/galaxy/scripts/components/ToolsView/ToolsView.vue
index fa3c43fcd4c0..879d5a932d79 100644
--- a/client/galaxy/scripts/components/ToolsView/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView/ToolsView.vue
@@ -31,12 +31,14 @@
                 @filter="filterOption = arguments[2]"
             >
                 <b-card v-for="(info, index) in buffer" :key="index" ref="cards" class="m-2" style="width: 23rem;">
-                    <div slot="header">
-                        <b-link :href="info.url" target="_blank">
-                            <h4 class="tools-view-name">{{ info.name }}</h4>
-                        </b-link>
-                        <b-badge class="tools-view-section">{{ info.section }}</b-badge>
-                    </div>
+                    <template v-slot:header>
+                        <div>
+                            <b-link :href="info.url" target="_blank">
+                                <h4 class="tools-view-name">{{ info.name }}</h4>
+                            </b-link>
+                            <b-badge class="tools-view-section">{{ info.section }}</b-badge>
+                        </div>
+                    </template>
                     <p class="card-text" v-html="helpSummary(info.help) || info.description" />
                     <p class="card-text">
                         <b-btn :index="index" v-b-modal="'modal-' + '-' + index">Info</b-btn>

From 8d8d3d08f56587cdb728cfd2b7d0541a5d1c4275 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Tue, 17 Mar 2020 22:36:52 +0100
Subject: [PATCH 454/853] Update model path

---
 doc/source/admin/galaxy_options.rst         | 5 ++---
 lib/galaxy/config/sample/galaxy.yml.sample  | 5 ++---
 lib/galaxy/webapps/galaxy/config_schema.yml | 3 +--
 lib/galaxy_test/api/test_workflows.py       | 2 +-
 4 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index e35ffb48af7c..d1a682905375 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -4058,9 +4058,8 @@
 
 :Description:
     Set remote path of the trained model (HDF5 file) for tool
-    recommendation. It is required to be set if
-    'enable_tool_recommendations' property is enabled and set to true.
-:Default: ``https://github.com/anuprulez/download_store/raw/tool_recommendation_model/tool_recommendation_model/tool_recommendation_model.hdf5``
+    recommendation.
+:Default: ``https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model.hdf5``
 :Type: str
 
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 3b39066b03fd..43450b70e820 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1981,9 +1981,8 @@ galaxy:
   #enable_tool_recommendations: false
 
   # Set remote path of the trained model (HDF5 file) for tool
-  # recommendation. It is required to be set if
-  # 'enable_tool_recommendations' property is enabled and set to true.
-  #tool_recommendation_model_path: https://github.com/anuprulez/download_store/raw/tool_recommendation_model/tool_recommendation_model/tool_recommendation_model.hdf5
+  # recommendation.
+  #tool_recommendation_model_path: https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model.hdf5
 
   # Set the number of predictions/recommendations to be made by the
   # model
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 66ed954360a6..0180a2a1a5ac 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2991,11 +2991,10 @@ mapping:
 
       tool_recommendation_model_path:
         type: str
-        default: 'https://github.com/anuprulez/download_store/raw/tool_recommendation_model/tool_recommendation_model/tool_recommendation_model.hdf5'
+        default: 'https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model.hdf5'
         required: false
         desc: |
           Set remote path of the trained model (HDF5 file) for tool recommendation.
-          It is required to be set if 'enable_tool_recommendations' property is enabled and set to true.
 
       topk_recommendations:
         type: int
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index 45eb96e26463..bb0a662896a1 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -332,7 +332,7 @@ def __test_upload(self, use_deprecated_route=False, name="test_import", workflow
         return upload_response
 
     def test_get_tool_predictions(self):
-        request = {"tool_sequence": "Cut1", "remote_model_url": "https://github.com/anuprulez/download_store/raw/tool_recommendation_model/tool_recommendation_model/tool_recommendation_model.hdf5"}
+        request = {"tool_sequence": "Cut1", "remote_model_url": "https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model.hdf5"}
         actual_recommendations = ['Filter1', 'cat1', 'addValue', 'comp1', 'Grep1']
         route = "workflows/get_tool_predictions"
         response = self._post(route, data=request)

From 26bfb80f4c885b0c55720a8354d664f297ff13c7 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Tue, 17 Mar 2020 23:10:37 +0100
Subject: [PATCH 455/853] ES6 strings for URL

---
 client/galaxy/scripts/components/ToolRecommendation.vue | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index ff46367d6418..c15c9774be3e 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -50,13 +50,13 @@ export default {
         loadRecommendations: function() {
             const self = this,
                 toolId = this.getToolId,
-                url = getAppRoot() + "api/workflows/get_tool_predictions";
+                url = `${getAppRoot()}api/workflows/get_tool_predictions`;
             axios
                 .post(url, {
                     tool_sequence: toolId
                 })
                 .then(response => {
-                    axios.get(getAppRoot() + "api/datatypes/mapping").then(responseMapping => {
+                    axios.get(`${getAppRoot()}api/datatypes/mapping`).then(responseMapping => {
                         const predData = response.data.predicted_data,
                             datatypesMapping = responseMapping.data,
                             extToType = datatypesMapping.ext_to_class_name,
@@ -222,8 +222,9 @@ export default {
                     d._children = null;
                 }
                 update(d);
-                if (d.tool_id !== undefined && d.tool_id !== "undefined" && d.tool_id !== null && d.tool_id !== "") {
-                    document.location.href = getAppRoot() + "tool_runner?tool_id=" + d.tool_id;
+                const tId = d.tool_id;
+                if (tId !== undefined && tId !== "undefined" && tId !== null && tId !== "") {
+                    document.location.href = `${getAppRoot()}tool_runner?tool_id=${tId}`;
                 }
             }
             function collapse(d) {

From 70645f2a177e437a982fc0ee31fd213fd054b436 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Tue, 17 Mar 2020 23:26:18 +0100
Subject: [PATCH 456/853] Use theme colors

---
 client/galaxy/style/scss/base.scss | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index c8ec6e2aee78..9865e9e5e3be 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1655,8 +1655,8 @@ body.reports {
 .node {
     cursor: pointer;
     circle {
-        fill: rgb(0, 0, 0);
-        stroke: rgb(194, 235, 194);
+        fill: none;
+        stroke: lighten($brand-success, 20%);
         stroke-width: 0.3rem;
     }
     text {
@@ -1680,6 +1680,6 @@ body.reports {
 
 .link {
     fill: none;
-    stroke: rgb(194, 235, 194);
+    stroke: lighten($brand-success, 20%);
     stroke-width: 0.3rem;
 }

From 9290d489ccafa44dbb0ed6b89eca71948d69d748 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 17 Mar 2020 18:38:33 -0400
Subject: [PATCH 457/853] Drop old-school 'one var' declaration rule; enforce a
 standard style.

---
 client/.eslintrc.js | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/client/.eslintrc.js b/client/.eslintrc.js
index 392057590fdb..50e8fe35157f 100644
--- a/client/.eslintrc.js
+++ b/client/.eslintrc.js
@@ -1,7 +1,7 @@
 module.exports = {
     extends: [
         "eslint:recommended",
-        "plugin:vue/strongly-recommended",
+        "plugin:vue/strongly-recommended"
         //"airbnb-base", eventually
     ],
     env: {
@@ -20,9 +20,10 @@ module.exports = {
         "no-console": "off",
         "no-unused-vars": ["error", { args: "none" }],
         "prefer-const": "error",
+        "one-var": ["error", "never"],
 
         "vue/valid-v-slot": "error",
-        "vue/v-slot-style": ["error", {"atComponent": "v-slot", "default": "v-slot", "named": "longform"}],
+        "vue/v-slot-style": ["error", { atComponent: "v-slot", default: "v-slot", named: "longform" }],
 
         // Vue TODO (enable these)
         "vue/require-default-prop": "warn",

From 5133716e48d0a8f2cd56ff38090ce33cc74bb0c5 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Tue, 17 Mar 2020 23:49:11 +0100
Subject: [PATCH 458/853] Remove margin vars

---
 .../scripts/components/ToolRecommendation.vue | 30 +++++++++----------
 1 file changed, 14 insertions(+), 16 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index c15c9774be3e..be74228e5f59 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -18,8 +18,6 @@ import * as d3 from "d3";
 import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 
-const margin = { top: 20, right: 30, bottom: 20, left: 250 };
-
 export default {
     props: {
         toolId: {
@@ -108,19 +106,19 @@ export default {
                 });
         },
         renderD3Tree: function(predictedTools) {
-            const width = 900 - margin.right - margin.left,
-                height = 300 - margin.top - margin.bottom,
-                duration = 750;
-            const tree = d3.layout.tree().size([height, width]);
-            const diagonal = d3.svg.diagonal().projection(d => {
-                return [d.y, d.x];
-            });
-            const svg = d3
-                .select("#tool-recommendation-view")
-                .append("svg")
-                .attr("class", "tree-size")
-                .append("g")
-                .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+            const duration = 750,
+                x = 620,
+                y = 260,
+                tree = d3.layout.tree().size([y, x]),
+                diagonal = d3.svg.diagonal().projection(d => {
+                    return [d.y, d.x];
+                }),
+                svg = d3
+                    .select("#tool-recommendation-view")
+                    .append("svg")
+                    .attr("class", "tree-size")
+                    .append("g")
+                    .attr("transform", "translate(" + 250 + "," + 20 + ")");
             let i = 0,
                 root = null;
             function update(source) {
@@ -235,7 +233,7 @@ export default {
                 }
             }
             root = predictedTools;
-            root.x0 = height / 2;
+            root.x0 = y / 2;
             root.y0 = 0;
             root.children.forEach(collapse);
             update(root);

From 7978de09729e0179ed731d1cb20672711be5b29f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 17 Mar 2020 18:51:52 -0400
Subject: [PATCH 459/853] Fix one-var to match airbnb spec.

---
 .../galaxy/scripts/components/HistoryView.vue |  4 +--
 .../scripts/components/Markdown/Markdown.vue  |  6 ++--
 .../components/RuleCollectionBuilder.vue      | 10 +++++--
 client/galaxy/scripts/i18n.js                 | 30 ++++++++++---------
 .../mvc/collection/list-collection-creator.js |  4 ++-
 .../scripts/mvc/rules/rule-definitions.js     |  8 ++---
 client/galaxy/scripts/mvc/tool/tool-form.js   |  3 +-
 client/galaxy/scripts/utils/color.js          |  4 ++-
 client/galaxy/scripts/utils/utils.js          |  6 ++--
 client/galaxy/scripts/viz/sweepster.js        |  6 ++--
 .../galaxy/scripts/viz/trackster/painters.js  |  4 +--
 11 files changed, 48 insertions(+), 37 deletions(-)

diff --git a/client/galaxy/scripts/components/HistoryView.vue b/client/galaxy/scripts/components/HistoryView.vue
index 2fd40422f20f..acb4e13b4901 100644
--- a/client/galaxy/scripts/components/HistoryView.vue
+++ b/client/galaxy/scripts/components/HistoryView.vue
@@ -105,8 +105,8 @@ export default {
         },
         showStructure: function() {
             const Galaxy = getGalaxyInstance();
-            const displayStructureInstance = Vue.extend(DisplayStructure),
-                mountView = document.createElement("div");
+            const displayStructureInstance = Vue.extend(DisplayStructure);
+            const mountView = document.createElement("div");
             Galaxy.page.center.display(mountView);
             new displayStructureInstance({ propsData: { id: QueryStringParsing.get("id") } }).$mount(mountView);
         },
diff --git a/client/galaxy/scripts/components/Markdown/Markdown.vue b/client/galaxy/scripts/components/Markdown/Markdown.vue
index 4e620ccc0613..12643fc415c3 100644
--- a/client/galaxy/scripts/components/Markdown/Markdown.vue
+++ b/client/galaxy/scripts/components/Markdown/Markdown.vue
@@ -117,9 +117,9 @@ const RENDER_FUNCTIONS = {
 };
 
 md.renderer.rules.fence = function(tokens, idx, options, env, slf) {
-    const token = tokens[idx],
-        info = token.info ? token.info.trim() : "",
-        content = token.content;
+    const token = tokens[idx];
+    const info = token.info ? token.info.trim() : "";
+    const content = token.content;
     if (info == "galaxy") {
         const arr = FUNCTION_CALL_LINE_TEMPLATE.exec(content);
         const action = arr[1];
diff --git a/client/galaxy/scripts/components/RuleCollectionBuilder.vue b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
index 5670b6d983f4..2e80d4ead504 100644
--- a/client/galaxy/scripts/components/RuleCollectionBuilder.vue
+++ b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
@@ -933,7 +933,8 @@ const RuleModalFooter = {
 export default {
     data: function() {
         let orientation = "vertical";
-        let mapping, rules;
+        let mapping;
+        let rules;
         if (this.initialRules) {
             mapping = this.initialRules.mapping.slice();
             rules = this.initialRules.rules.slice();
@@ -1334,7 +1335,9 @@ export default {
             return valid;
         },
         hotData() {
-            let data, sources, columns;
+            let data;
+            let sources;
+            let columns;
             if (
                 this.elementsType == "datasets" ||
                 this.elementsType == "library_datasets" ||
@@ -1593,7 +1596,8 @@ export default {
             } else {
                 const Galaxy = getGalaxyInstance();
                 const historyId = Galaxy.currHistoryPanel.model.id;
-                let elements, targets;
+                let elements;
+                let targets;
                 if (collectionType) {
                     targets = [];
                     const elementsByCollectionName = this.creationElementsForFetch();
diff --git a/client/galaxy/scripts/i18n.js b/client/galaxy/scripts/i18n.js
index 39133a94cb4e..a4a4a3c283c6 100644
--- a/client/galaxy/scripts/i18n.js
+++ b/client/galaxy/scripts/i18n.js
@@ -102,17 +102,17 @@
                     masterConfig.locale = config.locale;
                 }
 
-                var masterName,
-                    match = nlsRegExp.exec(name),
-                    prefix = match[1],
-                    locale = match[4],
-                    suffix = match[5],
-                    parts = locale.split("-"),
-                    toLoad = [],
-                    value = {},
-                    i,
-                    part,
-                    current = "";
+                var masterName;
+                var match = nlsRegExp.exec(name);
+                var prefix = match[1];
+                var locale = match[4];
+                var suffix = match[5];
+                var parts = locale.split("-");
+                var toLoad = [];
+                var value = {};
+                var i;
+                var part;
+                var current = "";
 
                 //If match[5] is blank, it means this is the top bundle definition,
                 //so it does not have to be handled. Locale-specific requests
@@ -158,8 +158,8 @@
                     //First, fetch the master bundle, it knows what locales are available.
                     req([masterName], function(master) {
                         //Figure out the best fit
-                        var needed = [],
-                            part;
+                        var needed = [];
+                        var part;
 
                         //Always allow for root, then do the rest of the locale parts.
                         addPart("root", master, needed, toLoad, prefix, suffix);
@@ -171,7 +171,9 @@
 
                         //Load all the parts missing.
                         req(toLoad, function() {
-                            var i, partBundle, part;
+                            var i;
+                            var partBundle;
+                            var part;
                             for (i = needed.length - 1; i > -1 && needed[i]; i--) {
                                 part = needed[i];
                                 partBundle = master[part];
diff --git a/client/galaxy/scripts/mvc/collection/list-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
index 1de9d6eae87f..f739ed317ba7 100644
--- a/client/galaxy/scripts/mvc/collection/list-collection-creator.js
+++ b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
@@ -1131,7 +1131,9 @@ function createListCollection(contents, defaultHideSourceItems) {
 }
 
 function createCollectionViaRules(selection, defaultHideSourceItems) {
-    let elements, elementsType, importType;
+    let elements;
+    let elementsType;
+    let importType;
     const selectionType = selection.selectionType;
     const copyElements = !defaultHideSourceItems;
     if (!selectionType) {
diff --git a/client/galaxy/scripts/mvc/rules/rule-definitions.js b/client/galaxy/scripts/mvc/rules/rule-definitions.js
index 29909912306f..bbd294dfdf92 100644
--- a/client/galaxy/scripts/mvc/rules/rule-definitions.js
+++ b/client/galaxy/scripts/mvc/rules/rule-definitions.js
@@ -357,8 +357,8 @@ const RULES = {
             function newRow(row) {
                 const newRow = row.slice();
                 const originalValue = row[target];
-                let start = 0,
-                    end = originalValue.length;
+                let start = 0;
+                let end = originalValue.length;
                 if (type == "keep_prefix") {
                     end = length;
                 } else if (type == "drop_prefix") {
@@ -727,8 +727,8 @@ const RULES = {
             const targets1 = rule.target_columns_1;
 
             const splitRow = function(row) {
-                const newRow0 = [],
-                    newRow1 = [];
+                const newRow0 = [];
+                const newRow1 = [];
                 for (let index in row) {
                     index = parseInt(index, 10);
                     if (targets0.indexOf(index) > -1) {
diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index 89bdb4d3f289..0682b2f58409 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -159,7 +159,8 @@ const View = Backbone.View.extend({
 
         // remap feature
         if (options.job_id && options.job_remap) {
-            let label, help;
+            let label;
+            let help;
             if (options.job_remap === "job_produced_collection_elements") {
                 label = "Replace elements in collection ?";
                 help =
diff --git a/client/galaxy/scripts/utils/color.js b/client/galaxy/scripts/utils/color.js
index 20ee5b6b772a..bcca21a12224 100644
--- a/client/galaxy/scripts/utils/color.js
+++ b/client/galaxy/scripts/utils/color.js
@@ -28,7 +28,9 @@ export function contrastingColor(r, g, b) {
  * @return  {Array}           The RGB representation
  */
 export function hslToRgb(h, s, l) {
-    var r, g, b;
+    var r;
+    var g;
+    var b;
 
     if (s == 0) {
         r = g = b = l; // achromatic
diff --git a/client/galaxy/scripts/utils/utils.js b/client/galaxy/scripts/utils/utils.js
index eda5d6e37c5e..9c7b3fed1413 100644
--- a/client/galaxy/scripts/utils/utils.js
+++ b/client/galaxy/scripts/utils/utils.js
@@ -357,9 +357,9 @@ export function setWindowTitle(title) {
  * @returns {integer}
  */
 export function hashFnv32a(str) {
-    var i,
-        l,
-        hval = 0x811c9dc5;
+    var i;
+    var l;
+    var hval = 0x811c9dc5;
 
     for (i = 0, l = str.length; i < l; i++) {
         hval ^= str.charCodeAt(i);
diff --git a/client/galaxy/scripts/viz/sweepster.js b/client/galaxy/scripts/viz/sweepster.js
index 360430e21747..3e941e69ae61 100644
--- a/client/galaxy/scripts/viz/sweepster.js
+++ b/client/galaxy/scripts/viz/sweepster.js
@@ -116,9 +116,9 @@ var ToolParameterTree = Backbone.Model.extend({
 
         var // Creates tree data recursively.
             create_tree_data = (params_samples, index) => {
-                var param_samples = params_samples[index],
-                    param = param_samples.param,
-                    settings = param_samples.samples;
+                var param_samples = params_samples[index];
+                var param = param_samples.param;
+                var settings = param_samples.samples;
 
                 // Create leaves when last parameter setting is reached.
                 if (params_samples.length - 1 === index) {
diff --git a/client/galaxy/scripts/viz/trackster/painters.js b/client/galaxy/scripts/viz/trackster/painters.js
index 9ffc89b654d4..da31494b4be6 100644
--- a/client/galaxy/scripts/viz/trackster/painters.js
+++ b/client/galaxy/scripts/viz/trackster/painters.js
@@ -818,8 +818,8 @@ class ReadPainter extends FeaturePainter {
         var // Parse cigar operations out and update/create blocks as needed.
             parsed_cigar = _.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g), op => {
                 // Get operation length, character.
-                var op_len = parseInt(op.slice(0, -1), 10),
-                    op_char = op.slice(-1);
+                var op_len = parseInt(op.slice(0, -1), 10);
+                var op_char = op.slice(-1);
 
                 // Update drawing block.
                 if (op_char === "N") {

From ae3f4629ca649dc6996f00e44cc6c74391eb0f4c Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 18 Mar 2020 00:36:48 +0100
Subject: [PATCH 460/853] Add header and brand-primary bg color

---
 client/galaxy/scripts/components/ToolRecommendation.vue | 1 +
 client/galaxy/style/scss/base.scss                      | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index be74228e5f59..048912558624 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -1,6 +1,7 @@
 <template>
     <div id="tool-recommendation-view">
         <div v-if="deprecated == false" class="infomessagelarge">
+            <h4>Tool recommendation</h4>
             You have used {{ getToolId }} tool. For further analysis, you could try using the following/recommended
             tools. The recommended tools are shown in the decreasing order of their scores predicted using machine
             learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index 9865e9e5e3be..e9a1de43595f 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1656,7 +1656,7 @@ body.reports {
     cursor: pointer;
     circle {
         fill: none;
-        stroke: lighten($brand-success, 20%);
+        stroke: lighten($brand-primary, 20%);
         stroke-width: 0.3rem;
     }
     text {
@@ -1680,6 +1680,6 @@ body.reports {
 
 .link {
     fill: none;
-    stroke: lighten($brand-success, 20%);
+    stroke: lighten($brand-primary, 20%);
     stroke-width: 0.3rem;
 }

From 12a3b1b58fb483328612229110ecdb333a976c00 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 18 Mar 2020 01:37:19 +0100
Subject: [PATCH 461/853] Fix review comments

---
 .../scripts/components/ToolRecommendation.vue | 77 +++++++++----------
 client/galaxy/scripts/mvc/tool/tool-form.js   |  2 +-
 2 files changed, 39 insertions(+), 40 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 048912558624..717c313ec921 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -47,20 +47,19 @@ export default {
     },
     methods: {
         loadRecommendations: function() {
-            const self = this,
-                toolId = this.getToolId,
-                url = `${getAppRoot()}api/workflows/get_tool_predictions`;
+            const toolId = this.getToolId;
+            const url = `${getAppRoot()}api/workflows/get_tool_predictions`;
             axios
                 .post(url, {
                     tool_sequence: toolId
                 })
                 .then(response => {
                     axios.get(`${getAppRoot()}api/datatypes/mapping`).then(responseMapping => {
-                        const predData = response.data.predicted_data,
-                            datatypesMapping = responseMapping.data,
-                            extToType = datatypesMapping.ext_to_class_name,
-                            typeToType = datatypesMapping.class_to_classes;
-                        self.deprecated = predData.is_deprecated;
+                        const predData = response.data.predicted_data;
+                        const datatypesMapping = responseMapping.data;
+                        const extToType = datatypesMapping.ext_to_class_name;
+                        const typeToType = datatypesMapping.class_to_classes;
+                        this.deprecated = predData.is_deprecated;
 
                         if (response.data !== null && predData.children.length > 0) {
                             const filteredData = {},
@@ -80,7 +79,7 @@ export default {
                                             out_t[1] === "_sniff_" ||
                                             out_t[1] === "input_collection"
                                         ) {
-                                            compatibleTools[nameObj[1]["tool_id"]] = nameObj[1]["name"];
+                                            compatibleTools[nameObj[1].tool_id] = nameObj[1].name;
                                             break;
                                         }
                                     }
@@ -88,44 +87,44 @@ export default {
                             }
                             for (const id in compatibleTools) {
                                 for (const nameObj of children.entries()) {
-                                    if (nameObj[1]["tool_id"] === id) {
+                                    if (nameObj[1].tool_id === id) {
                                         filteredChildren.push(nameObj[1]);
                                         break;
                                     }
                                 }
                             }
-                            filteredData["o_extensions"] = predData.o_extensions;
-                            filteredData["name"] = predData.name;
-                            filteredData["children"] = filteredChildren;
-                            if (filteredChildren.length > 0 && self.deprecated === false) {
-                                self.renderD3Tree(filteredData);
-                            } else if (self.deprecated === true) {
-                                self.deprecatedMessage = predData.message;
+                            filteredData.o_extensions = predData.o_extensions;
+                            filteredData.name = predData.name;
+                            filteredData.children = filteredChildren;
+                            if (filteredChildren.length > 0 && this.deprecated === false) {
+                                this.renderD3Tree(filteredData);
+                            } else if (this.deprecated === true) {
+                                this.deprecatedMessage = predData.message;
                             }
                         }
                     });
                 });
         },
-        renderD3Tree: function(predictedTools) {
-            const duration = 750,
-                x = 620,
-                y = 260,
-                tree = d3.layout.tree().size([y, x]),
-                diagonal = d3.svg.diagonal().projection(d => {
-                    return [d.y, d.x];
-                }),
-                svg = d3
-                    .select("#tool-recommendation-view")
-                    .append("svg")
-                    .attr("class", "tree-size")
-                    .append("g")
-                    .attr("transform", "translate(" + 250 + "," + 20 + ")");
+        renderD3Tree: predictedTools => {
+            const duration = 750;
+            const x = 620;
+            const y = 260;
+            const tree = d3.layout.tree().size([y, x]);
+            const diagonal = d3.svg.diagonal().projection(d => {
+                return [d.y, d.x];
+            });
+            const svg = d3
+                .select("#tool-recommendation-view")
+                .append("svg")
+                .attr("class", "tree-size")
+                .append("g")
+                .attr("transform", "translate(" + 250 + "," + 20 + ")");
             let i = 0,
                 root = null;
-            function update(source) {
+            const update = source => {
                 // Compute the new tree layout.
-                const nodes = tree.nodes(root).reverse(),
-                    links = tree.links(nodes);
+                const nodes = tree.nodes(root).reverse();
+                const links = tree.links(nodes);
                 // Normalize for fixed-depth.
                 nodes.forEach(d => {
                     d.y = d.depth * 180;
@@ -210,9 +209,9 @@ export default {
                     d.x0 = d.x;
                     d.y0 = d.y;
                 });
-            }
+            };
             // Toggle children on click.
-            function click(d) {
+            const click = d => {
                 if (d.children) {
                     d._children = d.children;
                     d.children = null;
@@ -225,14 +224,14 @@ export default {
                 if (tId !== undefined && tId !== "undefined" && tId !== null && tId !== "") {
                     document.location.href = `${getAppRoot()}tool_runner?tool_id=${tId}`;
                 }
-            }
-            function collapse(d) {
+            };
+            const collapse = d => {
                 if (d.children) {
                     d._children = d.children;
                     d._children.forEach(collapse);
                     d.children = null;
                 }
-            }
+            };
             root = predictedTools;
             root.x0 = y / 2;
             root.y0 = 0;
diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index 212134fc247c..1309e96dd012 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -268,7 +268,7 @@ const View = Backbone.View.extend({
                     }
                 }
                 this.$el.append(this._templateSuccess(response, job_def));
-                const enable_tool_recommendations = window.Galaxy.config.enable_tool_recommendations;
+                const enable_tool_recommendations = Galaxy.config.enable_tool_recommendations;
                 if (enable_tool_recommendations === true || enable_tool_recommendations === "true") {
                     // show tool recommendations
                     const ToolRecommendationInstance = Vue.extend(ToolRecommendation);

From bf5860db630fd8fb683566f201d5e700fd2a68e1 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 18 Mar 2020 11:10:25 +0100
Subject: [PATCH 462/853] Fix styles

---
 client/galaxy/scripts/components/ToolRecommendation.vue | 6 +++---
 client/galaxy/style/scss/base.scss                      | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 717c313ec921..9a5316d29e7a 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -32,11 +32,11 @@ export default {
             deprecatedMessage: ""
         };
     },
-    created: function() {
+    created() {
         this.loadRecommendations();
     },
     computed: {
-        getToolId: function() {
+        getToolId() {
             let toolId = this.toolId || "";
             if (toolId.indexOf("/") > 0) {
                 const toolIdSlash = toolId.split("/");
@@ -46,7 +46,7 @@ export default {
         }
     },
     methods: {
-        loadRecommendations: function() {
+        loadRecommendations() {
             const toolId = this.getToolId;
             const url = `${getAppRoot()}api/workflows/get_tool_predictions`;
             axios
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index e9a1de43595f..c9088cc51c8a 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1673,9 +1673,9 @@ body.reports {
 }
 
 .tree-size {
-    width: 100%;
-    height: 100%;
-    position: fixed;
+    width: 96%;
+    height: 50%;
+    position: absolute;
 }
 
 .link {

From d12acb464246727dcd299639065351149d8c72ed Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 18 Mar 2020 12:24:56 +0100
Subject: [PATCH 463/853] Free space before running tests

---
 .github/workflows/integration.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index dc8656359942..3d11cf634cad 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -21,6 +21,8 @@ jobs:
         ports:
           - 5432:5432
     steps:
+    - name: Prune unused docker image, volumes and containers
+      run: docker system prune -a -f
     - name: Setup Minikube
       if: matrix.subset == 'kubernetes'
       id: minikube

From 24c34afe8eed304e64aeb943d7e6d4410fb153d2 Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Wed, 18 Mar 2020 12:37:37 -0400
Subject: [PATCH 464/853] Add assertion for history count.

---
 lib/galaxy_test/selenium/test_history_multi_view.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy_test/selenium/test_history_multi_view.py b/lib/galaxy_test/selenium/test_history_multi_view.py
index 65123c244172..a80cb26b07ce 100644
--- a/lib/galaxy_test/selenium/test_history_multi_view.py
+++ b/lib/galaxy_test/selenium/test_history_multi_view.py
@@ -110,6 +110,8 @@ def test_switch_history(self):
         original_history_id = self.current_history_id()
         # Load the multi-view
         self.components.history_panel.multi_view_button.wait_for_and_click()
+        # There should be only one
+        self.assert_history(original_history_id, histories_number=1)
         # Creating a new history should automatically switch to it
         self.components.multi_history_view.create_new_button.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)

From 6af42d76a626d5830408572981d40001844f0bca Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 18 Mar 2020 18:20:19 +0100
Subject: [PATCH 465/853] Add wrapper for CSS

---
 .../scripts/components/ToolRecommendation.vue |  4 +-
 client/galaxy/style/scss/base.scss            | 52 ++++++++++---------
 2 files changed, 29 insertions(+), 27 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 9a5316d29e7a..9f5f6dcb65d7 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -1,5 +1,5 @@
 <template>
-    <div id="tool-recommendation-view">
+    <div id="tool-recommendation" class="tool-recommendation-view">
         <div v-if="deprecated == false" class="infomessagelarge">
             <h4>Tool recommendation</h4>
             You have used {{ getToolId }} tool. For further analysis, you could try using the following/recommended
@@ -114,7 +114,7 @@ export default {
                 return [d.y, d.x];
             });
             const svg = d3
-                .select("#tool-recommendation-view")
+                .select("#tool-recommendation")
                 .append("svg")
                 .attr("class", "tree-size")
                 .append("g")
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index c9088cc51c8a..87cc9b6ca410 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1652,34 +1652,36 @@ body.reports {
 }
 
 /* Used for tree in tool recommendations */
-.node {
-    cursor: pointer;
-    circle {
-        fill: none;
-        stroke: lighten($brand-primary, 20%);
-        stroke-width: 0.3rem;
-    }
-    text {
-        font: 0.75rem sans-serif;
+.tool-recommendation-view {
+    .node {
+        cursor: pointer;
+        circle {
+            fill: none;
+            stroke: lighten($brand-primary, 20%);
+            stroke-width: 0.3rem;
+        }
+        text {
+            font: 0.75rem sans-serif;
+        }
     }
-}
 
-.node-enter {
-    fill-opacity: 1e-6;
-}
+    .node-enter {
+        fill-opacity: 1e-6;
+    }
 
-.node-update {
-    fill-opacity: 1;
-}
+    .node-update {
+        fill-opacity: 1;
+    }
 
-.tree-size {
-    width: 96%;
-    height: 50%;
-    position: absolute;
-}
+    .tree-size {
+        width: 96%;
+        height: 50%;
+        position: absolute;
+    }
 
-.link {
-    fill: none;
-    stroke: lighten($brand-primary, 20%);
-    stroke-width: 0.3rem;
+    .link {
+        fill: none;
+        stroke: lighten($brand-primary, 20%);
+        stroke-width: 0.3rem;
+    }
 }

From 640a4a5c744267a89932ff3c40c3781329714495 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 18 Mar 2020 18:53:00 +0100
Subject: [PATCH 466/853] Fill tree's circles

---
 client/galaxy/style/scss/base.scss | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index 87cc9b6ca410..ac567172780c 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1656,7 +1656,7 @@ body.reports {
     .node {
         cursor: pointer;
         circle {
-            fill: none;
+            fill: lighten($brand-primary, 20%);
             stroke: lighten($brand-primary, 20%);
             stroke-width: 0.3rem;
         }

From 8ef37d260506b64cb4e11d3c02b53ddfdbd6637b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 18 Mar 2020 17:41:13 +0100
Subject: [PATCH 467/853] Set HDA state to job state on history import

Prior to this you could export histories with failed datasets,
but on import the dataset state would be set to OK (despite the
job state being correctly set to error).
---
 lib/galaxy/model/store/__init__.py    |  2 ++
 lib/galaxy_test/api/test_histories.py | 26 +++++++++++++++++++++++---
 2 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 99121f2029cc..830f4dbfedaf 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -828,6 +828,7 @@ def _connect_job_io(self, imported_job, job_attrs, _find_hda, _find_hdca):
         for output_key in job_attrs['output_datasets']:
             output_hda = _find_hda(output_key)
             if output_hda:
+                output_hda.state = imported_job.state
                 imported_job.add_output_dataset(output_hda.name, output_hda)
 
         if 'input_mapping' in job_attrs:
@@ -890,6 +891,7 @@ def _connect_job_io(self, imported_job, job_attrs, _find_hda, _find_hdca):
                 for output_key in output_keys:
                     output_hda = _find_hda(output_key)
                     if output_hda:
+                        output_hda.state = imported_job.state
                         imported_job.add_output_dataset(output_name, output_hda)
 
         if 'output_dataset_collection_mapping' in job_attrs:
diff --git a/lib/galaxy_test/api/test_histories.py b/lib/galaxy_test/api/test_histories.py
index 1be49800e902..4868949fd2b5 100644
--- a/lib/galaxy_test/api/test_histories.py
+++ b/lib/galaxy_test/api/test_histories.py
@@ -9,6 +9,7 @@
 from galaxy_test.base.populators import (
     DatasetCollectionPopulator,
     DatasetPopulator,
+    skip_without_tool,
 )
 from ._framework import ApiTestCase
 
@@ -235,6 +236,24 @@ def check_ok(hda):
         )
         assert imported_content == "1 2 3\n"
 
+    @skip_without_tool("job_properties")
+    def test_import_export_failed_job(self):
+        history_name = "for_export_include_deleted"
+        history_id = self.dataset_populator.new_history(name=history_name)
+        self.dataset_populator.run_tool('job_properties', inputs={'failbool': True}, history_id=history_id, assert_ok=False)
+        self.dataset_populator.wait_for_history(history_id, assert_ok=False)
+
+        imported_history_id = self._reimport_history(history_id, history_name, assert_ok=False, wait_on_history_length=4, export_kwds={"include_deleted": "True"})
+        self._assert_history_length(imported_history_id, 4)
+
+        def check_failed(hda_or_job):
+            print(hda_or_job)
+            assert hda_or_job["state"] == "error", hda_or_job
+
+        self.dataset_populator._summarize_history(imported_history_id)
+
+        self._check_imported_dataset(history_id=imported_history_id, hid=1, assert_ok=False, hda_checker=check_failed, job_checker=check_failed)
+
     def test_import_metadata_regeneration(self):
         history_name = "for_import_metadata_regeneration"
         history_id = self.dataset_populator.new_history(name=history_name)
@@ -303,9 +322,9 @@ def check_elements(elements):
 
         self._check_imported_collection(imported_history_id, hid=1, collection_type="list:paired", elements_checker=check_elements)
 
-    def _reimport_history(self, history_id, history_name, wait_on_history_length=None, export_kwds={}):
+    def _reimport_history(self, history_id, history_name, wait_on_history_length=None, assert_ok=True, export_kwds={}):
         # Ensure the history is ready to go...
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+        self.dataset_populator.wait_for_history(history_id, assert_ok=assert_ok)
 
         return self.dataset_populator.reimport_history(
             history_id, history_name, wait_on_history_length=wait_on_history_length, export_kwds=export_kwds, url=self.url, api_key=self.galaxy_interactor.api_key
@@ -326,10 +345,11 @@ def _assert_history_length(self, history_id, n):
         contents = contents_response.json()
         assert len(contents) == n, contents
 
-    def _check_imported_dataset(self, history_id, hid, has_job=True, hda_checker=None, job_checker=None):
+    def _check_imported_dataset(self, history_id, hid, assert_ok=True, has_job=True, hda_checker=None, job_checker=None):
         imported_dataset_metadata = self.dataset_populator.get_history_dataset_details(
             history_id=history_id,
             hid=hid,
+            assert_ok=assert_ok,
         )
         assert imported_dataset_metadata["history_content_type"] == "dataset"
         assert imported_dataset_metadata["history_id"] == history_id

From 5519fa79ab73e50e020120d720091aeb9b5c59e4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 18 Mar 2020 19:06:18 +0100
Subject: [PATCH 468/853] Serialize HDA state during history export, fallback
 to job state

---
 lib/galaxy/model/__init__.py       |  1 +
 lib/galaxy/model/store/__init__.py | 14 +++++++++++---
 test/unit/test_model_store.py      | 19 +++++++++++++++++--
 3 files changed, 29 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 0f61eab86aa7..621124e9ccd6 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3136,6 +3136,7 @@ def serialize(self, id_encoder, serialization_options, for_link=False):
             return rval
 
         rval = super(HistoryDatasetAssociation, self).serialize(id_encoder, serialization_options)
+        rval['state'] = self.state
         rval["hid"] = self.hid
         rval["annotation"] = unicodify(getattr(self, 'annotation', ''))
         rval["tags"] = self.make_tag_string_list()
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 830f4dbfedaf..ba8fa4d1f52b 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -82,6 +82,7 @@ def __init__(self, import_options=None, app=None, user=None, object_store=None):
             self.sessionless = True
         self.user = user
         self.import_options = import_options or ImportOptions()
+        self.dataset_state_serialized = True
 
     @abc.abstractmethod
     def defines_new_history(self):
@@ -184,6 +185,9 @@ def _import_datasets(self, object_import_tracker, datasets_attrs, history, new_h
 
         for dataset_attrs in datasets_attrs:
 
+            if 'state' not in dataset_attrs:
+                self.dataset_state_serialized = False
+
             def handle_dataset_object_edit(dataset_instance):
                 if "dataset" in dataset_attrs:
                     assert self.import_options.allow_dataset_object_edit
@@ -321,7 +325,7 @@ def remap_objects(p, k, obj):
                         dataset_instance.dataset.deleted = True
                         dataset_instance.dataset.purged = True
                     else:
-                        dataset_instance.state = dataset_instance.states.OK
+                        dataset_instance.state = dataset_attrs.get('state', dataset_instance.states.OK)
                         self.object_store.update_from_file(dataset_instance.dataset, file_name=temp_dataset_file_name, create=True)
 
                         # Import additional files if present. Histories exported previously might not have this attribute set.
@@ -828,7 +832,9 @@ def _connect_job_io(self, imported_job, job_attrs, _find_hda, _find_hdca):
         for output_key in job_attrs['output_datasets']:
             output_hda = _find_hda(output_key)
             if output_hda:
-                output_hda.state = imported_job.state
+                if not self.dataset_state_serialized:
+                    # dataset state has not been serialized, get state from job
+                    output_hda.state = imported_job.state
                 imported_job.add_output_dataset(output_hda.name, output_hda)
 
         if 'input_mapping' in job_attrs:
@@ -891,7 +897,9 @@ def _connect_job_io(self, imported_job, job_attrs, _find_hda, _find_hdca):
                 for output_key in output_keys:
                     output_hda = _find_hda(output_key)
                     if output_hda:
-                        output_hda.state = imported_job.state
+                        if not self.dataset_state_serialized:
+                            # dataset state has not been serialized, get state from job
+                            output_hda.state = imported_job.state
                         imported_job.add_output_dataset(output_name, output_hda)
 
         if 'output_dataset_collection_mapping' in job_attrs:
diff --git a/test/unit/test_model_store.py b/test/unit/test_model_store.py
index 4f26f5b25741..58fd0d5d2ceb 100644
--- a/test/unit/test_model_store.py
+++ b/test/unit/test_model_store.py
@@ -21,6 +21,17 @@ def test_import_export_history():
     _assert_simple_cat_job_imported(imported_history)
 
 
+def test_import_export_history_failed_job():
+    """Test a simple job import/export, make sure state is maintained correctly."""
+    app = _mock_app()
+
+    u, h, d1, d2, j = _setup_simple_cat_job(app, state='error')
+
+    imported_history = _import_export_history(app, h, export_files="copy")
+
+    _assert_simple_cat_job_imported(imported_history, state='error')
+
+
 def test_import_export_bag_archive():
     """Test a simple job import/export using a BagIt archive."""
     dest_parent = mkdtemp()
@@ -402,13 +413,15 @@ def _setup_simple_export(export_kwds):
     return app, h, temp_directory, import_history
 
 
-def _assert_simple_cat_job_imported(imported_history):
+def _assert_simple_cat_job_imported(imported_history, state='ok'):
     assert imported_history.name == "imported from archive: Test History"
 
     datasets = imported_history.datasets
     assert len(datasets) == 2
+    assert datasets[0].state == datasets[1].state == state
     imported_job = datasets[1].creating_job
     assert imported_job
+    assert imported_job.state == state
     assert imported_job.output_datasets
     assert imported_job.output_datasets[0].dataset == datasets[1]
 
@@ -421,17 +434,19 @@ def _assert_simple_cat_job_imported(imported_history):
         assert f.read().startswith("chr1\t147962192\t147962580\tNM_005997_cds_0_0_chr1_147962193_r\t0\t-")
 
 
-def _setup_simple_cat_job(app):
+def _setup_simple_cat_job(app, state='ok'):
     sa_session = app.model.context
 
     u = model.User(email="collection@example.com", password="password")
     h = model.History(name="Test History", user=u)
 
     d1, d2 = _create_datasets(sa_session, h, 2)
+    d1.state = d2.state = state
 
     j = model.Job()
     j.user = u
     j.tool_id = "cat1"
+    j.state = state
 
     j.add_input_dataset("input1", d1)
     j.add_output_dataset("out_file1", d2)

From 274ed99b3d882bd8e3f570825a33ca3214bd3362 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 18 Mar 2020 13:27:54 +0100
Subject: [PATCH 469/853] Make history import/export test more stable

We need to wait for the second HDA to be finished, otherwise
deleting the dataset wil cancel the job (if it is still running)
and then the dataset will be in discarded state (either because
that's what cancelling the job does, or if the export starts first
it's the import logic that sets state discarded if the file was not
exported).
This means sometimes the state will be OK and sometimes it would
be discarded. With this change the state will be OK.
---
 lib/galaxy_test/api/test_histories.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy_test/api/test_histories.py b/lib/galaxy_test/api/test_histories.py
index 4868949fd2b5..9ea6961cad81 100644
--- a/lib/galaxy_test/api/test_histories.py
+++ b/lib/galaxy_test/api/test_histories.py
@@ -182,7 +182,7 @@ def test_import_export(self):
         history_name = "for_export_default"
         history_id = self.dataset_populator.new_history(name=history_name)
         self.dataset_populator.new_dataset(history_id, content="1 2 3")
-        deleted_hda = self.dataset_populator.new_dataset(history_id, content="1 2 3")
+        deleted_hda = self.dataset_populator.new_dataset(history_id, content="1 2 3", wait=True)
         self.dataset_populator.delete_dataset(history_id, deleted_hda["id"])
         deleted_details = self.dataset_populator.get_history_dataset_details(history_id, id=deleted_hda["id"])
         assert deleted_details["deleted"]
@@ -214,7 +214,7 @@ def test_import_export_include_deleted(self):
         history_name = "for_export_include_deleted"
         history_id = self.dataset_populator.new_history(name=history_name)
         self.dataset_populator.new_dataset(history_id, content="1 2 3")
-        deleted_hda = self.dataset_populator.new_dataset(history_id, content="1 2 3")
+        deleted_hda = self.dataset_populator.new_dataset(history_id, content="1 2 3", wait=True)
         self.dataset_populator.delete_dataset(history_id, deleted_hda["id"])
 
         imported_history_id = self._reimport_history(history_id, history_name, wait_on_history_length=2, export_kwds={"include_deleted": "True"})
@@ -223,12 +223,13 @@ def test_import_export_include_deleted(self):
         def upload_job_check(job):
             assert job["tool_id"] == "upload1"
 
-        def check_ok(hda):
+        def check_deleted_not_purged(hda):
             assert hda["state"] == "ok", hda
             assert hda["deleted"] is True, hda
+            assert hda["purged"] is False, hda
 
         self._check_imported_dataset(history_id=imported_history_id, hid=1, job_checker=upload_job_check)
-        self._check_imported_dataset(history_id=imported_history_id, hid=2, hda_checker=check_ok, job_checker=upload_job_check)
+        self._check_imported_dataset(history_id=imported_history_id, hid=2, hda_checker=check_deleted_not_purged, job_checker=upload_job_check)
 
         imported_content = self.dataset_populator.get_history_dataset_content(
             history_id=imported_history_id,

From 71c1935a817023cc28f141d0d44e74cf07fee4e6 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 18 Mar 2020 19:25:02 +0100
Subject: [PATCH 470/853] Fix JS linting

---
 .../scripts/components/ToolRecommendation.vue  | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 9f5f6dcb65d7..86f4795ae92b 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -62,17 +62,17 @@ export default {
                         this.deprecated = predData.is_deprecated;
 
                         if (response.data !== null && predData.children.length > 0) {
-                            const filteredData = {},
-                                compatibleTools = {},
-                                filteredChildren = [],
-                                outputDatatypes = predData.o_extensions,
-                                children = predData.children;
+                            const filteredData = {};
+                            const compatibleTools = {};
+                            const filteredChildren = [];
+                            const outputDatatypes = predData.o_extensions;
+                            const children = predData.children;
                             for (const nameObj of children.entries()) {
                                 const inputDatatypes = nameObj[1].i_extensions;
                                 for (const out_t of outputDatatypes.entries()) {
                                     for (const in_t of inputDatatypes.entries()) {
-                                        const child = extToType[out_t[1]],
-                                            parent = extToType[in_t[1]];
+                                        const child = extToType[out_t[1]];
+                                        const parent = extToType[in_t[1]];
                                         if (
                                             (typeToType[child] && parent in typeToType[child]) === true ||
                                             out_t[1] === "input" ||
@@ -119,8 +119,8 @@ export default {
                 .attr("class", "tree-size")
                 .append("g")
                 .attr("transform", "translate(" + 250 + "," + 20 + ")");
-            let i = 0,
-                root = null;
+            let i = 0;
+            let root = null;
             const update = source => {
                 // Compute the new tree layout.
                 const nodes = tree.nodes(root).reverse();

From fa08def5363989de592fab542fc107d0cea4fc2d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 18 Mar 2020 19:52:42 +0100
Subject: [PATCH 471/853] Unit test fix

---
 test/unit/tools/test_history_imp_exp.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/unit/tools/test_history_imp_exp.py b/test/unit/tools/test_history_imp_exp.py
index 7f9f63610ee8..63eb9d71dc16 100644
--- a/test/unit/tools/test_history_imp_exp.py
+++ b/test/unit/tools/test_history_imp_exp.py
@@ -115,10 +115,12 @@ def test_export_dataset():
     app, sa_session, h = _setup_history_for_export("Datasets History")
 
     d1, d2 = _create_datasets(sa_session, h, 2)
+    d1.state = d2.state = 'ok'
 
     j = model.Job()
     j.user = h.user
     j.tool_id = "cat1"
+    j.state = 'ok'
 
     j.add_input_dataset("input1", d1)
     j.add_output_dataset("out_file1", d2)

From 563969082eb16127166c292d15cb8e7497a98d07 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 18 Mar 2020 20:59:34 +0100
Subject: [PATCH 472/853] Make test history name unique

---
 lib/galaxy_test/api/test_histories.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy_test/api/test_histories.py b/lib/galaxy_test/api/test_histories.py
index 9ea6961cad81..7da3695a87aa 100644
--- a/lib/galaxy_test/api/test_histories.py
+++ b/lib/galaxy_test/api/test_histories.py
@@ -239,7 +239,7 @@ def check_deleted_not_purged(hda):
 
     @skip_without_tool("job_properties")
     def test_import_export_failed_job(self):
-        history_name = "for_export_include_deleted"
+        history_name = "for_export_include_failed_job"
         history_id = self.dataset_populator.new_history(name=history_name)
         self.dataset_populator.run_tool('job_properties', inputs={'failbool': True}, history_id=history_id, assert_ok=False)
         self.dataset_populator.wait_for_history(history_id, assert_ok=False)

From 0d118fcb40cb26facd9673db5d2e21d6a3eca8b9 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 18 Mar 2020 22:58:18 +0100
Subject: [PATCH 473/853] Downgrades tensorflow to the same version as EU

---
 lib/galaxy/dependencies/conditional-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index 239441722983..b1f96df95255 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -31,4 +31,4 @@ influxdb
 
 # Deep learning packages for tool recommendation
 keras==2.2.4
-tensorflow==1.15.0
+tensorflow==1.12.2

From 74efc01ccd9f283d8af028fd004fcfa1ecae6111 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 19 Mar 2020 12:16:37 +0100
Subject: [PATCH 474/853] Retry reading tool conf on IOError

I think that might stabilize the test_tool_reload* unit tests.
---
 lib/galaxy/tools/toolbox/watcher.py | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/tools/toolbox/watcher.py b/lib/galaxy/tools/toolbox/watcher.py
index 2a165cae02ec..032ba55ec2d5 100644
--- a/lib/galaxy/tools/toolbox/watcher.py
+++ b/lib/galaxy/tools/toolbox/watcher.py
@@ -71,6 +71,8 @@ class ToolConfWatcher(object):
 
     def __init__(self, reload_callback, tool_cache=None):
         self.paths = {}
+        self.drop_on_next_loop = set()
+        self.drop_now = set()
         self.cache = tool_cache
         self._active = False
         self._lock = threading.Lock()
@@ -131,11 +133,16 @@ def check(self):
                     # in rare cases `path` may be deleted between `os.path.exists` calls
                     # and reading the file from the filesystem. We do not want the watcher
                     # thread to die in these cases.
-                    try:
-                        del hashes[path]
-                        del paths[path]
-                    except KeyError:
-                        pass
+                    if path in self.drop_now:
+                        log.warning("'%s' could not be read, removing from watched files")
+                        try:
+                            del hashes[path]
+                            del paths[path]
+                        except KeyError:
+                            pass
+                    else:
+                        log.debug("'%s could not be read")
+                        self.drop_on_next_loop.add(path)
                     if self.cache:
                         self.cache.cleanup()
                     do_reload = True
@@ -145,6 +152,8 @@ def check(self):
                     do_reload = True
             if do_reload:
                 self.reload_callback()
+            self.drop_now = self.drop_on_next_loop
+            self.drop_on_next_loop = set()
             self.exit.wait(1)
 
     def monitor(self, path):

From eb70313708e9c6a660f0e0a91dc0dd29a8a27105 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 19 Mar 2020 12:33:06 +0100
Subject: [PATCH 475/853] Fix minor comments

---
 client/galaxy/scripts/components/ToolRecommendation.vue     | 6 +++---
 .../tools/{tool_recommendations.py => recommendations.py}   | 0
 lib/galaxy/webapps/galaxy/api/workflows.py                  | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)
 rename lib/galaxy/tools/{tool_recommendations.py => recommendations.py} (100%)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 86f4795ae92b..35abb369a5de 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -1,6 +1,6 @@
 <template>
     <div id="tool-recommendation" class="tool-recommendation-view">
-        <div v-if="deprecated == false" class="infomessagelarge">
+        <div v-if="!deprecated" class="infomessagelarge">
             <h4>Tool recommendation</h4>
             You have used {{ getToolId }} tool. For further analysis, you could try using the following/recommended
             tools. The recommended tools are shown in the decreasing order of their scores predicted using machine
@@ -8,7 +8,7 @@
             tool than a tool with a lower score. Please click on one of the following/recommended tools to open its
             definition.
         </div>
-        <div v-if="deprecated == true" class="warningmessagelarge">
+        <div v-else-if="deprecated" class="warningmessagelarge">
             You have used {{ getToolId }} tool. {{ deprecatedMessage }}
         </div>
     </div>
@@ -105,7 +105,7 @@ export default {
                     });
                 });
         },
-        renderD3Tree: predictedTools => {
+        renderD3Tree(predictedTools) {
             const duration = 750;
             const x = 620;
             const y = 260;
diff --git a/lib/galaxy/tools/tool_recommendations.py b/lib/galaxy/tools/recommendations.py
similarity index 100%
rename from lib/galaxy/tools/tool_recommendations.py
rename to lib/galaxy/tools/recommendations.py
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 1dee03f7000e..9cfe322b53fb 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -26,7 +26,7 @@
 from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
-from galaxy.tools import tool_recommendations
+from galaxy.tools import recommendations
 from galaxy.tools.parameters import populate_state
 from galaxy.tools.parameters.basic import workflow_building_modes
 from galaxy.util.sanitize_html import sanitize_html
@@ -58,7 +58,7 @@ def __init__(self, app):
         self.history_manager = histories.HistoryManager(app)
         self.workflow_manager = workflows.WorkflowsManager(app)
         self.workflow_contents_manager = workflows.WorkflowContentsManager(app)
-        self.tool_recommendations = tool_recommendations.ToolRecommendations()
+        self.tool_recommendations = recommendations.ToolRecommendations()
 
     def __get_full_shed_url(self, url):
         for name, shed_url in self.app.tool_shed_registry.tool_sheds.items():

From 1d4e511d324aef4322364170de1042b5f888cdad Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 19 Mar 2020 15:47:12 +0100
Subject: [PATCH 476/853] Fix v-else

---
 client/galaxy/scripts/components/ToolRecommendation.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 35abb369a5de..264c59482b67 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -8,7 +8,7 @@
             tool than a tool with a lower score. Please click on one of the following/recommended tools to open its
             definition.
         </div>
-        <div v-else-if="deprecated" class="warningmessagelarge">
+        <div v-else class="warningmessagelarge">
             You have used {{ getToolId }} tool. {{ deprecatedMessage }}
         </div>
     </div>

From c46524a198ffb1a39bd30443766ab74346cca032 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Thu, 19 Mar 2020 15:56:23 +0100
Subject: [PATCH 477/853] wait for histories to be present

---
 lib/galaxy_test/selenium/test_history_multi_view.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy_test/selenium/test_history_multi_view.py b/lib/galaxy_test/selenium/test_history_multi_view.py
index a80cb26b07ce..14b59d137ee5 100644
--- a/lib/galaxy_test/selenium/test_history_multi_view.py
+++ b/lib/galaxy_test/selenium/test_history_multi_view.py
@@ -127,6 +127,7 @@ def test_switch_history(self):
         self.assertEqual(original_history_id, self.current_history_id())
 
     def assert_history(self, history_id, histories_number=1, should_exist=True):
+        self.components.multi_history_view.histories.wait_for_present()
         histories = self.components.multi_history_view.histories.all()
         assert len(histories) == histories_number
         # search for history with history_id

From 2185db9785074068b4661490049d956b7636be37 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 19 Mar 2020 16:19:56 +0100
Subject: [PATCH 478/853] Run prettier

---
 client/galaxy/scripts/components/ToolRecommendation.vue | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 264c59482b67..880f3aa93cb5 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -8,9 +8,7 @@
             tool than a tool with a lower score. Please click on one of the following/recommended tools to open its
             definition.
         </div>
-        <div v-else class="warningmessagelarge">
-            You have used {{ getToolId }} tool. {{ deprecatedMessage }}
-        </div>
+        <div v-else class="warningmessagelarge">You have used {{ getToolId }} tool. {{ deprecatedMessage }}</div>
     </div>
 </template>
 

From e86b237e6e4f52e1e8c385b6d7a600b161bfd74c Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Thu, 19 Mar 2020 18:48:56 +0100
Subject: [PATCH 479/853] fix citation ids

---
 client/galaxy/scripts/components/Citations.vue               | 2 +-
 client/galaxy/scripts/components/ToolsView/ToolsView.test.js | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/Citations.vue b/client/galaxy/scripts/components/Citations.vue
index e138738d76e7..71d4934c72e5 100644
--- a/client/galaxy/scripts/components/Citations.vue
+++ b/client/galaxy/scripts/components/Citations.vue
@@ -34,7 +34,7 @@
         <div v-else-if="citations.length">
             <b-btn v-b-toggle="id" variant="primary">Citations</b-btn>
             <b-collapse
-                :id="id"
+                :id="id.replace(/ /g, '_')"
                 class="mt-2"
                 @show="$emit('show')"
                 @shown="$emit('shown')"
diff --git a/client/galaxy/scripts/components/ToolsView/ToolsView.test.js b/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
index f12b524ca8ac..c7f605a02cbc 100644
--- a/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
+++ b/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
@@ -68,7 +68,7 @@ describe("ToolsView/ToolsView.vue", () => {
             .findAll('[type="button"]')
             .filter(button => button.text() === "Citations")
             .at(0);
-        const citation = wrapper.find("#" + infoButton.attributes("aria-controls"));
+        const citation = wrapper.find("#" + infoButton.attributes("aria-controls").replace(/ /g, "_"));
 
         assert(citation.isVisible() === false, "citation is visible before being triggered!");
         assert(infoButton.attributes("aria-expanded") === "false", "citation is expanded before being triggered!");

From 254cca9ddeb699df2501eb822b42fbe7427a05f4 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 19 Mar 2020 16:36:59 -0400
Subject: [PATCH 480/853] Passing the resource name in to create method, since
 now we can have multiple resources (S3, unix file system, etc.)

---
 lib/galaxy/objectstore/irods.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index a9ec524cfb11..14f99b22339b 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -440,7 +440,7 @@ def _download(self, rel_path):
 
         log.debug("Pulled data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
         
-        with data_obj.open('rb') as data_obj_fp, open(self._get_cache_path(rel_path), "wb") as cache_fp:
+        with data_obj.open('r') as data_obj_fp, open(self._get_cache_path(rel_path), "wb") as cache_fp:
             content = data_obj_fp.read()
             cache_fp.write(content)
         return True
@@ -470,7 +470,7 @@ def _push_to_os(self, rel_path, source_file=None, from_string=None):
                 log.debug("Wanted to push file '%s' to iRODS collection '%s' but its size is 0; skipping.", source_file, rel_path)
                 return True
             if from_string:
-                data_obj = self.session.data_objects.create(data_object_path, recurse=True, **options)
+                data_obj = self.session.data_objects.create(data_object_path, self.resource, **options)
                 with data_obj.open('w') as data_obj_fp:
                     data_obj_fp.write(from_string)
                 log.debug("Pushed data from string '%s' to collection '%s'", from_string, data_object_path)
@@ -486,7 +486,7 @@ def _push_to_os(self, rel_path, source_file=None, from_string=None):
                     file_content = content_file.read()
                 
                 # Write to file in subcollection created above
-                data_obj = self.session.data_objects.create(data_object_path, recurse=True, **options)
+                data_obj = self.session.data_objects.create(data_object_path, self.resource, **options)
                 with data_obj.open('w') as data_obj_fp:
                     data_obj_fp.write(file_content)
 
@@ -548,7 +548,6 @@ def exists(self, obj, **kwargs):
 
     def create(self, obj, **kwargs):
         if not self.exists(obj, **kwargs):
-
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
             extra_dir_at_root = kwargs.get('extra_dir_at_root', False)

From 5ad5939615fe5c3e708b353a168172df786b861e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 19 Mar 2020 21:54:52 +0000
Subject: [PATCH 481/853] Bump tensorflow from 1.12.2 to 1.15.2 in
 /lib/galaxy/dependencies

Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 1.12.2 to 1.15.2.
- [Release notes](https://github.com/tensorflow/tensorflow/releases)
- [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md)
- [Commits](https://github.com/tensorflow/tensorflow/compare/v1.12.2...v1.15.2)

Signed-off-by: dependabot[bot] <support@github.com>
---
 lib/galaxy/dependencies/conditional-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index b1f96df95255..44f61faf1a81 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -31,4 +31,4 @@ influxdb
 
 # Deep learning packages for tool recommendation
 keras==2.2.4
-tensorflow==1.12.2
+tensorflow==1.15.2

From fbc70dae1904391fd91a53048ebf4a3d68d7e6c5 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Fri, 20 Mar 2020 09:17:45 +0100
Subject: [PATCH 482/853] fix logging

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/tools/toolbox/watcher.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/toolbox/watcher.py b/lib/galaxy/tools/toolbox/watcher.py
index 032ba55ec2d5..75b5902eff44 100644
--- a/lib/galaxy/tools/toolbox/watcher.py
+++ b/lib/galaxy/tools/toolbox/watcher.py
@@ -134,7 +134,7 @@ def check(self):
                     # and reading the file from the filesystem. We do not want the watcher
                     # thread to die in these cases.
                     if path in self.drop_now:
-                        log.warning("'%s' could not be read, removing from watched files")
+                        log.warning("'%s' could not be read, removing from watched files", path)
                         try:
                             del hashes[path]
                             del paths[path]

From 6aea38443f7675d5d704033a1d876ac41cd48df1 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 20 Mar 2020 09:19:32 +0100
Subject: [PATCH 483/853] Make drop_now and drop_on_next_loop local variables

---
 lib/galaxy/tools/toolbox/watcher.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/tools/toolbox/watcher.py b/lib/galaxy/tools/toolbox/watcher.py
index 75b5902eff44..f224bba505a0 100644
--- a/lib/galaxy/tools/toolbox/watcher.py
+++ b/lib/galaxy/tools/toolbox/watcher.py
@@ -71,8 +71,6 @@ class ToolConfWatcher(object):
 
     def __init__(self, reload_callback, tool_cache=None):
         self.paths = {}
-        self.drop_on_next_loop = set()
-        self.drop_now = set()
         self.cache = tool_cache
         self._active = False
         self._lock = threading.Lock()
@@ -103,6 +101,8 @@ def check(self):
         hashes = {}
         while self._active and not self.exit.isSet():
             do_reload = False
+            drop_on_next_loop = set()
+            drop_now = set()
             with self._lock:
                 paths = list(self.paths.keys())
             for path in paths:
@@ -133,7 +133,7 @@ def check(self):
                     # in rare cases `path` may be deleted between `os.path.exists` calls
                     # and reading the file from the filesystem. We do not want the watcher
                     # thread to die in these cases.
-                    if path in self.drop_now:
+                    if path in drop_now:
                         log.warning("'%s' could not be read, removing from watched files", path)
                         try:
                             del hashes[path]
@@ -142,7 +142,7 @@ def check(self):
                             pass
                     else:
                         log.debug("'%s could not be read")
-                        self.drop_on_next_loop.add(path)
+                        drop_on_next_loop.add(path)
                     if self.cache:
                         self.cache.cleanup()
                     do_reload = True
@@ -152,8 +152,8 @@ def check(self):
                     do_reload = True
             if do_reload:
                 self.reload_callback()
-            self.drop_now = self.drop_on_next_loop
-            self.drop_on_next_loop = set()
+            drop_now = drop_on_next_loop
+            drop_on_next_loop = set()
             self.exit.wait(1)
 
     def monitor(self, path):

From 14a52c20fc7a72758a3e5c17d38713badb699db0 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 7 Feb 2020 15:31:53 -0500
Subject: [PATCH 484/853] Refactor toward testing workflow collection
 outputs...

... by Planemo via tool_util.
---
 lib/galaxy/tool_util/cwl/util.py          |  28 ++++--
 lib/galaxy/tool_util/verify/interactor.py | 103 ++++++++++++----------
 2 files changed, 78 insertions(+), 53 deletions(-)

diff --git a/lib/galaxy/tool_util/cwl/util.py b/lib/galaxy/tool_util/cwl/util.py
index 29c6f0aa9d5c..3892b6aeebac 100644
--- a/lib/galaxy/tool_util/cwl/util.py
+++ b/lib/galaxy/tool_util/cwl/util.py
@@ -354,17 +354,17 @@ def __str__(self):
         return "DirectoryUploadTarget[tar_path=%s]" % self.tar_path
 
 
-GalaxyOutput = namedtuple("GalaxyOutput", ["history_id", "history_content_type", "history_content_id"])
+GalaxyOutput = namedtuple("GalaxyOutput", ["history_id", "history_content_type", "history_content_id", "metadata"])
 
 
 def tool_response_to_output(tool_response, history_id, output_id):
     for output in tool_response["outputs"]:
         if output["output_name"] == output_id:
-            return GalaxyOutput(history_id, "dataset", output["id"])
+            return GalaxyOutput(history_id, "dataset", output["id"], None)
 
     for output_collection in tool_response["output_collections"]:
         if output_collection["output_name"] == output_id:
-            return GalaxyOutput(history_id, "dataset_collection", output_collection["id"])
+            return GalaxyOutput(history_id, "dataset_collection", output_collection["id"], None)
 
     raise Exception("Failed to find output with label [%s]" % output_id)
 
@@ -372,10 +372,10 @@ def tool_response_to_output(tool_response, history_id, output_id):
 def invocation_to_output(invocation, history_id, output_id):
     if output_id in invocation["outputs"]:
         dataset = invocation["outputs"][output_id]
-        galaxy_output = GalaxyOutput(history_id, "dataset", dataset["id"])
+        galaxy_output = GalaxyOutput(history_id, "dataset", dataset["id"], None)
     elif output_id in invocation["output_collections"]:
         collection = invocation["output_collections"][output_id]
-        galaxy_output = GalaxyOutput(history_id, "dataset_collection", collection["id"])
+        galaxy_output = GalaxyOutput(history_id, "dataset_collection", collection["id"], None)
     else:
         raise Exception("Failed to find output with label [%s] in [%s]" % (output_id, invocation))
 
@@ -391,14 +391,26 @@ def output_to_cwl_json(
     interface via Galaxy.
     """
     def element_to_cwl_json(element):
+        object = element["object"]
+        content_type = object.get("history_content_type")
+        metadata = None
+        if content_type is None:
+            content_type = "dataset_collection"
+            metadata = element["object"]
+            metadata["history_content_type"] = content_type
         element_output = GalaxyOutput(
             galaxy_output.history_id,
-            element["object"]["history_content_type"],
-            element["object"]["id"],
+            content_type,
+            object["id"],
+            metadata,
         )
         return output_to_cwl_json(element_output, get_metadata, get_dataset, get_extra_files, pseduo_location=pseduo_location)
 
-    output_metadata = get_metadata(galaxy_output.history_content_type, galaxy_output.history_content_id)
+    output_metadata = galaxy_output.metadata
+    if output_metadata is None:
+        output_metadata = get_metadata(galaxy_output.history_content_type, galaxy_output.history_content_id)
+
+    print(output_metadata)
 
     def dataset_dict_to_json_content(dataset_dict):
         if "content" in dataset_dict:
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index 2f6cfb5c4bd3..792448d9369a 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -147,54 +147,19 @@ def get_tool_tests(self, tool_id, tool_version=None):
         return response.json()
 
     def verify_output_collection(self, output_collection_def, output_collection_id, history, tool_id):
-        name = output_collection_def.name
         data_collection = self._get("dataset_collections/%s" % output_collection_id, data={"instance_type": "history"}).json()
 
-        def get_element(elements, id):
-            for element in elements:
-                if element["element_identifier"] == id:
-                    return element
-            return False
-
-        expected_collection_type = output_collection_def.collection_type
-        if expected_collection_type:
-            collection_type = data_collection["collection_type"]
-            if expected_collection_type != collection_type:
-                template = "Expected output collection [%s] to be of type [%s], was of type [%s]."
-                message = template % (name, expected_collection_type, collection_type)
-                raise AssertionError(message)
-
-        expected_element_count = output_collection_def.count
-        if expected_element_count:
-            actual_element_count = len(data_collection["elements"])
-            if expected_element_count != actual_element_count:
-                template = "Expected output collection [%s] to have %s elements, but it had %s."
-                message = template % (name, expected_element_count, actual_element_count)
-                raise AssertionError(message)
+        def verify_dataset(element, element_attrib, element_outfile):
+            hda = element["object"]
+            self.verify_output_dataset(
+                history,
+                hda_id=hda["id"],
+                outfile=element_outfile,
+                attributes=element_attrib,
+                tool_id=tool_id
+            )
 
-        def verify_elements(element_objects, element_tests):
-            for element_identifier, (element_outfile, element_attrib) in element_tests.items():
-                element = get_element(element_objects, element_identifier)
-                if not element:
-                    template = "Failed to find identifier [%s] for testing, tool generated collection elements [%s]"
-                    message = template % (element_identifier, element_objects)
-                    raise AssertionError(message)
-
-                element_type = element["element_type"]
-                if element_type != "dataset_collection":
-                    hda = element["object"]
-                    self.verify_output_dataset(
-                        history,
-                        hda_id=hda["id"],
-                        outfile=element_outfile,
-                        attributes=element_attrib,
-                        tool_id=tool_id
-                    )
-                if element_type == "dataset_collection":
-                    elements = element["object"]["elements"]
-                    verify_elements(elements, element_attrib.get("elements", {}))
-
-        verify_elements(data_collection["elements"], output_collection_def.element_tests)
+        verify_collection(output_collection_def, data_collection, verify_dataset)
 
     def verify_output(self, history_id, jobs, output_data, output_testdef, tool_id, maxseconds):
         outfile = output_testdef.outfile
@@ -724,6 +689,54 @@ def verify_extra_files(extra_files):
     )
 
 
+def verify_collection(output_collection_def, data_collection, verify_dataset):
+    name = output_collection_def.name
+
+    def get_element(elements, id):
+        for element in elements:
+            if element["element_identifier"] == id:
+                return element
+        return False
+
+    expected_collection_type = output_collection_def.collection_type
+    if expected_collection_type:
+        collection_type = data_collection["collection_type"]
+        if expected_collection_type != collection_type:
+            template = "Expected output collection [%s] to be of type [%s], was of type [%s]."
+            message = template % (name, expected_collection_type, collection_type)
+            raise AssertionError(message)
+
+    expected_element_count = output_collection_def.count
+    if expected_element_count:
+        actual_element_count = len(data_collection["elements"])
+        if expected_element_count != actual_element_count:
+            template = "Expected output collection [%s] to have %s elements, but it had %s."
+            message = template % (name, expected_element_count, actual_element_count)
+            raise AssertionError(message)
+
+    def verify_elements(element_objects, element_tests):
+        for element_identifier, element_test in element_tests.items():
+            if isinstance(element_test, dict):
+                element_outfile, element_attrib = None, element_test
+            else:
+                element_outfile, element_attrib = element_test
+
+            element = get_element(element_objects, element_identifier)
+            if not element:
+                template = "Failed to find identifier [%s] for testing, tool generated collection elements [%s]"
+                message = template % (element_identifier, element_objects)
+                raise AssertionError(message)
+
+            element_type = element["element_type"]
+            if element_type != "dataset_collection":
+                verify_dataset(element, element_attrib, element_outfile)
+            if element_type == "dataset_collection":
+                elements = element["object"]["elements"]
+                verify_elements(elements, element_attrib.get("elements", {}))
+
+    verify_elements(data_collection["elements"], output_collection_def.element_tests)
+
+
 def _verify_composite_datatype_file_content(file_name, hda_id, base_name=None, attributes=None, dataset_fetcher=None, test_data_downloader=None, keep_outputs_dir=False, mode='file'):
     assert dataset_fetcher is not None
 

From a22e35eea5a81449eb5d614c1949a50400867618 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 7 Feb 2020 16:50:54 -0500
Subject: [PATCH 485/853] Spelling fix.

---
 lib/galaxy/tool_util/verify/interactor.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index 792448d9369a..d9c3b29c99d2 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -167,7 +167,7 @@ def verify_output(self, history_id, jobs, output_data, output_testdef, tool_id,
         name = output_testdef.name
         self.wait_for_jobs(history_id, jobs, maxseconds)
         hid = self.__output_id(output_data)
-        # TODO: Twill version verifys dataset is 'ok' in here.
+        # TODO: Twill version verifies dataset is 'ok' in here.
         self.verify_output_dataset(history_id=history_id, hda_id=hid, outfile=outfile, attributes=attributes, tool_id=tool_id)
 
         primary_datasets = attributes.get('primary_datasets', {})

From 6208552e187fb67426dbd003be031de6e4ef1e32 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Fri, 20 Mar 2020 18:00:30 +0100
Subject: [PATCH 486/853] Fix removing tools from watched paths

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/tools/toolbox/watcher.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tools/toolbox/watcher.py b/lib/galaxy/tools/toolbox/watcher.py
index f224bba505a0..8f0a753fedbe 100644
--- a/lib/galaxy/tools/toolbox/watcher.py
+++ b/lib/galaxy/tools/toolbox/watcher.py
@@ -135,11 +135,9 @@ def check(self):
                     # thread to die in these cases.
                     if path in drop_now:
                         log.warning("'%s' could not be read, removing from watched files", path)
-                        try:
+                        del paths[path]
+                        if path in hashes:
                             del hashes[path]
-                            del paths[path]
-                        except KeyError:
-                            pass
                     else:
                         log.debug("'%s could not be read")
                         drop_on_next_loop.add(path)

From c9ca69075c6500a34d05c9691c781995b3740157 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 20 Mar 2020 18:17:54 +0100
Subject: [PATCH 487/853] fix documentation for data checksum attribute

the separator seems to be `$`: https://github.com/galaxyproject/galaxy/blob/519e35e9682a3d8ce8de0f3736b97e84fba583c4/lib/galaxy/tool_util/verify/__init__.py#L76
---
 lib/galaxy/tool_util/xsd/galaxy.xsd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index a812c6dc04d2..e074d8811aa8 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -1291,8 +1291,8 @@ and this can be used instead.
         <xs:documentation xml:lang="en"><![CDATA[
 
 If specified, the target output's checksum should match the value specified
-here. This value should have the form ``hash_type:hash_value``
-(e.g. ``sha1:8156d7ca0f46ed7abac98f82e36cfaddb2aca041``). For large static files
+here. This value should have the form ``hash_type$hash_value``
+(e.g. ``sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041``). For large static files
 it may be inconvenient to upload the entiry file and this can be used instead.
 
 ]]></xs:documentation>

From bc3733204af57c82b118bb06c807b01e3c95c584 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@gmail.com>
Date: Fri, 20 Mar 2020 18:21:15 +0100
Subject: [PATCH 488/853] Fix another logging

---
 lib/galaxy/tools/toolbox/watcher.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/toolbox/watcher.py b/lib/galaxy/tools/toolbox/watcher.py
index 8f0a753fedbe..7733ded05ab6 100644
--- a/lib/galaxy/tools/toolbox/watcher.py
+++ b/lib/galaxy/tools/toolbox/watcher.py
@@ -139,7 +139,7 @@ def check(self):
                         if path in hashes:
                             del hashes[path]
                     else:
-                        log.debug("'%s could not be read")
+                        log.debug("'%s could not be read", path)
                         drop_on_next_loop.add(path)
                     if self.cache:
                         self.cache.cleanup()

From 25332bdd2f3228cba76fd8c921d41810db96198e Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 20 Mar 2020 17:24:32 +0000
Subject: [PATCH 489/853] Ensure miniumum virtualenv version for py27-unit
 build

---
 .circleci/config.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index a87c6269b746..3afbbc0bb985 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -95,7 +95,8 @@ jobs:
     <<: *set_workdir
     steps:
       - *restore_repo_cache
-      - *install_tox
+      # Ensure minimum virtualenv version due to https://github.com/pypa/virtualenv/issues/1670
+      - run: sudo pip install tox 'virtualenv>=20.0.8'
       - run: tox -e py27-unit
   py35_docstring:
     docker:

From 8f4c1be9a11eb825ab9d4f4fe03e296eb5bdc9ee Mon Sep 17 00:00:00 2001
From: Juan David Mendez Solano <juan.mendez@imtek.uni-freiburg.de>
Date: Fri, 20 Mar 2020 19:26:24 +0100
Subject: [PATCH 490/853] Created a function to return a random password
 Deleted the hard coded passwords to use random passwords

---
 lib/galaxy/selenium/navigates_galaxy.py         |  3 +++
 .../selenium/test_change_password.py            | 17 +++++++++++------
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index 6cc481fbcda0..e9359560aa5c 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -389,6 +389,9 @@ def _get_random_email(self, username=None, domain=None):
         domain = domain or 'test.test'
         return self._get_random_name(prefix=username, suffix="@" + domain)
 
+    def _get_random_password(self, len=6):
+        return ''.join(random.SystemRandom().choice(string.ascii_uppercase + string.digits) for _ in range(len))
+
     def submit_login(self, email, password=None, assert_valid=True, retries=0):
         if password is None:
             password = self.default_password
diff --git a/lib/galaxy_test/selenium/test_change_password.py b/lib/galaxy_test/selenium/test_change_password.py
index f088b992b6e0..c7bbedeef6e0 100644
--- a/lib/galaxy_test/selenium/test_change_password.py
+++ b/lib/galaxy_test/selenium/test_change_password.py
@@ -13,32 +13,37 @@ def test_change_password(self):
         self.click_masthead_user()
         self.components.masthead.preferences.wait_for_and_click()
         self.components.preferences.change_password.wait_for_and_click()
-        self.fill_input_fields(self.default_password, "123123", "123123")
+        new_password = self._get_random_password()
+        self.fill_input_fields(self.default_password, new_password, new_password)
         self.logout_if_needed()
-        self.submit_login(email, "123123")
+        self.submit_login(email, new_password)
 
     @selenium_test
     def test_new_password_password(self):
         self.register_and_change_password()
-        self.fill_input_fields(self.default_password, "", "123123")
+        self.fill_input_fields(self.default_password, "", self._get_random_password())
         self.assert_error_message(contains='Please provide a new password.')
 
     @selenium_test
     def test_no_password_confirmation(self):
         self.register_and_change_password()
-        self.fill_input_fields(self.default_password, "123123", "5444484")
+        password = self._get_random_password()
+        confirmation = self._get_random_password()
+        self.fill_input_fields(self.default_password, password, confirmation)
         self.assert_error_message(contains='Passwords do not match.')
 
     @selenium_test
     def test_currect_password_incorrect(self):
         self.register_and_change_password()
-        self.fill_input_fields("4444444", "123123", "123123")
+        password = self._get_random_password()
+        self.fill_input_fields("4444444", password, password)
         self.assert_error_message(contains='Invalid current password.')
 
     @selenium_test
     def test_new_password_short(self):
         self.register_and_change_password()
-        self.fill_input_fields(self.default_password, "123", "123")
+        password = self._get_random_password(len=3)
+        self.fill_input_fields(self.default_password, password, password)
         self.assert_error_message(contains='Use a password of at least 6 characters.')
 
     @selenium_test

From 2ae3ed1c5a33f340c9b07a5558d8c820b6bbe88b Mon Sep 17 00:00:00 2001
From: Juan David Mendez Solano <juan.mendez@imtek.uni-freiburg.de>
Date: Fri, 20 Mar 2020 21:42:25 +0100
Subject: [PATCH 491/853] Implementation of Selenium test for signout from user
 preferences

---
 lib/galaxy/selenium/navigation.yml        |  1 +
 lib/galaxy_test/selenium/test_sign_out.py | 22 ++++++++++++++++++++++
 2 files changed, 23 insertions(+)
 create mode 100644 lib/galaxy_test/selenium/test_sign_out.py

diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index f35dab23a0ba..50f81ed50165 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -70,6 +70,7 @@ masthead:
 
 preferences:
   selectors:
+    sign_out: "#edit-preferences-custom-builds"
     change_password: "#edit-preferences-password"
     manage_information: '#edit-preferences-information'
     current_email: "#user-preferences-current-email"
diff --git a/lib/galaxy_test/selenium/test_sign_out.py b/lib/galaxy_test/selenium/test_sign_out.py
new file mode 100644
index 000000000000..9a160bef9ac6
--- /dev/null
+++ b/lib/galaxy_test/selenium/test_sign_out.py
@@ -0,0 +1,22 @@
+from .framework import (
+    selenium_test,
+    SeleniumTestCase
+)
+
+
+class SignOutTestCase(SeleniumTestCase):
+    @selenium_test
+    def test_sign_out(self):
+        email = self._get_random_email()
+        self.register(email)
+        self.click_masthead_user()
+        self.components.masthead.preferences.wait_for_and_click()
+        self.components.preferences.sign_out.wait_for_and_click()
+        cancel_button = self.driver.find_element_by_xpath("//button[@id='button-0']")
+        cancel_button.click()
+        assert self.is_logged_in()
+        new_email = self.driver.find_element_by_id("user-preferences-current-email").text
+        self.assertTrue(email == new_email)
+        signout_button = self.driver.find_element_by_xpath("//button[@id='button-1']")
+        signout_button.click()
+        assert not self.is_logged_in()

From 9d4f6ab0cde15e3dd5106568496d7b0590e0a1cf Mon Sep 17 00:00:00 2001
From: Juan David Mendez Solano <mendezj@tf.uni-freiburg.de>
Date: Fri, 20 Mar 2020 22:57:57 +0100
Subject: [PATCH 492/853] Change id link id from custome-builds into sign-out

---
 client/galaxy/scripts/components/User/UserPreferencesModel.js | 2 +-
 lib/galaxy/selenium/navigation.yml                            | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/User/UserPreferencesModel.js b/client/galaxy/scripts/components/User/UserPreferencesModel.js
index 702d038ae394..847c0b226c8b 100644
--- a/client/galaxy/scripts/components/User/UserPreferencesModel.js
+++ b/client/galaxy/scripts/components/User/UserPreferencesModel.js
@@ -83,7 +83,7 @@ export const getUserPreferencesModel = () => {
         },
         logout: {
             title: _l("Sign Out"),
-            id: "edit-preferences-custom-builds",
+            id: "edit-preferences-sign-out",
             description: _l("Click here to sign out of all sessions."),
             icon: "fa-sign-out",
             shouldRender: !!Galaxy.session_csrf_token
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index 50f81ed50165..9e4b125817fb 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -70,7 +70,7 @@ masthead:
 
 preferences:
   selectors:
-    sign_out: "#edit-preferences-custom-builds"
+    sign_out: "#edit-preferences-sign-out"
     change_password: "#edit-preferences-password"
     manage_information: '#edit-preferences-information'
     current_email: "#user-preferences-current-email"

From 2bb2f0989f0098e8c752632cd7d409f5c5887c76 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 20 Mar 2020 10:51:21 +0100
Subject: [PATCH 493/853] Make build_ts_whoosh_index.py py3 compatible

---
 scripts/tool_shed/build_ts_whoosh_index.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/tool_shed/build_ts_whoosh_index.py b/scripts/tool_shed/build_ts_whoosh_index.py
index cc96cb5dbc36..c3f3a659413a 100644
--- a/scripts/tool_shed/build_ts_whoosh_index.py
+++ b/scripts/tool_shed/build_ts_whoosh_index.py
@@ -190,10 +190,10 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
 
         # Load all changesets of the repo for lineage.
         repo_path = hgwcm.get_entry(os.path.join("repos", repo.user.username, repo.name))
-        hg_repo = hg.repository(ui.ui(), repo_path)
+        hg_repo = hg.repository(ui.ui(), repo_path.encode('utf-8'))
         lineage = []
         for changeset in hg_repo.changelog:
-            lineage.append(str(changeset) + ":" + str(hg_repo[changeset]))
+            lineage.append(unicodify(changeset) + ":" + unicodify(hg_repo[changeset]))
         repo_lineage = str(lineage)
 
         #  Parse all the tools within repo for a separate index.

From afce65249f6631e133027be5b971ca78110d4db4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 20 Mar 2020 13:23:15 +0100
Subject: [PATCH 494/853] Implement incremental indexing

---
 scripts/tool_shed/build_ts_whoosh_index.py | 143 +++++++++------------
 1 file changed, 63 insertions(+), 80 deletions(-)

diff --git a/scripts/tool_shed/build_ts_whoosh_index.py b/scripts/tool_shed/build_ts_whoosh_index.py
index c3f3a659413a..155cca876673 100644
--- a/scripts/tool_shed/build_ts_whoosh_index.py
+++ b/scripts/tool_shed/build_ts_whoosh_index.py
@@ -15,13 +15,12 @@
 import argparse
 import logging
 import os
-import shutil
 import sys
-import tempfile
-from distutils.dir_util import copy_tree
 
+import profilehooks
 from mercurial import hg, ui
-from whoosh.filedb.filestore import FileStorage
+from whoosh import index
+from whoosh.writing import AsyncWriter
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
 
@@ -74,6 +73,22 @@ def parse_arguments():
     return args
 
 
+def get_or_create_index(whoosh_index_dir):
+    tool_index_dir = os.path.join(whoosh_index_dir, 'tools')
+    if not os.path.exists(whoosh_index_dir):
+        os.makedirs(whoosh_index_dir)
+        os.makedirs(tool_index_dir)
+    return _get_or_create_index(whoosh_index_dir, repo_schema), _get_or_create_index(tool_index_dir, tool_schema)
+
+
+def _get_or_create_index(index_dir, schema):
+    try:
+        return index.open_dir(index_dir, schema=schema)
+    except index.EmptyIndexError:
+        return index.create_in(index_dir, schema=schema)
+
+
+@profilehooks.profile
 def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs):
     """
     Build two search indexes simultaneously
@@ -81,57 +96,35 @@ def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs):
     """
     model = ts_mapping.init(file_path, dburi, engine_options={}, create_tables=False)
     sa_session = model.context.current
+    repo_index, tool_index = get_or_create_index(whoosh_index_dir)
 
-    #  Rare race condition exists here and below
-    tool_index_dir = os.path.join(whoosh_index_dir, 'tools')
-    if not os.path.exists(whoosh_index_dir):
-        os.makedirs(whoosh_index_dir)
-        os.makedirs(tool_index_dir)
-        work_repo_dir = whoosh_index_dir
-        work_tool_dir = tool_index_dir
-    else:
-        # Index exists, prevent in-place index regeneration
-        work_repo_dir = tempfile.mkdtemp(prefix="tmp-whoosh-repo")
-        work_tool_dir = tempfile.mkdtemp(prefix="tmp-whoosh-tool")
-
-    repo_index_storage = FileStorage(work_repo_dir)
-    tool_index_storage = FileStorage(work_tool_dir)
-    repo_index = repo_index_storage.create_index(repo_schema)
-    tool_index = tool_index_storage.create_index(tool_schema)
-    repo_index_writer = repo_index.writer()
-    tool_index_writer = tool_index.writer()
+    repo_index_writer = AsyncWriter(repo_index)
+    tool_index_writer = AsyncWriter(tool_index)
     repos_indexed = 0
     tools_indexed = 0
 
     execution_timer = ExecutionTimer()
-    for repo in get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
-
-        repo_index_writer.add_document(id=repo.get('id'),
-                             name=unicodify(repo.get('name')),
-                             description=unicodify(repo.get('description')),
-                             long_description=unicodify(repo.get('long_description')),
-                             homepage_url=unicodify(repo.get('homepage_url')),
-                             remote_repository_url=unicodify(repo.get('remote_repository_url')),
-                             repo_owner_username=unicodify(repo.get('repo_owner_username')),
-                             categories=unicodify(repo.get('categories')),
-                             times_downloaded=repo.get('times_downloaded'),
-                             approved=repo.get('approved'),
-                             last_updated=repo.get('last_updated'),
-                             full_last_updated=repo.get('full_last_updated'),
-                             repo_lineage=unicodify(repo.get('repo_lineage')))
-        #  Tools get their own index
-        for tool in repo.get('tools_list'):
-            tool_index_writer.add_document(id=unicodify(tool.get('id')),
-                                           name=unicodify(tool.get('name')),
-                                           version=unicodify(tool.get('version')),
-                                           description=unicodify(tool.get('description')),
-                                           help=unicodify(tool.get('help')),
-                                           repo_owner_username=unicodify(repo.get('repo_owner_username')),
-                                           repo_name=unicodify(repo.get('name')),
-                                           repo_id=repo.get('id'))
-            tools_indexed += 1
-
-        repos_indexed += 1
+    with repo_index.searcher() as searcher:
+        for repo in get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
+            tools_list = repo.pop('tools_list')
+            repo_id = repo['id']
+            indexed_document = searcher.document(id=repo_id)
+            if indexed_document:
+                if indexed_document['full_last_updated'] == repo.get('full_last_updated'):
+                    # We're done, since we sorted repos by update time
+                    break
+                else:
+                    # Got an update, delete the previous document
+                    repo_index_writer.delete_by_term('id', repo_id)
+
+            repo_index_writer.add_document(**repo)
+
+            #  Tools get their own index
+            for tool in tools_list:
+                tool_index_writer.add_document(**tool)
+                tools_indexed += 1
+
+            repos_indexed += 1
 
     tool_index_writer.commit()
     repo_index_writer.commit()
@@ -139,25 +132,18 @@ def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs):
     log.info("Indexed repos: %s, tools: %s", repos_indexed, tools_indexed)
     log.info("Toolbox index finished %s", execution_timer)
 
-    # Copy the built indexes if we were working in a tmp folder.
-    if work_repo_dir is not whoosh_index_dir:
-        shutil.rmtree(whoosh_index_dir)
-        os.makedirs(whoosh_index_dir)
-        os.makedirs(tool_index_dir)
-        copy_tree(work_repo_dir, whoosh_index_dir)
-        copy_tree(work_tool_dir, tool_index_dir)
-        shutil.rmtree(work_repo_dir)
 
-
-def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
+def get_repos(sa_session, file_path, hgweb_config_dir, update_time=None, **kwargs):
     """
     Load repos from DB and included tools from .xml configs.
     """
     hgwcm = HgWebConfigManager()
     hgwcm.hgweb_config_dir = hgweb_config_dir
-    results = []
     # Do not index deleted, deprecated, or "tool_dependency_definition" type repositories.
-    for repo in sa_session.query(ts_model.Repository).filter_by(deleted=False).filter_by(deprecated=False).filter(ts_model.Repository.type != 'tool_dependency_definition'):
+    q = sa_session.query(ts_model.Repository).filter_by(deleted=False).filter_by(deprecated=False).order_by(ts_model.Repository.update_time.desc())
+    q = q.filter(ts_model.Repository.type != 'tool_dependency_definition')
+
+    for repo in q:
         category_names = []
         for rca in sa_session.query(ts_model.RepositoryCategoryAssociation).filter(ts_model.RepositoryCategoryAssociation.repository_id == repo.id):
             for category in sa_session.query(ts_model.Category).filter(ts_model.Category.id == rca.category.id):
@@ -170,9 +156,7 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
         homepage_url = repo.homepage_url
         remote_repository_url = repo.remote_repository_url
 
-        times_downloaded = repo.times_downloaded
-        if not isinstance(times_downloaded, (int, long)):
-            times_downloaded = 0
+        times_downloaded = repo.times_downloaded or 0
 
         repo_owner_username = ''
         if repo.user_id is not None:
@@ -209,21 +193,20 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
                     tools_in_dir = load_one_dir(os.path.join(root, dirname))
                     tools_list.extend(tools_in_dir)
 
-        results.append(dict(id=repo_id,
-                            name=name,
-                            description=description,
-                            long_description=long_description,
-                            homepage_url=homepage_url,
-                            remote_repository_url=remote_repository_url,
-                            repo_owner_username=repo_owner_username,
-                            times_downloaded=times_downloaded,
-                            approved=approved,
-                            last_updated=last_updated,
-                            full_last_updated=full_last_updated,
-                            tools_list=tools_list,
-                            repo_lineage=repo_lineage,
-                            categories=categories))
-    return results
+        yield (dict(id=repo_id,
+                    name=name,
+                    description=description,
+                    long_description=long_description,
+                    homepage_url=homepage_url,
+                    remote_repository_url=remote_repository_url,
+                    repo_owner_username=repo_owner_username,
+                    times_downloaded=times_downloaded,
+                    approved=approved,
+                    last_updated=last_updated,
+                    full_last_updated=full_last_updated,
+                    tools_list=tools_list,
+                    repo_lineage=repo_lineage,
+                    categories=categories))
 
 
 def load_one_dir(path):

From faf8d698970edb548cdb7790157b728c2194f728 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 20 Mar 2020 15:27:31 +0100
Subject: [PATCH 495/853] Make repository id numeric, allows recovering unique
 documents

---
 lib/tool_shed/webapp/search/repo_search.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/tool_shed/webapp/search/repo_search.py b/lib/tool_shed/webapp/search/repo_search.py
index 94ab0793b7cb..6b40d0aca43d 100644
--- a/lib/tool_shed/webapp/search/repo_search.py
+++ b/lib/tool_shed/webapp/search/repo_search.py
@@ -5,7 +5,7 @@
 
 import whoosh.index
 from whoosh import scoring
-from whoosh.fields import KEYWORD, Schema, STORED, TEXT
+from whoosh.fields import NUMERIC, KEYWORD, Schema, STORED, TEXT
 from whoosh.qparser import MultifieldParser
 from whoosh.query import And, Every, Term
 
@@ -18,7 +18,7 @@
 log = logging.getLogger(__name__)
 
 schema = Schema(
-    id=STORED,
+    id=NUMERIC(stored=True),
     name=TEXT(field_boost=1.7, stored=True),
     description=TEXT(field_boost=1.5, stored=True),
     long_description=TEXT(stored=True),

From 159a94b95dabf0189134a60838cdefda03f52b9f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 20 Mar 2020 15:28:35 +0100
Subject: [PATCH 496/853] Move index logic to lib.tool_shed.util.shed_index

Since we need the index for browsing repos in the new client
we should incrementally build the index with every repo update.
Having this in tool_shed will make re-use easier.
---
 lib/tool_shed/util/shed_index.py           | 187 ++++++++++++++++++++
 scripts/tool_shed/build_ts_whoosh_index.py | 188 +--------------------
 2 files changed, 189 insertions(+), 186 deletions(-)
 create mode 100644 lib/tool_shed/util/shed_index.py

diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
new file mode 100644
index 000000000000..11de0ed61dc1
--- /dev/null
+++ b/lib/tool_shed/util/shed_index.py
@@ -0,0 +1,187 @@
+import logging
+import os
+
+from mercurial import hg, ui
+from whoosh import index
+from whoosh.writing import AsyncWriter
+
+import tool_shed.webapp.model.mapping as ts_mapping
+
+from galaxy.tool_util.loader_directory import load_tool_elements_from_path
+from galaxy.util import (
+    directory_hash_id,
+    ExecutionTimer,
+    pretty_print_time_interval,
+    unicodify
+)
+from tool_shed.webapp import model
+from tool_shed.webapp.search.repo_search import schema as repo_schema
+from tool_shed.webapp.search.tool_search import schema as tool_schema
+from tool_shed.webapp.util.hgweb_config import HgWebConfigManager
+
+log = logging.getLogger(__name__)
+
+
+def get_or_create_index(whoosh_index_dir):
+    tool_index_dir = os.path.join(whoosh_index_dir, 'tools')
+    if not os.path.exists(whoosh_index_dir):
+        os.makedirs(whoosh_index_dir)
+        os.makedirs(tool_index_dir)
+    return _get_or_create_index(whoosh_index_dir, repo_schema), _get_or_create_index(tool_index_dir, tool_schema)
+
+
+def _get_or_create_index(index_dir, schema):
+    if index.exists_in(index_dir):
+        idx = index.open_dir(index_dir)
+        try:
+            assert idx.schema == repo_schema
+            return idx
+        except AssertionError:
+            log.warning("Index at '%s' uses outdated schema, creating new index", index_dir)
+    return index.create_in(index_dir, schema=schema)
+
+
+def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs):
+    """
+    Build two search indexes simultaneously
+    One is for repositories and the other for tools.
+    """
+    model = ts_mapping.init(file_path, dburi, engine_options={}, create_tables=False)
+    sa_session = model.context.current
+    repo_index, tool_index = get_or_create_index(whoosh_index_dir)
+
+    repo_index_writer = AsyncWriter(repo_index)
+    tool_index_writer = AsyncWriter(tool_index)
+    repos_indexed = 0
+    tools_indexed = 0
+
+    execution_timer = ExecutionTimer()
+    with repo_index.searcher() as searcher:
+        for repo in get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
+            tools_list = repo.pop('tools_list')
+            repo_id = repo['id']
+            indexed_document = searcher.document(id=repo_id)
+            if indexed_document:
+                if indexed_document['full_last_updated'] == repo.get('full_last_updated'):
+                    # We're done, since we sorted repos by update time
+                    break
+                else:
+                    # Got an update, delete the previous document
+                    repo_index_writer.delete_by_term('id', repo_id)
+
+            repo_index_writer.add_document(**repo)
+
+            #  Tools get their own index
+            for tool in tools_list:
+                tool_index_writer.add_document(**tool)
+                tools_indexed += 1
+
+            repos_indexed += 1
+
+    tool_index_writer.commit()
+    repo_index_writer.commit()
+
+    log.info("Indexed repos: %s, tools: %s", repos_indexed, tools_indexed)
+    log.info("Toolbox index finished %s", execution_timer)
+
+
+def get_repos(sa_session, file_path, hgweb_config_dir, update_time=None, **kwargs):
+    """
+    Load repos from DB and included tools from .xml configs.
+    """
+    hgwcm = HgWebConfigManager()
+    hgwcm.hgweb_config_dir = hgweb_config_dir
+    # Do not index deleted, deprecated, or "tool_dependency_definition" type repositories.
+    q = sa_session.query(model.Repository).filter_by(deleted=False).filter_by(deprecated=False).order_by(model.Repository.update_time.desc())
+    q = q.filter(model.Repository.type != 'tool_dependency_definition')
+    for repo in q:
+        category_names = []
+        for rca in sa_session.query(model.RepositoryCategoryAssociation).filter(model.RepositoryCategoryAssociation.repository_id == repo.id):
+            for category in sa_session.query(model.Category).filter(model.Category.id == rca.category.id):
+                category_names.append(category.name.lower())
+        categories = (",").join(category_names)
+        repo_id = repo.id
+        name = repo.name
+        description = repo.description
+        long_description = repo.long_description
+        homepage_url = repo.homepage_url
+        remote_repository_url = repo.remote_repository_url
+
+        times_downloaded = repo.times_downloaded or 0
+
+        repo_owner_username = ''
+        if repo.user_id is not None:
+            user = sa_session.query(model.User).filter(model.User.id == repo.user_id).one()
+            repo_owner_username = user.username.lower()
+
+        approved = 'no'
+        for review in repo.reviews:
+            if review.approved == 'yes':
+                approved = 'yes'
+                break
+
+        last_updated = pretty_print_time_interval(repo.update_time)
+        full_last_updated = repo.update_time.strftime("%Y-%m-%d %I:%M %p")
+
+        # Load all changesets of the repo for lineage.
+        repo_path = hgwcm.get_entry(os.path.join("repos", repo.user.username, repo.name))
+        hg_repo = hg.repository(ui.ui(), repo_path.encode('utf-8'))
+        lineage = []
+        for changeset in hg_repo.changelog:
+            lineage.append(unicodify(changeset) + ":" + unicodify(hg_repo[changeset]))
+        repo_lineage = str(lineage)
+
+        #  Parse all the tools within repo for a separate index.
+        tools_list = []
+        path = os.path.join(file_path, *directory_hash_id(repo.id))
+        path = os.path.join(path, "repo_%d" % repo.id)
+        if os.path.exists(path):
+            tools_list.extend(load_one_dir(path))
+            for root, dirs, files in os.walk(path):
+                if '.hg' in dirs:
+                    dirs.remove('.hg')
+                for dirname in dirs:
+                    tools_in_dir = load_one_dir(os.path.join(root, dirname))
+                    tools_list.extend(tools_in_dir)
+
+        yield (dict(id=repo_id,
+                    name=name,
+                    description=description,
+                    long_description=long_description,
+                    homepage_url=homepage_url,
+                    remote_repository_url=remote_repository_url,
+                    repo_owner_username=repo_owner_username,
+                    times_downloaded=times_downloaded,
+                    approved=approved,
+                    last_updated=last_updated,
+                    full_last_updated=full_last_updated,
+                    tools_list=tools_list,
+                    repo_lineage=repo_lineage,
+                    categories=categories))
+
+
+def debug_handler(path, exc_info):
+    """
+    By default the underlying tool parsing logs warnings for each exception.
+    This is very chatty hence this metod changes it to debug level.
+    """
+    log.debug("Failed to load tool with path %s." % path, exc_info=exc_info)
+
+
+def load_one_dir(path):
+    tools_in_dir = []
+    tool_elems = load_tool_elements_from_path(path, load_exception_handler=debug_handler)
+    if tool_elems:
+        for elem in tool_elems:
+            root = elem[1].getroot()
+            if root.tag == 'tool':
+                tool = {}
+                if root.find('help') is not None:
+                    tool.update(dict(help=root.find('help').text))
+                if root.find('description') is not None:
+                    tool.update(dict(description=root.find('description').text))
+                tool.update(dict(id=root.attrib.get('id'),
+                                 name=root.attrib.get('name'),
+                                 version=root.attrib.get('version')))
+                tools_in_dir.append(tool)
+    return tools_in_dir
diff --git a/scripts/tool_shed/build_ts_whoosh_index.py b/scripts/tool_shed/build_ts_whoosh_index.py
index 155cca876673..6a39f75adff1 100644
--- a/scripts/tool_shed/build_ts_whoosh_index.py
+++ b/scripts/tool_shed/build_ts_whoosh_index.py
@@ -17,35 +17,14 @@
 import os
 import sys
 
-import profilehooks
-from mercurial import hg, ui
-from whoosh import index
-from whoosh.writing import AsyncWriter
-
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
 
-import tool_shed.webapp.model.mapping as ts_mapping
-from galaxy.tool_util.loader_directory import load_tool_elements_from_path
-from galaxy.util import (
-    directory_hash_id,
-    ExecutionTimer,
-    pretty_print_time_interval,
-    unicodify
-)
 from galaxy.util.script import (
     app_properties_from_args,
     populate_config_args
 )
-from tool_shed.webapp import (
-    config as ts_config,
-    model as ts_model
-)
-from tool_shed.webapp.search.repo_search import schema as repo_schema
-from tool_shed.webapp.search.tool_search import schema as tool_schema
-from tool_shed.webapp.util.hgweb_config import HgWebConfigManager
-
-if sys.version_info > (3,):
-    long = int
+from tool_shed.webapp import config as ts_config
+from tool_shed.util.shed_index import build_index
 
 log = logging.getLogger()
 log.addHandler(logging.StreamHandler(sys.stdout))
@@ -73,169 +52,6 @@ def parse_arguments():
     return args
 
 
-def get_or_create_index(whoosh_index_dir):
-    tool_index_dir = os.path.join(whoosh_index_dir, 'tools')
-    if not os.path.exists(whoosh_index_dir):
-        os.makedirs(whoosh_index_dir)
-        os.makedirs(tool_index_dir)
-    return _get_or_create_index(whoosh_index_dir, repo_schema), _get_or_create_index(tool_index_dir, tool_schema)
-
-
-def _get_or_create_index(index_dir, schema):
-    try:
-        return index.open_dir(index_dir, schema=schema)
-    except index.EmptyIndexError:
-        return index.create_in(index_dir, schema=schema)
-
-
-@profilehooks.profile
-def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs):
-    """
-    Build two search indexes simultaneously
-    One is for repositories and the other for tools.
-    """
-    model = ts_mapping.init(file_path, dburi, engine_options={}, create_tables=False)
-    sa_session = model.context.current
-    repo_index, tool_index = get_or_create_index(whoosh_index_dir)
-
-    repo_index_writer = AsyncWriter(repo_index)
-    tool_index_writer = AsyncWriter(tool_index)
-    repos_indexed = 0
-    tools_indexed = 0
-
-    execution_timer = ExecutionTimer()
-    with repo_index.searcher() as searcher:
-        for repo in get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
-            tools_list = repo.pop('tools_list')
-            repo_id = repo['id']
-            indexed_document = searcher.document(id=repo_id)
-            if indexed_document:
-                if indexed_document['full_last_updated'] == repo.get('full_last_updated'):
-                    # We're done, since we sorted repos by update time
-                    break
-                else:
-                    # Got an update, delete the previous document
-                    repo_index_writer.delete_by_term('id', repo_id)
-
-            repo_index_writer.add_document(**repo)
-
-            #  Tools get their own index
-            for tool in tools_list:
-                tool_index_writer.add_document(**tool)
-                tools_indexed += 1
-
-            repos_indexed += 1
-
-    tool_index_writer.commit()
-    repo_index_writer.commit()
-
-    log.info("Indexed repos: %s, tools: %s", repos_indexed, tools_indexed)
-    log.info("Toolbox index finished %s", execution_timer)
-
-
-def get_repos(sa_session, file_path, hgweb_config_dir, update_time=None, **kwargs):
-    """
-    Load repos from DB and included tools from .xml configs.
-    """
-    hgwcm = HgWebConfigManager()
-    hgwcm.hgweb_config_dir = hgweb_config_dir
-    # Do not index deleted, deprecated, or "tool_dependency_definition" type repositories.
-    q = sa_session.query(ts_model.Repository).filter_by(deleted=False).filter_by(deprecated=False).order_by(ts_model.Repository.update_time.desc())
-    q = q.filter(ts_model.Repository.type != 'tool_dependency_definition')
-
-    for repo in q:
-        category_names = []
-        for rca in sa_session.query(ts_model.RepositoryCategoryAssociation).filter(ts_model.RepositoryCategoryAssociation.repository_id == repo.id):
-            for category in sa_session.query(ts_model.Category).filter(ts_model.Category.id == rca.category.id):
-                category_names.append(category.name.lower())
-        categories = (",").join(category_names)
-        repo_id = repo.id
-        name = repo.name
-        description = repo.description
-        long_description = repo.long_description
-        homepage_url = repo.homepage_url
-        remote_repository_url = repo.remote_repository_url
-
-        times_downloaded = repo.times_downloaded or 0
-
-        repo_owner_username = ''
-        if repo.user_id is not None:
-            user = sa_session.query(ts_model.User).filter(ts_model.User.id == repo.user_id).one()
-            repo_owner_username = user.username.lower()
-
-        approved = 'no'
-        for review in repo.reviews:
-            if review.approved == 'yes':
-                approved = 'yes'
-                break
-
-        last_updated = pretty_print_time_interval(repo.update_time)
-        full_last_updated = repo.update_time.strftime("%Y-%m-%d %I:%M %p")
-
-        # Load all changesets of the repo for lineage.
-        repo_path = hgwcm.get_entry(os.path.join("repos", repo.user.username, repo.name))
-        hg_repo = hg.repository(ui.ui(), repo_path.encode('utf-8'))
-        lineage = []
-        for changeset in hg_repo.changelog:
-            lineage.append(unicodify(changeset) + ":" + unicodify(hg_repo[changeset]))
-        repo_lineage = str(lineage)
-
-        #  Parse all the tools within repo for a separate index.
-        tools_list = []
-        path = os.path.join(file_path, *directory_hash_id(repo.id))
-        path = os.path.join(path, "repo_%d" % repo.id)
-        if os.path.exists(path):
-            tools_list.extend(load_one_dir(path))
-            for root, dirs, files in os.walk(path):
-                if '.hg' in dirs:
-                    dirs.remove('.hg')
-                for dirname in dirs:
-                    tools_in_dir = load_one_dir(os.path.join(root, dirname))
-                    tools_list.extend(tools_in_dir)
-
-        yield (dict(id=repo_id,
-                    name=name,
-                    description=description,
-                    long_description=long_description,
-                    homepage_url=homepage_url,
-                    remote_repository_url=remote_repository_url,
-                    repo_owner_username=repo_owner_username,
-                    times_downloaded=times_downloaded,
-                    approved=approved,
-                    last_updated=last_updated,
-                    full_last_updated=full_last_updated,
-                    tools_list=tools_list,
-                    repo_lineage=repo_lineage,
-                    categories=categories))
-
-
-def load_one_dir(path):
-    tools_in_dir = []
-    tool_elems = load_tool_elements_from_path(path, load_exception_handler=debug_handler)
-    if tool_elems:
-        for elem in tool_elems:
-            root = elem[1].getroot()
-            if root.tag == 'tool':
-                tool = {}
-                if root.find('help') is not None:
-                    tool.update(dict(help=root.find('help').text))
-                if root.find('description') is not None:
-                    tool.update(dict(description=root.find('description').text))
-                tool.update(dict(id=root.attrib.get('id'),
-                                 name=root.attrib.get('name'),
-                                 version=root.attrib.get('version')))
-                tools_in_dir.append(tool)
-    return tools_in_dir
-
-
-def debug_handler(path, exc_info):
-    """
-    By default the underlying tool parsing logs warnings for each exception.
-    This is very chatty hence this metod changes it to debug level.
-    """
-    log.debug("Failed to load tool with path %s." % path, exc_info=exc_info)
-
-
 def main():
     args = parse_arguments()
     build_index(**vars(args))

From aa91b65d4c21d23a26a529f5f85f02e30083f2dd Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 20 Mar 2020 16:31:44 +0100
Subject: [PATCH 497/853] Add unit test for build_index

---
 lib/tool_shed/util/shed_index.py       |  4 ++
 test/unit/shed_unit/test_shed_index.py | 64 ++++++++++++++++++++++++++
 2 files changed, 68 insertions(+)
 create mode 100644 test/unit/shed_unit/test_shed_index.py

diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
index 11de0ed61dc1..ee5b0e523d78 100644
--- a/lib/tool_shed/util/shed_index.py
+++ b/lib/tool_shed/util/shed_index.py
@@ -26,6 +26,7 @@ def get_or_create_index(whoosh_index_dir):
     tool_index_dir = os.path.join(whoosh_index_dir, 'tools')
     if not os.path.exists(whoosh_index_dir):
         os.makedirs(whoosh_index_dir)
+    if not os.path.exists(tool_index_dir):
         os.makedirs(tool_index_dir)
     return _get_or_create_index(whoosh_index_dir, repo_schema), _get_or_create_index(tool_index_dir, tool_schema)
 
@@ -45,6 +46,8 @@ def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs):
     """
     Build two search indexes simultaneously
     One is for repositories and the other for tools.
+
+    Returns a tuple with number of repos and tools that were indexed.
     """
     model = ts_mapping.init(file_path, dburi, engine_options={}, create_tables=False)
     sa_session = model.context.current
@@ -83,6 +86,7 @@ def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs):
 
     log.info("Indexed repos: %s, tools: %s", repos_indexed, tools_indexed)
     log.info("Toolbox index finished %s", execution_timer)
+    return repos_indexed, tools_indexed
 
 
 def get_repos(sa_session, file_path, hgweb_config_dir, update_time=None, **kwargs):
diff --git a/test/unit/shed_unit/test_shed_index.py b/test/unit/shed_unit/test_shed_index.py
new file mode 100644
index 000000000000..492d46482feb
--- /dev/null
+++ b/test/unit/shed_unit/test_shed_index.py
@@ -0,0 +1,64 @@
+import os
+import requests
+import shutil
+import tarfile
+import tempfile
+from collections import namedtuple
+
+import pytest
+from tool_shed.util.shed_index import build_index
+from whoosh import index
+
+URL = 'https://github.com/mvdbeek/toolshed-test-data/blob/master/toolshed_community_files.tgz?raw=true'
+
+
+@pytest.fixture
+def whoosh_index_dir():
+    try:
+        whoosh_index_dir = tempfile.mkdtemp(suffix='_whoosh_index_test')
+        yield whoosh_index_dir
+    finally:
+        shutil.rmtree(whoosh_index_dir)
+
+
+@pytest.fixture(scope='module')
+def community_file_dir():
+    extracted_archive_dir = tempfile.mkdtemp()
+    with tempfile.NamedTemporaryFile(suffix='_test_shed_index_archive.tgz', mode='wb') as outfile:
+        outfile.write(requests.get(URL).content)
+        tarfile.open(outfile.name, "r:gz").extractall(extracted_archive_dir)
+    try:
+        yield extracted_archive_dir
+    finally:
+        shutil.rmtree(extracted_archive_dir)
+
+
+@pytest.fixture()
+def community_file_structure(community_file_dir):
+    cf = namedtuple('community', 'file_path hgweb_config_dir dburi')
+    return cf(
+        file_path=os.path.join(community_file_dir, 'database', 'community_files'),
+        hgweb_config_dir=community_file_dir,
+        dburi="sqlite:///%s" % os.path.join(community_file_dir, 'database', 'community.sqlite')
+    )
+
+
+def test_build_index(whoosh_index_dir, community_file_structure):
+    repos_indexed, tools_indexed = build_index(whoosh_index_dir, community_file_structure.file_path, community_file_structure.hgweb_config_dir, community_file_structure.dburi)
+    assert repos_indexed == 1
+    assert tools_indexed == 1
+    idx = index.open_dir(whoosh_index_dir)
+    assert idx.doc_count() == 1
+    repos_indexed, tools_indexed = build_index(whoosh_index_dir, community_file_structure.file_path, community_file_structure.hgweb_config_dir, community_file_structure.dburi)
+    assert repos_indexed == 0
+    assert tools_indexed == 0
+    idx = index.open_dir(whoosh_index_dir)
+    assert idx.doc_count() == 1
+    writer = idx.writer()
+    writer.delete_by_term('id', 1)
+    writer.commit()
+    idx = index.open_dir(whoosh_index_dir)
+    assert idx.doc_count() == 0
+    repos_indexed, tools_indexed = build_index(whoosh_index_dir, community_file_structure.file_path, community_file_structure.hgweb_config_dir, community_file_structure.dburi)
+    assert repos_indexed == 1
+    assert tools_indexed == 1

From 7105de2fb0538aa46f32b5165eb657175186188d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 20 Mar 2020 16:56:33 +0100
Subject: [PATCH 498/853] Fix import order

---
 lib/tool_shed/util/shed_index.py           | 1 -
 lib/tool_shed/webapp/search/repo_search.py | 2 +-
 scripts/tool_shed/build_ts_whoosh_index.py | 2 +-
 test/unit/shed_unit/test_shed_index.py     | 5 +++--
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
index ee5b0e523d78..39fe3cd0c399 100644
--- a/lib/tool_shed/util/shed_index.py
+++ b/lib/tool_shed/util/shed_index.py
@@ -6,7 +6,6 @@
 from whoosh.writing import AsyncWriter
 
 import tool_shed.webapp.model.mapping as ts_mapping
-
 from galaxy.tool_util.loader_directory import load_tool_elements_from_path
 from galaxy.util import (
     directory_hash_id,
diff --git a/lib/tool_shed/webapp/search/repo_search.py b/lib/tool_shed/webapp/search/repo_search.py
index 6b40d0aca43d..a501fb8a9d69 100644
--- a/lib/tool_shed/webapp/search/repo_search.py
+++ b/lib/tool_shed/webapp/search/repo_search.py
@@ -5,7 +5,7 @@
 
 import whoosh.index
 from whoosh import scoring
-from whoosh.fields import NUMERIC, KEYWORD, Schema, STORED, TEXT
+from whoosh.fields import KEYWORD, NUMERIC, Schema, STORED, TEXT
 from whoosh.qparser import MultifieldParser
 from whoosh.query import And, Every, Term
 
diff --git a/scripts/tool_shed/build_ts_whoosh_index.py b/scripts/tool_shed/build_ts_whoosh_index.py
index 6a39f75adff1..b3e5f13148fe 100644
--- a/scripts/tool_shed/build_ts_whoosh_index.py
+++ b/scripts/tool_shed/build_ts_whoosh_index.py
@@ -23,8 +23,8 @@
     app_properties_from_args,
     populate_config_args
 )
-from tool_shed.webapp import config as ts_config
 from tool_shed.util.shed_index import build_index
+from tool_shed.webapp import config as ts_config
 
 log = logging.getLogger()
 log.addHandler(logging.StreamHandler(sys.stdout))
diff --git a/test/unit/shed_unit/test_shed_index.py b/test/unit/shed_unit/test_shed_index.py
index 492d46482feb..7a758bd39825 100644
--- a/test/unit/shed_unit/test_shed_index.py
+++ b/test/unit/shed_unit/test_shed_index.py
@@ -1,14 +1,15 @@
 import os
-import requests
 import shutil
 import tarfile
 import tempfile
 from collections import namedtuple
 
 import pytest
-from tool_shed.util.shed_index import build_index
+import requests
 from whoosh import index
 
+from tool_shed.util.shed_index import build_index
+
 URL = 'https://github.com/mvdbeek/toolshed-test-data/blob/master/toolshed_community_files.tgz?raw=true'
 
 

From 497061b3eaf59da9f739e1769440409c1afcbb56 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 20 Mar 2020 18:20:14 +0100
Subject: [PATCH 499/853] Figure out absolute path to repos

---
 lib/tool_shed/util/shed_index.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
index 39fe3cd0c399..4d6c0bb7b7b9 100644
--- a/lib/tool_shed/util/shed_index.py
+++ b/lib/tool_shed/util/shed_index.py
@@ -88,7 +88,7 @@ def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs):
     return repos_indexed, tools_indexed
 
 
-def get_repos(sa_session, file_path, hgweb_config_dir, update_time=None, **kwargs):
+def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
     """
     Load repos from DB and included tools from .xml configs.
     """
@@ -127,7 +127,7 @@ def get_repos(sa_session, file_path, hgweb_config_dir, update_time=None, **kwarg
         full_last_updated = repo.update_time.strftime("%Y-%m-%d %I:%M %p")
 
         # Load all changesets of the repo for lineage.
-        repo_path = hgwcm.get_entry(os.path.join("repos", repo.user.username, repo.name))
+        repo_path = os.path.join(hgweb_config_dir, hgwcm.get_entry(os.path.join("repos", repo.user.username, repo.name)))
         hg_repo = hg.repository(ui.ui(), repo_path.encode('utf-8'))
         lineage = []
         for changeset in hg_repo.changelog:

From 85f2bef43cc8bdbfe286a55c90113b6c23a894f4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 20 Mar 2020 18:51:37 +0100
Subject: [PATCH 500/853] Use BytesIO instead of writing to temp file

---
 test/unit/shed_unit/test_shed_index.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/unit/shed_unit/test_shed_index.py b/test/unit/shed_unit/test_shed_index.py
index 7a758bd39825..468efb2f7a9c 100644
--- a/test/unit/shed_unit/test_shed_index.py
+++ b/test/unit/shed_unit/test_shed_index.py
@@ -3,6 +3,7 @@
 import tarfile
 import tempfile
 from collections import namedtuple
+from io import BytesIO
 
 import pytest
 import requests
@@ -25,9 +26,8 @@ def whoosh_index_dir():
 @pytest.fixture(scope='module')
 def community_file_dir():
     extracted_archive_dir = tempfile.mkdtemp()
-    with tempfile.NamedTemporaryFile(suffix='_test_shed_index_archive.tgz', mode='wb') as outfile:
-        outfile.write(requests.get(URL).content)
-        tarfile.open(outfile.name, "r:gz").extractall(extracted_archive_dir)
+    b = BytesIO(requests.get(URL).content)
+    tarfile.open(fileobj=b, mode="r:gz").extractall(extracted_archive_dir)
     try:
         yield extracted_archive_dir
     finally:

From d3a51bafb73f994184b9dce0ac0f66d9ff0e6e7e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 21 Mar 2020 12:13:38 +0100
Subject: [PATCH 501/853] Whoosh needs unicode for indexed fields

---
 lib/tool_shed/util/shed_index.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
index 4d6c0bb7b7b9..206be3a3ce94 100644
--- a/lib/tool_shed/util/shed_index.py
+++ b/lib/tool_shed/util/shed_index.py
@@ -180,11 +180,11 @@ def load_one_dir(path):
             if root.tag == 'tool':
                 tool = {}
                 if root.find('help') is not None:
-                    tool.update(dict(help=root.find('help').text))
+                    tool.update(dict(help=unicodify(root.find('help').text)))
                 if root.find('description') is not None:
-                    tool.update(dict(description=root.find('description').text))
-                tool.update(dict(id=root.attrib.get('id'),
-                                 name=root.attrib.get('name'),
-                                 version=root.attrib.get('version')))
+                    tool.update(dict(description=unicodify(root.find('description').text)))
+                tool.update(dict(id=unicodify(root.attrib.get('id')),
+                                 name=unicodify(root.attrib.get('name')),
+                                 version=unicodify(root.attrib.get('version'))))
                 tools_in_dir.append(tool)
     return tools_in_dir

From 762e4efe69ebd158e58bed503aeacfe129479a23 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Sat, 21 Mar 2020 19:14:36 +0100
Subject: [PATCH 502/853] Center svg and responsive

---
 .../scripts/components/ToolRecommendation.vue | 44 +++++++++++++++----
 client/galaxy/style/scss/base.scss            |  5 +--
 2 files changed, 38 insertions(+), 11 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 880f3aa93cb5..84ea88541ccf 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -105,20 +105,48 @@ export default {
         },
         renderD3Tree(predictedTools) {
             const duration = 750;
-            const x = 620;
-            const y = 260;
-            const tree = d3.layout.tree().size([y, x]);
-            const diagonal = d3.svg.diagonal().projection(d => {
-                return [d.y, d.x];
-            });
+            //const x = 0 //620;
+            //const y = 0 //260;
             const svg = d3
                 .select("#tool-recommendation")
                 .append("svg")
                 .attr("class", "tree-size")
-                .append("g")
-                .attr("transform", "translate(" + 250 + "," + 20 + ")");
+                .append("g");
+                //.attr("transform", "translate(" + 250 + "," + 20 + ")");
             let i = 0;
             let root = null;
+            let x = 0,
+            y = 0,
+            translateX = 0,
+            clientH = 0,
+            clientW = 0;
+            
+            //.attr("viewBox", "0 0 " + w + " " + h )
+            //.attr("preserveAspectRatio", "xMinYMin meet")
+
+            console.log(svg);
+            
+            // temp1[0]["0"].parentNode.setAttribute("viewBox", "50 0 427 146")
+
+            clientH = svg[0]["0"].parentNode.clientHeight;
+            clientW = svg[0]["0"].parentNode.clientWidth;
+            y = parseInt(clientH * 0.5);
+            x = parseInt(clientW * 0.5);
+            translateX = parseInt(clientW * 0.2);
+
+            console.log(clientH, clientW, y, x);
+            console.log(translateX);
+            
+            let svgElem = svg[0][0].parentNode;
+            svgElem.setAttribute("viewBox", "0 0 " + x + " " + y);
+            svgElem.setAttribute("preserveAspectRatio", "xMinYMin");
+            svg[0][0].setAttribute("transform", "translate(" + translateX + ", 0)");
+
+            const tree = d3.layout.tree().size([y, x]);
+            
+            const diagonal = d3.svg.diagonal().projection(d => {
+                return [d.y, d.x];
+            });
             const update = source => {
                 // Compute the new tree layout.
                 const nodes = tree.nodes(root).reverse();
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index ac567172780c..8d1ef127dc39 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1661,7 +1661,7 @@ body.reports {
             stroke-width: 0.3rem;
         }
         text {
-            font: 0.75rem sans-serif;
+            font: 0.4rem sans-serif;
         }
     }
 
@@ -1675,8 +1675,7 @@ body.reports {
 
     .tree-size {
         width: 96%;
-        height: 50%;
-        position: absolute;
+        height: 40%;
     }
 
     .link {

From c4bbda6958b455c32e8f7ab7bca965a3e5852e82 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Sat, 21 Mar 2020 23:28:55 +0100
Subject: [PATCH 503/853] responsive d3 tree

---
 .../scripts/components/ToolRecommendation.vue | 39 +++++++------------
 client/galaxy/style/scss/base.scss            | 10 ++---
 2 files changed, 19 insertions(+), 30 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 84ea88541ccf..c5a5d93639e7 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -105,42 +105,31 @@ export default {
         },
         renderD3Tree(predictedTools) {
             const duration = 750;
-            //const x = 0 //620;
-            //const y = 0 //260;
             const svg = d3
                 .select("#tool-recommendation")
                 .append("svg")
                 .attr("class", "tree-size")
                 .append("g");
-                //.attr("transform", "translate(" + 250 + "," + 20 + ")");
             let i = 0;
             let root = null;
-            let x = 0,
-            y = 0,
-            translateX = 0,
-            clientH = 0,
-            clientW = 0;
-            
-            //.attr("viewBox", "0 0 " + w + " " + h )
-            //.attr("preserveAspectRatio", "xMinYMin meet")
+            let x = 0;
+            let y = 0;
+            let translateX = 0;
+            let clientH = 0;
+            let clientW = 0;
 
-            console.log(svg);
-            
-            // temp1[0]["0"].parentNode.setAttribute("viewBox", "50 0 427 146")
+            const gElem = svg[0][0];
+            const svgElem = gElem.parentNode;
 
-            clientH = svg[0]["0"].parentNode.clientHeight;
-            clientW = svg[0]["0"].parentNode.clientWidth;
-            y = parseInt(clientH * 0.5);
-            x = parseInt(clientW * 0.5);
-            translateX = parseInt(clientW * 0.2);
+            clientH = svgElem.clientHeight;
+            clientW = svgElem.clientWidth;
+            y = parseInt(clientH * 0.9);
+            x = parseInt(clientW * 0.6);
+            translateX = parseInt(clientW * 0.15);
 
-            console.log(clientH, clientW, y, x);
-            console.log(translateX);
-            
-            let svgElem = svg[0][0].parentNode;
-            svgElem.setAttribute("viewBox", "0 0 " + x + " " + y);
+            svgElem.setAttribute("viewBox", "0 0 " + x + " " + clientH);
             svgElem.setAttribute("preserveAspectRatio", "xMinYMin");
-            svg[0][0].setAttribute("transform", "translate(" + translateX + ", 0)");
+            gElem.setAttribute("transform", "translate(" + translateX + ", 5)");
 
             const tree = d3.layout.tree().size([y, x]);
             
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index 8d1ef127dc39..edae50527f71 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1658,10 +1658,10 @@ body.reports {
         circle {
             fill: lighten($brand-primary, 20%);
             stroke: lighten($brand-primary, 20%);
-            stroke-width: 0.3rem;
+            stroke-width: 0.1rem;
         }
         text {
-            font: 0.4rem sans-serif;
+            font: 0.35rem sans-serif;
         }
     }
 
@@ -1674,13 +1674,13 @@ body.reports {
     }
 
     .tree-size {
-        width: 96%;
-        height: 40%;
+        width: 100%;
+        height: 50%;
     }
 
     .link {
         fill: none;
         stroke: lighten($brand-primary, 20%);
-        stroke-width: 0.3rem;
+        stroke-width: 0.2rem;
     }
 }

From 867c2c919cade9bc5f09a89f6820d3d8e6299b78 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Sat, 21 Mar 2020 23:45:05 +0100
Subject: [PATCH 504/853] adjust font

---
 client/galaxy/scripts/components/ToolRecommendation.vue | 9 +++------
 client/galaxy/style/scss/base.scss                      | 2 +-
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index c5a5d93639e7..e0500e6eb15b 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -115,14 +115,11 @@ export default {
             let x = 0;
             let y = 0;
             let translateX = 0;
-            let clientH = 0;
-            let clientW = 0;
 
             const gElem = svg[0][0];
             const svgElem = gElem.parentNode;
-
-            clientH = svgElem.clientHeight;
-            clientW = svgElem.clientWidth;
+            const clientH = svgElem.clientHeight;
+            const clientW = svgElem.clientWidth;
             y = parseInt(clientH * 0.9);
             x = parseInt(clientW * 0.6);
             translateX = parseInt(clientW * 0.15);
@@ -132,7 +129,7 @@ export default {
             gElem.setAttribute("transform", "translate(" + translateX + ", 5)");
 
             const tree = d3.layout.tree().size([y, x]);
-            
+
             const diagonal = d3.svg.diagonal().projection(d => {
                 return [d.y, d.x];
             });
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index edae50527f71..05fdce4b8132 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1661,7 +1661,7 @@ body.reports {
             stroke-width: 0.1rem;
         }
         text {
-            font: 0.35rem sans-serif;
+            font: 0.4rem sans-serif;
         }
     }
 

From 52ceb8b23e6dd5d395890516d062339487696bd0 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 22 Mar 2020 14:03:27 +0100
Subject: [PATCH 505/853] Prevent exception in toolshed if userid is 'current'

and the user is not already logged in (=trans.user is None).

Fixes https://sentry.galaxyproject.org/sentry/toolshed/issues/568664/
---
 lib/tool_shed/webapp/api/users.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/lib/tool_shed/webapp/api/users.py b/lib/tool_shed/webapp/api/users.py
index 1216052904ee..bb4b43145520 100644
--- a/lib/tool_shed/webapp/api/users.py
+++ b/lib/tool_shed/webapp/api/users.py
@@ -106,11 +106,7 @@ def show(self, trans, id, **kwd):
         """
         user = None
         # user is requesting data about themselves
-        if id == "current" and trans.user:
-            user = trans.user
-        else:
-            user = suc.get_user(trans.app, id)
-
+        user = trans.user if id == 'current' else suc.get_user(trans.app, id)
         if user is None:
             user_dict = dict(message='Unable to locate user record for id %s.' % (str(id)),
                              status='error')

From 8ef36e974b6bab9684806aa4d15ea3ea0bb1e53b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 22 Mar 2020 16:41:38 +0100
Subject: [PATCH 506/853] Fix setting annotation that contains only integers

This fixes https://sentry.galaxyproject.org/sentry/main/issues/572478/:
```
TypeError: argument cannot be of 'int' type, must be of text type
  File "galaxy/web/framework/decorators.py", line 157, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/controllers/dataset.py", line 353, in set_edit
    annotation = sanitize_html(payload.get('annotation'))
  File "galaxy/util/sanitize_html.py", line 48, in sanitize_html
    return bleach.clean(htmlSource, **kwd)
  File "bleach/__init__.py", line 84, in clean
    return cleaner.clean(text)
  File "bleach/sanitizer.py", line 162, in clean
    raise TypeError(message)
```
---
 lib/galaxy/util/sanitize_html.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/util/sanitize_html.py b/lib/galaxy/util/sanitize_html.py
index b2c66b2cdb3b..1ff4b8c2ec40 100644
--- a/lib/galaxy/util/sanitize_html.py
+++ b/lib/galaxy/util/sanitize_html.py
@@ -3,6 +3,9 @@
 """
 import bleach
 
+from galaxy.util import unicodify
+
+
 _acceptable_elements = ['a', 'abbr', 'acronym', 'address', 'area', 'article',
         'aside', 'audio', 'b', 'big', 'blockquote', 'br', 'button', 'canvas',
         'caption', 'center', 'cite', 'code', 'col', 'colgroup', 'command',
@@ -45,4 +48,4 @@ def sanitize_html(htmlSource, allow_data_urls=False):
     kwd = dict(tags=_acceptable_elements, attributes=_acceptable_attributes, strip=True)
     if allow_data_urls:
         kwd["protocols"] = bleach.ALLOWED_PROTOCOLS + ["data"]
-    return bleach.clean(htmlSource, **kwd)
+    return bleach.clean(unicodify(htmlSource), **kwd)

From 401b163e7125ffa7dec307f6b76ba06d4b2e7477 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sun, 22 Mar 2020 17:08:04 +0000
Subject: [PATCH 507/853] Fix docs to update conda from conda-forge

---
 doc/source/admin/conda_faq.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/source/admin/conda_faq.rst b/doc/source/admin/conda_faq.rst
index 96aeadea7c15..566fcecbf41c 100644
--- a/doc/source/admin/conda_faq.rst
+++ b/doc/source/admin/conda_faq.rst
@@ -399,7 +399,7 @@ following command:
 
 .. code-block:: bash
 
-   $ <tool_dependency_dir/_conda/bin/conda install conda==4.6.14
+   $ <tool_dependency_dir/_conda/bin/conda install -c conda-forge conda==4.6.14
 
 The command can obviously be adapted to install any version of Conda. If the
 above command fails with an error like:
@@ -417,7 +417,7 @@ specification, which for the example error above would be ``python==3.6``:
 
 .. code-block:: bash
 
-   $ <tool_dependency_dir/_conda/bin/conda install conda==4.6.14 python==3.6
+   $ <tool_dependency_dir/_conda/bin/conda install -c conda-forge conda==4.6.14 python==3.6
 
 
 .. _Conda documentation: https://conda.io/docs/

From 7f5d93a3bc93d0ea74124964a52b4977ded25372 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sun, 22 Mar 2020 17:22:04 +0000
Subject: [PATCH 508/853] Fix bad merge of release_20.01

---
 .circleci/config.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 6dd34eb5be25..3afbbc0bb985 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -95,9 +95,8 @@ jobs:
     <<: *set_workdir
     steps:
       - *restore_repo_cache
-      # Temporary virtualenv pin added due to https://github.com/pypa/virtualenv/issues/1670
-      #- *install_tox
-      - run: sudo pip install tox virtualenv==20.0.4
+      # Ensure minimum virtualenv version due to https://github.com/pypa/virtualenv/issues/1670
+      - run: sudo pip install tox 'virtualenv>=20.0.8'
       - run: tox -e py27-unit
   py35_docstring:
     docker:

From 6418b3d699c2d9f3317ca6f4798e7b2ad91c25d7 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 22 Mar 2020 16:28:19 -0400
Subject: [PATCH 509/853] Upgrade to prettier 2.0

---
 client/package.json | 2 +-
 client/yarn.lock    | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/package.json b/client/package.json
index 2f6982dfe5f6..1e3229a7f6dc 100644
--- a/client/package.json
+++ b/client/package.json
@@ -123,7 +123,7 @@
     "phantomjs-polyfill": "0.0.2",
     "phantomjs-prebuilt": "^2.1.7",
     "postcss-loader": "^3.0.0",
-    "prettier": "^1.19.1",
+    "prettier": "^2.0.1",
     "qunit": "^2.9.3",
     "raw-loader": "^4.0.0",
     "sass-loader": "^8.0.2",
diff --git a/client/yarn.lock b/client/yarn.lock
index f54ba943e00c..0a41e99c61f4 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -10836,10 +10836,10 @@ prettier@^1.18.2:
   resolved "https://registry.yarnpkg.com/prettier/-/prettier-1.18.2.tgz#6823e7c5900017b4bd3acf46fe9ac4b4d7bda9ea"
   integrity sha512-OeHeMc0JhFE9idD4ZdtNibzY0+TPHSpSSb9h8FqtP+YnoZZ1sl8Vc9b1sasjfymH3SonAF4QcA2+mzHPhMvIiw==
 
-prettier@^1.19.1:
-  version "1.19.1"
-  resolved "https://registry.yarnpkg.com/prettier/-/prettier-1.19.1.tgz#f7d7f5ff8a9cd872a7be4ca142095956a60797cb"
-  integrity sha512-s7PoyDv/II1ObgQunCbB9PdLmUcBZcnWOcxDh7O0N/UwDEsHyqkW+Qh28jW+mVuCdx7gLB0BotYI1Y6uI9iyew==
+prettier@^2.0.1:
+  version "2.0.1"
+  resolved "https://registry.yarnpkg.com/prettier/-/prettier-2.0.1.tgz#3f00ac71263be34684b2b2c8d7e7f63737592dac"
+  integrity sha512-piXGBcY1zoFOG0MvHpNE5reAGseLmaCRifQ/fmfF49BcYkInEs/naD/unxGNAeOKFA5+JxVrPyMvMlpzcd20UA==
 
 pretty-hrtime@^1.0.0:
   version "1.0.3"

From 0e7c5b2de62c8bbbcbd810606fb4d585c28ca9d4 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 22 Mar 2020 16:38:21 -0400
Subject: [PATCH 510/853] Run prettier 2.0

---
 client/galaxy/scripts/app/galaxy.js           |  12 +-
 client/galaxy/scripts/app/monitor.js          |   8 +-
 client/galaxy/scripts/bundleEntries.js        |   8 +-
 client/galaxy/scripts/components/Alert.vue    |  14 +-
 .../galaxy/scripts/components/Citations.vue   |  40 +-
 .../components/Common/DelayedInput.vue        |  20 +-
 .../galaxy/scripts/components/Common/Tags.vue |  12 +-
 .../components/DataDialog/DataDialog.test.js  |  14 +-
 .../components/DataDialog/DataDialog.vue      |  38 +-
 .../scripts/components/DataDialog/model.js    |   2 +-
 .../scripts/components/DataDialog/services.js |   6 +-
 .../components/Dataset/DatasetHistory.vue     |   6 +-
 .../components/Dataset/DatasetList.vue        |  40 +-
 .../components/Dataset/DatasetName.vue        |   8 +-
 .../scripts/components/Dataset/services.js    |   4 +-
 .../scripts/components/DisplayStructured.vue  |  32 +-
 .../scripts/components/GalaxyLoader.vue       |  10 +-
 .../components/History/HistoryDropdown.vue    |   6 +-
 .../scripts/components/HistoryImport.vue      |  14 +-
 .../galaxy/scripts/components/HistoryView.vue |  36 +-
 .../InteractiveTools/InteractiveTools.test.js |  12 +-
 .../InteractiveTools/InteractiveTools.vue     |  36 +-
 .../components/InteractiveTools/services.js   |   2 +-
 .../components/JobMetrics/JobMetrics.test.js  |  24 +-
 .../components/JobMetrics/JobMetrics.vue      |  26 +-
 .../JobParameters/JobParameters.vue           |  34 +-
 .../JobStates/CollectionJobStates.vue         |   8 +-
 .../scripts/components/JobStates/mixin.js     |   6 +-
 .../galaxy/scripts/components/LoadingSpan.vue |  10 +-
 .../scripts/components/Markdown/Markdown.vue  |  28 +-
 .../components/Markdown/MarkdownEditor.vue    |  30 +-
 .../galaxy/scripts/components/MaskedInput.js  |  12 +-
 .../scripts/components/Masthead/index.vue     |   4 +-
 .../components/Masthead/initMasthead.js       |   2 +-
 client/galaxy/scripts/components/Message.vue  |   8 +-
 .../scripts/components/Nametags/Nametag.vue   |   8 +-
 .../scripts/components/Nametags/Nametags.vue  |  12 +-
 .../components/PageDisplay/PageDisplay.vue    |  26 +-
 .../components/PageEditor/PageEditor.vue      |  22 +-
 .../components/PageEditor/PageEditorHtml.vue  | 118 +--
 .../PageEditor/PageEditorMarkdown.vue         |  20 +-
 .../components/PageEditor/markdownHelp.js     |   2 +-
 .../scripts/components/PageEditor/util.js     |   2 +-
 .../Panels/Buttons/FavoritesButton.vue        |   8 +-
 .../Panels/Buttons/UploadButton.vue           |  10 +-
 .../components/Panels/Common/Tool.test.js     |  16 +-
 .../scripts/components/Panels/Common/Tool.vue |  18 +-
 .../components/Panels/Common/ToolSearch.vue   |  22 +-
 .../Panels/Common/ToolSection.test.js         |  30 +-
 .../components/Panels/Common/ToolSection.vue  |  30 +-
 .../scripts/components/Panels/SidePanel.vue   |  10 +-
 .../scripts/components/Panels/ToolBox.vue     |  28 +-
 .../components/Panels/ToolBoxWorkflow.vue     |  30 +-
 .../scripts/components/Panels/utilities.js    |   8 +-
 .../galaxy/scripts/components/PluginList.vue  |  22 +-
 .../galaxy/scripts/components/ProgressBar.vue |   8 +-
 .../components/RuleCollectionBuilder.vue      | 215 ++--
 .../scripts/components/RulesDisplay.vue       |  42 +-
 client/galaxy/scripts/components/Select2.js   |  26 +-
 .../SelectionDialog/DataDialogSearch.vue      |   8 +-
 .../SelectionDialog/DataDialogTable.vue       |  32 +-
 .../DatasetCollectionDialog.test.js           |   4 +-
 .../DatasetCollectionDialog.vue               |  24 +-
 .../SelectionDialog/SelectionDialog.test.js   |   8 +-
 .../SelectionDialog/SelectionDialog.vue       |  16 +-
 .../SelectionDialog/SelectionDialogMixin.js   |   8 +-
 .../SelectionDialog/WorkflowDialog.test.js    |   6 +-
 .../SelectionDialog/WorkflowDialog.vue        |  20 +-
 client/galaxy/scripts/components/Sharing.vue  |  54 +-
 .../components/Tags/StatelessTags.test.js     |   4 +-
 .../scripts/components/Tags/StatelessTags.vue |  18 +-
 .../scripts/components/Tags/Tags.test.js      |  24 +-
 .../galaxy/scripts/components/Tags/Tags.vue   |  20 +-
 .../galaxy/scripts/components/Tags/model.js   |  22 +-
 .../galaxy/scripts/components/Tags/mounts.js  |   6 +-
 .../scripts/components/Tags/tagService.js     |  14 +-
 .../components/Tags/tagService.test.js        |  14 +-
 .../ToolEntryPoints/ToolEntryPoints.vue       |  24 +-
 .../scripts/components/ToolRecommendation.vue |  62 +-
 .../ToolsView/ToolsSchemaJson/ToolsJson.vue   |  14 +-
 .../components/ToolsView/ToolsView.test.js    |   8 +-
 .../components/ToolsView/ToolsView.vue        |  36 +-
 .../scripts/components/Toolshed/Index.vue     |  14 +-
 .../Toolshed/InstalledList/Details.test.js    |   6 +-
 .../Toolshed/InstalledList/Details.vue        |  12 +-
 .../Toolshed/InstalledList/Index.test.js      |  16 +-
 .../Toolshed/InstalledList/Index.vue          |  20 +-
 .../Toolshed/InstalledList/Monitor.test.js    |   6 +-
 .../Toolshed/InstalledList/Monitor.vue        |  20 +-
 .../Toolshed/RepositoryDetails/Index.test.js  |   8 +-
 .../Toolshed/RepositoryDetails/Index.vue      |  36 +-
 .../InstallationButton.test.js                |   8 +-
 .../RepositoryDetails/InstallationButton.vue  |   8 +-
 .../InstallationSettings.test.js              |   8 +-
 .../InstallationSettings.vue                  |  24 +-
 .../RepositoryDetails/RepositoryTools.test.js |  20 +-
 .../RepositoryDetails/RepositoryTools.vue     |   8 +-
 .../Toolshed/SearchList/Categories.test.js    |  14 +-
 .../Toolshed/SearchList/Categories.vue        |  14 +-
 .../components/Toolshed/SearchList/Index.vue  |  12 +-
 .../Toolshed/SearchList/Repositories.test.js  |  10 +-
 .../Toolshed/SearchList/Repositories.vue      |  20 +-
 .../SearchList/ServerSelection.test.js        |   4 +-
 .../Toolshed/SearchList/ServerSelection.vue   |   6 +-
 .../scripts/components/Toolshed/services.js   |  20 +-
 .../components/Toolshed/services.test.js      |  12 +-
 .../components/Upload/Collection.test.js      |   2 +-
 .../scripts/components/Upload/Collection.vue  |  40 +-
 .../scripts/components/Upload/Composite.vue   |  56 +-
 .../scripts/components/Upload/Default.test.js |   2 +-
 .../scripts/components/Upload/Default.vue     |  36 +-
 .../scripts/components/Upload/RulesInput.vue  |  32 +-
 .../components/Upload/UploadBoxMixin.js       |  94 +-
 .../components/Upload/UploadModal.test.js     |   8 +-
 .../scripts/components/Upload/UploadModal.vue |  56 +-
 .../components/Upload/UploadWrapper.vue       |  16 +-
 .../scripts/components/Upload/test_helpers.js |  16 +-
 .../User/CloudAuth/CloudAuth.test.js          |   6 +-
 .../components/User/CloudAuth/CloudAuth.vue   |  26 +-
 .../User/CloudAuth/CloudAuthItem.vue          |  10 +-
 .../User/CloudAuth/CredentialConfig.vue       |   8 +-
 .../User/CloudAuth/CredentialForm.vue         |  12 +-
 .../User/CloudAuth/model/AwsConfig.js         |   6 +-
 .../User/CloudAuth/model/AzureConfig.js       |  10 +-
 .../User/CloudAuth/model/BaseModel.js         |   4 +-
 .../User/CloudAuth/model/Credential.js        |   4 +-
 .../User/CloudAuth/model/Credential.test.js   |   8 +-
 .../User/CloudAuth/model/ResourceProviders.js |   4 +-
 .../User/CloudAuth/model/service.js           |   4 +-
 .../scripts/components/User/CustomBuilds.vue  |  42 +-
 .../components/User/RecentInvocations.vue     |  10 +-
 .../components/User/UserPreferences.vue       |  34 +-
 .../components/User/UserPreferencesModel.js   |  22 +-
 client/galaxy/scripts/components/UtcDate.vue  |  14 +-
 .../galaxy/scripts/components/WaitButton.vue  |  18 +-
 .../Workflow/Editor/Attributes.test.js        |   4 +-
 .../components/Workflow/Editor/Attributes.vue |  30 +-
 .../Workflow/Editor/EditorPanel.vue           |   8 +-
 .../components/Workflow/Editor/Index.vue      |  58 +-
 .../components/Workflow/Editor/Node.test.js   |   4 +-
 .../components/Workflow/Editor/Node.vue       |  18 +-
 .../components/Workflow/Editor/Options.vue    |   6 +-
 .../components/Workflow/Editor/ReportHelp.vue |   4 +-
 .../Workflow/Editor/ZoomControl.test.js       |   4 +-
 .../Workflow/Editor/ZoomControl.vue           |  12 +-
 .../components/Workflow/Editor/mount.js       |   4 +-
 .../components/Workflow/Editor/utilities.js   |  26 +-
 .../components/Workflow/Invocations.vue       |  18 +-
 .../components/Workflow/Run/WorkflowRun.vue   |  16 +-
 .../Workflow/Run/WorkflowRunSuccess.vue       |  18 +-
 .../components/Workflow/WorkflowDropdown.vue  |  22 +-
 .../components/Workflow/WorkflowImport.vue    |  14 +-
 .../components/Workflow/WorkflowList.vue      |  60 +-
 .../scripts/components/Workflow/icons.js      |   2 +-
 .../scripts/components/Workflow/services.js   |   2 +-
 .../components/WorkflowInvocationReport.vue   |  30 +-
 .../WorkflowInvocationState.vue               |  54 +-
 .../WorkflowInvocationState/services.js       |   2 +-
 .../components/admin/ActiveInvocations.vue    |  10 +-
 .../scripts/components/admin/BaseGrid.vue     |  12 +-
 .../scripts/components/admin/BaseList.test.js |  12 +-
 .../scripts/components/admin/BaseList.vue     |  54 +-
 .../admin/DataManager/DataManager.vue         |  20 +-
 .../admin/DataManager/DataManagerJob.vue      |  34 +-
 .../admin/DataManager/DataManagerJobs.vue     |  28 +-
 .../admin/DataManager/DataManagerRouter.vue   |  14 +-
 .../admin/DataManager/DataManagerTable.vue    |  28 +-
 .../admin/DataManager/DataManagerView.vue     |   4 +-
 .../components/admin/DataManagerGrid.vue      |  14 +-
 .../scripts/components/admin/DataTables.vue   |  34 +-
 .../components/admin/DataTablesGrid.vue       |  16 +-
 .../scripts/components/admin/DataTypes.vue    |  22 +-
 .../Dependencies/ContainerDescription.vue     |  20 +-
 .../admin/Dependencies/ContainerIndex.vue     |  34 +-
 .../ContainerResolutionDetails.vue            |  10 +-
 .../admin/Dependencies/ContainerResolver.vue  |  18 +-
 .../Dependencies/DependencyIndexMixin.js      |  10 +-
 .../Dependencies/DependencyIndexWrapper.vue   |  12 +-
 .../admin/Dependencies/DependencyResolver.vue |  12 +-
 .../admin/Dependencies/DisplayRaw.vue         |  10 +-
 .../components/admin/Dependencies/Landing.vue |   8 +-
 .../admin/Dependencies/Requirement.vue        |   6 +-
 .../admin/Dependencies/Requirements.vue       |   6 +-
 .../admin/Dependencies/ResolutionDetails.vue  |  18 +-
 .../admin/Dependencies/ResolutionIndex.vue    |  32 +-
 .../admin/Dependencies/StatusDisplay.vue      |  24 +-
 .../admin/Dependencies/Statuses.vue           |  12 +-
 .../admin/Dependencies/ToolDisplay.vue        |  12 +-
 .../components/admin/Dependencies/Tools.vue   |  12 +-
 .../admin/Dependencies/UnusedIndex.vue        |  18 +-
 .../components/admin/DisplayApplications.vue  |   8 +-
 .../scripts/components/admin/ErrorStack.vue   |  18 +-
 .../galaxy/scripts/components/admin/Home.vue  |  14 +-
 .../scripts/components/admin/JobDetails.vue   |  10 +-
 .../scripts/components/admin/JobLock.vue      |  12 +-
 .../galaxy/scripts/components/admin/Jobs.vue  |  26 +-
 .../components/admin/ResetMetadata.vue        |   8 +-
 .../galaxy/scripts/components/login/Index.vue |  28 +-
 .../galaxy/scripts/components/login/Login.vue |  38 +-
 .../scripts/components/login/Password.vue     |  16 +-
 .../scripts/components/login/Register.vue     |  28 +-
 client/galaxy/scripts/components/xrefs.vue    |  16 +-
 .../galaxy/scripts/entry/admin/AdminRouter.js |  90 +-
 client/galaxy/scripts/entry/admin/index.js    |   4 +-
 .../scripts/entry/analysis/AnalysisRouter.js  | 120 +--
 client/galaxy/scripts/entry/analysis/index.js |   4 +-
 client/galaxy/scripts/entry/login/index.js    |   4 +-
 .../scripts/entry/panels/admin-panel.js       |  78 +-
 .../scripts/entry/panels/history-panel.js     |  28 +-
 .../galaxy/scripts/entry/panels/tool-panel.js |  22 +-
 .../galaxy.interactive_environments.js        |  46 +-
 client/galaxy/scripts/galaxy.library.js       |  52 +-
 client/galaxy/scripts/galaxy.pages.js         |   8 +-
 client/galaxy/scripts/i18n.js                 |  14 +-
 .../layout/communication-server-view.js       |  24 +-
 client/galaxy/scripts/layout/masthead.js      |  34 +-
 client/galaxy/scripts/layout/menu.js          | 132 +--
 client/galaxy/scripts/layout/modal.js         |  34 +-
 client/galaxy/scripts/layout/page.js          |  50 +-
 client/galaxy/scripts/layout/panel.js         |  66 +-
 client/galaxy/scripts/layout/router.js        |  20 +-
 client/galaxy/scripts/layout/scratchbook.js   |  64 +-
 .../galaxy/scripts/legacy/grid/grid-model.js  |  18 +-
 .../scripts/legacy/grid/grid-template.js      |  22 +-
 .../galaxy/scripts/legacy/grid/grid-view.js   | 128 ++-
 .../galaxy/scripts/mocha/tests/rules_tests.js |   4 +-
 client/galaxy/scripts/mvc/annotation.js       |  26 +-
 client/galaxy/scripts/mvc/base-mvc.js         | 120 +--
 .../mvc/base/controlled-fetch-collection.js   |  78 +-
 .../scripts/mvc/collection/base-creator.js    |  44 +-
 .../mvc/collection/collection-li-edit.js      |  30 +-
 .../scripts/mvc/collection/collection-li.js   |  64 +-
 .../mvc/collection/collection-model.js        |  78 +-
 .../mvc/collection/collection-view-edit.js    |  20 +-
 .../scripts/mvc/collection/collection-view.js |  46 +-
 .../mvc/collection/list-collection-creator.js | 232 +++--
 .../list-of-pairs-collection-creator.js       | 348 +++----
 .../mvc/collection/pair-collection-creator.js |  62 +-
 client/galaxy/scripts/mvc/dataset/data.js     | 121 +--
 .../scripts/mvc/dataset/dataset-choice.js     |  76 +-
 .../mvc/dataset/dataset-edit-attributes.js    |  90 +-
 .../scripts/mvc/dataset/dataset-error.js      |  66 +-
 .../scripts/mvc/dataset/dataset-li-edit.js    | 118 +--
 .../galaxy/scripts/mvc/dataset/dataset-li.js  | 108 +-
 .../scripts/mvc/dataset/dataset-list.js       |   8 +-
 .../scripts/mvc/dataset/dataset-model.js      |  86 +-
 client/galaxy/scripts/mvc/dataset/states.js   |   4 +-
 client/galaxy/scripts/mvc/embedded-objects.js |  18 +-
 client/galaxy/scripts/mvc/entrypoints/poll.js |   2 +-
 client/galaxy/scripts/mvc/entrypoints/view.js |  12 +-
 client/galaxy/scripts/mvc/form/form-data.js   |  26 +-
 client/galaxy/scripts/mvc/form/form-input.js  |  20 +-
 .../scripts/mvc/form/form-parameters.js       |  62 +-
 client/galaxy/scripts/mvc/form/form-repeat.js |  38 +-
 .../galaxy/scripts/mvc/form/form-section.js   |  48 +-
 client/galaxy/scripts/mvc/form/form-view.js   |  32 +-
 .../galaxy/scripts/mvc/form/form-wrapper.js   |  40 +-
 client/galaxy/scripts/mvc/grid/grid-model.js  |  16 +-
 client/galaxy/scripts/mvc/grid/grid-shared.js |  14 +-
 .../galaxy/scripts/mvc/grid/grid-template.js  |  22 +-
 client/galaxy/scripts/mvc/grid/grid-view.js   | 136 ++-
 .../galaxy/scripts/mvc/history/copy-dialog.js |  35 +-
 .../galaxy/scripts/mvc/history/hda-li-edit.js |  22 +-
 client/galaxy/scripts/mvc/history/hda-li.js   |  16 +-
 .../galaxy/scripts/mvc/history/hda-model.js   |   6 +-
 .../scripts/mvc/history/hdca-li-edit.js       |  22 +-
 client/galaxy/scripts/mvc/history/hdca-li.js  |  24 +-
 .../galaxy/scripts/mvc/history/hdca-model.js  |  10 +-
 .../mvc/history/history-content-model.js      |  18 +-
 .../scripts/mvc/history/history-contents.js   | 132 +--
 .../scripts/mvc/history/history-list.js       |  28 +-
 .../scripts/mvc/history/history-model.js      | 120 +--
 .../mvc/history/history-preferences.js        |  26 +-
 .../mvc/history/history-view-annotated.js     |  35 +-
 .../mvc/history/history-view-edit-current.js  | 135 ++-
 .../scripts/mvc/history/history-view-edit.js  | 162 +--
 .../scripts/mvc/history/history-view.js       | 158 ++-
 client/galaxy/scripts/mvc/history/job-dag.js  |  20 +-
 .../scripts/mvc/history/job-states-model.js   |  60 +-
 .../galaxy/scripts/mvc/history/multi-panel.js | 195 ++--
 .../scripts/mvc/history/options-menu.js       |  66 +-
 client/galaxy/scripts/mvc/job/job-li.js       |  42 +-
 client/galaxy/scripts/mvc/job/job-model.js    |  56 +-
 .../galaxy/scripts/mvc/lazy/lazy-limited.js   |  14 +-
 .../mvc/library/library-dataset-view.js       | 200 ++--
 .../mvc/library/library-folder-view.js        |  66 +-
 .../mvc/library/library-folderlist-view.js    |  98 +-
 .../mvc/library/library-folderrow-view.js     |  70 +-
 .../mvc/library/library-foldertoolbar-view.js | 332 +++---
 .../mvc/library/library-library-view.js       |  78 +-
 .../mvc/library/library-librarylist-view.js   |  67 +-
 .../mvc/library/library-libraryrow-view.js    |  48 +-
 .../library/library-librarytoolbar-view.js    |  38 +-
 .../scripts/mvc/library/library-model.js      |  52 +-
 .../scripts/mvc/library/library-util.js       |   2 +-
 client/galaxy/scripts/mvc/list/list-item.js   | 106 +-
 client/galaxy/scripts/mvc/list/list-view.js   | 259 +++--
 .../scripts/mvc/rules/rule-definitions.js     |  96 +-
 .../galaxy/scripts/mvc/tool/tool-form-base.js |  96 +-
 .../scripts/mvc/tool/tool-form-composite.js   | 142 ++-
 client/galaxy/scripts/mvc/tool/tool-form.js   |  88 +-
 client/galaxy/scripts/mvc/tours.js            |  56 +-
 client/galaxy/scripts/mvc/ui/error-modal.js   |  15 +-
 client/galaxy/scripts/mvc/ui/icon-button.js   |  30 +-
 client/galaxy/scripts/mvc/ui/popup-menu.js    |  53 +-
 client/galaxy/scripts/mvc/ui/ui-buttons.js    |  82 +-
 .../galaxy/scripts/mvc/ui/ui-color-picker.js  |  26 +-
 .../galaxy/scripts/mvc/ui/ui-data-picker.js   |  19 +-
 client/galaxy/scripts/mvc/ui/ui-drilldown.js  |  32 +-
 client/galaxy/scripts/mvc/ui/ui-frames.js     | 150 ++-
 client/galaxy/scripts/mvc/ui/ui-list.js       |  34 +-
 client/galaxy/scripts/mvc/ui/ui-misc.js       | 101 +-
 client/galaxy/scripts/mvc/ui/ui-modal.js      |  35 +-
 client/galaxy/scripts/mvc/ui/ui-options.js    | 106 +-
 client/galaxy/scripts/mvc/ui/ui-popover.js    |  14 +-
 client/galaxy/scripts/mvc/ui/ui-portlet.js    |  68 +-
 client/galaxy/scripts/mvc/ui/ui-rules-edit.js |  42 +-
 .../scripts/mvc/ui/ui-select-content.js       | 140 ++-
 .../scripts/mvc/ui/ui-select-default.js       | 123 +--
 client/galaxy/scripts/mvc/ui/ui-select-ftp.js |  18 +-
 .../scripts/mvc/ui/ui-select-library.js       |  38 +-
 client/galaxy/scripts/mvc/ui/ui-select.js     |  44 +-
 client/galaxy/scripts/mvc/ui/ui-slider.js     |  22 +-
 client/galaxy/scripts/mvc/ui/ui-table.js      |  44 +-
 client/galaxy/scripts/mvc/ui/ui-tabs.js       |  64 +-
 .../mvc/upload/collection/collection-row.js   |  26 +-
 .../mvc/upload/composite/composite-row.js     |  78 +-
 .../scripts/mvc/upload/default/default-row.js |  58 +-
 .../scripts/mvc/upload/upload-extension.js    |  12 +-
 .../galaxy/scripts/mvc/upload/upload-ftp.js   |  36 +-
 .../galaxy/scripts/mvc/upload/upload-model.js |  10 +-
 .../scripts/mvc/upload/upload-settings.js     |  22 +-
 .../galaxy/scripts/mvc/upload/upload-utils.js |  18 +-
 .../scripts/mvc/upload/uploadbox-row.js       |  22 +-
 client/galaxy/scripts/mvc/user/tab-updates.js |   2 +-
 client/galaxy/scripts/mvc/user/user-model.js  |  34 +-
 .../scripts/mvc/user/user-quotameter.js       |  28 +-
 .../mvc/visualization/chart/chart-client.js   |  10 +-
 .../visualization/chart/components/model.js   |  30 +-
 .../chart/components/screenshot.js            |  22 +-
 .../visualization/chart/utilities/datasets.js |  32 +-
 .../mvc/visualization/chart/utilities/jobs.js |  36 +-
 .../visualization/chart/utilities/series.js   |  34 +-
 .../visualization/chart/views/description.js  |   8 +-
 .../mvc/visualization/chart/views/editor.js   |  10 +-
 .../mvc/visualization/chart/views/groups.js   |  42 +-
 .../mvc/visualization/chart/views/menu.js     |  52 +-
 .../mvc/visualization/chart/views/settings.js |  16 +-
 .../mvc/visualization/chart/views/viewer.js   |  18 +-
 .../mvc/visualization/visualization-model.js  |  26 +-
 client/galaxy/scripts/mvc/webhooks.js         |  24 +-
 .../scripts/mvc/workflow/workflow-canvas.js   |  31 +-
 .../mvc/workflow/workflow-connector.js        |  10 +-
 .../scripts/mvc/workflow/workflow-forms.js    |  84 +-
 .../scripts/mvc/workflow/workflow-manager.js  |  32 +-
 .../scripts/mvc/workflow/workflow-node.js     |  28 +-
 .../mvc/workflow/workflow-terminals.js        |  74 +-
 .../mvc/workflow/workflow-view-data.js        |  18 +-
 .../mvc/workflow/workflow-view-node.js        |  10 +-
 .../mvc/workflow/workflow-view-terminals.js   |  50 +-
 client/galaxy/scripts/nls/de/locale.js        |   2 +-
 client/galaxy/scripts/nls/es/locale.js        |   2 +-
 client/galaxy/scripts/nls/fr/locale.js        |   2 +-
 client/galaxy/scripts/nls/ja/locale.js        |   2 +-
 client/galaxy/scripts/nls/locale.js           |   4 +-
 client/galaxy/scripts/nls/zh/locale.js        |   2 +-
 .../scripts/onload/defaultAppFactory.js       |   2 +-
 .../galaxy/scripts/onload/defaultConfigs.js   |   4 +-
 .../scripts/onload/getRootFromIndexLink.js    |   2 +-
 .../onload/globalInits/iframesAreTerrible.js  |   2 +-
 .../globalInits/init_refresh_on_change.js     |   6 +-
 .../onload/globalInits/onloadWebhooks.js      |   6 +-
 .../onload/globalInits/panelManagement.js     |  10 +-
 .../globalInits/replace_big_select_inputs.js  |   4 +-
 client/galaxy/scripts/onload/initQueue.js     |   2 +-
 client/galaxy/scripts/onload/loadConfig.js    |   4 +-
 client/galaxy/scripts/onload/standardInit.js  |   4 +-
 client/galaxy/scripts/polyfills.js            |  26 +-
 client/galaxy/scripts/qunit/test-app.js       |  14 +-
 .../scripts/qunit/test-data/bootstrapped.js   |   6 +-
 .../scripts/qunit/test-data/fakeserver.js     |   8 +-
 .../scripts/qunit/test-data/job-dag-1.js      | 148 +--
 .../paired-collection-creator.data.js         |  64 +-
 .../galaxy/scripts/qunit/tests/form_tests.js  |  31 +-
 .../qunit/tests/galaxy_app_base_tests.js      |  28 +-
 .../galaxy/scripts/qunit/tests/graph_tests.js | 134 +--
 .../scripts/qunit/tests/hda_base_tests.js     |  10 +-
 .../tests/history_contents_model_tests.js     |  16 +-
 .../scripts/qunit/tests/job_dag_tests.js      | 118 +--
 .../qunit/tests/jquery_plugin_tests.js        |   8 +-
 .../list_of_pairs_collection_creator_tests.js |  26 +-
 .../scripts/qunit/tests/masthead_tests.js     |  12 +-
 .../qunit/tests/metrics_logger_tests.js       |  96 +-
 .../galaxy/scripts/qunit/tests/modal_tests.js |  24 +-
 client/galaxy/scripts/qunit/tests/ui_tests.js | 192 ++--
 .../galaxy/scripts/qunit/tests/utils_tests.js |   8 +-
 .../qunit/tests/workflow_editor_tests.js      | 376 +++----
 client/galaxy/scripts/reports/run_stats.js    |  55 +-
 .../galaxy/scripts/store/configStore/index.js |   8 +-
 .../galaxy/scripts/store/gridSearchStore.js   |   8 +-
 client/galaxy/scripts/store/historyStore.js   |  16 +-
 client/galaxy/scripts/store/index.js          |   8 +-
 .../galaxy/scripts/store/invocationStore.js   |  14 +-
 .../galaxy/scripts/store/jobMetricsStore.js   |  14 +-
 .../scripts/store/jobMetricsStore.test.js     |   4 +-
 client/galaxy/scripts/store/tagStore.js       |  12 +-
 client/galaxy/scripts/store/tagStore.test.js  |   4 +-
 .../scripts/store/userStore/userStore.js      |  10 +-
 client/galaxy/scripts/store/workflowStore.js  |  12 +-
 .../toolshed/groups/group-detail-view.js      |  20 +-
 .../toolshed/groups/group-list-view.js        |  22 +-
 .../toolshed/groups/group-listrow-view.js     |  12 +-
 .../scripts/toolshed/groups/group-model.js    |   6 +-
 .../scripts/toolshed/toolshed.groups.js       |  14 +-
 client/galaxy/scripts/ui/editable-text.js     |  10 +-
 client/galaxy/scripts/ui/fa-icon-button.js    |  13 +-
 client/galaxy/scripts/ui/hoverhighlight.js    |  12 +-
 client/galaxy/scripts/ui/loading-indicator.js |  25 +-
 client/galaxy/scripts/ui/mode-button.js       |   4 +-
 client/galaxy/scripts/ui/pagination.js        |   8 +-
 .../galaxy/scripts/ui/peek-column-selector.js |  50 +-
 client/galaxy/scripts/ui/popupmenu.js         |  22 +-
 client/galaxy/scripts/ui/scroll-panel.js      |   6 +-
 client/galaxy/scripts/ui/search-input.js      |  29 +-
 client/galaxy/scripts/utils/add-logging.js    |   4 +-
 client/galaxy/scripts/utils/ajax-queue.js     |  10 +-
 client/galaxy/scripts/utils/ariaAlert.js      |   2 +-
 .../galaxy/scripts/utils/async-save-text.js   |  16 +-
 client/galaxy/scripts/utils/config.js         | 113 +-
 client/galaxy/scripts/utils/data.js           |  28 +-
 client/galaxy/scripts/utils/deferred.js       |  16 +-
 client/galaxy/scripts/utils/genericConfig.js  |   2 +-
 client/galaxy/scripts/utils/graph.js          | 120 +--
 client/galaxy/scripts/utils/installMonitor.js |   2 +-
 client/galaxy/scripts/utils/localization.js   |   4 +-
 client/galaxy/scripts/utils/metrics-logger.js |  18 +-
 client/galaxy/scripts/utils/mock.js           |   4 +-
 .../galaxy/scripts/utils/mountVueComponent.js |   4 +-
 .../scripts/utils/query-string-parsing.js     |   6 +-
 client/galaxy/scripts/utils/safeAssign.js     |   4 +-
 client/galaxy/scripts/utils/uploadbox.js      |  80 +-
 client/galaxy/scripts/utils/utils.js          |  26 +-
 client/galaxy/scripts/viz/bbi-data-manager.js |  12 +-
 client/galaxy/scripts/viz/circster.js         | 284 +++---
 client/galaxy/scripts/viz/phyloviz.js         | 224 ++--
 client/galaxy/scripts/viz/sweepster.js        | 295 +++---
 client/galaxy/scripts/viz/tools.js            | 102 +-
 client/galaxy/scripts/viz/trackster.js        | 105 +-
 .../galaxy/scripts/viz/trackster/filters.js   | 139 ++-
 .../galaxy/scripts/viz/trackster/painters.js  |  40 +-
 .../galaxy/scripts/viz/trackster/slotting.js  |  14 +-
 client/galaxy/scripts/viz/trackster/tracks.js | 964 ++++++++----------
 client/galaxy/scripts/viz/trackster/util.js   |  16 +-
 client/galaxy/scripts/viz/visualization.js    | 284 +++---
 client/galaxy/scripts/viz/viz_views.js        |  33 +-
 client/galaxy/style/scss/jquery.rating.scss   |  88 +-
 client/galaxy/style/scss/theme/blue.scss      |   2 +-
 457 files changed, 8570 insertions(+), 9221 deletions(-)

diff --git a/client/galaxy/scripts/app/galaxy.js b/client/galaxy/scripts/app/galaxy.js
index dff9e9d1bb05..86dd4f59728b 100644
--- a/client/galaxy/scripts/app/galaxy.js
+++ b/client/galaxy/scripts/app/galaxy.js
@@ -39,7 +39,7 @@ try {
 }
 
 /** initalize options and sub-components */
-GalaxyApp.prototype._init = function(options, bootstrapped) {
+GalaxyApp.prototype._init = function (options, bootstrapped) {
     _.extend(this, Backbone.Events);
     if (localDebugging) {
         this.logger = console;
@@ -98,7 +98,7 @@ GalaxyApp.prototype.defaultOptions = {
     patchExisting: true,
     /** root url of this app */
     root: "/",
-    session_csrf_token: null
+    session_csrf_token: null,
 };
 
 /** filter to options present in defaultOptions (and default to them) */
@@ -162,8 +162,8 @@ GalaxyApp.prototype._initLogger = function _initLogger(loggerOptions) {
 
     this.logger = new metricsLogger.MetricsLogger(loggerOptions);
     this.emit = {};
-    ["log", "debug", "info", "warn", "error", "metric"].map(i => {
-        this.emit[i] = data => {
+    ["log", "debug", "info", "warn", "error", "metric"].map((i) => {
+        this.emit[i] = (data) => {
             this.logger.emit(i, arguments[0], Array.prototype.slice.call(arguments, 1));
         };
     });
@@ -240,7 +240,7 @@ GalaxyApp.prototype._setUpListeners = function _setUpListeners() {
 
         this.lastAjax = {
             url: location.href.slice(0, -1) + options.url,
-            data: data
+            data: data,
         };
         //TODO:?? we might somehow manage to *retry* ajax using either this hook or Backbone.sync
     });
@@ -301,5 +301,5 @@ GalaxyApp.prototype.toString = function toString() {
 
 // ============================================================================
 export default {
-    GalaxyApp: GalaxyApp
+    GalaxyApp: GalaxyApp,
 };
diff --git a/client/galaxy/scripts/app/monitor.js b/client/galaxy/scripts/app/monitor.js
index 253a834fb059..42b48f0de0c7 100644
--- a/client/galaxy/scripts/app/monitor.js
+++ b/client/galaxy/scripts/app/monitor.js
@@ -8,20 +8,20 @@ import { serverPath } from "utils/serverPath";
 
 const galaxyStub = {
     root: getAppRoot(),
-    config: {}
+    config: {},
 };
 
 if (!window.Galaxy) {
     Object.defineProperty(window, "Galaxy", {
         enumerable: true,
-        get: function() {
+        get: function () {
             console.warn("accessing (get) window.Galaxy", serverPath());
             return getGalaxyInstance() || galaxyStub;
         },
-        set: function(newValue) {
+        set: function (newValue) {
             console.warn("accessing (set) window.Galaxy", serverPath());
             setGalaxyInstance(newValue);
-        }
+        },
     });
 } else {
     console.error("Detected redefinition of window.Galaxy -- skipping, but this should be investigated.", serverPath());
diff --git a/client/galaxy/scripts/bundleEntries.js b/client/galaxy/scripts/bundleEntries.js
index 6dce4ad39a69..2818689602fb 100644
--- a/client/galaxy/scripts/bundleEntries.js
+++ b/client/galaxy/scripts/bundleEntries.js
@@ -52,14 +52,14 @@ export function multiHistory(options) {
         order: options.order,
         limitOnFirstFetch: options.limit,
         limitPerFetch: options.limit,
-        currentHistoryId: options.current_history_id
+        currentHistoryId: options.current_history_id,
     });
     const multipanel = new MultiPanel.MultiPanelColumns({
         el: $("#center").get(0),
-        histories: histories
+        histories: histories,
     });
 
-    histories.fetchFirst({ silent: true }).done(function() {
+    histories.fetchFirst({ silent: true }).done(function () {
         multipanel.createColumns();
         multipanel.render(0);
     });
@@ -85,7 +85,7 @@ export function chart(options) {
 export const chartUtilities = {
     Datasets: Datasets,
     Jobs: Jobs,
-    Series: Series
+    Series: Series,
 };
 
 export { initMasthead } from "components/Masthead/initMasthead";
diff --git a/client/galaxy/scripts/components/Alert.vue b/client/galaxy/scripts/components/Alert.vue
index f33a3bf6bd61..232e1d54f67e 100644
--- a/client/galaxy/scripts/components/Alert.vue
+++ b/client/galaxy/scripts/components/Alert.vue
@@ -13,21 +13,21 @@ export default {
          */
         message: {
             type: String,
-            default: ""
+            default: "",
         },
         /**
          * Alias for variant, takes precedence if both are set
          */
         status: {
             type: String,
-            default: ""
+            default: "",
         },
         /**
          * Alert type, one of done/success, info, warning, error/danger
          */
         variant: {
             type: String,
-            default: "done"
+            default: "done",
         },
         /** Display a close button in the alert that allows it to be dismissed */
         dismissible: Boolean,
@@ -36,7 +36,7 @@ export default {
         /** If a number, number of seconds to show before dismissing */
         show: [Boolean, Number],
         /** Should the alert fade out */
-        fade: Boolean
+        fade: Boolean,
     },
     computed: {
         galaxyKwdToBootstrap() {
@@ -48,7 +48,7 @@ export default {
                 done: "success",
                 info: "info",
                 warning: "warning",
-                error: "danger"
+                error: "danger",
             };
             if (variant in galaxyKwdToBoostrapDict) {
                 return galaxyKwdToBoostrapDict[variant];
@@ -66,7 +66,7 @@ export default {
             } else {
                 return false;
             }
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Citations.vue b/client/galaxy/scripts/components/Citations.vue
index 71d4934c72e5..b15df077da50 100644
--- a/client/galaxy/scripts/components/Citations.vue
+++ b/client/galaxy/scripts/components/Citations.vue
@@ -64,29 +64,29 @@ export default {
     props: {
         source: {
             type: String,
-            required: true
+            required: true,
         },
         id: {
             type: String,
-            required: true
+            required: true,
         },
         viewRender: {
             type: Boolean,
             requried: false,
-            default: true
+            default: true,
         },
         simple: {
             type: Boolean,
             required: false,
-            default: false
-        }
+            default: false,
+        },
     },
     data() {
         return {
             citations: [],
             content: "",
             errors: [],
-            showCollapse: false
+            showCollapse: false,
         };
     },
     computed: {
@@ -95,7 +95,7 @@ export default {
                 (a, b) => a.concat(`<p class="formatted-reference">${this.formattedReference(b)}</p>`),
                 ""
             );
-        }
+        },
     },
     updated() {
         this.$nextTick(() => {
@@ -105,19 +105,19 @@ export default {
     created() {
         axios
             .get(`${getAppRoot()}api/${this.source}/${this.id}/citations`)
-            .then(response => {
+            .then((response) => {
                 this.content = "";
-                response.data.forEach(rawCitation => {
+                response.data.forEach((rawCitation) => {
                     try {
                         const citation = {
                             fields: {},
-                            entryType: undefined
+                            entryType: undefined,
                         };
                         let parsed = bibtexParse.toJSON(rawCitation.content);
                         if (parsed) {
                             parsed = _.first(parsed);
                             citation.entryType = parsed.entryType || undefined;
-                            Object.keys(parsed.entryTags).forEach(key => {
+                            Object.keys(parsed.entryTags).forEach((key) => {
                                 citation.fields[key.toLowerCase()] = parsed.entryTags[key];
                             });
                         }
@@ -128,7 +128,7 @@ export default {
                     }
                 });
             })
-            .catch(e => {
+            .catch((e) => {
                 console.error(e);
             });
     },
@@ -148,17 +148,21 @@ export default {
                     (fields.volume ? fields.volume : "") +
                     (fields.number ? ` (${fields.number})` : "") +
                     (pages ? `, ${pages}` : "");
-                ref = `${authorsAndYear +
+                ref = `${
+                    authorsAndYear +
                     this.asSentence(title) +
                     (fields.journal ? `In <em>${fields.journal}, ` : "") +
                     this.asSentence(volume) +
-                    this.asSentence(fields.address)}</em>`;
+                    this.asSentence(fields.address)
+                }</em>`;
             } else if (entryType === "inproceedings" || entryType === "proceedings") {
-                ref = `${authorsAndYear +
+                ref = `${
+                    authorsAndYear +
                     this.asSentence(title) +
                     (fields.booktitle ? `In <em>${fields.booktitle}, ` : "") +
                     (pages || "") +
-                    (address ? `, ${address}` : "")}.</em>`;
+                    (address ? `, ${address}` : "")
+                }.</em>`;
             } else if (entryType === "mastersthesis" || entryType === "phdthesis") {
                 ref =
                     authorsAndYear +
@@ -220,8 +224,8 @@ export default {
         },
         toggleViewRender() {
             this.viewRender = !this.viewRender;
-        }
-    }
+        },
+    },
 };
 </script>
 <style>
diff --git a/client/galaxy/scripts/components/Common/DelayedInput.vue b/client/galaxy/scripts/components/Common/DelayedInput.vue
index f8ec55fc4052..a6fee0ab9509 100644
--- a/client/galaxy/scripts/components/Common/DelayedInput.vue
+++ b/client/galaxy/scripts/components/Common/DelayedInput.vue
@@ -30,35 +30,35 @@ library.add(faTimesCircle);
 
 export default {
     components: {
-        FontAwesomeIcon
+        FontAwesomeIcon,
     },
     props: {
         query: {
-            type: String
+            type: String,
         },
         loading: {
-            type: Boolean
+            type: Boolean,
         },
         placeholder: {
             type: String,
-            default: "Enter your search term here."
+            default: "Enter your search term here.",
         },
         delay: {
             type: Number,
-            default: 1000
-        }
+            default: 1000,
+        },
     },
     data() {
         return {
             queryInput: null,
             queryTimer: null,
-            queryCurrent: null
+            queryCurrent: null,
         };
     },
     watch: {
         query(queryNew) {
             this.setQuery(queryNew);
-        }
+        },
     },
     methods: {
         clearTimer() {
@@ -82,7 +82,7 @@ export default {
                 this.queryCurrent = this.queryInput = queryNew;
                 this.$emit("onChange", this.queryCurrent);
             }
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Common/Tags.vue b/client/galaxy/scripts/components/Common/Tags.vue
index dc997330135b..3b23df71d719 100644
--- a/client/galaxy/scripts/components/Common/Tags.vue
+++ b/client/galaxy/scripts/components/Common/Tags.vue
@@ -5,20 +5,20 @@
 import StatelessTags from "components/Tags/StatelessTags";
 export default {
     components: {
-        StatelessTags
+        StatelessTags,
     },
     props: {
         index: {
-            type: Number
+            type: Number,
         },
         tags: {
-            type: Array
-        }
+            type: Array,
+        },
     },
     methods: {
         onInput(tags) {
             this.$emit("input", tags, this.index);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/DataDialog/DataDialog.test.js b/client/galaxy/scripts/components/DataDialog/DataDialog.test.js
index 7b53ef1ea654..af79e6e9d816 100644
--- a/client/galaxy/scripts/components/DataDialog/DataDialog.test.js
+++ b/client/galaxy/scripts/components/DataDialog/DataDialog.test.js
@@ -11,7 +11,7 @@ const mockOptions = {
     host: "host",
     root: "root",
     history: "history",
-    modalStatic: true
+    modalStatic: true,
 };
 
 describe("model.js", () => {
@@ -92,7 +92,7 @@ describe("services.js/Services", () => {
             hid: 1,
             id: 1,
             history_id: 0,
-            name: "name_1"
+            name: "name_1",
         };
         const services = new Services(mockOptions);
         const items = services.getItems(rawData);
@@ -111,19 +111,19 @@ describe("DataDialog.vue", () => {
             id: 1,
             hid: 1,
             name: "dataset_1",
-            history_content_type: "dataset"
+            history_content_type: "dataset",
         },
         {
             id: 2,
             name: "dataset_2",
-            type: "file"
+            type: "file",
         },
         {
             id: 3,
             hid: 3,
             name: "collection_1",
-            history_content_type: "dataset_collection"
-        }
+            history_content_type: "dataset_collection",
+        },
     ];
 
     const mockServices = class {
@@ -144,7 +144,7 @@ describe("DataDialog.vue", () => {
         wrapper = mount(DataDialog, {
             propsData: mockOptions,
             attachToDocument: true,
-            localVue
+            localVue,
         });
     });
 
diff --git a/client/galaxy/scripts/components/DataDialog/DataDialog.vue b/client/galaxy/scripts/components/DataDialog/DataDialog.vue
index f98988239723..f7dd42fa8fa1 100644
--- a/client/galaxy/scripts/components/DataDialog/DataDialog.vue
+++ b/client/galaxy/scripts/components/DataDialog/DataDialog.vue
@@ -52,32 +52,32 @@ export default {
     props: {
         multiple: {
             type: Boolean,
-            default: false
+            default: false,
         },
         format: {
             type: String,
-            default: "download"
+            default: "download",
         },
         library: {
             type: Boolean,
-            default: true
+            default: true,
         },
         root: {
             type: String,
-            required: true
+            required: true,
         },
         host: {
             type: String,
-            required: true
+            required: true,
         },
         history: {
             type: String,
-            required: true
+            required: true,
         },
         modalStatic: {
             type: Boolean,
-            default: false
-        }
+            default: false,
+        },
     },
     data() {
         return {
@@ -87,10 +87,10 @@ export default {
             modalShow: true,
             optionsShow: false,
             undoShow: false,
-            hasValue: false
+            hasValue: false,
         };
     },
-    created: function() {
+    created: function () {
         this.services = new Services({ root: this.root, host: this.host });
         this.urlTracker = new UrlTracker(this.getHistoryUrl());
         this.model = new Model({ multiple: this.multiple, format: this.format });
@@ -98,7 +98,7 @@ export default {
     },
     methods: {
         /** Returns the default url i.e. the url of the current history **/
-        getHistoryUrl: function() {
+        getHistoryUrl: function () {
             return `${this.root}api/histories/${this.history}/contents?deleted=false`;
         },
         /** Add highlighting for record variations, i.e. datasets vs. libraries/collections **/
@@ -112,7 +112,7 @@ export default {
             }
         },
         /** Collects selected datasets in value array **/
-        clicked: function(record) {
+        clicked: function (record) {
             if (record.isLeaf) {
                 this.model.add(record);
                 this.hasValue = this.model.count() > 0;
@@ -126,34 +126,34 @@ export default {
             }
         },
         /** Called when selection is complete, values are formatted and parsed to external callback **/
-        finalize: function() {
+        finalize: function () {
             const results = this.model.finalize();
             this.modalShow = false;
             this.callback(results);
         },
         /** Performs server request to retrieve data records **/
-        load: function(url) {
+        load: function (url) {
             url = this.urlTracker.getUrl(url);
             this.filter = null;
             this.optionsShow = false;
             this.undoShow = !this.urlTracker.atRoot();
             this.services
                 .get(url)
-                .then(items => {
+                .then((items) => {
                     if (this.library && this.urlTracker.atRoot()) {
                         items.unshift({
                             label: "Data Libraries",
-                            url: `${this.root}api/libraries`
+                            url: `${this.root}api/libraries`,
                         });
                     }
                     this.items = items;
                     this.formatRows();
                     this.optionsShow = true;
                 })
-                .catch(errorMessage => {
+                .catch((errorMessage) => {
                     this.errorMessage = errorMessage;
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/DataDialog/model.js b/client/galaxy/scripts/components/DataDialog/model.js
index 5163a01f4698..b704f2266ca3 100644
--- a/client/galaxy/scripts/components/DataDialog/model.js
+++ b/client/galaxy/scripts/components/DataDialog/model.js
@@ -35,7 +35,7 @@ export class Model {
     /** Finalizes the results from added records **/
     finalize() {
         let results = [];
-        Object.values(this.values).forEach(v => {
+        Object.values(this.values).forEach((v) => {
             let value = null;
             if (this.format) {
                 value = v[this.format];
diff --git a/client/galaxy/scripts/components/DataDialog/services.js b/client/galaxy/scripts/components/DataDialog/services.js
index 7b260f8988fa..20027162c2db 100644
--- a/client/galaxy/scripts/components/DataDialog/services.js
+++ b/client/galaxy/scripts/components/DataDialog/services.js
@@ -11,11 +11,11 @@ export class Services {
         return new Promise((resolve, reject) => {
             axios
                 .get(url)
-                .then(response => {
+                .then((response) => {
                     const items = this.getItems(response.data);
                     resolve(items);
                 })
-                .catch(e => {
+                .catch((e) => {
                     let errorMessage = "Request failed.";
                     if (e.response) {
                         errorMessage = e.response.data.err_msg || `${e.response.statusText} (${e.response.status})`;
@@ -32,7 +32,7 @@ export class Services {
         while (stack.length > 0) {
             const root = stack.pop();
             if (Array.isArray(root)) {
-                root.forEach(element => {
+                root.forEach((element) => {
                     stack.push(element);
                 });
             } else if (root.elements) {
diff --git a/client/galaxy/scripts/components/Dataset/DatasetHistory.vue b/client/galaxy/scripts/components/Dataset/DatasetHistory.vue
index 24cf43101523..02051c3e1d63 100644
--- a/client/galaxy/scripts/components/Dataset/DatasetHistory.vue
+++ b/client/galaxy/scripts/components/Dataset/DatasetHistory.vue
@@ -8,13 +8,13 @@ import { mapGetters } from "vuex";
 
 export default {
     props: {
-        item: Object
+        item: Object,
     },
     computed: {
         ...mapGetters(["getHistoryNameById"]),
         historyName() {
             return this.getHistoryNameById(this.item.history_id);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Dataset/DatasetList.vue b/client/galaxy/scripts/components/Dataset/DatasetList.vue
index 510ab721a861..285c75d31d44 100644
--- a/client/galaxy/scripts/components/Dataset/DatasetList.vue
+++ b/client/galaxy/scripts/components/Dataset/DatasetList.vue
@@ -48,7 +48,7 @@ export default {
         LoadingSpan,
         DelayedInput,
         UtcDate,
-        Tags
+        Tags,
     },
     data() {
         return {
@@ -57,31 +57,31 @@ export default {
             fields: [
                 {
                     key: "name",
-                    sortable: true
+                    sortable: true,
                 },
                 {
                     key: "tags",
-                    sortable: false
+                    sortable: false,
                 },
                 {
                     label: "History",
                     key: "history_id",
-                    sortable: true
+                    sortable: true,
                 },
                 {
                     key: "extension",
-                    sortable: true
+                    sortable: true,
                 },
                 {
                     label: "Updated",
                     key: "update_time",
-                    sortable: true
+                    sortable: true,
                 },
                 {
                     key: "context",
                     label: "",
-                    sortable: false
-                }
+                    sortable: false,
+                },
             ],
             query: "",
             limit: 50,
@@ -91,7 +91,7 @@ export default {
             loading: true,
             message: null,
             messageVariant: null,
-            rows: []
+            rows: [],
         };
     },
     computed: {
@@ -103,7 +103,7 @@ export default {
         },
         showMessage() {
             return !!this.message;
-        }
+        },
     },
     created() {
         this.fetchHistories();
@@ -121,9 +121,9 @@ export default {
                     sortBy: this.sortBy,
                     sortDesc: this.sortDesc,
                     offset: this.offset,
-                    limit: this.limit
+                    limit: this.limit,
                 })
-                .then(datasets => {
+                .then((datasets) => {
                     if (concat) {
                         this.rows = this.rows.concat(datasets);
                     } else {
@@ -131,7 +131,7 @@ export default {
                     }
                     this.loading = false;
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.error = error;
                 });
         },
@@ -142,10 +142,10 @@ export default {
             const history_id = history.model.id;
             this.services
                 .copyDataset(dataset_id, history_id)
-                .then(response => {
+                .then((response) => {
                     history.loadCurrentHistory();
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.onError(error);
                 });
         },
@@ -153,17 +153,17 @@ export default {
             const Galaxy = getGalaxyInstance();
             this.services
                 .setHistory(item.history_id)
-                .then(history => {
+                .then((history) => {
                     Galaxy.currHistoryPanel.loadCurrentHistory();
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.onError(error);
                 });
         },
         onTags(tags, index) {
             const item = this.rows[index];
             item.tags = tags;
-            this.services.updateTags(item.id, "HistoryDatasetAssociation", tags).catch(error => {
+            this.services.updateTags(item.id, "HistoryDatasetAssociation", tags).catch((error) => {
                 this.onError(error);
             });
         },
@@ -193,7 +193,7 @@ export default {
         onError(message) {
             this.message = message;
             this.messageVariant = "danger";
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Dataset/DatasetName.vue b/client/galaxy/scripts/components/Dataset/DatasetName.vue
index 136eb43e75fd..2abd8318b0cc 100644
--- a/client/galaxy/scripts/components/Dataset/DatasetName.vue
+++ b/client/galaxy/scripts/components/Dataset/DatasetName.vue
@@ -42,7 +42,7 @@ Vue.use(BootstrapVue);
 
 export default {
     props: {
-        item: Object
+        item: Object,
     },
     computed: {
         getName() {
@@ -53,7 +53,7 @@ export default {
         },
         isPaused() {
             return this.item.state === "paused";
-        }
+        },
     },
     methods: {
         copyDataset(item) {
@@ -61,8 +61,8 @@ export default {
         },
         showDataset(item) {
             this.$emit("showDataset", this.item);
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/Dataset/services.js b/client/galaxy/scripts/components/Dataset/services.js
index 5d885189288a..4d836372d5f9 100644
--- a/client/galaxy/scripts/components/Dataset/services.js
+++ b/client/galaxy/scripts/components/Dataset/services.js
@@ -36,7 +36,7 @@ export class Services {
             const response = await axios.post(url, {
                 type: "dataset",
                 source: "hda",
-                content: dataset_id
+                content: dataset_id,
             });
             return response.data;
         } catch (e) {
@@ -60,7 +60,7 @@ export class Services {
             const response = await axios.put(url, {
                 item_id: item_id,
                 item_class: item_class,
-                item_tags: item_tags
+                item_tags: item_tags,
             });
             return response.data;
         } catch (e) {
diff --git a/client/galaxy/scripts/components/DisplayStructured.vue b/client/galaxy/scripts/components/DisplayStructured.vue
index 9fdc6cda8d87..a9403fb24a9e 100644
--- a/client/galaxy/scripts/components/DisplayStructured.vue
+++ b/client/galaxy/scripts/components/DisplayStructured.vue
@@ -20,18 +20,18 @@ export default {
     props: {
         id: {
             type: String,
-            required: false
-        }
+            required: false,
+        },
     },
     data() {
         return {
             historyTemplate: "",
             historyJSON: {},
             // TODO: Error message standardization -- use bootstrap-vue component or the like.
-            errorMessages: []
+            errorMessages: [],
         };
     },
-    created: function() {
+    created: function () {
         const historyId = this.id;
         let url = "";
         if (historyId !== undefined && historyId !== "" && historyId !== null) {
@@ -42,52 +42,52 @@ export default {
         this.ajaxCall(url);
     },
     methods: {
-        ajaxCall: function(url) {
+        ajaxCall: function (url) {
             axios
                 .get(url)
-                .then(response => {
+                .then((response) => {
                     this._updateHistoryData(response);
                 })
-                .catch(e => {
+                .catch((e) => {
                     console.error(e);
                     this.errorMessages.push(
                         "Error fetching history data -- reload the page to retry this request.  Please contact an administrator if the problem persists."
                     );
                 });
         },
-        _updateHistoryData: function(response) {
+        _updateHistoryData: function (response) {
             const historyItems = response.data;
             this.historyTemplate = historyItems.template;
             this.historyJSON = historyItems.history_json;
         },
-        makeHistoryView: function(historyDict) {
-            window.hdas = historyDict.map(hda => {
+        makeHistoryView: function (historyDict) {
+            window.hdas = historyDict.map((hda) => {
                 const Galaxy = getGalaxyInstance();
                 return new HDAListItemEdit.HDAListItemEdit({
                     model: new HDAModel.HistoryDatasetAssociation(hda),
                     el: $("#hda-" + hda.id),
                     linkTarget: "galaxy_main",
                     purgeAllowed: Galaxy.config.allow_user_dataset_purge,
-                    logger: Galaxy.logger
+                    logger: Galaxy.logger,
                 }).render(0);
             });
             // toggle the body section of each item in the structure
-            $(function() {
+            $(function () {
                 $(".workflow, .tool").each((index, element) => {
                     const body = $(element).children(".body");
                     $(element)
                         .children(".header")
-                        .click(e => {
+                        .click((e) => {
                             body.toggle();
                         })
                         .addClass("clickable");
                 });
             });
-        }
+        },
     },
-    updated: function() {
+    updated: function () {
         this.makeHistoryView(this.historyJSON);
-    }
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/GalaxyLoader.vue b/client/galaxy/scripts/components/GalaxyLoader.vue
index 0e9d7bb6c402..fe2c4298471a 100644
--- a/client/galaxy/scripts/components/GalaxyLoader.vue
+++ b/client/galaxy/scripts/components/GalaxyLoader.vue
@@ -15,17 +15,17 @@ export default {
     props: {
         style: {
             type: String,
-            default: "light"
+            default: "light",
         },
         size: {
             type: Number,
-            default: 100
+            default: 100,
         },
         center: {
             type: Boolean,
-            default: false
-        }
-    }
+            default: false,
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/History/HistoryDropdown.vue b/client/galaxy/scripts/components/History/HistoryDropdown.vue
index becdb4169f60..7400e8a034ef 100644
--- a/client/galaxy/scripts/components/History/HistoryDropdown.vue
+++ b/client/galaxy/scripts/components/History/HistoryDropdown.vue
@@ -35,13 +35,13 @@ export default {
         },
         urlSharing() {
             return `${getAppRoot()}histories/sharing?id=${this.history.id}`;
-        }
+        },
     },
     methods: {
         onSwitch() {
             const Galaxy = getGalaxyInstance();
             Galaxy.currHistoryPanel.switchToHistory(this.history.id);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/HistoryImport.vue b/client/galaxy/scripts/components/HistoryImport.vue
index 042b5b7b91e2..5a3314bd1124 100644
--- a/client/galaxy/scripts/components/HistoryImport.vue
+++ b/client/galaxy/scripts/components/HistoryImport.vue
@@ -22,16 +22,16 @@ export default {
         return {
             sourceFile: null,
             sourceURL: null,
-            errorMessage: null
+            errorMessage: null,
         };
     },
     computed: {
         hasErrorMessage() {
             return this.errorMessage != null;
-        }
+        },
     },
     methods: {
-        submit: function(ev) {
+        submit: function (ev) {
             ev.preventDefault();
             if (!this.sourceFile && !this.sourceURL) {
                 this.errorMessage = "You must provide a history archive URL or file.";
@@ -41,17 +41,17 @@ export default {
                 formData.append("archive_source", this.sourceURL);
                 axios
                     .post(`${getAppRoot()}api/histories`, formData)
-                    .then(response => {
+                    .then((response) => {
                         window.location = `${getAppRoot()}histories/list?message=${
                             response.data.message
                         }&status=success`;
                     })
-                    .catch(error => {
+                    .catch((error) => {
                         const message = error.response.data && error.response.data.err_msg;
                         this.errorMessage = message || "Import failed for an unknown reason.";
                     });
             }
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/HistoryView.vue b/client/galaxy/scripts/components/HistoryView.vue
index acb4e13b4901..17139e4066bb 100644
--- a/client/galaxy/scripts/components/HistoryView.vue
+++ b/client/galaxy/scripts/components/HistoryView.vue
@@ -47,45 +47,45 @@ export default {
     props: {
         id: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
             historyData: {},
             historyHistory: {},
             // TODO: Pick a standard messaging convention and use a child component for it here.
-            errorMessages: []
+            errorMessages: [],
         };
     },
-    created: function() {
+    created: function () {
         const url = getAppRoot() + "history/view/" + this.id;
         this.ajaxCall(url, this.updateHistoryView);
     },
     methods: {
-        ajaxCall: function(url, callBack) {
+        ajaxCall: function (url, callBack) {
             axios
                 .get(url)
-                .then(response => {
+                .then((response) => {
                     callBack(response);
                 })
-                .catch(e => {
+                .catch((e) => {
                     this.showError(
                         "Error fetching histories -- reload the page to retry this request.  Please contact an administrator if the problem persists.",
                         e
                     );
                 });
         },
-        updateHistoryView: function(response) {
+        updateHistoryView: function (response) {
             this.historyData = response.data;
             this.historyHistory = response.data.history;
         },
-        showError: function(errorMsg, verbose) {
+        showError: function (errorMsg, verbose) {
             console.error(verbose);
             this.errorMessages.push(errorMsg);
         },
-        makeHistoryView: function(history) {
-            $(function() {
+        makeHistoryView: function (history) {
+            $(function () {
                 const options = {
                     hasMasthead: history.use_panels ? "true" : "false",
                     userIsOwner: history.user_is_owner ? "true" : "false",
@@ -95,7 +95,7 @@ export default {
                     showHiddenJson: history.show_hidden,
                     initialModeDeleted: history.show_deleted ? "showing_deleted" : "not_showing_deleted",
                     initialModeHidden: history.show_hidden ? "showing_hidden" : "not_showing_hidden",
-                    allowUserDatasetPurge: history.allow_user_dataset_purge ? "true" : "false"
+                    allowUserDatasetPurge: history.allow_user_dataset_purge ? "true" : "false",
                 };
                 options.viewToUse = options.userIsOwner
                     ? { location: "mvc/history/history-view-edit", className: "HistoryViewEdit" }
@@ -103,24 +103,24 @@ export default {
                 HistoryView.historyEntry(options);
             });
         },
-        showStructure: function() {
+        showStructure: function () {
             const Galaxy = getGalaxyInstance();
             const displayStructureInstance = Vue.extend(DisplayStructure);
             const mountView = document.createElement("div");
             Galaxy.page.center.display(mountView);
             new displayStructureInstance({ propsData: { id: QueryStringParsing.get("id") } }).$mount(mountView);
         },
-        switchHistory: function() {
+        switchHistory: function () {
             const url = getAppRoot() + "history/switch_to_history?hist_id=" + this.historyHistory["id"];
             this.ajaxCall(url, this.reloadPage);
         },
-        reloadPage: function() {
+        reloadPage: function () {
             window.location.reload();
-        }
+        },
     },
-    updated: function() {
+    updated: function () {
         this.makeHistoryView(this.historyData);
-    }
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.test.js b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.test.js
index e904c8030d9f..0d8c93f9c8c2 100644
--- a/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.test.js
+++ b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.test.js
@@ -9,7 +9,7 @@ import axios from "axios";
 
 describe("ToolsView/ToolsView.vue", () => {
     const localVue = createLocalVue();
-    localVue.filter("localize", value => _l(value));
+    localVue.filter("localize", (value) => _l(value));
     let wrapper, emitted, axiosMock;
 
     beforeEach(async () => {
@@ -18,10 +18,10 @@ describe("ToolsView/ToolsView.vue", () => {
             computed: {
                 currentHistory() {
                     return {
-                        loadCurrentHistory() {}
+                        loadCurrentHistory() {},
                     };
-                }
-            }
+                },
+            },
         });
         emitted = wrapper.emitted();
         axiosMock.onGet("/api/entry_points?running=true").reply(200, testInteractiveToolsResponse);
@@ -46,7 +46,7 @@ describe("ToolsView/ToolsView.vue", () => {
         }
 
         const toolId = testInteractiveToolsResponse[0].id;
-        const tool = wrapper.vm.activeInteractiveTools.find(tool => tool.id === toolId);
+        const tool = wrapper.vm.activeInteractiveTools.find((tool) => tool.id === toolId);
 
         assert(checkIfExists("#link-", toolId) === true, "tool is not rendered!");
         // ensure that the tool is not marked
@@ -65,7 +65,7 @@ describe("ToolsView/ToolsView.vue", () => {
         await Vue.nextTick();
         await Vue.nextTick();
 
-        const toolExists = wrapper.vm.activeInteractiveTools.includes(tool => tool.id === toolId);
+        const toolExists = wrapper.vm.activeInteractiveTools.includes((tool) => tool.id === toolId);
         // ensure that the tool was deleted from the list
         assert(toolExists === false, "tool was not deleted from the list!");
         assert(checkIfExists("#link-", toolId) === false, "tool is rendered after deletion!");
diff --git a/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue
index fb5ee6b0b1be..543632dc7ba7 100644
--- a/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue
+++ b/client/galaxy/scripts/components/InteractiveTools/InteractiveTools.vue
@@ -79,7 +79,7 @@ Vue.use(BootstrapVue);
 
 export default {
     components: {
-        UtcDate
+        UtcDate,
     },
     data() {
         return {
@@ -87,34 +87,34 @@ export default {
             fields: [
                 {
                     label: "",
-                    key: "checkbox"
+                    key: "checkbox",
                 },
                 {
                     label: "Name",
                     key: "name",
-                    sortable: true
+                    sortable: true,
                 },
                 {
                     label: "Job Info",
                     key: "job_info",
-                    sortable: true
+                    sortable: true,
                 },
                 {
                     label: "Created",
                     key: "created_time",
-                    sortable: true
+                    sortable: true,
                 },
                 {
                     label: "Last Updated",
                     key: "last_updated",
-                    sortable: true
-                }
+                    sortable: true,
+                },
             ],
             filter: "",
             message: null,
             messageVariant: null,
             nInteractiveTools: 0,
-            activeInteractiveTools: []
+            activeInteractiveTools: [],
         };
     },
     computed: {
@@ -122,7 +122,7 @@ export default {
             return this.nInteractiveTools === 0 && this.filter && !this.isActiveToolsListEmpty;
         },
         isCheckboxMarked() {
-            return this.activeInteractiveTools.some(tool => tool.marked);
+            return this.activeInteractiveTools.some((tool) => tool.marked);
         },
         isActiveToolsListEmpty() {
             return this.activeInteractiveTools.length === 0;
@@ -132,7 +132,7 @@ export default {
         },
         currentHistory() {
             return getGalaxyInstance().currHistoryPanel;
-        }
+        },
     },
     created() {
         this.root = getAppRoot();
@@ -144,29 +144,29 @@ export default {
             this.filter = "";
             this.services
                 .getActiveInteractiveTools()
-                .then(activeInteractiveTools => {
+                .then((activeInteractiveTools) => {
                     this.activeInteractiveTools = activeInteractiveTools;
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.error = error;
                 });
         },
-        filtered: function(items) {
+        filtered: function (items) {
             this.nInteractiveTools = items.length;
         },
         stopInteractiveToolSession() {
-            const idsToStop = this.activeInteractiveTools.filter(tool => tool.marked).map(tool => tool.id);
-            this.services.stopInteractiveTool(idsToStop).then(response => {
+            const idsToStop = this.activeInteractiveTools.filter((tool) => tool.marked).map((tool) => tool.id);
+            this.services.stopInteractiveTool(idsToStop).then((response) => {
                 if (response.status === "ok") this.messageVariant = "success";
                 else this.messageVariant = "danger";
                 this.message = response.message;
-                this.activeInteractiveTools = this.activeInteractiveTools.filter(tool => !tool.marked);
+                this.activeInteractiveTools = this.activeInteractiveTools.filter((tool) => !tool.marked);
                 this.currentHistory.loadCurrentHistory();
             });
         },
         createId(tagLabel, id) {
             return tagLabel + "-" + id;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/InteractiveTools/services.js b/client/galaxy/scripts/components/InteractiveTools/services.js
index 9003754f871d..48a358872cf2 100644
--- a/client/galaxy/scripts/components/InteractiveTools/services.js
+++ b/client/galaxy/scripts/components/InteractiveTools/services.js
@@ -21,7 +21,7 @@ export class Services {
         const url = `${this.root}interactivetool/list`;
         const formData = new FormData();
         formData.append("operation", "stop");
-        ids.forEach(id => formData.append("id", id));
+        ids.forEach((id) => formData.append("id", id));
         const response = await axios.post(url, formData);
         return response.data;
     }
diff --git a/client/galaxy/scripts/components/JobMetrics/JobMetrics.test.js b/client/galaxy/scripts/components/JobMetrics/JobMetrics.test.js
index 554982bc016a..0a97c76206ea 100644
--- a/client/galaxy/scripts/components/JobMetrics/JobMetrics.test.js
+++ b/client/galaxy/scripts/components/JobMetrics/JobMetrics.test.js
@@ -25,12 +25,12 @@ describe("JobMetrics/JobMetrics.vue", () => {
 
     it("should not render a div if no plugins found in store", async () => {
         const propsData = {
-            jobId: JOB_ID
+            jobId: JOB_ID,
         };
         const wrapper = mount(JobMetrics, {
             store: testStore,
             propsData,
-            localVue
+            localVue,
         });
         await wrapper.vm.$nextTick();
         expect(wrapper.isEmpty()).to.equals(true);
@@ -38,18 +38,18 @@ describe("JobMetrics/JobMetrics.vue", () => {
 
     it("should group plugins by type", async () => {
         const propsData = {
-            jobId: JOB_ID
+            jobId: JOB_ID,
         };
         const metricsResponse = [
             { plugin: "core", title: "runtime", value: 145 },
             { plugin: "core", title: "memory", value: 146 },
-            { plugin: "extended", title: "awesomeness", value: 42 }
+            { plugin: "extended", title: "awesomeness", value: 42 },
         ];
         axiosMock.onGet(`/api/jobs/${JOB_ID}/metrics`).reply(200, metricsResponse);
         const wrapper = mount(JobMetrics, {
             store: testStore,
             propsData,
-            localVue
+            localVue,
         });
         // Wait for axios and rendering.
         await flushPromises();
@@ -60,19 +60,9 @@ describe("JobMetrics/JobMetrics.vue", () => {
         // Three metrics, begin metrics for two plugins
         const metricsTables = wrapper.findAll(".metrics_plugin");
         expect(metricsTables.length).to.equals(2);
-        expect(
-            metricsTables
-                .at(0)
-                .find(".metrics_plugin_title")
-                .text()
-        ).to.equals("core");
+        expect(metricsTables.at(0).find(".metrics_plugin_title").text()).to.equals("core");
         expect(metricsTables.at(0).findAll("tr").length).to.equals(2);
-        expect(
-            metricsTables
-                .at(1)
-                .find(".metrics_plugin_title")
-                .text()
-        ).to.equals("extended");
+        expect(metricsTables.at(1).find(".metrics_plugin_title").text()).to.equals("extended");
         expect(metricsTables.at(1).findAll("tr").length).to.equals(1);
     });
 });
diff --git a/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue b/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue
index 7fc4cd3f00c4..f0bcd2702588 100644
--- a/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue
+++ b/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue
@@ -22,24 +22,24 @@ import { mapGetters } from "vuex";
 export default {
     props: {
         jobId: {
-            type: String
+            type: String,
         },
         datasetId: {
-            type: String
+            type: String,
         },
         datasetType: {
             type: String,
-            default: "hda"
+            default: "hda",
         },
         includeTitle: {
             type: Boolean,
-            default: true
-        }
+            default: true,
+        },
     },
     data() {
         return {};
     },
-    created: function() {
+    created: function () {
         if (this.jobId) {
             this.fetchJobMetricsForJobId(this.jobId);
         } else {
@@ -48,17 +48,17 @@ export default {
     },
     computed: {
         ...mapGetters(["getJobMetricsByDatasetId", "getJobMetricsByJobId"]),
-        jobMetrics: function() {
+        jobMetrics: function () {
             if (this.jobId) {
                 return this.getJobMetricsByJobId(this.jobId);
             } else {
                 return this.getJobMetricsByDatasetId(this.datasetId, this.datasetType);
             }
         },
-        metricsByPlugins: function() {
+        metricsByPlugins: function () {
             const metricsByPlugins = {};
             const metrics = this.jobMetrics;
-            metrics.forEach(metric => {
+            metrics.forEach((metric) => {
                 if (!(metric.plugin in metricsByPlugins)) {
                     metricsByPlugins[metric.plugin] = {};
                 }
@@ -67,12 +67,12 @@ export default {
             });
             return metricsByPlugins;
         },
-        orderedPlugins: function() {
+        orderedPlugins: function () {
             return Object.keys(this.metricsByPlugins).sort();
-        }
+        },
     },
     methods: {
-        ...mapCacheActions(["fetchJobMetricsForDatasetId", "fetchJobMetricsForJobId"])
-    }
+        ...mapCacheActions(["fetchJobMetricsForDatasetId", "fetchJobMetricsForJobId"]),
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/JobParameters/JobParameters.vue b/client/galaxy/scripts/components/JobParameters/JobParameters.vue
index 2ce3d6dfa996..d168c49db13c 100644
--- a/client/galaxy/scripts/components/JobParameters/JobParameters.vue
+++ b/client/galaxy/scripts/components/JobParameters/JobParameters.vue
@@ -53,27 +53,27 @@ Vue.use(BootstrapVue);
 export default {
     props: {
         jobId: {
-            type: String
+            type: String,
         },
         datasetId: {
-            type: String
+            type: String,
         },
         datasetType: {
             type: String,
-            default: "hda"
+            default: "hda",
         },
         includeTitle: {
             type: Boolean,
-            default: true
-        }
+            default: true,
+        },
     },
     data() {
         return {
             parameters: [],
-            hasParameterErrors: false
+            hasParameterErrors: false,
         };
     },
-    created: function() {
+    created: function () {
         let url;
         if (this.jobId) {
             url = `${getAppRoot()}api/jobs/${this.jobId}/parameters_display`;
@@ -83,31 +83,31 @@ export default {
         this.ajaxCall(url);
     },
     computed: {
-        anyNotes: function() {
+        anyNotes: function () {
             let hasNotes = false;
-            this.parameters.forEach(parameter => {
+            this.parameters.forEach((parameter) => {
                 hasNotes = hasNotes || parameter.notes;
             });
             return hasNotes;
-        }
+        },
     },
     methods: {
-        appRoot: function() {
+        appRoot: function () {
             return getAppRoot();
         },
-        ajaxCall: function(url) {
+        ajaxCall: function (url) {
             axios
                 .get(url)
-                .then(response => response.data)
-                .then(data => {
+                .then((response) => response.data)
+                .then((data) => {
                     this.hasParameterErrors = data.has_parameter_errors;
                     this.parameters = data.parameters;
                 })
-                .catch(e => {
+                .catch((e) => {
                     console.error(e);
                 });
-        }
-    }
+        },
+    },
 };
 </script>
 <style scoped>
diff --git a/client/galaxy/scripts/components/JobStates/CollectionJobStates.vue b/client/galaxy/scripts/components/JobStates/CollectionJobStates.vue
index 246bcf46c673..5839d9003c9f 100644
--- a/client/galaxy/scripts/components/JobStates/CollectionJobStates.vue
+++ b/client/galaxy/scripts/components/JobStates/CollectionJobStates.vue
@@ -28,10 +28,10 @@ import ProgressBar from "components/ProgressBar";
 export default {
     props: {
         collection: { type: Object, required: true }, // backbone model
-        jobStatesSummary: { required: true }
+        jobStatesSummary: { required: true },
     },
     components: {
-        ProgressBar
+        ProgressBar,
     },
     mixins: [mixin],
     computed: {
@@ -54,7 +54,7 @@ export default {
             var jobCount = this.jobCount;
             var errorCount = this.jobStatesSummary.numInError();
             return `a ${this.collectionTypeDescription} with ${errorCount} / ${jobCount} jobs in error`;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/JobStates/mixin.js b/client/galaxy/scripts/components/JobStates/mixin.js
index a350c9fdcd18..9d9652bd3721 100644
--- a/client/galaxy/scripts/components/JobStates/mixin.js
+++ b/client/galaxy/scripts/components/JobStates/mixin.js
@@ -37,7 +37,7 @@ export default {
         },
         otherPercent() {
             return 1.0 - this.okPercent - this.runningPercent - this.errorPercent;
-        }
+        },
     },
     methods: {
         countStates(states) {
@@ -48,6 +48,6 @@ export default {
                 }
             }
             return count;
-        }
-    }
+        },
+    },
 };
diff --git a/client/galaxy/scripts/components/LoadingSpan.vue b/client/galaxy/scripts/components/LoadingSpan.vue
index 732bf12e62df..0f61f08d9eed 100644
--- a/client/galaxy/scripts/components/LoadingSpan.vue
+++ b/client/galaxy/scripts/components/LoadingSpan.vue
@@ -10,17 +10,17 @@ export default {
         classes: {
             type: String,
             required: false,
-            default: null
+            default: null,
         },
         message: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     computed: {
         spinnerClasses() {
             return ["loading-icon", "fa", "fa-spinner", "fa-spin"].concat(this.classes ? this.classes.split(" ") : []);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Markdown/Markdown.vue b/client/galaxy/scripts/components/Markdown/Markdown.vue
index 12643fc415c3..6e2b872be04a 100644
--- a/client/galaxy/scripts/components/Markdown/Markdown.vue
+++ b/client/galaxy/scripts/components/Markdown/Markdown.vue
@@ -113,10 +113,10 @@ const RENDER_FUNCTIONS = {
     job_parameters: (action, args, content) => {
         const jobId = args.job_id;
         return `<div class="job-parameters" job_id="${jobId}"></div>`;
-    }
+    },
 };
 
-md.renderer.rules.fence = function(tokens, idx, options, env, slf) {
+md.renderer.rules.fence = function (tokens, idx, options, env, slf) {
     const token = tokens[idx];
     const info = token.info ? token.info.trim() : "";
     const content = token.content;
@@ -142,25 +142,23 @@ function render_fenced_output(tag, objects, idAttr, metadataKey) {
     $("." + tag).each((i, el) => {
         const objectId = $(el).attr(idAttr);
         const meta = objects[objectId][metadataKey];
-        $(el)
-            .find("code")
-            .text(meta);
+        $(el).find("code").text(meta);
     });
 }
 
 export default {
     props: {
         markdownConfig: {
-            type: Object
+            type: Object,
         },
         readOnly: {
             type: Boolean,
-            default: true
+            default: true,
         },
         exportLink: {
             type: String,
-            required: false
-        }
+            required: false,
+        },
     },
     data() {
         return {
@@ -168,17 +166,17 @@ export default {
             historyDatasets: {},
             historyDatasetCollections: {},
             workflows: {},
-            jobs: {}
+            jobs: {},
         };
     },
     computed: {
         effectiveExportLink() {
             const Galaxy = getGalaxyInstance();
             return Galaxy.config.enable_beta_markdown_export ? this.exportLink : null;
-        }
+        },
     },
     watch: {
-        markdownConfig: function(mConfig, oldVal) {
+        markdownConfig: function (mConfig, oldVal) {
             const markdown = mConfig.markdown;
             this.markdownRendered = md.render(markdown);
             this.historyDatasets = mConfig.history_datasets || {};
@@ -222,12 +220,12 @@ export default {
                         el: $(el),
                         linkTarget: "galaxy_main",
                         purgeAllowed: Galaxy.config.allow_user_dataset_purge,
-                        logger: Galaxy.logger
+                        logger: Galaxy.logger,
                     }).render(0);
                 });
             });
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/Markdown/MarkdownEditor.vue b/client/galaxy/scripts/components/Markdown/MarkdownEditor.vue
index e20c5b5bec7c..3660847f991a 100644
--- a/client/galaxy/scripts/components/Markdown/MarkdownEditor.vue
+++ b/client/galaxy/scripts/components/Markdown/MarkdownEditor.vue
@@ -1,5 +1,5 @@
 <template>
-    <div style="display: flex; flex: 1; flex-direction: column">
+    <div style="display: flex; flex: 1; flex-direction: column;">
         <ul class="galaxymark-toolbar" ref="menu" v-if="toolbar">
             <li>
                 <a
@@ -87,28 +87,28 @@ export default {
     props: {
         initialMarkdown: {
             required: true,
-            type: String
+            type: String,
         },
         toolbar: {
             type: Boolean,
-            default: false
+            default: false,
         },
         showMarkdownHelp: {
             // only used if toolbar is True - waiting on a general toolbar refactor
             type: Function,
-            required: false
+            required: false,
         },
         onupdate: {
-            type: Function
-        }
+            type: Function,
+        },
     },
-    data: function() {
+    data: function () {
         return {
-            input: this.initialMarkdown
+            input: this.initialMarkdown,
         };
     },
     methods: {
-        update: _.debounce(function(e) {
+        update: _.debounce(function (e) {
             if (this.onupdate) {
                 this.onupdate(this.input);
             }
@@ -126,14 +126,14 @@ export default {
         },
         _selectDataset(galaxyCall) {
             dialog(
-                response => {
+                (response) => {
                     const datasetId = response.id;
                     this.insertGalaxyMarkdownBlock(`${galaxyCall}(history_dataset_id=${datasetId})`);
                 },
                 {
                     multiple: false,
                     format: null,
-                    library: false // TODO: support?
+                    library: false, // TODO: support?
                 }
             );
         },
@@ -144,18 +144,18 @@ export default {
             this._selectDataset("history_dataset_as_image");
         },
         selectDatasetCollection() {
-            datasetCollectionDialog(response => {
+            datasetCollectionDialog((response) => {
                 this.insertGalaxyMarkdownBlock(
                     `history_dataset_collection_display(history_dataset_collection_id=${response.id})`
                 );
             }, {});
         },
         selectWorkflow() {
-            workflowDialog(response => {
+            workflowDialog((response) => {
                 this.insertGalaxyMarkdownBlock(`workflow_display(workflow_id=${response.id})`);
             }, {});
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/MaskedInput.js b/client/galaxy/scripts/components/MaskedInput.js
index f838bb22cf85..6e0e74166762 100644
--- a/client/galaxy/scripts/components/MaskedInput.js
+++ b/client/galaxy/scripts/components/MaskedInput.js
@@ -7,15 +7,15 @@ export default {
         mask: {
             type: String,
             required: false,
-            default: ""
-        }
+            default: "",
+        },
     },
     computed: {
         masker() {
             return createMask({
-                mask: this.mask
+                mask: this.mask,
             });
-        }
+        },
     },
     methods: {
         getFormatted(value) {
@@ -24,6 +24,6 @@ export default {
                 return this.masker.resolve(result);
             }
             return result;
-        }
-    }
+        },
+    },
 };
diff --git a/client/galaxy/scripts/components/Masthead/index.vue b/client/galaxy/scripts/components/Masthead/index.vue
index f232e2302b09..225459d8afd1 100644
--- a/client/galaxy/scripts/components/Masthead/index.vue
+++ b/client/galaxy/scripts/components/Masthead/index.vue
@@ -32,8 +32,8 @@ export default {
             // bolt the rendered DOM onto the vue component's element
             const backboneDom = galaxy.masthead.render();
             this.$el.appendChild(backboneDom.$el[0]);
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/Masthead/initMasthead.js b/client/galaxy/scripts/components/Masthead/initMasthead.js
index 9df6e15e2305..5eba73b2ecdf 100644
--- a/client/galaxy/scripts/components/Masthead/initMasthead.js
+++ b/client/galaxy/scripts/components/Masthead/initMasthead.js
@@ -11,6 +11,6 @@ export function initMasthead(config, container) {
     return new Component({
         props: Object.keys(config),
         propsData: config,
-        el: container
+        el: container,
     });
 }
diff --git a/client/galaxy/scripts/components/Message.vue b/client/galaxy/scripts/components/Message.vue
index 5779f83ca6cc..de1b0420ab0d 100644
--- a/client/galaxy/scripts/components/Message.vue
+++ b/client/galaxy/scripts/components/Message.vue
@@ -8,12 +8,12 @@ export default {
     props: {
         message: {
             type: String,
-            required: true
+            required: true,
         },
         status: {
             type: String,
-            default: "done"
-        }
-    }
+            default: "done",
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Nametags/Nametag.vue b/client/galaxy/scripts/components/Nametags/Nametag.vue
index 89cfc4a6251a..3fe004fcc3fa 100644
--- a/client/galaxy/scripts/components/Nametags/Nametag.vue
+++ b/client/galaxy/scripts/components/Nametags/Nametag.vue
@@ -7,7 +7,7 @@ import { keyedColorScheme } from "utils/color";
 
 export default {
     props: {
-        tag: { type: String, required: true }
+        tag: { type: String, required: true },
     },
     computed: {
         tagLabel() {
@@ -18,10 +18,10 @@ export default {
             return {
                 "background-color": primary,
                 color: contrasting,
-                "border-color": darker
+                "border-color": darker,
             };
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/Nametags/Nametags.vue b/client/galaxy/scripts/components/Nametags/Nametags.vue
index adb4078a7736..e98ee23b6dcf 100644
--- a/client/galaxy/scripts/components/Nametags/Nametags.vue
+++ b/client/galaxy/scripts/components/Nametags/Nametags.vue
@@ -8,27 +8,27 @@ import { mapActions } from "vuex";
 
 export default {
     components: {
-        Nametag
+        Nametag,
     },
     props: {
         storeKey: { type: String, required: true },
-        tags: { type: Array, required: false, default: () => [] }
+        tags: { type: Array, required: false, default: () => [] },
     },
     computed: {
         // only display tags that start with name:
         nameTags() {
-            return this.$store.getters.getTagsById(this.storeKey).filter(tag => tag.startsWith("name:"));
+            return this.$store.getters.getTagsById(this.storeKey).filter((tag) => tag.startsWith("name:"));
         },
         title() {
             return `${this.nameTags.length} nametags`;
-        }
+        },
     },
     methods: {
-        ...mapActions(["updateTags", "initializeTags"])
+        ...mapActions(["updateTags", "initializeTags"]),
     },
     mounted() {
         this.initializeTags({ key: this.storeKey, tags: this.tags });
-    }
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/PageDisplay/PageDisplay.vue b/client/galaxy/scripts/components/PageDisplay/PageDisplay.vue
index 0f2bc6337669..87b4cd62d631 100644
--- a/client/galaxy/scripts/components/PageDisplay/PageDisplay.vue
+++ b/client/galaxy/scripts/components/PageDisplay/PageDisplay.vue
@@ -9,41 +9,41 @@ import Markdown from "components/Markdown/Markdown.vue";
 
 export default {
     components: {
-        Markdown
+        Markdown,
     },
     props: {
         pageId: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     computed: {
-        dataUrl: function() {
+        dataUrl: function () {
             return getAppRoot() + `api/pages/${this.pageId}`;
         },
-        exportUrl: function() {
+        exportUrl: function () {
             return this.dataUrl + ".pdf";
-        }
+        },
     },
     data() {
         return {
-            markdownConfig: {}
+            markdownConfig: {},
         };
     },
-    created: function() {
+    created: function () {
         this.ajaxCall();
     },
     methods: {
-        ajaxCall: function() {
+        ajaxCall: function () {
             axios
                 .get(this.dataUrl)
-                .then(response => {
+                .then((response) => {
                     this.markdownConfig = { ...response.data, markdown: response.data.content };
                 })
-                .catch(e => {
+                .catch((e) => {
                     console.error(e);
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/PageEditor/PageEditor.vue b/client/galaxy/scripts/components/PageEditor/PageEditor.vue
index f77e804f2596..d1eb0e0dbada 100644
--- a/client/galaxy/scripts/components/PageEditor/PageEditor.vue
+++ b/client/galaxy/scripts/components/PageEditor/PageEditor.vue
@@ -36,29 +36,29 @@ export default {
     props: {
         pageId: {
             required: true,
-            type: String
+            type: String,
         },
         publicUrl: {
             required: true,
-            type: String
+            type: String,
         },
         content: {
-            type: String
+            type: String,
         },
         contentFormat: {
             type: String,
-            default: "html"
+            default: "html",
         },
         title: {
-            type: String
-        }
+            type: String,
+        },
     },
     computed: {},
     methods: {
-        saveContent: function() {
+        saveContent: function () {
             this.$refs.contentEditor.saveContent();
         },
-        viewContent: function() {
+        viewContent: function () {
             // TODO: Future iteration, contentEditor should have an entry point that can decide
             // if it has changed content.
             const r = window.confirm(
@@ -67,11 +67,11 @@ export default {
             if (r === true) {
                 window.location = `${getAppRoot()}${this.publicUrl}`;
             }
-        }
+        },
     },
     components: {
         PageEditorHtml,
-        PageEditorMarkdown
-    }
+        PageEditorMarkdown,
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/PageEditor/PageEditorHtml.vue b/client/galaxy/scripts/components/PageEditor/PageEditorHtml.vue
index a715567a63ab..64e8f71dfc00 100644
--- a/client/galaxy/scripts/components/PageEditor/PageEditorHtml.vue
+++ b/client/galaxy/scripts/components/PageEditor/PageEditorHtml.vue
@@ -51,7 +51,7 @@ var CONTROLS = {
     DIALOG_EMBED_DATASET: "embed_dataset",
     DIALOG_EMBED_WORKFLOW: "embed_workflow",
     DIALOG_EMBED_PAGE: "embed_page",
-    DIALOG_EMBED_VISUALIZATION: "embed_visualization"
+    DIALOG_EMBED_VISUALIZATION: "embed_visualization",
 };
 
 // Based on the dialog type, return a dictionary of information about an item
@@ -103,7 +103,7 @@ function get_item_info(dialog_type) {
         plural: item_plural,
         controller: item_controller,
         iclass: item_class,
-        list_ajax_url: ajax_url
+        list_ajax_url: ajax_url,
     };
 }
 
@@ -114,14 +114,14 @@ function make_item_importable(item_controller, item_id, item_type) {
         type: "POST",
         url: ajax_url,
         data: { id: item_id, accessible: "True" },
-        error: function() {
+        error: function () {
             alert(`Making ${item_type} accessible failed`);
-        }
+        },
     });
 }
 
 // Completely replace WYM's dialog handling
-WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtml) {
+WYMeditor.editor.prototype.dialog = function (dialogType, dialogFeatures, bodyHtml) {
     var wym = this;
     var sStamp = wym.uniqueStamp();
     var selected = wym.selected();
@@ -129,7 +129,7 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
     // Swap out URL attribute for id/name attribute in link creation to enable anchor creation in page.
     function set_link_id() {
         // When "set link id" link clicked, update UI.
-        $("#set_link_id").click(function() {
+        $("#set_link_id").click(function () {
             // Set label.
             $("#link_attribute_label").text("ID/Name");
 
@@ -166,7 +166,7 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
             "Create Link",
             `<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='javascript:void(0)' role="button" id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='${curURL}' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='${curTitle}' size='40' /></div><div>`,
             {
-                "Make link": function() {
+                "Make link": function () {
                     // Get URL, name/title.
                     var sUrl = $(wym._options.hrefSelector).val() || "";
 
@@ -179,9 +179,7 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
 
                         // Set link attributes.
                         var link = $(`a[href=${sStamp}]`, wym._doc.body);
-                        link.attr(WYMeditor.HREF, sUrl)
-                            .attr(WYMeditor.TITLE, sName)
-                            .attr("id", sId);
+                        link.attr(WYMeditor.HREF, sUrl).attr(WYMeditor.TITLE, sName).attr("id", sId);
 
                         // If link's text is default (wym-...), change it to the title.
                         if (link.text().indexOf("wym-") === 0) {
@@ -190,9 +188,9 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
                     }
                     hide_modal();
                 },
-                Cancel: function() {
+                Cancel: function () {
                     hide_modal();
-                }
+                },
             },
             {},
             set_link_id
@@ -227,7 +225,7 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
                 "<input type='text' class='wym_title' value='' size='40' />" +
                 "</div>",
             {
-                Insert: function() {
+                Insert: function () {
                     var sUrl = $(wym._options.srcSelector).val();
                     if (sUrl.length > 0) {
                         wym._exec(WYMeditor.INSERT_IMAGE, sStamp);
@@ -238,9 +236,9 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
                     }
                     hide_modal();
                 },
-                Cancel: function() {
+                Cancel: function () {
                     hide_modal();
-                }
+                },
             }
         );
         return;
@@ -267,7 +265,7 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
                 "<input type='text' class='wym_cols' value='2' size='3' />" +
                 "</div>",
             {
-                Insert: function() {
+                Insert: function () {
                     var iRows = $(wym._options.rowsSelector).val();
                     var iCols = $(wym._options.colsSelector).val();
 
@@ -299,9 +297,9 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
                     }
                     hide_modal();
                 },
-                Cancel: function() {
+                Cancel: function () {
                     hide_modal();
-                }
+                },
             }
         );
     }
@@ -336,7 +334,7 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
 
         var grid = new GridView({
             url_base: item_info.list_ajax_url,
-            embedded: true
+            embedded: true,
         });
         const Galaxy = getGalaxyInstance();
         Galaxy.modal.show({
@@ -352,13 +350,13 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
                 ),
             closing_events: true,
             buttons: {
-                Insert: function() {
+                Insert: function () {
                     // Make selected items accessible (importable) ?
                     var make_importable = false;
                     if ($("#make-importable:checked").val() != null) make_importable = true;
 
                     // Insert links to history for each checked item.
-                    grid.$("input[name=id]:checked").each(function() {
+                    grid.$("input[name=id]:checked").each(function () {
                         var item_id = $(this).val();
 
                         // Make item importable?
@@ -367,7 +365,7 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
                         // Insert link(s) to item(s). This is done by getting item info and then manipulating wym.
                         var url_template = configs.get_name_and_link_url + item_id;
                         var ajax_url = url_template.replace("ITEM_CONTROLLER", item_info.controller);
-                        $.getJSON(ajax_url, returned_item_info => {
+                        $.getJSON(ajax_url, (returned_item_info) => {
                             // Get link text.
                             wym._exec(WYMeditor.CREATE_LINK, sStamp);
                             var link_text = $(`a[href=${sStamp}]`, wym._doc.body).text();
@@ -391,10 +389,10 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
                     });
                     Galaxy.modal.hide();
                 },
-                Close: function() {
+                Close: function () {
                     Galaxy.modal.hide();
-                }
-            }
+                },
+            },
         });
     }
     // EMBED GALAXY OBJECT DIALOGS
@@ -427,7 +425,7 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
 
         const grid = new GridView({
             url_base: item_info.list_ajax_url,
-            embedded: true
+            embedded: true,
         });
         const Galaxy = getGalaxyInstance();
         Galaxy.modal.show({
@@ -444,21 +442,17 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
             closing_events: true,
             extra_class: "pages-embed",
             buttons: {
-                Embed: function() {
+                Embed: function () {
                     // Make selected items accessible (importable) ?
                     var make_importable = false;
                     if ($("#make-importable:checked").val() != null) make_importable = true;
 
-                    grid.$("input[name=id]:checked").each(function() {
+                    grid.$("input[name=id]:checked").each(function () {
                         var elt = $(this);
                         // Get item ID and name.
                         var item_id = elt.val();
                         // Use ':first' because there are many labels in table; the first one is the item name.
-                        var item_name = elt
-                            .closest("td")
-                            .next("td")
-                            .find("label")
-                            .text();
+                        var item_name = elt.closest("td").next("td").find("label").text();
 
                         if (make_importable) make_item_importable(item_info.controller, item_id, item_info.singular);
 
@@ -484,7 +478,7 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
                             item_info.singular.toLowerCase(),
                             " when it is displayed.]",
                             "</p>",
-                            "</div>"
+                            "</div>",
                         ].join("");
 
                         // Insert embedded item into document.
@@ -492,10 +486,10 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
                     });
                     Galaxy.modal.hide();
                 },
-                Close: function() {
+                Close: function () {
                     Galaxy.modal.hide();
-                }
-            }
+                },
+            },
         });
     }
 };
@@ -509,7 +503,7 @@ function renderEditorWithContent(pageId, content) {
         set_accessible_url: `${appRoot}ITEM_CONTROLLER/set_accessible_async`,
         get_name_and_link_url: `${appRoot}ITEM_CONTROLLER/get_name_and_link_async?id=`,
         editor_base_path: `${appRoot}static/wymeditor/`,
-        iframe_base_path: `${appRoot}static/wymeditor/iframe/galaxy/`
+        iframe_base_path: `${appRoot}static/wymeditor/iframe/galaxy/`,
     };
     setPageConfigs(pageConfigs);
 
@@ -540,22 +534,22 @@ function renderEditorWithContent(pageId, content) {
                 {
                     name: "Superscript",
                     title: _l("Superscript"),
-                    css: "wym_tools_superscript"
+                    css: "wym_tools_superscript",
                 },
                 {
                     name: "Subscript",
                     title: _l("Subscript"),
-                    css: "wym_tools_subscript"
+                    css: "wym_tools_subscript",
                 },
                 {
                     name: "InsertOrderedList",
                     title: "Ordered_List",
-                    css: "wym_tools_ordered_list"
+                    css: "wym_tools_ordered_list",
                 },
                 {
                     name: "InsertUnorderedList",
                     title: "Unordered_List",
-                    css: "wym_tools_unordered_list"
+                    css: "wym_tools_unordered_list",
                 },
                 { name: "Indent", title: "Indent", css: "wym_tools_indent" },
                 { name: "Outdent", title: "Outdent", css: "wym_tools_outdent" },
@@ -564,8 +558,8 @@ function renderEditorWithContent(pageId, content) {
                 { name: "CreateLink", title: "Link", css: "wym_tools_link" },
                 { name: "Unlink", title: "Unlink", css: "wym_tools_unlink" },
                 { name: "InsertImage", title: "Image", css: "wym_tools_image" },
-                { name: "InsertTable", title: "Table", css: "wym_tools_table" }
-            ]
+                { name: "InsertTable", title: "Table", css: "wym_tools_table" },
+            ],
         });
     // Get the editor object
     editor = $.wymeditors(0);
@@ -600,21 +594,21 @@ function renderEditorWithContent(pageId, content) {
 
     // Add menu options.
     make_popupmenu(insert_link_menu_button, {
-        "Insert History Link": function() {
+        "Insert History Link": function () {
             editor.dialog(CONTROLS.DIALOG_HISTORY_LINK);
         },
-        "Insert Dataset Link": function() {
+        "Insert Dataset Link": function () {
             editor.dialog(CONTROLS.DIALOG_DATASET_LINK);
         },
-        "Insert Workflow Link": function() {
+        "Insert Workflow Link": function () {
             editor.dialog(CONTROLS.DIALOG_WORKFLOW_LINK);
         },
-        "Insert Page Link": function() {
+        "Insert Page Link": function () {
             editor.dialog(CONTROLS.DIALOG_PAGE_LINK);
         },
-        "Insert Visualization Link": function() {
+        "Insert Visualization Link": function () {
             editor.dialog(CONTROLS.DIALOG_VISUALIZATION_LINK);
-        }
+        },
     });
 
     //
@@ -629,18 +623,18 @@ function renderEditorWithContent(pageId, content) {
 
     // Add menu options.
     make_popupmenu(embed_object_button, {
-        "Embed History": function() {
+        "Embed History": function () {
             editor.dialog(CONTROLS.DIALOG_EMBED_HISTORY);
         },
-        "Embed Dataset": function() {
+        "Embed Dataset": function () {
             editor.dialog(CONTROLS.DIALOG_EMBED_DATASET);
         },
-        "Embed Workflow": function() {
+        "Embed Workflow": function () {
             editor.dialog(CONTROLS.DIALOG_EMBED_WORKFLOW);
         },
-        "Embed Visualization": function() {
+        "Embed Visualization": function () {
             editor.dialog(CONTROLS.DIALOG_EMBED_VISUALIZATION);
-        }
+        },
         //"Embed Page": function() {
         //    editor.dialog(CONTROLS.DIALOG_EMBED_PAGE);
         //}
@@ -651,22 +645,22 @@ export default {
     props: {
         pageId: {
             required: true,
-            type: String
+            type: String,
         },
         content: {
-            type: String
-        }
+            type: String,
+        },
     },
-    created: function() {
+    created: function () {
         this.$nextTick(() => {
             renderEditorWithContent(this.pageId, this.content);
         });
     },
     methods: {
-        saveContent: function() {
+        saveContent: function () {
             save(this.pageId, editor.xhtml());
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/PageEditor/PageEditorMarkdown.vue b/client/galaxy/scripts/components/PageEditor/PageEditorMarkdown.vue
index ed88992ce6d1..14447395f5c5 100644
--- a/client/galaxy/scripts/components/PageEditor/PageEditorMarkdown.vue
+++ b/client/galaxy/scripts/components/PageEditor/PageEditorMarkdown.vue
@@ -18,31 +18,31 @@ import { save } from "./util";
 
 export default {
     components: {
-        MarkdownEditor
+        MarkdownEditor,
     },
-    data: function() {
+    data: function () {
         return {
             content: "",
-            showMarkdownHelp: showMarkdownHelp
+            showMarkdownHelp: showMarkdownHelp,
         };
     },
     props: {
         pageId: {
             required: true,
-            type: String
+            type: String,
         },
         initialContent: {
-            type: String
-        }
+            type: String,
+        },
     },
     methods: {
-        onUpdate: function(content) {
+        onUpdate: function (content) {
             this.content = content;
         },
-        saveContent: function() {
+        saveContent: function () {
             save(this.pageId, this.content);
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/PageEditor/markdownHelp.js b/client/galaxy/scripts/components/PageEditor/markdownHelp.js
index bd008b5b7f6e..11651fe61084 100644
--- a/client/galaxy/scripts/components/PageEditor/markdownHelp.js
+++ b/client/galaxy/scripts/components/PageEditor/markdownHelp.js
@@ -82,6 +82,6 @@ import { hide_modal, show_modal } from "layout/modal";
 export function showMarkdownHelp() {
     const markdownHelpBody = $(markdownHelp);
     show_modal("Pages Markdown Help", markdownHelpBody, {
-        Ok: hide_modal
+        Ok: hide_modal,
     });
 }
diff --git a/client/galaxy/scripts/components/PageEditor/util.js b/client/galaxy/scripts/components/PageEditor/util.js
index de6c96c92a4b..f9253ce23f27 100644
--- a/client/galaxy/scripts/components/PageEditor/util.js
+++ b/client/galaxy/scripts/components/PageEditor/util.js
@@ -11,5 +11,5 @@ export const save = (pageId, content) => {
     axios
         .post(`${getAppRoot()}api/pages/${pageId}/revisions`, { content: content })
         .finally(hide_modal)
-        .catch(error_message => Toast.error("Failed to save page: " + errorMessageAsString(error_message)));
+        .catch((error_message) => Toast.error("Failed to save page: " + errorMessageAsString(error_message)));
 };
diff --git a/client/galaxy/scripts/components/Panels/Buttons/FavoritesButton.vue b/client/galaxy/scripts/components/Panels/Buttons/FavoritesButton.vue
index c87c5d1814f9..82fb53f2251f 100644
--- a/client/galaxy/scripts/components/Panels/Buttons/FavoritesButton.vue
+++ b/client/galaxy/scripts/components/Panels/Buttons/FavoritesButton.vue
@@ -24,16 +24,16 @@ export default {
     components: { FontAwesomeIcon },
     data() {
         return {
-            tooltipText: "Show favorites"
+            tooltipText: "Show favorites",
         };
     },
     directives: {
-        "v-b-tooltip": VBTooltip
+        "v-b-tooltip": VBTooltip,
     },
     methods: {
         onFavorites() {
             this.$emit("onFavorites", "#favorites");
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Panels/Buttons/UploadButton.vue b/client/galaxy/scripts/components/Panels/Buttons/UploadButton.vue
index fcd2a68fa83a..5633012f57f1 100644
--- a/client/galaxy/scripts/components/Panels/Buttons/UploadButton.vue
+++ b/client/galaxy/scripts/components/Panels/Buttons/UploadButton.vue
@@ -5,7 +5,7 @@
                 class="progress-bar progress-bar-notransition"
                 :class="`progress-bar-${status}`"
                 :style="{
-                    width: `${percentage}%`
+                    width: `${percentage}%`,
                 }"
             ></div>
             <a
@@ -37,12 +37,12 @@ export default {
     name: "UploadButton",
     components: { FontAwesomeIcon },
     directives: {
-        "v-b-tooltip": VBTooltip
+        "v-b-tooltip": VBTooltip,
     },
     data() {
         return {
             status: "",
-            percentage: 0
+            percentage: 0,
         };
     },
     methods: {
@@ -50,7 +50,7 @@ export default {
             const Galaxy = getGalaxyInstance();
             e.preventDefault();
             Galaxy.upload.show();
-        }
+        },
     },
     created() {
         const Galaxy = getGalaxyInstance();
@@ -59,7 +59,7 @@ export default {
             this.status = Galaxy.upload.model.attributes.status;
             this.percentage = Galaxy.upload.model.attributes.percentage;
         });
-    }
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/Panels/Common/Tool.test.js b/client/galaxy/scripts/components/Panels/Common/Tool.test.js
index 38f6192b8368..cc022b172dd2 100644
--- a/client/galaxy/scripts/components/Panels/Common/Tool.test.js
+++ b/client/galaxy/scripts/components/Panels/Common/Tool.test.js
@@ -5,8 +5,8 @@ describe("Tool", () => {
     it("test tool", () => {
         const wrapper = mount(Tool, {
             propsData: {
-                tool: {}
-            }
+                tool: {},
+            },
         });
         const nameElement = wrapper.findAll(".name");
         expect(nameElement.at(0).text()).to.equal("");
@@ -23,11 +23,11 @@ describe("Tool", () => {
         const wrapper = mount(Tool, {
             propsData: {
                 tool: {
-                    name: "name"
+                    name: "name",
                 },
                 operationIcon: "operationIconClass",
-                operationTitle: "operationTitle"
-            }
+                operationTitle: "operationTitle",
+            },
         });
         const nameElement = wrapper.findAll(".name");
         expect(nameElement.at(0).text()).to.equal("name");
@@ -41,10 +41,10 @@ describe("Tool", () => {
             propsData: {
                 tool: {
                     name: "name",
-                    description: "description"
+                    description: "description",
                 },
-                hideName: true
-            }
+                hideName: true,
+            },
         });
         const nameElement = wrapper.findAll(".name");
         expect(nameElement.length).to.equal(0);
diff --git a/client/galaxy/scripts/components/Panels/Common/Tool.vue b/client/galaxy/scripts/components/Panels/Common/Tool.vue
index cc72cc6afcf2..4687d89af294 100644
--- a/client/galaxy/scripts/components/Panels/Common/Tool.vue
+++ b/client/galaxy/scripts/components/Panels/Common/Tool.vue
@@ -38,20 +38,20 @@ export default {
     props: {
         tool: {
             type: Object,
-            required: true
+            required: true,
         },
         operationTitle: {
-            type: String
+            type: String,
         },
         operationIcon: {
-            type: String
+            type: String,
         },
         hideName: {
-            type: Boolean
+            type: Boolean,
         },
         toolKey: {
-            type: String
-        }
+            type: String,
+        },
     },
     computed: {
         targetClass() {
@@ -60,7 +60,7 @@ export default {
             } else {
                 return null;
             }
-        }
+        },
     },
     methods: {
         onClick(evt) {
@@ -70,7 +70,7 @@ export default {
         onOperation(evt) {
             ariaAlert(`${this.tool.name} operation selected from panel`);
             this.$emit("onOperation", this.tool, evt);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Panels/Common/ToolSearch.vue b/client/galaxy/scripts/components/Panels/Common/ToolSearch.vue
index 1a7d0fe99342..a09dfe7c382a 100644
--- a/client/galaxy/scripts/components/Panels/Common/ToolSearch.vue
+++ b/client/galaxy/scripts/components/Panels/Common/ToolSearch.vue
@@ -11,28 +11,28 @@ import DelayedInput from "components/Common/DelayedInput";
 export default {
     name: "ToolSearch",
     components: {
-        DelayedInput
+        DelayedInput,
     },
     props: {
         query: {
-            type: String
+            type: String,
         },
         placeholder: {
-            type: String
-        }
+            type: String,
+        },
     },
     data() {
         return {
             favorites: ["#favs", "#favorites", "#favourites"],
             minQueryLength: 3,
-            loading: false
+            loading: false,
         };
     },
     computed: {
         favoritesResults() {
             const Galaxy = getGalaxyInstance();
             return Galaxy.user.getFavorites().tools;
-        }
+        },
     },
     methods: {
         checkQuery(q) {
@@ -44,13 +44,13 @@ export default {
                     this.loading = true;
                     axios
                         .get(`${getAppRoot()}api/tools`, {
-                            params: { q }
+                            params: { q },
                         })
-                        .then(response => {
+                        .then((response) => {
                             this.loading = false;
                             this.$emit("onResults", response.data);
                         })
-                        .catch(err => {
+                        .catch((err) => {
                             this.loading = false;
                             this.$emit("onError", err);
                         });
@@ -58,7 +58,7 @@ export default {
             } else {
                 this.$emit("onResults", null);
             }
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Panels/Common/ToolSection.test.js b/client/galaxy/scripts/components/Panels/Common/ToolSection.test.js
index 90ba6136894c..ba2674b20255 100644
--- a/client/galaxy/scripts/components/Panels/Common/ToolSection.test.js
+++ b/client/galaxy/scripts/components/Panels/Common/ToolSection.test.js
@@ -7,9 +7,9 @@ describe("ToolSection", () => {
         const wrapper = mount(ToolSection, {
             propsData: {
                 category: {
-                    name: "name"
-                }
-            }
+                    name: "name",
+                },
+            },
         });
         const nameElement = wrapper.findAll(".name");
         expect(nameElement.at(0).text()).to.equal("name");
@@ -24,14 +24,14 @@ describe("ToolSection", () => {
                     title: "tool_section",
                     elems: [
                         {
-                            name: "name"
+                            name: "name",
                         },
                         {
-                            text: "text"
-                        }
-                    ]
-                }
-            }
+                            text: "text",
+                        },
+                    ],
+                },
+            },
         });
         expect(wrapper.vm.opened).to.equal(false);
         const $sectionName = wrapper.find(".name");
@@ -54,15 +54,15 @@ describe("ToolSection", () => {
                     title: "tool_section",
                     elems: [
                         {
-                            name: "name"
+                            name: "name",
                         },
                         {
-                            text: "text"
-                        }
-                    ]
+                            text: "text",
+                        },
+                    ],
                 },
-                queryFilter: "test"
-            }
+                queryFilter: "test",
+            },
         });
         expect(wrapper.vm.opened).to.equal(true);
         const $sectionName = wrapper.find(".name");
diff --git a/client/galaxy/scripts/components/Panels/Common/ToolSection.vue b/client/galaxy/scripts/components/Panels/Common/ToolSection.vue
index cac178c39e05..69e8377ffe4b 100644
--- a/client/galaxy/scripts/components/Panels/Common/ToolSection.vue
+++ b/client/galaxy/scripts/components/Panels/Common/ToolSection.vue
@@ -56,45 +56,45 @@ import ariaAlert from "utils/ariaAlert";
 export default {
     name: "ToolSection",
     components: {
-        Tool
+        Tool,
     },
     props: {
         category: {
             type: Object,
-            required: true
+            required: true,
         },
         queryFilter: {
-            type: String
+            type: String,
         },
         disableFilter: {
-            type: Boolean
+            type: Boolean,
         },
         hideName: {
-            type: Boolean
+            type: Boolean,
         },
         operationTitle: {
-            type: String
+            type: String,
         },
         operationIcon: {
-            type: String
+            type: String,
         },
         toolKey: {
-            type: String
+            type: String,
         },
         sectionName: {
             type: String,
-            default: "default"
-        }
+            default: "default",
+        },
     },
     data() {
         return {
-            opened: this.checkFilter()
+            opened: this.checkFilter(),
         };
     },
     watch: {
         queryFilter() {
             this.opened = this.checkFilter();
-        }
+        },
     },
     computed: {
         name() {
@@ -105,7 +105,7 @@ export default {
         },
         hasElements() {
             return this.category.elems && this.category.elems.length > 0;
-        }
+        },
     },
     methods: {
         checkFilter() {
@@ -121,8 +121,8 @@ export default {
             this.opened = !this.opened;
             const currentState = this.opened ? "opened" : "closed";
             ariaAlert(`${this.name} tools menu ${currentState}`);
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/Panels/SidePanel.vue b/client/galaxy/scripts/components/Panels/SidePanel.vue
index 85e232d0c932..ef14219380d6 100644
--- a/client/galaxy/scripts/components/Panels/SidePanel.vue
+++ b/client/galaxy/scripts/components/Panels/SidePanel.vue
@@ -9,7 +9,7 @@
                 :class="{
                     left: side === 'left',
                     right: side === 'right',
-                    hidden: !show
+                    hidden: !show,
                 }"
                 @click="toggle"
             />
@@ -28,7 +28,7 @@ export default {
     data() {
         return {
             show: true,
-            width: 288
+            width: 288,
         };
     },
     computed: {
@@ -37,7 +37,7 @@ export default {
             styles[this.side] = this.show ? "0" : `-${this.width}px`;
             styles["width"] = this.width + "px";
             return styles;
-        }
+        },
     },
     methods: {
         dragHandler(e) {
@@ -92,8 +92,8 @@ export default {
             setTimeout(() => {
                 document.getElementById("center").style.transition = "";
             }, 250);
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/Panels/ToolBox.vue b/client/galaxy/scripts/components/Panels/ToolBox.vue
index 29e49d4abb27..c834ff0e5ae1 100644
--- a/client/galaxy/scripts/components/Panels/ToolBox.vue
+++ b/client/galaxy/scripts/components/Panels/ToolBox.vue
@@ -55,28 +55,28 @@ export default {
         UploadButton,
         FavoritesButton,
         ToolSection,
-        ToolSearch
+        ToolSearch,
     },
     data() {
         return {
             query: null,
             results: null,
-            workflow: null
+            workflow: null,
         };
     },
     props: {
         toolbox: {
             type: Array,
-            required: true
+            required: true,
         },
         stored_workflow_menu_entries: {
             type: Array,
-            required: true
+            required: true,
         },
         workflowTitle: {
             type: String,
-            default: _l("Workflows")
-        }
+            default: _l("Workflows"),
+        },
     },
     computed: {
         categories() {
@@ -91,17 +91,17 @@ export default {
                 {
                     title: _l("All workflows"),
                     href: `${getAppRoot()}workflows/list`,
-                    id: "list"
+                    id: "list",
                 },
-                ...this.stored_workflow_menu_entries.map(menuEntry => {
+                ...this.stored_workflow_menu_entries.map((menuEntry) => {
                     return {
                         id: menuEntry.id,
                         title: menuEntry.name,
-                        href: `${getAppRoot()}workflows/run?id=${menuEntry.id}`
+                        href: `${getAppRoot()}workflows/run?id=${menuEntry.id}`,
                     };
-                })
+                }),
             ];
-        }
+        },
     },
     methods: {
         onQuery(query) {
@@ -122,10 +122,10 @@ export default {
                 evt.preventDefault();
                 Galaxy.router.push("/", {
                     tool_id: tool.id,
-                    version: tool.version
+                    version: tool.version,
                 });
             }
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue b/client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue
index cb378e226000..a44c15ee5aec 100644
--- a/client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue
+++ b/client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue
@@ -62,58 +62,58 @@ export default {
     name: "ToolBox",
     components: {
         ToolSection,
-        ToolSearch
+        ToolSearch,
     },
     data() {
         return {
             query: null,
-            results: null
+            results: null,
         };
     },
     props: {
         toolbox: {
             type: Array,
-            required: true
+            required: true,
         },
         workflows: {
-            type: Array
+            type: Array,
         },
         dataManagers: {
-            type: Array
+            type: Array,
         },
         moduleSections: {
-            type: Array
-        }
+            type: Array,
+        },
     },
     computed: {
         workflowSection() {
             return {
                 name: _l("Workflows"),
-                elems: this.workflows
+                elems: this.workflows,
             };
         },
         dataManagerSection() {
             return {
                 name: _l("Data Managers"),
-                elems: this.dataManagers
+                elems: this.dataManagers,
             };
         },
         categories() {
             return filterToolSections(this.toolsLayout, this.results);
         },
         toolsLayout() {
-            return this.toolbox.map(section => {
+            return this.toolbox.map((section) => {
                 return {
                     ...section,
                     elems:
                         section.elems &&
-                        section.elems.map(el => {
+                        section.elems.map((el) => {
                             el.disabled = !el.is_workflow_compatible;
                             return el;
-                        })
+                        }),
                 };
             });
-        }
+        },
     },
     methods: {
         onQuery(query) {
@@ -136,7 +136,7 @@ export default {
         },
         onInsertWorkflowSteps(workflow) {
             this.$emit("onInsertWorkflowSteps", workflow.id, workflow.step_count);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Panels/utilities.js b/client/galaxy/scripts/components/Panels/utilities.js
index 9842e6cbc5ad..9038db655f52 100644
--- a/client/galaxy/scripts/components/Panels/utilities.js
+++ b/client/galaxy/scripts/components/Panels/utilities.js
@@ -1,16 +1,16 @@
 export function filterToolSections(layout, results) {
     if (results) {
-        const filteredLayout = layout.map(category => {
+        const filteredLayout = layout.map((category) => {
             return {
                 ...category,
                 elems:
                     category.elems &&
-                    category.elems.filter(el => {
+                    category.elems.filter((el) => {
                         return !el.text && results.includes(el.id);
-                    })
+                    }),
             };
         });
-        return filteredLayout.filter(category => {
+        return filteredLayout.filter((category) => {
             const isSection = category.elems && category.elems.length > 0;
             const isMatchedTool = !category.text && results.includes(category.id);
             return isSection || isMatchedTool;
diff --git a/client/galaxy/scripts/components/PluginList.vue b/client/galaxy/scripts/components/PluginList.vue
index cf88c5c2d7e1..53cb80954a47 100644
--- a/client/galaxy/scripts/components/PluginList.vue
+++ b/client/galaxy/scripts/components/PluginList.vue
@@ -76,7 +76,7 @@ export default {
             selected: null,
             name: null,
             error: null,
-            fixed: false
+            fixed: false,
         };
     },
     created() {
@@ -90,15 +90,15 @@ export default {
         }
         axios
             .get(url)
-            .then(response => {
+            .then((response) => {
                 this.plugins = response.data;
             })
-            .catch(e => {
+            .catch((e) => {
                 this.error = this._errorMessage(e);
             });
     },
     methods: {
-        select: function(plugin) {
+        select: function (plugin) {
             if (this.fixed) {
                 this.create(plugin);
             } else {
@@ -107,14 +107,14 @@ export default {
                 if (history_id) {
                     axios
                         .get(`${getAppRoot()}api/plugins/${plugin.name}?history_id=${history_id}`)
-                        .then(response => {
+                        .then((response) => {
                             this.name = plugin.name;
                             this.hdas = response.data && response.data.hdas;
                             if (this.hdas && this.hdas.length > 0) {
                                 this.selected = this.hdas[0].id;
                             }
                         })
-                        .catch(e => {
+                        .catch((e) => {
                             this.error = this._errorMessage(e);
                         });
                 } else {
@@ -122,7 +122,7 @@ export default {
                 }
             }
         },
-        create: function(plugin) {
+        create: function (plugin) {
             const href = `${plugin.href}?dataset_id=${this.selected}`;
             if (plugin.target == "_top") {
                 window.location.href = href;
@@ -130,17 +130,17 @@ export default {
                 $("#galaxy_main").attr("src", href);
             }
         },
-        match: function(plugin) {
+        match: function (plugin) {
             return (
                 !this.search ||
                 plugin.name.indexOf(this.search) != -1 ||
                 (plugin.description && plugin.description.indexOf(this.search) != -1)
             );
         },
-        _errorMessage: function(e) {
+        _errorMessage: function (e) {
             const message = e && e.response && e.response.data && e.response.data.err_msg;
             return message || "Request failed for an unknown reason.";
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/ProgressBar.vue b/client/galaxy/scripts/components/ProgressBar.vue
index c2bc9ae86f52..5a9b7a58c2da 100644
--- a/client/galaxy/scripts/components/ProgressBar.vue
+++ b/client/galaxy/scripts/components/ProgressBar.vue
@@ -25,12 +25,12 @@ export default {
         newProgress: { type: Number, default: 0.0 },
         newMessage: { type: String, default: null },
         errorProgress: { type: Number, default: 0.0 },
-        errorMessage: { type: String, default: null }
+        errorMessage: { type: String, default: null },
     },
     methods: {
-        styleFromProgress: function(progress) {
+        styleFromProgress: function (progress) {
             return { width: `${progress * 100}%` };
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/RuleCollectionBuilder.vue b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
index 2e80d4ead504..d4d99436d373 100644
--- a/client/galaxy/scripts/components/RuleCollectionBuilder.vue
+++ b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
@@ -40,7 +40,7 @@
                         :class="{
                             'rules-container-vertical': initialElements && vertical,
                             'rules-container-horizontal': initialElements && horizontal,
-                            'rules-container-full': initialElements == null
+                            'rules-container-full': initialElements == null,
                         }"
                     >
                         <rule-component rule-type="sort" :display-rule-type="displayRuleType" :builder="this">
@@ -351,8 +351,8 @@
                                     :key="map.type"
                                     @remove="removeMapping(index)"
                                     @edit="displayRuleType = 'mapping'"
-                                    @mouseover.native="map.columns.forEach(col => highlightColumn(col))"
-                                    @mouseout.native="map.columns.forEach(col => unhighlightColumn(col))"
+                                    @mouseover.native="map.columns.forEach((col) => highlightColumn(col))"
+                                    @mouseout.native="map.columns.forEach((col) => unhighlightColumn(col))"
                                     :col-headers="colHeaders"
                                 />
                                 <div v-if="mapping.length == 0">
@@ -620,47 +620,47 @@ const ColumnSelector = {
             </ol>
         </div>
     `,
-    data: function() {
+    data: function () {
         return {
-            l: _l
+            l: _l,
         };
     },
     props: {
         target: {
-            required: true
+            required: true,
         },
         label: {
             required: false,
             type: String,
-            default: _l("From Column")
+            default: _l("From Column"),
         },
         help: {
-            required: false
+            required: false,
         },
         colHeaders: {
             type: Array,
-            required: true
+            required: true,
         },
         multiple: {
             type: Boolean,
             required: false,
-            default: false
+            default: false,
         },
         ordered: {
             type: Boolean,
             required: false,
-            default: false
+            default: false,
         },
         valueAsList: {
             type: Boolean,
             required: false,
-            default: false
+            default: false,
         },
         orderedEdit: {
             type: Boolean,
             required: false,
-            default: false
-        }
+            default: false,
+        },
     },
     computed: {
         remainingHeaders() {
@@ -678,13 +678,13 @@ const ColumnSelector = {
         },
         title() {
             return _l("Select a column");
-        }
+        },
     },
     methods: {
         handleInput(value) {
             if (this.multiple) {
                 // https://stackoverflow.com/questions/262427/why-does-parseint-yield-nan-with-arraymap
-                const val = value.map(idx => parseInt(idx));
+                const val = value.map((idx) => parseInt(idx));
                 this.$emit("update:target", val);
             } else {
                 let val = parseInt(value);
@@ -705,11 +705,11 @@ const ColumnSelector = {
             const swapVal = this.target[value - 1];
             Vue.set(this.target, value - 1, this.target[value]);
             Vue.set(this.target, value, swapVal);
-        }
+        },
     },
     components: {
-        Select2
-    }
+        Select2,
+    },
 };
 
 const RegularExpressionInput = {
@@ -722,8 +722,8 @@ const RegularExpressionInput = {
     `,
     props: {
         target: {
-            required: true
-        }
+            required: true,
+        },
     },
     computed: {
         label() {
@@ -739,8 +739,8 @@ const RegularExpressionInput = {
             return _l(
                 `Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in <a href="https://pythonforbiologists.com/regular-expressions/">this Python for Biologists tutorial</a>.`
             );
-        }
-    }
+        },
+    },
 };
 
 const RuleDisplay = {
@@ -762,12 +762,12 @@ const RuleDisplay = {
     props: {
         rule: {
             required: true,
-            type: Object
+            type: Object,
         },
         colHeaders: {
             type: Array,
-            required: true
-        }
+            required: true,
+        },
     },
     computed: {
         title() {
@@ -779,7 +779,7 @@ const RuleDisplay = {
         },
         removeTitle() {
             return _l("Remove this rule.");
-        }
+        },
     },
     methods: {
         edit() {
@@ -787,8 +787,8 @@ const RuleDisplay = {
         },
         remove() {
             this.$emit("remove");
-        }
-    }
+        },
+    },
 };
 
 const IdentifierDisplay = {
@@ -802,15 +802,15 @@ const IdentifierDisplay = {
     props: {
         type: {
             type: String,
-            required: true
+            required: true,
         },
         columns: {
-            required: true
+            required: true,
         },
         colHeaders: {
             type: Array,
-            required: true
-        }
+            required: true,
+        },
     },
     methods: {
         remove() {
@@ -818,7 +818,7 @@ const IdentifierDisplay = {
         },
         edit() {
             this.$emit("edit");
-        }
+        },
     },
     computed: {
         typeDisplay() {
@@ -835,8 +835,8 @@ const IdentifierDisplay = {
         },
         columnsLabel() {
             return RuleDefs.columnDisplay(this.columns, this.colHeaders);
-        }
-    }
+        },
+    },
 };
 
 const RuleTargetComponent = {
@@ -844,11 +844,11 @@ const RuleTargetComponent = {
     props: {
         ruleType: {
             type: String,
-            required: true
+            required: true,
         },
         builder: {
-            required: true
-        }
+            required: true,
+        },
     },
     computed: {
         linkClassName() {
@@ -856,8 +856,8 @@ const RuleTargetComponent = {
         },
         title() {
             return RULES[this.ruleType].title;
-        }
-    }
+        },
+    },
 };
 
 const RuleComponent = {
@@ -869,23 +869,23 @@ const RuleComponent = {
            <button type="button" class="btn btn-primary rule-editor-ok" @click="okay">{{ applyLabel }}</button>
         </div>
     </div>`,
-    data: function() {
+    data: function () {
         return {
             applyLabel: _l("Apply"),
-            cancelLabel: _l("Cancel")
+            cancelLabel: _l("Cancel"),
         };
     },
     props: {
         ruleType: {
             type: String,
-            required: true
+            required: true,
         },
         displayRuleType: {
-            required: true
+            required: true,
         },
         builder: {
-            required: true
-        }
+            required: true,
+        },
     },
     methods: {
         cancel() {
@@ -894,28 +894,28 @@ const RuleComponent = {
         okay() {
             this.builder.handleRuleSave(this.ruleType);
             this.cancel();
-        }
+        },
     },
     computed: {
         typeToClass() {
             return "rule-edit-" + this.ruleType.replace(/_/g, "-");
-        }
-    }
+        },
+    },
 };
 
 const StateDiv = {
     template: `
         <div class="rule-collection-creator collection-creator flex-row-container">
             <slot></slot>
-        </div>`
+        </div>`,
 };
 
 const RuleModalHeader = {
-    template: `<div class="header flex-row no-flex"><slot></slot></div>`
+    template: `<div class="header flex-row no-flex"><slot></slot></div>`,
 };
 
 const RuleModalMiddle = {
-    template: `<div class="middle flex-row flex-row-container"><slot></slot></div>`
+    template: `<div class="middle flex-row flex-row-container"><slot></slot></div>`,
 };
 
 const RuleModalFooter = {
@@ -927,11 +927,11 @@ const RuleModalFooter = {
                     <slot></slot>
                 </div>
             </div>
-        </div>`
+        </div>`,
 };
 
 export default {
-    data: function() {
+    data: function () {
         let orientation = "vertical";
         let mapping;
         let rules;
@@ -954,7 +954,7 @@ export default {
                     for (const index in collectionTypeRanks) {
                         rules.push({
                             type: "add_column_metadata",
-                            value: "identifier" + index
+                            value: "identifier" + index,
                         });
                     }
                 } else {
@@ -962,29 +962,29 @@ export default {
                     // just assume a list is given by default.
                     rules.push({
                         type: "add_column_metadata",
-                        value: "identifier0"
+                        value: "identifier0",
                     });
                 }
             } else if (this.elementsType == "datasets") {
                 rules.push(
                     {
                         type: "add_column_metadata",
-                        value: "hid"
+                        value: "hid",
                     },
                     {
                         type: "add_column_metadata",
-                        value: "name"
+                        value: "name",
                     }
                 );
             } else if (this.elementsType == "library_datasets") {
                 rules.push({
                     type: "add_column_metadata",
-                    value: "name"
+                    value: "name",
                 });
             } else if (this.elementsType == "ftp") {
                 rules.push({
                     type: "add_column_metadata",
-                    value: "path"
+                    value: "path",
                 });
             }
         }
@@ -1065,58 +1065,58 @@ export default {
             genome: null,
             hideSourceItems: this.defaultHideSourceItems,
             addNameTag: false,
-            orientation: orientation
+            orientation: orientation,
         };
     },
     props: {
         initialElements: {
-            required: true
+            required: true,
         },
         importType: {
             type: String,
             required: false,
-            default: "collections"
+            default: "collections",
         },
         elementsType: {
             type: String,
             required: false,
-            default: "datasets"
+            default: "datasets",
         },
         // required if elementsType is "datasets" - hook into Backbone code for creating
         // collections from HDAs, etc...
         creationFn: {
             required: false,
-            type: Function
+            type: Function,
         },
         // required if elementsType is "collection_contents" - hook into tool form to update
         // rule parameter
         saveRulesFn: {
             required: false,
-            type: Function
+            type: Function,
         },
         initialRules: {
             required: false,
-            type: Object
+            type: Object,
         },
         defaultHideSourceItems: {
             type: Boolean,
             required: false,
-            default: true
+            default: true,
         },
         // Callbacks sent in by modal code.
         oncancel: {
             required: true,
-            type: Function
+            type: Function,
         },
         oncreate: {
             required: true,
-            type: Function
+            type: Function,
         },
         ftpUploadSite: {
             type: String,
             required: false,
-            default: null
-        }
+            default: null,
+        },
     },
     computed: {
         exisistingDatasets() {
@@ -1169,7 +1169,7 @@ export default {
             }
         },
         hasActiveMappingEdit() {
-            const has = _.any(_.values(this.mapping), mapping => mapping.editing);
+            const has = _.any(_.values(this.mapping), (mapping) => mapping.editing);
             return has;
         },
         activeRule() {
@@ -1237,7 +1237,7 @@ export default {
                 } else if (mappingDisplay.length > 1) {
                     formattedHeaders[colIndex] += ` (${[
                         mappingDisplay.slice(0, -1).join(", "),
-                        mappingDisplay.slice(-1)[0]
+                        mappingDisplay.slice(-1)[0],
                     ].join(" & ")})`;
                 }
             }
@@ -1292,7 +1292,7 @@ export default {
             if (this.mappingAsDict.list_identifiers) {
                 identifierColumns = this.mappingAsDict.list_identifiers.columns;
             }
-            let collectionType = identifierColumns.map(col => "list").join(":");
+            let collectionType = identifierColumns.map((col) => "list").join(":");
             if (this.mappingAsDict.paired_identifier) {
                 if (collectionType) {
                     collectionType += ":paired";
@@ -1344,7 +1344,7 @@ export default {
                 this.elementsType == "ftp"
             ) {
                 sources = this.initialElements.slice();
-                data = sources.map(el => []);
+                data = sources.map((el) => []);
                 columns = [];
             } else if (this.elementsType == "collection_contents") {
                 const collection = this.initialElements;
@@ -1363,7 +1363,7 @@ export default {
                 }
             } else {
                 data = this.initialElements.slice();
-                sources = data.map(el => null);
+                sources = data.map((el) => null);
                 columns = [];
                 if (this.initialElements) {
                     this.initialElements[0].forEach(() => columns.push("new"));
@@ -1373,7 +1373,7 @@ export default {
         },
         colHeadersPerRule() {
             return this.hotData.colHeadersPerRule;
-        }
+        },
     },
     methods: {
         l(str) {
@@ -1416,7 +1416,7 @@ export default {
             this.ruleView = "source";
         },
         resetSource() {
-            const replacer = function(key, value) {
+            const replacer = function (key, value) {
                 if (key == "error" || key == "warn") {
                     return undefined;
                 }
@@ -1424,7 +1424,7 @@ export default {
             };
             const asJson = {
                 rules: this.rules,
-                mapping: this.mapping
+                mapping: this.mapping,
             };
             if (!this.exisistingDatasets) {
                 if (this.extension !== UploadUtils.DEFAULT_EXTENSION) {
@@ -1497,7 +1497,7 @@ export default {
         },
         waitOnJob(response) {
             const jobId = response.data.jobs[0].id;
-            const handleJobShow = jobResponse => {
+            const handleJobShow = (jobResponse) => {
                 const state = jobResponse.data.state;
                 this.waitingJobState = state;
                 if (JobStatesModel.NON_TERMINAL_STATES.indexOf(state) !== -1) {
@@ -1515,15 +1515,12 @@ export default {
                 }
             };
             const doJobCheck = () => {
-                axios
-                    .get(`${getAppRoot()}api/jobs/${jobId}`)
-                    .then(handleJobShow)
-                    .catch(this.renderFetchError);
+                axios.get(`${getAppRoot()}api/jobs/${jobId}`).then(handleJobShow).catch(this.renderFetchError);
             };
             setTimeout(doJobCheck, 1000);
         },
         doFullJobCheck(jobId) {
-            const handleJobShow = jobResponse => {
+            const handleJobShow = (jobResponse) => {
                 const stderr = jobResponse.data.stderr;
                 if (stderr) {
                     let errorMessage = "An error was encountered while running your upload job. ";
@@ -1535,10 +1532,7 @@ export default {
                     this.errorMessage = errorMessage;
                 }
             };
-            axios
-                .get(`${getAppRoot()}api/jobs/${jobId}?full=True`)
-                .then(handleJobShow)
-                .catch(this.renderFetchError);
+            axios.get(`${getAppRoot()}api/jobs/${jobId}?full=True`).then(handleJobShow).catch(this.renderFetchError);
         },
         renderFetchError(error) {
             this.state = "error";
@@ -1554,17 +1548,17 @@ export default {
             this.orientation = this.orientation == "horizontal" ? "vertical" : "horizontal";
             const hotTable = this.$refs.hotTable.table;
             if (this.orientation == "horizontal") {
-                this.$nextTick(function() {
+                this.$nextTick(function () {
                     const fullWidth = $(".rule-builder-body").width();
                     hotTable.updateSettings({
-                        width: fullWidth
+                        width: fullWidth,
                     });
                 });
             } else {
-                this.$nextTick(function() {
+                this.$nextTick(function () {
                     const fullWidth = $(".rule-builder-body").width();
                     hotTable.updateSettings({
-                        width: fullWidth - 270
+                        width: fullWidth - 270,
                     });
                 });
             }
@@ -1606,7 +1600,7 @@ export default {
                             destination: { type: "hdca" },
                             elements: elementsByCollectionName[collectionName],
                             collection_type: collectionType,
-                            name: collectionName
+                            name: collectionName,
                         };
                         if (this.addNameTag) {
                             target["tags"] = ["name:" + collectionName];
@@ -1619,8 +1613,8 @@ export default {
                         {
                             destination: { type: "hdas" },
                             elements: elements,
-                            name: name
-                        }
+                            name: name,
+                        },
                     ];
                 }
 
@@ -1629,7 +1623,7 @@ export default {
                         .post(`${getAppRoot()}api/tools/fetch`, {
                             history_id: historyId,
                             targets: targets,
-                            auto_decompress: true
+                            auto_decompress: true,
                         })
                         .then(this.refreshAndWait)
                         .catch(this.renderFetchError);
@@ -1722,10 +1716,7 @@ export default {
                             identifiersAtDepth.push(identifier);
                         } else {
                             // Create nesting for this element.
-                            collectionTypeAtDepth = collectionTypeAtDepth
-                                .split(":")
-                                .slice(1)
-                                .join(":");
+                            collectionTypeAtDepth = collectionTypeAtDepth.split(":").slice(1).join(":");
                             let found = false;
                             for (const element of elementsAtDepth) {
                                 if (element["name"] == identifier) {
@@ -1765,7 +1756,7 @@ export default {
                     const src = this.elementsType == "datasets" ? "hda" : "ldda";
                     return { id: source["id"], name: identifier, src: src, tags: res.tags };
                 },
-                identifier => {
+                (identifier) => {
                     return { name: identifier, src: "new_collection" };
                 },
                 "element_identifiers"
@@ -1783,7 +1774,7 @@ export default {
                     res["name"] = identifier;
                     return res;
                 },
-                identifier => {
+                (identifier) => {
                     return { name: identifier };
                 },
                 "elements"
@@ -1916,7 +1907,7 @@ export default {
                 res["tags"] = tags;
             }
             return res;
-        }
+        },
     },
     created() {
         if (this.elementsType !== "collection_contents") {
@@ -1942,28 +1933,28 @@ export default {
                 }
             }
             UploadUtils.getUploadDatatypes(
-                extensions => {
+                (extensions) => {
                     this.extensions = extensions;
                     this.extension = UploadUtils.DEFAULT_EXTENSION;
                 },
                 false,
                 UploadUtils.AUTO_EXTENSION
             );
-            UploadUtils.getUploadGenomes(genomes => {
+            UploadUtils.getUploadGenomes((genomes) => {
                 this.genomes = genomes;
                 this.genome = UploadUtils.DEFAULT_GENOME;
             }, UploadUtils.DEFAULT_GENOME);
         }
     },
     watch: {
-        addColumnRegexType: function(val) {
+        addColumnRegexType: function (val) {
             if (val == "groups") {
                 this.addColumnRegexGroupCount = 1;
             }
             if (val == "replacement") {
                 this.addColumnRegexReplacement = "\0";
             }
-        }
+        },
     },
     components: {
         HotTable,
@@ -1977,8 +1968,8 @@ export default {
         RuleModalHeader,
         RuleModalMiddle,
         RuleModalFooter,
-        Select2
-    }
+        Select2,
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/RulesDisplay.vue b/client/galaxy/scripts/components/RulesDisplay.vue
index 56109a307dc7..f3e0accf6c66 100644
--- a/client/galaxy/scripts/components/RulesDisplay.vue
+++ b/client/galaxy/scripts/components/RulesDisplay.vue
@@ -38,20 +38,20 @@ const RuleDisplayPreview = {
     props: {
         rule: {
             required: true,
-            type: Object
+            type: Object,
         },
         colHeaders: {
             type: Array,
-            required: false
-        }
+            required: false,
+        },
     },
     computed: {
         title() {
             const ruleType = this.rule.type;
             return RuleDefs.RULES[ruleType].display(this.rule, this.colHeaders);
-        }
+        },
     },
-    methods: {}
+    methods: {},
 };
 
 const IdentifierDisplayPreview = {
@@ -63,15 +63,15 @@ const IdentifierDisplayPreview = {
     props: {
         type: {
             type: String,
-            required: true
+            required: true,
         },
         columns: {
-            required: true
+            required: true,
         },
         colHeaders: {
             type: Array,
-            required: true
-        }
+            required: true,
+        },
     },
     computed: {
         typeDisplay() {
@@ -82,40 +82,40 @@ const IdentifierDisplayPreview = {
         },
         columnsLabel() {
             return RuleDefs.columnDisplay(this.columns, this.colHeaders);
-        }
-    }
+        },
+    },
 };
 
 export default {
-    data: function() {
+    data: function () {
         return {};
     },
     computed: {
-        mapping: function() {
+        mapping: function () {
             return this.inputRules ? this.inputRules.mapping : [];
         },
-        rules: function() {
+        rules: function () {
             return this.inputRules ? this.inputRules.rules : [];
         },
-        columnData: function() {
+        columnData: function () {
             const colHeadersPerRule = [];
             const hotData = RuleDefs.applyRules([], [], [], this.rules, colHeadersPerRule);
             return { colHeadersPerRule: colHeadersPerRule, columns: hotData.columns };
         },
-        colHeaders: function() {
+        colHeaders: function () {
             const columns = this.columnData.columns;
             return RuleDefs.colHeadersFor([], columns);
-        }
+        },
     },
     props: {
         inputRules: {
             required: false,
-            type: Object
-        }
+            type: Object,
+        },
     },
     components: {
         RuleDisplayPreview,
-        IdentifierDisplayPreview
-    }
+        IdentifierDisplayPreview,
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Select2.js b/client/galaxy/scripts/components/Select2.js
index e8e23a1b7d33..e76f5563210d 100644
--- a/client/galaxy/scripts/components/Select2.js
+++ b/client/galaxy/scripts/components/Select2.js
@@ -5,7 +5,7 @@ import $ from "jquery";
 export default {
     props: ["options", "value", "placeholder", "containerClass", "enabled"],
     template: `<select><slot></slot></select>`,
-    mounted: function() {
+    mounted: function () {
         const vm = this;
         // TODO: refactor property list to objects that allow defaults and types
         let enabled = this.enabled;
@@ -17,7 +17,7 @@ export default {
             placeholder: this.placeholder,
             allowClear: !!this.placeholder,
             enable: enabled,
-            dropdownAutoWidth: true
+            dropdownAutoWidth: true,
         };
         if (this.containerClass) {
             select2Options.containerCssClass = this.containerClass;
@@ -28,28 +28,24 @@ export default {
             .val(this.value)
             .trigger("change")
             // emit event on change.
-            .on("change", function(event) {
+            .on("change", function (event) {
                 vm.$emit("input", event.val);
             });
     },
     watch: {
-        value: function(value) {
+        value: function (value) {
             // update value
             $(this.$el).val(value);
         },
-        options: function(options) {
+        options: function (options) {
             // update options
-            $(this.$el)
-                .empty()
-                .select2({ data: options });
+            $(this.$el).empty().select2({ data: options });
         },
-        enabled: function(value) {
+        enabled: function (value) {
             $(this.$el).select2("enable", value);
-        }
+        },
+    },
+    destroyed: function () {
+        $(this.$el).off().select2("destroy");
     },
-    destroyed: function() {
-        $(this.$el)
-            .off()
-            .select2("destroy");
-    }
 };
diff --git a/client/galaxy/scripts/components/SelectionDialog/DataDialogSearch.vue b/client/galaxy/scripts/components/SelectionDialog/DataDialogSearch.vue
index ed57a831eada..d562dec6b99d 100644
--- a/client/galaxy/scripts/components/SelectionDialog/DataDialogSearch.vue
+++ b/client/galaxy/scripts/components/SelectionDialog/DataDialogSearch.vue
@@ -2,7 +2,7 @@
     <b-input-group>
         <b-input v-model="filter" placeholder="Type to Search" />
         <b-input-group-append>
-            <b-btn :disabled="!filter" @click="filter = ''"><i class="fa fa-times"/></b-btn>
+            <b-btn :disabled="!filter" @click="filter = ''"><i class="fa fa-times" /></b-btn>
         </b-input-group-append>
     </b-input-group>
 </template>
@@ -22,8 +22,8 @@ export default {
             },
             set(val) {
                 this.$emit("input", val);
-            }
-        }
-    }
+            },
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/SelectionDialog/DataDialogTable.vue b/client/galaxy/scripts/components/SelectionDialog/DataDialogTable.vue
index fa4c076b7522..a953f058a85b 100644
--- a/client/galaxy/scripts/components/SelectionDialog/DataDialogTable.vue
+++ b/client/galaxy/scripts/components/SelectionDialog/DataDialogTable.vue
@@ -43,20 +43,20 @@ export default {
     props: {
         items: {
             type: Array,
-            required: true
+            required: true,
         },
         filter: {
             type: String,
-            default: null
+            default: null,
         },
         multiple: {
             type: Boolean,
-            default: false
+            default: false,
         },
         leafIcon: {
             type: String,
-            default: "fa fa-file-o"
-        }
+            default: "fa fa-file-o",
+        },
     },
     data() {
         return {
@@ -64,19 +64,19 @@ export default {
             fields: [
                 {
                     key: "label",
-                    sortable: true
+                    sortable: true,
                 },
                 {
                     key: "details",
-                    sortable: true
+                    sortable: true,
                 },
                 {
                     key: "time",
-                    sortable: true
-                }
+                    sortable: true,
+                },
             ],
             nItems: 0,
-            perPage: 100
+            perPage: 100,
         };
     },
     watch: {
@@ -84,19 +84,19 @@ export default {
             immediate: true,
             handler(items) {
                 this.filtered(items);
-            }
-        }
+            },
+        },
     },
     methods: {
         /** Resets pagination when a filter/search word is entered **/
-        filtered: function(items) {
+        filtered: function (items) {
             this.nItems = items.length;
             this.currentPage = 1;
         },
         /** Collects selected datasets in value array **/
-        clicked: function(record) {
+        clicked: function (record) {
             this.$emit("clicked", record);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/SelectionDialog/DatasetCollectionDialog.test.js b/client/galaxy/scripts/components/SelectionDialog/DatasetCollectionDialog.test.js
index d3e8d0235753..50dddfe3624e 100644
--- a/client/galaxy/scripts/components/SelectionDialog/DatasetCollectionDialog.test.js
+++ b/client/galaxy/scripts/components/SelectionDialog/DatasetCollectionDialog.test.js
@@ -9,7 +9,7 @@ import { shallowMount, createLocalVue } from "@vue/test-utils";
 const mockOptions = {
     callback: () => {},
     modalStatic: true,
-    history: "f2db41e1fa331b3e"
+    history: "f2db41e1fa331b3e",
 };
 
 describe("DatasetCollectionDialog.vue", () => {
@@ -23,7 +23,7 @@ describe("DatasetCollectionDialog.vue", () => {
         localVue = createLocalVue();
         wrapper = shallowMount(DatasetCollectionDialog, {
             propsData: mockOptions,
-            localVue: localVue
+            localVue: localVue,
         });
     });
 
diff --git a/client/galaxy/scripts/components/SelectionDialog/DatasetCollectionDialog.vue b/client/galaxy/scripts/components/SelectionDialog/DatasetCollectionDialog.vue
index 742688f7b231..d980d687d931 100644
--- a/client/galaxy/scripts/components/SelectionDialog/DatasetCollectionDialog.vue
+++ b/client/galaxy/scripts/components/SelectionDialog/DatasetCollectionDialog.vue
@@ -33,8 +33,8 @@ export default {
     props: {
         history: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
@@ -43,42 +43,42 @@ export default {
             items: [],
             modalShow: true,
             optionsShow: false,
-            hasValue: false
+            hasValue: false,
         };
     },
-    created: function() {
+    created: function () {
         this.load();
     },
     methods: {
         formatRows() {},
-        clicked: function(record) {
+        clicked: function (record) {
             this.modalShow = false;
             this.callback(record);
         },
         /** Performs server request to retrieve data records **/
-        load: function() {
+        load: function () {
             this.filter = null;
             this.optionsShow = false;
             const Galaxy = getGalaxyInstance();
             const url = `${Galaxy.root}api/histories/${this.history}/contents?type=dataset_collection`;
             axios
                 .get(url)
-                .then(response => {
-                    this.items = response.data.map(item => {
+                .then((response) => {
+                    this.items = response.data.map((item) => {
                         return {
                             id: item.id,
                             label: item.name,
                             time: item.created_time,
-                            isLeaf: true
+                            isLeaf: true,
                         };
                     });
                     this.formatRows();
                     this.optionsShow = true;
                 })
-                .catch(errorMessage => {
+                .catch((errorMessage) => {
                     this.errorMessage = errorMessageAsString(errorMessage);
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/SelectionDialog/SelectionDialog.test.js b/client/galaxy/scripts/components/SelectionDialog/SelectionDialog.test.js
index 249cc99dfb15..a101f7c7a221 100644
--- a/client/galaxy/scripts/components/SelectionDialog/SelectionDialog.test.js
+++ b/client/galaxy/scripts/components/SelectionDialog/SelectionDialog.test.js
@@ -3,7 +3,7 @@ import { mount, createLocalVue } from "@vue/test-utils";
 
 const mockOptions = {
     callback: () => {},
-    modalStatic: true
+    modalStatic: true,
 };
 
 describe("SelectionDialog.vue", () => {
@@ -19,14 +19,14 @@ describe("SelectionDialog.vue", () => {
         wrapper = mount(SelectionDialog, {
             slots: {
                 options: "<tree-options />",
-                search: "<cool-search />"
+                search: "<cool-search />",
             },
             stubs: {
                 "tree-options": "<div id='tree-options'/>",
-                "cool-search": "<div id='cool-search'/>"
+                "cool-search": "<div id='cool-search'/>",
             },
             propsData: mockOptions,
-            localVue
+            localVue,
         });
     });
 
diff --git a/client/galaxy/scripts/components/SelectionDialog/SelectionDialog.vue b/client/galaxy/scripts/components/SelectionDialog/SelectionDialog.vue
index 9028f9921456..b0e38b87b886 100644
--- a/client/galaxy/scripts/components/SelectionDialog/SelectionDialog.vue
+++ b/client/galaxy/scripts/components/SelectionDialog/SelectionDialog.vue
@@ -34,29 +34,29 @@ export default {
     props: {
         multiple: {
             type: Boolean,
-            default: false
+            default: false,
         },
         modalStatic: {
             type: Boolean,
-            default: false
+            default: false,
         },
         errorMessage: {
             type: String,
-            default: null
+            default: null,
         },
         optionsShow: {
             type: Boolean,
-            default: false
+            default: false,
         },
         modalShow: {
             type: Boolean,
-            default: true
+            default: true,
         },
         hideModal: {
             type: Function,
-            required: true
-        }
-    }
+            required: true,
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/SelectionDialog/SelectionDialogMixin.js b/client/galaxy/scripts/components/SelectionDialog/SelectionDialogMixin.js
index 9529f860c568..1da6a8d00581 100644
--- a/client/galaxy/scripts/components/SelectionDialog/SelectionDialogMixin.js
+++ b/client/galaxy/scripts/components/SelectionDialog/SelectionDialogMixin.js
@@ -6,12 +6,12 @@ export default {
     components: {
         "selection-dialog": SelectionDialog,
         "data-dialog-table": DataDialogTable,
-        "data-dialog-search": DataDialogSearch
+        "data-dialog-search": DataDialogSearch,
     },
     props: {
         callback: {
             type: Function,
-            required: true
-        }
-    }
+            required: true,
+        },
+    },
 };
diff --git a/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js b/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js
index 556054a438c9..409e371fff42 100644
--- a/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js
+++ b/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js
@@ -9,7 +9,7 @@ import { shallowMount, createLocalVue } from "@vue/test-utils";
 
 const mockOptions = {
     callback: () => {},
-    modalStatic: true
+    modalStatic: true,
 };
 
 describe("WorkflowDialog.vue", () => {
@@ -20,11 +20,11 @@ describe("WorkflowDialog.vue", () => {
     beforeEach(() => {
         axiosMock = new MockAdapter(axios);
         setupTestGalaxy();
-        rewire.__Rewire__("_addAttributes", workflow => workflow);
+        rewire.__Rewire__("_addAttributes", (workflow) => workflow);
         localVue = createLocalVue();
         wrapper = shallowMount(WorkflowDialog, {
             propsData: mockOptions,
-            localVue: localVue
+            localVue: localVue,
         });
     });
 
diff --git a/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.vue b/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.vue
index 0adbf7458ad4..ee3d040ede94 100644
--- a/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.vue
+++ b/client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.vue
@@ -36,41 +36,41 @@ export default {
             items: [],
             modalShow: true,
             optionsShow: false,
-            hasValue: false
+            hasValue: false,
         };
     },
-    created: function() {
+    created: function () {
         this.services = new Services();
         this.load();
     },
     methods: {
         formatRows() {},
-        clicked: function(record) {
+        clicked: function (record) {
             this.modalShow = false;
             this.callback(record);
         },
         /** Performs server request to retrieve data records **/
-        load: function() {
+        load: function () {
             this.filter = null;
             this.optionsShow = false;
             this.services
                 .getWorkflows()
-                .then(items => {
-                    this.items = items.map(item => {
+                .then((items) => {
+                    this.items = items.map((item) => {
                         return {
                             id: item.id,
                             label: item.name,
                             time: item.create_time,
-                            isLeaf: true
+                            isLeaf: true,
                         };
                     });
                     this.formatRows();
                     this.optionsShow = true;
                 })
-                .catch(errorMessage => {
+                .catch((errorMessage) => {
                     this.errorMessage = errorMessage.toString();
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Sharing.vue b/client/galaxy/scripts/components/Sharing.vue
index d0624563fc02..e44dfce69a5e 100644
--- a/client/galaxy/scripts/components/Sharing.vue
+++ b/client/galaxy/scripts/components/Sharing.vue
@@ -22,7 +22,7 @@
                     <p>Anyone can view and import this {{ model_class_lc }} by visiting the following URL:</p>
                     <blockquote>
                         <a id="item-url" :href="item_url" target="_top">{{ item_url }}</a>
-                        <span id="item-url-text" style="display: none">
+                        <span id="item-url-text" style="display: none;">
                             {{ item_url_parts[0] }}<span id="item-identifier">{{ item_url_parts[1] }}</span>
                         </span>
                         <a href="javascript:void(0)" id="edit-identifier"
@@ -150,16 +150,16 @@ export default {
     props: {
         id: {
             type: String,
-            required: true
+            required: true,
         },
         plural_name: {
             type: String,
-            required: true
+            required: true,
         },
         model_class: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     computed: {
         model_class_lc() {
@@ -196,7 +196,7 @@ export default {
         },
         show_danger() {
             return this.err_msg !== null;
-        }
+        },
     },
     data() {
         const Galaxy = getGalaxyInstance();
@@ -211,68 +211,68 @@ export default {
                 username_and_slug: "username_and_slug",
                 importable: false,
                 published: false,
-                users_shared_with: []
+                users_shared_with: [],
             },
             share_fields: ["email", { key: "id", label: "" }],
-            make_members_public: false
+            make_members_public: false,
         };
     },
-    created: function() {
+    created: function () {
         this.getModel();
     },
-    updated: function() {
+    updated: function () {
         this.createSlugHandler();
     },
     methods: {
-        getModel: function() {
+        getModel: function () {
             this.ready = false;
             axios
                 .get(`${getAppRoot()}api/${this.plural_name_lc}/${this.id}/sharing`)
-                .then(response => {
+                .then((response) => {
                     this.item = response.data;
                     this.ready = true;
                 })
-                .catch(error => (this.err_msg = error.response.data.err_msg));
+                .catch((error) => (this.err_msg = error.response.data.err_msg));
         },
-        setUsername: function() {
+        setUsername: function () {
             const Galaxy = getGalaxyInstance();
             axios
                 .put(`${getAppRoot()}api/users/${Galaxy.user.id}/information/inputs`, {
-                    username: this.new_username || ""
+                    username: this.new_username || "",
                 })
-                .then(response => {
+                .then((response) => {
                     this.err_msg = null;
                     this.has_username = true;
                     this.getModel();
                 })
-                .catch(error => (this.err_msg = error.response.data.err_msg));
+                .catch((error) => (this.err_msg = error.response.data.err_msg));
         },
-        setSharing: function(action, user_id) {
+        setSharing: function (action, user_id) {
             const data = {
                 action: action,
-                user_id: user_id
+                user_id: user_id,
             };
             if (this.has_possible_members) {
                 data.make_members_public = this.make_members_public;
             }
             axios
                 .post(`${getAppRoot()}api/${this.plural_name_lc}/${this.id}/sharing`, data)
-                .then(response => {
+                .then((response) => {
                     Object.assign(this.item, response.data);
                     if (response.data.skipped) {
                         this.err_msg = "Some of the items within this object were not published due to an error.";
                     }
                 })
-                .catch(error => (this.err_msg = error.response.data.err_msg));
+                .catch((error) => (this.err_msg = error.response.data.err_msg));
         },
-        createSlugHandler: function() {
-            const on_start = function(text_elt) {
+        createSlugHandler: function () {
+            const on_start = function (text_elt) {
                 // Replace URL with URL text.
                 $("#item-url").hide();
                 $("#item-url-text").show();
 
                 // Allow only lowercase alphanumeric and '-' characters in slug.
-                text_elt.keyup(function() {
+                text_elt.keyup(function () {
                     text_elt.val(
                         $(this)
                             .val()
@@ -282,7 +282,7 @@ export default {
                     );
                 });
             };
-            const on_finish = function(text_elt) {
+            const on_finish = function (text_elt) {
                 // Replace URL text with URL.
                 $("#item-url-text").hide();
                 $("#item-url").show();
@@ -304,7 +304,7 @@ export default {
                 on_start,
                 on_finish
             );
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Tags/StatelessTags.test.js b/client/galaxy/scripts/components/Tags/StatelessTags.test.js
index fa8ca82a5230..48900ecb0621 100644
--- a/client/galaxy/scripts/components/Tags/StatelessTags.test.js
+++ b/client/galaxy/scripts/components/Tags/StatelessTags.test.js
@@ -5,7 +5,7 @@ import Vue from "vue";
 
 describe("Tags/StatelessTags.vue", () => {
     const localVue = createLocalVue();
-    localVue.filter("localize", value => _l(value));
+    localVue.filter("localize", (value) => _l(value));
 
     let testTags = ["abc", "def", "ghi"];
     let wrapper, emitted;
@@ -13,7 +13,7 @@ describe("Tags/StatelessTags.vue", () => {
     beforeEach(async () => {
         wrapper = mount(StatelessTags, { localVue });
         wrapper.setProps({
-            value: testTags
+            value: testTags,
         });
         emitted = wrapper.emitted();
         await Vue.nextTick();
diff --git a/client/galaxy/scripts/components/Tags/StatelessTags.vue b/client/galaxy/scripts/components/Tags/StatelessTags.vue
index 94712aa1f317..0706212f7ab8 100644
--- a/client/galaxy/scripts/components/Tags/StatelessTags.vue
+++ b/client/galaxy/scripts/components/Tags/StatelessTags.vue
@@ -39,14 +39,14 @@ import { createTag } from "./model";
 
 export default {
     components: {
-        VueTagsInput
+        VueTagsInput,
     },
     props: {
         value: { type: Array, required: false, default: () => [] },
         autocompleteItems: { type: Array, required: false, default: () => [] },
         maxVisibleTags: { type: Number, required: false, default: 5 },
         useToggleLink: { type: Boolean, required: false, default: true },
-        disabled: { type: Boolean, required: false, default: false }
+        disabled: { type: Boolean, required: false, default: false },
     },
     data() {
         // initialize toggle value
@@ -55,13 +55,13 @@ export default {
         return {
             tagText: "",
             tagToggle: !isClosed,
-            triggerKeys: [13, " "]
+            triggerKeys: [13, " "],
         };
     },
     computed: {
         tagContainerClasses() {
             return {
-                disabled: this.disabled
+                disabled: this.disabled,
             };
         },
         tagModels() {
@@ -78,19 +78,19 @@ export default {
         },
         tagsVisible() {
             return this.useToggleLink ? this.tagToggle : true;
-        }
+        },
     },
     watch: {
         tagText(newValue) {
             this.$emit("tag-input-changed", newValue);
-        }
+        },
     },
     methods: {
         tagsChanged(newTags) {
             this.$emit("input", this.pluckLabels(newTags));
         },
         pluckLabels(newTags) {
-            return newTags.map(t => createTag(t).toString());
+            return newTags.map((t) => createTag(t).toString());
         },
         toggleTagDisplay() {
             this.tagToggle = !this.tagToggle;
@@ -117,8 +117,8 @@ export default {
         },
         hasHandler(eventName) {
             return Object.keys(this.$listeners).includes(eventName);
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/Tags/Tags.test.js b/client/galaxy/scripts/components/Tags/Tags.test.js
index aede53f1d54e..649dea99f748 100644
--- a/client/galaxy/scripts/components/Tags/Tags.test.js
+++ b/client/galaxy/scripts/components/Tags/Tags.test.js
@@ -10,7 +10,7 @@ import { createTag } from "./model";
 
 describe("Tags/Tags.vue", () => {
     const localVue = createLocalVue();
-    localVue.filter("localize", value => _l(value));
+    localVue.filter("localize", (value) => _l(value));
     localVue.use(Vuex);
 
     let id = "testId",
@@ -37,15 +37,15 @@ describe("Tags/Tags.vue", () => {
 
         tagService = new TagService({ id, itemClass, context });
 
-        tagService.save = async function(tag) {
+        tagService.save = async function (tag) {
             return createTag(tag);
         };
 
-        tagService.delete = async function(tag) {
+        tagService.delete = async function (tag) {
             return createTag(tag);
         };
 
-        tagService.autocomplete = async function(txt) {
+        tagService.autocomplete = async function (txt) {
             return [txt].map(createTag);
         };
 
@@ -57,8 +57,8 @@ describe("Tags/Tags.vue", () => {
             propsData: {
                 tags: startingTags,
                 storeKey,
-                tagService
-            }
+                tagService,
+            },
         });
 
         emitted = wrapper.emitted();
@@ -121,11 +121,11 @@ describe("Tags/Tags.vue", () => {
             }
         });
 
-        it("should generate autocomplete items when you set the search text", done => {
+        it("should generate autocomplete items when you set the search text", (done) => {
             let sampleTxt = "floobar";
-            subscription = tagService.autocompleteOptions.subscribe(results => {
+            subscription = tagService.autocompleteOptions.subscribe((results) => {
                 expect(results.length).equal(1);
-                results.forEach(r => {
+                results.forEach((r) => {
                     expect(r.text).equal(sampleTxt);
                 });
                 done();
@@ -133,11 +133,11 @@ describe("Tags/Tags.vue", () => {
             tagService.autocompleteSearchText = sampleTxt;
         });
 
-        it("should debounce autocomplete requests", done => {
+        it("should debounce autocomplete requests", (done) => {
             let sampleTxt = "floobar";
-            subscription = tagService.autocompleteOptions.subscribe(results => {
+            subscription = tagService.autocompleteOptions.subscribe((results) => {
                 expect(results.length).equal(1);
-                results.forEach(r => {
+                results.forEach((r) => {
                     expect(r.text).equal(sampleTxt);
                 });
                 done();
diff --git a/client/galaxy/scripts/components/Tags/Tags.vue b/client/galaxy/scripts/components/Tags/Tags.vue
index 2fd42ced6298..9966e71d0cae 100644
--- a/client/galaxy/scripts/components/Tags/Tags.vue
+++ b/client/galaxy/scripts/components/Tags/Tags.vue
@@ -23,7 +23,7 @@ Vue.use(VueRx);
 
 export default {
     components: {
-        StatelessTags
+        StatelessTags,
     },
 
     props: {
@@ -37,7 +37,7 @@ export default {
         storeKey: { type: String, required: true },
 
         // allows user to edit tag list
-        disabled: { type: Boolean, required: false, default: false }
+        disabled: { type: Boolean, required: false, default: false },
     },
 
     computed: {
@@ -47,16 +47,16 @@ export default {
             },
             set(tags) {
                 this.updateTags({ key: this.storeKey, tags });
-            }
-        }
+            },
+        },
     },
 
     subscriptions() {
         return {
             autocompleteItems: this.tagService.autocompleteOptions.pipe(
                 // without the ones we've already selected
-                map(resultTags => diffTags(resultTags, this.tags))
-            )
+                map((resultTags) => diffTags(resultTags, this.tags))
+            ),
         };
     },
 
@@ -69,14 +69,14 @@ export default {
             this.tagService
                 .save(tag)
                 .then(() => addTag(tag))
-                .catch(err => console.warn("Unable to save tag", err));
+                .catch((err) => console.warn("Unable to save tag", err));
         },
 
         beforeDeletingTag({ tag, deleteTag }) {
             this.tagService
                 .delete(tag)
                 .then(() => deleteTag(tag))
-                .catch(err => console.warn("Unable to delete tag", err));
+                .catch((err) => console.warn("Unable to delete tag", err));
         },
 
         // Set search value on tag service input proprety and eventually search
@@ -87,11 +87,11 @@ export default {
             this.tagService.autocompleteSearchText = searchTxt;
         },
 
-        ...mapActions(["updateTags", "initializeTags"])
+        ...mapActions(["updateTags", "initializeTags"]),
     },
 
     mounted() {
         this.initializeTags({ key: this.storeKey, tags: this.tags });
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Tags/model.js b/client/galaxy/scripts/components/Tags/model.js
index de079521a947..957a88b6258e 100644
--- a/client/galaxy/scripts/components/Tags/model.js
+++ b/client/galaxy/scripts/components/Tags/model.js
@@ -19,47 +19,47 @@ function TagModel(props = {}) {
     // style enumerable for vue-tags-input
     Object.defineProperty(this, "style", {
         enumerable: true,
-        get: function() {
+        get: function () {
             if (this.text.startsWith("name:")) {
                 const { primary, contrasting, darker } = keyedColorScheme(this.text);
 
                 const styles = {
                     "background-color": primary,
                     color: contrasting,
-                    "border-color": darker
+                    "border-color": darker,
                 };
 
                 return Object.keys(styles)
-                    .map(prop => `${prop}: ${styles[prop]}`)
+                    .map((prop) => `${prop}: ${styles[prop]}`)
                     .join(";");
             }
             return "";
-        }
+        },
     });
 
     // Changes name:foo to #foo
     Object.defineProperty(this, "label", {
         enumerable: true,
-        get: function() {
+        get: function () {
             return this.text.startsWith("name:") ? this.text.replace("name:", "#") : this.text;
-        }
+        },
     });
 
     // valid flag
     Object.defineProperty(this, "valid", {
         enumerable: false,
-        get: function() {
+        get: function () {
             if (!this.text.length) return false;
             return this.text != "name:";
-        }
+        },
     });
 }
 
-TagModel.prototype.equals = function(otherTag) {
+TagModel.prototype.equals = function (otherTag) {
     return this.text == otherTag.text;
 };
 
-TagModel.prototype.toString = function() {
+TagModel.prototype.toString = function () {
     return this.text;
 };
 
@@ -83,5 +83,5 @@ export function createTag(data) {
 export const diffTags = (newTags, existingTags) => {
     const newModels = newTags.map(createTag);
     const existingModels = existingTags.map(createTag);
-    return newModels.filter(tag => !existingModels.some(st => st.equals(tag)));
+    return newModels.filter((tag) => !existingModels.some((st) => st.equals(tag)));
 };
diff --git a/client/galaxy/scripts/components/Tags/mounts.js b/client/galaxy/scripts/components/Tags/mounts.js
index 2ac287cdcc43..6c6f0747dce9 100644
--- a/client/galaxy/scripts/components/Tags/mounts.js
+++ b/client/galaxy/scripts/components/Tags/mounts.js
@@ -20,7 +20,7 @@ export const mountMakoTags = (options = {}, el) => {
         storeKey: `${itemClass}-${id}`,
         tagService: new TagService({ id, itemClass, context }),
         tags,
-        disabled
+        disabled,
     };
 
     const fn = mountVueComponent(Tags);
@@ -35,7 +35,7 @@ export const mountMakoTags = (options = {}, el) => {
  * @param {object} options Passed options from mount fn
  */
 const makoClickHandler = (options, vm) =>
-    function(tag) {
+    function (tag) {
         if (!tag) {
             return;
         }
@@ -74,7 +74,7 @@ export const mountModelTags = (options = {}, el) => {
         storeKey: `${itemClass}-${id}`,
         tagService: new BackboneTagService({ id, itemClass, context, model }),
         tags,
-        disabled
+        disabled,
     };
 
     const fn = mountVueComponent(Tags);
diff --git a/client/galaxy/scripts/components/Tags/tagService.js b/client/galaxy/scripts/components/Tags/tagService.js
index 7d600e1b4517..fb643ea5e79b 100644
--- a/client/galaxy/scripts/components/Tags/tagService.js
+++ b/client/galaxy/scripts/components/Tags/tagService.js
@@ -31,11 +31,11 @@ export class TagService {
      */
     get autocompleteOptions() {
         return this._searchText.pipe(
-            map(txt => txt.replace("name:", "")),
-            filter(txt => txt.length),
+            map((txt) => txt.replace("name:", "")),
+            filter((txt) => txt.length),
             debounceTime(this.debounceInterval),
             distinctUntilChanged(),
-            switchMap(txt => this.autocomplete(txt))
+            switchMap((txt) => this.autocomplete(txt))
         );
     }
 
@@ -105,8 +105,8 @@ export class TagService {
 export function parseAutocompleteResults(rawResponse) {
     return rawResponse
         .split("\n")
-        .filter(line => line.includes("|"))
-        .map(line => line.split("|")[0])
-        .filter(label => label.length)
-        .filter(label => label !== "#Header");
+        .filter((line) => line.includes("|"))
+        .map((line) => line.split("|")[0])
+        .filter((label) => label.length)
+        .filter((label) => label !== "#Header");
 }
diff --git a/client/galaxy/scripts/components/Tags/tagService.test.js b/client/galaxy/scripts/components/Tags/tagService.test.js
index ee4b3d77c2fa..0bb3e1b65fa6 100644
--- a/client/galaxy/scripts/components/Tags/tagService.test.js
+++ b/client/galaxy/scripts/components/Tags/tagService.test.js
@@ -13,13 +13,13 @@ describe("Tags/tagService.js", () => {
         id: 123,
         itemClass: "fooClass",
         context: "",
-        debounceInterval: 50 // shorter value than default for unit tests
+        debounceInterval: 50, // shorter value than default for unit tests
     };
 
     let svc = new TagService(svcParams);
 
     let mockAxios = {
-        get: () => null
+        get: () => null,
     };
 
     let stub;
@@ -87,10 +87,10 @@ describe("Tags/tagService.js", () => {
 
         let successResponse = {
             status: 200,
-            data: autocompleteResponse
+            data: autocompleteResponse,
         };
 
-        let checkAutocompleteResult = result => {
+        let checkAutocompleteResult = (result) => {
             assert(result);
             assert(result instanceof Array);
             assert(result.length == 2);
@@ -109,7 +109,7 @@ describe("Tags/tagService.js", () => {
 
         // hit the search input with multiple entries, only one ajax call
         // should result because of debouncing
-        it("should debounce autocomplete search inputs", done => {
+        it("should debounce autocomplete search inputs", (done) => {
             let searchResult;
 
             // ends subscription to observable so test doesn't go on forever
@@ -121,8 +121,8 @@ describe("Tags/tagService.js", () => {
             stub = sinon.stub(mockAxios, "get").resolves(successResponse);
 
             svc.autocompleteOptions.pipe(takeUntil(timer)).subscribe(
-                result => (searchResult = result),
-                err => console.log("error", err),
+                (result) => (searchResult = result),
+                (err) => console.log("error", err),
                 () => {
                     assert(stub.called, "Ajax call not made");
                     assert(stub.callCount == 1, `Wrong number of ajax calls: ${stub.callCount}`);
diff --git a/client/galaxy/scripts/components/ToolEntryPoints/ToolEntryPoints.vue b/client/galaxy/scripts/components/ToolEntryPoints/ToolEntryPoints.vue
index 90e9f53120f0..f36f04ff0fa1 100644
--- a/client/galaxy/scripts/components/ToolEntryPoints/ToolEntryPoints.vue
+++ b/client/galaxy/scripts/components/ToolEntryPoints/ToolEntryPoints.vue
@@ -38,35 +38,35 @@ export default {
     props: {
         jobId: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
-            entryPoints: []
+            entryPoints: [],
         };
     },
-    created: function() {
+    created: function () {
         this.pollEntryPoints();
     },
-    beforeDestroy: function() {
+    beforeDestroy: function () {
         clearPolling();
     },
     computed: {
-        interactiveToolsLink: function() {
+        interactiveToolsLink: function () {
             return getAppRoot() + "interactivetool_entry_points/list";
-        }
+        },
     },
     methods: {
-        pollEntryPoints: function() {
-            const onUpdate = entryPoints => {
+        pollEntryPoints: function () {
+            const onUpdate = (entryPoints) => {
                 this.entryPoints = entryPoints;
             };
-            const onError = e => {
+            const onError = (e) => {
                 console.error(e);
             };
             pollUntilActive(onUpdate, onError, { job_id: this.jobId });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index e0500e6eb15b..674f62f0e5e8 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -21,13 +21,13 @@ export default {
     props: {
         toolId: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
             deprecated: null,
-            deprecatedMessage: ""
+            deprecatedMessage: "",
         };
     },
     created() {
@@ -41,7 +41,7 @@ export default {
                 toolId = toolIdSlash[toolIdSlash.length - 2];
             }
             return toolId;
-        }
+        },
     },
     methods: {
         loadRecommendations() {
@@ -49,10 +49,10 @@ export default {
             const url = `${getAppRoot()}api/workflows/get_tool_predictions`;
             axios
                 .post(url, {
-                    tool_sequence: toolId
+                    tool_sequence: toolId,
                 })
-                .then(response => {
-                    axios.get(`${getAppRoot()}api/datatypes/mapping`).then(responseMapping => {
+                .then((response) => {
+                    axios.get(`${getAppRoot()}api/datatypes/mapping`).then((responseMapping) => {
                         const predData = response.data.predicted_data;
                         const datatypesMapping = responseMapping.data;
                         const extToType = datatypesMapping.ext_to_class_name;
@@ -105,11 +105,7 @@ export default {
         },
         renderD3Tree(predictedTools) {
             const duration = 750;
-            const svg = d3
-                .select("#tool-recommendation")
-                .append("svg")
-                .attr("class", "tree-size")
-                .append("g");
+            const svg = d3.select("#tool-recommendation").append("svg").attr("class", "tree-size").append("g");
             let i = 0;
             let root = null;
             let x = 0;
@@ -130,19 +126,19 @@ export default {
 
             const tree = d3.layout.tree().size([y, x]);
 
-            const diagonal = d3.svg.diagonal().projection(d => {
+            const diagonal = d3.svg.diagonal().projection((d) => {
                 return [d.y, d.x];
             });
-            const update = source => {
+            const update = (source) => {
                 // Compute the new tree layout.
                 const nodes = tree.nodes(root).reverse();
                 const links = tree.links(nodes);
                 // Normalize for fixed-depth.
-                nodes.forEach(d => {
+                nodes.forEach((d) => {
                     d.y = d.depth * 180;
                 });
                 // Update the nodes…
-                const node = svg.selectAll("g.node").data(nodes, d => {
+                const node = svg.selectAll("g.node").data(nodes, (d) => {
                     return d.id || (d.id = ++i);
                 });
                 // Enter any new nodes at the parent's previous position.
@@ -150,32 +146,32 @@ export default {
                     .enter()
                     .append("g")
                     .attr("class", "node")
-                    .attr("transform", d => {
+                    .attr("transform", (d) => {
                         return "translate(" + source.y0 + "," + source.x0 + ")";
                     })
                     .on("click", click);
                 nodeEnter.append("circle").attr("r", 1e-6);
                 nodeEnter
                     .append("text")
-                    .attr("x", d => {
+                    .attr("x", (d) => {
                         return d.children || d._children ? -10 : 10;
                     })
                     .attr("dy", ".35em")
-                    .attr("text-anchor", d => {
+                    .attr("text-anchor", (d) => {
                         return d.children || d._children ? "end" : "start";
                     })
-                    .text(d => {
+                    .text((d) => {
                         return d.name;
                     })
                     .attr("class", "node-enter");
-                nodeEnter.append("title").text(d => {
+                nodeEnter.append("title").text((d) => {
                     return d.children || d._children ? "Click to collapse" : "Click to open tool definition";
                 });
                 // Transition nodes to their new position.
                 const nodeUpdate = node
                     .transition()
                     .duration(duration)
-                    .attr("transform", d => {
+                    .attr("transform", (d) => {
                         return "translate(" + d.y + "," + d.x + ")";
                     });
                 nodeUpdate.select("circle").attr("r", 4.5);
@@ -185,45 +181,43 @@ export default {
                     .exit()
                     .transition()
                     .duration(duration)
-                    .attr("transform", d => {
+                    .attr("transform", (d) => {
                         return "translate(" + source.y + "," + source.x + ")";
                     })
                     .remove();
                 nodeExit.select("circle").attr("r", 1e-6);
                 nodeExit.select("text").attr("class", "node-enter");
                 // Update the links
-                const link = svg.selectAll("path.link").data(links, d => {
+                const link = svg.selectAll("path.link").data(links, (d) => {
                     return d.target.id;
                 });
                 // Enter any new links at the parent's previous position.
                 link.enter()
                     .insert("path", "g")
                     .attr("class", "link")
-                    .attr("d", d => {
+                    .attr("d", (d) => {
                         const o = { x: source.x0, y: source.y0 };
                         return diagonal({ source: o, target: o });
                     });
                 // Transition links to their new position.
-                link.transition()
-                    .duration(duration)
-                    .attr("d", diagonal);
+                link.transition().duration(duration).attr("d", diagonal);
                 // Transition exiting nodes to the parent's new position.
                 link.exit()
                     .transition()
                     .duration(duration)
-                    .attr("d", d => {
+                    .attr("d", (d) => {
                         const o = { x: source.x, y: source.y };
                         return diagonal({ source: o, target: o });
                     })
                     .remove();
                 // Stash the old positions for transition.
-                nodes.forEach(d => {
+                nodes.forEach((d) => {
                     d.x0 = d.x;
                     d.y0 = d.y;
                 });
             };
             // Toggle children on click.
-            const click = d => {
+            const click = (d) => {
                 if (d.children) {
                     d._children = d.children;
                     d.children = null;
@@ -237,7 +231,7 @@ export default {
                     document.location.href = `${getAppRoot()}tool_runner?tool_id=${tId}`;
                 }
             };
-            const collapse = d => {
+            const collapse = (d) => {
                 if (d.children) {
                     d._children = d.children;
                     d._children.forEach(collapse);
@@ -249,7 +243,7 @@ export default {
             root.y0 = 0;
             root.children.forEach(collapse);
             update(root);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.vue b/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.vue
index 00d933adb075..7e4f7b1c10f2 100644
--- a/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.vue
+++ b/client/galaxy/scripts/components/ToolsView/ToolsSchemaJson/ToolsJson.vue
@@ -24,8 +24,8 @@ export default {
                                   name: tool.name,
                                   description: tool.help || tool.description,
                                   softwareVersion: tool.version,
-                                  url: getAppRoot() + String(tool.link).substring(1)
-                              }
+                                  url: getAppRoot() + String(tool.link).substring(1),
+                              },
                           ]
                         : _acc;
                 }
@@ -37,14 +37,14 @@ export default {
             }
             return {
                 "@context": "http://schema.org",
-                "@graph": tools.reduce(extractSections, [])
+                "@graph": tools.reduce(extractSections, []),
             };
-        }
+        },
     },
     created() {
         axios
             .get(`${getAppRoot()}api/tools?tool_help=True`)
-            .then(response => {
+            .then((response) => {
                 this.schemaTagObj = this.createToolsJson(response.data);
                 const el = document.createElement("script");
                 el.id = "schema-json";
@@ -52,9 +52,9 @@ export default {
                 el.text = JSON.stringify(this.schemaTagObj);
                 document.head.appendChild(el);
             })
-            .catch(error => {
+            .catch((error) => {
                 console.error(error);
             });
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/ToolsView/ToolsView.test.js b/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
index c7f605a02cbc..0721b8963834 100644
--- a/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
+++ b/client/galaxy/scripts/components/ToolsView/ToolsView.test.js
@@ -12,7 +12,7 @@ import axios from "axios";
 
 describe("ToolsView/ToolsView.vue", () => {
     const localVue = createLocalVue();
-    localVue.filter("localize", value => _l(value));
+    localVue.filter("localize", (value) => _l(value));
     let wrapper, emitted, axiosMock;
 
     beforeEach(async () => {
@@ -38,7 +38,7 @@ describe("ToolsView/ToolsView.vue", () => {
     });
 
     it("should render only specific number of tools, equal to current buffer", async () => {
-        let buttons = wrapper.findAll('[type="button"]').filter(button => button.text() === "Info");
+        let buttons = wrapper.findAll('[type="button"]').filter((button) => button.text() === "Info");
         // one 'info' button per tool
         assert(wrapper.vm.buffer.length === buttons.length, "Number of 'info' buttons do not equal the buffer size!");
     });
@@ -47,7 +47,7 @@ describe("ToolsView/ToolsView.vue", () => {
         // findAll() returns WrapperArray, thus regular array.find() won't work
         let infoButton = wrapper
             .findAll('[type="button"]')
-            .filter(button => button.text() === "Info")
+            .filter((button) => button.text() === "Info")
             .at(0);
         const modalId = "modal--" + infoButton.attributes().index;
         const modal = wrapper.find("#" + modalId);
@@ -66,7 +66,7 @@ describe("ToolsView/ToolsView.vue", () => {
 
         let infoButton = wrapper
             .findAll('[type="button"]')
-            .filter(button => button.text() === "Citations")
+            .filter((button) => button.text() === "Citations")
             .at(0);
         const citation = wrapper.find("#" + infoButton.attributes("aria-controls").replace(/ /g, "_"));
 
diff --git a/client/galaxy/scripts/components/ToolsView/ToolsView.vue b/client/galaxy/scripts/components/ToolsView/ToolsView.vue
index 879d5a932d79..480c15d826c5 100644
--- a/client/galaxy/scripts/components/ToolsView/ToolsView.vue
+++ b/client/galaxy/scripts/components/ToolsView/ToolsView.vue
@@ -1,6 +1,6 @@
 <template>
     <div v-infinite-scroll="loadMore" infinite-scroll-disabled="busy">
-        <h2 class="mb-3" style="text-align: center">
+        <h2 class="mb-3" style="text-align: center;">
             <span id="tools-view">Consolidated view of {{ tools.length }} available tools.</span>
         </h2>
         <div v-if="!loading">
@@ -74,14 +74,14 @@ import { setTimeout } from "timers";
 export default {
     components: {
         Citations,
-        isotope
+        isotope,
     },
     directives: { infiniteScroll },
     props: {
         transitionDuration: {
             type: Number,
-            default: 200
-        }
+            default: 200,
+        },
     },
     data() {
         return {
@@ -90,7 +90,7 @@ export default {
             filterOption: null,
             filterText: "",
             busy: false,
-            loading: true
+            loading: true,
         };
     },
     computed: {
@@ -98,24 +98,24 @@ export default {
             return {
                 transitionDuration: this.transitionDuration,
                 masonry: {
-                    fitWidth: true
+                    fitWidth: true,
                 },
                 getFilterData: {
-                    filterByText: el => {
+                    filterByText: (el) => {
                         const re = new RegExp(this.filterText, "i");
                         return el.name.match(re) || el.description.match(re) || el.help.match(re);
-                    }
-                }
+                    },
+                },
             };
-        }
+        },
     },
     created() {
         axios
             .get(`${getAppRoot()}api/tools?tool_help=True`)
-            .then(response => {
+            .then((response) => {
                 this.initialize(response.data);
             })
-            .catch(error => {
+            .catch((error) => {
                 console.error(error);
             });
     },
@@ -151,8 +151,8 @@ export default {
                                   description: tool.description,
                                   url: getAppRoot() + String(tool.link).substring(1),
                                   version: tool.version,
-                                  help: tool.help
-                              }
+                                  help: tool.help,
+                              },
                           ]
                         : _acc;
                 }
@@ -163,9 +163,9 @@ export default {
             }
             return tools
                 .reduce(extractSections, [])
-                .map(a => [Math.random(), a])
+                .map((a) => [Math.random(), a])
                 .sort((a, b) => a[0] - b[0])
-                .map(a => a[1]);
+                .map((a) => a[1]);
         },
         loadMore() {
             if (this.buffer.length < this.tools.length) {
@@ -203,7 +203,7 @@ export default {
             this.tools = this.toolsExtracted(tools);
             this.buffer = this.tools.slice(0, 20);
             this.loading = false;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Toolshed/Index.vue b/client/galaxy/scripts/components/Toolshed/Index.vue
index 41dbbbd47364..81506b3f3482 100644
--- a/client/galaxy/scripts/components/Toolshed/Index.vue
+++ b/client/galaxy/scripts/components/Toolshed/Index.vue
@@ -33,7 +33,7 @@ import InstalledList from "./InstalledList/Index.vue";
 export default {
     components: {
         SearchList,
-        InstalledList
+        InstalledList,
     },
     data() {
         return {
@@ -49,19 +49,19 @@ export default {
             tabValue: true,
             tabOptions: [
                 { text: "Search All", value: true },
-                { text: "Installed Only", value: false }
-            ]
+                { text: "Installed Only", value: false },
+            ],
         };
     },
     watch: {
         tabValue() {
             this.setQuery("");
-        }
+        },
     },
     computed: {
         queryEmpty() {
             return !this.query || this.query.length < this.queryLength;
-        }
+        },
     },
     methods: {
         clearTimer() {
@@ -88,7 +88,7 @@ export default {
         },
         onScroll({ target: { scrollTop, clientHeight, scrollHeight } }) {
             this.scrolled = scrollTop + clientHeight >= scrollHeight;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Toolshed/InstalledList/Details.test.js b/client/galaxy/scripts/components/Toolshed/InstalledList/Details.test.js
index f362b289db04..1294174e027d 100644
--- a/client/galaxy/scripts/components/Toolshed/InstalledList/Details.test.js
+++ b/client/galaxy/scripts/components/Toolshed/InstalledList/Details.test.js
@@ -24,9 +24,9 @@ describe("Details", () => {
                 repo: {
                     tool_shed_url: "tool_shed_url",
                     name: "name",
-                    owner: "owner"
-                }
-            }
+                    owner: "owner",
+                },
+            },
         });
         expect(wrapper.findAll("loading-span-stub").length).to.equal(1);
         expect(wrapper.find("loading-span-stub").attributes("message")).to.equal(
diff --git a/client/galaxy/scripts/components/Toolshed/InstalledList/Details.vue b/client/galaxy/scripts/components/Toolshed/InstalledList/Details.vue
index 8fd02251f8d8..10b167cacdae 100644
--- a/client/galaxy/scripts/components/Toolshed/InstalledList/Details.vue
+++ b/client/galaxy/scripts/components/Toolshed/InstalledList/Details.vue
@@ -23,13 +23,13 @@ export default {
     props: ["repo"],
     components: {
         LoadingSpan,
-        RepositoryDetails
+        RepositoryDetails,
     },
     data() {
         return {
             loading: true,
             toolshedRepository: null,
-            error: null
+            error: null,
         };
     },
     created() {
@@ -42,14 +42,14 @@ export default {
             this.loading = true;
             this.services
                 .getRepositoryByName(this.repo.tool_shed_url, this.repo.name, this.repo.owner)
-                .then(toolshedRepository => {
+                .then((toolshedRepository) => {
                     this.toolshedRepository = toolshedRepository;
                     this.loading = false;
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.error = error;
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Toolshed/InstalledList/Index.test.js b/client/galaxy/scripts/components/Toolshed/InstalledList/Index.test.js
index f9f96c0b65c9..4ae5e2dddd30 100644
--- a/client/galaxy/scripts/components/Toolshed/InstalledList/Index.test.js
+++ b/client/galaxy/scripts/components/Toolshed/InstalledList/Index.test.js
@@ -14,16 +14,16 @@ describe("InstalledList", () => {
                             name: "name_0",
                             description: "description_0",
                             tool_shed_status: {
-                                latest_installable_revision: false
-                            }
+                                latest_installable_revision: false,
+                            },
                         },
                         {
                             name: "name_1",
                             description: "description_1",
                             tool_shed_status: {
-                                latest_installable_revision: true
-                            }
-                        }
+                                latest_installable_revision: true,
+                            },
+                        },
                     ];
                 }
             }
@@ -33,11 +33,11 @@ describe("InstalledList", () => {
     it("test installed list", async () => {
         const wrapper = mount(Index, {
             propsData: {
-                filter: ""
+                filter: "",
             },
             stubs: {
-                RepositoryDetails: true
-            }
+                RepositoryDetails: true,
+            },
         });
         expect(wrapper.find(".loading-message").text()).to.equal("Loading installed repositories...");
         await Vue.nextTick();
diff --git a/client/galaxy/scripts/components/Toolshed/InstalledList/Index.vue b/client/galaxy/scripts/components/Toolshed/InstalledList/Index.vue
index a72225f47625..5cd31cedf644 100644
--- a/client/galaxy/scripts/components/Toolshed/InstalledList/Index.vue
+++ b/client/galaxy/scripts/components/Toolshed/InstalledList/Index.vue
@@ -71,7 +71,7 @@ export default {
     components: {
         LoadingSpan,
         Monitor,
-        RepositoryDetails
+        RepositoryDetails,
     },
     props: ["filter"],
     data() {
@@ -83,12 +83,12 @@ export default {
                     sortable: true,
                     sortByFormatted: (value, key, item) => {
                         return `${this.isLatest(item)}_${value}`;
-                    }
+                    },
                 },
                 {
                     key: "owner",
-                    sortable: true
-                }
+                    sortable: true,
+                },
             ],
             loading: true,
             message: null,
@@ -96,7 +96,7 @@ export default {
             nRepositories: 0,
             repositories: [],
             showMonitor: false,
-            sortBy: "name"
+            sortBy: "name",
         };
     },
     computed: {
@@ -108,7 +108,7 @@ export default {
         },
         showMessage() {
             return !!this.message;
-        }
+        },
     },
     created() {
         this.root = getAppRoot();
@@ -124,12 +124,12 @@ export default {
             this.loading = true;
             this.services
                 .getInstalledRepositories()
-                .then(repositories => {
+                .then((repositories) => {
                     this.repositories = repositories;
                     this.nRepositories = repositories.length;
                     this.loading = false;
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.error = error;
                 });
         },
@@ -141,7 +141,7 @@ export default {
         },
         onQuery(query) {
             this.$emit("onQuery", query);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Toolshed/InstalledList/Monitor.test.js b/client/galaxy/scripts/components/Toolshed/InstalledList/Monitor.test.js
index 9a5ce15b5767..24ae47986eb1 100644
--- a/client/galaxy/scripts/components/Toolshed/InstalledList/Monitor.test.js
+++ b/client/galaxy/scripts/components/Toolshed/InstalledList/Monitor.test.js
@@ -14,14 +14,14 @@ describe("Monitor", () => {
                             name: "name_0",
                             owner: "owner_0",
                             status: "status_0_0",
-                            description: "description_0_0"
+                            description: "description_0_0",
                         },
                         {
                             name: "name_1",
                             owner: "owner_1",
                             status: "status_1",
-                            description: "description_1"
-                        }
+                            description: "description_1",
+                        },
                     ];
                 }
             }
diff --git a/client/galaxy/scripts/components/Toolshed/InstalledList/Monitor.vue b/client/galaxy/scripts/components/Toolshed/InstalledList/Monitor.vue
index d89246b81315..f2f918115f0b 100644
--- a/client/galaxy/scripts/components/Toolshed/InstalledList/Monitor.vue
+++ b/client/galaxy/scripts/components/Toolshed/InstalledList/Monitor.vue
@@ -40,7 +40,7 @@ Vue.use(BootstrapVue);
 
 export default {
     components: {
-        InstallationButton
+        InstallationButton,
     },
     data() {
         return {
@@ -48,7 +48,7 @@ export default {
             loading: true,
             error: null,
             items: [],
-            fields: ["name", "status"]
+            fields: ["name", "status"],
         };
     },
     computed: {
@@ -57,7 +57,7 @@ export default {
         },
         showEmpty() {
             return !this.loading && this.items.length === 0;
-        }
+        },
     },
     created() {
         this.root = getAppRoot();
@@ -82,26 +82,26 @@ export default {
         load() {
             this.services
                 .getInstalledRepositories({
-                    filter: x => x.status !== "Installed"
+                    filter: (x) => x.status !== "Installed",
                 })
-                .then(items => {
+                .then((items) => {
                     this.items = items;
                     this.loading = false;
                     this.setTimeout();
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.error = error;
                 });
         },
         onQuery(q) {
             this.$emit("onQuery", q);
         },
-        uninstallRepository: function(repository) {
-            this.services.uninstallRepository(repository).catch(error => {
+        uninstallRepository: function (repository) {
+            this.services.uninstallRepository(repository).catch((error) => {
                 this.error = error;
             });
-        }
-    }
+        },
+    },
 };
 </script>
 <style>
diff --git a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/Index.test.js b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/Index.test.js
index 7abcf12bfc9e..2c2d47fb36c0 100644
--- a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/Index.test.js
+++ b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/Index.test.js
@@ -29,15 +29,15 @@ describe("RepositoryDetails", () => {
                     id: "id",
                     name: "name",
                     owner: "owner",
-                    description: "description"
+                    description: "description",
                 },
-                toolshedUrl: "toolshedUrl"
+                toolshedUrl: "toolshedUrl",
             },
             stubs: {
                 RepositoryDetails: true,
                 InstallationSettings: true,
-                RepositoryTools: true
-            }
+                RepositoryTools: true,
+            },
         });
         expect(wrapper.find(".loading-message").text()).to.equal("Loading repository details...");
         await Vue.nextTick();
diff --git a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/Index.vue b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/Index.vue
index 004be321da26..17d6d998d765 100644
--- a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/Index.vue
+++ b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/Index.vue
@@ -65,7 +65,7 @@ export default {
     components: {
         InstallationSettings,
         InstallationButton,
-        RepositoryTools
+        RepositoryTools,
     },
     props: ["repo", "toolshedUrl"],
     data() {
@@ -80,12 +80,12 @@ export default {
                 { key: "tools", label: "Tools and Versions" },
                 { key: "profile", label: "Requires" },
                 { key: "missing_test_components", label: "Tests" },
-                { key: "actions", label: "" }
+                { key: "actions", label: "" },
             ],
             showSettings: false,
             error: null,
             loading: true,
-            delay: 2000
+            delay: 2000,
         };
     },
     created() {
@@ -110,11 +110,11 @@ export default {
         load() {
             this.services
                 .getRepository(this.toolshedUrl, this.repo.id)
-                .then(response => {
+                .then((response) => {
                     this.repoTable = response;
                     this.loadInstalledRepositories();
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.error = error;
                     this.loading = false;
                 });
@@ -122,9 +122,9 @@ export default {
         loadInstalledRepositories() {
             this.services
                 .getInstalledRepositoriesByName(this.repo.name, this.repo.owner)
-                .then(revisions => {
+                .then((revisions) => {
                     let changed = false;
-                    this.repoTable.forEach(x => {
+                    this.repoTable.forEach((x) => {
                         const revision = revisions[x.changeset_revision];
                         if (revision && revision.status !== x.status) {
                             x.status = revision.status;
@@ -139,43 +139,43 @@ export default {
                     this.setTimeout();
                     this.loading = false;
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.error = error;
                     this.loading = false;
                 });
         },
-        onOk: function(details) {
+        onOk: function (details) {
             this.services
                 .installRepository(details)
-                .then(response => {
+                .then((response) => {
                     this.showSettings = false;
                 })
-                .catch(error => {
+                .catch((error) => {
                     console.log(error);
                 });
         },
-        onHide: function() {
+        onHide: function () {
             this.showSettings = false;
         },
-        setupRepository: function(details) {
+        setupRepository: function (details) {
             this.selectedChangeset = details.changeset_revision;
             this.selectedRequiresPanel =
                 details.includes_tools_for_display_in_tool_panel ||
                 details.repository.type == "repository_suite_definition";
             this.showSettings = true;
         },
-        uninstallRepository: function(details) {
+        uninstallRepository: function (details) {
             this.services
                 .uninstallRepository({
                     tool_shed_url: this.toolshedUrl,
                     name: this.repo.name,
                     owner: this.repo.owner,
-                    changeset_revision: details.changeset_revision
+                    changeset_revision: details.changeset_revision,
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.error = error;
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationButton.test.js b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationButton.test.js
index ea854a43634d..175aa86acec1 100644
--- a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationButton.test.js
+++ b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationButton.test.js
@@ -6,8 +6,8 @@ describe("InstallationButton", () => {
         const wrapper = mount(InstallationButton, {
             propsData: {
                 installed: true,
-                status: "Installed"
-            }
+                status: "Installed",
+            },
         });
         const $el = wrapper.find("button");
         expect($el.classes()).to.include("btn-danger");
@@ -19,8 +19,8 @@ describe("InstallationButton", () => {
         const wrapper = mount(InstallationButton, {
             propsData: {
                 installed: false,
-                status: "Uninstalled"
-            }
+                status: "Uninstalled",
+            },
         });
         const $el = wrapper.find("button");
         expect($el.classes()).to.include("btn-primary");
diff --git a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationButton.vue b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationButton.vue
index 88b93472a35e..aebfbd8b2e3d 100644
--- a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationButton.vue
+++ b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationButton.vue
@@ -24,7 +24,7 @@ export default {
     props: ["installed", "status"],
     data() {
         return {
-            buttonClass: "btn-sm text-nowrap"
+            buttonClass: "btn-sm text-nowrap",
         };
     },
     computed: {
@@ -36,7 +36,7 @@ export default {
         },
         errorState() {
             return this.status == "Error";
-        }
+        },
     },
     methods: {
         onInstall() {
@@ -49,7 +49,7 @@ export default {
             if (window.confirm(`Do you want to reset this repository?`)) {
                 this.$emit("onUninstall");
             }
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.test.js b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.test.js
index a35f853324cb..ec846fd1ee63 100644
--- a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.test.js
+++ b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.test.js
@@ -6,7 +6,7 @@ describe("InstallationSettings", () => {
     beforeEach(() => {
         rewire.__Rewire__("getGalaxyInstance", () => {
             return {
-                config: {}
+                config: {},
             };
         });
     });
@@ -19,12 +19,12 @@ describe("InstallationSettings", () => {
                     long_description: "long_description",
                     description: "description",
                     owner: "owner",
-                    name: "name"
+                    name: "name",
                 },
                 changesetRevision: "changesetRevision",
                 requiresPanel: true,
-                toolshedUrl: "toolshedUrl"
-            }
+                toolshedUrl: "toolshedUrl",
+            },
         });
         expect(wrapper.find(".title").text()).to.equal("Installing 'name'");
         expect(wrapper.find(".description").text()).to.equal("long_description");
diff --git a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.vue b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.vue
index 26a0703426a5..cca78c921c9e 100644
--- a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.vue
+++ b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.vue
@@ -68,7 +68,7 @@ export default {
             toolConfigs: [],
             toolConfig: null,
             toolSections: [],
-            toolSection: null
+            toolSection: null,
         };
     },
     computed: {
@@ -80,16 +80,16 @@ export default {
         },
         showConfig() {
             return this.toolConfigs.length > 1;
-        }
+        },
     },
     created() {
         this.load();
     },
     methods: {
-        findSection: function(name) {
+        findSection: function (name) {
             const result = ["", ""];
             if (name) {
-                const found = this.toolSections.find(s => {
+                const found = this.toolSections.find((s) => {
                     return s.name.toLowerCase().trim() == name.toLowerCase().trim();
                 });
                 if (found) {
@@ -100,21 +100,21 @@ export default {
             }
             return result;
         },
-        load: function() {
+        load: function () {
             const galaxy = getGalaxyInstance();
             const sections = galaxy.config.toolbox;
             if (sections) {
-                this.toolSections = sections.filter(x => x.elems);
+                this.toolSections = sections.filter((x) => x.elems);
             }
             this.toolConfigs = galaxy.config.tool_dynamic_configs || [];
             if (this.toolConfigs.length > 0) {
                 this.toolConfig = this.toolConfigs[0];
             }
         },
-        onAdvanced: function() {
+        onAdvanced: function () {
             this.advancedShow = !this.advancedShow;
         },
-        onOk: function() {
+        onOk: function () {
             const [sectionId, sectionLabel] = this.findSection(this.toolSection);
             this.$emit("ok", {
                 tool_shed_url: this.toolshedUrl,
@@ -126,12 +126,12 @@ export default {
                 shed_tool_conf: this.toolConfig,
                 install_resolver_dependencies: this.installResolverDependencies,
                 install_tool_dependencies: this.installToolDependencies,
-                install_repository_dependencies: this.installRepositoryDependencies
+                install_repository_dependencies: this.installRepositoryDependencies,
             });
         },
-        onHide: function() {
+        onHide: function () {
             this.$emit("hide");
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/RepositoryTools.test.js b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/RepositoryTools.test.js
index eb020a50af66..4cfec3c5389b 100644
--- a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/RepositoryTools.test.js
+++ b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/RepositoryTools.test.js
@@ -10,10 +10,10 @@ describe("RepositoryTools", () => {
                     {
                         guid: "guid",
                         id: "id",
-                        version: "version"
-                    }
-                ]
-            }
+                        version: "version",
+                    },
+                ],
+            },
         });
         const $el = wrapper.findAll("td");
         const $first = $el.at(0);
@@ -29,20 +29,20 @@ describe("RepositoryTools", () => {
                     {
                         guid: "guid_1",
                         id: "id_1",
-                        version: "version_1"
+                        version: "version_1",
                     },
                     {
                         guid: "guid_2",
                         id: "id_2",
-                        version: "version_2"
+                        version: "version_2",
                     },
                     {
                         guid: "guid_3",
                         id: "id_3",
-                        version: "version_3"
-                    }
-                ]
-            }
+                        version: "version_3",
+                    },
+                ],
+            },
         });
         const $el = wrapper.findAll("tr");
         expect($el.length).to.equal(3);
diff --git a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/RepositoryTools.vue b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/RepositoryTools.vue
index 27d3a9667848..c7b2b6e5565d 100644
--- a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/RepositoryTools.vue
+++ b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/RepositoryTools.vue
@@ -41,7 +41,7 @@ export default {
             clsFirstColumn: "p-0 w-50 text-left",
             clsSecondColumn: "p-0 w-50 text-center",
             expanded: false,
-            preview: 2
+            preview: 2,
         };
     },
     computed: {
@@ -56,12 +56,12 @@ export default {
                 return this.tools.slice(0, this.preview);
             }
             return this.tools;
-        }
+        },
     },
     methods: {
         onExpand() {
             this.expanded = !this.expanded;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Toolshed/SearchList/Categories.test.js b/client/galaxy/scripts/components/Toolshed/SearchList/Categories.test.js
index e13d9b74bdd3..c69c8eb6af62 100644
--- a/client/galaxy/scripts/components/Toolshed/SearchList/Categories.test.js
+++ b/client/galaxy/scripts/components/Toolshed/SearchList/Categories.test.js
@@ -13,13 +13,13 @@ describe("Categories", () => {
                         {
                             name: "name_0",
                             description: "description_0",
-                            repositories: "repositories_0"
+                            repositories: "repositories_0",
                         },
                         {
                             name: "name_1",
                             description: "description_1",
-                            repositories: "repositories_1"
-                        }
+                            repositories: "repositories_1",
+                        },
                     ];
                 }
             }
@@ -30,8 +30,8 @@ describe("Categories", () => {
         const wrapper = mount(Categories, {
             propsData: {
                 loading: true,
-                toolshedUrl: "toolshedUrl"
-            }
+                toolshedUrl: "toolshedUrl",
+            },
         });
         expect(wrapper.find(".loading-message").text()).to.equal("Loading categories...");
     });
@@ -40,8 +40,8 @@ describe("Categories", () => {
         const wrapper = mount(Categories, {
             propsData: {
                 loading: false,
-                toolshedUrl: "toolshedUrl"
-            }
+                toolshedUrl: "toolshedUrl",
+            },
         });
         await Vue.nextTick();
         const links = wrapper.findAll("a");
diff --git a/client/galaxy/scripts/components/Toolshed/SearchList/Categories.vue b/client/galaxy/scripts/components/Toolshed/SearchList/Categories.vue
index 7929920880fc..88e999cbf197 100644
--- a/client/galaxy/scripts/components/Toolshed/SearchList/Categories.vue
+++ b/client/galaxy/scripts/components/Toolshed/SearchList/Categories.vue
@@ -32,8 +32,8 @@ export default {
             fields: [
                 { key: "name", label: "Category", sortable: true },
                 { key: "description", sortable: false },
-                { key: "repositories", sortable: true }
-            ]
+                { key: "repositories", sortable: true },
+            ],
         };
     },
     created() {
@@ -43,27 +43,27 @@ export default {
     watch: {
         toolshedUrl() {
             this.load();
-        }
+        },
     },
     methods: {
         load() {
             this.$emit("onLoading", true);
             this.services
                 .getCategories(this.toolshedUrl)
-                .then(categories => {
+                .then((categories) => {
                     this.categories = categories;
                     const reducer = (value, entry) => value + entry.repositories;
                     this.$emit("onTotal", this.categories.reduce(reducer, 0));
                     this.$emit("onLoading", false);
                 })
-                .catch(errorMessage => {
+                .catch((errorMessage) => {
                     this.$emit("onError", errorMessage);
                     this.$emit("onLoading", false);
                 });
         },
         onCategory(category) {
             this.$emit("onCategory", `category:'${category}'`);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Toolshed/SearchList/Index.vue b/client/galaxy/scripts/components/Toolshed/SearchList/Index.vue
index 87dc9ab4d3a8..63dba70f2c10 100644
--- a/client/galaxy/scripts/components/Toolshed/SearchList/Index.vue
+++ b/client/galaxy/scripts/components/Toolshed/SearchList/Index.vue
@@ -38,7 +38,7 @@ export default {
     components: {
         Categories,
         Repositories,
-        ServerSelection
+        ServerSelection,
     },
     data() {
         return {
@@ -51,8 +51,8 @@ export default {
             tabCurrent: "true",
             tabOptions: [
                 { text: "Search All", value: true },
-                { text: "Installed Only", value: false }
-            ]
+                { text: "Installed Only", value: false },
+            ],
         };
     },
     created() {
@@ -61,7 +61,7 @@ export default {
     computed: {
         queryEmpty() {
             return !this.query || this.query.length < this.queryLength;
-        }
+        },
     },
     methods: {
         configureToolsheds() {
@@ -88,7 +88,7 @@ export default {
         },
         setLoading(loading) {
             this.loading = loading;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Toolshed/SearchList/Repositories.test.js b/client/galaxy/scripts/components/Toolshed/SearchList/Repositories.test.js
index da51702c9840..b046c19c0e7d 100644
--- a/client/galaxy/scripts/components/Toolshed/SearchList/Repositories.test.js
+++ b/client/galaxy/scripts/components/Toolshed/SearchList/Repositories.test.js
@@ -15,14 +15,14 @@ describe("Repositories", () => {
                             name: "name_0",
                             owner: "owner_0",
                             last_updated: "last_updated_0",
-                            times_downloaded: "times_downloaded_0"
+                            times_downloaded: "times_downloaded_0",
                         },
                         {
                             name: "name_1",
                             owner: "owner_1",
                             last_updated: "last_updated_1",
-                            times_downloaded: "times_downloaded_1"
-                        }
+                            times_downloaded: "times_downloaded_1",
+                        },
                     ];
                 }
             }
@@ -34,8 +34,8 @@ describe("Repositories", () => {
             propsData: {
                 query: true,
                 scrolled: false,
-                toolshedUrl: "toolshedUrl"
-            }
+                toolshedUrl: "toolshedUrl",
+            },
         });
         // Test initial state prior to the data fetch tick -- should be loading.
         expect(wrapper.find(".loading-message").text()).to.equal("Loading repositories...");
diff --git a/client/galaxy/scripts/components/Toolshed/SearchList/Repositories.vue b/client/galaxy/scripts/components/Toolshed/SearchList/Repositories.vue
index c9ce61cee977..8325f7b5b46d 100644
--- a/client/galaxy/scripts/components/Toolshed/SearchList/Repositories.vue
+++ b/client/galaxy/scripts/components/Toolshed/SearchList/Repositories.vue
@@ -32,7 +32,7 @@ const COMPLETE = 2;
 export default {
     components: {
         LoadingSpan,
-        RepositoryDetails
+        RepositoryDetails,
     },
     props: ["query", "scrolled", "toolshedUrl"],
     data() {
@@ -42,12 +42,12 @@ export default {
                 { key: "name" },
                 { key: "owner", label: "Owner" },
                 { key: "times_downloaded", label: "Downloaded" },
-                { key: "last_updated", label: "Updated" }
+                { key: "last_updated", label: "Updated" },
             ],
             page: 1,
             pageSize: 50,
             pageState: READY,
-            error: null
+            error: null,
         };
     },
     watch: {
@@ -61,7 +61,7 @@ export default {
             if (this.scrolled && this.pageState === READY) {
                 this.load(this.page + 1);
             }
-        }
+        },
     },
     computed: {
         pageLoading() {
@@ -69,7 +69,7 @@ export default {
         },
         noResultsFound() {
             return this.repositories.length === 0 && !this.pageLoading;
-        }
+        },
     },
     created() {
         this.services = new Services();
@@ -87,9 +87,9 @@ export default {
                     tool_shed_url: this.toolshedUrl,
                     q: this.query,
                     page: this.page,
-                    page_size: this.pageSize
+                    page_size: this.pageSize,
                 })
-                .then(incoming => {
+                .then((incoming) => {
                     this.repositories = this.repositories.concat(incoming);
                     if (incoming.length < this.pageSize) {
                         this.pageState = COMPLETE;
@@ -97,10 +97,10 @@ export default {
                         this.pageState = READY;
                     }
                 })
-                .catch(errorMessage => {
+                .catch((errorMessage) => {
                     this.$emit("onError", errorMessage);
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Toolshed/SearchList/ServerSelection.test.js b/client/galaxy/scripts/components/Toolshed/SearchList/ServerSelection.test.js
index 73d45b61f5c5..1a2645e817e6 100644
--- a/client/galaxy/scripts/components/Toolshed/SearchList/ServerSelection.test.js
+++ b/client/galaxy/scripts/components/Toolshed/SearchList/ServerSelection.test.js
@@ -8,8 +8,8 @@ describe("ServerSelection", () => {
                 toolshedUrl: "url_0",
                 toolshedUrls: ["url_0", "url_1"],
                 loading: false,
-                total: "total"
-            }
+                total: "total",
+            },
         });
         expect(wrapper.find(".description").text()).to.equal("total repositories available at");
         const $options = wrapper.findAll("a");
diff --git a/client/galaxy/scripts/components/Toolshed/SearchList/ServerSelection.vue b/client/galaxy/scripts/components/Toolshed/SearchList/ServerSelection.vue
index 6e3572f7a95a..8a7701feb3fa 100644
--- a/client/galaxy/scripts/components/Toolshed/SearchList/ServerSelection.vue
+++ b/client/galaxy/scripts/components/Toolshed/SearchList/ServerSelection.vue
@@ -42,13 +42,13 @@ export default {
     computed: {
         showDropdown() {
             return this.toolshedUrls.length > 1;
-        }
+        },
     },
     methods: {
         onToolshed(url) {
             this.$emit("onToolshed", url);
-        }
-    }
+        },
+    },
 };
 </script>
 <style scoped>
diff --git a/client/galaxy/scripts/components/Toolshed/services.js b/client/galaxy/scripts/components/Toolshed/services.js
index b887ceda47d2..0aab5f52fc93 100644
--- a/client/galaxy/scripts/components/Toolshed/services.js
+++ b/client/galaxy/scripts/components/Toolshed/services.js
@@ -21,8 +21,8 @@ export class Services {
         try {
             const response = await axios.get(url);
             const data = response.data;
-            const incoming = data.hits.map(x => x.repository);
-            incoming.forEach(x => {
+            const incoming = data.hits.map((x) => x.repository);
+            incoming.forEach((x) => {
                 x.owner = x.repo_owner_username;
                 x.times_downloaded = this._formatCount(x.times_downloaded);
                 x.repository_url = `${data.hostname}repository?repository_id=${x.id}`;
@@ -38,12 +38,12 @@ export class Services {
         try {
             const response = await axios.get(url);
             const data = response.data;
-            const table = Object.keys(data).map(key => data[key]);
+            const table = Object.keys(data).map((key) => data[key]);
             if (table.length === 0) {
                 throw "Repository does not contain any installable revisions.";
             }
             table.sort((a, b) => b.numeric_revision - a.numeric_revision);
-            table.forEach(x => {
+            table.forEach((x) => {
                 if (Array.isArray(x.tools)) {
                     x.profile = x.tools.reduce(
                         (value, current) => (current.profile > value ? current.profile : value),
@@ -92,10 +92,10 @@ export class Services {
             const response = await axios.get(url);
             const data = response.data;
             const result = {};
-            data.forEach(x => {
+            data.forEach((x) => {
                 const d = {
                     status: x.status,
-                    installed: !x.deleted && !x.uninstalled
+                    installed: !x.deleted && !x.uninstalled,
                 };
                 result[x.changeset_revision] = result[x.installed_changeset_revision] = d;
             });
@@ -114,7 +114,7 @@ export class Services {
         }
     }
     async uninstallRepository(params) {
-        const paramsString = Object.keys(params).reduce(function(previous, key) {
+        const paramsString = Object.keys(params).reduce(function (previous, key) {
             return `${previous}${key}=${params[key]}&`;
         }, "");
         const url = `${getAppRoot()}api/tool_shed_repositories?${paramsString}`;
@@ -128,7 +128,7 @@ export class Services {
     _groupByNameOwner(incoming, filter) {
         const hash = {};
         const repositories = [];
-        incoming.forEach(x => {
+        incoming.forEach((x) => {
             const hashCode = `${x.name}_${x.owner}`;
             if (!filter || filter(x)) {
                 if (!hash[hashCode]) {
@@ -140,7 +140,7 @@ export class Services {
         return repositories;
     }
     _fixToolshedUrls(incoming, urls) {
-        incoming.forEach(x => {
+        incoming.forEach((x) => {
             for (const url of urls) {
                 if (url.includes(x.tool_shed)) {
                     x.tool_shed_url = url;
@@ -155,7 +155,7 @@ export class Services {
     }
     _getParamsString(params) {
         if (params) {
-            return Object.keys(params).reduce(function(previous, key) {
+            return Object.keys(params).reduce(function (previous, key) {
                 return `${previous}${key}=${params[key]}&`;
             }, "");
         } else {
diff --git a/client/galaxy/scripts/components/Toolshed/services.test.js b/client/galaxy/scripts/components/Toolshed/services.test.js
index 2f0c1c77725d..b8ad73622bbb 100644
--- a/client/galaxy/scripts/components/Toolshed/services.test.js
+++ b/client/galaxy/scripts/components/Toolshed/services.test.js
@@ -7,35 +7,35 @@ describe("Toolshed service helpers", () => {
             owner: "owner_0",
             status: "status_0_0",
             description: "description_0_0",
-            tool_shed: "url_1"
+            tool_shed: "url_1",
         },
         {
             name: "name_0",
             owner: "owner_0",
             status: "status_0_1",
             description: "description_0_1",
-            tool_shed: "url_1"
+            tool_shed: "url_1",
         },
         {
             name: "name_1",
             owner: "owner_1",
             status: "status_1",
             description: "description_1",
-            tool_shed: "url_2"
+            tool_shed: "url_2",
         },
         {
             name: "name_2",
             owner: "owner_2",
             status: "Installed",
             description: "description_2",
-            tool_shed: "url_2"
-        }
+            tool_shed: "url_2",
+        },
     ];
     const urls = ["http://url_1.com", "http://url_2.com"];
 
     it("test fix toolshed helper", () => {
         const services = new Services();
-        const filter = x => x.status !== "Installed";
+        const filter = (x) => x.status !== "Installed";
         const grouped = services._groupByNameOwner(incoming, filter);
         services._fixToolshedUrls(grouped, urls);
         expect(grouped.length).to.equal(2);
diff --git a/client/galaxy/scripts/components/Upload/Collection.test.js b/client/galaxy/scripts/components/Upload/Collection.test.js
index 6e9cfcc514c7..5f4eb4ff4f9d 100644
--- a/client/galaxy/scripts/components/Upload/Collection.test.js
+++ b/client/galaxy/scripts/components/Upload/Collection.test.js
@@ -22,7 +22,7 @@ describe("Collection.vue", () => {
         const { wrapper } = mountWithApp(Collection, {
             currentFtp: () => {
                 return null;
-            }
+            },
         });
         expect(wrapper.findAll("#btn-ftp").length).to.equals(0);
     });
diff --git a/client/galaxy/scripts/components/Upload/Collection.vue b/client/galaxy/scripts/components/Upload/Collection.vue
index d120e81f1cbf..ff32856fd301 100644
--- a/client/galaxy/scripts/components/Upload/Collection.vue
+++ b/client/galaxy/scripts/components/Upload/Collection.vue
@@ -158,7 +158,7 @@ export default {
             btnBuildTitle: _l("Build"),
             btnStopTitle: _l("Pause"),
             btnResetTitle: _l("Reset"),
-            btnCloseTitle: _l("Close")
+            btnCloseTitle: _l("Close"),
         };
     },
     created() {
@@ -174,7 +174,7 @@ export default {
             announce: (index, file) => {
                 this._eventAnnounce(index, file);
             },
-            initialize: index => {
+            initialize: (index) => {
                 return this.app.toData([this.collection.get(index)], this.history_id);
             },
             progress: (index, percentage) => {
@@ -197,32 +197,32 @@ export default {
             },
             ondragleave: () => {
                 this.highlightBox = false;
-            }
+            },
         });
-        this.collection.on("remove", model => {
+        this.collection.on("remove", (model) => {
             this._eventRemove(model);
         });
         this._updateStateForCounters();
     },
     computed: {
         extensions() {
-            const result = _.filter(this.listExtensions, ext => !ext.composite_files);
+            const result = _.filter(this.listExtensions, (ext) => !ext.composite_files);
             return result;
         },
         appModel() {
             return this.app.model;
-        }
+        },
     },
     watch: {
-        extension: function(value) {
+        extension: function (value) {
             this.updateExtension(value);
         },
-        genome: function(value) {
+        genome: function (value) {
             this.updateGenome(value);
-        }
+        },
     },
     methods: {
-        _newUploadModelProps: function(index, file) {
+        _newUploadModelProps: function (index, file) {
             return {
                 id: index,
                 file_name: file.name,
@@ -231,12 +231,12 @@ export default {
                 file_path: file.path,
                 file_data: file,
                 extension: this.extension,
-                genome: this.genome
+                genome: this.genome,
             };
         },
 
         /** Success */
-        _eventSuccess: function(index, message) {
+        _eventSuccess: function (index, message) {
             var hids = _.pluck(message["outputs"], "hid");
             var it = this.collection.get(index);
             it.set({ percentage: 100, status: "success", hids: hids });
@@ -245,13 +245,13 @@ export default {
             Galaxy.currHistoryPanel.refreshContents();
         },
 
-        _eventBuild: function() {
+        _eventBuild: function () {
             const Galaxy = getGalaxyInstance();
             var allHids = [];
-            _.forEach(this.collection.models, upload => {
+            _.forEach(this.collection.models, (upload) => {
                 allHids.push.apply(allHids, upload.get("hids"));
             });
-            var models = _.map(allHids, hid => Galaxy.currHistoryPanel.collection.getByHid(hid));
+            var models = _.map(allHids, (hid) => Galaxy.currHistoryPanel.collection.getByHid(hid));
             var selection = new Galaxy.currHistoryPanel.collection.constructor(models);
             // I'm building the selection wrong because I need to set this historyId directly.
             selection.historyId = Galaxy.currHistoryPanel.collection.historyId;
@@ -263,13 +263,13 @@ export default {
         },
 
         /** Start upload process */
-        _eventStart: function() {
+        _eventStart: function () {
             if (this.counterAnnounce == 0 || this.counterRunning > 0) {
                 return;
             }
             this.uploadSize = 0;
             this.uploadCompleted = 0;
-            this.collection.each(model => {
+            this.collection.each((model) => {
                 if (model.get("status") == "init") {
                     model.set("status", "queued");
                     this.uploadSize += model.get("file_size");
@@ -285,7 +285,7 @@ export default {
         },
 
         /** Remove all */
-        _eventReset: function() {
+        _eventReset: function () {
             if (this.counterRunning == 0) {
                 this.collection.reset();
                 this.counterAnnounce = 0;
@@ -298,7 +298,7 @@ export default {
                 this.appModel.set("percentage", 0);
                 this._updateStateForCounters();
             }
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Upload/Composite.vue b/client/galaxy/scripts/components/Upload/Composite.vue
index 46b9694d4b76..693074c4fe89 100644
--- a/client/galaxy/scripts/components/Upload/Composite.vue
+++ b/client/galaxy/scripts/components/Upload/Composite.vue
@@ -75,7 +75,7 @@ export default {
             btnResetTitle: _l("Reset"),
             btnStartTitle: _l("Start"),
             btnCloseTitle: _l("Close"),
-            readyStart: false
+            readyStart: false,
         };
     },
     created() {
@@ -84,15 +84,15 @@ export default {
     },
     computed: {
         extensions() {
-            const result = _.filter(this.listExtensions, ext => ext.composite_files);
+            const result = _.filter(this.listExtensions, (ext) => ext.composite_files);
             result.unshift({ id: "_select_", text: "Select" });
             return result;
-        }
+        },
     },
     mounted() {
         this.initExtensionInfo();
         // listener for collection triggers on change in composite datatype and extension selection
-        this.collection.on("add", model => {
+        this.collection.on("add", (model) => {
             this._eventAnnounce(model);
         });
         this.collection.on("change add", () => {
@@ -101,7 +101,7 @@ export default {
         this.renderNonReactiveComponents();
     },
     methods: {
-        renderNonReactiveComponents: function() {
+        renderNonReactiveComponents: function () {
             var model = this.collection.first();
             if (model && model.get("status") == "running") {
                 this.running = true;
@@ -125,40 +125,38 @@ export default {
         //
 
         /** Builds the basic ui with placeholder rows for each composite data type file */
-        _eventAnnounce: function(model) {
+        _eventAnnounce: function (model) {
             var upload_row = new UploadRow(this, { model: model });
-            this.$uploadTable()
-                .find("tbody:first")
-                .append(upload_row.$el);
+            this.$uploadTable().find("tbody:first").append(upload_row.$el);
             this.showHelper = this.collection.length == 0;
             upload_row.render();
         },
 
         /** Start upload process */
-        _eventStart: function() {
-            this.collection.each(model => {
+        _eventStart: function () {
+            this.collection.each((model) => {
                 model.set({
                     genome: this.genome,
-                    extension: this.extension
+                    extension: this.extension,
                 });
             });
             $.uploadpost({
                 url: this.app.uploadPath,
                 data: this.app.toData(this.collection.filter()),
-                success: message => {
+                success: (message) => {
                     this._eventSuccess(message);
                 },
-                error: message => {
+                error: (message) => {
                     this._eventError(message);
                 },
-                progress: percentage => {
+                progress: (percentage) => {
                     this._eventProgress(percentage);
-                }
+                },
             });
         },
 
         /** Remove all */
-        _eventReset: function() {
+        _eventReset: function () {
             if (this.collection.where({ status: "running" }).length == 0) {
                 this.collection.reset();
                 this.extension = this.app.defaultExtension;
@@ -168,42 +166,42 @@ export default {
         },
 
         /** Refresh progress state */
-        _eventProgress: function(percentage) {
-            this.collection.each(it => {
+        _eventProgress: function (percentage) {
+            this.collection.each((it) => {
                 it.set("percentage", percentage);
             });
         },
 
         /** Refresh success state */
-        _eventSuccess: function(message) {
+        _eventSuccess: function (message) {
             const Galaxy = getGalaxyInstance();
-            this.collection.each(it => {
+            this.collection.each((it) => {
                 it.set("status", "success");
             });
             Galaxy.currHistoryPanel.refreshContents();
         },
 
         /** Refresh error state */
-        _eventError: function(message) {
-            this.collection.each(it => {
+        _eventError: function (message) {
+            this.collection.each((it) => {
                 it.set({ status: "error", info: message });
             });
-        }
+        },
     },
     watch: {
-        extension: function(value) {
+        extension: function (value) {
             this.collection.reset();
             const details = this.extensionDetails(value);
             if (details && details.composite_files) {
-                _.each(details.composite_files, item => {
+                _.each(details.composite_files, (item) => {
                     this.collection.add({
                         id: this.collection.size(),
                         file_desc: item.description || item.name,
-                        optional: item.optional
+                        optional: item.optional,
                     });
                 });
             }
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Upload/Default.test.js b/client/galaxy/scripts/components/Upload/Default.test.js
index b86f9bb037d9..c8c132613b46 100644
--- a/client/galaxy/scripts/components/Upload/Default.test.js
+++ b/client/galaxy/scripts/components/Upload/Default.test.js
@@ -31,7 +31,7 @@ describe("Default.vue", () => {
         const { wrapper } = mountWithApp(Default, {
             currentFtp: () => {
                 return null;
-            }
+            },
         });
         expect(wrapper.findAll("#btn-ftp").length).to.equals(0);
     });
diff --git a/client/galaxy/scripts/components/Upload/Default.vue b/client/galaxy/scripts/components/Upload/Default.vue
index fcfee878da40..023a9d9b51ff 100644
--- a/client/galaxy/scripts/components/Upload/Default.vue
+++ b/client/galaxy/scripts/components/Upload/Default.vue
@@ -137,7 +137,7 @@ export default {
             btnStartTitle: _l("Start"),
             btnStopTitle: _l("Pause"),
             btnResetTitle: _l("Reset"),
-            btnCloseTitle: _l("Close")
+            btnCloseTitle: _l("Close"),
         };
     },
     created() {
@@ -153,7 +153,7 @@ export default {
             announce: (index, file) => {
                 this._eventAnnounce(index, file);
             },
-            initialize: index => {
+            initialize: (index) => {
                 return this.app.toData([this.collection.get(index)], this.history_id);
             },
             progress: (index, percentage) => {
@@ -176,56 +176,56 @@ export default {
             },
             ondragleave: () => {
                 this.highlightBox = false;
-            }
+            },
         });
-        this.collection.on("remove", model => {
+        this.collection.on("remove", (model) => {
             this._eventRemove(model);
         });
         this._updateStateForCounters();
     },
     computed: {
         extensions() {
-            const result = _.filter(this.listExtensions, ext => !ext.composite_files);
+            const result = _.filter(this.listExtensions, (ext) => !ext.composite_files);
             return result;
         },
         appModel() {
             return this.app.model;
-        }
+        },
     },
     watch: {
-        extension: function(value) {
+        extension: function (value) {
             this.updateExtension(value);
         },
-        genome: function(value) {
+        genome: function (value) {
             this.updateGenome(value);
-        }
+        },
     },
     methods: {
-        _newUploadModelProps: function(index, file) {
+        _newUploadModelProps: function (index, file) {
             return {
                 id: index,
                 file_name: file.name,
                 file_size: file.size,
                 file_mode: file.mode || "local",
                 file_path: file.path,
-                file_data: file
+                file_data: file,
             };
         },
 
         /** Success */
-        _eventSuccess: function(index, message) {
+        _eventSuccess: function (index, message) {
             var it = this.collection.get(index);
             it.set({ percentage: 100, status: "success" });
             this._updateStateForSuccess(it);
         },
 
         /** Start upload process */
-        _eventStart: function() {
+        _eventStart: function () {
             if (this.counterAnnounce !== 0 && this.counterRunning === 0) {
                 // prepare upload process
                 this.uploadSize = 0;
                 this.uploadCompleted = 0;
-                this.collection.each(model => {
+                this.collection.each((model) => {
                     if (model.get("status") == "init") {
                         model.set("status", "queued");
                         this.uploadSize += model.get("file_size");
@@ -242,14 +242,14 @@ export default {
                 const Galaxy = getGalaxyInstance();
                 this.uploadbox.start({
                     id: Galaxy.user.id,
-                    chunk_upload_size: this.app.chunkUploadSize
+                    chunk_upload_size: this.app.chunkUploadSize,
                 });
                 this._updateStateForCounters();
             }
         },
 
         /** Remove all */
-        _eventReset: function() {
+        _eventReset: function () {
             if (this.counterRunning === 0) {
                 this.collection.reset();
                 this.counterAnnounce = 0;
@@ -262,7 +262,7 @@ export default {
                 this.appModel.set("percentage", 0);
                 this._updateStateForCounters();
             }
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Upload/RulesInput.vue b/client/galaxy/scripts/components/Upload/RulesInput.vue
index ca469b21b4bf..b3ddaad9b135 100644
--- a/client/galaxy/scripts/components/Upload/RulesInput.vue
+++ b/client/galaxy/scripts/components/Upload/RulesInput.vue
@@ -1,6 +1,6 @@
 <template>
     <upload-wrapper ref="wrapper" :top-info="topInfo">
-        <span style="width: 25%; display: inline; height: 100%" class="float-left">
+        <span style="width: 25%; display: inline; height: 100%;" class="float-left">
             <div class="upload-rule-option">
                 <div class="upload-rule-option-title">{{ l("Upload data as") }}</div>
                 <div class="rule-data-type">
@@ -36,10 +36,10 @@
                 </div>
             </div>
         </span>
-        <span style="display: inline; float: right; width: 75%; height: 300px">
+        <span style="display: inline; float: right; width: 75%; height: 300px;">
             <textarea
                 class="upload-rule-source-content form-control"
-                style="height: 100%"
+                style="height: 100%;"
                 v-model="sourceContent"
                 :disabled="selectionType != 'paste'"
             ></textarea>
@@ -100,7 +100,7 @@ export default {
             selectionType: "paste",
             btnBuildTitle: _l("Build"),
             btnResetTitle: _l("Reset"),
-            btnCloseTitle: _l("Close")
+            btnCloseTitle: _l("Close"),
         };
     },
     created() {
@@ -108,7 +108,7 @@ export default {
         this.initAppProperties();
     },
     watch: {
-        selectionType: function(selectionType) {
+        selectionType: function (selectionType) {
             if (selectionType == "dataset" && !this.datasetsSet) {
                 const Galaxy = getGalaxyInstance();
                 const history = Galaxy && Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model;
@@ -122,13 +122,13 @@ export default {
                 }
                 this.datasetsSet = true;
             } else if (selectionType == "ftp") {
-                UploadUtils.getRemoteFiles(ftp_files => {
-                    this.sourceContent = ftp_files.map(file => file["path"]).join("\n");
+                UploadUtils.getRemoteFiles((ftp_files) => {
+                    this.sourceContent = ftp_files.map((file) => file["path"]).join("\n");
                     this.ftpFiles = ftp_files;
                 });
             }
         },
-        selectedDatasetId: function(selectedDatasetId) {
+        selectedDatasetId: function (selectedDatasetId) {
             if (!selectedDatasetId) {
                 this.sourceContent = "";
                 return;
@@ -140,23 +140,23 @@ export default {
                         Galaxy.currHistoryPanel.model.id
                     }/contents/${selectedDatasetId}/display`
                 )
-                .then(response => {
+                .then((response) => {
                     this.sourceContent = response.data;
                 })
-                .catch(error => console.log(error));
-        }
+                .catch((error) => console.log(error));
+        },
     },
     methods: {
-        _eventReset: function() {
+        _eventReset: function () {
             this.selectedDatasetId = null;
             this.sourceContent = "";
         },
 
-        _eventBuild: function() {
+        _eventBuild: function () {
             this._buildSelection(this.sourceContent);
         },
 
-        _buildSelection: function(content) {
+        _buildSelection: function (content) {
             const selectionType = this.selectionType;
             const selection = {};
             const Galaxy = getGalaxyInstance();
@@ -171,7 +171,7 @@ export default {
             selection.dataType = this.dataType;
             Galaxy.currHistoryPanel.buildCollection("rules", selection, true);
             this.app.hide();
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Upload/UploadBoxMixin.js b/client/galaxy/scripts/components/Upload/UploadBoxMixin.js
index a96e4ab23054..4ae9925ef45f 100644
--- a/client/galaxy/scripts/components/Upload/UploadBoxMixin.js
+++ b/client/galaxy/scripts/components/Upload/UploadBoxMixin.js
@@ -13,17 +13,17 @@ import LazyLimited from "mvc/lazy/lazy-limited";
 export default {
     components: {
         UploadWrapper,
-        Select2
+        Select2,
     },
     props: {
         app: {
             type: Object,
-            required: true
+            required: true,
         },
         lazyLoadMax: {
             type: Number,
-            default: null
-        }
+            default: null,
+        },
     },
     methods: {
         $uploadBox() {
@@ -38,19 +38,19 @@ export default {
                     $container: $uploadBox,
                     collection: this.collection,
                     max: this.lazyLoadMax,
-                    new_content: model => {
+                    new_content: (model) => {
                         return this.renderNewModel(model);
-                    }
+                    },
                 });
             }
         },
-        uploadSelect: function() {
+        uploadSelect: function () {
             this.uploadbox.select();
         },
         /** Package and upload ftp files in a single request */
-        _uploadFtp: function() {
+        _uploadFtp: function () {
             const list = [];
-            this.collection.each(model => {
+            this.collection.each((model) => {
                 if (model.get("status") == "queued" && model.get("file_mode") == "ftp") {
                     this.uploadbox.remove(model.id);
                     list.push(model);
@@ -60,34 +60,32 @@ export default {
                 $.uploadpost({
                     data: this.app.toData(list),
                     url: this.app.uploadPath,
-                    success: message => {
-                        _.each(list, model => {
+                    success: (message) => {
+                        _.each(list, (model) => {
                             this._eventSuccess(model.id, message);
                         });
                     },
-                    error: message => {
-                        _.each(list, model => {
+                    error: (message) => {
+                        _.each(list, (model) => {
                             self._eventError(model.id, message);
                         });
-                    }
+                    },
                 });
             }
         },
-        renderNewModel: function(model) {
+        renderNewModel: function (model) {
             // Turn backbone upload model into row model and place in table,
             // render in next tick so table can respond first and dynamic
             // sizing works.
             var uploadRow = new this.rowUploadModel(this, { model: model });
-            this.$uploadTable()
-                .find("tbody:first")
-                .append(uploadRow.$el);
+            this.$uploadTable().find("tbody:first").append(uploadRow.$el);
             this._updateStateForCounters();
             this.$nextTick(() => {
                 uploadRow.render();
             });
             return uploadRow;
         },
-        _updateStateForCounters: function() {
+        _updateStateForCounters: function () {
             this.setTopInfoBasedOnCounters();
             this.enableReset =
                 this.counterRunning == 0 && this.counterAnnounce + this.counterSuccess + this.counterError > 0;
@@ -101,7 +99,7 @@ export default {
             var show_table = this.counterAnnounce + this.counterSuccess + this.counterError > 0;
             this.showHelper = !show_table;
         },
-        setTopInfoBasedOnCounters: function() {
+        setTopInfoBasedOnCounters: function () {
             var message = "";
             if (this.counterAnnounce == 0) {
                 if (this.uploadbox.compatible()) {
@@ -120,16 +118,16 @@ export default {
             this.topInfo = message;
         },
         /** Progress */
-        _eventProgress: function(index, percentage) {
+        _eventProgress: function (index, percentage) {
             var it = this.collection.get(index);
             it.set("percentage", percentage);
             this.appModel.set("percentage", this._uploadPercentage(percentage, it.get("file_size")));
         },
         /** Calculate percentage of all queued uploads */
-        _uploadPercentage: function(percentage, size) {
+        _uploadPercentage: function (percentage, size) {
             return (this.uploadCompleted + percentage * size) / this.uploadSize;
         },
-        _updateStateForSuccess: function(model) {
+        _updateStateForSuccess: function (model) {
             this.appModel.set("percentage", this._uploadPercentage(100, model.get("file_size")));
             this.uploadCompleted += model.get("file_size") * 100;
             this.counterAnnounce--;
@@ -139,7 +137,7 @@ export default {
             Galaxy.currHistoryPanel.refreshContents();
         },
         /** A new file has been dropped/selected through the uploadbox plugin */
-        _eventAnnounce: function(index, file) {
+        _eventAnnounce: function (index, file) {
             this.counterAnnounce++;
             const modelProps = this._newUploadModelProps(index, file);
             var newModel = new UploadModel.Model(modelProps);
@@ -152,12 +150,12 @@ export default {
             }
         },
         /** Error */
-        _eventError: function(index, message) {
+        _eventError: function (index, message) {
             var it = this.collection.get(index);
             it.set({ percentage: 100, status: "error", info: message });
             this.appModel.set({
                 percentage: this._uploadPercentage(100, it.get("file_size")),
-                status: "danger"
+                status: "danger",
             });
             this.uploadCompleted += it.get("file_size") * 100;
             this.counterAnnounce--;
@@ -165,15 +163,15 @@ export default {
             this._updateStateForCounters();
         },
         /** Queue is done */
-        _eventComplete: function() {
-            this.collection.each(model => {
+        _eventComplete: function () {
+            this.collection.each((model) => {
                 model.get("status") == "queued" && model.set("status", "init");
             });
             this.counterRunning = 0;
             this._updateStateForCounters();
         },
         /** Remove model from upload list */
-        _eventRemove: function(model) {
+        _eventRemove: function (model) {
             var status = model.get("status");
             if (status == "success") {
                 this.counterSuccess--;
@@ -186,40 +184,40 @@ export default {
             this._updateStateForCounters();
         },
         /** Show/hide ftp popup */
-        _eventFtp: function() {
+        _eventFtp: function () {
             this.ftp.show(
                 new UploadFtp({
                     collection: this.collection,
                     ftp_upload_site: this.ftpUploadSite,
-                    onadd: ftp_file => {
+                    onadd: (ftp_file) => {
                         return this.uploadbox.add([
                             {
                                 mode: "ftp",
                                 name: ftp_file.path,
                                 size: ftp_file.size,
-                                path: ftp_file.path
-                            }
+                                path: ftp_file.path,
+                            },
                         ]);
                     },
-                    onremove: function(model_index) {
+                    onremove: function (model_index) {
                         this.collection.remove(model_index);
-                    }
+                    },
                 }).$el
             );
         },
         /** Create a new file */
-        _eventCreate: function() {
+        _eventCreate: function () {
             this.uploadbox.add([{ name: "New File", size: 0, mode: "new" }]);
         },
         /** Pause upload process */
-        _eventStop: function() {
+        _eventStop: function () {
             if (this.counterRunning > 0) {
                 this.appModel.set("status", "info");
                 this.topInfo = "Queue will pause after completing the current file...";
                 this.uploadbox.stop();
             }
         },
-        _eventWarning: function(index, message) {
+        _eventWarning: function (index, message) {
             var it = this.collection.get(index);
             it.set({ status: "warning", info: message });
         },
@@ -228,13 +226,13 @@ export default {
         },
         extensionDetails(extension) {
             var details = _.findWhere(this.listExtensions, {
-                id: extension
+                id: extension,
             });
             return details;
         },
         initExtensionInfo() {
             $(this.$refs.footerExtensionInfo)
-                .on("click", e => {
+                .on("click", (e) => {
                     const details = this.extensionDetails(this.extension);
                     if (details) {
                         new UploadExtension({
@@ -242,11 +240,11 @@ export default {
                             title: details && details.text,
                             extension: details && details.id,
                             list: this.listExtensions,
-                            placement: "top"
+                            placement: "top",
                         });
                     }
                 })
-                .on("mousedown", e => {
+                .on("mousedown", (e) => {
                     e.preventDefault();
                 });
         },
@@ -262,13 +260,13 @@ export default {
             // add ftp file viewer
             this.ftp = new Popover({
                 title: _l("FTP files"),
-                container: $(this.$refs.btnFtp)
+                container: $(this.$refs.btnFtp),
             });
         },
         /* walk collection and update un-modified default values when globals
            change */
         updateExtension(extension, defaults_only) {
-            this.collection.each(model => {
+            this.collection.each((model) => {
                 if (
                     model.get("status") == "init" &&
                     (model.get("extension") == this.app.defaultExtension || !defaults_only)
@@ -277,8 +275,8 @@ export default {
                 }
             });
         },
-        updateGenome: function(genome, defaults_only) {
-            this.collection.each(model => {
+        updateGenome: function (genome, defaults_only) {
+            this.collection.each((model) => {
                 if (
                     model.get("status") == "init" &&
                     (model.get("genome") == this.app.defaultGenome || !defaults_only)
@@ -286,6 +284,6 @@ export default {
                     model.set("genome", genome);
                 }
             });
-        }
-    }
+        },
+    },
 };
diff --git a/client/galaxy/scripts/components/Upload/UploadModal.test.js b/client/galaxy/scripts/components/Upload/UploadModal.test.js
index 3314e19b8591..89f0e30c26f4 100644
--- a/client/galaxy/scripts/components/Upload/UploadModal.test.js
+++ b/client/galaxy/scripts/components/Upload/UploadModal.test.js
@@ -7,7 +7,7 @@ import { shallowMount, createLocalVue } from "@vue/test-utils";
 
 const propsData = {
     chunkUploadSize: 1024,
-    uploadPath: "/api/tools"
+    uploadPath: "/api/tools",
 };
 
 describe("UploadModal.vue", () => {
@@ -22,14 +22,14 @@ describe("UploadModal.vue", () => {
             display_in_upload: true,
             extension: "fasta",
             description:
-                "A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than ('>') symbol in the first column. All lines should be shorter than 80 characters."
+                "A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than ('>') symbol in the first column. All lines should be shorter than 80 characters.",
         };
         const datatypesResponse = [fastaResponse];
         axiosMock.onGet(`/api/datatypes?extension_only=False`).reply(200, datatypesResponse);
         const genomesResponse = [
             ["Scarlet macaw Jun 2013 (SMACv1.1/araMac1) (araMac1)", "araMac1"],
             ["Cat Dec. 2008 (NHGRI/GTB V17e/felCat4) (felCat4)", "felCat4"],
-            ["Cat Sep. 2011 (ICGSC Felis_catus 6.2/felCat5) (felCat5)", "felCat5"]
+            ["Cat Sep. 2011 (ICGSC Felis_catus 6.2/felCat5) (felCat5)", "felCat5"],
         ];
         axiosMock.onGet(`/api/genomes`).reply(200, genomesResponse);
 
@@ -37,7 +37,7 @@ describe("UploadModal.vue", () => {
         setupTestGalaxy();
         wrapper = shallowMount(UploadModal, {
             propsData: propsData,
-            localVue: localVue
+            localVue: localVue,
         });
     });
 
diff --git a/client/galaxy/scripts/components/Upload/UploadModal.vue b/client/galaxy/scripts/components/Upload/UploadModal.vue
index a8179cc32ec1..3c77fe8c7059 100644
--- a/client/galaxy/scripts/components/Upload/UploadModal.vue
+++ b/client/galaxy/scripts/components/Upload/UploadModal.vue
@@ -52,70 +52,70 @@ export default {
         Collection,
         Composite,
         Default,
-        RulesInput
+        RulesInput,
     },
     props: {
         modalStatic: {
             type: Boolean,
-            default: true
+            default: true,
         },
         chunkUploadSize: {
             type: Number,
-            required: true
+            required: true,
         },
         uploadPath: {
             type: String,
-            required: true
+            required: true,
         },
         modalShow: {
             type: Boolean,
-            default: false
+            default: false,
         },
         ftpUploadSite: {
             type: String,
-            default: "n/a"
+            default: "n/a",
         },
         defaultGenome: {
             type: String,
-            default: UploadUtils.DEFAULT_GENOME
+            default: UploadUtils.DEFAULT_GENOME,
         },
         defaultExtension: {
             type: String,
-            default: UploadUtils.DEFAULT_EXTENSION
+            default: UploadUtils.DEFAULT_EXTENSION,
         },
         datatypesDisableAuto: {
             type: Boolean,
-            default: false
+            default: false,
         },
         auto: {
             type: Object,
-            default: function() {
+            default: function () {
                 return UploadUtils.AUTO_EXTENSION;
-            }
-        }
+            },
+        },
     },
-    data: function() {
+    data: function () {
         return {
             title: _l("Download from web or upload from disk"),
             historyAvailable: false,
             currentUser: null,
             listGenomes: [],
-            listExtensions: []
+            listExtensions: [],
         };
     },
-    created: function() {
+    created: function () {
         this.model = new Backbone.Model({
             label: "Load Data",
             percentage: 0,
             status: "",
-            onunload: function() {},
-            onclick: function() {}
+            onunload: function () {},
+            onclick: function () {},
         });
         $(window).on("beforeunload", () => this.model.get("onunload")());
 
         // load extensions
         UploadUtils.getUploadDatatypes(
-            listExtensions => {
+            (listExtensions) => {
                 this.listExtensions = listExtensions;
             },
             this.datatypesDisableSuto,
@@ -123,7 +123,7 @@ export default {
         );
 
         // load genomes
-        UploadUtils.getUploadGenomes(listGenomes => {
+        UploadUtils.getUploadGenomes((listGenomes) => {
             this.listGenomes = listGenomes;
         }, this.defaultGenome);
 
@@ -148,11 +148,11 @@ export default {
             this.historyAvailable = true;
             this.currentUser = Galaxy.user.id;
         },
-        currentFtp: function() {
+        currentFtp: function () {
             return this.currentUser && this.ftpUploadSite;
         },
         /** Refresh user and current history */
-        currentHistory: function() {
+        currentHistory: function () {
             const Galaxy = getGalaxyInstance();
             return this.currentUser && Galaxy.currHistoryPanel.model.get("id");
         },
@@ -160,16 +160,16 @@ export default {
          * Package API data from array of models
          * @param{Array} items - Upload items/rows filtered from a collection
          */
-        toData: function(items, history_id) {
+        toData: function (items, history_id) {
             // create dictionary for data submission
             var data = {
                 payload: {
                     tool_id: "upload1",
                     history_id: history_id || this.currentHistory(),
-                    inputs: {}
+                    inputs: {},
                 },
                 files: [],
-                error_message: null
+                error_message: null,
             };
             // add upload tools input data
             if (items && items.length > 0) {
@@ -178,7 +178,7 @@ export default {
                     dbkey: items[0].get("genome", "?"),
                     // sometimes extension set to "" in automated testing after first upload of
                     // a session. https://github.com/galaxyproject/galaxy/issues/5169
-                    file_type: items[0].get("extension") || "auto"
+                    file_type: items[0].get("extension") || "auto",
                 };
                 for (var index in items) {
                     var it = items[index];
@@ -203,7 +203,7 @@ export default {
                             case "local":
                                 data.files.push({
                                     name: `${prefix}file_data`,
-                                    file: it.get("file_data")
+                                    file: it.get("file_data"),
                                 });
                         }
                     } else if (it.get("optional")) {
@@ -218,8 +218,8 @@ export default {
                 data.payload.inputs = JSON.stringify(inputs);
             }
             return data;
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/Upload/UploadWrapper.vue b/client/galaxy/scripts/components/Upload/UploadWrapper.vue
index 8666b30be05e..1e4226e24f71 100644
--- a/client/galaxy/scripts/components/Upload/UploadWrapper.vue
+++ b/client/galaxy/scripts/components/Upload/UploadWrapper.vue
@@ -22,16 +22,16 @@ export default {
     props: {
         topInfo: {
             type: String,
-            default: "&nbsp;"
+            default: "&nbsp;",
         },
         wrapperClass: {
             type: String,
-            default: "upload-view-default"
+            default: "upload-view-default",
         },
         highlightBox: {
             type: Boolean,
-            default: false
-        }
+            default: false,
+        },
     },
     computed: {
         hasFooter() {
@@ -39,11 +39,11 @@ export default {
             const name = "footer";
             return !!this.$slots[name] || !!this.$scopedSlots[name];
         },
-        boxStyle: function() {
+        boxStyle: function () {
             return {
-                height: this.hasFooter ? "300px" : "335px"
+                height: this.hasFooter ? "300px" : "335px",
             };
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Upload/test_helpers.js b/client/galaxy/scripts/components/Upload/test_helpers.js
index 9382534ae5c7..776530bd548f 100644
--- a/client/galaxy/scripts/components/Upload/test_helpers.js
+++ b/client/galaxy/scripts/components/Upload/test_helpers.js
@@ -20,16 +20,16 @@ export function mountWithApp(component, options = {}, propsData_ = {}) {
                     {
                         name: "%s.pheno",
                         optional: false,
-                        description: "Phenodata tab text file"
+                        description: "Phenodata tab text file",
                     },
                     {
                         name: "%s.affybatch",
                         optional: false,
-                        description: "AffyBatch R object saved to file"
-                    }
-                ]
-            }
-        ]
+                        description: "AffyBatch R object saved to file",
+                    },
+                ],
+            },
+        ],
     });
     const propsData = _.defaults(propsData_, { app });
     const localVue = createLocalVue();
@@ -38,8 +38,8 @@ export function mountWithApp(component, options = {}, propsData_ = {}) {
         localVue,
         attachToDocument: true,
         stubs: {
-            select2: true
-        }
+            select2: true,
+        },
     });
     return { wrapper, localVue };
 }
diff --git a/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.test.js b/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.test.js
index 979f8a0e9d55..a3624866065f 100644
--- a/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.test.js
+++ b/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.test.js
@@ -14,13 +14,13 @@ import listCredentials from "./testdata/listCredentials.json";
 
 const localVue = createLocalVue();
 localVue.use(BootstrapVue);
-localVue.filter("localize", value => _l(value));
+localVue.filter("localize", (value) => _l(value));
 
 describe("CloudAuth component", () => {
     let stub, wrapper;
 
     const mockSvc = {
-        listCredentials: async () => null
+        listCredentials: async () => null,
     };
 
     rewire.__Rewire__("svc", mockSvc);
@@ -82,7 +82,7 @@ describe("CloudAuth component", () => {
             results = wrapper.vm.filteredItems;
             assert(results.length == 3, `Wrong number of items: ${results.length}`);
 
-            const blank = results.find(i => i.id == null);
+            const blank = results.find((i) => i.id == null);
             assert(blank, "missing blank key");
             assert(blank.id == null);
         });
diff --git a/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.vue b/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.vue
index 74bc81e5592a..e61552833aa2 100644
--- a/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.vue
+++ b/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.vue
@@ -107,7 +107,7 @@ Vue.use(BootstrapVue);
 
 export default {
     components: {
-        CloudAuthItem
+        CloudAuthItem,
     },
     data() {
         return {
@@ -117,12 +117,12 @@ export default {
             showFilter: false,
             loading: false,
             doomedItem: null,
-            errorMessage: null
+            errorMessage: null,
         };
     },
     computed: {
         filteredItems() {
-            return this.items.filter(o => o.match(this.filter));
+            return this.items.filter((o) => o.match(this.filter));
         },
         filterDescription() {
             return `${this.filteredItems.length} matches out of ${this.items.length} items`;
@@ -136,19 +136,19 @@ export default {
             },
             // This setter is here because vue-bootstrap modal
             // tries to set this property for unfathomable reasons
-            set() {}
-        }
+            set() {},
+        },
     },
     watch: {
         showDeleted(deleted) {
             this.loadCredentials({ deleted });
-        }
+        },
     },
     methods: {
         loadCredentials(params = {}) {
             this.loading = true;
             svc.listCredentials(params)
-                .then(items => (this.items = items))
+                .then((items) => (this.items = items))
                 .catch(this.setError("Unable to load cloud keys."))
                 .finally(() => (this.loading = false));
         },
@@ -162,7 +162,7 @@ export default {
             }
             item.loading = true;
             svc.saveCredential(item)
-                .then(result => {
+                .then((result) => {
                     item.id = result.id;
                     item.updateState();
                 })
@@ -190,25 +190,25 @@ export default {
         expand(credential, { expanded }) {
             credential.expanded = expanded;
             if (expanded) {
-                this.items.filter(i => i !== credential).forEach(i => (i.expanded = false));
+                this.items.filter((i) => i !== credential).forEach((i) => (i.expanded = false));
             }
         },
         addItem(item) {
             this.items = [...this.items, item];
         },
         removeItem(item) {
-            this.items = this.items.filter(o => o !== item);
+            this.items = this.items.filter((o) => o !== item);
         },
         setError(msg) {
-            return err => {
+            return (err) => {
                 this.errorMessage = msg;
                 console.warn(err);
             };
-        }
+        },
     },
     created() {
         this.loadCredentials();
-    }
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/User/CloudAuth/CloudAuthItem.vue b/client/galaxy/scripts/components/User/CloudAuth/CloudAuthItem.vue
index 39d8c43f7d55..dc7a13d35589 100644
--- a/client/galaxy/scripts/components/User/CloudAuth/CloudAuthItem.vue
+++ b/client/galaxy/scripts/components/User/CloudAuth/CloudAuthItem.vue
@@ -59,10 +59,10 @@ import CredentialForm from "./CredentialForm";
 
 export default {
     components: {
-        CredentialForm
+        CredentialForm,
     },
     props: {
-        credential: { type: Credential, required: true }
+        credential: { type: Credential, required: true },
     },
     computed: {
         statusClasses() {
@@ -83,13 +83,13 @@ export default {
         },
         expanded() {
             return this.credential.expanded;
-        }
+        },
     },
     methods: {
         expand(forceState) {
             const expanded = forceState !== undefined ? forceState : !this.expanded;
             this.$emit("expand", { expanded });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/User/CloudAuth/CredentialConfig.vue b/client/galaxy/scripts/components/User/CloudAuth/CredentialConfig.vue
index 8314cb93bb80..03eda18b03e9 100644
--- a/client/galaxy/scripts/components/User/CloudAuth/CredentialConfig.vue
+++ b/client/galaxy/scripts/components/User/CloudAuth/CredentialConfig.vue
@@ -27,10 +27,10 @@ import MaskedInput from "components/MaskedInput";
 
 export default {
     components: {
-        MaskedInput
+        MaskedInput,
     },
     props: {
-        value: { type: Object, required: true }
+        value: { type: Object, required: true },
     },
     computed: {
         config() {
@@ -38,7 +38,7 @@ export default {
         },
         fieldDefs() {
             return this.value.constructor.fields;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/User/CloudAuth/CredentialForm.vue b/client/galaxy/scripts/components/User/CloudAuth/CredentialForm.vue
index 0dd4d16a332a..e27decdc2e51 100644
--- a/client/galaxy/scripts/components/User/CloudAuth/CredentialForm.vue
+++ b/client/galaxy/scripts/components/User/CloudAuth/CredentialForm.vue
@@ -61,14 +61,14 @@ import CredentialConfig from "./CredentialConfig";
 
 export default {
     components: {
-        CredentialConfig
+        CredentialConfig,
     },
     props: {
-        value: { type: Credential, required: true }
+        value: { type: Credential, required: true },
     },
     data() {
         return {
-            identityProviders: []
+            identityProviders: [],
         };
     },
     computed: {
@@ -93,16 +93,16 @@ export default {
         },
         saveButtonTitle() {
             return this.loading ? "Saving Key..." : "Save Key";
-        }
+        },
     },
     created() {
-        getIdentityProviders().then(result => {
+        getIdentityProviders().then((result) => {
             if (!this.credential.authn_id && result.length == 1) {
                 this.credential.authn_id = result[0].authn_id;
                 this.credential.updateState();
             }
             this.identityProviders = result;
         });
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/AwsConfig.js b/client/galaxy/scripts/components/User/CloudAuth/model/AwsConfig.js
index 269d75578a38..c9e34a7d3659 100644
--- a/client/galaxy/scripts/components/User/CloudAuth/model/AwsConfig.js
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/AwsConfig.js
@@ -10,7 +10,7 @@ export class AwsConfig extends BaseModel {
     }
 }
 
-AwsConfig.setValidator(function(model) {
+AwsConfig.setValidator(function (model) {
     const errors = {};
     if (!model.role_arn.length) {
         errors.role_arn = "Missing role_arn";
@@ -22,6 +22,6 @@ AwsConfig.fields = {
     role_arn: {
         label: "Role ARN",
         description: "The Amazon resource name (ARN) of the role to be assumed by Galaxy.",
-        placeholder: "arn:aws:iam::XXXXXXXXXXXX:role/XXXXXXXXXXX"
-    }
+        placeholder: "arn:aws:iam::XXXXXXXXXXXX:role/XXXXXXXXXXX",
+    },
 };
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/AzureConfig.js b/client/galaxy/scripts/components/User/CloudAuth/model/AzureConfig.js
index 7cee6dacf069..fbf8eb70f9e1 100644
--- a/client/galaxy/scripts/components/User/CloudAuth/model/AzureConfig.js
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/AzureConfig.js
@@ -12,7 +12,7 @@ export class AzureConfig extends BaseModel {
     }
 }
 
-AzureConfig.setValidator(function(model) {
+AzureConfig.setValidator(function (model) {
     const errors = {};
 
     if (model.tenant_id.length < 36) {
@@ -42,20 +42,20 @@ AzureConfig.fields = {
         mask: "********-****-****-****-************",
         placeholder: "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx",
         maxlength: 36,
-        description: "Your Tenant ID (or Directory ID) on Azure."
+        description: "Your Tenant ID (or Directory ID) on Azure.",
     },
     client_id: {
         label: "Client ID",
         mask: "********-****-****-****-************",
         placeholder: "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx",
         maxlength: 36,
-        description: "The Client ID (or Application ID) you defined for Galaxy on your Azure directory."
+        description: "The Client ID (or Application ID) you defined for Galaxy on your Azure directory.",
     },
     client_secret: {
         label: "Client Secret",
         mask: "",
         placeholder: "Client Secret",
         description:
-            "A secret string you obtained from Azure portal that Galaxy can use to prove its identity when requesting tokens to access your resources."
-    }
+            "A secret string you obtained from Azure portal that Galaxy can use to prove its identity when requesting tokens to access your resources.",
+    },
 };
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/BaseModel.js b/client/galaxy/scripts/components/User/CloudAuth/model/BaseModel.js
index 651ce0d0ab10..5dede7517def 100644
--- a/client/galaxy/scripts/components/User/CloudAuth/model/BaseModel.js
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/BaseModel.js
@@ -30,7 +30,7 @@ export class BaseModel {
     get state() {
         // build state JSON ignoring transient fields
         const tFields = this.transientFields;
-        return JSON.stringify(this, function(key) {
+        return JSON.stringify(this, function (key) {
             if (!tFields.has(key)) {
                 return this[key];
             }
@@ -63,7 +63,7 @@ export class BaseModel {
         }
 
         const fields = transients.get(klass);
-        fieldNames.forEach(fieldName => fields.add(fieldName));
+        fieldNames.forEach((fieldName) => fields.add(fieldName));
         transients.set(klass, fields);
     }
 
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/Credential.js b/client/galaxy/scripts/components/User/CloudAuth/model/Credential.js
index defa15e67df5..d3fc13fe28e0 100644
--- a/client/galaxy/scripts/components/User/CloudAuth/model/Credential.js
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/Credential.js
@@ -65,7 +65,7 @@ export class Credential extends BaseModel {
         return {
             authn_id: null,
             provider: "aws",
-            expanded: false
+            expanded: false,
         };
     }
 
@@ -85,7 +85,7 @@ Credential.setTransient("expanded", "loading");
  * where the keys are field names and the values are
  * error messages.
  */
-Credential.setValidator(function(model) {
+Credential.setValidator(function (model) {
     const errors = {};
 
     if (!model.provider) {
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/Credential.test.js b/client/galaxy/scripts/components/User/CloudAuth/model/Credential.test.js
index ee2be51b3151..219b3a196204 100644
--- a/client/galaxy/scripts/components/User/CloudAuth/model/Credential.test.js
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/Credential.test.js
@@ -84,8 +84,8 @@ describe("Credential model", () => {
                 authn_id: "asdfasdf",
                 provider: "aws",
                 config: {
-                    role_arn: "floobar"
-                }
+                    role_arn: "floobar",
+                },
             };
             let instance = new Credential(props);
             assert(instance.valid);
@@ -96,8 +96,8 @@ describe("Credential model", () => {
                 authn_id: "asdfasdf",
                 provider: "aws",
                 config: {
-                    role_arn: ""
-                }
+                    role_arn: "",
+                },
             };
             let instance = new Credential(props);
             assert(!instance.valid);
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/ResourceProviders.js b/client/galaxy/scripts/components/User/CloudAuth/model/ResourceProviders.js
index 965e254b2f11..cefcbb63faa6 100644
--- a/client/galaxy/scripts/components/User/CloudAuth/model/ResourceProviders.js
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/ResourceProviders.js
@@ -5,10 +5,10 @@ export const ResourceProviders = new Map();
 
 ResourceProviders.set("aws", {
     klass: AwsConfig,
-    label: "Amazon Web Services (AWS)"
+    label: "Amazon Web Services (AWS)",
 });
 
 ResourceProviders.set("azure", {
     klass: AzureConfig,
-    label: "Microsoft Azure"
+    label: "Microsoft Azure",
 });
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/service.js b/client/galaxy/scripts/components/User/CloudAuth/model/service.js
index 4c33eae865c2..c4fcc3d0c2fe 100644
--- a/client/galaxy/scripts/components/User/CloudAuth/model/service.js
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/service.js
@@ -6,7 +6,7 @@ import axios from "axios";
 import { Credential, IdentityProvider } from "./index";
 import { getRootFromIndexLink } from "onload";
 
-const getUrl = path => getRootFromIndexLink() + path;
+const getUrl = (path) => getRootFromIndexLink() + path;
 
 export async function listCredentials() {
     const url = getUrl("api/cloud/authz");
@@ -76,5 +76,5 @@ export default {
     getCredential,
     saveCredential,
     deleteCredential,
-    getIdentityProviders
+    getIdentityProviders,
 };
diff --git a/client/galaxy/scripts/components/User/CustomBuilds.vue b/client/galaxy/scripts/components/User/CustomBuilds.vue
index c1bdd012af39..7da484c44250 100644
--- a/client/galaxy/scripts/components/User/CustomBuilds.vue
+++ b/client/galaxy/scripts/components/User/CustomBuilds.vue
@@ -164,7 +164,7 @@ Vue.use(BootstrapVue);
 
 export default {
     components: {
-        Multiselect
+        Multiselect,
     },
     data() {
         const Galaxy = getGalaxyInstance();
@@ -178,7 +178,7 @@ export default {
                 { key: "name", label: "Name" },
                 { key: "id", label: "Key" },
                 { key: "count", label: "Number of chroms/contigs" },
-                { key: "action", label: "" }
+                { key: "action", label: "" },
             ],
             customBuilds: [],
             alertType: "info",
@@ -189,25 +189,25 @@ export default {
                 id: "",
                 name: "",
                 file: "",
-                text: ""
+                text: "",
             },
             dataSources: [
                 { value: "fasta", text: "FASTA-file from history" },
                 { value: "file", text: "Len-file from disk" },
-                { value: "text", text: "Len-file by copy/paste" }
+                { value: "text", text: "Len-file by copy/paste" },
             ],
             selectedDataSource: "fasta",
             fastaFilesLoading: true,
             fastaFilesSelectDisabled: true,
             fastaFiles: [],
-            selectedFastaFile: null
+            selectedFastaFile: null,
         };
     },
     computed: {
-        lengthType: function() {
+        lengthType: function () {
             return this.selectedDataSource || "";
         },
-        lengthValue: function() {
+        lengthValue: function () {
             let value = "";
             if (this.lengthType === "fasta") {
                 value = this.selectedFastaFile || "";
@@ -217,7 +217,7 @@ export default {
                 value = this.form.text;
             }
             return value;
-        }
+        },
     },
     created() {
         const Galaxy = getGalaxyInstance();
@@ -233,10 +233,10 @@ export default {
         loadCustomBuilds() {
             axios
                 .get(this.customBuildsUrl)
-                .then(response => {
+                .then((response) => {
                     this.customBuilds = response.data;
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.showAlert("danger", error.response);
                 });
         },
@@ -244,7 +244,7 @@ export default {
             const Galaxy = getGalaxyInstance();
             axios
                 .get(`${Galaxy.root}api/histories/${historyId}/custom_builds_metadata`)
-                .then(response => {
+                .then((response) => {
                     const fastaHdas = response.data.fasta_hdas;
                     for (let i = 0; i < fastaHdas.length; i++) {
                         fastaHdas[i].text = fastaHdas[i].label;
@@ -260,7 +260,7 @@ export default {
                         this.installedBuilds[i].text = this.installedBuilds[i].label;
                     }
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.showAlert("danger", error.response);
                     this.fastaFilesLoading = false;
                 });
@@ -270,7 +270,7 @@ export default {
                 id: this.form.id,
                 name: this.form.name,
                 "len|type": this.lengthType,
-                "len|value": this.lengthValue
+                "len|value": this.lengthValue,
             };
             if (!data.id.trim() || !data.name.trim() || !data["len|value"].trim()) {
                 this.showAlert("danger", "All inputs are required.");
@@ -278,7 +278,7 @@ export default {
             }
             axios
                 .put(`${this.customBuildsUrl}/${data.id}`, data)
-                .then(response => {
+                .then((response) => {
                     if (response.data.message) {
                         this.showAlert("warning", response.data.message);
                     } else {
@@ -286,7 +286,7 @@ export default {
                     }
                     this.loadCustomBuilds();
                 })
-                .catch(error => {
+                .catch((error) => {
                     const message = error.response.data.err_msg;
                     this.showAlert("danger", message || "Failed to create custom build.");
                 });
@@ -294,10 +294,10 @@ export default {
         deleteBuild(id) {
             axios
                 .delete(`${this.customBuildsUrl}/${id}`)
-                .then(response => {
-                    this.customBuilds = this.customBuilds.filter(i => i.id !== id);
+                .then((response) => {
+                    this.customBuilds = this.customBuilds.filter((i) => i.id !== id);
                 })
-                .catch(error => {
+                .catch((error) => {
                     const message = error.response.data.err_msg;
                     this.showAlert("danger", message || "Failed to delete custom build.");
                 });
@@ -306,7 +306,7 @@ export default {
             const file = event.target.files && event.target.files[0];
             if (file) {
                 const reader = new FileReader();
-                reader.onprogress = e => {
+                reader.onprogress = (e) => {
                     if (e.lengthComputable) {
                         this.fileLoaded = Math.round(e.loaded / e.total) * 100;
                     }
@@ -325,8 +325,8 @@ export default {
         },
         countDownChanged(dismissCountDown) {
             this.dismissCountDown = dismissCountDown;
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/User/RecentInvocations.vue b/client/galaxy/scripts/components/User/RecentInvocations.vue
index dbf82f300d4a..eb11ebc129e0 100644
--- a/client/galaxy/scripts/components/User/RecentInvocations.vue
+++ b/client/galaxy/scripts/components/User/RecentInvocations.vue
@@ -14,17 +14,17 @@ import { getRecentInvocations } from "./UserServices";
 
 export default {
     components: {
-        Invocations
+        Invocations,
     },
     data() {
         return {
             invocationItems: [],
-            loading: true
+            loading: true,
         };
     },
     created() {
         getRecentInvocations()
-            .then(response => {
+            .then((response) => {
                 this.invocationItems = response.data;
                 this.loading = false;
             })
@@ -33,7 +33,7 @@ export default {
     methods: {
         handleError(error) {
             console.error(error);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/User/UserPreferences.vue b/client/galaxy/scripts/components/User/UserPreferences.vue
index 2d7453652f15..fab04469d612 100644
--- a/client/galaxy/scripts/components/User/UserPreferences.vue
+++ b/client/galaxy/scripts/components/User/UserPreferences.vue
@@ -58,12 +58,12 @@ export default {
     props: {
         userId: {
             type: String,
-            required: true
+            required: true,
         },
         enableQuotas: {
             type: Boolean,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
@@ -72,7 +72,7 @@ export default {
             quotaUsageString: "",
             baseUrl: `${getAppRoot()}user`,
             messageVariant: null,
-            message: null
+            message: null,
         };
     },
     created() {
@@ -82,7 +82,7 @@ export default {
             this.message = message;
             this.messageVariant = status;
         }
-        axios.get(`${getAppRoot()}api/users/${this.userId}`).then(response => {
+        axios.get(`${getAppRoot()}api/users/${this.userId}`).then((response) => {
             this.email = response.data.email;
             this.diskUsage = response.data.nice_total_disk_usage;
             this.quotaUsageString = this.enableQuotas
@@ -114,15 +114,15 @@ export default {
             }
 
             return activeLinks;
-        }
+        },
     },
     methods: {
         toggleNotifications() {
-            Notification.requestPermission().then(function(permission) {
+            Notification.requestPermission().then(function (permission) {
                 //If the user accepts, let's create a notification
                 if (permission === "granted") {
                     new Notification("Notifications enabled", {
-                        icon: "static/favicon.ico"
+                        icon: "static/favicon.ico",
                     });
                 } else {
                     alert("Notifications disabled, please re-enable through browser settings.");
@@ -148,15 +148,15 @@ export default {
                     )
                 )
             ) {
-                axios.post(`${getAppRoot()}history/make_private?all_histories=true`).then(response => {
+                axios.post(`${getAppRoot()}history/make_private?all_histories=true`).then((response) => {
                     Galaxy.modal.show({
                         title: _l("Datasets are now private"),
                         body: `All of your histories and datsets have been made private.  If you'd like to make all *future* histories private please use the <a href="${Galaxy.root}user/permissions">User Permissions</a> interface.`,
                         buttons: {
                             Close: () => {
                                 Galaxy.modal.hide();
-                            }
-                        }
+                            },
+                        },
                     });
                 });
             }
@@ -167,18 +167,18 @@ export default {
                 title: _l("Sign out"),
                 body: "Do you want to continue and sign out of all active sessions?",
                 buttons: {
-                    Cancel: function() {
+                    Cancel: function () {
                         Galaxy.modal.hide();
                     },
-                    "Sign out": function() {
+                    "Sign out": function () {
                         window.location.href = `${getAppRoot()}user/logout?session_csrf_token=${
                             Galaxy.session_csrf_token
                         }`;
-                    }
-                }
+                    },
+                },
             });
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/User/UserPreferencesModel.js b/client/galaxy/scripts/components/User/UserPreferencesModel.js
index 702d038ae394..9f18625916ca 100644
--- a/client/galaxy/scripts/components/User/UserPreferencesModel.js
+++ b/client/galaxy/scripts/components/User/UserPreferencesModel.js
@@ -12,7 +12,7 @@ export const getUserPreferencesModel = () => {
             url: `api/users/${Galaxy.user.id}/information/inputs`,
             icon: "fa-user",
             redirect: "user",
-            shouldRender: !config.use_remote_user
+            shouldRender: !config.use_remote_user,
         },
         password: {
             title: _l("Change Password"),
@@ -22,7 +22,7 @@ export const getUserPreferencesModel = () => {
             url: `api/users/${Galaxy.user.id}/password/inputs`,
             submit_title: "Save Password",
             redirect: "user",
-            shouldRender: !config.use_remote_user
+            shouldRender: !config.use_remote_user,
         },
         communication: {
             title: _l("Change Communication Settings"),
@@ -31,7 +31,7 @@ export const getUserPreferencesModel = () => {
             url: `api/users/${Galaxy.user.id}/communication/inputs`,
             icon: "fa-comments-o",
             redirect: "user",
-            shouldRender: !!config.enable_communication_server
+            shouldRender: !!config.enable_communication_server,
         },
         permissions: {
             title: _l("Set Dataset Permissions for new Histories"),
@@ -41,13 +41,13 @@ export const getUserPreferencesModel = () => {
             url: `api/users/${Galaxy.user.id}/permissions/inputs`,
             icon: "fa-users",
             submit_title: "Save Permissions",
-            redirect: "user"
+            redirect: "user",
         },
         make_data_private: {
             title: _l("Make all Data Private"),
             id: "edit-preferences-make-data-private",
             description: _l("Click here to make all data private."),
-            icon: "fa-lock"
+            icon: "fa-lock",
         },
         api_key: {
             title: _l("Manage API Key"),
@@ -56,7 +56,7 @@ export const getUserPreferencesModel = () => {
             url: `api/users/${Galaxy.user.id}/api_key/inputs`,
             icon: "fa-key",
             submit_title: "Create a new Key",
-            submit_icon: "fa-check"
+            submit_icon: "fa-check",
         },
         cloud_auth: {
             id: "edit-preferences-cloud-auth",
@@ -64,7 +64,7 @@ export const getUserPreferencesModel = () => {
             description: _l("Add or modify the configuration that grants Galaxy to access your cloud-based resources."),
             icon: "fa-cloud",
             submit_title: "Create a new Key",
-            submit_icon: "fa-check"
+            submit_icon: "fa-check",
         },
         toolbox_filters: {
             title: _l("Manage Toolbox Filters"),
@@ -74,19 +74,19 @@ export const getUserPreferencesModel = () => {
             icon: "fa-filter",
             submit_title: "Save Filters",
             redirect: "user",
-            shouldRender: !!config.has_user_tool_filters
+            shouldRender: !!config.has_user_tool_filters,
         },
         custom_builds: {
             title: _l("Manage Custom Builds"),
             description: _l("Add or remove custom builds using history datasets."),
-            icon: "fa-cubes"
+            icon: "fa-cubes",
         },
         logout: {
             title: _l("Sign Out"),
             id: "edit-preferences-custom-builds",
             description: _l("Click here to sign out of all sessions."),
             icon: "fa-sign-out",
-            shouldRender: !!Galaxy.session_csrf_token
-        }
+            shouldRender: !!Galaxy.session_csrf_token,
+        },
     };
 };
diff --git a/client/galaxy/scripts/components/UtcDate.vue b/client/galaxy/scripts/components/UtcDate.vue
index 80539145ed9a..4ebd16b3a6f1 100644
--- a/client/galaxy/scripts/components/UtcDate.vue
+++ b/client/galaxy/scripts/components/UtcDate.vue
@@ -14,20 +14,20 @@ export default {
     props: {
         date: {
             type: String,
-            required: true
+            required: true,
         },
         mode: {
             type: String,
-            default: "date" // or elapsed
-        }
+            default: "date", // or elapsed
+        },
     },
     computed: {
-        elapsedTime: function() {
+        elapsedTime: function () {
             return moment(moment.utc(this.date)).from(moment().utc());
         },
-        fullDate: function() {
+        fullDate: function () {
             return moment.utc(this.date).format();
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/WaitButton.vue b/client/galaxy/scripts/components/WaitButton.vue
index 884c01bd52d2..27f0942481b6 100644
--- a/client/galaxy/scripts/components/WaitButton.vue
+++ b/client/galaxy/scripts/components/WaitButton.vue
@@ -14,28 +14,28 @@ export default {
     props: {
         title: {
             type: String,
-            default: ""
+            default: "",
         },
         icon: {
             type: String,
-            deafult: ""
+            deafult: "",
         },
         percentage: {
             type: Number,
-            default: -1
+            default: -1,
         },
         waiting: {
             type: Boolean,
-            default: false
+            default: false,
         },
         waitText: {
             type: String,
-            default: "Sending..."
+            default: "Sending...",
         },
         variant: {
             type: String,
-            default: "info"
-        }
+            default: "info",
+        },
     },
     computed: {
         progressWidth() {
@@ -61,7 +61,7 @@ export default {
             } else {
                 return this.title;
             }
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Attributes.test.js b/client/galaxy/scripts/components/Workflow/Editor/Attributes.test.js
index 59ede8ebf10b..0f2ec364e836 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Attributes.test.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/Attributes.test.js
@@ -21,8 +21,8 @@ describe("Attributes", () => {
                 name: "workflow_name",
                 tags: ["workflow_tag_0", "workflow_tag_1"],
                 parameters: ["workflow_parameter_0", "workflow_parameter_1"],
-                versions: ["workflow_version_0"]
-            }
+                versions: ["workflow_version_0"],
+            },
         });
         const name = wrapper.find("#workflow-name");
         expect(name.element.value).to.equal("workflow_name");
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Attributes.vue b/client/galaxy/scripts/components/Workflow/Editor/Attributes.vue
index abad5bf2cf55..a37bcd95591c 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Attributes.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Attributes.vue
@@ -51,40 +51,40 @@ Vue.use(BootstrapVue);
 export default {
     name: "Attributes",
     components: {
-        Tags
+        Tags,
     },
     props: {
         id: {
             type: String,
-            required: true
+            required: true,
         },
         name: {
             type: String,
-            required: true
+            required: true,
         },
         tags: {
             type: Array,
-            required: true
+            required: true,
         },
         annotation: {
-            type: String
+            type: String,
         },
         version: {
-            type: Number
+            type: Number,
         },
         versions: {
-            type: Array
+            type: Array,
         },
         parameters: {
-            type: Array
-        }
+            type: Array,
+        },
     },
     data() {
         return {
             message: null,
             messageVariant: null,
             tagsCurrent: this.tags,
-            versionCurrent: this.version
+            versionCurrent: this.version,
         };
     },
     created() {
@@ -104,11 +104,11 @@ export default {
                 }
                 versions.push({
                     version: i,
-                    label: label
+                    label: label,
                 });
             }
             return versions;
-        }
+        },
     },
     methods: {
         onTags(tags) {
@@ -130,10 +130,10 @@ export default {
             this.messageVariant = "danger";
         },
         onAttributes(data) {
-            this.services.updateWorkflow(this.id, data).catch(error => {
+            this.services.updateWorkflow(this.id, data).catch((error) => {
                 this.onError(error);
             });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/EditorPanel.vue b/client/galaxy/scripts/components/Workflow/Editor/EditorPanel.vue
index f68ad5681441..fff5e0f55e6f 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/EditorPanel.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/EditorPanel.vue
@@ -21,13 +21,13 @@ import ReportHelp from "./ReportHelp";
 export default {
     name: "EditorPanel",
     components: {
-        ReportHelp
+        ReportHelp,
     },
     props: {
         canvas: {
             type: Boolean,
-            required: true
-        }
-    }
+            required: true,
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Index.vue b/client/galaxy/scripts/components/Workflow/Editor/Index.vue
index 2aada23c39dd..4c3e9938739d 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Index.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Index.vue
@@ -83,7 +83,7 @@ import {
     getWorkflowParameters,
     showAttributes,
     showForm,
-    saveAs
+    saveAs,
 } from "./utilities";
 import WorkflowManager from "mvc/workflow/workflow-manager";
 import WorkflowOptions from "./Options";
@@ -105,47 +105,47 @@ export default {
         ToolBoxWorkflow,
         WorkflowOptions,
         WorkflowAttributes,
-        ZoomControl
+        ZoomControl,
     },
     props: {
         id: {
-            type: String
+            type: String,
         },
         version: {
-            type: Number
+            type: Number,
         },
         name: {
-            type: String
+            type: String,
         },
         tags: {
-            type: Array
+            type: Array,
         },
         annotation: {
-            type: String
+            type: String,
         },
         module_sections: {
-            type: Array
+            type: Array,
         },
         data_managers: {
-            type: Array
+            type: Array,
         },
         workflows: {
-            type: Array
+            type: Array,
         },
         toolbox: {
-            type: Array
-        }
+            type: Array,
+        },
     },
     data() {
         return {
             isCanvas: true,
             versions: [],
             parameters: [],
-            zoomLevel: 7
+            zoomLevel: 7,
         };
     },
     created() {
-        getDatatypes().then(response => {
+        getDatatypes().then((response) => {
             const datatypes = response.datatypes;
             const datatypes_mapping = response.datatypes_mapping;
             this.manager = new WorkflowManager({ datatypes_mapping }, this.$refs.canvas);
@@ -153,7 +153,7 @@ export default {
                 .on("onRemoveNode", () => {
                     showAttributes();
                 })
-                .on("onActiveNode", node => {
+                .on("onActiveNode", (node) => {
                     showForm(this.manager, node, datatypes);
                 })
                 .on("onNodeChange", () => {
@@ -172,9 +172,9 @@ export default {
             const requestData = {
                 type: "tool",
                 tool_id: tool_id,
-                _: "true"
+                _: "true",
             };
-            getModule(requestData).then(response => {
+            getModule(requestData).then((response) => {
                 this.manager.set_node(node, response);
             });
         },
@@ -186,9 +186,9 @@ export default {
             var node = this.manager.create_node(module_id, module_name);
             const requestData = {
                 type: module_id,
-                _: "true"
+                _: "true",
             };
-            getModule(requestData).then(response => {
+            getModule(requestData).then((response) => {
                 this.manager.set_node(node, response);
             });
         },
@@ -201,9 +201,9 @@ export default {
             const requestData = {
                 type: "subworkflow",
                 content_id: workflow_id,
-                _: "true"
+                _: "true",
             };
-            getModule(requestData).then(response => {
+            getModule(requestData).then((response) => {
                 this.manager.set_node(node, response);
             });
         },
@@ -248,14 +248,14 @@ export default {
         onSave() {
             show_message("Saving workflow...", "progress");
             saveWorkflow(this.manager, this.id)
-                .then(data => {
+                .then((data) => {
                     showWarnings(data);
-                    getVersions(this.id).then(versions => {
+                    getVersions(this.id).then((versions) => {
                         this.versions = versions;
                         hide_modal();
                     });
                 })
-                .catch(response => {
+                .catch((response) => {
                     show_modal("Saving workflow failed...", response, { Ok: hide_modal });
                 });
         },
@@ -277,19 +277,19 @@ export default {
         loadCurrent(id, version) {
             show_message("Loading workflow...", "progress");
             loadWorkflow(this.manager, id, version)
-                .then(data => {
+                .then((data) => {
                     const report = data.report || {};
                     const markdown = report.markdown || reportDefault;
                     this.$refs["report-editor"].input = markdown;
                     showUpgradeMessage(this.manager, data);
-                    getVersions(this.id).then(versions => {
+                    getVersions(this.id).then((versions) => {
                         this.versions = versions;
                     });
                 })
-                .catch(response => {
+                .catch((response) => {
                     show_modal("Loading workflow failed...", response, { Ok: hide_modal });
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.test.js b/client/galaxy/scripts/components/Workflow/Editor/Node.test.js
index c0599c340441..0b142a25849e 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.test.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.test.js
@@ -8,8 +8,8 @@ describe("Node", () => {
             propsData: {
                 id: "node-id",
                 title: "node-title",
-                type: "tool"
-            }
+                type: "tool",
+            },
         });
         const icon = wrapper.findAll("i");
         expect(icon.at(2).classes()).to.contain("fa-wrench");
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 93070869e0a7..d3d91f178869 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -41,23 +41,23 @@ Vue.use(BootstrapVue);
 
 export default {
     components: {
-        LoadingSpan
+        LoadingSpan,
     },
     props: {
         id: {
-            type: String
+            type: String,
         },
         title: {
             type: String,
-            default: "title"
+            default: "title",
         },
         type: {
             type: String,
-            default: "tool"
+            default: "tool",
         },
         node: {
-            type: Object
-        }
+            type: Object,
+        },
     },
     computed: {
         iconClass() {
@@ -69,7 +69,7 @@ export default {
         },
         canClone() {
             return this.type != "subworkflow";
-        }
+        },
     },
     methods: {
         onDestroy() {
@@ -77,7 +77,7 @@ export default {
         },
         onClone() {
             this.node.clone();
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Options.vue b/client/galaxy/scripts/components/Workflow/Editor/Options.vue
index 4bf53aeada58..8ed339efa5d8 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Options.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Options.vue
@@ -74,8 +74,8 @@ export default {
     props: {
         canvas: {
             type: Boolean,
-            required: true
-        }
-    }
+            required: true,
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/ReportHelp.vue b/client/galaxy/scripts/components/Workflow/Editor/ReportHelp.vue
index 1f40ebd61245..bba0f6f764dc 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/ReportHelp.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/ReportHelp.vue
@@ -69,8 +69,8 @@ export default {
     data() {
         return {
             datasetCommandsHtml,
-            markdownGeneralHelpHtml
+            markdownGeneralHelpHtml,
         };
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/ZoomControl.test.js b/client/galaxy/scripts/components/Workflow/Editor/ZoomControl.test.js
index 5ec9518b234d..e18a805532af 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/ZoomControl.test.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/ZoomControl.test.js
@@ -6,8 +6,8 @@ describe("ZoomControl", () => {
     it("test zoom control", async () => {
         const wrapper = mount(ZoomControl, {
             propsData: {
-                zoomLevel: 10
-            }
+                zoomLevel: 10,
+            },
         });
         const buttons = wrapper.findAll("button");
         expect(buttons.length).to.equal(3);
diff --git a/client/galaxy/scripts/components/Workflow/Editor/ZoomControl.vue b/client/galaxy/scripts/components/Workflow/Editor/ZoomControl.vue
index fb0a734cd9ce..faa49bf94e9e 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/ZoomControl.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/ZoomControl.vue
@@ -44,18 +44,18 @@ export default {
     props: {
         zoomLevel: {
             type: Number,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
-            zoomDefault: this.zoomLevel
+            zoomDefault: this.zoomLevel,
         };
     },
     computed: {
         zoomPercentage() {
             return Math.floor(zoomLevels[this.zoomLevel] * 100);
-        }
+        },
     },
     methods: {
         onZoomIn() {
@@ -66,8 +66,8 @@ export default {
         },
         onZoomReset() {
             this.$emit("onZoom", this.zoomDefault);
-        }
-    }
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/Workflow/Editor/mount.js b/client/galaxy/scripts/components/Workflow/Editor/mount.js
index 5ebdea19dd7e..f0263b10f28e 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/mount.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/mount.js
@@ -5,11 +5,11 @@ import Vue from "vue";
 import Index from "./Index";
 import Node from "./Node";
 
-export const mountWorkflowEditor = propsData => {
+export const mountWorkflowEditor = (propsData) => {
     const component = Vue.extend(Index);
     return new component({
         propsData: propsData,
-        el: "#columns"
+        el: "#columns",
     });
 };
 
diff --git a/client/galaxy/scripts/components/Workflow/Editor/utilities.js b/client/galaxy/scripts/components/Workflow/Editor/utilities.js
index aa966a976c11..dcd01b05aaf8 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/utilities.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/utilities.js
@@ -12,7 +12,7 @@ export function copyIntoWorkflow(workflow, id = null, stepCount = null) {
     const _copy_into_workflow_ajax = () => {
         // Load workflow definition
         show_message("Importing workflow", "progress");
-        loadWorkflow(workflow, id, null).then(data => {
+        loadWorkflow(workflow, id, null).then((data) => {
             workflow.from_simple(data, false);
             // Determine if any parameters were 'upgraded' and provide message
             var upgrade_message = "";
@@ -40,7 +40,7 @@ export function copyIntoWorkflow(workflow, id = null, stepCount = null) {
         // don't ruin the workflow by adding 50 steps unprompted.
         show_modal(_l("Warning"), `This will copy ${stepCount} new steps into your workflow.`, {
             Cancel: hide_modal,
-            Copy: _copy_into_workflow_ajax
+            Copy: _copy_into_workflow_ajax,
         });
     }
 }
@@ -51,9 +51,7 @@ export function showWarnings(data) {
         body.addClass("warningmark");
         var errlist = $("<ul/>");
         $.each(data.errors, (i, v) => {
-            $("<li/>")
-                .text(v)
-                .appendTo(errlist);
+            $("<li/>").text(v).appendTo(errlist);
         });
         body.append(errlist);
     } else {
@@ -61,7 +59,7 @@ export function showWarnings(data) {
     }
     if (data.errors) {
         show_modal("Saving workflow", body, {
-            Ok: hide_modal
+            Ok: hide_modal,
         });
     } else {
         hide_modal();
@@ -110,7 +108,7 @@ export function showUpgradeMessage(workflow, data) {
         if (step.errors) {
             details += `<li>${step.errors}</li>`;
         }
-        _.each(data.upgrade_messages[step_id], m => {
+        _.each(data.upgrade_messages[step_id], (m) => {
             details += `<li>${m}</li>`;
         });
         if (details) {
@@ -136,7 +134,7 @@ export function getWorkflowParameters(nodes) {
     let matches = [];
     Object.entries(nodes).forEach(([k, node]) => {
         if (node.config_form && node.config_form.inputs) {
-            Utils.deepeach(node.config_form.inputs, d => {
+            Utils.deepeach(node.config_form.inputs, (d) => {
                 if (typeof d.value == "string") {
                     var form_matches = d.value.match(parameter_re);
                     if (form_matches) {
@@ -179,7 +177,7 @@ export function saveAs(workflow) {
             '<br><label style="display:inline-block; width: 100%;">Annotation: </label><input type="text" id="wf_annotation" style="width: 80%;" /></form>'
     );
     show_modal("Save As a New Workflow", body, {
-        OK: function() {
+        OK: function () {
             var rename_name =
                 $("#workflow_rename").val().length > 0 ? $("#workflow_rename").val() : `SavedAs_${workflow.name}`;
             var rename_annotation = $("#wf_annotation").val().length > 0 ? $("#wf_annotation").val() : "";
@@ -190,12 +188,12 @@ export function saveAs(workflow) {
                     workflow_name: rename_name,
                     workflow_annotation: rename_annotation,
                     from_tool_form: true,
-                    workflow_data: function() {
+                    workflow_data: function () {
                         return JSON.stringify(workflow.to_simple());
-                    }
-                }
+                    },
+                },
             })
-                .done(id => {
+                .done((id) => {
                     window.onbeforeunload = undefined;
                     window.location = `${getAppRoot()}workflow/editor?id=${id}`;
                     hide_modal();
@@ -205,6 +203,6 @@ export function saveAs(workflow) {
                     alert("Saving this workflow failed. Please contact this site's administrator.");
                 });
         },
-        Cancel: hide_modal
+        Cancel: hide_modal,
     });
 }
diff --git a/client/galaxy/scripts/components/Workflow/Invocations.vue b/client/galaxy/scripts/components/Workflow/Invocations.vue
index 713e673d7e5c..bc49ac4d31e5 100644
--- a/client/galaxy/scripts/components/Workflow/Invocations.vue
+++ b/client/galaxy/scripts/components/Workflow/Invocations.vue
@@ -84,14 +84,14 @@ export default {
         WorkflowInvocationState,
         LoadingSpan,
         WorkflowDropdown,
-        HistoryDropdown
+        HistoryDropdown,
     },
     props: {
         invocationItems: { type: Array, default: () => [] },
         loading: { type: Boolean, default: true },
         noInvocationsMessage: { type: String },
         headerMessage: { type: String, default: "" },
-        ownerGrid: { type: Boolean, default: true }
+        ownerGrid: { type: Boolean, default: true },
     },
     data() {
         const fields = [
@@ -101,19 +101,19 @@ export default {
             { key: "id", label: "Invocation ID" },
             { key: "state" },
             { key: "update_time", label: "Last Update" },
-            { key: "create_time", label: "Invocation Time" }
+            { key: "create_time", label: "Invocation Time" },
         ];
         return {
             invocationItemsModel: [],
             invocationFields: fields,
-            status: ""
+            status: "",
         };
     },
     computed: {
         ...mapGetters(["getWorkflowByInstanceId", "getHistoryById"]),
         invocationItemsComputed() {
             return this.computeItems(this.invocationItems);
-        }
+        },
     },
     methods: {
         ...mapCacheActions(["fetchWorkflowForInstanceId", "fetchHistoryForId"]),
@@ -121,7 +121,7 @@ export default {
             return getRootFromIndexLink() + "workflow/editor?id=" + this.getWorkflowByInstanceId(workflowId).id;
         },
         computeItems(items) {
-            return items.map(invocation => {
+            return items.map((invocation) => {
                 if (this.ownerGrid) {
                     this.fetchWorkflowForInstanceId(invocation["workflow_id"]);
                     this.fetchHistoryForId(invocation["history_id"]);
@@ -133,7 +133,7 @@ export default {
                     workflow_id: invocation["workflow_id"],
                     history_id: invocation["history_id"],
                     state: invocation["state"],
-                    _showDetails: false
+                    _showDetails: false,
                 };
             });
         },
@@ -142,7 +142,7 @@ export default {
         },
         handleError(error) {
             console.error(error);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Run/WorkflowRun.vue b/client/galaxy/scripts/components/Workflow/Run/WorkflowRun.vue
index be0c65ed819e..955379b2d42e 100644
--- a/client/galaxy/scripts/components/Workflow/Run/WorkflowRun.vue
+++ b/client/galaxy/scripts/components/Workflow/Run/WorkflowRun.vue
@@ -55,10 +55,10 @@ export default {
     components: {
         LoadingSpan,
         WaitButton,
-        WorkflowRunSuccess
+        WorkflowRunSuccess,
     },
     props: {
-        workflowId: { type: String }
+        workflowId: { type: String },
     },
     data() {
         return {
@@ -71,14 +71,14 @@ export default {
             runButtonEnabled: true,
             runButtonWaitText: "",
             runButtonPercentage: -1,
-            invocations: null
+            invocations: null,
         };
     },
     created() {
         const url = `${getAppRoot()}api/workflows/${this.workflowId}/download?style=run`;
         axios
             .get(url)
-            .then(response => {
+            .then((response) => {
                 const runData = response.data;
                 this.hasUpgradeMessages = runData.has_upgrade_messages;
                 this.hasStepVersionChanges = runData.step_version_changes && runData.step_version_changes.length > 0;
@@ -89,12 +89,12 @@ export default {
                     const formProps = {
                         el,
                         setRunButtonStatus: this.setRunButtonStatus,
-                        handleInvocations: this.handleInvocations
+                        handleInvocations: this.handleInvocations,
                     };
                     this.runForm = new ToolFormComposite.View(Object.assign({}, runData, formProps));
                 });
             })
-            .catch(response => {
+            .catch((response) => {
                 this.error = errorMessageAsString(response);
             });
     },
@@ -109,7 +109,7 @@ export default {
         },
         handleInvocations(invocations) {
             this.invocations = invocations;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Run/WorkflowRunSuccess.vue b/client/galaxy/scripts/components/Workflow/Run/WorkflowRunSuccess.vue
index 1e6426db4305..933d112d7497 100644
--- a/client/galaxy/scripts/components/Workflow/Run/WorkflowRunSuccess.vue
+++ b/client/galaxy/scripts/components/Workflow/Run/WorkflowRunSuccess.vue
@@ -32,21 +32,21 @@ import { getGalaxyInstance } from "app";
 
 export default {
     components: {
-        WorkflowInvocationState
+        WorkflowInvocationState,
     },
     props: {
         workflowName: {
             type: String,
-            required: true
+            required: true,
         },
         invocations: {
             type: Array,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
-            refreshHistoryTimeout: null
+            refreshHistoryTimeout: null,
         };
     },
     computed: {
@@ -74,7 +74,7 @@ export default {
                     Galaxy.currHistoryPanel.model.id != this.invocations[0].history_id) ||
                 false
             );
-        }
+        },
     },
     methods: {
         _refreshHistory() {
@@ -92,15 +92,15 @@ export default {
                     }
                 });
             }
-        }
+        },
     },
     mounted() {
         new Webhooks.WebhookView({
             type: "workflow",
             toolId: null,
-            toolVersion: null
+            toolVersion: null,
         });
         this._refreshHistory();
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/WorkflowDropdown.vue b/client/galaxy/scripts/components/Workflow/WorkflowDropdown.vue
index 57f9a23ad1a2..b023c53afd0f 100644
--- a/client/galaxy/scripts/components/Workflow/WorkflowDropdown.vue
+++ b/client/galaxy/scripts/components/Workflow/WorkflowDropdown.vue
@@ -81,43 +81,43 @@ export default {
                 return "fa fa-share-alt";
             }
             return "fa fa-caret-down";
-        }
+        },
     },
     created() {
         this.root = getAppRoot();
         this.services = new Services({ root: this.root });
     },
     methods: {
-        onCopy: function() {
+        onCopy: function () {
             this.services
                 .copyWorkflow(this.workflow)
-                .then(newWorkflow => {
+                .then((newWorkflow) => {
                     this.$emit("onAdd", newWorkflow);
                     this.$emit(
                         "onSuccess",
                         `Successfully copied workflow '${this.workflow.name}' to '${newWorkflow.name}'.`
                     );
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.$emit("onError", error);
                 });
         },
-        onDelete: function() {
+        onDelete: function () {
             const id = this.workflow.id;
             const name = this.workflow.name;
             if (window.confirm(`Are you sure you want to delete workflow '${name}'?`)) {
                 this.services
                     .deleteWorkflow(id)
-                    .then(message => {
+                    .then((message) => {
                         this.$emit("onRemove", id);
                         this.$emit("onSuccess", message);
                     })
-                    .catch(error => {
+                    .catch((error) => {
                         this.$emit("onError", error);
                     });
             }
         },
-        onRename: function() {
+        onRename: function () {
             const id = this.workflow.id;
             const name = this.workflow.name;
             const newName = window.prompt(`Enter a new name for workflow '${name}'`, name);
@@ -129,11 +129,11 @@ export default {
                         this.$emit("onUpdate", id, data);
                         this.$emit("onSuccess", `Successfully changed name of workflow '${name}' to '${newName}'.`);
                     })
-                    .catch(error => {
+                    .catch((error) => {
                         this.$emit("onError", error);
                     });
             }
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/WorkflowImport.vue b/client/galaxy/scripts/components/Workflow/WorkflowImport.vue
index 8136a936443e..e4debbab586f 100644
--- a/client/galaxy/scripts/components/Workflow/WorkflowImport.vue
+++ b/client/galaxy/scripts/components/Workflow/WorkflowImport.vue
@@ -36,16 +36,16 @@ export default {
             sourceFile: null,
             sourceURL: null,
             errorMessage: null,
-            myexperiment_target_url: `http://${Galaxy.config.myexperiment_target_url}/galaxy?galaxy_url=${window.location.protocol}//${window.location.host}`
+            myexperiment_target_url: `http://${Galaxy.config.myexperiment_target_url}/galaxy?galaxy_url=${window.location.protocol}//${window.location.host}`,
         };
     },
     computed: {
         hasErrorMessage() {
             return this.errorMessage != null;
-        }
+        },
     },
     methods: {
-        submit: function(ev) {
+        submit: function (ev) {
             ev.preventDefault();
             if (!this.sourceFile && !this.sourceURL) {
                 this.errorMessage = "You must provide a workflow archive URL or file.";
@@ -55,17 +55,17 @@ export default {
                 formData.append("archive_source", this.sourceURL);
                 axios
                     .post(`${getAppRoot()}api/workflows`, formData)
-                    .then(response => {
+                    .then((response) => {
                         window.location = `${getAppRoot()}workflows/list?message=${
                             response.data.message
                         }&status=success`;
                     })
-                    .catch(error => {
+                    .catch((error) => {
                         const message = error.response.data && error.response.data.err_msg;
                         this.errorMessage = message || "Import failed for an unknown reason.";
                     });
             }
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/WorkflowList.vue b/client/galaxy/scripts/components/Workflow/WorkflowList.vue
index 403d291ee12c..c559d4deb11f 100644
--- a/client/galaxy/scripts/components/Workflow/WorkflowList.vue
+++ b/client/galaxy/scripts/components/Workflow/WorkflowList.vue
@@ -102,7 +102,7 @@ export default {
         FontAwesomeIcon,
         UtcDate,
         Tags,
-        WorkflowDropdown
+        WorkflowDropdown,
     },
     data() {
         return {
@@ -110,31 +110,31 @@ export default {
             fields: [
                 {
                     key: "name",
-                    sortable: true
+                    sortable: true,
                 },
                 {
                     key: "tags",
-                    sortable: true
+                    sortable: true,
                 },
                 {
                     label: "Created",
                     key: "create_time",
-                    sortable: true
+                    sortable: true,
                 },
                 {
-                    key: "bookmark"
+                    key: "bookmark",
                 },
                 {
                     key: "execute",
-                    label: ""
-                }
+                    label: "",
+                },
             ],
             filter: "",
             loading: true,
             message: null,
             messageVariant: null,
             nWorkflows: 0,
-            workflows: []
+            workflows: [],
         };
     },
     computed: {
@@ -146,7 +146,7 @@ export default {
         },
         showMessage() {
             return !!this.message;
-        }
+        },
     },
     created() {
         this.root = getAppRoot();
@@ -159,28 +159,28 @@ export default {
             this.filter = "";
             this.services
                 .getWorkflows()
-                .then(workflows => {
+                .then((workflows) => {
                     this.workflows = workflows;
                     this.nWorkflows = workflows.length;
                     this.loading = false;
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.error = error;
                 });
         },
-        filtered: function(items) {
+        filtered: function (items) {
             this.nWorkflows = items.length;
         },
-        createWorkflow: function(workflow) {
+        createWorkflow: function (workflow) {
             window.location = `${this.root}workflows/create`;
         },
-        importWorkflow: function(workflow) {
+        importWorkflow: function (workflow) {
             window.location = `${this.root}workflows/import`;
         },
-        executeWorkflow: function(workflow) {
+        executeWorkflow: function (workflow) {
             window.location = `${this.root}workflows/run?id=${workflow.id}`;
         },
-        bookmarkWorkflow: function(workflow) {
+        bookmarkWorkflow: function (workflow) {
             // This reloads the whole page, so that the workflow appears in the tool panel.
             // Ideally we would notify only the tool panel of a change
             const id = workflow.id;
@@ -188,50 +188,50 @@ export default {
             const tags = workflow.tags;
             const data = {
                 show_in_tool_panel: !show_in_tool_panel,
-                tags: tags
+                tags: tags,
             };
             this.services
                 .updateWorkflow(id, data)
                 .then(() => {
                     window.location = `${getAppRoot()}workflows/list`;
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.onError(error);
                 });
         },
-        onTags: function(tags, index) {
+        onTags: function (tags, index) {
             const workflow = this.workflows[index];
             workflow.tags = tags;
             this.services
                 .updateWorkflow(workflow.id, {
                     show_in_tool_panel: workflow.show_in_tool_panel,
-                    tags: workflow.tags
+                    tags: workflow.tags,
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.onError(error);
                 });
         },
-        onAdd: function(workflow) {
+        onAdd: function (workflow) {
             this.workflows.unshift(workflow);
             this.nWorkflows = this.workflows.length;
         },
-        onRemove: function(id) {
-            this.workflows = this.workflows.filter(item => item.id !== id);
+        onRemove: function (id) {
+            this.workflows = this.workflows.filter((item) => item.id !== id);
             this.nWorkflows = this.workflows.length;
         },
-        onUpdate: function(id, data) {
-            const workflow = this.workflows.find(item => item.id === id);
+        onUpdate: function (id, data) {
+            const workflow = this.workflows.find((item) => item.id === id);
             Object.assign(workflow, data);
             this.workflows = [...this.workflows];
         },
-        onSuccess: function(message) {
+        onSuccess: function (message) {
             this.message = message;
             this.messageVariant = "success";
         },
-        onError: function(message) {
+        onError: function (message) {
             this.message = message;
             this.messageVariant = "danger";
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/icons.js b/client/galaxy/scripts/components/Workflow/icons.js
index a3b84c4e543e..69401bcd581f 100644
--- a/client/galaxy/scripts/components/Workflow/icons.js
+++ b/client/galaxy/scripts/components/Workflow/icons.js
@@ -4,5 +4,5 @@ export default {
     data_collection_input: "fa-folder-o",
     subworkflow: "fa-sitemap fa-rotate-270",
     parameter_input: "fa-pencil",
-    pause: "fa-pause"
+    pause: "fa-pause",
 };
diff --git a/client/galaxy/scripts/components/Workflow/services.js b/client/galaxy/scripts/components/Workflow/services.js
index 6ecab09440b4..e9b1bf47de76 100644
--- a/client/galaxy/scripts/components/Workflow/services.js
+++ b/client/galaxy/scripts/components/Workflow/services.js
@@ -46,7 +46,7 @@ export class Services {
         try {
             const response = await axios.get(url);
             const workflows = response.data;
-            workflows.forEach(workflow => {
+            workflows.forEach((workflow) => {
                 this._addAttributes(workflow);
             });
             return workflows;
diff --git a/client/galaxy/scripts/components/WorkflowInvocationReport.vue b/client/galaxy/scripts/components/WorkflowInvocationReport.vue
index c4c7d11f22a4..56ff6d7eabb7 100644
--- a/client/galaxy/scripts/components/WorkflowInvocationReport.vue
+++ b/client/galaxy/scripts/components/WorkflowInvocationReport.vue
@@ -16,30 +16,30 @@ import MarkdownEditor from "components/Markdown/MarkdownEditor.vue";
 export default {
     components: {
         Markdown,
-        MarkdownEditor
+        MarkdownEditor,
     },
     props: {
         invocationId: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
             markdownConfig: {},
             invocationMarkdown: null,
-            edit: false
+            edit: false,
         };
     },
-    created: function() {
+    created: function () {
         this.loadMarkdownConfig();
         window.addEventListener("keyup", this.keyListener);
     },
-    destroyed: function() {
+    destroyed: function () {
         window.removeEventListener("keyup", this.keyListener);
     },
     methods: {
-        keyListener: function(event) {
+        keyListener: function (event) {
             const which = event.which || event.keyCode;
             // ctrl + e
             if (event.ctrlKey && which == 69) {
@@ -50,17 +50,17 @@ export default {
                 }
             }
         },
-        viewReport: function() {
+        viewReport: function () {
             this.edit = false;
             this.loadMarkdownConfig();
         },
-        editReport: function() {
+        editReport: function () {
             this.edit = true;
         },
-        onupdate: function(newMarkdown) {
+        onupdate: function (newMarkdown) {
             this.invocationMarkdown = newMarkdown;
         },
-        loadMarkdownConfig: function() {
+        loadMarkdownConfig: function () {
             const invocationId = this.invocationId;
             const url = getAppRoot() + `api/invocations/${invocationId}/report`;
             const params = {};
@@ -69,13 +69,13 @@ export default {
             }
             axios
                 .get(url, { params: params })
-                .then(response => {
+                .then((response) => {
                     this.markdownConfig = response.data;
                 })
-                .catch(e => {
+                .catch((e) => {
                     console.error(e);
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/WorkflowInvocationState/WorkflowInvocationState.vue b/client/galaxy/scripts/components/WorkflowInvocationState/WorkflowInvocationState.vue
index 30d704ab49a1..17542e426e01 100644
--- a/client/galaxy/scripts/components/WorkflowInvocationState/WorkflowInvocationState.vue
+++ b/client/galaxy/scripts/components/WorkflowInvocationState/WorkflowInvocationState.vue
@@ -75,47 +75,47 @@ import ProgressBar from "components/ProgressBar";
 
 import { mapGetters, mapActions } from "vuex";
 
-const getUrl = path => getRootFromIndexLink() + path;
+const getUrl = (path) => getRootFromIndexLink() + path;
 
 Vue.use(BootstrapVue);
 
 export default {
     components: {
-        ProgressBar
+        ProgressBar,
     },
     mixins: [mixin],
     props: {
         invocationId: {
             type: String,
-            required: true
+            required: true,
         },
         provideContext: {
             type: Boolean,
-            default: true
-        }
+            default: true,
+        },
     },
     data() {
         return {
             stepStatesInterval: null,
-            jobStatesInterval: null
+            jobStatesInterval: null,
         };
     },
-    created: function() {
+    created: function () {
         this.pollStepStatesUntilTerminal();
         this.pollJobStatesUntilTerminal();
     },
     computed: {
         ...mapGetters(["getInvocationById", "getInvocationJobsSummaryById"]),
-        invocationState: function() {
+        invocationState: function () {
             const invocation = this.getInvocationById(this.invocationId);
             const state = invocation ? invocation.state : "new";
             return state;
         },
-        createdTime: function() {
+        createdTime: function () {
             const invocation = this.getInvocationById(this.invocationId);
             return invocation ? this.getInvocationById(this.invocationId).create_time : null;
         },
-        stepCount: function() {
+        stepCount: function () {
             const invocation = this.getInvocationById(this.invocationId);
             if (invocation) {
                 return invocation.steps.length;
@@ -123,7 +123,7 @@ export default {
                 return null;
             }
         },
-        stepStates: function() {
+        stepStates: function () {
             const stepStates = {};
             const invocation = this.getInvocationById(this.invocationId);
             if (!invocation) {
@@ -138,37 +138,37 @@ export default {
             }
             return stepStates;
         },
-        invocationLink: function() {
+        invocationLink: function () {
             return getUrl(`workflows/invocations/report?id=${this.invocationId}`);
         },
-        invocationPdfLink: function() {
+        invocationPdfLink: function () {
             return getUrl(`api/invocations/${this.invocationId}/report.pdf`);
         },
-        invocationSchedulingTerminal: function() {
+        invocationSchedulingTerminal: function () {
             return (
                 this.invocationState == "scheduled" ||
                 this.invocationState == "cancelled" ||
                 this.invocationState == "failed"
             );
         },
-        jobStatesTerminal: function() {
+        jobStatesTerminal: function () {
             return this.jobStatesSummary && this.jobStatesSummary.terminal();
         },
-        stepScheduledPercent: function() {
+        stepScheduledPercent: function () {
             let percent = 0.0;
             if (this.stepCount !== null) {
                 percent = (this.stepStates["scheduled"] || 0) / this.stepCount;
             }
             return percent;
         },
-        stepOtherPercent: function() {
+        stepOtherPercent: function () {
             const percent = 1.0 - this.stepScheduledPercent;
             return percent;
         },
-        stepStatesStr: function() {
+        stepStatesStr: function () {
             return `${this.stepStates["scheduled"] || 0} of ${this.stepCount} steps successfully scheduled`;
         },
-        jobStatesStr: function() {
+        jobStatesStr: function () {
             let jobStr = `${this.jobStatesSummary.states()["ok"] || 0} of ${this.jobCount} jobs complete`;
             if (!this.invocationSchedulingTerminal) {
                 jobStr += " (total number of jobs will change until all steps fully scheduled)";
@@ -187,35 +187,35 @@ export default {
         jobStatesSummary() {
             const jobsSummary = this.getInvocationJobsSummaryById(this.invocationId);
             return !jobsSummary ? null : new JOB_STATES_MODEL.JobStatesSummary(jobsSummary);
-        }
+        },
     },
     methods: {
         ...mapActions(["fetchInvocationForId", "fetchInvocationJobsSummaryForId"]),
-        pollStepStatesUntilTerminal: function() {
+        pollStepStatesUntilTerminal: function () {
             clearInterval(this.stepStatesInterval);
             if (!this.invocationSchedulingTerminal) {
                 this.fetchInvocationForId(this.invocationId);
                 this.stepStatesInterval = setInterval(this.pollStepStatesUntilTerminal, 3000);
             }
         },
-        pollJobStatesUntilTerminal: function() {
+        pollJobStatesUntilTerminal: function () {
             clearInterval(this.jobStatesInterval);
             if (!this.jobStatesTerminal) {
                 this.fetchInvocationJobsSummaryForId(this.invocationId);
                 this.jobStatesInterval = setInterval(this.pollJobStatesUntilTerminal, 3000);
             }
         },
-        onError: function(e) {
+        onError: function (e) {
             console.error(e);
         },
-        cancelWorkflowScheduling: function() {
+        cancelWorkflowScheduling: function () {
             cancelWorkflowScheduling(this.invocationId).catch(this.onError);
-        }
+        },
     },
-    beforeDestroy: function() {
+    beforeDestroy: function () {
         clearInterval(this.jobStatesInterval);
         clearInterval(this.stepStatesInterval);
-    }
+    },
 };
 </script>
 <style scoped>
diff --git a/client/galaxy/scripts/components/WorkflowInvocationState/services.js b/client/galaxy/scripts/components/WorkflowInvocationState/services.js
index 76fb7fec0339..0af7eb3077c4 100644
--- a/client/galaxy/scripts/components/WorkflowInvocationState/services.js
+++ b/client/galaxy/scripts/components/WorkflowInvocationState/services.js
@@ -1,7 +1,7 @@
 import { getRootFromIndexLink } from "onload";
 import axios from "axios";
 
-const getUrl = path => getRootFromIndexLink() + path;
+const getUrl = (path) => getRootFromIndexLink() + path;
 
 export function getInvocationJobsSummary(invocationId) {
     const url = getUrl(`api/invocations/${invocationId}/jobs_summary`);
diff --git a/client/galaxy/scripts/components/admin/ActiveInvocations.vue b/client/galaxy/scripts/components/admin/ActiveInvocations.vue
index d0d166e522e1..d21bf79364f9 100644
--- a/client/galaxy/scripts/components/admin/ActiveInvocations.vue
+++ b/client/galaxy/scripts/components/admin/ActiveInvocations.vue
@@ -15,17 +15,17 @@ import { getActiveInvocations } from "./AdminServices";
 
 export default {
     components: {
-        Invocations
+        Invocations,
     },
     data() {
         return {
             invocationItems: [],
-            loading: true
+            loading: true,
         };
     },
     created() {
         getActiveInvocations()
-            .then(response => {
+            .then((response) => {
                 this.invocationItems = response.data;
                 this.loading = false;
             })
@@ -34,7 +34,7 @@ export default {
     methods: {
         handleError(error) {
             console.error(error);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/BaseGrid.vue b/client/galaxy/scripts/components/admin/BaseGrid.vue
index bc1b500581aa..1abcf110de51 100644
--- a/client/galaxy/scripts/components/admin/BaseGrid.vue
+++ b/client/galaxy/scripts/components/admin/BaseGrid.vue
@@ -28,18 +28,18 @@
 export default {
     props: {
         isLoaded: {
-            type: Boolean
+            type: Boolean,
         },
         title: {
-            type: String
+            type: String,
         },
         columns: {
-            type: Array
+            type: Array,
         },
         rows: {
-            type: Array
-        }
-    }
+            type: Array,
+        },
+    },
 };
 </script>
 <style>
diff --git a/client/galaxy/scripts/components/admin/BaseList.test.js b/client/galaxy/scripts/components/admin/BaseList.test.js
index 34a2ff550c15..442f5609ee8d 100644
--- a/client/galaxy/scripts/components/admin/BaseList.test.js
+++ b/client/galaxy/scripts/components/admin/BaseList.test.js
@@ -8,13 +8,13 @@ describe("Categories", () => {
             data: [
                 {
                     col_0: "col_0_0",
-                    col_1: "col_0_1"
+                    col_1: "col_0_1",
                 },
                 {
                     col_0: "col_0_2",
-                    col_1: "col_0_3"
-                }
-            ]
+                    col_1: "col_0_3",
+                },
+            ],
         };
     };
     const setter = async () => {
@@ -29,8 +29,8 @@ describe("Categories", () => {
                 success: "success",
                 fields: ["execute", "col_0", "col_1"],
                 getter: getter,
-                setter: setter
-            }
+                setter: setter,
+            },
         });
         await Vue.nextTick();
         expect(wrapper.find(".card-header").text()).contains("There are 2");
diff --git a/client/galaxy/scripts/components/admin/BaseList.vue b/client/galaxy/scripts/components/admin/BaseList.vue
index 7c5fc66355da..77b892cdb712 100644
--- a/client/galaxy/scripts/components/admin/BaseList.vue
+++ b/client/galaxy/scripts/components/admin/BaseList.vue
@@ -43,83 +43,83 @@ Vue.use(BootstrapVue);
 export default {
     props: {
         icon: {
-            type: String
+            type: String,
         },
         tooltip: {
-            type: String
+            type: String,
         },
         plural: {
-            type: String
+            type: String,
         },
         success: {
-            type: String
+            type: String,
         },
         fields: {
-            type: Array
+            type: Array,
         },
         getter: {
-            type: Function
+            type: Function,
         },
         setter: {
-            type: Function
-        }
+            type: Function,
+        },
     },
     data() {
         return {
             items: [],
             busy: false,
             messageText: null,
-            messageVariant: null
+            messageVariant: null,
         };
     },
     computed: {
-        tooltipAll: function() {
+        tooltipAll: function () {
             return `${this.tooltip} all`;
         },
-        itemsIndex: function() {
+        itemsIndex: function () {
             return this.items.reduce((r, v) => {
                 r[v.id] = v;
                 return r;
             }, {});
         },
-        itemsAll: function() {
-            return this.items.map(v => v.id);
+        itemsAll: function () {
+            return this.items.map((v) => v.id);
         },
-        itemsVisible: function() {
+        itemsVisible: function () {
             return this.items.length > 0;
         },
-        itemsLength: function() {
+        itemsLength: function () {
             return this.items.length;
         },
-        messageVisible: function() {
+        messageVisible: function () {
             return this.messageText != null;
-        }
+        },
     },
     created() {
         this.messageText = null;
         this.getter()
-            .then(response => {
+            .then((response) => {
                 this.items = response.data;
                 if (!this.itemsVisible) {
                     this.messageVariant = "warning";
                     this.messageText = `No ${this.plural} available.`;
                 }
             })
-            .catch(e => {
+            .catch((e) => {
                 this._errorMessage(e);
             });
     },
     methods: {
-        executeAll: function() {
+        executeAll: function () {
             this.execute(this.itemsAll);
         },
-        execute: function(ids) {
+        execute: function (ids) {
             this.busy = true;
             this.messageVariant = "warning";
             this.messageText = "Executing request. Please wait...";
             this._highlightRows(this.itemsAll, "default");
             this.setter(ids)
-                .then(response => {
+                .then((response) => {
                     const data = response.data;
                     if (data) {
                         this.messageVariant = "info";
@@ -129,12 +129,12 @@ export default {
                     }
                     this.busy = false;
                 })
-                .catch(e => {
+                .catch((e) => {
                     this._errorMessage(e);
                     this.busy = false;
                 });
         },
-        _highlightRows: function(ids, status) {
+        _highlightRows: function (ids, status) {
             if (ids) {
                 for (const id of ids) {
                     const item = this.itemsIndex[id];
@@ -144,11 +144,11 @@ export default {
                 }
             }
         },
-        _errorMessage: function(e) {
+        _errorMessage: function (e) {
             const message = e && e.response && e.response.data && e.response.data.err_msg;
             this.messageText = message || "Request failed for an unknown reason.";
             this.messageVariant = "danger";
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManager.vue b/client/galaxy/scripts/components/admin/DataManager/DataManager.vue
index 5f60232b00fb..b94709efa6d2 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManager.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManager.vue
@@ -47,7 +47,7 @@
                                 <b-button
                                     :to="{
                                         name: 'DataManagerJobs',
-                                        params: { id: encodeURIComponent(dataManager['id']) }
+                                        params: { id: encodeURIComponent(dataManager['id']) },
                                     }"
                                     :id="kebabCase(dataManager['name']) + '-jobs'"
                                 >
@@ -85,7 +85,7 @@ import Alert from "components/Alert.vue";
 
 export default {
     components: {
-        Alert
+        Alert,
     },
     data() {
         return {
@@ -95,26 +95,26 @@ export default {
             viewOnly: false,
             message: "",
             status: "",
-            loading: true
+            loading: true,
         };
     },
     computed: {
         dataManagersFiltered() {
-            return this.dataManagers.filter(d => d["name"].match(new RegExp(this.filter, "i")));
+            return this.dataManagers.filter((d) => d["name"].match(new RegExp(this.filter, "i")));
         },
         dataTablesFiltered() {
-            return this.dataTables.filter(d => d["name"].match(new RegExp(this.filter, "i")));
-        }
+            return this.dataTables.filter((d) => d["name"].match(new RegExp(this.filter, "i")));
+        },
     },
     methods: {
         kebabCase(s) {
             return s.toLowerCase().replace(/ /g, "-");
-        }
+        },
     },
     created() {
         axios
             .get(`${getAppRoot()}data_manager/data_managers_list`)
-            .then(response => {
+            .then((response) => {
                 this.dataManagers = response.data.dataManagers;
                 this.dataTables = response.data.dataTables;
                 this.viewOnly = response.data.viewOnly;
@@ -122,9 +122,9 @@ export default {
                 this.status = response.data.status;
                 this.loading = false;
             })
-            .catch(error => {
+            .catch((error) => {
                 console.error(error);
             });
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue b/client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue
index 0db0cc7e88f3..3d1a2a72dcc5 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue
@@ -82,13 +82,13 @@ import Alert from "components/Alert.vue";
 
 export default {
     components: {
-        Alert
+        Alert,
     },
     props: {
         id: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
@@ -105,13 +105,13 @@ export default {
                 {
                     key: "fileName",
                     label: "Full path",
-                    tdClass: "table-cell-break-word"
-                }
+                    tdClass: "table-cell-break-word",
+                },
             ],
             viewOnly: false,
             message: "",
             status: "",
-            loading: true
+            loading: true,
         };
     },
     computed: {
@@ -119,36 +119,36 @@ export default {
             return [
                 {
                     text: "Data Managers",
-                    to: "/"
+                    to: "/",
                 },
                 {
                     text: this.dataManager["name"] + " ( " + this.dataManager["description"] + " )",
                     href: this.dataManager["toolUrl"],
-                    target: "_blank"
+                    target: "_blank",
                 },
                 {
                     text: "Jobs",
                     to: {
                         name: "DataManagerJobs",
-                        params: { id: this.dataManager["id"] }
-                    }
+                        params: { id: this.dataManager["id"] },
+                    },
                 },
                 {
                     text: "Job " + this.jobId,
-                    active: true
-                }
+                    active: true,
+                },
             ];
-        }
+        },
     },
     methods: {
         outputFields(output) {
             return Object.keys(output).reduce((acc, c) => [...acc, { key: c, label: c }], []);
-        }
+        },
     },
     created() {
         axios
             .get(`${getAppRoot()}data_manager/job_info?id=${this.id}`)
-            .then(response => {
+            .then((response) => {
                 this.jobId = response.data.jobId;
                 this.exitCode = response.data.exitCode;
                 this.runUrl = response.data.runUrl;
@@ -161,10 +161,10 @@ export default {
                 this.status = response.data.status;
                 this.loading = false;
             })
-            .catch(error => {
+            .catch((error) => {
                 console.error(error);
             });
-    }
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue b/client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
index 69e5756e8c57..8e62b9853d6d 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
@@ -83,13 +83,13 @@ import Alert from "components/Alert.vue";
 
 export default {
     components: {
-        Alert
+        Alert,
     },
     props: {
         id: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
@@ -102,14 +102,14 @@ export default {
                 { key: "state" },
                 { key: "actions" },
                 { key: "jobRunnerName", label: "Job Runner" },
-                { key: "jobRunnerExternalId", label: "PID/Cluster ID", sortable: true }
+                { key: "jobRunnerExternalId", label: "PID/Cluster ID", sortable: true },
             ],
             showCommandLine: true,
             filter: "",
             viewOnly: false,
             message: "",
             status: "",
-            loading: true
+            loading: true,
         };
     },
     computed: {
@@ -117,17 +117,17 @@ export default {
             return [
                 {
                     text: "Data Managers",
-                    to: "/"
+                    to: "/",
                 },
                 {
                     text: this.dataManager["name"] + " ( " + this.dataManager["description"] + " )",
                     href: this.dataManager["toolUrl"],
-                    target: "_blank"
+                    target: "_blank",
                 },
                 {
                     text: "Jobs",
-                    active: true
-                }
+                    active: true,
+                },
             ];
         },
         tableFields() {
@@ -135,7 +135,7 @@ export default {
             if (this.showCommandLine) {
                 tableFields.splice(5, 0, {
                     key: "commandLine",
-                    tdClass: ["code", "command-line"]
+                    tdClass: ["code", "command-line"],
                 });
             }
             return tableFields;
@@ -171,12 +171,12 @@ export default {
                 }
             }
             return tableItems;
-        }
+        },
     },
     created() {
         axios
             .get(`${getAppRoot()}data_manager/jobs_list?id=${decodeURIComponent(this.id)}`)
-            .then(response => {
+            .then((response) => {
                 this.dataManager = response.data.dataManager;
                 this.jobs = response.data.jobs;
                 this.viewOnly = response.data.viewOnly;
@@ -184,10 +184,10 @@ export default {
                 this.status = response.data.status;
                 this.loading = false;
             })
-            .catch(error => {
+            .catch((error) => {
                 console.error(error);
             });
-    }
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue b/client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
index 14eec488586c..32b2b3aeacd8 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
@@ -16,30 +16,30 @@ export default new VueRouter({
         {
             path: "/",
             name: "DataManager",
-            component: DataManager
+            component: DataManager,
         },
         {
             path: "/jobs/:id",
             name: "DataManagerJobs",
             component: DataManagerJobs,
-            props: true
+            props: true,
         },
         {
             path: "/job/:id",
             name: "DataManagerJob",
             component: DataManagerJob,
-            props: true
+            props: true,
         },
         {
             path: "/table/:name",
             name: "DataManagerTable",
             component: DataManagerTable,
-            props: true
+            props: true,
         },
         {
             path: "*",
-            redirect: "/"
-        }
-    ]
+            redirect: "/",
+        },
+    ],
 });
 </script>
diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue b/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
index 972612a81160..5c5888509dfc 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
@@ -48,13 +48,13 @@ import Alert from "components/Alert.vue";
 
 export default {
     components: {
-        Alert
+        Alert,
     },
     props: {
         name: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
@@ -62,7 +62,7 @@ export default {
             viewOnly: false,
             message: "",
             status: "",
-            loading: true
+            loading: true,
         };
     },
     computed: {
@@ -76,13 +76,13 @@ export default {
             return [
                 {
                     text: "Tool Data Tables",
-                    to: "/"
+                    to: "/",
                 },
                 {
-                    text: this.dataTableName
-                }
+                    text: this.dataTableName,
+                },
             ];
-        }
+        },
     },
     methods: {
         fields(columns) {
@@ -93,31 +93,31 @@ export default {
         reload() {
             axios
                 .get(`${getAppRoot()}data_manager/reload_tool_data_tables?table_name=${this.dataTableName}`)
-                .then(response => {
+                .then((response) => {
                     if (response.data.dataTable) {
                         this.dataTable = response.data.dataTable;
                     }
                     this.message = response.data.message;
                     this.status = response.data.status;
                 })
-                .catch(error => {
+                .catch((error) => {
                     console.error(error);
                 });
-        }
+        },
     },
     created() {
         axios
             .get(`${getAppRoot()}data_manager/tool_data_table_info?table_name=${this.name}`)
-            .then(response => {
+            .then((response) => {
                 this.dataTable = response.data.dataTable;
                 this.viewOnly = response.data.viewOnly;
                 this.message = response.data.message;
                 this.status = response.data.status;
                 this.loading = false;
             })
-            .catch(error => {
+            .catch((error) => {
                 console.error(error);
             });
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue b/client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
index 4e9e9a3869f3..9d9f4bdb5fce 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
@@ -19,7 +19,7 @@ export default {
     computed: {
         toolShedLink() {
             return `${getAppRoot()}admin_toolshed/browse_tool_sheds`;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/DataManagerGrid.vue b/client/galaxy/scripts/components/admin/DataManagerGrid.vue
index 8435fde7f36a..64b3f3221724 100644
--- a/client/galaxy/scripts/components/admin/DataManagerGrid.vue
+++ b/client/galaxy/scripts/components/admin/DataManagerGrid.vue
@@ -2,7 +2,7 @@
     <table class="tabletip">
         <thead>
             <tr>
-                <th :colspan="dataManagerColumns.length" style="font-size:120%">
+                <th :colspan="dataManagerColumns.length" style="font-size: 120%;">
                     Data Manager: {{ dataManagerTableName }}
                     <a
                         class="icon-btn"
@@ -32,21 +32,21 @@ export default {
     props: {
         dataManagerTableName: {
             type: String,
-            required: true
+            required: true,
         },
         dataManagerColumns: {
             type: Array,
-            required: true
+            required: true,
         },
         dataManagerItems: {
             type: Array,
-            required: true
-        }
+            required: true,
+        },
     },
     methods: {
         handleReloadButtonClick(event) {
             this.$emit("reloaddatamanager", this.dataManagerTableName);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/DataTables.vue b/client/galaxy/scripts/components/admin/DataTables.vue
index 3df7ad29ab38..0bfa36ee4824 100644
--- a/client/galaxy/scripts/components/admin/DataTables.vue
+++ b/client/galaxy/scripts/components/admin/DataTables.vue
@@ -29,14 +29,14 @@ export default {
             dataManagerColumns: [],
             dataManagerItems: [],
             message: "",
-            status: ""
+            status: "",
         };
     },
 
     components: {
         message: Message,
         "data-tables-grid": DataTablesGrid,
-        "data-manager-grid": DataManagerGrid
+        "data-manager-grid": DataManagerGrid,
     },
 
     computed: {
@@ -46,18 +46,18 @@ export default {
             if (this.currentView === "data-tables-grid") {
                 props = {
                     isLoaded: this.isLoaded,
-                    rows: this.dataTables
+                    rows: this.dataTables,
                 };
             } else {
                 props = {
                     dataManagerTableName: this.dataManagerTableName,
                     dataManagerColumns: this.dataManagerColumns,
-                    dataManagerItems: this.dataManagerItems
+                    dataManagerItems: this.dataManagerItems,
                 };
             }
 
             return props;
-        }
+        },
     },
 
     methods: {
@@ -65,10 +65,10 @@ export default {
             axios
                 .get(`${getAppRoot()}data_manager/tool_data_table_items`, {
                     params: {
-                        table_name: dataManagerTableName
-                    }
+                        table_name: dataManagerTableName,
+                    },
                 })
-                .then(response => {
+                .then((response) => {
                     this.message = response.data.message;
                     this.status = response.data.status;
 
@@ -79,7 +79,7 @@ export default {
                         this.currentView = "data-manager-grid";
                     }
                 })
-                .catch(error => {
+                .catch((error) => {
                     console.error(error);
                 });
         },
@@ -88,10 +88,10 @@ export default {
             axios
                 .get(`${getAppRoot()}data_manager/reload_tool_data_table`, {
                     params: {
-                        table_name: dataManagerTableName
-                    }
+                        table_name: dataManagerTableName,
+                    },
                 })
-                .then(response => {
+                .then((response) => {
                     this.message = response.data.message;
                     this.status = response.data.status;
 
@@ -99,24 +99,24 @@ export default {
                         this.dataManagerItems = response.data.data.items;
                     }
                 })
-                .catch(error => {
+                .catch((error) => {
                     console.error(error);
                 });
-        }
+        },
     },
 
     created() {
         axios
             .get(`${getAppRoot()}admin/data_tables_list`)
-            .then(response => {
+            .then((response) => {
                 this.isLoaded = true;
                 this.dataTables = response.data.data;
                 this.message = response.data.message;
                 this.status = response.data.status;
             })
-            .catch(error => {
+            .catch((error) => {
                 console.error(error);
             });
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/DataTablesGrid.vue b/client/galaxy/scripts/components/admin/DataTablesGrid.vue
index f62df0ef06b8..af5d56c72ad8 100644
--- a/client/galaxy/scripts/components/admin/DataTablesGrid.vue
+++ b/client/galaxy/scripts/components/admin/DataTablesGrid.vue
@@ -23,12 +23,12 @@ export default {
     props: {
         isLoaded: {
             type: Boolean,
-            required: true
+            required: true,
         },
         rows: {
             type: Array,
-            required: true
-        }
+            required: true,
+        },
     },
 
     data() {
@@ -37,19 +37,19 @@ export default {
                 { text: "Name", dataIndex: "name" },
                 { text: "Filename", dataIndex: "filename" },
                 { text: "Tool data path", dataIndex: "tool_data_path" },
-                { text: "Errors", dataIndex: "errors" }
-            ]
+                { text: "Errors", dataIndex: "errors" },
+            ],
         };
     },
 
     components: {
-        "base-grid": BaseGrid
+        "base-grid": BaseGrid,
     },
 
     methods: {
         handleTableNameClick(event) {
             this.$emit("changeview", event.target.text);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/DataTypes.vue b/client/galaxy/scripts/components/admin/DataTypes.vue
index 544ccdb0360f..c46a4f307b62 100644
--- a/client/galaxy/scripts/components/admin/DataTypes.vue
+++ b/client/galaxy/scripts/components/admin/DataTypes.vue
@@ -26,7 +26,7 @@ import BaseGrid from "./BaseGrid.vue";
 export default {
     components: {
         Message,
-        BaseGrid
+        BaseGrid,
     },
 
     data() {
@@ -36,7 +36,7 @@ export default {
             keys: [],
             dataTypes: [],
             message: "",
-            status: ""
+            status: "",
         };
     },
 
@@ -47,9 +47,9 @@ export default {
                 { text: "Extension", dataIndex: "extension" },
                 { text: "Type", dataIndex: "type" },
                 { text: "MIME Type", dataIndex: "mimetype" },
-                { text: "Display in Upload", dataIndex: "display_in_upload" }
+                { text: "Display in Upload", dataIndex: "display_in_upload" },
             ];
-        }
+        },
     },
 
     computed: {
@@ -64,16 +64,16 @@ export default {
                     let keys = this.keys;
                     // Filter out the predefined column headers
                     for (const c of columns) {
-                        keys = keys.filter(k => k !== c["dataIndex"]);
+                        keys = keys.filter((k) => k !== c["dataIndex"]);
                     }
                     // Create column headers from each remaining key and merge
                     // with predefined column headers
-                    columns = keys.reduce(function(m, k) {
+                    columns = keys.reduce(function (m, k) {
                         let text = k[0].toUpperCase();
                         text += k.slice(1).replace(/_/g, " ");
                         m.push({
                             text: text,
-                            dataIndex: k
+                            dataIndex: k,
                         });
                         return m;
                     }, columns);
@@ -83,21 +83,21 @@ export default {
         },
         isDataLoaded() {
             return status !== "" || this.dataTypes.length > 0;
-        }
+        },
     },
 
     created() {
         axios
             .get(`${getAppRoot()}admin/data_types_list`)
-            .then(response => {
+            .then((response) => {
                 this.keys = response.data.keys;
                 this.dataTypes = response.data.data;
                 this.message = response.data.message;
                 this.status = response.data.status;
             })
-            .catch(error => {
+            .catch((error) => {
                 console.error(error);
             });
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/ContainerDescription.vue b/client/galaxy/scripts/components/admin/Dependencies/ContainerDescription.vue
index 68b78d5b5694..4b5adbc034d0 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/ContainerDescription.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/ContainerDescription.vue
@@ -20,27 +20,27 @@ export default {
     components: { DisplayRaw },
     props: {
         containerDescription: {
-            type: Object
+            type: Object,
         },
         compact: {
             type: Boolean,
-            default: true
-        }
+            default: true,
+        },
     },
     computed: {
-        title: function() {
+        title: function () {
             return this.compact ? this.description : "";
         },
-        description: function() {
+        description: function () {
             return `This is a ${this.containerDescription.type} container. ${this.shellDescription}`;
         },
-        shellDescription: function() {
+        shellDescription: function () {
             return `This container uses shell [${this.containerDescription.shell}].`;
         },
-        identifier: function() {
+        identifier: function () {
             return this.containerDescription && this.containerDescription.identifier;
         },
-        externalUrl: function() {
+        externalUrl: function () {
             const identifier = this.identifier;
             if (identifier) {
                 if (identifier.startsWith("quay.io")) {
@@ -48,7 +48,7 @@ export default {
                 }
             }
             return null;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/ContainerIndex.vue b/client/galaxy/scripts/components/admin/Dependencies/ContainerIndex.vue
index a568b4a87334..26630ffd8318 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/ContainerIndex.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/ContainerIndex.vue
@@ -107,7 +107,7 @@ import { DESCRIPTION } from "./ContainerResolver";
 
 Vue.use(BootstrapVue);
 
-const RESOLVER_TYPE_OPTIONS = _.keys(DESCRIPTION).map(resolverType => ({ value: resolverType, text: resolverType }));
+const RESOLVER_TYPE_OPTIONS = _.keys(DESCRIPTION).map((resolverType) => ({ value: resolverType, text: resolverType }));
 RESOLVER_TYPE_OPTIONS.splice(0, 0, { value: null, text: "*any*" });
 
 export default {
@@ -123,20 +123,20 @@ export default {
                 { key: "requirement", label: "Requirements" },
                 { key: "resolution" },
                 { key: "resolver" },
-                { key: "container" }
+                { key: "container" },
             ],
             containerType: null,
             containerTypeOptions: [
                 { value: null, text: "*any*" },
                 { value: "docker", text: "Docker" },
-                { value: "singularity", text: "Singularity" }
+                { value: "singularity", text: "Singularity" },
             ],
             resolverType: null,
             resolverTypeOptions: RESOLVER_TYPE_OPTIONS,
             filterResolution: null,
             filterResolverType: null,
             filterContainerType: null,
-            resolutions: []
+            resolutions: [],
         };
     },
     methods: {
@@ -144,7 +144,7 @@ export default {
             this.loading = true;
             const params = this.apiParams();
             getContainerResolutionToolbox(params)
-                .then(resolutions => {
+                .then((resolutions) => {
                     this.resolutions = resolutions;
                     this.loading = false;
                 })
@@ -153,7 +153,7 @@ export default {
         installSelected() {
             this.loading = true;
             resolveContainersWithInstall(this.selectedToolIds(), this.apiParams())
-                .then(resolutions => {
+                .then((resolutions) => {
                     this.resolutions = resolutions;
                     this.loading = false;
                 })
@@ -180,26 +180,26 @@ export default {
                 }
             }
             return toolIds;
-        }
+        },
     },
     watch: {
-        containerType: function(val) {
+        containerType: function (val) {
             this.load();
         },
-        resolverType: function(val) {
+        resolverType: function (val) {
             this.load();
         },
-        filterResolution: function(val) {
+        filterResolution: function (val) {
             if (val == "unresolved") {
                 this.filterResolverType = null;
                 this.filterContainerType = null;
             }
-        }
+        },
     },
     computed: {
-        items: function() {
+        items: function () {
             return this.resolutions
-                .filter(resolution => {
+                .filter((resolution) => {
                     if (this.filterResolution == "unresolved" && resolution.status.dependency_type != null) {
                         return false;
                     }
@@ -224,16 +224,16 @@ export default {
                     }
                     return true;
                 })
-                .map(resolution => {
+                .map((resolution) => {
                     return {
                         selected: false,
                         requirements: resolution.requirements,
                         status: resolution.status,
                         tool_id: resolution.tool_id,
-                        _showDetails: false
+                        _showDetails: false,
                     };
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/ContainerResolutionDetails.vue b/client/galaxy/scripts/components/admin/Dependencies/ContainerResolutionDetails.vue
index cbfc89c0e857..ccf79a6b2488 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/ContainerResolutionDetails.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/ContainerResolutionDetails.vue
@@ -65,13 +65,13 @@ export default {
     props: {
         resolution: {
             type: Object,
-            required: true
-        }
+            required: true,
+        },
     },
     computed: {
-        singleTool: function() {
+        singleTool: function () {
             return this.resolution.tool_id != undefined;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/ContainerResolver.vue b/client/galaxy/scripts/components/admin/Dependencies/ContainerResolver.vue
index b31baedbc990..fd8f34bc0323 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/ContainerResolver.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/ContainerResolver.vue
@@ -27,31 +27,31 @@ export const DESCRIPTION = {
     cached_mulled_singularity:
         "The cached_mulled_singularity container resolver finds mulled containers cached in a directory mounted by the Galaxy server.",
     build_mulled: "",
-    build_mulled_cached: ""
+    build_mulled_cached: "",
 };
 
 export default {
     components: { DisplayRaw },
     props: {
         containerResolver: {
-            type: Object
+            type: Object,
         },
         compact: {
             type: Boolean,
-            default: true
-        }
+            default: true,
+        },
     },
     computed: {
-        title: function() {
+        title: function () {
             return this.compact ? this.description : "";
         },
-        description: function() {
+        description: function () {
             const description = DESCRIPTION[this.resolverType] || `Container resolver of type ${this.resolverType}.`;
             return `${description}`;
         },
-        resolverType: function() {
+        resolverType: function () {
             return this.containerResolver && this.containerResolver.resolver_type;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/DependencyIndexMixin.js b/client/galaxy/scripts/components/admin/Dependencies/DependencyIndexMixin.js
index ee3ca7110b20..1c80d58a3169 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/DependencyIndexMixin.js
+++ b/client/galaxy/scripts/components/admin/Dependencies/DependencyIndexMixin.js
@@ -19,14 +19,14 @@ export default {
         StatusDisplay,
         Statuses,
         ToolDisplay,
-        Tools
+        Tools,
     },
     created() {
         this.root = getAppRoot();
         this.load();
     },
     computed: {
-        hasSelection: function() {
+        hasSelection: function () {
             // Not reactive yet...
             for (const item of this.items) {
                 if (item["selected"]) {
@@ -34,7 +34,7 @@ export default {
                 }
             }
             return false;
-        }
+        },
     },
     methods: {
         showRowDetails(row, index, e) {
@@ -44,6 +44,6 @@ export default {
         },
         handleError(e) {
             this.error = e;
-        }
-    }
+        },
+    },
 };
diff --git a/client/galaxy/scripts/components/admin/Dependencies/DependencyIndexWrapper.vue b/client/galaxy/scripts/components/admin/Dependencies/DependencyIndexWrapper.vue
index 32b413e3fce4..b633f1815b3f 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/DependencyIndexWrapper.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/DependencyIndexWrapper.vue
@@ -17,21 +17,21 @@ import LoadingSpan from "components/LoadingSpan";
 
 export default {
     components: {
-        LoadingSpan
+        LoadingSpan,
     },
     props: {
         loading: {
             type: Boolean,
-            required: true
+            required: true,
         },
         loadingMessage: {
             type: String,
-            required: true
+            required: true,
         },
         error: {
             type: String,
-            default: null
-        }
-    }
+            default: null,
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/DependencyResolver.vue b/client/galaxy/scripts/components/admin/Dependencies/DependencyResolver.vue
index 177a8f7761ee..eb8820565a18 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/DependencyResolver.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/DependencyResolver.vue
@@ -31,17 +31,17 @@ export default {
     components: { DisplayRaw },
     props: {
         dependencyResolver: {
-            type: Object
+            type: Object,
         },
         compact: {
             type: Boolean,
-            default: false
-        }
+            default: false,
+        },
     },
     computed: {
-        resolverType: function() {
+        resolverType: function () {
             return this.dependencyResolver && this.dependencyResolver.resolver_type;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/DisplayRaw.vue b/client/galaxy/scripts/components/admin/Dependencies/DisplayRaw.vue
index b046e1fd17de..f82413fc6de9 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/DisplayRaw.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/DisplayRaw.vue
@@ -7,13 +7,13 @@ export default {
     props: {
         object: {
             type: Object,
-            required: true
-        }
+            required: true,
+        },
     },
     computed: {
-        asJson: function() {
+        asJson: function () {
             return JSON.stringify(this.object);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/Landing.vue b/client/galaxy/scripts/components/admin/Dependencies/Landing.vue
index 8a33fe9fb9fa..5c2c6b281a25 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/Landing.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/Landing.vue
@@ -22,15 +22,15 @@ Vue.use(BootstrapVue);
 
 export default {
     components: { ContainerIndex, ResolutionIndex, UnusedIndex },
-    data: function() {
+    data: function () {
         return {
-            mode: "dependencies"
+            mode: "dependencies",
         };
     },
     methods: {
         setMode(mode) {
             this.mode = mode;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/Requirement.vue b/client/galaxy/scripts/components/admin/Dependencies/Requirement.vue
index d798df983d4e..7e55236faf5d 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/Requirement.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/Requirement.vue
@@ -9,8 +9,8 @@ export default {
     props: {
         requirement: {
             type: Object,
-            required: true
-        }
-    }
+            required: true,
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/Requirements.vue b/client/galaxy/scripts/components/admin/Dependencies/Requirements.vue
index fc111448423d..08d61b0234ce 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/Requirements.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/Requirements.vue
@@ -16,8 +16,8 @@ export default {
     props: {
         requirements: {
             type: Array,
-            required: true
-        }
-    }
+            required: true,
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/ResolutionDetails.vue b/client/galaxy/scripts/components/admin/Dependencies/ResolutionDetails.vue
index 26af797509b9..9a7c627e146d 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/ResolutionDetails.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/ResolutionDetails.vue
@@ -94,22 +94,22 @@ export default {
         Requirements,
         StatusDisplay,
         ToolDisplay,
-        Tools
+        Tools,
     },
     props: {
         resolution: {
             type: Object,
-            required: true
-        }
+            required: true,
+        },
     },
     computed: {
-        singleTool: function() {
+        singleTool: function () {
             return this.resolution.tool_id != undefined;
         },
-        isContainerResolution: function() {
+        isContainerResolution: function () {
             return this.resolution.status.length >= 1 && this.resolution.status[0].model_class == "ContainerDependency";
         },
-        containerResolution: function() {
+        containerResolution: function () {
             return { ...this.resolution, status: this.resolution.status[0] };
         },
         /*
@@ -121,11 +121,11 @@ export default {
             return !anyUnresolved;
         },
         */
-        separateDetails: function() {
+        separateDetails: function () {
             return (
                 this.resolution.status.length > 1 && this.resolution.status[0].model_class != "MergedCondaDependency"
             );
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/ResolutionIndex.vue b/client/galaxy/scripts/components/admin/Dependencies/ResolutionIndex.vue
index 7836212940d8..c22d512ac361 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/ResolutionIndex.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/ResolutionIndex.vue
@@ -94,11 +94,11 @@ export const RESOLVER_DESCRIPTIONS = {
     tool_shed_packages: "",
     galaxy_packages: "",
     lmod: "",
-    module: ""
+    module: "",
 };
-const RESOLVER_TYPE_OPTIONS = _.keys(RESOLVER_DESCRIPTIONS).map(resolverType => ({
+const RESOLVER_TYPE_OPTIONS = _.keys(RESOLVER_DESCRIPTIONS).map((resolverType) => ({
     value: resolverType,
-    text: resolverType
+    text: resolverType,
 }));
 RESOLVER_TYPE_OPTIONS.splice(0, 0, { value: null, text: "*any*" });
 
@@ -114,16 +114,16 @@ export default {
             resolverTypeOptions: RESOLVER_TYPE_OPTIONS,
             baseFields: [{ key: "selected", label: "" }, { key: "requirement" }, { key: "resolution" }],
             filterResolution: null,
-            requirements: []
+            requirements: [],
         };
     },
     watch: {
-        resolverType: function(val) {
+        resolverType: function (val) {
             this.load();
-        }
+        },
     },
     computed: {
-        fields: function() {
+        fields: function () {
             const fields = this.baseFields.slice();
             if (this.expandToolIds) {
                 fields.splice(1, 0, { key: "tool", label: "Tool" });
@@ -132,9 +132,9 @@ export default {
             }
             return fields;
         },
-        items: function() {
+        items: function () {
             let items = this.requirements
-                .filter(resolution => {
+                .filter((resolution) => {
                     if (this.filterResolution) {
                         let anyUnresolved = resolution.status.length == 0; // odd logic here, but we call no requirements unresolved in the GUI :(
                         for (const status of resolution.status) {
@@ -150,13 +150,13 @@ export default {
                     }
                     return true;
                 })
-                .map(resolution => {
+                .map((resolution) => {
                     return {
                         selected: false,
                         requirements: resolution.requirements,
                         status: resolution.status,
                         tool_ids: resolution.tool_ids,
-                        _showDetails: false
+                        _showDetails: false,
                     };
                 });
             if (this.expandToolIds) {
@@ -170,7 +170,7 @@ export default {
             }
             return items;
         },
-        selectedToolIds: function() {
+        selectedToolIds: function () {
             const toolIds = [];
             for (const item of this.items) {
                 if (item["selected"]) {
@@ -181,13 +181,13 @@ export default {
                 }
             }
             return toolIds;
-        }
+        },
     },
     methods: {
         load() {
             this.loading = true;
             getToolboxDependencies(this.apiParams())
-                .then(requirements => {
+                .then((requirements) => {
                     this.requirements = requirements;
                     this.loading = false;
                 })
@@ -222,7 +222,7 @@ export default {
         setExpandToolIds(expandToolIds) {
             this.expandToolIds = expandToolIds;
             this.load();
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/StatusDisplay.vue b/client/galaxy/scripts/components/admin/Dependencies/StatusDisplay.vue
index 3789f00f2e23..9365f0113124 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/StatusDisplay.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/StatusDisplay.vue
@@ -5,7 +5,7 @@
                 <span class="fa fa-check text-success"></span>{{ status.dependency_type }}
                 <span v-if="mergedMultiple">(merged)</span>
             </b>
-            <span v-if="!compact">{{ description }} <display-raw :object="status"/></span>
+            <span v-if="!compact">{{ description }} <display-raw :object="status" /></span>
         </span>
         <b v-else> <span class="fa fa-times text-danger"></span><i>unresolved</i> </b>
     </span>
@@ -16,7 +16,7 @@ const DESCRIPTIONS = {
     galaxy_package: "A manually configured Galaxy package directory will be used for resolution. ",
     tool_shed_packages: "Legacy Tool Shed package installations will be used for resolution. ",
     docker: "Resolution of dependencies is assumed to be handled by specified Docker container. ",
-    singularity: "Resolution of dependencies is assumed to be handled by specified Singularity container. "
+    singularity: "Resolution of dependencies is assumed to be handled by specified Singularity container. ",
 };
 
 function describeRequirement(status) {
@@ -41,27 +41,27 @@ export default {
     props: {
         status: {
             type: Object,
-            required: true
+            required: true,
         },
         allStatuses: {
             type: Array,
-            default: null
+            default: null,
         },
         compact: {
             type: Boolean,
-            default: true
-        }
+            default: true,
+        },
     },
     computed: {
-        merged: function() {
+        merged: function () {
             return (
                 this.status.model_class == "MergedCondaDependency" || this.status.model_class == "ContainerDependency"
             );
         },
-        mergedMultiple: function() {
+        mergedMultiple: function () {
             return this.merged && this.allStatuses != null && this.allStatuses.length > 1;
         },
-        description: function() {
+        description: function () {
             const dependencyType = this.status.dependency_type;
             let resolutionDescription =
                 DESCRIPTIONS[dependencyType] ||
@@ -78,9 +78,9 @@ export default {
             }
             return resolutionDescription;
         },
-        title: function() {
+        title: function () {
             return this.compact ? this.description : "";
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/Statuses.vue b/client/galaxy/scripts/components/admin/Dependencies/Statuses.vue
index eda9d1ffa2bd..3d9461204e84 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/Statuses.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/Statuses.vue
@@ -17,17 +17,17 @@ export default {
     props: {
         statuses: {
             type: Array,
-            required: true
+            required: true,
         },
         compact: {
             type: Boolean,
-            default: true
-        }
+            default: true,
+        },
     },
     computed: {
-        merged: function() {
+        merged: function () {
             return this.statuses.length >= 1 && this.statuses[0].model_class == "MergedCondaDependency";
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/ToolDisplay.vue b/client/galaxy/scripts/components/admin/Dependencies/ToolDisplay.vue
index 4769d0a38feb..114d4df07589 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/ToolDisplay.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/ToolDisplay.vue
@@ -9,17 +9,17 @@ export default {
     props: {
         toolId: {
             type: String,
-            required: true
+            required: true,
         },
         toolVersion: {
             type: String,
-            default: null
-        }
+            default: null,
+        },
     },
     computed: {
-        showVersion: function() {
+        showVersion: function () {
             return this.toolVersion && !this.toolId.endsWith(this.toolVersion);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/Tools.vue b/client/galaxy/scripts/components/admin/Dependencies/Tools.vue
index 96126dd41530..6ceb30952ce3 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/Tools.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/Tools.vue
@@ -17,17 +17,17 @@ export default {
     props: {
         toolIds: {
             type: Array,
-            required: true
+            required: true,
         },
         compact: {
             type: Boolean,
-            default: true
-        }
+            default: true,
+        },
     },
     computed: {
-        title: function() {
+        title: function () {
             return this.compact ? this.toolIds.join(", ") : "";
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Dependencies/UnusedIndex.vue b/client/galaxy/scripts/components/admin/Dependencies/UnusedIndex.vue
index 5239b8615046..94fbea2ac5bb 100644
--- a/client/galaxy/scripts/components/admin/Dependencies/UnusedIndex.vue
+++ b/client/galaxy/scripts/components/admin/Dependencies/UnusedIndex.vue
@@ -31,31 +31,31 @@ export default {
             error: null,
             loading: true,
             fields: [{ key: "selected", label: "" }, { key: "path" }],
-            paths: []
+            paths: [],
         };
     },
-    created: function() {
+    created: function () {
         this.load();
     },
     computed: {
-        items: function() {
-            return this.paths.map(path => {
+        items: function () {
+            return this.paths.map((path) => {
                 return { path: path, selected: false, _showDetails: false };
             });
         },
-        hasSelectedPaths: function() {
+        hasSelectedPaths: function () {
             for (const item of this.items) {
                 if (item["selected"]) {
                     return true;
                 }
             }
             return false;
-        }
+        },
     },
     methods: {
         load() {
             getDependencyUnusedPaths()
-                .then(response => {
+                .then((response) => {
                     this.paths = response;
                     this.loading = false;
                 })
@@ -77,7 +77,7 @@ export default {
         },
         handleError(e) {
             this.error = e;
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/DisplayApplications.vue b/client/galaxy/scripts/components/admin/DisplayApplications.vue
index da229aeb4713..36ae2d6fc490 100644
--- a/client/galaxy/scripts/components/admin/DisplayApplications.vue
+++ b/client/galaxy/scripts/components/admin/DisplayApplications.vue
@@ -15,7 +15,7 @@ import { getDisplayApplications, reloadDisplayApplications } from "./AdminServic
 
 export default {
     components: {
-        BaseList
+        BaseList,
     },
     data() {
         return {
@@ -24,11 +24,11 @@ export default {
                 { key: "name", sortable: true },
                 { key: "id", sortable: true },
                 { key: "version" },
-                { key: "links" }
+                { key: "links" },
             ],
             getter: getDisplayApplications,
-            setter: reloadDisplayApplications
+            setter: reloadDisplayApplications,
         };
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/ErrorStack.vue b/client/galaxy/scripts/components/admin/ErrorStack.vue
index d6ab056ef1c5..0a8a2ccfd899 100644
--- a/client/galaxy/scripts/components/admin/ErrorStack.vue
+++ b/client/galaxy/scripts/components/admin/ErrorStack.vue
@@ -17,32 +17,32 @@ export default {
                 { key: "time", sortable: true },
                 { key: "phase", sortable: true },
                 { key: "file", sortable: true },
-                { key: "error" }
+                { key: "error" },
             ],
-            messageText: null
+            messageText: null,
         };
     },
     computed: {
-        errorStackVisible: function() {
+        errorStackVisible: function () {
             return this.errorStack.length > 0;
         },
-        messageVisible: function() {
+        messageVisible: function () {
             return this.messageText != null;
         },
-        infoVisible: function() {
+        infoVisible: function () {
             return !this.errorStackVisible && this.errorStackLoaded;
-        }
+        },
     },
     created() {
         getErrorStack()
-            .then(response => {
+            .then((response) => {
                 this.errorStack = response.data;
                 this.errorStackLoaded = true;
             })
-            .catch(e => {
+            .catch((e) => {
                 const message = e && e.response && e.response.data && e.response.data.err_msg;
                 this.messageText = message || "Request failed for an unknown reason.";
             });
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Home.vue b/client/galaxy/scripts/components/admin/Home.vue
index 1eef4279d078..eb96e955ff0e 100644
--- a/client/galaxy/scripts/components/admin/Home.vue
+++ b/client/galaxy/scripts/components/admin/Home.vue
@@ -125,18 +125,18 @@ export default {
     props: {
         isRepoInstalled: {
             type: Boolean,
-            required: true
+            required: true,
         },
         isToolShedInstalled: {
             type: Boolean,
-            required: true
-        }
+            required: true,
+        },
     },
     methods: {
-        useRouter: function(ev) {
+        useRouter: function (ev) {
             const Galaxy = getGalaxyInstance();
             Galaxy.page.router.push(ev.target.pathname.slice(root.length));
-        }
+        },
     },
     computed: {
         migrationStagesUrl: () => `${root}admin/review_tool_migration_stages`, // NOT ROUTER
@@ -152,7 +152,7 @@ export default {
         adminRolesUrl: () => `${root}admin/roles`,
         adminFormsUrl: () => `${root}admin/forms`,
         adminToolshedUrl: () => `${root}admin/toolshed`,
-        adminToolVersionsUrl: () => `${root}admin/tool_versions`
-    }
+        adminToolVersionsUrl: () => `${root}admin/tool_versions`,
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/JobDetails.vue b/client/galaxy/scripts/components/admin/JobDetails.vue
index 16002d2e0f1c..e5a3e65ab782 100644
--- a/client/galaxy/scripts/components/admin/JobDetails.vue
+++ b/client/galaxy/scripts/components/admin/JobDetails.vue
@@ -16,18 +16,18 @@ import { JobParameters } from "components/JobParameters";
 export default {
     components: {
         JobMetrics,
-        JobParameters
+        JobParameters,
     },
     props: {
         commandLine: {
             type: String,
-            required: true
+            required: true,
         },
         jobId: {
             type: String,
-            required: true
-        }
-    }
+            required: true,
+        },
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/admin/JobLock.vue b/client/galaxy/scripts/components/admin/JobLock.vue
index d613b8236b6b..dcb8d6f9b4ee 100644
--- a/client/galaxy/scripts/components/admin/JobLock.vue
+++ b/client/galaxy/scripts/components/admin/JobLock.vue
@@ -15,13 +15,13 @@ export default {
     data() {
         return {
             jobLock: false,
-            jobLockDisplay: false
+            jobLockDisplay: false,
         };
     },
     watch: {
         jobLock(newVal) {
             this.handleJobLock(axios.put(`${getAppRoot()}api/job_lock`, { active: this.jobLock }));
-        }
+        },
     },
     methods: {
         initJobLock() {
@@ -29,17 +29,17 @@ export default {
         },
         handleJobLock(axiosPromise) {
             axiosPromise
-                .then(response => {
+                .then((response) => {
                     this.jobLock = response.data.active;
                     this.jobLockDisplay = response.data.active;
                 })
-                .catch(error => {
+                .catch((error) => {
                     console.error(error);
                 });
-        }
+        },
     },
     created() {
         this.initJobLock();
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/admin/Jobs.vue b/client/galaxy/scripts/components/admin/Jobs.vue
index 83a2690441f5..a6871ce88cd6 100644
--- a/client/galaxy/scripts/components/admin/Jobs.vue
+++ b/client/galaxy/scripts/components/admin/Jobs.vue
@@ -200,7 +200,7 @@ export default {
                 { key: "tool_id", label: "Tool", tdClass: ["break-word"] },
                 { key: "state" },
                 { key: "job_runner_name", label: "Job Runner" },
-                { key: "job_runner_external_id", label: "PID/Cluster ID", sortable: true }
+                { key: "job_runner_external_id", label: "PID/Cluster ID", sortable: true },
             ],
             cutoff: 180,
             cutoffDisplay: 180,
@@ -213,7 +213,7 @@ export default {
             message: "",
             status: "",
             loading: true,
-            busy: true
+            busy: true,
         };
     },
     watch: {
@@ -228,7 +228,7 @@ export default {
                 this.indeterminate = true;
                 this.allSelected = false;
             }
-        }
+        },
     },
     methods: {
         update() {
@@ -238,7 +238,7 @@ export default {
             params = params.join("&");
             axios
                 .get(`${getAppRoot()}admin/jobs_list?${params}`)
-                .then(response => {
+                .then((response) => {
                     this.jobsItems = response.data.jobs;
                     this.recentJobsItems = response.data.recent_jobs;
                     this.cutoffDisplay = response.data.cutoff;
@@ -247,7 +247,7 @@ export default {
                     this.loading = false;
                     this.busy = false;
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.message = error.response.data.err_msg;
                     this.status = "error";
                     console.log(error.response);
@@ -257,7 +257,7 @@ export default {
             this.update();
         },
         onStopJobs() {
-            axios.all(this.selectedStopJobIds.map(jobId => cancelJob(jobId, this.stopMessage))).then(res => {
+            axios.all(this.selectedStopJobIds.map((jobId) => cancelJob(jobId, this.stopMessage))).then((res) => {
                 this.update();
                 this.selectedStopJobIds = [];
                 this.stopMessage = "";
@@ -282,16 +282,16 @@ export default {
                 new: "primary",
                 queued: "secondary",
                 running: "info",
-                upload: "dark"
+                upload: "dark",
             };
             return translateDict[state] || "primary";
         },
         computeItems(items) {
-            return items.map(job => {
+            return items.map((job) => {
                 return {
                     ...job,
                     _showDetails: false,
-                    _cellVariants: { state: this.translateState(job.state) }
+                    _cellVariants: { state: this.translateState(job.state) },
                 };
             });
         },
@@ -311,14 +311,14 @@ export default {
                 done: "success",
                 info: "info",
                 warning: "warning",
-                error: "danger"
+                error: "danger",
             };
             if (variant in galaxyKwdToBoostrapDict) {
                 return galaxyKwdToBoostrapDict[variant];
             } else {
                 return variant;
             }
-        }
+        },
     },
     computed: {
         jobsItemsComputed() {
@@ -340,11 +340,11 @@ export default {
         },
         selectedJobUrl() {
             return `${getAppRoot()}admin/job_info?jobid=${this.selectedJobId}`;
-        }
+        },
     },
     created() {
         this.update();
-    }
+    },
 };
 </script>
 
diff --git a/client/galaxy/scripts/components/admin/ResetMetadata.vue b/client/galaxy/scripts/components/admin/ResetMetadata.vue
index ef6516d10308..40897d7f4569 100644
--- a/client/galaxy/scripts/components/admin/ResetMetadata.vue
+++ b/client/galaxy/scripts/components/admin/ResetMetadata.vue
@@ -15,7 +15,7 @@ import { getInstalledRepositories, resetRepositoryMetadata } from "./AdminServic
 
 export default {
     components: {
-        BaseList
+        BaseList,
     },
     data() {
         return {
@@ -23,11 +23,11 @@ export default {
                 { key: "execute", label: "Reset" },
                 { key: "name", label: "Metadata", sortable: true },
                 { key: "owner", sortable: true },
-                { key: "ctx_rev", label: "Revision" }
+                { key: "ctx_rev", label: "Revision" },
             ],
             getter: getInstalledRepositories,
-            setter: resetRepositoryMetadata
+            setter: resetRepositoryMetadata,
         };
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/login/Index.vue b/client/galaxy/scripts/components/login/Index.vue
index 92b55a0f6377..cea03f89b765 100644
--- a/client/galaxy/scripts/components/login/Index.vue
+++ b/client/galaxy/scripts/components/login/Index.vue
@@ -24,48 +24,48 @@ Vue.use(BootstrapVue);
 export default {
     data() {
         return {
-            login: true
+            login: true,
         };
     },
     computed: {
-        showLogin: function() {
+        showLogin: function () {
             return this.login;
-        }
+        },
     },
     components: {
         login: Login,
-        register: Register
+        register: Register,
     },
     methods: {
-        toggleLogin: function() {
+        toggleLogin: function () {
             this.login = !this.login;
-        }
+        },
     },
     props: {
         show_welcome_with_login: {
             type: Boolean,
-            required: false
+            required: false,
         },
         welcome_url: {
             type: String,
-            required: false
+            required: false,
         },
         terms_url: {
             type: String,
-            required: false
+            required: false,
         },
         registration_warning_message: {
             type: String,
-            required: false
+            required: false,
         },
         mailing_join_addr: {
             type: String,
-            required: false
+            required: false,
         },
         server_mail_configured: {
             type: Boolean,
-            required: false
-        }
-    }
+            required: false,
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/login/Login.vue b/client/galaxy/scripts/components/login/Login.vue
index 9189093645ea..e7c37e369d69 100644
--- a/client/galaxy/scripts/components/login/Login.vue
+++ b/client/galaxy/scripts/components/login/Login.vue
@@ -38,7 +38,7 @@
                         </b-card-footer>
                     </b-card>
                 </b-form>
-                <div v-for="idp in oidc_idps" :key="idp" style="margin:0.5em">
+                <div v-for="idp in oidc_idps" :key="idp" style="margin: 0.5em;">
                     <span v-if="oidc_idps_icons[idp]">
                         <b-button variant="link" class="d-block mt-3" @click="submitOIDCLogin(idp)">
                             <img :src="oidc_idps_icons[idp]" height="45" :alt="idp" />
@@ -71,19 +71,19 @@ export default {
     props: {
         show_welcome_with_login: {
             type: Boolean,
-            required: false
+            required: false,
         },
         welcome_url: {
             type: String,
-            required: false
-        }
+            required: false,
+        },
     },
     data() {
         const galaxy = getGalaxyInstance();
         // Icons to use for each IdP
         const oidc_idps_icons = {
             google: "https://developers.google.com/identity/images/btn_google_signin_light_normal_web.png",
-            elixir: "https://elixir-europe.org/sites/default/files/images/login-button-orange.png"
+            elixir: "https://elixir-europe.org/sites/default/files/images/login-button-orange.png",
         };
         return {
             login: null,
@@ -97,25 +97,25 @@ export default {
             session_csrf_token: galaxy.session_csrf_token,
             enable_oidc: galaxy.config.enable_oidc,
             oidc_idps: galaxy.config.oidc,
-            oidc_idps_icons: oidc_idps_icons
+            oidc_idps_icons: oidc_idps_icons,
         };
     },
     computed: {
         messageShow() {
             return this.messageText != null;
-        }
+        },
     },
     methods: {
-        toggleLogin: function() {
+        toggleLogin: function () {
             if (this.$root.toggleLogin) {
                 this.$root.toggleLogin();
             }
         },
-        submitGalaxyLogin: function(method) {
+        submitGalaxyLogin: function (method) {
             const rootUrl = getAppRoot();
             axios
                 .post(`${rootUrl}user/login`, this.$data)
-                .then(response => {
+                .then((response) => {
                     if (response.data.message && response.data.status) {
                         alert(response.data.message);
                     }
@@ -127,43 +127,43 @@ export default {
                         window.location = `${rootUrl}`;
                     }
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.messageVariant = "danger";
                     const message = error.response.data && error.response.data.err_msg;
                     this.messageText = message || "Login failed for an unknown reason.";
                 });
         },
-        submitOIDCLogin: function(idp) {
+        submitOIDCLogin: function (idp) {
             const rootUrl = getAppRoot();
             axios
                 .post(`${rootUrl}authnz/${idp}/login`)
-                .then(response => {
+                .then((response) => {
                     if (response.data.redirect_uri) {
                         window.location = response.data.redirect_uri;
                     }
                     // Else do something intelligent or maybe throw an error -- what else does this endpoint possibly return?
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.messageVariant = "danger";
                     const message = error.response.data && error.response.data.err_msg;
                     this.messageText = message || "Login failed for an unknown reason.";
                 });
         },
-        reset: function(ev) {
+        reset: function (ev) {
             const rootUrl = getAppRoot();
             ev.preventDefault();
             axios
                 .post(`${rootUrl}user/reset_password`, { email: this.login })
-                .then(response => {
+                .then((response) => {
                     this.messageVariant = "info";
                     this.messageText = response.data.message;
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.messageVariant = "danger";
                     const message = error.response.data && error.response.data.err_msg;
                     this.messageText = message || "Password reset failed for an unknown reason.";
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/login/Password.vue b/client/galaxy/scripts/components/login/Password.vue
index f50b6a6afb1d..c0e8149f35e0 100644
--- a/client/galaxy/scripts/components/login/Password.vue
+++ b/client/galaxy/scripts/components/login/Password.vue
@@ -30,16 +30,16 @@ export default {
             confirm: null,
             current: null,
             messageText: Galaxy.params.message,
-            messageVariant: Galaxy.params.status
+            messageVariant: Galaxy.params.status,
         };
     },
     computed: {
         messageShow() {
             return this.messageText != null;
-        }
+        },
     },
     methods: {
-        submit: function(ev) {
+        submit: function (ev) {
             const urlRoot = getAppRoot();
             ev.preventDefault();
             axios
@@ -48,17 +48,17 @@ export default {
                     id: this.user,
                     current: this.current,
                     password: this.password,
-                    confirm: this.confirm
+                    confirm: this.confirm,
                 })
-                .then(response => {
+                .then((response) => {
                     window.location = `${urlRoot}`;
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.messageVariant = "danger";
                     const message = error.response.data && error.response.data.err_msg;
                     this.messageText = message || "Password change failed for an unknown reason.";
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/login/Register.vue b/client/galaxy/scripts/components/login/Register.vue
index f247ec672985..80748b1b066c 100644
--- a/client/galaxy/scripts/components/login/Register.vue
+++ b/client/galaxy/scripts/components/login/Register.vue
@@ -62,24 +62,24 @@ export default {
     props: {
         registration_warning_message: {
             type: String,
-            required: false
+            required: false,
         },
         server_mail_configured: {
             type: Boolean,
-            required: false
+            required: false,
         },
         mailing_join_addr: {
             type: String,
-            required: false
+            required: false,
         },
         redirect: {
             type: String,
-            required: false
+            required: false,
         },
         terms_url: {
             type: String,
-            required: false
-        }
+            required: false,
+        },
     },
     data() {
         const galaxy = getGalaxyInstance();
@@ -93,7 +93,7 @@ export default {
             messageText: null,
             messageVariant: null,
             session_csrf_token: galaxy.session_csrf_token,
-            isAdmin: galaxy.user.isAdmin()
+            isAdmin: galaxy.user.isAdmin(),
         };
     },
     computed: {
@@ -102,32 +102,32 @@ export default {
         },
         showRegistrationWarning() {
             return this.registration_warning_message != null;
-        }
+        },
     },
     methods: {
-        toggleLogin: function() {
+        toggleLogin: function () {
             if (this.$root.toggleLogin) {
                 this.$root.toggleLogin();
             }
         },
-        submit: function(method) {
+        submit: function (method) {
             this.disableCreate = true;
             const rootUrl = getAppRoot();
             axios
                 .post(`${rootUrl}user/create`, this.$data)
-                .then(response => {
+                .then((response) => {
                     if (response.data.message && response.data.status) {
                         alert(response.data.message);
                     }
                     window.location = this.redirect || rootUrl;
                 })
-                .catch(error => {
+                .catch((error) => {
                     this.disableCreate = false;
                     this.messageVariant = "danger";
                     const message = error.response.data && error.response.data.err_msg;
                     this.messageText = message || "Registration failed for an unknown reason.";
                 });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/xrefs.vue b/client/galaxy/scripts/components/xrefs.vue
index 66d014311da5..75c9d54b973b 100644
--- a/client/galaxy/scripts/components/xrefs.vue
+++ b/client/galaxy/scripts/components/xrefs.vue
@@ -28,28 +28,28 @@ export default {
     props: {
         source: {
             type: String,
-            required: true
+            required: true,
         },
         id: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
             xrefs: [],
-            errors: []
+            errors: [],
         };
     },
-    created: function() {
+    created: function () {
         axios
             .get(`${getAppRoot()}api/${this.source}/${this.id}/xrefs`)
-            .then(response => {
+            .then((response) => {
                 this.xrefs = response.data;
             })
-            .catch(e => {
+            .catch((e) => {
                 console.error(e);
             });
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/entry/admin/AdminRouter.js b/client/galaxy/scripts/entry/admin/AdminRouter.js
index e634b74ec058..0298b26bbdec 100644
--- a/client/galaxy/scripts/entry/admin/AdminRouter.js
+++ b/client/galaxy/scripts/entry/admin/AdminRouter.js
@@ -45,108 +45,108 @@ export const getAdminRouter = (Galaxy, options) => {
             "(/)admin/toolbox_dependencies": "show_toolbox_dependencies",
             "(/)admin/data_manager*path": "show_data_manager",
             "(/)admin(/)reset_metadata": "show_reset_metadata",
-            "*notFound": "not_found"
+            "*notFound": "not_found",
         },
 
-        authenticate: function() {
+        authenticate: function () {
             const Galaxy = getGalaxyInstance();
             return Galaxy.user && Galaxy.user.id && Galaxy.user.get("is_admin");
         },
 
-        not_found: function() {
+        not_found: function () {
             window.location.reload(); // = window.location.href;
         },
 
-        show_home: function() {
+        show_home: function () {
             this._display_vue_helper(AdminHome, {
                 isRepoInstalled: options.settings.is_repo_installed,
-                isToolShedInstalled: options.settings.is_tool_shed_installed
+                isToolShedInstalled: options.settings.is_tool_shed_installed,
             });
         },
 
-        show_users: function() {
+        show_users: function () {
             this._show_grid_view("admin/users_list");
         },
 
-        show_users_create: function() {
+        show_users_create: function () {
             this._display_vue_helper(Register, {
                 redirect: "/admin/users",
                 registration_warning_message: options.config.registration_warning_message,
                 mailing_join_addr: options.config.mailing_join_addr,
-                server_mail_configured: options.config.server_mail_configured
+                server_mail_configured: options.config.server_mail_configured,
             });
         },
 
-        show_roles: function() {
+        show_roles: function () {
             this._show_grid_view("admin/roles_list");
         },
 
-        show_groups: function() {
+        show_groups: function () {
             this._show_grid_view("admin/groups_list");
         },
 
-        show_toolshed: function() {
+        show_toolshed: function () {
             this._display_vue_helper(Toolshed);
         },
 
-        show_tool_versions: function() {
+        show_tool_versions: function () {
             this._show_grid_view("admin/tool_versions_list");
         },
 
-        show_quotas: function() {
+        show_quotas: function () {
             this._show_grid_view("admin/quotas_list");
         },
 
-        _show_grid_view: function(urlSuffix) {
+        _show_grid_view: function (urlSuffix) {
             const Galaxy = getGalaxyInstance();
             this.page.display(
                 new GridView({
                     url_base: `${galaxyRoot}${urlSuffix}`,
-                    url_data: Galaxy.params
+                    url_data: Galaxy.params,
                 })
             );
         },
 
-        _display_vue_helper: function(component, propsData = {}) {
+        _display_vue_helper: function (component, propsData = {}) {
             const instance = Vue.extend(component);
             const container = document.createElement("div");
             this.page.display(container);
             new instance({ store, propsData }).$mount(container);
         },
 
-        show_data_tables: function() {
+        show_data_tables: function () {
             this._display_vue_helper(DataTables);
         },
 
-        show_data_types: function() {
+        show_data_types: function () {
             this._display_vue_helper(DataTypes);
         },
 
-        show_jobs: function() {
+        show_jobs: function () {
             this._display_vue_helper(Jobs);
         },
 
-        show_invocations: function() {
+        show_invocations: function () {
             this._display_vue_helper(ActiveInvocations);
         },
 
-        show_toolbox_dependencies: function() {
+        show_toolbox_dependencies: function () {
             this._display_vue_helper(Landing);
         },
 
-        show_error_stack: function() {
+        show_error_stack: function () {
             this._display_vue_helper(ErrorStack);
         },
 
-        show_display_applications: function() {
+        show_display_applications: function () {
             this._display_vue_helper(DisplayApplications);
         },
 
-        show_reset_metadata: function() {
+        show_reset_metadata: function () {
             this._display_vue_helper(ResetMetadata);
         },
 
-        show_data_manager: function(path) {
+        show_data_manager: function (path) {
             const Galaxy = getGalaxyInstance();
             console.log("show_data_manager");
             const vueMount = document.createElement("div");
@@ -155,14 +155,14 @@ export const getAdminRouter = (Galaxy, options) => {
             // `${galaxyRoot}admin/data_manager`
             Galaxy.debug("show_data_manager: path='" + path + "'");
             DataManagerRouter.replace(path || "/");
-            new Vue({ router: DataManagerRouter, render: h => h(DataManagerView) }).$mount(vueMount);
+            new Vue({ router: DataManagerRouter, render: (h) => h(DataManagerView) }).$mount(vueMount);
         },
 
-        show_forms: function() {
+        show_forms: function () {
             this._show_grid_view("forms/forms_list");
         },
 
-        show_form: function(form_id) {
+        show_form: function (form_id) {
             const id = `?id=${QueryStringParsing.get("id")}`;
             const form_defs = {
                 reset_user_password: {
@@ -170,67 +170,67 @@ export const getAdminRouter = (Galaxy, options) => {
                     url: `admin/reset_user_password${id}`,
                     icon: "fa-user",
                     submit_title: "Save new password",
-                    redirect: "admin/users"
+                    redirect: "admin/users",
                 },
                 manage_roles_and_groups_for_user: {
                     url: `admin/manage_roles_and_groups_for_user${id}`,
                     icon: "fa-users",
-                    redirect: "admin/users"
+                    redirect: "admin/users",
                 },
                 manage_users_and_groups_for_role: {
                     url: `admin/manage_users_and_groups_for_role${id}`,
-                    redirect: "admin/roles"
+                    redirect: "admin/roles",
                 },
                 manage_users_and_roles_for_group: {
                     url: `admin/manage_users_and_roles_for_group${id}`,
-                    redirect: "admin/groups"
+                    redirect: "admin/groups",
                 },
                 manage_users_and_groups_for_quota: {
                     url: `admin/manage_users_and_groups_for_quota${id}`,
-                    redirect: "admin/quotas"
+                    redirect: "admin/quotas",
                 },
                 create_role: {
                     url: "admin/create_role",
-                    redirect: "admin/roles"
+                    redirect: "admin/roles",
                 },
                 create_group: {
                     url: "admin/create_group",
-                    redirect: "admin/groups"
+                    redirect: "admin/groups",
                 },
                 create_quota: {
                     url: "admin/create_quota",
-                    redirect: "admin/quotas"
+                    redirect: "admin/quotas",
                 },
                 rename_role: {
                     url: `admin/rename_role${id}`,
-                    redirect: "admin/roles"
+                    redirect: "admin/roles",
                 },
                 rename_group: {
                     url: `admin/rename_group${id}`,
-                    redirect: "admin/groups"
+                    redirect: "admin/groups",
                 },
                 rename_quota: {
                     url: `admin/rename_quota${id}`,
-                    redirect: "admin/quotas"
+                    redirect: "admin/quotas",
                 },
                 edit_quota: {
                     url: `admin/edit_quota${id}`,
-                    redirect: "admin/quotas"
+                    redirect: "admin/quotas",
                 },
                 set_quota_default: {
                     url: `admin/set_quota_default${id}`,
-                    redirect: "admin/quotas"
+                    redirect: "admin/quotas",
                 },
                 create_form: {
                     url: "forms/create_form",
-                    redirect: "admin/forms"
+                    redirect: "admin/forms",
                 },
                 edit_form: {
                     url: `forms/edit_form${id}`,
-                    redirect: "admin/forms"
-                }
+                    redirect: "admin/forms",
+                },
             };
             this.page.display(new FormWrapper.View(form_defs[form_id]));
-        }
+        },
     });
 };
diff --git a/client/galaxy/scripts/entry/admin/index.js b/client/galaxy/scripts/entry/admin/index.js
index 7268210f20d2..cc6a76b98120 100644
--- a/client/galaxy/scripts/entry/admin/index.js
+++ b/client/galaxy/scripts/entry/admin/index.js
@@ -8,12 +8,12 @@ addInitialization((Galaxy, { options }) => {
     console.log("Admin custom page setup");
 
     Object.assign(options.config, {
-        active_view: "admin"
+        active_view: "admin",
     });
 
     const pageOptions = Object.assign({}, options, {
         Left: AdminPanel,
-        Router: getAdminRouter(Galaxy, options)
+        Router: getAdminRouter(Galaxy, options),
     });
 
     Utils.setWindowTitle("Administration");
diff --git a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
index 6d5239673bab..fd8d93605a75 100644
--- a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
+++ b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
@@ -48,7 +48,7 @@ import Vue from "vue";
 import store from "store";
 
 /** Routes */
-export const getAnalysisRouter = Galaxy =>
+export const getAnalysisRouter = (Galaxy) =>
     Router.extend({
         routes: {
             "(/)(#)(_=_)": "home",
@@ -86,17 +86,17 @@ export const getAnalysisRouter = Galaxy =>
             "(/)custom_builds": "show_custom_builds",
             "(/)datasets/edit": "show_dataset_edit_attributes",
             "(/)datasets/error": "show_dataset_error",
-            "(/)interactivetool_entry_points(/)list": "show_interactivetool_list"
+            "(/)interactivetool_entry_points(/)list": "show_interactivetool_list",
         },
 
         require_login: ["show_user", "show_user_form", "show_workflows", "show_cloud_auth"],
 
-        authenticate: function(args, name) {
+        authenticate: function (args, name) {
             const Galaxy = getGalaxyInstance();
             return (Galaxy.user && Galaxy.user.id) || this.require_login.indexOf(name) == -1;
         },
 
-        _display_vue_helper: function(component, propsData = {}, active_tab = null) {
+        _display_vue_helper: function (component, propsData = {}, active_tab = null) {
             const instance = Vue.extend(component);
             const container = document.createElement("div");
             if (active_tab) {
@@ -106,7 +106,7 @@ export const getAnalysisRouter = Galaxy =>
             new instance({ store, propsData }).$mount(container);
         },
 
-        show_tours: function(tour_id) {
+        show_tours: function (tour_id) {
             if (tour_id) {
                 Tours.giveTourById(tour_id);
             } else {
@@ -114,52 +114,52 @@ export const getAnalysisRouter = Galaxy =>
             }
         },
 
-        show_user: function() {
+        show_user: function () {
             const Galaxy = getGalaxyInstance();
             this._display_vue_helper(UserPreferences, {
                 enableQuotas: Galaxy.config.enable_quotas,
-                userId: Galaxy.user.id
+                userId: Galaxy.user.id,
             });
         },
 
-        show_user_form: function(form_id) {
+        show_user_form: function (form_id) {
             const Galaxy = getGalaxyInstance();
             const model = getUserPreferencesModel();
             model.user_id = Galaxy.params.id;
             this.page.display(new FormWrapper.View(_.extend(model[form_id], { active_tab: "user" })));
         },
 
-        show_interactivetool_list: function() {
+        show_interactivetool_list: function () {
             this._display_vue_helper(InteractiveTools);
         },
 
-        show_cloud_auth: function() {
+        show_cloud_auth: function () {
             this._display_vue_helper(CloudAuth);
         },
 
-        show_visualizations: function(action_id) {
+        show_visualizations: function (action_id) {
             const activeTab = action_id == "list_published" ? "shared" : "user";
             this.page.display(
                 new GridShared.View({
                     action_id: action_id,
                     plural: "Visualizations",
                     item: "visualization",
-                    active_tab: activeTab
+                    active_tab: activeTab,
                 })
             );
         },
 
-        show_visualizations_edit: function() {
+        show_visualizations_edit: function () {
             this.page.display(
                 new FormWrapper.View({
                     url: `visualization/edit?id=${QueryStringParsing.get("id")}`,
                     redirect: "visualizations/list",
-                    active_tab: "visualization"
+                    active_tab: "visualization",
                 })
             );
         },
 
-        show_visualizations_sharing: function() {
+        show_visualizations_sharing: function () {
             const sharingInstance = Vue.extend(Sharing);
             const vm = document.createElement("div");
             this.page.display(vm);
@@ -167,69 +167,69 @@ export const getAnalysisRouter = Galaxy =>
                 propsData: {
                     id: QueryStringParsing.get("id"),
                     plural_name: "Visualizations",
-                    model_class: "Visualization"
-                }
+                    model_class: "Visualization",
+                },
             }).$mount(vm);
         },
 
-        show_workflows_published: function() {
+        show_workflows_published: function () {
             const userFilter = QueryStringParsing.get("f-username");
             this.page.display(
                 new GridView({
                     url_base: `${getAppRoot()}workflow/list_published`,
                     active_tab: "shared",
                     url_data: {
-                        "f-username": userFilter == null ? "" : userFilter
-                    }
+                        "f-username": userFilter == null ? "" : userFilter,
+                    },
                 })
             );
         },
 
-        show_history_view: function() {
+        show_history_view: function () {
             const historyInstance = Vue.extend(HistoryView);
             const vm = document.createElement("div");
             this.page.display(vm);
             new historyInstance({ propsData: { id: QueryStringParsing.get("id") } }).$mount(vm);
         },
 
-        show_workflow_invocation_report: function() {
+        show_workflow_invocation_report: function () {
             const invocationId = QueryStringParsing.get("id");
             this._display_vue_helper(WorkflowInvocationReport, { invocationId: invocationId });
         },
 
-        show_workflow_invocations: function() {
+        show_workflow_invocations: function () {
             this._display_vue_helper(RecentInvocations, {});
         },
 
-        show_history_structure: function() {
+        show_history_structure: function () {
             const displayStructureInstance = Vue.extend(DisplayStructure);
             const vm = document.createElement("div");
             this.page.display(vm);
             new displayStructureInstance({ propsData: { id: QueryStringParsing.get(" id: ") } }).$mount(vm);
         },
 
-        show_histories: function(action_id) {
+        show_histories: function (action_id) {
             const view = new HistoryList.View({ action_id: action_id });
             this.page.display(view);
         },
 
-        show_history_citations: function() {
+        show_history_citations: function () {
             const citationInstance = Vue.extend(Citations);
             const vm = document.createElement("div");
             this.page.display(vm);
             new citationInstance({ propsData: { id: QueryStringParsing.get("id"), source: "histories" } }).$mount(vm);
         },
 
-        show_histories_rename: function() {
+        show_histories_rename: function () {
             this.page.display(
                 new FormWrapper.View({
                     url: `history/rename?id=${QueryStringParsing.get("id")}`,
-                    redirect: "histories/list"
+                    redirect: "histories/list",
                 })
             );
         },
 
-        show_histories_sharing: function() {
+        show_histories_sharing: function () {
             const sharingInstance = Vue.extend(Sharing);
             const vm = document.createElement("div");
             this.page.display(vm);
@@ -237,70 +237,70 @@ export const getAnalysisRouter = Galaxy =>
                 propsData: {
                     id: QueryStringParsing.get("id"),
                     plural_name: "Histories",
-                    model_class: "History"
-                }
+                    model_class: "History",
+                },
             }).$mount(vm);
         },
 
-        show_histories_import: function() {
+        show_histories_import: function () {
             this._display_vue_helper(HistoryImport);
         },
 
-        show_tools_view: function() {
+        show_tools_view: function () {
             this.page.toolPanel.getVueComponent().hide();
             this.page.panels.right.hide();
             this._display_vue_helper(ToolsView);
         },
 
-        show_tools_json: function() {
+        show_tools_json: function () {
             this._display_vue_helper(ToolsJson);
         },
-        show_histories_permissions: function() {
+        show_histories_permissions: function () {
             this.page.display(
                 new FormWrapper.View({
                     url: `history/permissions?id=${QueryStringParsing.get("id")}`,
-                    redirect: "histories/list"
+                    redirect: "histories/list",
                 })
             );
         },
 
-        show_datasets: function() {
+        show_datasets: function () {
             this._display_vue_helper(DatasetList);
         },
 
-        show_pages: function(action_id) {
+        show_pages: function (action_id) {
             const activeTab = action_id == "list_published" ? "shared" : "user";
             this.page.display(
                 new GridShared.View({
                     action_id: action_id,
                     plural: "Pages",
                     item: "page",
-                    active_tab: activeTab
+                    active_tab: activeTab,
                 })
             );
         },
 
-        show_pages_create: function() {
+        show_pages_create: function () {
             this.page.display(
                 new FormWrapper.View({
                     url: "page/create",
                     redirect: "pages/list",
-                    active_tab: "user"
+                    active_tab: "user",
                 })
             );
         },
 
-        show_pages_edit: function() {
+        show_pages_edit: function () {
             this.page.display(
                 new FormWrapper.View({
                     url: `page/edit?id=${QueryStringParsing.get("id")}`,
                     redirect: "pages/list",
-                    active_tab: "user"
+                    active_tab: "user",
                 })
             );
         },
 
-        show_pages_sharing: function() {
+        show_pages_sharing: function () {
             const sharingInstance = Vue.extend(Sharing);
             const vm = document.createElement("div");
             this.page.display(vm);
@@ -308,47 +308,47 @@ export const getAnalysisRouter = Galaxy =>
                 propsData: {
                     id: QueryStringParsing.get("id"),
                     plural_name: "Pages",
-                    model_class: "Page"
-                }
+                    model_class: "Page",
+                },
             }).$mount(vm);
         },
 
-        show_plugins: function() {
+        show_plugins: function () {
             const pluginListInstance = Vue.extend(PluginList);
             const vm = document.createElement("div");
             this.page.display(vm);
             new pluginListInstance().$mount(vm);
         },
 
-        show_workflows: function() {
+        show_workflows: function () {
             const workflowListInstance = Vue.extend(WorkflowList);
             const vm = document.createElement("div");
             this.page.display(vm);
             new workflowListInstance().$mount(vm);
         },
 
-        show_workflows_create: function() {
+        show_workflows_create: function () {
             this.page.display(
                 new FormWrapper.View({
                     url: "workflow/create",
                     redirect: "workflow/editor",
-                    active_tab: "workflow"
+                    active_tab: "workflow",
                 })
             );
         },
 
-        show_workflows_run: function() {
+        show_workflows_run: function () {
             this._loadWorkflow();
         },
 
-        show_workflows_import: function() {
+        show_workflows_import: function () {
             const workflowImportInstance = Vue.extend(WorkflowImport);
             const vm = document.createElement("div");
             this.page.display(vm);
             new workflowImportInstance().$mount(vm);
         },
 
-        show_custom_builds: function() {
+        show_custom_builds: function () {
             const historyPanel = this.page.historyPanel.historyView;
             if (!historyPanel || !historyPanel.model || !historyPanel.model.id) {
                 window.setTimeout(() => {
@@ -362,16 +362,16 @@ export const getAnalysisRouter = Galaxy =>
             new customBuildsInstance().$mount(vm);
         },
 
-        show_dataset_edit_attributes: function() {
+        show_dataset_edit_attributes: function () {
             this.page.display(new DatasetEditAttributes.View());
         },
 
-        show_dataset_error: function() {
+        show_dataset_error: function () {
             this.page.display(new DatasetError.View());
         },
 
         /**  */
-        home: function(params) {
+        home: function (params) {
             // TODO: to router, remove Globals
             // load a tool by id (tool_id) or rerun a previous tool execution (job_id)
             if (params.tool_id || params.job_id) {
@@ -396,7 +396,7 @@ export const getAnalysisRouter = Galaxy =>
         },
 
         /** load the center panel with a tool form described by the given params obj */
-        _loadToolForm: function(params) {
+        _loadToolForm: function (params) {
             //TODO: load tool form code async
             if (params.tool_id) {
                 params.id = decodeUriComponent(params.tool_id);
@@ -408,15 +408,15 @@ export const getAnalysisRouter = Galaxy =>
         },
 
         /** load the center panel iframe using the given url */
-        _loadCenterIframe: function(url, root) {
+        _loadCenterIframe: function (url, root) {
             root = root || getAppRoot();
             url = root + url;
             this.page.$("#galaxy_main").prop("src", url);
         },
 
         /** load workflow by its url in run mode */
-        _loadWorkflow: function() {
+        _loadWorkflow: function () {
             const workflowId = QueryStringParsing.get("id");
             this._display_vue_helper(WorkflowRun, { workflowId: workflowId }, "workflow");
-        }
+        },
     });
diff --git a/client/galaxy/scripts/entry/analysis/index.js b/client/galaxy/scripts/entry/analysis/index.js
index 1bac19b9eb19..6ede5034773c 100644
--- a/client/galaxy/scripts/entry/analysis/index.js
+++ b/client/galaxy/scripts/entry/analysis/index.js
@@ -10,11 +10,11 @@ addInitialization((Galaxy, { options = {} }) => {
     const pageOptions = Object.assign({}, options, {
         config: Object.assign({}, options.config, {
             hide_panels: Galaxy.params.hide_panels,
-            hide_masthead: Galaxy.params.hide_masthead
+            hide_masthead: Galaxy.params.hide_masthead,
         }),
         Left: ToolPanel,
         Right: HistoryPanel,
-        Router: getAnalysisRouter(Galaxy)
+        Router: getAnalysisRouter(Galaxy),
     });
 
     Galaxy.page = new Page.View(pageOptions);
diff --git a/client/galaxy/scripts/entry/login/index.js b/client/galaxy/scripts/entry/login/index.js
index 424832dc1403..bb7deb0625c1 100644
--- a/client/galaxy/scripts/entry/login/index.js
+++ b/client/galaxy/scripts/entry/login/index.js
@@ -18,8 +18,8 @@ export function initLoginView(Galaxy, { options }) {
             terms_url: options.config.terms_url,
             registration_warning_message: options.config.registration_warning_message,
             mailing_join_addr: options.config.mailing_join_addr,
-            server_mail_configured: options.config.server_mail_configured
-        }
+            server_mail_configured: options.config.server_mail_configured,
+        },
     }).$mount(vm);
 }
 
diff --git a/client/galaxy/scripts/entry/panels/admin-panel.js b/client/galaxy/scripts/entry/panels/admin-panel.js
index 64dfc86e0e8d..c44603784d89 100644
--- a/client/galaxy/scripts/entry/panels/admin-panel.js
+++ b/client/galaxy/scripts/entry/panels/admin-panel.js
@@ -5,13 +5,13 @@ import _l from "utils/localization";
 import { getGalaxyInstance } from "app";
 
 const AdminPanel = Backbone.View.extend({
-    initialize: function(page, options) {
+    initialize: function (page, options) {
         this.page = page;
         this.root = options.root;
         this.config = options.config;
         this.settings = options.settings;
         this.model = new Backbone.Model({
-            title: `Galaxy version ${getGalaxyInstance().config.version_major}`
+            title: `Galaxy version ${getGalaxyInstance().config.version_major}`,
         });
         this.categories = new Backbone.Collection([
             {
@@ -21,39 +21,39 @@ const AdminPanel = Backbone.View.extend({
                         title: _l("Data Types"),
                         url: "admin/data_types",
                         target: "__use_router__",
-                        id: "admin-link-datatypes"
+                        id: "admin-link-datatypes",
                     },
                     {
                         title: _l("Data Tables"),
                         url: "admin/data_tables",
                         target: "__use_router__",
-                        id: "admin-link-data-tables"
+                        id: "admin-link-data-tables",
                     },
                     {
                         title: _l("Display Applications"),
                         url: "admin/display_applications",
                         target: "__use_router__",
-                        id: "admin-link-display-applications"
+                        id: "admin-link-display-applications",
                     },
                     {
                         title: _l("Jobs"),
                         url: "admin/jobs",
                         target: "__use_router__",
-                        id: "admin-link-jobs"
+                        id: "admin-link-jobs",
                     },
                     {
                         title: _l("Workflow Invocations"),
                         url: "admin/invocations",
                         target: "__use_router__",
-                        id: "admin-link-invocations"
+                        id: "admin-link-invocations",
                     },
                     {
                         title: _l("Local Data"),
                         url: "admin/data_manager",
                         target: "__use_router__",
-                        id: "admin-link-local-data"
-                    }
-                ]
+                        id: "admin-link-local-data",
+                    },
+                ],
             },
             {
                 title: _l("User Management"),
@@ -62,33 +62,33 @@ const AdminPanel = Backbone.View.extend({
                         title: _l("Users"),
                         url: "admin/users",
                         target: "__use_router__",
-                        id: "admin-link-users"
+                        id: "admin-link-users",
                     },
                     {
                         title: _l("Quotas"),
                         url: "admin/quotas",
                         target: "__use_router__",
                         enabled: this.config.enable_quotas,
-                        id: "admin-link-quotas"
+                        id: "admin-link-quotas",
                     },
                     {
                         title: _l("Groups"),
                         url: "admin/groups",
                         target: "__use_router__",
-                        id: "admin-link-groups"
+                        id: "admin-link-groups",
                     },
                     {
                         title: _l("Roles"),
                         url: "admin/roles",
                         target: "__use_router__",
-                        id: "admin-link-roles"
+                        id: "admin-link-roles",
                     },
                     {
                         title: _l("Forms"),
                         url: "admin/forms",
-                        target: "__use_router__"
-                    }
-                ]
+                        target: "__use_router__",
+                    },
+                ],
             },
             {
                 title: _l("Tool Management"),
@@ -97,54 +97,54 @@ const AdminPanel = Backbone.View.extend({
                         title: _l("Install and Uninstall"),
                         url: "admin/toolshed",
                         target: "__use_router__",
-                        enabled: this.settings.is_tool_shed_installed
+                        enabled: this.settings.is_tool_shed_installed,
                     },
                     {
                         title: _l("Manage Metadata"),
                         url: "admin/reset_metadata",
                         enabled: this.settings.is_repo_installed,
-                        target: "__use_router__"
+                        target: "__use_router__",
                     },
                     {
                         title: _l("Manage Whitelist"),
-                        url: "admin/sanitize_whitelist"
+                        url: "admin/sanitize_whitelist",
                     },
                     {
                         title: _l("Manage Dependencies"),
                         url: "admin/toolbox_dependencies",
                         target: "__use_router__",
-                        id: "admin-link-manage-dependencies"
+                        id: "admin-link-manage-dependencies",
                     },
                     {
                         title: _l("Manage Dependencies (legacy)"),
-                        url: "admin/manage_tool_dependencies"
+                        url: "admin/manage_tool_dependencies",
                     },
                     {
                         title: _l("View Lineage"),
                         url: "admin/tool_versions",
-                        target: "__use_router__"
+                        target: "__use_router__",
                     },
                     {
                         title: _l("View Migration Stages"),
-                        url: "admin/review_tool_migration_stages"
+                        url: "admin/review_tool_migration_stages",
                     },
                     {
                         title: _l("View Error Logs"),
                         url: "admin/error_stack",
-                        target: "__use_router__"
-                    }
-                ]
-            }
+                        target: "__use_router__",
+                    },
+                ],
+            },
         ]);
         this.setElement(this._template());
     },
 
-    render: function() {
+    render: function () {
         this.$el.empty();
-        this.categories.each(category => {
+        this.categories.each((category) => {
             const $section = $(this._templateSection(category.attributes));
             const $entries = $section.find(".toolSectionBody");
-            _.each(category.get("items"), item => {
+            _.each(category.get("items"), (item) => {
                 if (item.enabled === undefined || item.enabled) {
                     const $link = $("<a/>")
                         .attr({ href: this.root + item.url })
@@ -153,38 +153,34 @@ const AdminPanel = Backbone.View.extend({
                         $link.attr("id", item.id);
                     }
                     if (item.target == "__use_router__") {
-                        $link.on("click", e => {
+                        $link.on("click", (e) => {
                             e.preventDefault();
                             this.page.router.push(item.url);
                         });
                     } else {
                         $link.attr("target", "galaxy_main");
                     }
-                    $entries.append(
-                        $("<div/>")
-                            .addClass("toolTitle")
-                            .append($link)
-                    );
+                    $entries.append($("<div/>").addClass("toolTitle").append($link));
                 }
             });
             this.$el.append($section);
         });
     },
 
-    _templateSection: function(options) {
+    _templateSection: function (options) {
         return `<div class="toolSectionWrapper">
                     <div class="toolSectionTitle pt-1 px-3">${_l(options.title)}</div>
                     <div class="toolSectionBody"/>
                 </div>`;
     },
 
-    _template: function() {
+    _template: function () {
         return '<div class="toolMenuContainer"/>';
     },
 
-    toString: function() {
+    toString: function () {
         return "adminPanel";
-    }
+    },
 });
 
 export default AdminPanel;
diff --git a/client/galaxy/scripts/entry/panels/history-panel.js b/client/galaxy/scripts/entry/panels/history-panel.js
index 95919e3cbc67..2841f2266589 100644
--- a/client/galaxy/scripts/entry/panels/history-panel.js
+++ b/client/galaxy/scripts/entry/panels/history-panel.js
@@ -7,7 +7,7 @@ import CurrentHistoryView from "mvc/history/history-view-edit-current";
 
 /** the right hand panel in the analysis page that shows the current history */
 const HistoryPanel = Backbone.View.extend({
-    initialize: function(page, options) {
+    initialize: function (page, options) {
         const Galaxy = getGalaxyInstance();
         const panelHeaderButtons = [];
 
@@ -19,7 +19,7 @@ const HistoryPanel = Backbone.View.extend({
         this.historyView = new CurrentHistoryView.CurrentHistoryView({
             className: `${CurrentHistoryView.CurrentHistoryView.prototype.className} middle`,
             purgeAllowed: this.allow_user_dataset_purge,
-            linkTarget: "galaxy_main"
+            linkTarget: "galaxy_main",
         });
 
         // add history panel to Galaxy object
@@ -34,7 +34,7 @@ const HistoryPanel = Backbone.View.extend({
             icon: "fa fa-refresh",
             onclick: () => {
                 this.historyView.loadCurrentHistory();
-            }
+            },
         });
         panelHeaderButtons.push(this.buttonRefresh);
 
@@ -44,9 +44,9 @@ const HistoryPanel = Backbone.View.extend({
                 title: _l("Create new history"),
                 cls: "panel-header-button",
                 icon: "fa fa-plus",
-                onclick: function() {
+                onclick: function () {
                     Galaxy.currHistoryPanel.createNewHistory();
-                }
+                },
             });
             panelHeaderButtons.push(this.buttonNew);
         }
@@ -56,7 +56,7 @@ const HistoryPanel = Backbone.View.extend({
             title: _l("View all histories"),
             cls: "panel-header-button",
             icon: "fa fa-columns",
-            href: `${this.root}history/view_multiple`
+            href: `${this.root}history/view_multiple`,
         });
         panelHeaderButtons.push(this.buttonViewMulti);
 
@@ -66,7 +66,7 @@ const HistoryPanel = Backbone.View.extend({
             cls: "panel-header-button",
             target: "galaxy_main",
             icon: "fa fa-cog",
-            href: `${this.root}root/history_options`
+            href: `${this.root}root/history_options`,
         });
         panelHeaderButtons.push(this.buttonOptions);
 
@@ -74,7 +74,7 @@ const HistoryPanel = Backbone.View.extend({
             // define components
             cls: "history-right-panel",
             title: _l("History"),
-            buttons: panelHeaderButtons
+            buttons: panelHeaderButtons,
         });
 
         // build body template and connect history view
@@ -86,28 +86,28 @@ const HistoryPanel = Backbone.View.extend({
         // fetch to update the quota meter adding 'current' for any anon-user's id
         Galaxy.listenTo(this.historyView, "history-size-change", () => {
             Galaxy.user.fetch({
-                url: `${Galaxy.user.urlRoot()}/${Galaxy.user.id || "current"}`
+                url: `${Galaxy.user.urlRoot()}/${Galaxy.user.id || "current"}`,
             });
         });
     },
 
-    render: function() {
+    render: function () {
         this.optionsMenu = historyOptionsMenu(this.buttonOptions.$el, {
             anonymous: this.userIsAnonymous,
             purgeAllowed: this.allow_user_dataset_purge,
-            root: this.root
+            root: this.root,
         });
         this.buttonViewMulti.$el[!this.userIsAnonymous ? "show" : "hide"]();
     },
 
     /** add history view div */
-    _template: function(data) {
+    _template: function (data) {
         return ['<div id="current-history-panel" class="history-panel middle"/>'].join("");
     },
 
-    toString: function() {
+    toString: function () {
         return "historyPanel";
-    }
+    },
 });
 
 export default HistoryPanel;
diff --git a/client/galaxy/scripts/entry/panels/tool-panel.js b/client/galaxy/scripts/entry/panels/tool-panel.js
index 7aa5e977544f..24f74feb26cf 100644
--- a/client/galaxy/scripts/entry/panels/tool-panel.js
+++ b/client/galaxy/scripts/entry/panels/tool-panel.js
@@ -10,7 +10,7 @@ import SidePanel from "../../components/Panels/SidePanel";
 import { mountVueComponent } from "../../utils/mountVueComponent";
 
 const ToolPanel = Backbone.View.extend({
-    initialize: function() {
+    initialize: function () {
         const Galaxy = getGalaxyInstance();
         const appRoot = getAppRoot();
 
@@ -21,12 +21,12 @@ const ToolPanel = Backbone.View.extend({
             chunkUploadSize: Galaxy.config.chunk_upload_size,
             ftpUploadSite: Galaxy.config.ftp_upload_site,
             defaultGenome: Galaxy.config.default_genome,
-            defaultExtension: Galaxy.config.default_extension
+            defaultExtension: Galaxy.config.default_extension,
         };
         const vm = document.createElement("div");
         $("body").append(vm);
         const upload = new modalInstance({
-            propsData: propsData
+            propsData: propsData,
         }).$mount(vm);
 
         // attach upload entrypoint to Galaxy object
@@ -34,39 +34,39 @@ const ToolPanel = Backbone.View.extend({
 
         // components for panel definition
         this.model = new Backbone.Model({
-            title: _l("Tools")
+            title: _l("Tools"),
         });
     },
 
     isVueWrapper: true,
 
-    mountVueComponent: function(el) {
+    mountVueComponent: function (el) {
         const Galaxy = getGalaxyInstance();
         return mountVueComponent(SidePanel)(
             {
                 side: "left",
                 currentPanel: ToolBox,
-                currentPanelProperties: Galaxy.config
+                currentPanelProperties: Galaxy.config,
             },
             el
         );
     },
 
-    getVueComponent: function() {
+    getVueComponent: function () {
         const Galaxy = getGalaxyInstance();
         const SidePanelClass = Vue.extend(SidePanel);
         return new SidePanelClass({
             propsData: {
                 side: "left",
                 currentPanel: ToolBox,
-                currentPanelProperties: Galaxy.config
-            }
+                currentPanelProperties: Galaxy.config,
+            },
         });
     },
 
-    toString: function() {
+    toString: function () {
         return "toolPanel";
-    }
+    },
 });
 
 export default ToolPanel;
diff --git a/client/galaxy/scripts/galaxy.interactive_environments.js b/client/galaxy/scripts/galaxy.interactive_environments.js
index 3f371508b090..c712a1fa4edb 100644
--- a/client/galaxy/scripts/galaxy.interactive_environments.js
+++ b/client/galaxy/scripts/galaxy.interactive_environments.js
@@ -15,9 +15,7 @@ export function append_notebook(url) {
 
 export function clear_main_area() {
     $("#spinner").remove();
-    $("#main")
-        .children()
-        .remove();
+    $("#main").children().remove();
 }
 
 export function display_spinner() {
@@ -44,7 +42,7 @@ export function make_spin_state(
         sleep_max: typeof sleep_max !== "undefined" ? sleep_max : 8000,
         sleep_step: typeof sleep_step !== "undefined" ? sleep_step : 100,
         log_attempts: typeof log_attempts !== "undefined" ? log_attempts : true,
-        count: 0
+        count: 0,
     };
 }
 
@@ -58,7 +56,7 @@ export function spin_error(console_msg, user_msg, clear) {
             closeButton: true,
             timeOut: 0,
             extendedTimeOut: 0,
-            tapToDismiss: false
+            tapToDismiss: false,
         });
     }
 }
@@ -70,9 +68,9 @@ function spin_again(spin_state) {
     }
     if (spin_state.log_attempts) {
         console.log(
-            `${spin_state.type} request ${spin_state.count} request timeout ${
-                spin_state.ajax_timeout
-            }ms sleeping ${spin_state.sleep / 1000}s`
+            `${spin_state.type} request ${spin_state.count} request timeout ${spin_state.ajax_timeout}ms sleeping ${
+                spin_state.sleep / 1000
+            }s`
         );
     }
     window.setTimeout(spin_state.spinner, spin_state.sleep);
@@ -88,17 +86,17 @@ export function spin(url, bool_response, success_callback, timeout_callback, err
         var ajax_params = {
             url: url,
             xhrFields: {
-                withCredentials: true
+                withCredentials: true,
             },
             type: "GET",
             timeout: spin_state.ajax_timeout,
-            success: function(data, status, jqxhr) {
+            success: function (data, status, jqxhr) {
                 if (!success_callback(data, status, jqxhr)) {
                     spin_state.count++;
                     spin_again(spin_state);
                 }
             },
-            error: function(jqxhr, status, error) {
+            error: function (jqxhr, status, error) {
                 if (status == "timeout") {
                     if (spin_state.ajax_timeout < spin_state.ajax_timeout_max) {
                         spin_state.ajax_timeout += spin_state.ajax_timeout_step;
@@ -109,7 +107,7 @@ export function spin(url, bool_response, success_callback, timeout_callback, err
                     spin_state.count++;
                     if (!error_callback(jqxhr, status, error)) spin_again(spin_state);
                 }
-            }
+            },
         };
         if (bool_response) ajax_params.dataType = "json";
         $.ajax(ajax_params);
@@ -134,11 +132,11 @@ function spin_until(url, bool_response, messages, success_callback, spin_state)
                 closeButton: true,
                 timeOut: 0,
                 extendedTimeOut: 0,
-                tapToDismiss: false
+                tapToDismiss: false,
             });
         }
     };
-    var wrapped_success = data => {
+    var wrapped_success = (data) => {
         if (!bool_response || (bool_response && data == true)) {
             console.log(messages.success);
             clear_main_area();
@@ -159,7 +157,7 @@ function spin_until(url, bool_response, messages, success_callback, spin_state)
                 closeButton: true,
                 timeOut: 0,
                 extendedTimeOut: 0,
-                tapToDismiss: false
+                tapToDismiss: false,
             });
         }
         return false; // keep spinning
@@ -181,7 +179,7 @@ export function test_ie_availability(url, success_callback) {
         wait_warn:
             "It is taking an usually long time to connect to the interactive environment. Attempts will continue but you may want to report this condition to a Galaxy administrator if it does not succeed soon.",
         error:
-            "An error was encountered while attempting to connect to the interactive environment, contact your administrator."
+            "An error was encountered while attempting to connect to the interactive environment, contact your administrator.",
     };
     var spin_state = make_spin_state("IE availability");
     spin_until(url, false, messages, success_callback, spin_state);
@@ -204,7 +202,7 @@ export function load_when_ready(url, success_callback) {
         wait_warn:
             "It is taking an usually long time to start a container. Attempts will continue but you may want to report this condition to a Galaxy administrator if it does not succeed soon.",
         error:
-            "Galaxy encountered an error while attempting to determine the readiness of this interactive environment's container, contact a Galaxy administrator."
+            "Galaxy encountered an error while attempting to determine the readiness of this interactive environment's container, contact a Galaxy administrator.",
     };
     var spin_state = make_spin_state("IE container readiness");
     spin_until(url, true, messages, success_callback, spin_state);
@@ -217,18 +215,18 @@ export function load_when_ready(url, success_callback) {
  */
 export function keepAlive(notebookAccessURL) {
     var request_count = 0;
-    var interval = window.setInterval(function() {
+    var interval = window.setInterval(function () {
         $.ajax({
             url: notebookAccessURL,
             xhrFields: {
-                withCredentials: true
+                withCredentials: true,
             },
             type: "GET",
             timeout: 500,
-            success: function() {
+            success: function () {
                 console.log("Connected to IE, returning");
             },
-            error: function(jqxhr, status, error) {
+            error: function (jqxhr, status, error) {
                 request_count++;
                 console.log("Request " + request_count);
                 if (request_count > 30) {
@@ -237,10 +235,10 @@ export function keepAlive(notebookAccessURL) {
                     Toast.error("Could not connect to IE, contact your administrator", "Error", {
                         closeButton: true,
                         timeOut: 20000,
-                        tapToDismiss: false
+                        tapToDismiss: false,
                     });
                 }
-            }
+            },
         });
     }, 10000);
 }
@@ -254,5 +252,5 @@ export default {
     spin,
     test_ie_availability,
     load_when_ready,
-    keepAlive
+    keepAlive,
 };
diff --git a/client/galaxy/scripts/galaxy.library.js b/client/galaxy/scripts/galaxy.library.js
index d1d9a9672b71..39305fa5d576 100644
--- a/client/galaxy/scripts/galaxy.library.js
+++ b/client/galaxy/scripts/galaxy.library.js
@@ -24,12 +24,12 @@ import mod_library_folder_view from "mvc/library/library-folder-view";
  * and sends users to proper pieces of the application.
  */
 var LibraryRouter = Backbone.Router.extend({
-    initialize: function() {
+    initialize: function () {
         this.routesHit = 0;
         // keep count of number of routes handled by the application
         Backbone.history.on(
             "route",
-            function() {
+            function () {
                 this.routesHit++;
             },
             this
@@ -49,7 +49,7 @@ var LibraryRouter = Backbone.Router.extend({
         "folders/:folder_id/datasets/:dataset_id/permissions": "dataset_permissions",
         "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id": "dataset_version",
         "folders/:folder_id/download/:format": "download",
-        "folders/:folder_id/import/:source": "import_datasets"
+        "folders/:folder_id/import/:source": "import_datasets",
     },
 
     /**
@@ -58,7 +58,7 @@ var LibraryRouter = Backbone.Router.extend({
      * Use replaceState if available so the navigation doesn't create an
      * extra history entry
      */
-    back: function() {
+    back: function () {
         if (this.routesHit > 1) {
             window.history.back();
         } else {
@@ -69,7 +69,7 @@ var LibraryRouter = Backbone.Router.extend({
     /**
      * Track every route change as a page view in Google Analytics.
      */
-    trackPageview: function() {
+    trackPageview: function () {
         var url = Backbone.history.getFragment();
         //prepend slash
         if (!/^\//.test(url) && url != "") {
@@ -78,7 +78,7 @@ var LibraryRouter = Backbone.Router.extend({
         if (typeof ga !== "undefined") {
             ga("send", "pageview", `${getAppRoot()}library/list${url}`);
         }
-    }
+    },
 });
 
 // ============================================================================
@@ -90,8 +90,8 @@ var LibraryPrefs = mod_baseMVC.SessionStorageModel.extend({
         sort_order: "asc",
         sort_by: "name",
         library_page_size: 20,
-        folder_page_size: 15
-    }
+        folder_page_size: 15,
+    },
 });
 
 // ============================================================================
@@ -108,7 +108,7 @@ var GalaxyLibrary = Backbone.View.extend({
     folderListView: null,
     datasetView: null,
 
-    initialize: function() {
+    initialize: function () {
         // This should go upstream in the js app once available
         const Galaxy = getGalaxyInstance();
         if (Galaxy.config.ga_code) {
@@ -116,7 +116,7 @@ var GalaxyLibrary = Backbone.View.extend({
                 i["GoogleAnalyticsObject"] = r;
                 (i[r] =
                     i[r] ||
-                    function() {
+                    function () {
                         (i[r].q = i[r].q || []).push(arguments);
                     }),
                     (i[r].l = 1 * new Date());
@@ -143,18 +143,18 @@ var GalaxyLibrary = Backbone.View.extend({
             Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView();
         });
 
-        this.library_router.on("route:libraries_page", show_page => {
+        this.library_router.on("route:libraries_page", (show_page) => {
             if (Galaxy.libraries.libraryToolbarView === null) {
                 Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView();
                 Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView({ show_page: show_page });
             } else {
                 Galaxy.libraries.libraryListView.render({
-                    show_page: show_page
+                    show_page: show_page,
                 });
             }
         });
 
-        this.library_router.on("route:folder_content", id => {
+        this.library_router.on("route:folder_content", (id) => {
             if (Galaxy.libraries.folderToolbarView) {
                 Galaxy.libraries.folderToolbarView.$el.unbind("click");
             }
@@ -167,12 +167,12 @@ var GalaxyLibrary = Backbone.View.extend({
                 Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({ id: id });
                 Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({
                     id: id,
-                    show_page: show_page
+                    show_page: show_page,
                 });
             } else {
                 Galaxy.libraries.folderListView.render({
                     id: id,
-                    show_page: parseInt(show_page)
+                    show_page: parseInt(show_page),
                 });
             }
         });
@@ -194,7 +194,7 @@ var GalaxyLibrary = Backbone.View.extend({
             Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({
                 id: dataset_id,
                 show_version: false,
-                show_permissions: false
+                show_permissions: false,
             });
         });
 
@@ -205,7 +205,7 @@ var GalaxyLibrary = Backbone.View.extend({
             Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({
                 id: dataset_id,
                 ldda_id: ldda_id,
-                show_version: true
+                show_version: true,
             });
         });
 
@@ -215,48 +215,48 @@ var GalaxyLibrary = Backbone.View.extend({
             }
             Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({
                 id: dataset_id,
-                show_permissions: true
+                show_permissions: true,
             });
         });
 
-        this.library_router.on("route:library_permissions", library_id => {
+        this.library_router.on("route:library_permissions", (library_id) => {
             if (Galaxy.libraries.libraryView) {
                 Galaxy.libraries.libraryView.$el.unbind("click");
             }
             Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({
                 id: library_id,
-                show_permissions: true
+                show_permissions: true,
             });
         });
 
-        this.library_router.on("route:folder_permissions", folder_id => {
+        this.library_router.on("route:folder_permissions", (folder_id) => {
             if (Galaxy.libraries.folderView) {
                 Galaxy.libraries.folderView.$el.unbind("click");
             }
             Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({
                 id: folder_id,
-                show_permissions: true
+                show_permissions: true,
             });
         });
 
         this.library_router.on("route:import_datasets", (folder_id, source) => {
             if (Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView) {
                 Galaxy.libraries.folderToolbarView.showImportModal({
-                    source: source
+                    source: source,
                 });
             } else {
                 Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({ id: folder_id });
                 Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({ id: folder_id });
                 Galaxy.libraries.folderToolbarView.showImportModal({
-                    source: source
+                    source: source,
                 });
             }
         });
 
         Backbone.history.start({ pushState: false });
-    }
+    },
 });
 
 export default {
-    GalaxyApp: GalaxyLibrary
+    GalaxyApp: GalaxyLibrary,
 };
diff --git a/client/galaxy/scripts/galaxy.pages.js b/client/galaxy/scripts/galaxy.pages.js
index 8ab624c80cb3..2ed3bd3289c6 100644
--- a/client/galaxy/scripts/galaxy.pages.js
+++ b/client/galaxy/scripts/galaxy.pages.js
@@ -9,7 +9,7 @@ export default function pagesEditorOnload() {
     const pageId = $("#page-editor-content").attr("page_id");
     axios
         .get(`${getAppRoot()}api/pages/${pageId}`)
-        .then(response => {
+        .then((response) => {
             const data = response.data;
             const pageEditorInstance = Vue.extend(PageEditor);
             new pageEditorInstance({
@@ -18,12 +18,12 @@ export default function pagesEditorOnload() {
                     pageId: pageId,
                     content: data.content,
                     contentFormat: data.content_format,
-                    title: data.title
+                    title: data.title,
                 },
-                el: "#page-editor-content"
+                el: "#page-editor-content",
             });
         })
-        .catch(e => {
+        .catch((e) => {
             const response = e.response;
             if (typeof response.responseJSON !== "undefined") {
                 Toast.error(response.responseJSON.err_msg);
diff --git a/client/galaxy/scripts/i18n.js b/client/galaxy/scripts/i18n.js
index a4a4a3c283c6..b6d9b68b6cfd 100644
--- a/client/galaxy/scripts/i18n.js
+++ b/client/galaxy/scripts/i18n.js
@@ -33,7 +33,7 @@
  * locale pieces into each other, then finally sets the context.defined value
  * for the nls/fr-fr/colors bundle to be that mixed in locale.
  */
-(function() {
+(function () {
     "use strict";
 
     //regexp for reconstructing the master bundle name from parts of the regexp match
@@ -87,7 +87,7 @@
         }
     }
 
-    define(["module"], function(module) {
+    define(["module"], function (module) {
         var masterConfig = module.config ? module.config() : {};
 
         return {
@@ -95,7 +95,7 @@
             /**
              * Called when a dependency needs to be loaded.
              */
-            load: function(name, req, onLoad, config) {
+            load: function (name, req, onLoad, config) {
                 config = config || {};
 
                 if (config.locale) {
@@ -151,12 +151,12 @@
                         addIfExists(req, current, toLoad, prefix, suffix);
                     }
 
-                    req(toLoad, function() {
+                    req(toLoad, function () {
                         onLoad();
                     });
                 } else {
                     //First, fetch the master bundle, it knows what locales are available.
-                    req([masterName], function(master) {
+                    req([masterName], function (master) {
                         //Figure out the best fit
                         var needed = [];
                         var part;
@@ -170,7 +170,7 @@
                         }
 
                         //Load all the parts missing.
-                        req(toLoad, function() {
+                        req(toLoad, function () {
                             var i;
                             var partBundle;
                             var part;
@@ -188,7 +188,7 @@
                         });
                     });
                 }
-            }
+            },
         };
     });
 })();
diff --git a/client/galaxy/scripts/layout/communication-server-view.js b/client/galaxy/scripts/layout/communication-server-view.js
index d71930ebb79b..830fc1dd73c8 100644
--- a/client/galaxy/scripts/layout/communication-server-view.js
+++ b/client/galaxy/scripts/layout/communication-server-view.js
@@ -7,12 +7,12 @@ import Modal from "mvc/ui/ui-modal";
 import { getGalaxyInstance } from "app";
 
 export const CommunicationServerView = Backbone.View.extend({
-    initialize: function() {
+    initialize: function () {
         this.modal = null;
     },
 
     /** makes bootstrap modal and iframe inside it */
-    makeModalIframe: function(e) {
+    makeModalIframe: function (e) {
         const Galaxy = getGalaxyInstance();
         // make modal
         const host = Galaxy.config.communication_server_host;
@@ -50,7 +50,7 @@ export const CommunicationServerView = Backbone.View.extend({
             width: frame_width,
             closing_events: true,
             title_separator: false,
-            cls: class_names
+            cls: class_names,
         });
 
         // shows modal
@@ -64,25 +64,21 @@ export const CommunicationServerView = Backbone.View.extend({
         $el_chat_modal_header.removeAttr("min-height padding border");
         $el_chat_modal_header.append(header_template);
         // click event of the close button for chat
-        $(".close-modal").click(e => {
+        $(".close-modal").click((e) => {
             $(".chat-modal").css("display", "none");
         });
         // click event of expand and compress icon
-        $(".expand-compress-modal").click(e => {
+        $(".expand-compress-modal").click((e) => {
             if ($(".expand-compress-modal").hasClass("fa-expand")) {
                 $(".chat-modal .modal-dialog").width("1000px");
                 $(".chat-modal .modal-body").height("575px");
-                $(".expand-compress-modal")
-                    .removeClass("fa-expand")
-                    .addClass("fa-compress");
+                $(".expand-compress-modal").removeClass("fa-expand").addClass("fa-compress");
                 $(".expand-compress-modal").attr("title", "Minimize");
                 $(".expand-compress-modal").css("margin-left", "96.2%");
             } else {
                 $(".chat-modal .modal-dialog").width(`${frame_width}px`);
                 $(".chat-modal .modal-body").height(`${frame_height}px`);
-                $(".expand-compress-modal")
-                    .removeClass("fa-compress")
-                    .addClass("fa-expand");
+                $(".expand-compress-modal").removeClass("fa-compress").addClass("fa-expand");
                 $(".expand-compress-modal").attr("title", "Maximize");
                 $(".expand-compress-modal").css("margin-left", "93.2%");
             }
@@ -91,13 +87,13 @@ export const CommunicationServerView = Backbone.View.extend({
     },
 
     /**renders the chat icon as a nav item*/
-    render: function() {
+    render: function () {
         return {
             id: "show-chat-online",
             icon: "fa-comment-o",
             tooltip: _l("Chat online"),
             visible: false,
-            onclick: this.makeModalIframe
+            onclick: this.makeModalIframe,
         };
-    }
+    },
 });
diff --git a/client/galaxy/scripts/layout/masthead.js b/client/galaxy/scripts/layout/masthead.js
index fc86c27d0e89..d5eb3816c09e 100644
--- a/client/galaxy/scripts/layout/masthead.js
+++ b/client/galaxy/scripts/layout/masthead.js
@@ -7,7 +7,7 @@ import { getGalaxyInstance } from "app";
 
 /** Masthead **/
 const View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         const Galaxy = getGalaxyInstance();
 
         const self = this;
@@ -22,14 +22,14 @@ const View = Backbone.View.extend({
         // build tabs
         this.collection = new Menu.Collection();
         this.collection
-            .on("add", model => {
+            .on("add", (model) => {
                 self.$navbarTabs.append(new Menu.Tab({ model: model }).render().$el);
             })
             .on("reset", () => {
                 self.$navbarTabs.empty();
             })
-            .on("dispatch", callback => {
-                self.collection.each(m => {
+            .on("dispatch", (callback) => {
+                self.collection.each((m) => {
                     callback(m);
                 });
             })
@@ -40,27 +40,23 @@ const View = Backbone.View.extend({
 
         // scratchbook
         Galaxy.frame = this.frame = new Scratchbook({
-            collection: this.collection
+            collection: this.collection,
         });
 
         // set up the quota meter (And fetch the current user data from trans)
         // add quota meter to masthead
         Galaxy.quotaMeter = this.quotaMeter = new QuotaMeter.UserQuotaMeter({
             model: Galaxy.user,
-            el: this.$quoteMeter
+            el: this.$quoteMeter,
         });
 
         // loop through beforeunload functions if the user attempts to unload the page
         $(window)
-            .on("click", e => {
+            .on("click", (e) => {
                 const $download_link = $(e.target).closest("a[download]");
                 if ($download_link.length == 1) {
                     if ($("iframe[id=download]").length === 0) {
-                        $("body").append(
-                            $("<iframe/>")
-                                .attr("id", "download")
-                                .hide()
-                        );
+                        $("body").append($("<iframe/>").attr("id", "download").hide());
                     }
                     $("iframe[id=download]").attr("src", $download_link.attr("href"));
                     e.preventDefault();
@@ -68,7 +64,7 @@ const View = Backbone.View.extend({
             })
             .on("beforeunload", () => {
                 let text = "";
-                self.collection.each(model => {
+                self.collection.each((model) => {
                     const q = model.get("onbeforeunload") && model.get("onbeforeunload")();
                     if (q) {
                         text += `${q} `;
@@ -80,7 +76,7 @@ const View = Backbone.View.extend({
             });
     },
 
-    render: function() {
+    render: function () {
         let brand = this.options.display_galaxy_brand ? "Galaxy " : "";
         if (this.options.brand) {
             brand += this.options.brand;
@@ -92,14 +88,14 @@ const View = Backbone.View.extend({
         return this;
     },
 
-    highlight: function(id) {
-        this.collection.forEach(function(model) {
+    highlight: function (id) {
+        this.collection.forEach(function (model) {
             model.set("active", model.id == id);
         });
     },
 
     /** body template */
-    _template: function() {
+    _template: function () {
         return `
             <nav id="masthead" class="navbar navbar-expand justify-content-center navbar-dark" role="navigation" aria-label="Main">
                 <a class="navbar-brand" aria-label="homepage">
@@ -109,9 +105,9 @@ const View = Backbone.View.extend({
                 <ul class="navbar-nav"/>
                 <div class="quota-meter-container"/>
             </nav>`;
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/layout/menu.js b/client/galaxy/scripts/layout/menu.js
index 9cd4fd36ecf2..bfa1bbfa7af7 100644
--- a/client/galaxy/scripts/layout/menu.js
+++ b/client/galaxy/scripts/layout/menu.js
@@ -27,7 +27,7 @@ function logoutClick() {
                 return {};
             }
         })
-        .then(response => {
+        .then((response) => {
             if (response.data && response.data.redirect_uri) {
                 window.top.location.href = response.data.redirect_uri;
             } else {
@@ -40,10 +40,10 @@ const Collection = Backbone.Collection.extend({
     model: Backbone.Model.extend({
         defaults: {
             visible: true,
-            target: "_parent"
-        }
+            target: "_parent",
+        },
     }),
-    fetch: function(options) {
+    fetch: function (options) {
         options = options || {};
         this.reset();
 
@@ -62,7 +62,7 @@ const Collection = Backbone.Collection.extend({
             id: "analysis",
             title: _l("Analyze Data"),
             url: "",
-            tooltip: _l("Analysis home view")
+            tooltip: _l("Analysis home view"),
         });
 
         //
@@ -74,7 +74,7 @@ const Collection = Backbone.Collection.extend({
             tooltip: _l("Chain tools into workflows"),
             disabled: !Galaxy.user.id,
             url: "workflows/list",
-            target: "__use_router__"
+            target: "__use_router__",
         });
 
         //
@@ -91,14 +91,14 @@ const Collection = Backbone.Collection.extend({
                     {
                         title: _l("Create Visualization"),
                         url: "visualizations",
-                        target: "__use_router__"
+                        target: "__use_router__",
                     },
                     {
                         title: _l("Interactive Environments"),
                         url: "visualization/gie_list",
-                        target: "galaxy_main"
-                    }
-                ]
+                        target: "galaxy_main",
+                    },
+                ],
             });
         }
 
@@ -113,29 +113,29 @@ const Collection = Backbone.Collection.extend({
             menu: [
                 {
                     title: _l("Data Libraries"),
-                    url: "library/list"
+                    url: "library/list",
                 },
                 {
                     title: _l("Histories"),
                     url: "histories/list_published",
-                    target: "__use_router__"
+                    target: "__use_router__",
                 },
                 {
                     title: _l("Workflows"),
                     url: "workflows/list_published",
-                    target: "__use_router__"
+                    target: "__use_router__",
                 },
                 {
                     title: _l("Visualizations"),
                     url: "visualizations/list_published",
-                    target: "__use_router__"
+                    target: "__use_router__",
                 },
                 {
                     title: _l("Pages"),
                     url: "pages/list_published",
-                    target: "__use_router__"
-                }
-            ]
+                    target: "__use_router__",
+                },
+            ],
         });
 
         //
@@ -143,9 +143,9 @@ const Collection = Backbone.Collection.extend({
         //
         Webhooks.load({
             type: "masthead",
-            callback: function(webhooks) {
+            callback: function (webhooks) {
                 $(document).ready(() => {
-                    webhooks.each(model => {
+                    webhooks.each((model) => {
                         const webhook = model.toJSON();
                         if (webhook.activate) {
                             const obj = {
@@ -154,7 +154,7 @@ const Collection = Backbone.Collection.extend({
                                 url: webhook.config.url,
                                 tooltip: webhook.config.tooltip,
                                 /*jslint evil: true */
-                                onclick: webhook.config.function && new Function(webhook.config.function)
+                                onclick: webhook.config.function && new Function(webhook.config.function),
                             };
 
                             // Galaxy.page is undefined for data libraries, workflows pages
@@ -170,7 +170,7 @@ const Collection = Backbone.Collection.extend({
                         }
                     });
                 });
-            }
+            },
         });
 
         //
@@ -182,7 +182,7 @@ const Collection = Backbone.Collection.extend({
                 title: _l("Admin"),
                 url: "admin",
                 tooltip: _l("Administer this Galaxy"),
-                cls: "admin-only"
+                cls: "admin-only",
             });
         }
 
@@ -198,51 +198,51 @@ const Collection = Backbone.Collection.extend({
                 {
                     title: _l("Support"),
                     url: options.support_url,
-                    target: "_blank"
+                    target: "_blank",
                 },
                 {
                     title: _l("Search"),
                     url: options.search_url,
-                    target: "_blank"
+                    target: "_blank",
                 },
                 {
                     title: _l("Mailing Lists"),
                     url: options.mailing_lists,
-                    target: "_blank"
+                    target: "_blank",
                 },
                 {
                     title: _l("Videos"),
                     url: options.screencasts_url,
-                    target: "_blank"
+                    target: "_blank",
                 },
                 {
                     title: _l("Wiki"),
                     url: options.wiki_url,
-                    target: "_blank"
+                    target: "_blank",
                 },
                 {
                     title: _l("How to Cite Galaxy"),
                     url: options.citation_url,
-                    target: "_blank"
+                    target: "_blank",
                 },
                 {
                     title: _l("Interactive Tours"),
-                    url: "tours"
-                }
-            ]
+                    url: "tours",
+                },
+            ],
         };
         if (options.terms_url) {
             helpTab.menu.push({
                 title: _l("Terms and Conditions"),
                 url: options.terms_url,
-                target: "_blank"
+                target: "_blank",
             });
         }
         if (options.helpsite_url) {
             helpTab.menu.unshift({
                 title: _l("Galaxy Help"),
                 url: options.helpsite_url,
-                target: "_blank"
+                target: "_blank",
             });
         }
         this.add(helpTab);
@@ -258,7 +258,7 @@ const Collection = Backbone.Collection.extend({
                     title: _l("Login or Register"),
                     cls: "loggedout-only",
                     url: "login",
-                    tooltip: _l("Log in or register a new account")
+                    tooltip: _l("Log in or register a new account"),
                 };
             } else {
                 userTab = {
@@ -267,7 +267,7 @@ const Collection = Backbone.Collection.extend({
                     cls: "loggedout-only",
                     tooltip: _l("Login"),
                     url: "login",
-                    noscratchbook: true
+                    noscratchbook: true,
                 };
             }
         } else {
@@ -280,55 +280,55 @@ const Collection = Backbone.Collection.extend({
                 menu: [
                     {
                         title: `${_l("Logged in as")} ${Galaxy.user.get("email")}`,
-                        class: "dropdown-item disabled"
+                        class: "dropdown-item disabled",
                     },
                     {
                         title: _l("Preferences"),
                         url: "user",
-                        target: "__use_router__"
+                        target: "__use_router__",
                     },
                     {
                         title: _l("Custom Builds"),
                         url: "custom_builds",
-                        target: "__use_router__"
+                        target: "__use_router__",
                     },
                     {
                         title: _l("Logout"),
                         divider: true,
-                        onclick: logoutClick
+                        onclick: logoutClick,
                     },
                     {
                         title: _l("Datasets"),
                         url: "datasets/list",
-                        target: "__use_router__"
+                        target: "__use_router__",
                     },
                     {
                         title: _l("Histories"),
                         url: "histories/list",
-                        target: "__use_router__"
+                        target: "__use_router__",
                     },
                     {
                         title: _l("Histories shared with me"),
                         url: "histories/list_shared",
-                        target: "__use_router__"
+                        target: "__use_router__",
                     },
                     {
                         title: _l("Pages"),
                         url: "pages/list",
-                        target: "__use_router__"
+                        target: "__use_router__",
                     },
                     {
                         title: _l("Workflow Invocations"),
                         url: "workflows/invocations",
-                        target: "__use_router__"
-                    }
-                ]
+                        target: "__use_router__",
+                    },
+                ],
             };
             if (Galaxy.config.visualizations_visible) {
                 userTab.menu.push({
                     title: _l("Visualizations"),
                     url: "visualizations/list",
-                    target: "__use_router__"
+                    target: "__use_router__",
                 });
             }
             if (Galaxy.config.interactivetools_enable) {
@@ -336,18 +336,18 @@ const Collection = Backbone.Collection.extend({
                 userTab.menu.push({
                     title: _l("Active InteractiveTools"),
                     url: "interactivetool_entry_points/list",
-                    target: "__use_router__"
+                    target: "__use_router__",
                 });
             }
         }
         this.add(userTab);
         return new $.Deferred().resolve().promise();
-    }
+    },
 });
 
 /** Masthead tab **/
 const Tab = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model = options.model;
         this.setElement(this._template());
         this.$link = this.$(".nav-link");
@@ -357,10 +357,10 @@ const Tab = Backbone.View.extend({
     },
 
     events: {
-        "click .nav-link": "_toggleClick"
+        "click .nav-link": "_toggleClick",
     },
 
-    render: function() {
+    render: function () {
         $(".tooltip").remove();
         this.$el
             .removeClass()
@@ -369,7 +369,7 @@ const Tab = Backbone.View.extend({
             .addClass(this.model.get("menu") && "dropdown")
             .attr("id", this.model.id)
             .css({
-                visibility: (this.model.get("visible") && "visible") || "hidden"
+                visibility: (this.model.get("visible") && "visible") || "hidden",
             });
         this.model.set("url", this._formatUrl(this.model.get("url")));
         this.$note
@@ -378,7 +378,7 @@ const Tab = Backbone.View.extend({
             .addClass("nav-note")
             .addClass(this.model.get("note_cls"))
             .css({
-                display: (this.model.get("show_note") && "block") || "none"
+                display: (this.model.get("show_note") && "block") || "none",
             });
         this.$link
             .html(this.model.get("title") || "")
@@ -412,7 +412,7 @@ const Tab = Backbone.View.extend({
         }
         this.$menu.empty().removeClass();
         if (this.model.get("menu")) {
-            _.each(this.model.get("menu"), menuItem => {
+            _.each(this.model.get("menu"), (menuItem) => {
                 this.$menu.append(this._buildMenuItem(menuItem));
                 if (menuItem.divider) {
                     this.$menu.append($("<div/>").addClass("dropdown-divider"));
@@ -427,12 +427,12 @@ const Tab = Backbone.View.extend({
     },
 
     /** Add new menu item */
-    _buildMenuItem: function(options) {
+    _buildMenuItem: function (options) {
         options = _.defaults(options || {}, {
             title: "",
             url: "",
             target: "_parent",
-            noscratchbook: false
+            noscratchbook: false,
         });
         options.url = this._formatUrl(options.url);
         return $("<a/>")
@@ -442,7 +442,7 @@ const Tab = Backbone.View.extend({
             .attr("class", options.class)
             .attr("role", "menuitem")
             .html(options.title)
-            .on("click", e => {
+            .on("click", (e) => {
                 e.preventDefault();
                 this.model.set("show_menu", false);
                 if (options.onclick) {
@@ -462,7 +462,7 @@ const Tab = Backbone.View.extend({
             });
     },
 
-    buildLink: function(label, url) {
+    buildLink: function (label, url) {
         return $("<div/>")
             .append(
                 $("<a/>")
@@ -473,11 +473,11 @@ const Tab = Backbone.View.extend({
     },
 
     /** Handle click event */
-    _toggleClick: function(e) {
+    _toggleClick: function (e) {
         const model = this.model;
         e.preventDefault();
         $(".tooltip").hide();
-        model.trigger("dispatch", m => {
+        model.trigger("dispatch", (m) => {
             if (model.id !== m.id && m.get("menu")) {
                 m.set("show_menu", false);
             }
@@ -505,7 +505,7 @@ const Tab = Backbone.View.extend({
                 .popover({
                     html: true,
                     placement: "bottom",
-                    content: `Please ${this.buildLink("login or register", "login")} to use this feature.`
+                    content: `Please ${this.buildLink("login or register", "login")} to use this feature.`,
                 })
                 .popover("show");
             window.setTimeout(() => {
@@ -515,7 +515,7 @@ const Tab = Backbone.View.extend({
     },
 
     /** Url formatting */
-    _formatUrl: function(url) {
+    _formatUrl: function (url) {
         return typeof url == "string" &&
             url.indexOf("mailto:") === -1 &&
             url.indexOf("//") === -1 &&
@@ -525,17 +525,17 @@ const Tab = Backbone.View.extend({
     },
 
     /** body tempate */
-    _template: function() {
+    _template: function () {
         return `
             <li class="nav-item">
                 <a class="nav-link"/>
                 <div class="nav-note"/>
                 <div class="dropdown-menu"/>
             </li>`;
-    }
+    },
 });
 
 export default {
     Collection: Collection,
-    Tab: Tab
+    Tab: Tab,
 };
diff --git a/client/galaxy/scripts/layout/modal.js b/client/galaxy/scripts/layout/modal.js
index dae640ea60ca..01a4b2f8b3af 100644
--- a/client/galaxy/scripts/layout/modal.js
+++ b/client/galaxy/scripts/layout/modal.js
@@ -1,7 +1,7 @@
 import $ from "jquery";
 
 // Modal dialog boxes
-export const Modal = function(options) {
+export const Modal = function (options) {
     this.$overlay = options.overlay;
     this.$dialog = options.dialog;
     this.$header = this.$dialog.find(".modal-header");
@@ -13,7 +13,7 @@ export const Modal = function(options) {
 };
 
 $.extend(Modal.prototype, {
-    setContent: function(options) {
+    setContent: function (options) {
         this.$header.hide();
         // Title
         if (options.title) {
@@ -31,26 +31,14 @@ $.extend(Modal.prototype, {
         const $buttons = this.$footer.find(".buttons").html("");
         if (options.buttons) {
             $.each(options.buttons, (name, value) => {
-                $buttons
-                    .append(
-                        $("<button></button> ")
-                            .text(name)
-                            .click(value)
-                    )
-                    .append(" ");
+                $buttons.append($("<button></button> ").text(name).click(value)).append(" ");
             });
             this.$footer.show();
         }
         const $extraButtons = this.$footer.find(".extra_buttons").html("");
         if (options.extra_buttons) {
             $.each(options.extra_buttons, (name, value) => {
-                $extraButtons
-                    .append(
-                        $("<button></button>")
-                            .text(name)
-                            .click(value)
-                    )
-                    .append(" ");
+                $extraButtons.append($("<button></button>").text(name).click(value)).append(" ");
             });
             this.$footer.show();
         }
@@ -63,7 +51,7 @@ $.extend(Modal.prototype, {
         }
         this.$body.html(body);
     },
-    show: function(options, callback) {
+    show: function (options, callback) {
         if (options.backdrop) {
             this.$backdrop.addClass("in");
         } else {
@@ -82,7 +70,7 @@ $.extend(Modal.prototype, {
             callback();
         }
     },
-    hide: function() {
+    hide: function () {
         const modal = this;
         modal.$dialog.fadeOut(() => {
             modal.$overlay.hide();
@@ -91,7 +79,7 @@ $.extend(Modal.prototype, {
             // Clear min-width to allow for modal to take size of new body.
             modal.$body.css("min-width", undefined);
         });
-    }
+    },
 });
 
 let modal;
@@ -101,7 +89,7 @@ $(() => {
     modal = new Modal({
         overlay: $("#top-modal"),
         dialog: $("#top-modal-dialog"),
-        backdrop: $("#top-modal-backdrop")
+        backdrop: $("#top-modal-backdrop"),
     });
 });
 
@@ -115,7 +103,7 @@ export function show_modal(title, body, buttons, extra_buttons, init_fn) {
         title: title,
         body: body,
         buttons: buttons,
-        extra_buttons: extra_buttons
+        extra_buttons: extra_buttons,
     });
     modal.show({ backdrop: true }, init_fn);
 }
@@ -125,7 +113,7 @@ export function show_message(title, body, buttons, extra_buttons, init_fn) {
         title: title,
         body: body,
         buttons: buttons,
-        extra_buttons: extra_buttons
+        extra_buttons: extra_buttons,
     });
     modal.show({ backdrop: false }, init_fn);
 }
@@ -143,7 +131,7 @@ export function show_in_overlay(options) {
         title: "&nbsp;",
         body: $(
             `<div style='margin: -5px;'><iframe style='margin: 0; padding: 0;' src='${options.url}' width='${width}' height='${height}' scrolling='${scroll}' frameborder='0'></iframe></div>`
-        )
+        ),
     });
     modal.show({ backdrop: true });
 }
diff --git a/client/galaxy/scripts/layout/page.js b/client/galaxy/scripts/layout/page.js
index f5954f7c93d4..3078d83c08d5 100644
--- a/client/galaxy/scripts/layout/page.js
+++ b/client/galaxy/scripts/layout/page.js
@@ -13,7 +13,7 @@ const View = Backbone.View.extend({
     className: "full-content",
     _panelids: ["left", "right"],
 
-    initialize: function(options) {
+    initialize: function (options) {
         const self = this;
         this.config = _.defaults(options.config || {}, {
             message_box_visible: false,
@@ -22,7 +22,7 @@ const View = Backbone.View.extend({
             show_inactivity_warning: false,
             inactivity_box_content: "",
             hide_panels: false,
-            hide_masthead: false
+            hide_masthead: false,
         });
 
         // attach global objects, build mastheads
@@ -33,7 +33,7 @@ const View = Backbone.View.extend({
         this.center = new Panel.CenterPanel();
 
         // display helper
-        Galaxy.display = this.display = view => {
+        Galaxy.display = this.display = (view) => {
             if (view.title) {
                 Utils.setWindowTitle(view.title);
                 view.allow_title_display = false;
@@ -69,7 +69,7 @@ const View = Backbone.View.extend({
         // build panels
         this.panels = {};
         if (!this.config.hide_panels) {
-            _.each(this._panelids, panel_id => {
+            _.each(this._panelids, (panel_id) => {
                 const panel_class_name = panel_id.charAt(0).toUpperCase() + panel_id.slice(1);
                 const panel_class = options[panel_class_name];
                 if (panel_class) {
@@ -79,7 +79,7 @@ const View = Backbone.View.extend({
                     self.panels[panel_id] = new Panel.SidePanel({
                         id: panel_id,
                         el: panel_el,
-                        view: panel_instance
+                        view: panel_instance,
                     });
                     if (this.config.hide_masthead) {
                         panel_el.css("top", 0);
@@ -93,12 +93,12 @@ const View = Backbone.View.extend({
         if (this.router) {
             Backbone.history.start({
                 root: getAppRoot(),
-                pushState: true
+                pushState: true,
             });
         }
     },
 
-    render: function() {
+    render: function () {
         // TODO: Remove this line after select2 update
         $(".select2-hidden-accessible").remove();
         if (!this.config.hide_masthead) {
@@ -112,16 +112,12 @@ const View = Backbone.View.extend({
     },
 
     /** Render message box */
-    renderMessageBox: function() {
+    renderMessageBox: function () {
         if (this.config.message_box_visible) {
             const content = this.config.message_box_content || "";
             const level = this.config.message_box_class || "info";
             this.$el.addClass("has-message-box");
-            this.$messagebox
-                .attr("class", `panel-${level}-message`)
-                .html(content)
-                .toggle(!!content)
-                .show();
+            this.$messagebox.attr("class", `panel-${level}-message`).html(content).toggle(!!content).show();
         } else {
             this.$el.removeClass("has-message-box");
             this.$messagebox.hide();
@@ -130,18 +126,14 @@ const View = Backbone.View.extend({
     },
 
     /** Render inactivity warning */
-    renderInactivityBox: function() {
+    renderInactivityBox: function () {
         if (this.config.show_inactivity_warning) {
             const content = this.config.inactivity_box_content || "";
             const verificationLink = $("<a/>")
                 .attr("href", `${getAppRoot()}user/resend_verification`)
                 .text("Resend verification");
             this.$el.addClass("has-inactivity-box");
-            this.$inactivebox
-                .html(`${content} `)
-                .append(verificationLink)
-                .toggle(!!content)
-                .show();
+            this.$inactivebox.html(`${content} `).append(verificationLink).toggle(!!content).show();
         } else {
             this.$el.removeClass("has-inactivity-box");
             this.$inactivebox.hide();
@@ -150,9 +142,9 @@ const View = Backbone.View.extend({
     },
 
     /** Render panels */
-    renderPanels: function() {
+    renderPanels: function () {
         const self = this;
-        _.each(this._panelids, panel_id => {
+        _.each(this._panelids, (panel_id) => {
             const panel = self.panels[panel_id];
             if (panel) {
                 panel.render();
@@ -165,7 +157,7 @@ const View = Backbone.View.extend({
     },
 
     /** body template */
-    _template: function() {
+    _template: function () {
         return [
             `<div id="everything">
                 <div id="background"/>
@@ -178,16 +170,16 @@ const View = Backbone.View.extend({
                     <div id="right" class="unified-panel" />
                 </div>
             </div>
-            <div id="dd-helper" />`
+            <div id="dd-helper" />`,
         ].join("");
     },
 
-    toString: function() {
+    toString: function () {
         return "PageLayoutView";
     },
 
     /** Check if the communication server is online and show the icon otherwise hide the icon */
-    _checkCommunicationServerOnline: function() {
+    _checkCommunicationServerOnline: function () {
         const Galaxy = getGalaxyInstance();
         const host = Galaxy.config.communication_server_host;
         const port = Galaxy.config.communication_server_port;
@@ -197,9 +189,9 @@ const View = Backbone.View.extend({
         if (preferences && ["1", "true"].indexOf(preferences.communication_server) != -1) {
             // See if the configured communication server is available
             $.ajax({
-                url: `${host}:${port}`
+                url: `${host}:${port}`,
             })
-                .success(data => {
+                .success((data) => {
                     // enable communication only when a user is logged in
                     if (Galaxy.user.id !== null) {
                         if ($chat_icon_element.css("visibility") === "hidden") {
@@ -207,14 +199,14 @@ const View = Backbone.View.extend({
                         }
                     }
                 })
-                .error(data => {
+                .error((data) => {
                     // hide the communication icon if the communication server is not available
                     $chat_icon_element.css("visibility", "hidden");
                 });
         } else {
             $chat_icon_element.css("visibility", "hidden");
         }
-    }
+    },
 });
 
 export default { View: View };
diff --git a/client/galaxy/scripts/layout/panel.js b/client/galaxy/scripts/layout/panel.js
index d69c4f215b1a..de1f3dada5fc 100644
--- a/client/galaxy/scripts/layout/panel.js
+++ b/client/galaxy/scripts/layout/panel.js
@@ -8,22 +8,22 @@ const MAX_PANEL_WIDTH = 800;
 
 /** View for left/right panels used by Page view */
 const SidePanel = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.view = options.view;
         this.hidden = false;
         this.saved_size = null;
         this.hiddenByTool = false;
     },
 
-    $center: function() {
+    $center: function () {
         return this.$el.siblings("#center");
     },
 
-    $toggleButton: function() {
+    $toggleButton: function () {
         return this.$(".unified-panel-footer > .panel-collapse");
     },
 
-    render: function() {
+    render: function () {
         const self = this;
         const panel = this.view;
         const components = this.view.model.attributes || {};
@@ -35,7 +35,7 @@ const SidePanel = Backbone.View.extend({
             this.view.mountVueComponent(node);
         } else {
             this.$el.html(this._templatePanel(this.id));
-            _.each(components.buttons, button => {
+            _.each(components.buttons, (button) => {
                 self.$(".panel-header-buttons").append(button.$el);
             });
             this.$el.addClass(components.cls);
@@ -46,12 +46,12 @@ const SidePanel = Backbone.View.extend({
     },
 
     /** panel dom template. id is 'right' or 'left' */
-    _templatePanel: function() {
+    _templatePanel: function () {
         return [this._templateHeader(), this._templateBody(), this._templateFooter()].join("");
     },
 
     /** panel dom template. id is 'right' or 'left' */
-    _templateHeader: function(data) {
+    _templateHeader: function (data) {
         return `<div class="unified-panel-header" unselectable="on">
                     <div class="unified-panel-header-inner">
                         <div class="panel-header-buttons"/>
@@ -62,28 +62,28 @@ const SidePanel = Backbone.View.extend({
     },
 
     /** panel dom template. id is 'right' or 'left' */
-    _templateBody: function(data) {
+    _templateBody: function (data) {
         return '<div class="unified-panel-body"/>';
     },
 
     /** panel dom template. id is 'right' or 'left' */
-    _templateFooter: function(data) {
+    _templateFooter: function (data) {
         return [
             '<div class="unified-panel-footer">',
             '<div class="panel-collapse ',
             _.escape(this.id),
             '"/>',
             '<div class="drag"/>',
-            "</div>"
+            "</div>",
         ].join("");
     },
 
     events: {
         "mousedown .unified-panel-footer > .drag": "_mousedownDragHandler",
-        "click .unified-panel-footer > .panel-collapse": "toggle"
+        "click .unified-panel-footer > .panel-collapse": "toggle",
     },
 
-    _mousedownDragHandler: function(ev) {
+    _mousedownDragHandler: function (ev) {
         const self = this;
         const draggingLeft = this.id === "left";
         // Save the mouse position and width of the element (panel) when the
@@ -105,22 +105,20 @@ const SidePanel = Backbone.View.extend({
         $("#dd-helper")
             .show()
             .on("mousemove", move)
-            .one("mouseup", function(e) {
-                $(this)
-                    .hide()
-                    .off("mousemove", move);
+            .one("mouseup", function (e) {
+                $(this).hide().off("mousemove", move);
             });
     },
 
     // TODO: the following three could be simplified I think
     // if panel is 'right' (this.id), move center right newSize number of pixels
-    resize: function(newSize) {
+    resize: function (newSize) {
         this.$el.css("width", newSize);
         this.$center().css(this.id, newSize);
         return this;
     },
 
-    show: function() {
+    show: function () {
         if (this.hidden && !this.motionQueue) {
             this.motionQueue = 2;
             const animation = {};
@@ -138,7 +136,7 @@ const SidePanel = Backbone.View.extend({
         return this;
     },
 
-    hide: function() {
+    hide: function () {
         if (!this.hidden && !this.motionQueue) {
             this.motionQueue = 2;
             const animation = {};
@@ -154,7 +152,7 @@ const SidePanel = Backbone.View.extend({
         return this;
     },
 
-    toggle: function(ev) {
+    toggle: function (ev) {
         this.hidden ? this.show() : this.hide();
         this.hiddenByTool = false;
         return this;
@@ -163,7 +161,7 @@ const SidePanel = Backbone.View.extend({
     // ..............................................................
     //TODO: only used in message.mako?
     /**   */
-    handle_minwidth_hint: function(hint) {
+    handle_minwidth_hint: function (hint) {
         const space = this.$center().width() - (this.hidden ? this.saved_size : 0);
         if (space < hint) {
             if (!this.hidden) {
@@ -180,7 +178,7 @@ const SidePanel = Backbone.View.extend({
     },
 
     /**   */
-    force_panel: function(op) {
+    force_panel: function (op) {
         if (op == "show") {
             return this.show();
         }
@@ -190,24 +188,24 @@ const SidePanel = Backbone.View.extend({
         return self;
     },
 
-    toString: function() {
+    toString: function () {
         return `SidePanel(${this.id})`;
-    }
+    },
 });
 
 // ----------------------------------------------------------------------------
 // TODO: side should be defined by page - not here
 const LeftPanel = SidePanel.extend({
-    id: "left"
+    id: "left",
 });
 
 const RightPanel = SidePanel.extend({
-    id: "right"
+    id: "right",
 });
 
 /** Center panel with the ability to switch between iframe and view */
 const CenterPanel = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.setElement($(this.template()));
         this.$frame = this.$(".center-frame");
         this.$panel = this.$(".center-panel");
@@ -215,7 +213,7 @@ const CenterPanel = Backbone.View.extend({
     },
 
     /** Display iframe if its target url changes, hide center panel */
-    _iframeChangeHandler: function(ev) {
+    _iframeChangeHandler: function (ev) {
         const iframe = ev.currentTarget;
         const location = iframe.contentWindow && iframe.contentWindow.location;
         const Galaxy = getGalaxyInstance();
@@ -229,7 +227,7 @@ const CenterPanel = Backbone.View.extend({
                     fullpath: location.pathname + location.search + location.hash,
                     pathname: location.pathname,
                     search: location.search,
-                    hash: location.hash
+                    hash: location.hash,
                 });
             }
         } catch (err) {
@@ -238,7 +236,7 @@ const CenterPanel = Backbone.View.extend({
     },
 
     /** Display a view in the center panel, hide iframe */
-    display: function(view) {
+    display: function (view) {
         const Galaxy = getGalaxyInstance();
         let contentWindow = this.$frame[0].contentWindow || {};
         let message;
@@ -263,7 +261,7 @@ const CenterPanel = Backbone.View.extend({
         }
     },
 
-    template: function() {
+    template: function () {
         return (
             '<div class="center-container">' +
             '<iframe id="galaxy_main" name="galaxy_main" frameborder="0" class="center-frame" title="galaxy main frame"/>' +
@@ -272,14 +270,14 @@ const CenterPanel = Backbone.View.extend({
         );
     },
 
-    toString: function() {
+    toString: function () {
         return "CenterPanel";
-    }
+    },
 });
 
 export default {
     SidePanel: SidePanel,
     LeftPanel: LeftPanel,
     RightPanel: RightPanel,
-    CenterPanel: CenterPanel
+    CenterPanel: CenterPanel,
 };
diff --git a/client/galaxy/scripts/layout/router.js b/client/galaxy/scripts/layout/router.js
index 9132d05f9a6d..748ccb249c0d 100644
--- a/client/galaxy/scripts/layout/router.js
+++ b/client/galaxy/scripts/layout/router.js
@@ -8,12 +8,12 @@ import Ui from "mvc/ui/ui-misc";
 const Router = Backbone.Router.extend({
     // TODO: not many client routes at this point - fill and remove from server.
     // since we're at root here, this may be the last to be routed entirely on the client.
-    initialize: function(page, options) {
+    initialize: function (page, options) {
         this.page = page;
         this.options = options;
     },
 
-    executeUseRouter: function(url) {
+    executeUseRouter: function (url) {
         const prefix = getAppRoot();
         if (url.startsWith(prefix)) {
             url = url.replace(prefix, "/");
@@ -22,11 +22,9 @@ const Router = Backbone.Router.extend({
     },
 
     /** helper to push a new navigation state */
-    push: function(url, data) {
+    push: function (url, data) {
         data = data || {};
-        data.__identifer = Math.random()
-            .toString(36)
-            .substr(2);
+        data.__identifer = Math.random().toString(36).substr(2);
         url += url.indexOf("?") == -1 ? "?" : "&";
         const bustParam = $.param(data, true);
         url += bustParam;
@@ -37,7 +35,7 @@ const Router = Backbone.Router.extend({
     },
 
     /** override to parse query string into obj and send to each route */
-    execute: function(callback, args, name) {
+    execute: function (callback, args, name) {
         const Galaxy = getGalaxyInstance();
         Galaxy.debug("router execute:", callback, args, name);
         const queryObj = QUERY_STRING.parse(args.pop());
@@ -51,19 +49,19 @@ const Router = Backbone.Router.extend({
         }
     },
 
-    authenticate: function(args, name) {
+    authenticate: function (args, name) {
         return true;
     },
 
-    access_denied: function() {
+    access_denied: function () {
         this.page.display(
             new Ui.Message({
                 status: "danger",
                 message: "You must be logged in with proper credentials to make this request.",
-                persistent: true
+                persistent: true,
             })
         );
-    }
+    },
 });
 
 export default Router;
diff --git a/client/galaxy/scripts/layout/scratchbook.js b/client/galaxy/scripts/layout/scratchbook.js
index eeb7953ef5d8..ba1d06cc0b6b 100644
--- a/client/galaxy/scripts/layout/scratchbook.js
+++ b/client/galaxy/scripts/layout/scratchbook.js
@@ -11,7 +11,7 @@ import { TracksterUI } from "viz/trackster";
 import _l from "utils/localization";
 
 export default Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         options = options || {};
         this.frames = new Frames.View({ visible: false });
         this.setElement(this.frames.$el);
@@ -25,7 +25,7 @@ export default Backbone.View.extend({
                 this.buttonActive.set({
                     toggle: this.active,
                     show_note: this.active,
-                    note_cls: this.active && "fa fa-check"
+                    note_cls: this.active && "fa fa-check",
                 });
                 if (!this.active) {
                     this.frames.hide();
@@ -35,7 +35,7 @@ export default Backbone.View.extend({
                 if (this.frames.length() > 0) {
                     return `You opened ${this.frames.length()} frame(s) which will be lost.`;
                 }
-            }
+            },
         });
         this.buttonLoad = options.collection.add({
             id: "show-scratchbook",
@@ -43,13 +43,13 @@ export default Backbone.View.extend({
             tooltip: _l("Show/Hide Scratchbook"),
             show_note: true,
             visible: false,
-            onclick: e => {
+            onclick: (e) => {
                 if (this.frames.visible) {
                     this.frames.hide();
                 } else {
                     this.frames.show();
                 }
-            }
+            },
         });
         this.frames
             .on("add remove", () => {
@@ -58,20 +58,20 @@ export default Backbone.View.extend({
                 }
                 this.buttonLoad.set({
                     note: this.frames.length(),
-                    visible: this.frames.length() > 0
+                    visible: this.frames.length() > 0,
                 });
             })
             .on("show hide ", () => {
                 this.buttonLoad.set({
                     toggle: this.frames.visible,
-                    icon: (this.frames.visible && "fa-eye") || "fa-eye-slash"
+                    icon: (this.frames.visible && "fa-eye") || "fa-eye-slash",
                 });
             });
         this.history_cache = {};
     },
 
     /** Add a dataset to the frames */
-    addDataset: function(dataset_id) {
+    addDataset: function (dataset_id) {
         const self = this;
         let current_dataset = null;
         const Galaxy = getGalaxyInstance();
@@ -79,9 +79,9 @@ export default Backbone.View.extend({
             const history_id = Galaxy.currHistoryPanel.collection.historyId;
             this.history_cache[history_id] = {
                 name: Galaxy.currHistoryPanel.model.get("name"),
-                dataset_ids: []
+                dataset_ids: [],
             };
-            Galaxy.currHistoryPanel.collection.each(model => {
+            Galaxy.currHistoryPanel.collection.each((model) => {
                 if (!model.get("deleted") && model.get("visible")) {
                     self.history_cache[history_id].dataset_ids.push(model.get("id"));
                 }
@@ -119,24 +119,24 @@ export default Backbone.View.extend({
                             {
                                 icon: "fa fa-chevron-circle-left",
                                 tooltip: _l("Previous in History"),
-                                onclick: function(frame) {
+                                onclick: function (frame) {
                                     _loadDatasetOffset(current_dataset, -1, frame);
                                 },
-                                disabled: function() {
+                                disabled: function () {
                                     return !_findDataset(current_dataset, -1);
-                                }
+                                },
                             },
                             {
                                 icon: "fa fa-chevron-circle-right",
                                 tooltip: _l("Next in History"),
-                                onclick: function(frame) {
+                                onclick: function (frame) {
                                     _loadDatasetOffset(current_dataset, 1, frame);
                                 },
-                                disabled: function() {
+                                disabled: function () {
                                     return !_findDataset(current_dataset, 1);
-                                }
-                            }
-                        ]
+                                },
+                            },
+                        ],
                     },
                     config
                 )
@@ -144,13 +144,13 @@ export default Backbone.View.extend({
         });
     },
 
-    _loadDataset: function(dataset_id, callback) {
+    _loadDataset: function (dataset_id, callback) {
         const self = this;
         const dataset = new Dataset({ id: dataset_id });
         $.when(dataset.fetch()).then(() => {
             const is_tabular = _.find(
                 ["tabular", "interval"],
-                data_type => dataset.get("data_type").indexOf(data_type) !== -1
+                (data_type) => dataset.get("data_type").indexOf(data_type) !== -1
             );
             let title = dataset.get("name");
             const history_details = self.history_cache[dataset.get("history_id")];
@@ -166,20 +166,20 @@ export default Backbone.View.extend({
                           content: createTabularDatasetChunkedView({
                               model: new TabularDataset(dataset.toJSON()),
                               embedded: true,
-                              height: "100%"
-                          }).$el
+                              height: "100%",
+                          }).$el,
                       }
                     : {
                           title: title,
                           url: `${getAppRoot()}datasets/${dataset_id}/display/?preview=True`,
-                          content: null
+                          content: null,
                       }
             );
         });
     },
 
     /** Add a trackster visualization to the frames. */
-    addTrackster: function(viz_id) {
+    addTrackster: function (viz_id) {
         const self = this;
         const viz = new visualization.Visualization({ id: viz_id });
         $.when(viz.fetch()).then(() => {
@@ -189,7 +189,7 @@ export default Backbone.View.extend({
             const frame_config = {
                 title: viz.get("name"),
                 type: "other",
-                content: function(parent_elt) {
+                content: function (parent_elt) {
                     // Create view config.
                     const view_config = {
                         container: parent_elt,
@@ -197,17 +197,17 @@ export default Backbone.View.extend({
                         id: viz.id,
                         // FIXME: this will not work with custom builds b/c the dbkey needed to be encoded.
                         dbkey: viz.get("dbkey"),
-                        stand_alone: false
+                        stand_alone: false,
                     };
 
                     const latest_revision = viz.get("latest_revision");
                     const drawables = latest_revision.config.view.drawables;
 
                     // Set up datasets in drawables.
-                    _.each(drawables, d => {
+                    _.each(drawables, (d) => {
                         d.dataset = {
                             hda_ldda: d.hda_ldda,
-                            id: d.dataset_id
+                            id: d.dataset_id,
                         };
                     });
                     ui.create_visualization(
@@ -217,14 +217,14 @@ export default Backbone.View.extend({
                         latest_revision.config.bookmarks,
                         false
                     );
-                }
+                },
             };
             self.add(frame_config);
         });
     },
 
     /** Add and display a new frame/window based on options. */
-    add: function(options) {
+    add: function (options) {
         if (options.target == "_blank") {
             window.open(options.url);
         } else if (options.target == "_top" || options.target == "_parent" || options.target == "_self") {
@@ -245,11 +245,11 @@ export default Backbone.View.extend({
     },
 
     /** Url helper */
-    _build_url: function(url, options) {
+    _build_url: function (url, options) {
         if (url) {
             url += url.indexOf("?") == -1 ? "?" : "&";
             url += $.param(options, true);
             return url;
         }
-    }
+    },
 });
diff --git a/client/galaxy/scripts/legacy/grid/grid-model.js b/client/galaxy/scripts/legacy/grid/grid-model.js
index f25a4313abed..57713eac5e13 100644
--- a/client/galaxy/scripts/legacy/grid/grid-model.js
+++ b/client/galaxy/scripts/legacy/grid/grid-model.js
@@ -12,20 +12,20 @@ export default Backbone.Model.extend({
         cur_page: 1,
         num_pages: 1,
         operation: undefined,
-        item_ids: undefined
+        item_ids: undefined,
     },
 
     /**
      * Return true if operation can be done asynchronously.
      */
-    can_async_op: function(op) {
+    can_async_op: function (op) {
         return _.indexOf(this.attributes.async_ops, op) !== -1;
     },
 
     /**
      * Add filtering criterion.
      */
-    add_filter: function(key, value, append) {
+    add_filter: function (key, value, append) {
         // Update URL arg with new condition.
         if (append) {
             // Update or append value.
@@ -61,7 +61,7 @@ export default Backbone.Model.extend({
     /**
      * Remove filtering criterion.
      */
-    remove_filter: function(key, condition) {
+    remove_filter: function (key, condition) {
         var cur_val = this.attributes.filters[key];
         if (cur_val === null || cur_val === undefined) {
             return false;
@@ -82,13 +82,13 @@ export default Backbone.Model.extend({
     /**
      * Returns URL data for obtaining a new grid.
      */
-    get_url_data: function() {
+    get_url_data: function () {
         var url_data = {
             async: this.attributes.async,
             sort: this.attributes.sort_key,
             page: this.attributes.cur_page,
             show_item_checkboxes: this.attributes.show_item_checkboxes,
-            advanced_search: this.attributes.advanced_search
+            advanced_search: this.attributes.advanced_search,
         };
 
         // Add operation, item_ids only if they have values.
@@ -101,14 +101,14 @@ export default Backbone.Model.extend({
 
         // Add filter arguments to data, placing "f-" in front of all arguments.
         var self = this;
-        _.each(_.pairs(self.attributes.filters), k => {
+        _.each(_.pairs(self.attributes.filters), (k) => {
             url_data[`f-${k[0]}`] = k[1];
         });
         return url_data;
     },
 
     // Return URL for obtaining a new grid
-    get_url: function(args) {
+    get_url: function (args) {
         return `${this.get("url_base")}?${$.param(this.get_url_data())}&${$.param(args)}`;
-    }
+    },
 });
diff --git a/client/galaxy/scripts/legacy/grid/grid-template.js b/client/galaxy/scripts/legacy/grid/grid-template.js
index 349f4fc0f1cd..59a15e695203 100644
--- a/client/galaxy/scripts/legacy/grid/grid-template.js
+++ b/client/galaxy/scripts/legacy/grid/grid-template.js
@@ -3,7 +3,7 @@ import Utils from "utils/utils";
 // grid view templates
 export default {
     // template
-    grid: function(options) {
+    grid: function (options) {
         var tmpl = "";
         if (options.embedded) {
             tmpl = this.grid_header(options) + this.grid_table(options);
@@ -25,7 +25,7 @@ export default {
     },
 
     // template
-    grid_table: function() {
+    grid_table: function () {
         return `
             <form method="post" onsubmit="return false;">
                 <table id="grid-table" class="grid">
@@ -37,7 +37,7 @@ export default {
     },
 
     // template
-    grid_header: function(options) {
+    grid_header: function (options) {
         var tmpl = '<div class="grid-header">';
         if (!options.embedded) {
             tmpl += `<h2>${options.title}</h2>`;
@@ -71,7 +71,7 @@ export default {
     },
 
     // template
-    header: function(options) {
+    header: function (options) {
         // start
         var tmpl = "<tr>";
 
@@ -107,7 +107,7 @@ export default {
     },
 
     // template
-    body: function(options) {
+    body: function (options) {
         // initialize
         var tmpl = "";
         var items_length = options.items.length;
@@ -192,7 +192,7 @@ export default {
     },
 
     // template
-    footer: function(options) {
+    footer: function (options) {
         // create template string
         var tmpl = "";
 
@@ -322,7 +322,7 @@ export default {
     },
 
     // template
-    message: function(options) {
+    message: function (options) {
         var status = options.status;
         if (["success", "ok"].indexOf(status) != -1) {
             status = "done";
@@ -333,7 +333,7 @@ export default {
     },
 
     // template
-    grid_filters: function(options) {
+    grid_filters: function (options) {
         // get filters
         var default_filter_dict = options.default_filter_dict;
         var filters = options.filters;
@@ -407,7 +407,7 @@ export default {
     },
 
     // template
-    grid_column_filter: function(options, column) {
+    grid_column_filter: function (options, column) {
         // collect parameters
         var filters = options.filters;
         var column_label = column.label;
@@ -532,8 +532,8 @@ export default {
     },
 
     // template for filter items
-    filter_element: function(filter_key, filter_value) {
+    filter_element: function (filter_key, filter_value) {
         filter_value = Utils.sanitize(filter_value);
         return `<span class="text-filter-val">${filter_value}<a href="javascript:void(0);" filter_key="${filter_key}" filter_val="${filter_value}"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>`;
-    }
+    },
 };
diff --git a/client/galaxy/scripts/legacy/grid/grid-view.js b/client/galaxy/scripts/legacy/grid/grid-view.js
index 3bb2c6083e4e..94b504e5ef9a 100644
--- a/client/galaxy/scripts/legacy/grid/grid-view.js
+++ b/client/galaxy/scripts/legacy/grid/grid-view.js
@@ -21,7 +21,7 @@ export default Backbone.View.extend({
     grid: null,
 
     // Initialize
-    initialize: function(grid_config) {
+    initialize: function (grid_config) {
         this.grid = new GridModel();
         this.dict_format = grid_config.dict_format;
         this.title = grid_config.title;
@@ -53,11 +53,11 @@ export default Backbone.View.extend({
                 });
                 $.ajax({
                     url: `${grid_config.url_base}?${$.param(url_data)}`,
-                    success: function(response) {
+                    success: function (response) {
                         response.embedded = grid_config.embedded;
                         response.filters = grid_config.filters || {};
                         self.init_grid(response);
-                    }
+                    },
                 });
             } else {
                 this.init_grid(grid_config);
@@ -71,13 +71,13 @@ export default Backbone.View.extend({
         if (grid_config.use_panels) {
             $("#center").css({
                 padding: "10px",
-                overflow: "auto"
+                overflow: "auto",
             });
         }
     },
 
     // refresh frames
-    handle_refresh: function(refresh_frames) {
+    handle_refresh: function (refresh_frames) {
         if (refresh_frames) {
             if ($.inArray("history", refresh_frames) > -1) {
                 if (window.top.Galaxy && window.top.Galaxy.currHistoryPanel) {
@@ -88,7 +88,7 @@ export default Backbone.View.extend({
     },
 
     // Initialize
-    init_grid: function(grid_config) {
+    init_grid: function (grid_config) {
         this.grid.set(grid_config);
 
         // get options
@@ -134,44 +134,44 @@ export default Backbone.View.extend({
     },
 
     // Initialize grid controls
-    init_grid_controls: function() {
+    init_grid_controls: function () {
         // link
         var self = this;
 
         // Initialize grid operation button.
-        this.$el.find(".operation-button").each(function() {
+        this.$el.find(".operation-button").each(function () {
             $(this).off();
-            $(this).click(function() {
+            $(this).click(function () {
                 self.submit_operation(this);
                 return false;
             });
         });
 
         // Initialize text filters to select text on click and use normal font when user is typing.
-        this.$el.find("input[type=text]").each(function() {
+        this.$el.find("input[type=text]").each(function () {
             $(this).off();
             $(this)
-                .click(function() {
+                .click(function () {
                     $(this).select();
                 })
-                .keyup(function() {
+                .keyup(function () {
                     $(this).css("font-style", "normal");
                 });
         });
 
         // Initialize sort links.
-        this.$el.find(".sort-link").each(function() {
+        this.$el.find(".sort-link").each(function () {
             $(this).off();
-            $(this).click(function() {
+            $(this).click(function () {
                 self.set_sort_condition($(this).attr("sort_key"));
                 return false;
             });
         });
 
         // Initialize text filters.
-        this.$el.find(".text-filter-form").each(function() {
+        this.$el.find(".text-filter-form").each(function () {
             $(this).off();
-            $(this).submit(function() {
+            $(this).submit(function () {
                 var column_key = $(this).attr("column_key");
                 var text_input_obj = $(`#input-${column_key}-filter`);
                 var text_input = text_input_obj.val();
@@ -182,13 +182,11 @@ export default Backbone.View.extend({
         });
 
         // Initialize categorical filters.
-        this.$el.find(".text-filter-val > a").each(function() {
+        this.$el.find(".text-filter-val > a").each(function () {
             $(this).off();
-            $(this).click(function() {
+            $(this).click(function () {
                 // Remove visible element.
-                $(this)
-                    .parent()
-                    .remove();
+                $(this).parent().remove();
 
                 // Remove filter condition.
                 self.remove_filter_condition($(this).attr("filter_key"), $(this).attr("filter_val"));
@@ -199,16 +197,16 @@ export default Backbone.View.extend({
         });
 
         // Initialize categorical filters.
-        this.$el.find(".categorical-filter > a").each(function() {
+        this.$el.find(".categorical-filter > a").each(function () {
             $(this).off();
-            $(this).click(function() {
+            $(this).click(function () {
                 self.set_categorical_filter($(this).attr("filter_key"), $(this).attr("filter_val"));
                 return false;
             });
         });
 
         // Initialize standard, advanced search toggles.
-        this.$el.find(".advanced-search-toggle").each(function() {
+        this.$el.find(".advanced-search-toggle").each(function () {
             $(this).off();
             $(this).click(() => {
                 self.$el.find("#standard-search").slideToggle("fast");
@@ -225,16 +223,16 @@ export default Backbone.View.extend({
     },
 
     // Initialize grid elements.
-    init_grid_elements: function() {
+    init_grid_elements: function () {
         // Initialize grid selection checkboxes.
-        this.$el.find(".grid").each(function() {
+        this.$el.find(".grid").each(function () {
             var checkboxes = $(this).find("input.grid-row-select-checkbox");
             var check_count = $(this).find("span.grid-selected-count");
             var update_checked = () => {
                 check_count.text($(checkboxes).filter(":checked").length);
             };
 
-            $(checkboxes).each(function() {
+            $(checkboxes).each(function () {
                 $(this).change(update_checked);
             });
             update_checked();
@@ -250,8 +248,8 @@ export default Backbone.View.extend({
         //
         // add page click events
         //
-        this.$el.find(".page-link > a").each(function() {
-            $(this).click(function() {
+        this.$el.find(".page-link > a").each(function () {
+            $(this).click(function () {
                 self.set_page($(this).attr("page_num"));
                 return false;
             });
@@ -260,11 +258,11 @@ export default Backbone.View.extend({
         //
         // add inbound/outbound events
         //
-        this.$el.find(".use-target").each(function() {
-            $(this).click(function() {
+        this.$el.find(".use-target").each(function () {
+            $(this).click(function () {
                 self.execute({
                     href: $(this).attr("href"),
-                    target: $(this).attr("target")
+                    target: $(this).attr("target"),
                 });
                 return false;
             });
@@ -280,14 +278,14 @@ export default Backbone.View.extend({
         _.each(options.items, (item, index) => {
             var button = self.$(`#grid-${item.encode_id}-popup`).off();
             var popup = new PopupMenu(button);
-            _.each(options.operations, operation => {
+            _.each(options.operations, (operation) => {
                 self._add_operation(popup, operation, item);
             });
         });
     },
 
     /** Add an operation to the items menu */
-    _add_operation: function(popup, operation, item) {
+    _add_operation: function (popup, operation, item) {
         var self = this;
         var settings = item.operation_config[operation.label];
         if (settings.allowed && operation.allow_popup) {
@@ -296,7 +294,7 @@ export default Backbone.View.extend({
                 href: settings.url_args,
                 target: settings.target,
                 confirmation_text: operation.confirm,
-                func: function(e) {
+                func: function (e) {
                     e.preventDefault();
                     var label = $(e.target).html();
                     if (operation.onclick) {
@@ -304,13 +302,13 @@ export default Backbone.View.extend({
                     } else {
                         self.execute(this.findItemByHtml(label));
                     }
-                }
+                },
             });
         }
     },
 
     // Add a condition to the grid filter; this adds the condition and refreshes the grid.
-    add_filter_condition: function(name, value) {
+    add_filter_condition: function (name, value) {
         // Do nothing is value is empty.
         if (value === "") {
             return false;
@@ -322,7 +320,7 @@ export default Backbone.View.extend({
         // Add button that displays filter and provides a button to delete it.
         var t = $(Templates.filter_element(name, value));
         var self = this;
-        t.click(function() {
+        t.click(function () {
             // Remove visible element.
             $(this).remove();
 
@@ -340,7 +338,7 @@ export default Backbone.View.extend({
     },
 
     // Remove a condition to the grid filter; this adds the condition and refreshes the grid.
-    remove_filter_condition: function(name, value) {
+    remove_filter_condition: function (name, value) {
         // Remove filter condition.
         this.grid.remove_filter(name, value);
 
@@ -350,7 +348,7 @@ export default Backbone.View.extend({
     },
 
     // Set sort condition for grid.
-    set_sort_condition: function(col_key) {
+    set_sort_condition: function (col_key) {
         // Set new sort condition. New sort is col_key if sorting new column; if reversing sort on
         // currently sorted column, sort is reversed.
         var cur_sort = this.grid.get("sort_key");
@@ -379,13 +377,13 @@ export default Backbone.View.extend({
     },
 
     // Set new value for categorical filter.
-    set_categorical_filter: function(name, new_value) {
+    set_categorical_filter: function (name, new_value) {
         // Update filter hyperlinks to reflect new filter value.
         var category_filter = this.grid.get("categorical_filters")[name];
 
         var cur_value = this.grid.get("filters")[name];
         var self = this;
-        this.$el.find(`.${name}-filter`).each(function() {
+        this.$el.find(`.${name}-filter`).each(function () {
             var text = $.trim($(this).text());
             var filter = category_filter[text];
             var filter_value = filter[name];
@@ -415,10 +413,10 @@ export default Backbone.View.extend({
     },
 
     // Set page to view.
-    set_page: function(new_page) {
+    set_page: function (new_page) {
         // Update page hyperlink to reflect new page.
         var self = this;
-        this.$el.find(".page-link").each(function() {
+        this.$el.find(".page-link").each(function () {
             var id = $(this).attr("id");
 
             var // Id has form 'page-link-<page_num>
@@ -429,9 +427,7 @@ export default Backbone.View.extend({
             if (page_num === new_page) {
                 // Remove link to page since grid will be on this page. It is assumed that
                 // this element has a single child, a hyperlink/anchor with text.
-                text = $(this)
-                    .children()
-                    .text();
+                text = $(this).children().text();
                 $(this).empty();
                 $(this).addClass("inactive-link");
                 $(this).text(text);
@@ -458,7 +454,7 @@ export default Backbone.View.extend({
     },
 
     // confirmation/submission of operation request
-    submit_operation: function(operation_button, confirmation_text) {
+    submit_operation: function (operation_button, confirmation_text) {
         // identify operation
         var operation_name = $(operation_button).val();
 
@@ -470,7 +466,7 @@ export default Backbone.View.extend({
 
         // Check to see if there's grid confirmation text for this operation
         var operation = _.findWhere(this.grid.attributes.operations, {
-            label: operation_name
+            label: operation_name,
         });
         if (operation && !confirmation_text) {
             confirmation_text = operation.confirm || "";
@@ -478,7 +474,7 @@ export default Backbone.View.extend({
 
         // collect ids
         var item_ids = [];
-        this.$el.find("input[name=id]:checked").each(function() {
+        this.$el.find("input[name=id]:checked").each(function () {
             item_ids.push($(this).val());
         });
 
@@ -486,29 +482,29 @@ export default Backbone.View.extend({
         var options = {
             operation: operation_name,
             id: item_ids,
-            confirmation_text: confirmation_text
+            confirmation_text: confirmation_text,
         };
         if (operation.target == "top" || operation.target == "center") {
             options = _.extend(options, {
                 href: operation.href,
-                target: operation.target
+                target: operation.target,
             });
         }
         this.execute(options);
         return true;
     },
 
-    check_all_items: function() {
+    check_all_items: function () {
         var check = this.$(".grid-row-select-checkbox");
         var state = this.$("#check_all").prop("checked");
-        _.each(check, c => {
+        _.each(check, (c) => {
             $(c).prop("checked", state);
         });
         this.init_grid_elements();
     },
 
     // Go back to page one; this is useful when a filter is applied.
-    go_page_one: function() {
+    go_page_one: function () {
         // Need to go back to page 1 if not showing all.
         var cur_page = this.grid.get("cur_page");
         if (cur_page !== null && cur_page !== undefined && cur_page !== "all") {
@@ -519,7 +515,7 @@ export default Backbone.View.extend({
     //
     // execute operations and hyperlink requests
     //
-    execute: function(options) {
+    execute: function (options) {
         // get url
         var id = null;
         var href = null;
@@ -574,7 +570,7 @@ export default Backbone.View.extend({
             // Update grid.
             this.grid.set({
                 operation: operation,
-                item_ids: id
+                item_ids: id,
             });
 
             // Do operation. If operation cannot be performed asynchronously, redirect to location.
@@ -610,7 +606,7 @@ export default Backbone.View.extend({
     },
 
     // go to url
-    go_to: function(target, href) {
+    go_to: function (target, href) {
         // get aysnc status
         var async = this.grid.get("async");
         this.grid.set("async", false);
@@ -628,7 +624,7 @@ export default Backbone.View.extend({
         this.grid.set({
             operation: undefined,
             item_ids: undefined,
-            async: async
+            async: async,
         });
         switch (target) {
             case "center":
@@ -643,7 +639,7 @@ export default Backbone.View.extend({
     },
 
     // Update grid.
-    update_grid: function() {
+    update_grid: function () {
         // If there's an operation, do POST; otherwise, do GET.
         var method = this.grid.get("operation") ? "POST" : "GET";
 
@@ -654,10 +650,10 @@ export default Backbone.View.extend({
             type: method,
             url: self.grid.get("url_base"),
             data: self.grid.get_url_data(),
-            error: function() {
+            error: function () {
                 alert("Grid refresh failed");
             },
-            success: function(response_text) {
+            success: function (response_text) {
                 // backup
                 var embedded = self.grid.get("embedded");
                 var insert = self.grid.get("insert");
@@ -677,13 +673,13 @@ export default Backbone.View.extend({
                 // Hide loading overlay.
                 self.$el.find(".loading-elt-overlay").hide();
             },
-            complete: function() {
+            complete: function () {
                 // Clear grid of transient request attributes.
                 self.grid.set({
                     operation: undefined,
-                    item_ids: undefined
+                    item_ids: undefined,
                 });
-            }
+            },
         });
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mocha/tests/rules_tests.js b/client/galaxy/scripts/mocha/tests/rules_tests.js
index b97f81130faa..8d6111f76247 100644
--- a/client/galaxy/scripts/mocha/tests/rules_tests.js
+++ b/client/galaxy/scripts/mocha/tests/rules_tests.js
@@ -15,7 +15,7 @@ function applyRules(rules, data, sources) {
 }
 
 function itShouldConform(specTestCase, i) {
-    it("should pass conformance test case " + i, function() {
+    it("should pass conformance test case " + i, function () {
         chai.assert.property(specTestCase, "rules");
         if (specTestCase.initial) {
             chai.assert.property(specTestCase, "final");
@@ -38,6 +38,6 @@ function itShouldConform(specTestCase, i) {
     });
 }
 
-describe("Rules DSL Spec", function() {
+describe("Rules DSL Spec", function () {
     SPEC_TEST_CASES.forEach(itShouldConform);
 });
diff --git a/client/galaxy/scripts/mvc/annotation.js b/client/galaxy/scripts/mvc/annotation.js
index 1c4454d0681d..3a0c90a2f434 100644
--- a/client/galaxy/scripts/mvc/annotation.js
+++ b/client/galaxy/scripts/mvc/annotation.js
@@ -13,39 +13,39 @@ var AnnotationEditor = Backbone.View.extend(baseMVC.LoggableMixin)
         className: "annotation-display",
 
         /** Set up listeners, parse options */
-        initialize: function(options) {
+        initialize: function (options) {
             options = options || {};
             this.tooltipConfig = options.tooltipConfig || {
-                placement: "bottom"
+                placement: "bottom",
             };
             //console.debug( this, options );
             // only listen to the model only for changes to annotations
-            this.listenTo(this.model, "change:annotation", function() {
+            this.listenTo(this.model, "change:annotation", function () {
                 this.render();
             });
             this.hiddenUntilActivated(options.$activator, options);
         },
 
         /** Build the DOM elements, call select to on the created input, and set up behaviors */
-        render: function() {
+        render: function () {
             var view = this;
             this.$el.html(this._template());
 
             //TODO: handle empties better
             this.$annotation().make_text_editable({
                 use_textarea: true,
-                on_finish: function(newAnnotation) {
+                on_finish: function (newAnnotation) {
                     view.$annotation().text(newAnnotation);
                     view.model.save({ annotation: newAnnotation }, { silent: true }).fail(() => {
                         view.$annotation().text(view.model.previous("annotation"));
                     });
-                }
+                },
             });
             return this;
         },
 
         /** @returns {String} the html text used to build the view's DOM */
-        _template: function() {
+        _template: function () {
             var annotation = this.model.get("annotation");
             return [
                 //TODO: make prompt optional
@@ -55,28 +55,28 @@ var AnnotationEditor = Backbone.View.extend(baseMVC.LoggableMixin)
                 // set up initial tags by adding as CSV to input vals (necc. to init select2)
                 '<div class="annotation">',
                 _.escape(annotation),
-                "</div>"
+                "</div>",
             ].join("");
         },
 
         /** @returns {jQuery} the main element for this view */
-        $annotation: function() {
+        $annotation: function () {
             return this.$el.find(".annotation");
         },
 
         /** shut down event listeners and remove this view's DOM */
-        remove: function() {
+        remove: function () {
             this.$annotation.off();
             this.stopListening(this.model);
             Backbone.View.prototype.remove.call(this);
         },
 
         /** string rep */
-        toString: function() {
+        toString: function () {
             return ["AnnotationEditor(", `${this.model}`, ")"].join("");
-        }
+        },
     });
 // =============================================================================
 export default {
-    AnnotationEditor: AnnotationEditor
+    AnnotationEditor: AnnotationEditor,
 };
diff --git a/client/galaxy/scripts/mvc/base-mvc.js b/client/galaxy/scripts/mvc/base-mvc.js
index 2bf9c8836196..961a02ff5906 100644
--- a/client/galaxy/scripts/mvc/base-mvc.js
+++ b/client/galaxy/scripts/mvc/base-mvc.js
@@ -33,7 +33,7 @@ var LoggableMixin = /** @lends LoggableMixin# */ {
      */
     logger: null,
     /** @type {String} a namespace for filtering/focusing log output */
-    _logNamespace: "."
+    _logNamespace: ".",
 };
 addLogging(LoggableMixin);
 
@@ -42,7 +42,7 @@ addLogging(LoggableMixin);
  *      This all largely happens behind the scenes and no special calls are required.
  */
 var SessionStorageModel = Backbone.Model.extend({
-    initialize: function(initialAttrs) {
+    initialize: function (initialAttrs) {
         // check for sessionStorage and error if no id is provided
         this._checkEnabledSessionStorage();
         if (!initialAttrs.id) {
@@ -55,16 +55,16 @@ var SessionStorageModel = Backbone.Model.extend({
         var existing = !this.isNew() ? this._read(this) : {};
         this.clear({ silent: true });
         this.save(_.extend({}, this.defaults, existing, initialAttrs), {
-            silent: true
+            silent: true,
         });
 
         // save on any change to it immediately
-        this.on("change", function() {
+        this.on("change", function () {
             this.save();
         });
     },
 
-    _checkEnabledSessionStorage: function() {
+    _checkEnabledSessionStorage: function () {
         try {
             return window.sessionStorage.length >= 0;
         } catch (err) {
@@ -76,7 +76,7 @@ var SessionStorageModel = Backbone.Model.extend({
     /** override of bbone sync to save to sessionStorage rather than REST
      *      bbone options (success, errror, etc.) should still apply
      */
-    sync: function(method, model, options) {
+    sync: function (method, model, options) {
         if (!options.silent) {
             model.trigger("request", model, {}, options);
         }
@@ -108,7 +108,7 @@ var SessionStorageModel = Backbone.Model.extend({
     },
 
     /** set storage to the stringified item */
-    _create: function(model) {
+    _create: function (model) {
         try {
             var json = model.toJSON();
             var set = sessionStorage.setItem(model.id, JSON.stringify(json));
@@ -125,31 +125,31 @@ var SessionStorageModel = Backbone.Model.extend({
     },
 
     /** read and parse json from storage */
-    _read: function(model) {
+    _read: function (model) {
         return JSON.parse(sessionStorage.getItem(model.id));
     },
 
     /** set storage to the item (alias to create) */
-    _update: function(model) {
+    _update: function (model) {
         return model._create(model);
     },
 
     /** remove the item from storage */
-    _delete: function(model) {
+    _delete: function (model) {
         return sessionStorage.removeItem(model.id);
     },
 
     /** T/F whether sessionStorage contains the model's id (data is present) */
-    isNew: function() {
+    isNew: function () {
         return !Object.prototype.hasOwnProperty.call(sessionStorage, this.id);
     },
 
-    _log: function() {
+    _log: function () {
         return JSON.stringify(this.toJSON(), null, "  ");
     },
-    toString: function() {
+    toString: function () {
         return `SessionStorageModel(${this.id})`;
-    }
+    },
 });
 (() => {
     SessionStorageModel.prototype = _.omit(SessionStorageModel.prototype, "url", "urlRoot");
@@ -194,7 +194,7 @@ var SearchableModelMixin = {
     },
 
     /** search the attribute with key attrKey for the string searchFor; T/F if found */
-    searchAttribute: function(attrKey, searchFor) {
+    searchAttribute: function (attrKey, searchFor) {
         var attrVal = this.get(attrKey);
         //this.debug( 'searchAttribute', attrKey, attrVal, searchFor );
         // bail if empty searchFor or unsearchable values
@@ -205,37 +205,25 @@ var SearchableModelMixin = {
         if (_.isArray(attrVal)) {
             return this._searchArrayAttribute(attrVal, searchFor);
         }
-        return (
-            attrVal
-                .toString()
-                .toLowerCase()
-                .indexOf(searchFor.toLowerCase()) !== -1
-        );
+        return attrVal.toString().toLowerCase().indexOf(searchFor.toLowerCase()) !== -1;
     },
 
     /** deep(er) search for array attributes; T/F if found */
-    _searchArrayAttribute: function(array, searchFor) {
+    _searchArrayAttribute: function (array, searchFor) {
         //this.debug( '_searchArrayAttribute', array, searchFor );
         searchFor = searchFor.toLowerCase();
         //precondition: searchFor has already been validated as non-empty string
         //precondition: assumes only 1 level array
         //TODO: could possibly break up searchFor more (CSV...)
-        return _.any(
-            array,
-            elem =>
-                elem
-                    .toString()
-                    .toLowerCase()
-                    .indexOf(searchFor.toLowerCase()) !== -1
-        );
+        return _.any(array, (elem) => elem.toString().toLowerCase().indexOf(searchFor.toLowerCase()) !== -1);
     },
 
     /** search all searchAttributes for the string searchFor,
      *      returning a list of keys of attributes that contain searchFor
      */
-    search: function(searchFor) {
+    search: function (searchFor) {
         var model = this;
-        return _.filter(this.searchAttributes, key => model.searchAttribute(key, searchFor));
+        return _.filter(this.searchAttributes, (key) => model.searchAttribute(key, searchFor));
     },
 
     /** alias of search, but returns a boolean; accepts attribute specifiers where
@@ -246,7 +234,7 @@ var SearchableModelMixin = {
      *  @param {String} term   plain text or ATTR_SPECIFIER sep. key=val pair
      *  @returns {Boolean} was term found in (any) attribute(s)
      */
-    matches: function(term) {
+    matches: function (term) {
         var ATTR_SPECIFIER = "=";
         var split = term.split(ATTR_SPECIFIER);
         // attribute is specified - search only that
@@ -265,15 +253,15 @@ var SearchableModelMixin = {
      *          an HDA would have to have attributes containing blah AND bler AND a genome_build == hg19
      *      To include whitespace in terms: wrap the term in double quotations (name="blah bler").
      */
-    matchesAll: function(terms) {
+    matchesAll: function (terms) {
         var model = this;
         // break the terms up by whitespace and filter out the empty strings
-        terms = terms.match(/(".*"|\w*=".*"|\S*)/g).filter(s => !!s);
-        return _.all(terms, term => {
+        terms = terms.match(/(".*"|\w*=".*"|\S*)/g).filter((s) => !!s);
+        return _.all(terms, (term) => {
             term = term.replace(/"/g, "");
             return model.matches(term);
         });
-    }
+    },
 };
 
 //==============================================================================
@@ -297,14 +285,14 @@ var HiddenUntilActivatedViewMixin = /** @lends hiddenUntilActivatedMixin# */ {
      *  @param {jQuery} $activator the 'button' that's clicked to show/hide the view
      *  @param {Object} hash with mixin options
      */
-    hiddenUntilActivated: function($activator, options) {
+    hiddenUntilActivated: function ($activator, options) {
         // call this in your view's initialize fn
         options = options || {};
         //TODO: flesh out options - show them all here
         this.HUAVOptions = {
             $elementShown: this.$el,
             showFn: $.prototype.toggle,
-            showSpeed: "fast"
+            showSpeed: "fast",
         };
         _.extend(this.HUAVOptions, options || {});
         /** has this been shown already (and onshowFirstTime called)? */
@@ -313,7 +301,7 @@ var HiddenUntilActivatedViewMixin = /** @lends hiddenUntilActivatedMixin# */ {
 
         if ($activator) {
             var mixin = this;
-            $activator.on("click", ev => {
+            $activator.on("click", (ev) => {
                 mixin.toggle(mixin.HUAVOptions.showSpeed);
             });
         }
@@ -321,12 +309,12 @@ var HiddenUntilActivatedViewMixin = /** @lends hiddenUntilActivatedMixin# */ {
 
     //TODO:?? remove? use .hidden?
     /** returns T/F if the view is hidden */
-    isHidden: function() {
+    isHidden: function () {
         return this.HUAVOptions.$elementShown.is(":hidden");
     },
 
     /** toggle the hidden state, show/hide $elementShown, call onshow/hide, trigger events */
-    toggle: function() {
+    toggle: function () {
         //TODO: more specific name - toggle is too general
         // can be called manually as well with normal toggle arguments
         //TODO: better as a callback (when the show/hide is actually done)
@@ -354,7 +342,7 @@ var HiddenUntilActivatedViewMixin = /** @lends hiddenUntilActivatedMixin# */ {
             this.hidden = true;
         }
         return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown, arguments);
-    }
+    },
 };
 
 //==============================================================================
@@ -366,20 +354,20 @@ var HiddenUntilActivatedViewMixin = /** @lends hiddenUntilActivatedMixin# */ {
  */
 var DraggableViewMixin = {
     /** set up instance vars to track whether this view is currently draggable */
-    initialize: function(attributes) {
+    initialize: function (attributes) {
         /** is the body of this hda view expanded/not? */
         this.draggable = attributes.draggable || false;
     },
 
     /** what part of the view's DOM triggers the dragging */
-    $dragHandle: function() {
+    $dragHandle: function () {
         //TODO: make abstract/general - move this to listItem
         // override to the element you want to be your view's handle
         return this.$(".title-bar");
     },
 
     /** toggle whether this view is draggable */
-    toggleDraggable: function() {
+    toggleDraggable: function () {
         if (this.draggable) {
             this.draggableOff();
         } else {
@@ -388,24 +376,20 @@ var DraggableViewMixin = {
     },
 
     /** allow the view to be dragged, set up event handlers */
-    draggableOn: function() {
+    draggableOn: function () {
         this.draggable = true;
         this.dragStartHandler = _.bind(this._dragStartHandler, this);
         this.dragEndHandler = _.bind(this._dragEndHandler, this);
 
-        var handle = this.$dragHandle()
-            .attr("draggable", true)
-            .get(0);
+        var handle = this.$dragHandle().attr("draggable", true).get(0);
         handle.addEventListener("dragstart", this.dragStartHandler, false);
         handle.addEventListener("dragend", this.dragEndHandler, false);
     },
 
     /** turn of view dragging and remove event listeners */
-    draggableOff: function() {
+    draggableOff: function () {
         this.draggable = false;
-        var handle = this.$dragHandle()
-            .attr("draggable", false)
-            .get(0);
+        var handle = this.$dragHandle().attr("draggable", false).get(0);
         handle.removeEventListener("dragstart", this.dragStartHandler, false);
         handle.removeEventListener("dragend", this.dragEndHandler, false);
     },
@@ -413,7 +397,7 @@ var DraggableViewMixin = {
     /** sets the dataTransfer data to the model's toJSON
      *  @fires draggable:dragstart (bbone event) which is passed the event and this view
      */
-    _dragStartHandler: function(event) {
+    _dragStartHandler: function (event) {
         event.dataTransfer.effectAllowed = "move";
         //ASSUMES: this.model
         //TODO: all except IE: should be 'application/json', IE: must be 'text'
@@ -425,10 +409,10 @@ var DraggableViewMixin = {
     /** handle the dragend
      *  @fires draggable:dragend (bbone event) which is passed the event and this view
      */
-    _dragEndHandler: function(event) {
+    _dragEndHandler: function (event) {
         this.trigger("draggable:dragend", event, this);
         return false;
-    }
+    },
 };
 
 //==============================================================================
@@ -442,7 +426,7 @@ var DraggableViewMixin = {
  */
 var SelectableViewMixin = {
     /** Set up instance state vars for whether the selector is shown and whether the view has been selected */
-    initialize: function(attributes) {
+    initialize: function (attributes) {
         /** is the view currently in selection mode? */
         this.selectable = attributes.selectable || false;
         /** is the view currently selected? */
@@ -450,12 +434,12 @@ var SelectableViewMixin = {
     },
 
     /** $el sub-element where the selector is rendered and what can be clicked to select. */
-    $selector: function() {
+    $selector: function () {
         return this.$(".selector");
     },
 
     /** How the selector is rendered - defaults to font-awesome checkbox */
-    _renderSelected: function() {
+    _renderSelected: function () {
         // override
         this.$selector()
             .find("span")
@@ -464,7 +448,7 @@ var SelectableViewMixin = {
     },
 
     /** Toggle whether the selector is shown */
-    toggleSelector: function() {
+    toggleSelector: function () {
         //TODO: use this.selectable
         if (!this.$selector().is(":visible")) {
             this.showSelector();
@@ -477,7 +461,7 @@ var SelectableViewMixin = {
      *  @param {Number} a jQuery fx speed
      *  @fires: selectable which is passed true (IOW, the selector is shown) and the view
      */
-    showSelector: function(speed) {
+    showSelector: function (speed) {
         speed = speed !== undefined ? speed : this.fxSpeed;
         // make sure selected state is represented properly
         this.selectable = true;
@@ -494,7 +478,7 @@ var SelectableViewMixin = {
      *  @param {Number} a jQuery fx speed
      *  @fires: selectable which is passed false (IOW, the selector is not shown) and the view
      */
-    hideSelector: function(speed) {
+    hideSelector: function (speed) {
         speed = speed !== undefined ? speed : this.fxSpeed;
         // reverse the process from showSelect
         this.selectable = false;
@@ -507,7 +491,7 @@ var SelectableViewMixin = {
     },
 
     /** Toggle whether the view is selected */
-    toggleSelect: function(event) {
+    toggleSelect: function (event) {
         if (this.selected) {
             this.deselect(event);
         } else {
@@ -519,7 +503,7 @@ var SelectableViewMixin = {
      *  @param {Event} a jQuery event that caused the selection
      *  @fires: selected which is passed the view and the DOM event that triggered it (optionally)
      */
-    select: function(event) {
+    select: function (event) {
         // switch icon, set selected, and trigger event
         if (!this.selected) {
             this.trigger("selected", this, event);
@@ -533,7 +517,7 @@ var SelectableViewMixin = {
      *  @param {Event} a jQuery event that caused the selection
      *  @fires: de-selected which is passed the view and the DOM event that triggered it (optionally)
      */
-    deselect: function(event) {
+    deselect: function (event) {
         // switch icon, set selected, and trigger event
         if (this.selected) {
             this.trigger("de-selected", this, event);
@@ -541,7 +525,7 @@ var SelectableViewMixin = {
             this._renderSelected();
         }
         return false;
-    }
+    },
 };
 
 //==============================================================================
@@ -599,5 +583,5 @@ export default {
     DraggableViewMixin: DraggableViewMixin,
     SelectableViewMixin: SelectableViewMixin,
     wrapTemplate: wrapTemplate,
-    buildComparator: buildComparator
+    buildComparator: buildComparator,
 };
diff --git a/client/galaxy/scripts/mvc/base/controlled-fetch-collection.js b/client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
index 848d85504b85..d9dadd3438c1 100644
--- a/client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
+++ b/client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
@@ -10,28 +10,28 @@ import BASE_MVC from "mvc/base-mvc";
  */
 var ControlledFetchCollection = Backbone.Collection.extend({
     /** call setOrder on initialization to build the comparator based on options */
-    initialize: function(models, options) {
+    initialize: function (models, options) {
         Backbone.Collection.prototype.initialize.call(this, models, options);
         this.setOrder(options.order || this.order, { silent: true });
     },
 
     /** set up to track order changes and re-sort when changed */
-    _setUpListeners: function() {
+    _setUpListeners: function () {
         return this.on({
-            "changed-order": this.sort
+            "changed-order": this.sort,
         });
     },
 
     /** override to provide order and offsets based on instance vars, set limit if passed,
      *  and set allFetched/fire 'all-fetched' when xhr returns
      */
-    fetch: function(options) {
+    fetch: function (options) {
         options = this._buildFetchOptions(options);
         return Backbone.Collection.prototype.fetch.call(this, options);
     },
 
     /** build ajax data/parameters from options */
-    _buildFetchOptions: function(options) {
+    _buildFetchOptions: function (options) {
         // note: we normally want options passed in to override the defaults built here
         // so most of these fns will generate defaults
         options = _.clone(options) || {};
@@ -57,7 +57,7 @@ var ControlledFetchCollection = Backbone.Collection.extend({
     },
 
     /** Build the dictionary to send to fetch's XHR as data */
-    _buildFetchData: function(options) {
+    _buildFetchData: function (options) {
         var defaults = {};
         if (this.order) {
             defaults.order = this.order;
@@ -76,21 +76,21 @@ var ControlledFetchCollection = Backbone.Collection.extend({
         /** what series of attributes to return (model dependent) */
         "view",
         /** individual keys to return for the models (see api/histories.index) */
-        "keys"
+        "keys",
     ],
 
     /** add any needed filters here based on collection state */
-    _buildFetchFilters: function(options) {
+    _buildFetchFilters: function (options) {
         // override
         return _.clone(options.filters || {});
     },
 
     /** Convert dictionary filters to qqv style arrays */
-    _fetchFiltersToAjaxData: function(filters) {
+    _fetchFiltersToAjaxData: function (filters) {
         // return as a map so ajax.data can extend from it
         var filterMap = {
             q: [],
-            qv: []
+            qv: [],
         };
         _.each(filters, (v, k) => {
             // don't send if filter value is empty
@@ -115,7 +115,7 @@ var ControlledFetchCollection = Backbone.Collection.extend({
     },
 
     /** override to reset allFetched flag to false */
-    reset: function(models, options) {
+    reset: function (models, options) {
         this.allFetched = false;
         return Backbone.Collection.prototype.reset.call(this, models, options);
     },
@@ -126,23 +126,23 @@ var ControlledFetchCollection = Backbone.Collection.extend({
     /** @type {Object} map of collection available sorting orders containing comparator fns */
     comparators: {
         update_time: BASE_MVC.buildComparator("update_time", {
-            ascending: false
+            ascending: false,
         }),
         "update_time-asc": BASE_MVC.buildComparator("update_time", {
-            ascending: true
+            ascending: true,
         }),
         create_time: BASE_MVC.buildComparator("create_time", {
-            ascending: false
+            ascending: false,
         }),
         "create_time-asc": BASE_MVC.buildComparator("create_time", {
-            ascending: true
-        })
+            ascending: true,
+        }),
     },
 
     /** set the order and comparator for this collection then sort with the new order
      *  @event 'changed-order' passed the new order and the collection
      */
-    setOrder: function(order, options) {
+    setOrder: function (order, options) {
         options = options || {};
         var collection = this;
         var comparator = collection.comparators[order];
@@ -161,7 +161,7 @@ var ControlledFetchCollection = Backbone.Collection.extend({
             collection.trigger("changed-order", options);
         }
         return collection;
-    }
+    },
 });
 
 //=============================================================================
@@ -172,41 +172,41 @@ var PaginatedCollection = ControlledFetchCollection.extend({
     /** @type {Number} limit used for each page's fetch */
     limitPerPage: 500,
 
-    initialize: function(models, options) {
+    initialize: function (models, options) {
         ControlledFetchCollection.prototype.initialize.call(this, models, options);
         this.currentPage = options.currentPage || 0;
     },
 
-    getTotalItemCount: function() {
+    getTotalItemCount: function () {
         return this.length;
     },
 
-    shouldPaginate: function() {
+    shouldPaginate: function () {
         return this.getTotalItemCount() >= this.limitPerPage;
     },
 
-    getLastPage: function() {
+    getLastPage: function () {
         return Math.floor(this.getTotalItemCount() / this.limitPerPage);
     },
 
-    getPageCount: function() {
+    getPageCount: function () {
         return this.getLastPage() + 1;
     },
 
-    getPageLimitOffset: function(pageNum) {
+    getPageLimitOffset: function (pageNum) {
         pageNum = this.constrainPageNum(pageNum);
         return {
             limit: this.limitPerPage,
-            offset: pageNum * this.limitPerPage
+            offset: pageNum * this.limitPerPage,
         };
     },
 
-    constrainPageNum: function(pageNum) {
+    constrainPageNum: function (pageNum) {
         return Math.max(0, Math.min(pageNum, this.getLastPage()));
     },
 
     /** fetch the next page of data */
-    fetchPage: function(pageNum, options) {
+    fetchPage: function (pageNum, options) {
         var self = this;
         pageNum = self.constrainPageNum(pageNum);
         self.currentPage = pageNum;
@@ -218,17 +218,17 @@ var PaginatedCollection = ControlledFetchCollection.extend({
         });
     },
 
-    fetchCurrentPage: function(options) {
+    fetchCurrentPage: function (options) {
         return this.fetchPage(this.currentPage, options);
     },
 
-    fetchPrevPage: function(options) {
+    fetchPrevPage: function (options) {
         return this.fetchPage(this.currentPage - 1, options);
     },
 
-    fetchNextPage: function(options) {
+    fetchNextPage: function (options) {
         return this.fetchPage(this.currentPage + 1, options);
-    }
+    },
 });
 
 //=============================================================================
@@ -241,7 +241,7 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
     /** @type {Number} limit used for each subsequent fetch */
     limitPerFetch: 100,
 
-    initialize: function(models, options) {
+    initialize: function (models, options) {
         ControlledFetchCollection.prototype.initialize.call(this, models, options);
         /** @type {Integer} number of contents to return from the first fetch */
         this.limitOnFirstFetch = options.limitOnFirstFetch || this.limitOnFirstFetch;
@@ -254,7 +254,7 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
     },
 
     /** build ajax data/parameters from options */
-    _buildFetchOptions: function(options) {
+    _buildFetchOptions: function (options) {
         // options (options for backbone.fetch and jquery.ajax generally)
         // backbone option; false here to make fetching an addititive process
         options.remove = options.remove || false;
@@ -262,20 +262,20 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
     },
 
     /** fetch the first 'page' of data */
-    fetchFirst: function(options) {
+    fetchFirst: function (options) {
         options = options ? _.clone(options) : {};
         this.allFetched = false;
         this.lastFetched = 0;
         return this.fetchMore(
             _.defaults(options, {
                 reset: true,
-                limit: this.limitOnFirstFetch
+                limit: this.limitOnFirstFetch,
             })
         );
     },
 
     /** fetch the next page of data */
-    fetchMore: function(options) {
+    fetchMore: function (options) {
         options = _.clone(options || {});
         var collection = this;
 
@@ -313,7 +313,7 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
     },
 
     /** fetch all the collection */
-    fetchAll: function(options) {
+    fetchAll: function (options) {
         // whitelist options to prevent allowing limit/offset/filters
         // (use vanilla fetch instead)
         options = options || {};
@@ -324,12 +324,12 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
             self.allFetched = true;
             self.trigger("all-fetched", self);
         });
-    }
+    },
 });
 
 //==============================================================================
 export default {
     ControlledFetchCollection: ControlledFetchCollection,
     PaginatedCollection: PaginatedCollection,
-    InfinitelyScrollingCollection: InfinitelyScrollingCollection
+    InfinitelyScrollingCollection: InfinitelyScrollingCollection,
 };
diff --git a/client/galaxy/scripts/mvc/collection/base-creator.js b/client/galaxy/scripts/mvc/collection/base-creator.js
index abe7c8dcdc59..1204cd556f4a 100644
--- a/client/galaxy/scripts/mvc/collection/base-creator.js
+++ b/client/galaxy/scripts/mvc/collection/base-creator.js
@@ -4,13 +4,11 @@
 import _ from "underscore";
 var CollectionCreatorMixin = {
     /** add (or clear if clear is truthy) a validation warning to the DOM element described in what */
-    _validationWarning: function(what, clear) {
+    _validationWarning: function (what, clear) {
         var VALIDATION_CLASS = "validation-warning";
         if (what === "name") {
             what = this.$(".collection-name").add(this.$(".collection-name-prompt"));
-            this.$(".collection-name")
-                .focus()
-                .select();
+            this.$(".collection-name").focus().select();
         }
         if (clear) {
             what = what || this.$(`.${VALIDATION_CLASS}`);
@@ -20,50 +18,50 @@ var CollectionCreatorMixin = {
         }
     },
 
-    _changeHideOriginals: function(ev) {
+    _changeHideOriginals: function (ev) {
         this.hideOriginals = this.$(".hide-originals").prop("checked");
     },
 
     // ........................................................................ footer
     /** handle a collection name change */
-    _changeName: function(ev) {
+    _changeName: function (ev) {
         this._validationWarning("name", !!this._getName());
     },
 
     /** check for enter key press when in the collection name and submit */
-    _nameCheckForEnter: function(ev) {
+    _nameCheckForEnter: function (ev) {
         if (ev.keyCode === 13 && !this.blocking) {
             this._clickCreate();
         }
     },
 
     /** get the current collection name */
-    _getName: function() {
+    _getName: function () {
         return _.escape(this.$(".collection-name").val());
     },
 
     // ........................................................................ header
     /** expand help */
-    _clickMoreHelp: function(ev) {
+    _clickMoreHelp: function (ev) {
         ev.stopPropagation();
         this.$(".main-help").addClass("expanded");
         this.$(".more-help").hide();
     },
     /** collapse help */
-    _clickLessHelp: function(ev) {
+    _clickLessHelp: function (ev) {
         ev.stopPropagation();
         this.$(".main-help").removeClass("expanded");
         this.$(".more-help").show();
     },
     /** toggle help */
-    _toggleHelp: function(ev) {
+    _toggleHelp: function (ev) {
         ev.stopPropagation();
         this.$(".main-help").toggleClass("expanded");
         this.$(".more-help").toggle();
     },
 
     /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*) */
-    _showAlert: function(message, alertClass) {
+    _showAlert: function (message, alertClass) {
         alertClass = alertClass || "alert-danger";
         this.$(".main-help").hide();
         this.$(".header .alert")
@@ -74,19 +72,19 @@ var CollectionCreatorMixin = {
             .html(message);
     },
     /** hide the alerts at the top */
-    _hideAlert: function(message) {
+    _hideAlert: function (message) {
         this.$(".main-help").show();
         this.$(".header .alert").hide();
     },
 
-    _cancelCreate: function(ev) {
+    _cancelCreate: function (ev) {
         if (typeof this.oncancel === "function") {
             this.oncancel.call(this);
         }
     },
 
     /** attempt to create the current collection */
-    _clickCreate: function(ev) {
+    _clickCreate: function (ev) {
         var name = this._getName();
         if (!name) {
             this._validationWarning("name");
@@ -95,16 +93,14 @@ var CollectionCreatorMixin = {
         }
     },
 
-    _setUpCommonSettings: function(attributes) {
+    _setUpCommonSettings: function (attributes) {
         this.hideOriginals = attributes.defaultHideSourceItems || false;
     },
 
     /** render the footer, completion controls, and cancel controls */
-    _renderFooter: function(speed, callback) {
+    _renderFooter: function (speed, callback) {
         var self = this;
-        var $footer = this.$(".footer")
-            .empty()
-            .html(this.templates.footer());
+        var $footer = this.$(".footer").empty().html(this.templates.footer());
         _.each(this.footerSettings, (property, selector) => {
             self.$(selector).prop("checked", self[property]);
         });
@@ -119,13 +115,13 @@ var CollectionCreatorMixin = {
             [
                 '<div class="header flex-row no-flex"></div>',
                 '<div class="middle flex-row flex-row-container"></div>',
-                '<div class="footer flex-row no-flex"></div>'
+                '<div class="footer flex-row no-flex"></div>',
             ].join("")
-        )
-    }
+        ),
+    },
 };
 
 //==============================================================================
 export default {
-    CollectionCreatorMixin: CollectionCreatorMixin
+    CollectionCreatorMixin: CollectionCreatorMixin,
 };
diff --git a/client/galaxy/scripts/mvc/collection/collection-li-edit.js b/client/galaxy/scripts/mvc/collection/collection-li-edit.js
index f0605101dcb7..2d6e286efe52 100644
--- a/client/galaxy/scripts/mvc/collection/collection-li-edit.js
+++ b/client/galaxy/scripts/mvc/collection/collection-li-edit.js
@@ -10,16 +10,16 @@ var DCListItemView = DC_LI.DCListItemView;
 var DCListItemEdit = DCListItemView.extend(
     /** @lends DCListItemEdit.prototype */ {
         /** override to add linkTarget */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             DCListItemView.prototype.initialize.call(this, attributes);
         },
 
         // ......................................................................... misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `DCListItemEdit(${modelString})`;
-        }
+        },
     }
 );
 
@@ -32,16 +32,16 @@ var DCEListItemEdit = DCEListItemView.extend(
         //TODO: this might be expendable - compacted with HDAListItemView
 
         /** set up */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             DCEListItemView.prototype.initialize.call(this, attributes);
         },
 
         // ......................................................................... misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `DCEListItemEdit(${modelString})`;
-        }
+        },
     }
 );
 
@@ -54,7 +54,7 @@ var DCEListItemEdit = DCEListItemView.extend(
 var DatasetDCEListItemEdit = DATASET_LI_EDIT.DatasetListItemEdit.extend(
     /** @lends DatasetDCEListItemEdit.prototype */ {
         /** set up */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             DATASET_LI_EDIT.DatasetListItemEdit.prototype.initialize.call(this, attributes);
         },
 
@@ -63,7 +63,7 @@ var DatasetDCEListItemEdit = DATASET_LI_EDIT.DatasetListItemEdit.extend(
         /** In this override, only get details if in the ready state.
          *  Note: fetch with no 'change' event triggering to prevent automatic rendering.
          */
-        _fetchModelDetails: function() {
+        _fetchModelDetails: function () {
             var view = this;
             if (view.model.inReadyState() && !view.model.hasDetails()) {
                 return view.model.fetch({ silent: true });
@@ -72,16 +72,16 @@ var DatasetDCEListItemEdit = DATASET_LI_EDIT.DatasetListItemEdit.extend(
         },
 
         /** Override to remove delete button */
-        _renderDeleteButton: function() {
+        _renderDeleteButton: function () {
             return null;
         },
 
         // ......................................................................... misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `DatasetDCEListItemEdit(${modelString})`;
-        }
+        },
     }
 );
 
@@ -89,7 +89,7 @@ var DatasetDCEListItemEdit = DATASET_LI_EDIT.DatasetListItemEdit.extend(
 /** underscore templates */
 DatasetDCEListItemEdit.prototype.templates = (() =>
     _.extend({}, DATASET_LI_EDIT.DatasetListItemEdit.prototype.templates, {
-        titleBar: DC_LI.DatasetDCEListItemView.prototype.templates.titleBar
+        titleBar: DC_LI.DatasetDCEListItemView.prototype.templates.titleBar,
     }))();
 
 //==============================================================================
@@ -99,10 +99,10 @@ DatasetDCEListItemEdit.prototype.templates = (() =>
 var NestedDCDCEListItemEdit = DC_LI.NestedDCDCEListItemView.extend(
     /** @lends NestedDCDCEListItemEdit.prototype */ {
         /** String representation */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `NestedDCDCEListItemEdit(${modelString})`;
-        }
+        },
     }
 );
 
@@ -111,5 +111,5 @@ export default {
     DCListItemEdit: DCListItemEdit,
     DCEListItemEdit: DCEListItemEdit,
     DatasetDCEListItemEdit: DatasetDCEListItemEdit,
-    NestedDCDCEListItemEdit: NestedDCDCEListItemEdit
+    NestedDCDCEListItemEdit: NestedDCDCEListItemEdit,
 };
diff --git a/client/galaxy/scripts/mvc/collection/collection-li.js b/client/galaxy/scripts/mvc/collection/collection-li.js
index 48c0b7cf88ce..6fdef8ea7baa 100644
--- a/client/galaxy/scripts/mvc/collection/collection-li.js
+++ b/client/galaxy/scripts/mvc/collection/collection-li.js
@@ -10,21 +10,21 @@ import _l from "utils/localization";
 var DCListItemView = FoldoutListItemView.extend(
     /** @lends DCListItemView.prototype */ {
         className: `${FoldoutListItemView.prototype.className} dataset-collection`,
-        id: function() {
+        id: function () {
             return ["dataset_collection", this.model.get("id")].join("-");
         },
 
         /** override to add linkTarget */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             this.linkTarget = attributes.linkTarget || "_blank";
             this.hasUser = attributes.hasUser;
             FoldoutListItemView.prototype.initialize.call(this, attributes);
         },
 
         /** event listeners */
-        _setUpListeners: function() {
+        _setUpListeners: function () {
             FoldoutListItemView.prototype._setUpListeners.call(this);
-            this.listenTo(this.model, "change", function(model, options) {
+            this.listenTo(this.model, "change", function (model, options) {
                 // if the model has changed deletion status render it entirely
                 if (_.has(model.changed, "deleted")) {
                     this.render();
@@ -39,31 +39,31 @@ var DCListItemView = FoldoutListItemView.extend(
 
         // ......................................................................... rendering
         /** render a subtitle to show the user what sort of collection this is */
-        _renderSubtitle: function() {
+        _renderSubtitle: function () {
             return $(this.templates.subtitle(this.model.toJSON(), this));
         },
 
         // ......................................................................... foldout
         /** override to add linktarget to sub-panel */
-        _getFoldoutPanelOptions: function() {
+        _getFoldoutPanelOptions: function () {
             var options = FoldoutListItemView.prototype._getFoldoutPanelOptions.call(this);
             return _.extend(options, {
                 linkTarget: this.linkTarget,
-                hasUser: this.hasUser
+                hasUser: this.hasUser,
             });
         },
 
         /** override to not catch sub-panel selectors */
-        $selector: function() {
+        $selector: function () {
             return this.$("> .selector");
         },
 
         // ......................................................................... misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `DCListItemView(${modelString})`;
-        }
+        },
     }
 );
 
@@ -78,14 +78,14 @@ DCListItemView.prototype.templates = (() => {
             _l("There was an error getting the data for this collection"),
             ": <%- model.error %>",
             "</div>",
-            "<% } %>"
+            "<% } %>",
         ]),
         purged: BASE_MVC.wrapTemplate([
             "<% if( model.purged ){ %>",
             '<div class="purged-msg warningmessagesmall">',
             _l("This collection has been deleted and removed from disk"),
             "</div>",
-            "<% } %>"
+            "<% } %>",
         ]),
         deleted: BASE_MVC.wrapTemplate([
             // deleted not purged
@@ -93,8 +93,8 @@ DCListItemView.prototype.templates = (() => {
             '<div class="deleted-msg warningmessagesmall">',
             _l("This collection has been deleted"),
             "</div>",
-            "<% } %>"
-        ])
+            "<% } %>",
+        ]),
     });
 
     // use element identifier
@@ -105,7 +105,7 @@ DCListItemView.prototype.templates = (() => {
             '<span class="name"><%- collection.element_identifier || collection.name %></span>',
             "</div>",
             '<div class="subtitle"></div>',
-            "</div>"
+            "</div>",
         ],
         "collection"
     );
@@ -124,7 +124,7 @@ DCListItemView.prototype.templates = (() => {
             '<% } else if( collection.collection_type === "list:list" ){ %>',
             _l("a list of <%- countText %>dataset lists"),
             "<% } %>",
-            "</div>"
+            "</div>",
         ],
         "collection"
     );
@@ -132,7 +132,7 @@ DCListItemView.prototype.templates = (() => {
     return _.extend({}, FoldoutListItemView.prototype.templates, {
         warnings: warnings,
         titleBar: titleBarTemplate,
-        subtitle: subtitleTemplate
+        subtitle: subtitleTemplate,
     });
 })();
 
@@ -145,7 +145,7 @@ var DCEListItemView = ListItemView.extend(
         className: `${ListItemView.prototype.className} dataset-collection-element`,
 
         /** set up */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             if (attributes.logger) {
                 this.logger = this.model.logger = attributes.logger;
             }
@@ -155,10 +155,10 @@ var DCEListItemView = ListItemView.extend(
 
         // ......................................................................... misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `DCEListItemView(${modelString})`;
-        }
+        },
     }
 );
 
@@ -173,13 +173,13 @@ DCEListItemView.prototype.templates = (() => {
             '<span class="name"><%- element.element_identifier %></span>',
             "</div>",
             '<div class="subtitle"></div>',
-            "</div>"
+            "</div>",
         ],
         "element"
     );
 
     return _.extend({}, ListItemView.prototype.templates, {
-        titleBar: titleBarTemplate
+        titleBar: titleBarTemplate,
     });
 })();
 
@@ -192,7 +192,7 @@ var DatasetDCEListItemView = DatasetListItemView.extend(
         className: `${DatasetListItemView.prototype.className} dataset-collection-element`,
 
         /** set up */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             if (attributes.logger) {
                 this.logger = this.model.logger = attributes.logger;
             }
@@ -203,7 +203,7 @@ var DatasetDCEListItemView = DatasetListItemView.extend(
         /** In this override, only get details if in the ready state.
          *  Note: fetch with no 'change' event triggering to prevent automatic rendering.
          */
-        _fetchModelDetails: function() {
+        _fetchModelDetails: function () {
             var view = this;
             if (view.model.inReadyState() && !view.model.hasDetails()) {
                 return view.model.fetch({ silent: true });
@@ -213,10 +213,10 @@ var DatasetDCEListItemView = DatasetListItemView.extend(
 
         // ......................................................................... misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `DatasetDCEListItemView(${modelString})`;
-        }
+        },
     }
 );
 
@@ -232,13 +232,13 @@ DatasetDCEListItemView.prototype.templates = (() => {
             '<div class="title">',
             '<span class="name"><%- element.element_identifier %></span>',
             "</div>",
-            "</div>"
+            "</div>",
         ],
         "element"
     );
 
     return _.extend({}, DatasetListItemView.prototype.templates, {
-        titleBar: titleBarTemplate
+        titleBar: titleBarTemplate,
     });
 })();
 
@@ -251,7 +251,7 @@ var NestedDCDCEListItemView = DCListItemView.extend(
         className: `${DCListItemView.prototype.className} dataset-collection-element`,
 
         /** In this override, add the state as a class for use with state-based CSS */
-        _swapNewRender: function($newRender) {
+        _swapNewRender: function ($newRender) {
             DCListItemView.prototype._swapNewRender.call(this, $newRender);
             var state = this.model.get("state") || "ok";
             this.$el.addClass(`state-${state}`);
@@ -260,10 +260,10 @@ var NestedDCDCEListItemView = DCListItemView.extend(
 
         // ......................................................................... misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `NestedDCDCEListItemView(${modelString})`;
-        }
+        },
     }
 );
 
@@ -272,5 +272,5 @@ export default {
     DCListItemView: DCListItemView,
     DCEListItemView: DCEListItemView,
     DatasetDCEListItemView: DatasetDCEListItemView,
-    NestedDCDCEListItemView: NestedDCDCEListItemView
+    NestedDCDCEListItemView: NestedDCDCEListItemView,
 };
diff --git a/client/galaxy/scripts/mvc/collection/collection-model.js b/client/galaxy/scripts/mvc/collection/collection-model.js
index 4f99ac3c0dbc..561358972646 100644
--- a/client/galaxy/scripts/mvc/collection/collection-model.js
+++ b/client/galaxy/scripts/mvc/collection/collection-model.js
@@ -58,11 +58,11 @@ var DatasetCollectionElementMixin = {
         model_class: "DatasetCollectionElement",
         element_identifier: null,
         element_index: null,
-        element_type: null
+        element_type: null,
     },
 
     /** merge the attributes of the sub-object 'object' into this model */
-    _mergeObject: function(attributes) {
+    _mergeObject: function (attributes) {
         // Don't let the dataset ID replace the DCE's ID so record it as the
         // element_id and when fetching dataset details below use the element_id
         // instead of this.id.
@@ -73,14 +73,14 @@ var DatasetCollectionElementMixin = {
             delete attributes.object.id;
         }
         _.extend(attributes, attributes.object, {
-            element_id: elementId
+            element_id: elementId,
         });
         delete attributes.object;
         return attributes;
     },
 
     /** override to merge this.object into this */
-    constructor: function(attributes, options) {
+    constructor: function (attributes, options) {
         // console.debug( '\t DatasetCollectionElement.constructor:', attributes, options );
         attributes = this._mergeObject(attributes);
         this.idAttribute = "element_id";
@@ -88,11 +88,11 @@ var DatasetCollectionElementMixin = {
     },
 
     /** when the model is fetched, merge this.object into this */
-    parse: function(response, options) {
+    parse: function (response, options) {
         var attributes = response;
         attributes = this._mergeObject(attributes);
         return attributes;
-    }
+    },
 };
 
 /** @class Concrete class of Generic DatasetCollectionElement */
@@ -112,9 +112,9 @@ var DCECollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(
         model: DatasetCollectionElement,
 
         /** String representation. */
-        toString: function() {
+        toString: function () {
             return ["DatasetCollectionElementCollection(", this.length, ")"].join("");
-        }
+        },
     }
 );
 
@@ -126,7 +126,7 @@ var DatasetDCE = DATASET_MODEL.DatasetAssociation.extend(
         DatasetCollectionElementMixin,
         /** @lends DatasetDCE.prototype */ {
             /** url fn */
-            url: function() {
+            url: function () {
                 // won't always be an hda
                 if (!this.has("history_id")) {
                     console.warn("no endpoint for non-hdas within a collection yet");
@@ -137,7 +137,7 @@ var DatasetDCE = DATASET_MODEL.DatasetAssociation.extend(
                 return `${getAppRoot()}api/histories/${this.get("history_id")}/contents/${datasetId}`;
             },
 
-            _getDatasetId: function() {
+            _getDatasetId: function () {
                 // I'm a DCE acting as dataset, this URL needs to be the dataset URL so
                 // use element_id instead of id. See note above in _mergeObject and
                 // discussion on #3782 for more context.
@@ -150,7 +150,7 @@ var DatasetDCE = DATASET_MODEL.DatasetAssociation.extend(
                 DatasetCollectionElementMixin.defaults
             ),
 
-            _downloadQueryParameters: function() {
+            _downloadQueryParameters: function () {
                 // Setting the file extension to just 'data' defers that
                 // decision to the serverside, setting based on the datatype.
                 var fileExt = this.get("file_ext") || "data";
@@ -163,22 +163,22 @@ var DatasetDCE = DATASET_MODEL.DatasetAssociation.extend(
             //  the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model
             //  - re-apply manually for now
             /** call the mixin constructor */
-            constructor: function(attributes, options) {
+            constructor: function (attributes, options) {
                 this.debug("\t DatasetDCE.constructor:", attributes, options);
                 //DATASET_MODEL.DatasetAssociation.prototype.constructor.call( this, attributes, options );
                 DatasetCollectionElementMixin.constructor.call(this, attributes, options);
             },
 
             /** Does this model already contain detailed data (as opposed to just summary level data)? */
-            hasDetails: function() {
+            hasDetails: function () {
                 return this.elements && this.elements.length;
             },
 
             /** String representation. */
-            toString: function() {
+            toString: function () {
                 var objStr = this.get("element_identifier");
                 return `DatasetDCE(${objStr})`;
-            }
+            },
         }
     )
 );
@@ -191,9 +191,9 @@ var DatasetDCECollection = DCECollection.extend(
         model: DatasetDCE,
 
         /** String representation. */
-        toString: function() {
+        toString: function () {
             return ["DatasetDCECollection(", this.length, ")"].join("");
-        }
+        },
     }
 );
 
@@ -217,11 +217,11 @@ var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin)
                 /* 'list', 'paired', or 'list:paired' */
                 collection_type: null,
                 //??
-                deleted: false
+                deleted: false,
             },
 
             /** Which class to use for elements */
-            collectionClass: function() {
+            collectionClass: function () {
                 if (this.attributes.collection_type.indexOf(":") > 0) {
                     return NestedDCDCECollection;
                 } else {
@@ -230,10 +230,10 @@ var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin)
             },
 
             /** set up: create elements instance var and (on changes to elements) update them  */
-            initialize: function(model, options) {
+            initialize: function (model, options) {
                 this.debug(`${this}(DatasetCollection).initialize:`, model, options, this);
                 this.elements = this._createElementsModel();
-                this.on("change:elements", function() {
+                this.on("change:elements", function () {
                     this.log("change:elements");
                     //TODO: prob. better to update the collection instead of re-creating it
                     this.elements = this._createElementsModel();
@@ -241,7 +241,7 @@ var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin)
             },
 
             /** move elements model attribute to full collection */
-            _createElementsModel: function() {
+            _createElementsModel: function () {
                 var collectionClass = this.collectionClass();
                 this.debug(`${this}._createElementsModel`, collectionClass, this.get("elements"), this.elements);
                 //TODO: same patterns as DatasetCollectionElement _createObjectModel - refactor to BASE_MVC.hasSubModel?
@@ -250,7 +250,7 @@ var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin)
                 var parentHdcaId = this.get("parent_hdca_id") || this.get("id");
                 _.each(elements, (element, index) => {
                     _.extend(element, {
-                        parent_hdca_id: parentHdcaId
+                        parent_hdca_id: parentHdcaId,
                     });
                 });
                 this.elements = new collectionClass(elements);
@@ -260,7 +260,7 @@ var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin)
 
             // ........................................................................ common queries
             /** pass the elements back within the model json when this is serialized */
-            toJSON: function() {
+            toJSON: function () {
                 var json = Backbone.Model.prototype.toJSON.call(this);
                 if (this.elements) {
                     json.elements = this.elements.toJSON();
@@ -271,26 +271,26 @@ var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin)
             /** Is this collection in a 'ready' state no processing (for the collection) is left
              *  to do on the server.
              */
-            inReadyState: function() {
+            inReadyState: function () {
                 var populated = this.get("populated");
                 return this.isDeletedOrPurged() || populated;
             },
 
             //TODO:?? the following are the same interface as DatasetAssociation - can we combine?
             /** Does the DC contain any elements yet? Is a fetch() required? */
-            hasDetails: function() {
+            hasDetails: function () {
                 return this.elements.length !== 0;
             },
 
             /** Given the filters, what models in this.elements would be returned? */
-            getVisibleContents: function(filters) {
+            getVisibleContents: function (filters) {
                 // filters unused for now
                 return this.elements;
             },
 
             // ........................................................................ ajax
             /** override to use actual Dates objects for create/update times */
-            parse: function(response, options) {
+            parse: function (response, options) {
                 var parsed = Backbone.Model.prototype.parse.call(this, response, options);
                 if (parsed.create_time) {
                     parsed.create_time = new Date(parsed.create_time);
@@ -302,7 +302,7 @@ var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin)
             },
 
             /** save this collection, _Mark_ing it as deleted (just a flag) */
-            delete: function(recursive, purge, options) {
+            delete: function (recursive, purge, options) {
                 recursive = recursive || false;
                 purge = purge || false;
                 if (this.get("deleted")) {
@@ -312,7 +312,7 @@ var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin)
                 return this.save({ deleted: true, recursive: recursive, purge: purge }, options);
             },
             /** save this collection, _Mark_ing it as undeleted */
-            undelete: function(options) {
+            undelete: function (options) {
                 if (!this.get("deleted")) {
                     return $.when();
                 }
@@ -320,7 +320,7 @@ var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin)
             },
 
             /** Is this collection deleted or purged? */
-            isDeletedOrPurged: function() {
+            isDeletedOrPurged: function () {
                 return this.get("deleted") || this.get("purged");
             },
 
@@ -330,10 +330,10 @@ var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin)
 
             // ........................................................................ misc
             /** String representation */
-            toString: function() {
+            toString: function () {
                 var idAndName = [this.get("id"), this.get("name") || this.get("element_identifier")];
                 return `DatasetCollection(${idAndName.join(",")})`;
-            }
+            },
         }
     );
 
@@ -352,16 +352,16 @@ var NestedDCDCE = DatasetCollection.extend(
             //  the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model
             //  - re-apply manually it now
             /** call the mixin constructor */
-            constructor: function(attributes, options) {
+            constructor: function (attributes, options) {
                 this.debug("\t NestedDCDCE.constructor:", attributes, options);
                 DatasetCollectionElementMixin.constructor.call(this, attributes, options);
             },
 
             /** String representation. */
-            toString: function() {
+            toString: function () {
                 var objStr = this.object ? `${this.object}` : this.get("element_identifier");
                 return ["NestedDCDCE(", objStr, ")"].join("");
-            }
+            },
         }
     )
 );
@@ -375,13 +375,13 @@ var NestedDCDCECollection = DCECollection.extend(
         model: NestedDCDCE,
 
         /** String representation. */
-        toString: function() {
+        toString: function () {
             return ["NestedDCDCECollection(", this.length, ")"].join("");
-        }
+        },
     }
 );
 
 //==============================================================================
 export default {
-    DatasetCollection: DatasetCollection
+    DatasetCollection: DatasetCollection,
 };
diff --git a/client/galaxy/scripts/mvc/collection/collection-view-edit.js b/client/galaxy/scripts/mvc/collection/collection-view-edit.js
index c77e59cc217e..b07e77ec5032 100644
--- a/client/galaxy/scripts/mvc/collection/collection-view-edit.js
+++ b/client/galaxy/scripts/mvc/collection/collection-view-edit.js
@@ -25,9 +25,9 @@ var CollectionViewEdit = _super.extend(
         /** sub view class used for nested collections */
         NestedDCDCEViewClass: DC_EDIT.NestedDCDCEListItemEdit,
 
-        getNestedDCDCEViewClass: function() {
+        getNestedDCDCEViewClass: function () {
             return DC_EDIT.NestedDCDCEListItemEdit.extend({
-                foldoutPanelClass: CollectionViewEdit
+                foldoutPanelClass: CollectionViewEdit,
             });
         },
 
@@ -35,13 +35,13 @@ var CollectionViewEdit = _super.extend(
         /** Set up the view, set up storage, bind listeners to HistoryContents events
          *  @param {Object} attributes optional settings for the panel
          */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             _super.prototype.initialize.call(this, attributes);
         },
 
         /** In this override, make the collection name editable
          */
-        _setUpBehaviors: function($where) {
+        _setUpBehaviors: function ($where) {
             $where = $where || this.$el;
             _super.prototype._setUpBehaviors.call(this, $where);
             if (!this.model) {
@@ -65,7 +65,7 @@ var CollectionViewEdit = _super.extend(
                 .attr("title", _l("Click to rename collection"))
                 .tooltip({ placement: "bottom" })
                 .make_text_editable({
-                    on_finish: function(newName) {
+                    on_finish: function (newName) {
                         var previousName = panel.model.get("name");
                         if (newName && newName !== previousName) {
                             panel.$el.find(nameSelector).text(newName);
@@ -75,14 +75,14 @@ var CollectionViewEdit = _super.extend(
                         } else {
                             panel.$el.find(nameSelector).text(previousName);
                         }
-                    }
+                    },
                 });
 
             const el = $where.find(".tags-display")[0];
             const propsData = {
                 model: this.model,
                 disabled: false,
-                context: "collection-view-edit"
+                context: "collection-view-edit",
             };
 
             const vm = mountModelTags(propsData, el);
@@ -102,13 +102,13 @@ var CollectionViewEdit = _super.extend(
 
         // ........................................................................ misc
         /** string rep */
-        toString: function() {
+        toString: function () {
             return `CollectionViewEdit(${this.model ? this.model.get("name") : ""})`;
-        }
+        },
     }
 );
 
 //==============================================================================
 export default {
-    CollectionViewEdit: CollectionViewEdit
+    CollectionViewEdit: CollectionViewEdit,
 };
diff --git a/client/galaxy/scripts/mvc/collection/collection-view.js b/client/galaxy/scripts/mvc/collection/collection-view.js
index ac49b0347898..07467adf885d 100644
--- a/client/galaxy/scripts/mvc/collection/collection-view.js
+++ b/client/galaxy/scripts/mvc/collection/collection-view.js
@@ -29,7 +29,7 @@ var CollectionView = _super.extend(
         /** Set up the view, set up storage, bind listeners to HistoryContents events
          *  @param {Object} attributes optional settings for the panel
          */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             _super.prototype.initialize.call(this, attributes);
             this.linkTarget = attributes.linkTarget || "_blank";
             this.dragItems = true;
@@ -43,13 +43,13 @@ var CollectionView = _super.extend(
             this.downloadUrl = `${getAppRoot()}api/dataset_collections/${this.model.attributes.id}/download`;
         },
 
-        getNestedDCDCEViewClass: function() {
+        getNestedDCDCEViewClass: function () {
             return DC_LI.NestedDCDCEListItemView.extend({
-                foldoutPanelClass: CollectionView
+                foldoutPanelClass: CollectionView,
             });
         },
 
-        _queueNewRender: function($newRender, speed) {
+        _queueNewRender: function ($newRender, speed) {
             speed = speed === undefined ? this.fxSpeed : speed;
             var panel = this;
             this.handleWarning($newRender);
@@ -61,7 +61,7 @@ var CollectionView = _super.extend(
             panel.trigger("rendered", panel);
         },
 
-        handleWarning: function($newRender) {
+        handleWarning: function ($newRender) {
             var viewLength = this.views.length;
             var elementCount = this.model.get("element_count");
             if (elementCount && elementCount !== viewLength) {
@@ -73,13 +73,13 @@ var CollectionView = _super.extend(
 
         // ------------------------------------------------------------------------ sub-views
         /** In this override, use model.getVisibleContents */
-        _filterCollection: function() {
+        _filterCollection: function () {
             //TODO: should *not* be model.getVisibleContents - visibility is not model related
             return this.model.getVisibleContents();
         },
 
         /** override to return proper view class based on element_type */
-        _getItemViewClass: function(model) {
+        _getItemViewClass: function (model) {
             //this.debug( this + '._getItemViewClass:', model );
             //TODO: subclasses use DCEViewClass - but are currently unused - decide
             switch (model.get("element_type")) {
@@ -92,47 +92,45 @@ var CollectionView = _super.extend(
         },
 
         /** override to add link target and anon */
-        _getItemViewOptions: function(model) {
+        _getItemViewOptions: function (model) {
             var options = _super.prototype._getItemViewOptions.call(this, model);
             return _.extend(options, {
                 linkTarget: this.linkTarget,
                 hasUser: this.hasUser,
                 //TODO: could move to only nested: list:paired
-                foldoutStyle: this.foldoutStyle
+                foldoutStyle: this.foldoutStyle,
             });
         },
 
         // ------------------------------------------------------------------------ collection sub-views
         /** In this override, add/remove expanded/collapsed model ids to/from web storage */
-        _setUpItemViewListeners: function(view) {
+        _setUpItemViewListeners: function (view) {
             var panel = this;
             _super.prototype._setUpItemViewListeners.call(panel, view);
 
             // use pub-sub to: handle drilldown expansion and collapse
             panel.listenTo(view, {
-                "expanded:drilldown": function(v, drilldown) {
+                "expanded:drilldown": function (v, drilldown) {
                     this._expandDrilldownPanel(drilldown);
                 },
-                "collapsed:drilldown": function(v, drilldown) {
+                "collapsed:drilldown": function (v, drilldown) {
                     this._collapseDrilldownPanel(drilldown);
-                }
+                },
             });
             return this;
         },
 
         /** Handle drill down by hiding this panels list and controls and showing the sub-panel */
-        _expandDrilldownPanel: function(drilldown) {
+        _expandDrilldownPanel: function (drilldown) {
             this.panelStack.push(drilldown);
             // hide this panel's controls and list, set the name for back navigation, and attach to the $el
-            this.$("> .controls")
-                .add(this.$list())
-                .hide();
+            this.$("> .controls").add(this.$list()).hide();
             drilldown.parentName = this.model.get("name");
             this.$el.append(drilldown.render().$el);
         },
 
         /** Handle drilldown close by freeing the panel and re-rendering this panel */
-        _collapseDrilldownPanel: function(drilldown) {
+        _collapseDrilldownPanel: function (drilldown) {
             this.panelStack.pop();
             this.render();
         },
@@ -140,20 +138,20 @@ var CollectionView = _super.extend(
         // ------------------------------------------------------------------------ panel events
         /** event map */
         events: {
-            "click .navigation .back": "close"
+            "click .navigation .back": "close",
         },
 
         /** close/remove this collection panel */
-        close: function(event) {
+        close: function (event) {
             this.remove();
             this.trigger("close");
         },
 
         // ........................................................................ misc
         /** string rep */
-        toString: function() {
+        toString: function () {
             return `CollectionView(${this.model ? this.model.get("name") : ""})`;
-        }
+        },
     }
 );
 
@@ -189,7 +187,7 @@ CollectionView.prototype.templates = (() => {
     };
 
     return _.extend(_.clone(_super.prototype.templates), {
-        controls: controlsTemplate
+        controls: controlsTemplate,
     });
 })();
 
@@ -228,5 +226,5 @@ function collectionDescription(collection) {
 export default {
     collectionTypeDescription: collectionTypeDescription,
     collectionDescription: collectionDescription,
-    CollectionView: CollectionView
+    CollectionView: CollectionView,
 };
diff --git a/client/galaxy/scripts/mvc/collection/list-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
index f739ed317ba7..f30bf474afd5 100644
--- a/client/galaxy/scripts/mvc/collection/list-collection-creator.js
+++ b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
@@ -33,12 +33,12 @@ var DatasetCollectionElementView = Backbone.View.extend(BASE_MVC.LoggableMixin).
     tagName: "li",
     className: "collection-element",
 
-    initialize: function(attributes) {
+    initialize: function (attributes) {
         this.element = attributes.element || {};
         this.selected = attributes.selected || false;
     },
 
-    render: function() {
+    render: function () {
         this.dragStartHandler = _.bind(this._dragstart, this);
         this.dragEndHandler = _.bind(this._dragend, this);
         var handle = this.$el
@@ -66,33 +66,33 @@ var DatasetCollectionElementView = Backbone.View.extend(BASE_MVC.LoggableMixin).
             _l("Remove this dataset from the list"),
             '">',
             _l("Discard"),
-            "</button>"
+            "</button>",
         ].join("")
     ),
 
     /** select this element and pub */
-    select: function(toggle) {
+    select: function (toggle) {
         this.$el.toggleClass("selected", toggle);
         this.trigger("select", {
             source: this,
-            selected: this.$el.hasClass("selected")
+            selected: this.$el.hasClass("selected"),
         });
     },
 
     /** animate the removal of this element and pub */
-    discard: function() {
+    discard: function () {
         var view = this;
         var parentWidth = this.$el.parent().width();
         this.$el.animate({ "margin-right": parentWidth }, "fast", () => {
             view.trigger("discard", {
-                source: view
+                source: view,
             });
             view.destroy();
         });
     },
 
     /** remove the DOM and any listeners */
-    destroy: function() {
+    destroy: function () {
         this.off();
         this.$el.remove();
     },
@@ -103,17 +103,17 @@ var DatasetCollectionElementView = Backbone.View.extend(BASE_MVC.LoggableMixin).
         "click .discard": "_clickDiscard",
 
         dragover: "_sendToParent",
-        drop: "_sendToParent"
+        drop: "_sendToParent",
     },
 
     /** select when the li is clicked */
-    _click: function(ev) {
+    _click: function (ev) {
         ev.stopPropagation();
         this.select(ev);
     },
 
     /** rename a pair when the name is clicked */
-    _clickName: function(ev) {
+    _clickName: function (ev) {
         ev.stopPropagation();
         ev.preventDefault();
 
@@ -127,13 +127,13 @@ var DatasetCollectionElementView = Backbone.View.extend(BASE_MVC.LoggableMixin).
     },
 
     /** discard when the discard button is clicked */
-    _clickDiscard: function(ev) {
+    _clickDiscard: function (ev) {
         ev.stopPropagation();
         this.discard();
     },
 
     /** dragging pairs for re-ordering */
-    _dragstart: function(ev) {
+    _dragstart: function (ev) {
         if (ev.originalEvent) {
             ev = ev.originalEvent;
         }
@@ -145,20 +145,20 @@ var DatasetCollectionElementView = Backbone.View.extend(BASE_MVC.LoggableMixin).
     },
 
     /** dragging for re-ordering */
-    _dragend: function(ev) {
+    _dragend: function (ev) {
         this.$el.removeClass("dragging");
         this.$el.parent().trigger("collection-element.dragend", [this]);
     },
 
     /** manually bubble up an event to the parent/container */
-    _sendToParent: function(ev) {
+    _sendToParent: function (ev) {
         this.$el.parent().trigger(ev);
     },
 
     /** string rep */
-    toString: function() {
+    toString: function () {
         return "DatasetCollectionElementView()";
-    }
+    },
 });
 
 // ============================================================================
@@ -181,25 +181,25 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         defaultAttributes: {
             //TODO: remove - use new collectionClass().save()
             /** takes elements and creates the proper collection - returns a promise */
-            creationFn: function() {
+            creationFn: function () {
                 throw new TypeError("no creation fn for creator");
             },
             /** fn to call when the collection is created (scoped to this) */
-            oncreate: function() {},
+            oncreate: function () {},
             /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */
-            oncancel: function() {},
+            oncancel: function () {},
             /** distance from list edge to begin autoscrolling list */
             autoscrollDist: 24,
             /** Color passed to hoverhighlight */
-            highlightClr: "rgba( 64, 255, 255, 1.0 )"
+            highlightClr: "rgba( 64, 255, 255, 1.0 )",
         },
 
         footerSettings: {
-            ".hide-originals": "hideOriginals"
+            ".hide-originals": "hideOriginals",
         },
 
         /** set up initial options, instance vars, behaviors */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             this.metric("ListCollectionCreator.initialize", attributes);
             var creator = this;
             _.each(this.defaultAttributes, (value, key) => {
@@ -217,7 +217,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** set up instance vars */
-        _instanceSetUp: function() {
+        _instanceSetUp: function () {
             /** Ids of elements that have been selected by the user - to preserve over renders */
             this.selectedIds = {};
             /** DOM elements currently being dragged */
@@ -228,7 +228,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
 
         // ------------------------------------------------------------------------ process raw list
         /** set up main data */
-        _elementsSetUp: function() {
+        _elementsSetUp: function () {
             //this.debug( '-- _dataSetUp' );
             /** a list of invalid elements and the reasons they aren't valid */
             this.invalidElements = [];
@@ -247,8 +247,8 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** add ids to dataset objs in initial list if none */
-        _ensureElementIds: function() {
-            this.workingElements.forEach(element => {
+        _ensureElementIds: function () {
+            this.workingElements.forEach((element) => {
                 if (!Object.prototype.hasOwnProperty.call(element, "id")) {
                     element.id = _.uniqueId();
                 }
@@ -257,16 +257,16 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** separate working list into valid and invalid elements for this collection */
-        _validateElements: function() {
+        _validateElements: function () {
             var creator = this;
             creator.invalidElements = [];
 
-            this.workingElements = this.workingElements.filter(element => {
+            this.workingElements = this.workingElements.filter((element) => {
                 var problem = creator._isElementInvalid(element);
                 if (problem) {
                     creator.invalidElements.push({
                         element: element,
-                        text: problem
+                        text: problem,
                     });
                 }
                 return !problem;
@@ -275,7 +275,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** describe what is wrong with a particular element if anything */
-        _isElementInvalid: function(element) {
+        _isElementInvalid: function (element) {
             if (element.history_content_type === "dataset_collection") {
                 return _l("is a collection, this is not allowed");
             }
@@ -290,11 +290,11 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** mangle duplicate names using a mac-like '(counter)' addition to any duplicates */
-        _mangleDuplicateNames: function() {
+        _mangleDuplicateNames: function () {
             var SAFETY = 900;
             var counter = 1;
             var existingNames = {};
-            this.workingElements.forEach(element => {
+            this.workingElements.forEach((element) => {
                 var currName = element.name;
                 while (Object.prototype.hasOwnProperty.call(existingNames, currName)) {
                     currName = `${element.name} (${counter})`;
@@ -309,7 +309,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** sort a list of elements */
-        _sortElements: function(list) {
+        _sortElements: function (list) {
             // // currently only natural sort by name
             // this.workingElements.sort( function( a, b ){ return naturalSort( a.name, b.name ); });
             // return this.workingElements;
@@ -318,7 +318,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         // ------------------------------------------------------------------------ rendering
         // templates : ListCollectionCreator.templates,
         /** render the entire interface */
-        render: function(speed, callback) {
+        render: function (speed, callback) {
             //this.debug( '-- _render' );
             if (this.workingElements.length < this.minElements) {
                 return this._renderInvalid(speed, callback);
@@ -335,12 +335,12 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** render a simplified interface aimed at telling the user why they can't move forward */
-        _renderInvalid: function(speed, callback) {
+        _renderInvalid: function (speed, callback) {
             //this.debug( '-- _render' );
             this.$el.empty().html(
                 this.templates.invalidInitial({
                     problems: this.invalidElements,
-                    elements: this.workingElements
+                    elements: this.workingElements,
                 })
             );
             if (typeof this.oncancel === "function") {
@@ -351,7 +351,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** render the header section */
-        _renderHeader: function(speed, callback) {
+        _renderHeader: function (speed, callback) {
             var $header = this.$(".header")
                 .empty()
                 .html(this.templates.header())
@@ -365,30 +365,28 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** render the middle including the elements */
-        _renderMiddle: function(speed, callback) {
-            var $middle = this.$(".middle")
-                .empty()
-                .html(this.templates.middle());
+        _renderMiddle: function (speed, callback) {
+            var $middle = this.$(".middle").empty().html(this.templates.middle());
             this._renderList(speed);
             return $middle;
         },
 
         /** add any jQuery/bootstrap/custom plugins to elements rendered */
-        _addPluginComponents: function() {
+        _addPluginComponents: function () {
             this.$(".help-content i").hoverhighlight(".collection-creator", this.highlightClr);
         },
 
         /** build and show an alert describing any elements that could not be included due to problems */
-        _invalidElementsAlert: function() {
+        _invalidElementsAlert: function () {
             this._showAlert(
                 this.templates.invalidElements({
-                    problems: this.invalidElements
+                    problems: this.invalidElements,
                 }),
                 "alert-warning"
             );
         },
 
-        _disableNameAndCreate: function(disable) {
+        _disableNameAndCreate: function (disable) {
             disable = !_.isUndefined(disable) ? disable : true;
             if (disable) {
                 this.$(".collection-name").prop("disabled", true);
@@ -401,12 +399,12 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
 
         // ------------------------------------------------------------------------ rendering elements
         /** conv. to the main list display DOM */
-        $list: function() {
+        $list: function () {
             return this.$(".collection-elements");
         },
 
         /** show or hide the clear selected control based on the num of selected elements */
-        _renderClearSelected: function() {
+        _renderClearSelected: function () {
             if (_.size(this.selectedIds)) {
                 this.$(".collection-elements-controls > .clear-selected").show();
             } else {
@@ -415,14 +413,14 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** render the elements in order (or a warning if no elements found) */
-        _renderList: function(speed, callback) {
+        _renderList: function (speed, callback) {
             //this.debug( '-- _renderList' );
             var creator = this;
 
             var $tmp = jQuery("<div/>");
             var $list = creator.$list();
 
-            _.each(this.elementViews, view => {
+            _.each(this.elementViews, (view) => {
                 view.destroy();
                 creator.removeElementView(view);
             });
@@ -432,7 +430,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
             //     return;
             // }
 
-            creator.workingElements.forEach(element => {
+            creator.workingElements.forEach((element) => {
                 var elementView = creator._createElementView(element);
                 $tmp.append(elementView.$el);
             });
@@ -449,12 +447,12 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** create an element view, cache in elementViews, set up listeners, and return */
-        _createElementView: function(element) {
+        _createElementView: function (element) {
             var elementView = new this.elementViewClass({
                 //TODO: use non-generic class or not all
                 // model : COLLECTION.DatasetDCE( element )
                 element: element,
-                selected: _.has(this.selectedIds, element.id)
+                selected: _.has(this.selectedIds, element.id),
             });
             this.elementViews.push(elementView);
             this._listenToElementView(elementView);
@@ -462,10 +460,10 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** listen to any element events */
-        _listenToElementView: function(view) {
+        _listenToElementView: function (view) {
             var creator = this;
             creator.listenTo(view, {
-                select: function(data) {
+                select: function (data) {
                     var element = data.source.element;
                     if (data.selected) {
                         creator.selectedIds[element.id] = true;
@@ -474,14 +472,14 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     }
                     creator.trigger("elements:select", data);
                 },
-                discard: function(data) {
+                discard: function (data) {
                     creator.trigger("elements:discard", data);
-                }
+                },
             });
         },
 
         /** add a new element view based on the json in element */
-        addElementView: function(element) {
+        addElementView: function (element) {
             //TODO: workingElements is sorted, add element in appropo index
             // add element, sort elements, find element index
             // var view = this._createElementView( element );
@@ -489,7 +487,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** stop listening to view and remove from caches */
-        removeElementView: function(view) {
+        removeElementView: function (view) {
             delete this.selectedIds[view.element.id];
             this._renderClearSelected();
 
@@ -498,7 +496,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** render a message in the list that no elements remain to create a collection */
-        _renderNoElementsLeft: function() {
+        _renderNoElementsLeft: function () {
             this._disableNameAndCreate(true);
             this.$(".collection-elements").append(this.templates.noElementsLeft());
         },
@@ -511,7 +509,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
 
         // ------------------------------------------------------------------------ API
         /** convert element into JSON compatible with the collections API */
-        _elementToJSON: function(element) {
+        _elementToJSON: function (element) {
             // return element.toJSON();
             return element;
         },
@@ -519,7 +517,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         /** create the collection via the API
          *  @returns {jQuery.xhr Object} the jquery ajax request
          */
-        createList: function(name) {
+        createList: function (name) {
             if (!this.workingElements.length) {
                 var message = `${_l("No valid elements for final list")}. `;
                 message += `<a class="cancel-create" href="javascript:void(0);" role="button">${_l("Cancel")}</a> `;
@@ -531,7 +529,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
 
             var creator = this;
 
-            var elements = this.workingElements.map(element => creator._elementToJSON(element));
+            var elements = this.workingElements.map((element) => creator._elementToJSON(element));
 
             creator.blocking = true;
             return creator
@@ -543,10 +541,10 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     creator.trigger("error", {
                         xhr: xhr,
                         status: status,
-                        message: _l("An error occurred while creating this collection")
+                        message: _l("An error occurred while creating this collection"),
                     });
                 })
-                .done(function(response, message, xhr) {
+                .done(function (response, message, xhr) {
                     creator.trigger("collection:created", response, message, xhr);
                     creator.metric("collection:created", response);
                     if (typeof creator.oncreate === "function") {
@@ -557,18 +555,18 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
 
         // ------------------------------------------------------------------------ events
         /** set up event handlers on self */
-        _setUpBehaviors: function() {
+        _setUpBehaviors: function () {
             this.on("error", this._errorHandler);
 
-            this.once("rendered", function() {
+            this.once("rendered", function () {
                 this.trigger("rendered:initial", this);
             });
 
-            this.on("elements:select", function(data) {
+            this.on("elements:select", function (data) {
                 this._renderClearSelected();
             });
 
-            this.on("elements:discard", function(data) {
+            this.on("elements:discard", function (data) {
                 var element = data.source.element;
                 this.removeElementView(data.source);
 
@@ -585,7 +583,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** handle errors with feedback and details to the user (if available) */
-        _errorHandler: function(data) {
+        _errorHandler: function (data) {
             this.error(data);
 
             var creator = this;
@@ -634,19 +632,19 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
             "keydown .collection-name": "_nameCheckForEnter",
             "change .hide-originals": "_changeHideOriginals",
             "click .cancel-create": "_cancelCreate",
-            "click .create-collection": "_clickCreate" //,
+            "click .create-collection": "_clickCreate", //,
         },
 
         // ........................................................................ elements
         /** reset all data to the initial state */
-        reset: function() {
+        reset: function () {
             this._instanceSetUp();
             this._elementsSetUp();
             this.render();
         },
 
         /** deselect all elements */
-        clearSelectedElements: function(ev) {
+        clearSelectedElements: function (ev) {
             this.$(".collection-elements .collection-element").removeClass("selected");
             this.$(".collection-elements-controls > .clear-selected").hide();
         },
@@ -660,7 +658,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         // },
 
         /** track the mouse drag over the list adding a placeholder to show where the drop would occur */
-        _dragoverElements: function(ev) {
+        _dragoverElements: function (ev) {
             //this.debug( '_dragoverElements:', ev );
             ev.preventDefault();
 
@@ -679,7 +677,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** If the mouse is near enough to the list's top or bottom, scroll the list */
-        _checkForAutoscroll: function($element, y) {
+        _checkForAutoscroll: function ($element, y) {
             var AUTOSCROLL_SPEED = 2;
             var offset = $element.offset();
             var scrollTop = $element.scrollTop();
@@ -695,7 +693,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         /** get the nearest element based on the mouse's Y coordinate.
          *  If the y is at the end of the list, return an empty jQuery object.
          */
-        _getNearestElement: function(y) {
+        _getNearestElement: function (y) {
             var WIGGLE = 4;
 
             var lis = this.$(".collection-elements li.collection-element").toArray();
@@ -712,7 +710,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** drop (dragged/selected elements) onto the list, re-ordering the internal list */
-        _dropElements: function(ev) {
+        _dropElements: function (ev) {
             if (ev.originalEvent) {
                 ev = ev.originalEvent;
             }
@@ -734,15 +732,15 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** resync the creator's list of elements based on the DOM order */
-        _syncOrderToDom: function() {
+        _syncOrderToDom: function () {
             var creator = this;
             var newElements = [];
             //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?
-            this.$(".collection-elements .collection-element").each(function() {
+            this.$(".collection-elements .collection-element").each(function () {
                 var id = $(this).attr("data-element-id");
 
                 var element = _.findWhere(creator.workingElements, {
-                    id: id
+                    id: id,
                 });
 
                 if (element) {
@@ -756,14 +754,14 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
         },
 
         /** drag communication with element sub-views: dragstart */
-        _elementDragstart: function(ev, element) {
+        _elementDragstart: function (ev, element) {
             // auto select the element causing the event and move all selected
             element.select(true);
             this.$dragging = this.$(".collection-elements .collection-element.selected");
         },
 
         /** drag communication with element sub-views: dragend - remove the placeholder */
-        _elementDragend: function(ev, element) {
+        _elementDragend: function (ev, element) {
             $(".element-drop-placeholder").remove();
             this.$dragging = null;
         },
@@ -793,7 +791,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     _l("Close and show more help"),
                     '" aria-hidden="true">&times;</button>',
                     '<span class="alert-message"></span>',
-                    "</div>"
+                    "</div>",
                 ].join("")
             ),
 
@@ -815,7 +813,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     "</a>",
                     "</div>",
                     '<div class="collection-elements scroll-container flex-row">',
-                    "</div>"
+                    "</div>",
                 ].join("")
             ),
 
@@ -867,7 +865,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     _l("Create list"),
                     "</button>",
                     "</div>",
-                    "</div>"
+                    "</div>",
                 ].join("")
             ),
 
@@ -879,7 +877,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                         [
                             "Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ",
                             "workflows in order to have analyses done on each member of the entire group. This interface allows ",
-                            "you to create a collection and re-order the final collection."
+                            "you to create a collection and re-order the final collection.",
                         ].join("")
                     ),
                     "</p>",
@@ -888,7 +886,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     _l(
                         [
                             "Rename elements in the list by clicking on ",
-                            '<i data-target=".collection-element .name">the existing name</i>.'
+                            '<i data-target=".collection-element .name">the existing name</i>.',
                         ].join("")
                     ),
                     "</li>",
@@ -896,7 +894,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     _l(
                         [
                             "Discard elements from the final created list by clicking on the ",
-                            '<i data-target=".collection-element .discard">"Discard"</i> button.'
+                            '<i data-target=".collection-element .discard">"Discard"</i> button.',
                         ].join("")
                     ),
                     "</li>",
@@ -906,7 +904,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                             "Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",
                             '<i data-target=".collection-element">them</i> and you can then move those selected by dragging the ',
                             "entire group. Deselect them by clicking them again or by clicking the ",
-                            'the <i data-target=".clear-selected">"Clear selected"</i> link.'
+                            'the <i data-target=".clear-selected">"Clear selected"</i> link.',
                         ].join("")
                     ),
                     "</li>",
@@ -914,7 +912,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     _l(
                         [
                             'Click the <i data-target=".reset">"Start over"</i> link to begin again as if you had just opened ',
-                            "the interface."
+                            "the interface.",
                         ].join("")
                     ),
                     "</li>",
@@ -930,10 +928,10 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     _l(
                         [
                             'Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ',
-                            'click <i data-target=".create-collection">"Create list"</i>.'
+                            'click <i data-target=".create-collection">"Create list"</i>.',
                         ].join("")
                     ),
-                    "</p>"
+                    "</p>",
                 ].join("")
             ),
 
@@ -943,7 +941,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     _l("The following selections could not be included due to problems:"),
                     "<ul><% _.each( problems, function( problem ){ %>",
                     "<li><b><%- problem.element.name %></b>: <%- problem.text %></li>",
-                    "<% }); %></ul>"
+                    "<% }); %></ul>",
                 ].join("")
             ),
 
@@ -956,7 +954,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     '<a class="reset" href="javascript:void(0)" role="button">',
                     _l("start over"),
                     "</a>?",
-                    "</li>"
+                    "</li>",
                 ].join("")
             ),
 
@@ -997,16 +995,16 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     // _l( 'Create a different kind of collection' ),
                     "</div>",
                     "</div>",
-                    "</div>"
+                    "</div>",
                 ].join("")
-            )
+            ),
         }),
 
         // ------------------------------------------------------------------------ misc
         /** string rep */
-        toString: function() {
+        toString: function () {
             return "ListCollectionCreator";
-        }
+        },
     });
 
 const collectionCreatorModalSetup = function _collectionCreatorModalSetup(options) {
@@ -1015,24 +1013,24 @@ const collectionCreatorModalSetup = function _collectionCreatorModalSetup(option
     const modal = Galaxy.modal || new UI_MODAL.View();
 
     const creatorOptions = _.defaults(options || {}, {
-        oncancel: function() {
+        oncancel: function () {
             modal.hide();
             deferred.reject("cancelled");
         },
-        oncreate: function(creator, response) {
+        oncreate: function (creator, response) {
             modal.hide();
             deferred.resolve(response);
-        }
+        },
     });
 
-    const showEl = function(el) {
+    const showEl = function (el) {
         modal.show({
             title: options.title || _l("Create a collection"),
             body: el,
             width: "85%",
             height: "100%",
             xlarge: true,
-            closing_events: true
+            closing_events: true,
         });
     };
 
@@ -1045,7 +1043,7 @@ const collectionCreatorModalSetup = function _collectionCreatorModalSetup(option
  */
 var collectionCreatorModal = function _collectionCreatorModal(elements, options, CreatorClass) {
     options = _.defaults(options || {}, {
-        elements: elements
+        elements: elements,
     });
     const { deferred, creatorOptions, showEl } = collectionCreatorModalSetup(options);
     var creator = new CreatorClass(creatorOptions);
@@ -1073,11 +1071,11 @@ var ruleBasedCollectionCreatorModal = function _ruleBasedCollectionCreatorModal(
         title = _l("Build Rules for Uploading Collections");
     }
     options = _.defaults(options || {}, {
-        title: title
+        title: title,
     });
     const { deferred, creatorOptions, showEl } = collectionCreatorModalSetup(options); // eslint-disable-line no-unused-vars
     return import(/* webpackChunkName: "ruleCollectionBuilder" */ "components/RuleCollectionBuilder.vue").then(
-        module => {
+        (module) => {
             var ruleCollectionBuilderInstance = Vue.extend(module.default);
             var vm = document.createElement("div");
             showEl(vm);
@@ -1092,8 +1090,8 @@ var ruleBasedCollectionCreatorModal = function _ruleBasedCollectionCreatorModal(
                     oncreate: options.oncreate,
                     defaultHideSourceItems: options.defaultHideSourceItems,
                     saveRulesFn: options.saveRulesFn,
-                    initialRules: options.initialRules
-                }
+                    initialRules: options.initialRules,
+                },
             }).$mount(vm);
             return deferred;
         }
@@ -1116,15 +1114,15 @@ function createListCollection(contents, defaultHideSourceItems) {
     const copyElements = !defaultHideSourceItems;
     const promise = listCollectionCreatorModal(elements, {
         defaultHideSourceItems: defaultHideSourceItems,
-        creationFn: function(elements, name, hideSourceItems) {
-            elements = elements.map(element => ({
+        creationFn: function (elements, name, hideSourceItems) {
+            elements = elements.map((element) => ({
                 id: element.id,
                 name: element.name,
                 //TODO: this allows for list:list even if the filter above does not - reconcile
-                src: element.history_content_type === "dataset" ? "hda" : "hdca"
+                src: element.history_content_type === "dataset" ? "hda" : "hdca",
             }));
             return contents.createHDCA(elements, "list", name, hideSourceItems, copyElements);
-        }
+        },
     });
 
     return promise;
@@ -1150,7 +1148,7 @@ function createCollectionViaRules(selection, defaultHideSourceItems) {
         // Have pasted data, data from a history dataset, or FTP list.
         const lines = selection.content
             .split(/[\n\r]/)
-            .filter(line => line.length > 0 && hasNonWhitespaceChars.exec(line));
+            .filter((line) => line.length > 0 && hasNonWhitespaceChars.exec(line));
 
         // Really poor tabular parser - we should get a library for this or expose options? I'm not
         // sure.
@@ -1162,16 +1160,16 @@ function createCollectionViaRules(selection, defaultHideSourceItems) {
             }
         }
         const regex = hasTabs ? /\t/ : /\s+/;
-        elements = lines.map(line => line.split(regex));
+        elements = lines.map((line) => line.split(regex));
         elementsType = selection.selectionType;
         importType = selection.dataType || "collections";
     }
     const promise = ruleBasedCollectionCreatorModal(elements, elementsType, importType, {
         ftpUploadSite: selection.ftpUploadSite,
         defaultHideSourceItems: defaultHideSourceItems,
-        creationFn: function(elements, collectionType, name, hideSourceItems) {
+        creationFn: function (elements, collectionType, name, hideSourceItems) {
             return selection.createHDCA(elements, collectionType, name, hideSourceItems, copyElements);
-        }
+        },
     });
     return promise;
 }
@@ -1184,5 +1182,5 @@ export default {
     listCollectionCreatorModal: listCollectionCreatorModal,
     createListCollection: createListCollection,
     createCollectionViaRules: createCollectionViaRules,
-    ruleBasedCollectionCreatorModal: ruleBasedCollectionCreatorModal
+    ruleBasedCollectionCreatorModal: ruleBasedCollectionCreatorModal,
 };
diff --git a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
index ea9e6746adbf..b06f9f5a9dd9 100644
--- a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
+++ b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
@@ -31,7 +31,7 @@ var PairView = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     tagName: "li",
     className: "dataset paired",
 
-    initialize: function(attributes) {
+    initialize: function (attributes) {
         this.pair = attributes.pair || {};
     },
 
@@ -41,11 +41,11 @@ var PairView = Backbone.View.extend(baseMVC.LoggableMixin).extend({
             '<span class="pair-name-column flex-column">',
             '<span class="pair-name"><%- pair.name %></span>',
             "</span>",
-            '<span class="reverse-dataset-name flex-column"><%- pair.reverse.name %></span>'
+            '<span class="reverse-dataset-name flex-column"><%- pair.reverse.name %></span>',
         ].join("")
     ),
 
-    render: function() {
+    render: function () {
         this.dragStartHandler = _.bind(this._dragstart, this);
         this.dragEndHandler = _.bind(this._dragend, this);
         var handle = this.$el
@@ -61,11 +61,11 @@ var PairView = Backbone.View.extend(baseMVC.LoggableMixin).extend({
 
     events: {
         dragover: "_sendToParent",
-        drop: "_sendToParent"
+        drop: "_sendToParent",
     },
 
     /** dragging pairs for re-ordering */
-    _dragstart: function(ev) {
+    _dragstart: function (ev) {
         ev.currentTarget.style.opacity = "0.4";
         if (ev.originalEvent) {
             ev = ev.originalEvent;
@@ -78,20 +78,20 @@ var PairView = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     },
 
     /** dragging pairs for re-ordering */
-    _dragend: function(ev) {
+    _dragend: function (ev) {
         ev.currentTarget.style.opacity = "1.0";
         this.$el.parent().trigger("pair.dragend", [this]);
     },
 
     /** manually bubble up an event to the parent/container */
-    _sendToParent: function(ev) {
+    _sendToParent: function (ev) {
         this.$el.parent().trigger(ev);
     },
 
     /** string rep */
-    toString: function() {
+    toString: function () {
         return `PairView(${this.pair.name})`;
-    }
+    },
 });
 
 // ============================================================================
@@ -129,7 +129,7 @@ function autoPairFnBuilder(options) {
             var regexps = getRegExps.call(this);
             return _.extend(params, {
                 matchTo: params.matchTo.name.replace(regexps[0], ""),
-                possible: params.possible.name.replace(regexps[1], "")
+                possible: params.possible.name.replace(regexps[1], ""),
             });
         };
 
@@ -143,7 +143,7 @@ function autoPairFnBuilder(options) {
 
         var bestMatch = {
             score: 0.0,
-            index: null
+            index: null,
         };
 
         var paired = [];
@@ -168,7 +168,7 @@ function autoPairFnBuilder(options) {
                             matchTo: matchTo,
                             possible: possible,
                             index: indexB,
-                            bestMatch: bestMatch
+                            bestMatch: bestMatch,
                         })
                     );
                     this.debug("bestMatch:", JSON.stringify(bestMatch, null, "  "));
@@ -189,7 +189,7 @@ function autoPairFnBuilder(options) {
                         listA: listA,
                         indexA: indexA,
                         listB: listB,
-                        indexB: bestMatch.index
+                        indexB: bestMatch.index,
                     })
                 );
                 //console.debug( 'list lens now:', listA.length, listB.length );
@@ -217,7 +217,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         className: "list-of-pairs-collection-creator collection-creator flex-row-container",
 
         /** set up initial options, instance vars, behaviors, and autopair (if set to do so) */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             this.metric("PairedCollectionCreator.initialize", attributes);
             //this.debug( '-- PairedCollectionCreator:', attributes );
 
@@ -227,7 +227,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                 automaticallyPair: true,
                 strategy: "lcs",
                 matchPercentage: 0.9,
-                twoPassAutopairing: true
+                twoPassAutopairing: true,
             });
 
             /** unordered, original list */
@@ -288,7 +288,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         /** map of common filter pairs by name */
         commonFilters: {
             illumina: ["_1", "_2"],
-            Rs: ["_R1", "_R2"]
+            Rs: ["_R1", "_R2"],
         },
         /** which commonFilter to use by default */
         DEFAULT_FILTERS: "illumina",
@@ -297,14 +297,14 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         strategies: {
             simple: "autopairSimple",
             lcs: "autopairLCS",
-            levenshtein: "autopairLevenshtein"
+            levenshtein: "autopairLevenshtein",
         },
         /** default autopair strategy name */
         DEFAULT_STRATEGY: "lcs",
 
         // ------------------------------------------------------------------------ process raw list
         /** set up main data: cache initialList, sort, and autopair */
-        _dataSetUp: function() {
+        _dataSetUp: function () {
             //this.debug( '-- _dataSetUp' );
 
             this.paired = [];
@@ -319,28 +319,28 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
             if (this.automaticallyPair) {
                 this.autoPair();
-                this.once("rendered:initial", function() {
+                this.once("rendered:initial", function () {
                     this.trigger("autopair");
                 });
             }
         },
 
         /** sort initial list */
-        _sortInitialList: function() {
+        _sortInitialList: function () {
             //this.debug( '-- _sortInitialList' );
             this._sortDatasetList(this.initialList);
         },
 
         /** sort a list of datasets */
-        _sortDatasetList: function(list) {
+        _sortDatasetList: function (list) {
             // currently only natural sort by name
             list.sort((a, b) => naturalSort(a.name, b.name));
             return list;
         },
 
         /** add ids to dataset objs in initial list if none */
-        _ensureIds: function() {
-            this.initialList.forEach(dataset => {
+        _ensureIds: function () {
+            this.initialList.forEach((dataset) => {
                 if (!Object.prototype.hasOwnProperty.call(dataset, "id")) {
                     dataset.id = _.uniqueId();
                 }
@@ -349,8 +349,8 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** split initial list into two lists, those that pass forward filters & those passing reverse */
-        _splitByFilters: function() {
-            var regexFilters = this.filters.map(stringFilter => new RegExp(stringFilter));
+        _splitByFilters: function () {
+            var regexFilters = this.filters.map((stringFilter) => new RegExp(stringFilter));
 
             var split = [[], []];
 
@@ -372,7 +372,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** add a dataset to the unpaired list in it's proper order */
-        _addToUnpaired: function(dataset) {
+        _addToUnpaired: function (dataset) {
             // currently, unpaired is natural sorted by name, use binary search to find insertion point
             var binSearchSortedIndex = (low, hi) => {
                 if (low === hi) {
@@ -402,7 +402,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         /** two passes to automatically create pairs:
          *  use both simpleAutoPair, then the fn mentioned in strategy
          */
-        autoPair: function(strategy) {
+        autoPair: function (strategy) {
             // split first using exact matching
             var split = this._splitByFilters();
 
@@ -410,7 +410,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             if (this.twoPassAutopairing) {
                 paired = this.autopairSimple({
                     listA: split[0],
-                    listB: split[1]
+                    listB: split[1],
                 });
                 split = this._splitByFilters();
             }
@@ -424,7 +424,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             paired = paired.concat(
                 this[strategy].call(this, {
                     listA: split[0],
-                    listB: split[1]
+                    listB: split[1],
                 })
             );
             return paired;
@@ -432,7 +432,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
         /** autopair by exact match */
         autopairSimple: autoPairFnBuilder({
-            scoreThreshold: function() {
+            scoreThreshold: function () {
                 return 0.6;
             },
             match: function _match(params) {
@@ -440,16 +440,16 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                 if (params.matchTo === params.possible) {
                     return {
                         index: params.index,
-                        score: 1.0
+                        score: 1.0,
                     };
                 }
                 return params.bestMatch;
-            }
+            },
         }),
 
         /** autopair by levenshtein edit distance scoring */
         autopairLevenshtein: autoPairFnBuilder({
-            scoreThreshold: function() {
+            scoreThreshold: function () {
                 return this.matchPercentage;
             },
             match: function _matches(params) {
@@ -462,16 +462,16 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                 if (score > params.bestMatch.score) {
                     return {
                         index: params.index,
-                        score: score
+                        score: score,
                     };
                 }
                 return params.bestMatch;
-            }
+            },
         }),
 
         /** autopair by longest common substrings scoring */
         autopairLCS: autoPairFnBuilder({
-            scoreThreshold: function() {
+            scoreThreshold: function () {
                 return this.matchPercentage;
             },
             match: function _matches(params) {
@@ -484,15 +484,15 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                 if (score > params.bestMatch.score) {
                     return {
                         index: params.index,
-                        score: score
+                        score: score,
                     };
                 }
                 return params.bestMatch;
-            }
+            },
         }),
 
         /** return the concat'd longest common prefix and suffix from two strings */
-        _naiveStartingAndEndingLCS: function(s1, s2) {
+        _naiveStartingAndEndingLCS: function (s1, s2) {
             var fwdLCS = "";
             var revLCS = "";
             var i = 0;
@@ -526,7 +526,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
         // ------------------------------------------------------------------------ pairing / unpairing
         /** create a pair from fwd and rev, removing them from unpaired, and placing the new pair in paired */
-        _pair: function(fwd, rev, options) {
+        _pair: function (fwd, rev, options) {
             options = options || {};
             this.debug("_pair:", fwd, rev);
             var pair = this._createPair(fwd, rev, options.name);
@@ -539,7 +539,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** create a pair Object from fwd and rev, adding the name attribute (will guess if not given) */
-        _createPair: function(fwd, rev, name) {
+        _createPair: function (fwd, rev, name) {
             // ensure existance and don't pair something with itself
             if (!(fwd && rev) || fwd === rev) {
                 throw new Error(`Bad pairing: ${[JSON.stringify(fwd), JSON.stringify(rev)]}`);
@@ -549,7 +549,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** try to find a good pair name for the given fwd and rev datasets */
-        _guessNameForPair: function(fwd, rev, removeExtensions) {
+        _guessNameForPair: function (fwd, rev, removeExtensions) {
             removeExtensions = removeExtensions !== undefined ? removeExtensions : this.removeExtensions;
             var fwdName = fwd.name;
             var revName = rev.name;
@@ -581,7 +581,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** unpair a pair, removing it from paired, and adding the fwd,rev datasets back into unpaired */
-        _unpair: function(pair, options) {
+        _unpair: function (pair, options) {
             options = options || {};
             if (!pair) {
                 throw new Error(`Bad pair: ${JSON.stringify(pair)}`);
@@ -597,7 +597,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** unpair all paired datasets */
-        unpairAll: function() {
+        unpairAll: function () {
             var pairs = [];
             while (this.paired.length) {
                 pairs.push(this._unpair(this.paired[0], { silent: true }));
@@ -607,7 +607,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
         // ------------------------------------------------------------------------ API
         /** convert a pair into JSON compatible with the collections API */
-        _pairToJSON: function(pair) {
+        _pairToJSON: function (pair) {
             //TODO: consider making this the pair structure when created instead
             return {
                 collection_type: "paired",
@@ -617,21 +617,21 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                     {
                         name: "forward",
                         id: pair.forward.id,
-                        src: pair.forward.src || "hda"
+                        src: pair.forward.src || "hda",
                     },
                     {
                         name: "reverse",
                         id: pair.reverse.id,
-                        src: pair.reverse.src || "hda"
-                    }
-                ]
+                        src: pair.reverse.src || "hda",
+                    },
+                ],
             };
         },
 
         /** create the collection via the API
          *  @returns {jQuery.xhr Object}    the jquery ajax request
          */
-        createList: function(name) {
+        createList: function (name) {
             var self = this;
 
             var url = `${getAppRoot()}api/histories/${this.historyId}/contents/dataset_collections`;
@@ -642,7 +642,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                 hide_source_items: self.hideOriginals || false,
                 copy_elements: self.copyElements,
                 name: _.escape(name || self.$(".collection-name").val()),
-                element_identifiers: self.paired.map(pair => self._pairToJSON(pair))
+                element_identifiers: self.paired.map((pair) => self._pairToJSON(pair)),
             };
             //this.debug( JSON.stringify( ajaxData ) );
             self.blocking = true;
@@ -650,7 +650,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                 type: "POST",
                 contentType: "application/json",
                 dataType: "json",
-                data: JSON.stringify(ajaxData)
+                data: JSON.stringify(ajaxData),
             })
                 .always(() => {
                     self.blocking = false;
@@ -658,7 +658,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                 .fail((xhr, status, message) => {
                     self._ajaxErrHandler(xhr, status, message);
                 })
-                .done(function(response, message, xhr) {
+                .done(function (response, message, xhr) {
                     //this.info( 'ok', response, message, xhr );
                     self.trigger("collection:created", response, message, xhr);
                     self.metric("collection:created", response);
@@ -669,7 +669,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** handle ajax errors with feedback and details to the user (if available) */
-        _ajaxErrHandler: function(xhr, status, message) {
+        _ajaxErrHandler: function (xhr, status, message) {
             this.error(xhr, status, message);
             var self = this;
             var content = _l("An error occurred while creating this collection");
@@ -689,7 +689,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
         // ------------------------------------------------------------------------ rendering
         /** render the entire interface */
-        render: function(speed, callback) {
+        render: function (speed, callback) {
             //this.debug( '-- _render' );
             //this.$el.empty().html( this.templates.main() );
             this.$el.empty().html(this.templates.main());
@@ -702,7 +702,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** render the header section */
-        _renderHeader: function(speed, callback) {
+        _renderHeader: function (speed, callback) {
             //this.debug( '-- _renderHeader' );
             var $header = this.$(".header")
                 .empty()
@@ -714,17 +714,15 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             return $header;
         },
         /** fill the filter inputs with the filter values */
-        _renderFilters: function() {
+        _renderFilters: function () {
             return this.$(".forward-column .column-header input")
                 .val(this.filters[0])
                 .add(this.$(".reverse-column .column-header input").val(this.filters[1]));
         },
 
         /** render the middle including unpaired and paired sections (which may be hidden) */
-        _renderMiddle: function(speed, callback) {
-            var $middle = this.$(".middle")
-                .empty()
-                .html(this.templates.middle());
+        _renderMiddle: function (speed, callback) {
+            var $middle = this.$(".middle").empty().html(this.templates.middle());
 
             // (re-) hide the un/paired panels based on instance vars
             if (this.unpairedPanelHidden) {
@@ -738,7 +736,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             return $middle;
         },
         /** render the unpaired section, showing datasets accrd. to filters, update the unpaired counts */
-        _renderUnpaired: function(speed, callback) {
+        _renderUnpaired: function (speed, callback) {
             //this.debug( '-- _renderUnpaired' );
             var self = this;
 
@@ -773,7 +771,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                 }
                 return self._renderUnpairedDataset(dataset);
             });
-            $fwd = split[0].map(dataset => self._renderUnpairedDataset(dataset));
+            $fwd = split[0].map((dataset) => self._renderUnpairedDataset(dataset));
 
             if (!$fwd.length && !$rev.length) {
                 this._renderUnpairedNotShown();
@@ -789,11 +787,11 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             this._adjUnpairedOnScrollbar();
         },
         /** return a string to display the count of filtered out datasets */
-        _renderUnpairedDisplayStr: function(numFiltered) {
+        _renderUnpairedDisplayStr: function (numFiltered) {
             return ["(", numFiltered, " ", _l("filtered out"), ")"].join("");
         },
         /** return an unattached jQuery DOM element to represent an unpaired dataset */
-        _renderUnpairedDataset: function(dataset) {
+        _renderUnpairedDataset: function (dataset) {
             //TODO: to underscore template
             return (
                 $("<li/>")
@@ -801,48 +799,36 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                     .addClass("dataset unpaired")
                     .attr("draggable", true)
                     .addClass(dataset.selected ? "selected" : "")
-                    .append(
-                        $("<span/>")
-                            .addClass("dataset-name")
-                            .text(dataset.name)
-                    )
+                    .append($("<span/>").addClass("dataset-name").text(dataset.name))
                     //??
                     .data("dataset", dataset)
             );
         },
         /** render the button that may go between unpaired datasets, allowing the user to pair a row */
-        _renderPairButton: function() {
+        _renderPairButton: function () {
             //TODO: *not* a dataset - don't pretend like it is
             return $("<li/>")
                 .addClass("dataset unpaired")
-                .append(
-                    $("<span/>")
-                        .addClass("dataset-name")
-                        .text(_l("Pair these datasets"))
-                );
+                .append($("<span/>").addClass("dataset-name").text(_l("Pair these datasets")));
         },
         /** a message to display when no unpaired left */
-        _renderUnpairedEmpty: function() {
+        _renderUnpairedEmpty: function () {
             //this.debug( '-- renderUnpairedEmpty' );
             var $msg = $('<div class="empty-message"></div>').text(`(${_l("no remaining unpaired datasets")})`);
-            this.$(".unpaired-columns .paired-column .column-datasets")
-                .empty()
-                .prepend($msg);
+            this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend($msg);
             return $msg;
         },
         /** a message to display when no unpaired can be shown with the current filters */
-        _renderUnpairedNotShown: function() {
+        _renderUnpairedNotShown: function () {
             //this.debug( '-- renderUnpairedEmpty' );
             var $msg = $('<div class="empty-message"></div>').text(
                 `(${_l("no datasets were found matching the current filters")})`
             );
-            this.$(".unpaired-columns .paired-column .column-datasets")
-                .empty()
-                .prepend($msg);
+            this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend($msg);
             return $msg;
         },
         /** try to detect if the unpaired section has a scrollbar and adjust left column for better centering of all */
-        _adjUnpairedOnScrollbar: function() {
+        _adjUnpairedOnScrollbar: function () {
             var $unpairedColumns = this.$(".unpaired-columns").last();
 
             var $firstDataset = this.$(".unpaired-columns .reverse-column .dataset").first();
@@ -861,7 +847,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** render the paired section and update counts of paired datasets */
-        _renderPaired: function(speed, callback) {
+        _renderPaired: function (speed, callback) {
             //this.debug( '-- _renderPaired' );
             this.$(".paired-column-title .title").text([this.paired.length, _l("paired")].join(" "));
             // show/hide the unpair all link
@@ -888,33 +874,31 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                             '<span class="fa fa-unlink" title="',
                             _l("Unpair"),
                             '"></span>',
-                            "</button>"
+                            "</button>",
                         ].join("")
                     );
             });
         },
         /** a message to display when none paired */
-        _renderPairedEmpty: function() {
+        _renderPairedEmpty: function () {
             var $msg = $('<div class="empty-message"></div>').text(`(${_l("no paired datasets yet")})`);
-            this.$(".paired-columns .column-datasets")
-                .empty()
-                .prepend($msg);
+            this.$(".paired-columns .column-datasets").empty().prepend($msg);
             return $msg;
         },
 
         footerSettings: {
             ".hide-originals": "hideOriginals",
-            ".remove-extensions": "removeExtensions"
+            ".remove-extensions": "removeExtensions",
         },
 
         /** add any jQuery/bootstrap/custom plugins to elements rendered */
-        _addPluginComponents: function() {
+        _addPluginComponents: function () {
             this._chooseFiltersPopover(".choose-filters-link");
             this.$(".help-content i").hoverhighlight(".collection-creator", "rgba( 64, 255, 255, 1.0 )");
         },
 
         /** build a filter selection popover allowing selection of common filter pairs */
-        _chooseFiltersPopover: function(selector) {
+        _chooseFiltersPopover: function (selector) {
             function filterChoice(val1, val2) {
                 return [
                     '<button class="filter-choice btn" ',
@@ -930,7 +914,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                     _l("Reverse"),
                     ": ",
                     val2,
-                    "</button>"
+                    "</button>",
                 ].join("");
             }
             var $popoverContent = $(
@@ -941,9 +925,9 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                         _l("Choose from the following filters to change which unpaired reads are shown in the display"),
                         ":</div>",
                         _.values(this.commonFilters)
-                            .map(filterSet => filterChoice(filterSet[0], filterSet[1]))
+                            .map((filterSet) => filterChoice(filterSet[0], filterSet[1]))
                             .join(""),
-                        "</div>"
+                        "</div>",
                     ].join("")
                 )({})
             );
@@ -953,18 +937,16 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                 placement: "bottom",
                 html: true,
                 //animation   : false,
-                content: $popoverContent
+                content: $popoverContent,
             });
         },
 
         /** add (or clear if clear is truthy) a validation warning to what */
-        _validationWarning: function(what, clear) {
+        _validationWarning: function (what, clear) {
             var VALIDATION_CLASS = "validation-warning";
             if (what === "name") {
                 what = this.$(".collection-name").add(this.$(".collection-name-prompt"));
-                this.$(".collection-name")
-                    .focus()
-                    .select();
+                this.$(".collection-name").focus().select();
             }
             if (clear) {
                 what = what || this.$(`.${VALIDATION_CLASS}`);
@@ -976,12 +958,12 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
         // ------------------------------------------------------------------------ events
         /** set up event handlers on self */
-        _setUpBehaviors: function() {
-            this.once("rendered", function() {
+        _setUpBehaviors: function () {
+            this.once("rendered", function () {
                 this.trigger("rendered:initial", this);
             });
 
-            this.on("pair:new", function() {
+            this.on("pair:new", function () {
                 //TODO: ideally only re-render the columns (or even elements) involved
                 this._renderUnpaired();
                 this._renderPaired();
@@ -994,24 +976,24 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                 //this.debug( $pairedView.height() )
                 this.$(".paired-columns").scrollTop(8000000);
             });
-            this.on("pair:unpair", function(pairs) {
+            this.on("pair:unpair", function (pairs) {
                 //TODO: ideally only re-render the columns (or even elements) involved
                 this._renderUnpaired();
                 this._renderPaired();
                 this.splitView();
             });
 
-            this.on("filter-change", function() {
+            this.on("filter-change", function () {
                 this.filters = [
                     this.$(".forward-unpaired-filter input").val(),
-                    this.$(".reverse-unpaired-filter input").val()
+                    this.$(".reverse-unpaired-filter input").val(),
                 ];
                 this.metric("filter-change", this.filters);
                 this._renderFilters();
                 this._renderUnpaired();
             });
 
-            this.on("autopair", function() {
+            this.on("autopair", function () {
                 this._renderUnpaired();
                 this._renderPaired();
 
@@ -1030,7 +1012,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                         [
                             "Could not automatically create any pairs from the given dataset names.",
                             "You may want to choose or enter different filters and try auto-pairing again.",
-                            "Close this message using the X on the right to view more help."
+                            "Close this message using the X on the right to view more help.",
                         ].join(" ")
                     );
                 }
@@ -1053,19 +1035,19 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             "click .reverse-column .column-title": "_clickShowOnlyUnpaired",
             "click .unpair-all-link": "_clickUnpairAll",
             //TODO: this seems kinda backasswards - re-sending jq event as a backbone event, can we listen directly?
-            "change .forward-unpaired-filter input": function(ev) {
+            "change .forward-unpaired-filter input": function (ev) {
                 this.trigger("filter-change");
             },
-            "focus .forward-unpaired-filter input": function(ev) {
+            "focus .forward-unpaired-filter input": function (ev) {
                 $(ev.currentTarget).select();
             },
             "click .autopair-link": "_clickAutopair",
             "click .choose-filters .filter-choice": "_clickFilterChoice",
             "click .clear-filters-link": "_clearFilters",
-            "change .reverse-unpaired-filter input": function(ev) {
+            "change .reverse-unpaired-filter input": function (ev) {
                 this.trigger("filter-change");
             },
-            "focus .reverse-unpaired-filter input": function(ev) {
+            "focus .reverse-unpaired-filter input": function (ev) {
                 $(ev.currentTarget).select();
             },
             // unpaired
@@ -1092,18 +1074,18 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             "pair.dragend   .paired-columns .column-datasets": "_pairDragend",
 
             // footer
-            "change .remove-extensions": function(ev) {
+            "change .remove-extensions": function (ev) {
                 this.toggleExtensions();
             },
             "change .collection-name": "_changeName",
             "keydown .collection-name": "_nameCheckForEnter",
             "change .hide-originals": "_changeHideOriginals",
             "click .cancel-create": "_cancelCreate",
-            "click .create-collection": "_clickCreate" //,
+            "click .create-collection": "_clickCreate", //,
         },
 
         /** toggle between showing only unpaired and split view */
-        _clickShowOnlyUnpaired: function(ev) {
+        _clickShowOnlyUnpaired: function (ev) {
             //this.debug( 'click unpaired', ev.currentTarget );
             if (this.$(".paired-columns").is(":visible")) {
                 this.hidePaired();
@@ -1112,7 +1094,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             }
         },
         /** toggle between showing only paired and split view */
-        _clickShowOnlyPaired: function(ev) {
+        _clickShowOnlyPaired: function (ev) {
             //this.debug( 'click paired' );
             if (this.$(".unpaired-columns").is(":visible")) {
                 this.hideUnpaired();
@@ -1122,39 +1104,39 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** hide unpaired, show paired */
-        hideUnpaired: function(speed, callback) {
+        hideUnpaired: function (speed, callback) {
             this.unpairedPanelHidden = true;
             this.pairedPanelHidden = false;
             this._renderMiddle(speed, callback);
         },
         /** hide paired, show unpaired */
-        hidePaired: function(speed, callback) {
+        hidePaired: function (speed, callback) {
             this.unpairedPanelHidden = false;
             this.pairedPanelHidden = true;
             this._renderMiddle(speed, callback);
         },
         /** show both paired and unpaired (splitting evenly) */
-        splitView: function(speed, callback) {
+        splitView: function (speed, callback) {
             this.unpairedPanelHidden = this.pairedPanelHidden = false;
             this._renderMiddle(speed, callback);
             return this;
         },
 
         /** unpair all paired and do other super neat stuff which I'm not really sure about yet... */
-        _clickUnpairAll: function(ev) {
+        _clickUnpairAll: function (ev) {
             this.metric("unpairAll");
             this.unpairAll();
         },
 
         /** attempt to autopair */
-        _clickAutopair: function(ev) {
+        _clickAutopair: function (ev) {
             var paired = this.autoPair();
             this.metric("autopair", paired.length, this.unpaired.length);
             this.trigger("autopair");
         },
 
         /** set the filters based on the data attributes of the button click target */
-        _clickFilterChoice: function(ev) {
+        _clickFilterChoice: function (ev) {
             var $selected = $(ev.currentTarget);
             this.$(".forward-unpaired-filter input").val($selected.data("forward"));
             this.$(".reverse-unpaired-filter input").val($selected.data("reverse"));
@@ -1163,7 +1145,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** hide the choose filters popover */
-        _hideChooseFilters: function() {
+        _hideChooseFilters: function () {
             //TODO: update bootstrap and remove the following hack
             //  see also: https://github.com/twbs/bootstrap/issues/10260
             this.$(".choose-filters-link").popover("hide");
@@ -1171,7 +1153,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** clear both filters */
-        _clearFilters: function(ev) {
+        _clearFilters: function (ev) {
             this.$(".forward-unpaired-filter input").val("");
             this.$(".reverse-unpaired-filter input").val("");
             this.trigger("filter-change");
@@ -1179,7 +1161,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
         // ........................................................................ unpaired
         /** select an unpaired dataset */
-        _clickUnpairedDataset: function(ev) {
+        _clickUnpairedDataset: function (ev) {
             ev.stopPropagation();
             return this.toggleSelectUnpaired($(ev.currentTarget));
         },
@@ -1188,7 +1170,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
          *  @param [jQuery] $dataset        the unpaired dataset dom rep to select
          *  @param [Boolean] options.force  if defined, force selection based on T/F; otherwise, toggle
          */
-        toggleSelectUnpaired: function($dataset, options) {
+        toggleSelectUnpaired: function ($dataset, options) {
             options = options || {};
             var dataset = $dataset.data("dataset");
 
@@ -1212,16 +1194,16 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** pair all the currently selected unpaired datasets */
-        pairAllSelected: function(options) {
+        pairAllSelected: function (options) {
             options = options || {};
             var self = this;
             var fwds = [];
             var revs = [];
             var pairs = [];
-            self.$(".unpaired-columns .forward-column .dataset.selected").each(function() {
+            self.$(".unpaired-columns .forward-column .dataset.selected").each(function () {
                 fwds.push($(this).data("dataset"));
             });
-            self.$(".unpaired-columns .reverse-column .dataset.selected").each(function() {
+            self.$(".unpaired-columns .reverse-column .dataset.selected").each(function () {
                 revs.push($(this).data("dataset"));
             });
             fwds.length = revs.length = Math.min(fwds.length, revs.length);
@@ -1243,26 +1225,24 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** clear the selection on all unpaired datasets */
-        clearSelectedUnpaired: function() {
+        clearSelectedUnpaired: function () {
             this.$(".unpaired-columns .dataset.selected").removeClass("selected");
         },
 
         /** when holding down the shift key on a click, 'paint' the moused over datasets as selected */
-        _mousedownUnpaired: function(ev) {
+        _mousedownUnpaired: function (ev) {
             if (ev.shiftKey) {
                 var self = this;
                 var $startTarget = $(ev.target).addClass("selected");
 
-                var moveListener = ev => {
-                    self.$(ev.target)
-                        .filter(".dataset")
-                        .addClass("selected");
+                var moveListener = (ev) => {
+                    self.$(ev.target).filter(".dataset").addClass("selected");
                 };
 
                 $startTarget.parent().on("mousemove", moveListener);
 
                 // on any mouseup, stop listening to the move and try to pair any selected
-                $(document).one("mouseup", ev => {
+                $(document).one("mouseup", (ev) => {
                     $startTarget.parent().off("mousemove", moveListener);
                     self.pairAllSelected();
                 });
@@ -1270,17 +1250,13 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** attempt to pair two datasets directly across from one another */
-        _clickPairRow: function(ev) {
+        _clickPairRow: function (ev) {
             //if( !ev.currentTarget ){ return true; }
             var rowIndex = $(ev.currentTarget).index();
 
-            var fwd = $(".unpaired-columns .forward-column .dataset")
-                .eq(rowIndex)
-                .data("dataset");
+            var fwd = $(".unpaired-columns .forward-column .dataset").eq(rowIndex).data("dataset");
 
-            var rev = $(".unpaired-columns .reverse-column .dataset")
-                .eq(rowIndex)
-                .data("dataset");
+            var rev = $(".unpaired-columns .reverse-column .dataset").eq(rowIndex).data("dataset");
 
             //this.debug( 'row:', rowIndex, fwd, rev );
             this._pair(fwd, rev);
@@ -1288,7 +1264,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
         // ........................................................................ divider/partition
         /** start dragging the visible divider/partition between unpaired and paired panes */
-        _startPartitionDrag: function(ev) {
+        _startPartitionDrag: function (ev) {
             var self = this;
             var startingY = ev.pageY;
             //this.debug( 'partition drag START:', ev );
@@ -1297,9 +1273,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
             function endDrag(ev) {
                 self.$(".flexible-partition-drag").css("color", "");
-                $("body")
-                    .css("cursor", "")
-                    .unbind("mousemove", trackMouse);
+                $("body").css("cursor", "").unbind("mousemove", trackMouse);
             }
             function trackMouse(ev) {
                 var offset = ev.pageY - startingY;
@@ -1314,7 +1288,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** adjust the parition up/down +/-adj pixels */
-        adjPartition: function(adj) {
+        adjPartition: function (adj) {
             var $unpaired = this.$(".unpaired-columns");
             var $paired = this.$(".paired-columns");
             var unpairedHi = parseInt($unpaired.css("height"), 10);
@@ -1357,25 +1331,25 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
             $unpaired.css({
                 height: `${unpairedHi}px`,
-                flex: "0 0 auto"
+                flex: "0 0 auto",
             });
             return true;
         },
 
         // ........................................................................ paired
         /** select a pair when clicked */
-        selectPair: function(ev) {
+        selectPair: function (ev) {
             ev.stopPropagation();
             $(ev.currentTarget).toggleClass("selected");
         },
 
         /** deselect all pairs */
-        clearSelectedPaired: function(ev) {
+        clearSelectedPaired: function (ev) {
             this.$(".paired-columns .dataset.selected").removeClass("selected");
         },
 
         /** rename a pair when the pair name is clicked */
-        _clickPairName: function(ev) {
+        _clickPairName: function (ev) {
             ev.stopPropagation();
             var $name = $(ev.currentTarget);
             var $pair = $name.parent().parent();
@@ -1393,7 +1367,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** unpair this pair */
-        _clickUnpair: function(ev) {
+        _clickUnpair: function (ev) {
             //if( !ev.currentTarget ){ return true; }
             var pairIndex = Math.floor($(ev.currentTarget).index(".unpair-btn"));
             //this.debug( 'pair:', pairIndex );
@@ -1408,7 +1382,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         //    //this.debug( '_dragleavePairedColumns:', ev );
         //},
         /** track the mouse drag over the paired list adding a placeholder to show where the drop would occur */
-        _dragoverPairedColumns: function(ev) {
+        _dragoverPairedColumns: function (ev) {
             //this.debug( '_dragoverPairedColumns:', ev );
             ev.preventDefault();
 
@@ -1427,7 +1401,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** If the mouse is near enough to the list's top or bottom, scroll the list */
-        _checkForAutoscroll: function($element, y) {
+        _checkForAutoscroll: function ($element, y) {
             var AUTOSCROLL_SPEED = 2;
             var offset = $element.offset();
             var scrollTop = $element.scrollTop();
@@ -1444,7 +1418,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         /** get the nearest *previous* paired dataset PairView based on the mouse's Y coordinate.
          *      If the y is at the end of the list, return an empty jQuery object.
          */
-        _getNearestPairedDatasetLi: function(y) {
+        _getNearestPairedDatasetLi: function (y) {
             var WIGGLE = 4;
             var lis = this.$(".paired-columns .column-datasets li").toArray();
             for (var i = 0; i < lis.length; i++) {
@@ -1459,7 +1433,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             return $();
         },
         /** drop (dragged/selected PairViews) onto the list, re-ordering both the DOM and the internal array of pairs */
-        _dropPairedColumns: function(ev) {
+        _dropPairedColumns: function (ev) {
             // both required for firefox
             ev.preventDefault();
             ev.dataTransfer.dropEffect = "move";
@@ -1476,10 +1450,10 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             return false;
         },
         /** resync the creator's list of paired based on the DOM order of pairs */
-        _syncPairsToDom: function() {
+        _syncPairsToDom: function () {
             var newPaired = [];
             //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?
-            this.$(".paired-columns .dataset.paired").each(function() {
+            this.$(".paired-columns .dataset.paired").each(function () {
                 newPaired.push($(this).data("pair"));
             });
             //this.debug( newPaired );
@@ -1487,25 +1461,25 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             this._renderPaired();
         },
         /** drag communication with pair sub-views: dragstart */
-        _pairDragstart: function(ev, pair) {
+        _pairDragstart: function (ev, pair) {
             //this.debug( '_pairDragstart', ev, pair )
             // auto select the pair causing the event and move all selected
             pair.$el.addClass("selected");
             this.$dragging = this.$(".paired-columns .dataset.selected");
         },
         /** drag communication with pair sub-views: dragend - remove the placeholder */
-        _pairDragend: function(ev, pair) {
+        _pairDragend: function (ev, pair) {
             //this.debug( '_pairDragend', ev, pair )
             $(".element-drop-placeholder").remove();
             this.$dragging = null;
         },
 
         // ........................................................................ footer
-        toggleExtensions: function(force) {
+        toggleExtensions: function (force) {
             var self = this;
             self.removeExtensions = force !== undefined ? force : !self.removeExtensions;
 
-            _.each(self.paired, pair => {
+            _.each(self.paired, (pair) => {
                 // don't overwrite custom names
                 if (pair.customizedName) {
                     return;
@@ -1519,9 +1493,9 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
         // ------------------------------------------------------------------------ misc
         /** debug a dataset list */
-        _printList: function(list) {
+        _printList: function (list) {
             var self = this;
-            _.each(list, e => {
+            _.each(list, (e) => {
                 if (list === self.paired) {
                     self._printPair(e);
                 } else {
@@ -1531,12 +1505,12 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** print a pair Object */
-        _printPair: function(pair) {
+        _printPair: function (pair) {
             this.debug(pair.forward.name, pair.reverse.name, ": ->", pair.name);
         },
 
         /** string rep */
-        toString: function() {
+        toString: function () {
             return "PairedCollectionCreator";
         },
 
@@ -1603,7 +1577,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                     "</div>",
                     "</div>",
                     "</div>",
-                    "</div>"
+                    "</div>",
                 ].join("")
             ),
 
@@ -1637,7 +1611,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                     "</div>",
                     '<div class="paired-columns flex-column-container scroll-container flex-row">',
                     '<ol class="column-datasets"></ol>',
-                    "</div>"
+                    "</div>",
                 ].join("")
             ),
 
@@ -1694,7 +1668,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                     _l("Create list"),
                     "</button>",
                     "</div>",
-                    "</div>"
+                    "</div>",
                 ].join("")
             ),
 
@@ -1707,7 +1681,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                             "Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ",
                             "These collections can be passed to tools and workflows in order to have analyses done on each member of ",
                             "the entire group. This interface allows you to create a collection, choose which datasets are paired, ",
-                            "and re-order the final collection."
+                            "and re-order the final collection.",
                         ].join("")
                     ),
                     "</p>",
@@ -1733,7 +1707,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                             '<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',
                             "to have your datasets automatically paired based on name.",
                             "</li>",
-                            "</ul>"
+                            "</ul>",
                         ].join("")
                     ),
                     "</p>",
@@ -1756,7 +1730,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                             "<li>Clearing the filters by clicking the ",
                             '<i data-target=".clear-filters-link">"Clear filters" link</i>.',
                             "</li>",
-                            "</ul>"
+                            "</ul>",
                         ].join("")
                     ),
                     "</p>",
@@ -1765,7 +1739,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                         [
                             "To unpair individual dataset pairs, click the ",
                             '<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ',
-                            'Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'
+                            'Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.',
                         ].join("")
                     ),
                     "</p>",
@@ -1773,7 +1747,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                     _l(
                         [
                             'You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ',
-                            '<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.'
+                            '<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.',
                         ].join("")
                     ),
                     "</p>",
@@ -1782,13 +1756,13 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                         [
                             'Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ',
                             'click <i data-target=".create-collection">"Create list"</i>. ',
-                            "(Note: you do not have to pair all unpaired datasets to finish.)"
+                            "(Note: you do not have to pair all unpaired datasets to finish.)",
                         ].join("")
                     ),
-                    "</p>"
+                    "</p>",
                 ].join("")
-            )
-        })
+            ),
+        }),
     });
 
 //=============================================================================
@@ -1800,15 +1774,15 @@ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal(datase
 
     options = _.defaults(options || {}, {
         datasets: datasets,
-        oncancel: function() {
+        oncancel: function () {
             Galaxy.modal.hide();
             deferred.reject("cancelled");
         },
-        oncreate: function(creator, response) {
+        oncreate: function (creator, response) {
             Galaxy.modal.hide();
             deferred.resolve(response);
         },
-        title: _l("Create a collection of paired datasets")
+        title: _l("Create a collection of paired datasets"),
     });
 
     if (!Galaxy || !Galaxy.modal) {
@@ -1821,7 +1795,7 @@ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal(datase
         body: creator.$el,
         width: "80%",
         height: "800px",
-        closing_events: true
+        closing_events: true,
     });
     creator.render();
     window.creator = creator;
@@ -1837,7 +1811,7 @@ function createListOfPairsCollection(collection, defaultHideSourceItems) {
     return pairedCollectionCreatorModal(elements, {
         historyId: collection.historyId,
         defaultHideSourceItems: defaultHideSourceItems,
-        copyElements: !defaultHideSourceItems
+        copyElements: !defaultHideSourceItems,
     });
 }
 
@@ -1845,5 +1819,5 @@ function createListOfPairsCollection(collection, defaultHideSourceItems) {
 export default {
     PairedCollectionCreator: PairedCollectionCreator,
     pairedCollectionCreatorModal: pairedCollectionCreatorModal,
-    createListOfPairsCollection: createListOfPairsCollection
+    createListOfPairsCollection: createListOfPairsCollection,
 };
diff --git a/client/galaxy/scripts/mvc/collection/pair-collection-creator.js b/client/galaxy/scripts/mvc/collection/pair-collection-creator.js
index 9842db8c164c..18731c4fb91d 100644
--- a/client/galaxy/scripts/mvc/collection/pair-collection-creator.js
+++ b/client/galaxy/scripts/mvc/collection/pair-collection-creator.js
@@ -23,16 +23,16 @@ var PairedDatasetCollectionElementView = Backbone.View.extend(BASE_MVC.LoggableM
     tagName: "li",
     className: "collection-element",
 
-    initialize: function(attributes) {
+    initialize: function (attributes) {
         this.element = attributes.element || {};
         this.identifier = attributes.identifier;
     },
 
-    render: function() {
+    render: function () {
         this.$el.attr("data-element-id", this.element.id).html(
             this.template({
                 identifier: this.identifier,
-                element: this.element
+                element: this.element,
             })
         );
         return this;
@@ -44,15 +44,15 @@ var PairedDatasetCollectionElementView = Backbone.View.extend(BASE_MVC.LoggableM
     ),
 
     /** remove the DOM and any listeners */
-    destroy: function() {
+    destroy: function () {
         this.off();
         this.$el.remove();
     },
 
     /** string rep */
-    toString: function() {
+    toString: function () {
         return "DatasetCollectionElementView()";
-    }
+    },
 });
 
 // ============================================================================
@@ -68,13 +68,13 @@ var PairCollectionCreator = _super.extend({
     className: "pair-collection-creator collection-creator flex-row-container",
 
     /** override to no-op */
-    _mangleDuplicateNames: function() {},
+    _mangleDuplicateNames: function () {},
 
     // TODO: this whole pattern sucks. There needs to be two classes of problem area:
     //      bad inital choices and
     //      when the user has painted his/her self into a corner during creation/use-of-the-creator
     /** render the entire interface */
-    render: function(speed, callback) {
+    render: function (speed, callback) {
         if (this.workingElements.length === 2) {
             return _super.prototype.render.call(this, speed, callback);
         }
@@ -83,7 +83,7 @@ var PairCollectionCreator = _super.extend({
 
     // ------------------------------------------------------------------------ rendering elements
     /** render forward/reverse */
-    _renderList: function(speed, callback) {
+    _renderList: function (speed, callback) {
         //this.debug( '-- _renderList' );
         //precondition: there are two valid elements in workingElements
         var creator = this;
@@ -92,7 +92,7 @@ var PairCollectionCreator = _super.extend({
         var $list = creator.$list();
 
         // lose the original views, create the new, append all at once, then call their renders
-        _.each(this.elementViews, view => {
+        _.each(this.elementViews, (view) => {
             view.destroy();
             creator.removeElementView(view);
         });
@@ -103,24 +103,24 @@ var PairCollectionCreator = _super.extend({
     },
 
     /** create the forward element view */
-    _createForwardElementView: function() {
+    _createForwardElementView: function () {
         return this._createElementView(this.workingElements[0], {
-            identifier: "forward"
+            identifier: "forward",
         });
     },
 
     /** create the forward element view */
-    _createReverseElementView: function() {
+    _createReverseElementView: function () {
         return this._createElementView(this.workingElements[1], {
-            identifier: "reverse"
+            identifier: "reverse",
         });
     },
 
     /** create an element view, cache in elementViews, and return */
-    _createElementView: function(element, options) {
+    _createElementView: function (element, options) {
         var elementView = new this.elementViewClass(
             _.extend(options, {
-                element: element
+                element: element,
             })
         );
         this.elementViews.push(elementView);
@@ -128,13 +128,13 @@ var PairCollectionCreator = _super.extend({
     },
 
     /** swap the forward, reverse elements and re-render */
-    swap: function() {
+    swap: function () {
         this.workingElements = [this.workingElements[1], this.workingElements[0]];
         this._renderList();
     },
 
     events: _.extend(_.clone(_super.prototype.events), {
-        "click .swap": "swap"
+        "click .swap": "swap",
     }),
 
     // ------------------------------------------------------------------------ templates
@@ -154,7 +154,7 @@ var PairCollectionCreator = _super.extend({
                 "</a>",
                 "</div>",
                 '<div class="collection-elements scroll-container flex-row">',
-                "</div>"
+                "</div>",
             ].join("")
         ),
 
@@ -167,7 +167,7 @@ var PairCollectionCreator = _super.extend({
                         "Pair collections are permanent collections containing two datasets: one forward and one reverse. ",
                         "Often these are forward and reverse reads. The pair collections can be passed to tools and ",
                         "workflows in order to have analyses done on both datasets. This interface allows ",
-                        "you to create a pair, name it, and swap which is forward and which reverse."
+                        "you to create a pair, name it, and swap which is forward and which reverse.",
                     ].join("")
                 ),
                 "</p>",
@@ -176,7 +176,7 @@ var PairCollectionCreator = _super.extend({
                 _l(
                     [
                         'Click the <i data-target=".swap">"Swap"</i> link to make your forward dataset the reverse ',
-                        "and the reverse dataset forward."
+                        "and the reverse dataset forward.",
                     ].join("")
                 ),
                 "</li>",
@@ -188,10 +188,10 @@ var PairCollectionCreator = _super.extend({
                 _l(
                     [
                         'Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ',
-                        'click <i data-target=".create-collection">"Create list"</i>.'
+                        'click <i data-target=".create-collection">"Create list"</i>.',
                     ].join("")
                 ),
-                "</p>"
+                "</p>",
             ].join("")
         ),
 
@@ -237,16 +237,16 @@ var PairCollectionCreator = _super.extend({
                 // _l( 'Create a different kind of collection' ),
                 "</div>",
                 "</div>",
-                "</div>"
+                "</div>",
             ].join("")
-        )
+        ),
     }),
 
     // ------------------------------------------------------------------------ misc
     /** string rep */
-    toString: function() {
+    toString: function () {
         return "PairCollectionCreator";
-    }
+    },
 });
 
 //==============================================================================
@@ -267,13 +267,13 @@ function createPairCollection(contents, defaultHideSourceItems) {
 
     var promise = pairCollectionCreatorModal(elements, {
         defaultHideSourceItems: defaultHideSourceItems,
-        creationFn: function(elements, name, hideSourceItems) {
+        creationFn: function (elements, name, hideSourceItems) {
             elements = [
                 { name: "forward", src: "hda", id: elements[0].id },
-                { name: "reverse", src: "hda", id: elements[1].id }
+                { name: "reverse", src: "hda", id: elements[1].id },
             ];
             return contents.createHDCA(elements, "paired", name, hideSourceItems, copyElements);
-        }
+        },
     });
 
     return promise;
@@ -283,5 +283,5 @@ function createPairCollection(contents, defaultHideSourceItems) {
 export default {
     PairCollectionCreator: PairCollectionCreator,
     pairCollectionCreatorModal: pairCollectionCreatorModal,
-    createPairCollection: createPairCollection
+    createPairCollection: createPairCollection,
 };
diff --git a/client/galaxy/scripts/mvc/dataset/data.js b/client/galaxy/scripts/mvc/dataset/data.js
index c054946753d6..11c77430da75 100644
--- a/client/galaxy/scripts/mvc/dataset/data.js
+++ b/client/galaxy/scripts/mvc/dataset/data.js
@@ -21,10 +21,10 @@ export var Dataset = Backbone.Model.extend({
         type: "",
         name: "",
         hda_ldda: "hda",
-        metadata: null
+        metadata: null,
     },
 
-    initialize: function() {
+    initialize: function () {
         // Metadata can be passed in as a model or a set of attributes; if it's
         // already a model, there's no need to set metadata.
         if (!this.get("metadata")) {
@@ -35,13 +35,13 @@ export var Dataset = Backbone.Model.extend({
         this.on("change", this._set_metadata, this);
     },
 
-    _set_metadata: function() {
+    _set_metadata: function () {
         var metadata = new DatasetMetadata();
 
         // Move metadata from dataset attributes to metadata object.
         _.each(
             _.keys(this.attributes),
-            function(k) {
+            function (k) {
                 if (k.indexOf("metadata_") === 0) {
                     // Found metadata.
                     var new_key = k.split("metadata_")[1];
@@ -59,11 +59,11 @@ export var Dataset = Backbone.Model.extend({
     /**
      * Returns dataset metadata for a given attribute.
      */
-    get_metadata: function(attribute) {
+    get_metadata: function (attribute) {
         return this.attributes.metadata.get(attribute);
     },
 
-    urlRoot: `${getAppRoot()}api/datasets`
+    urlRoot: `${getAppRoot()}api/datasets`,
 });
 
 /**
@@ -74,10 +74,10 @@ export var TabularDataset = Dataset.extend({
         chunk_url: null,
         first_data_chunk: null,
         offset: 0,
-        at_eof: false
+        at_eof: false,
     }),
 
-    initialize: function(options) {
+    initialize: function (options) {
         Dataset.prototype.initialize.call(this);
 
         // If first data chunk is available, next chunk is 1.
@@ -91,7 +91,7 @@ export var TabularDataset = Dataset.extend({
     /**
      * Returns a jQuery Deferred object that resolves to the next data chunk or null if at EOF.
      */
-    get_next_chunk: function() {
+    get_next_chunk: function () {
         // If already at end of file, do nothing.
         if (this.attributes.at_eof) {
             return null;
@@ -102,8 +102,8 @@ export var TabularDataset = Dataset.extend({
 
         var next_chunk = $.Deferred();
         $.getJSON(this.attributes.chunk_url, {
-            offset: self.attributes.offset
-        }).success(chunk => {
+            offset: self.attributes.offset,
+        }).success((chunk) => {
             var rval;
             if (chunk.ck_data !== "") {
                 // Found chunk.
@@ -118,11 +118,11 @@ export var TabularDataset = Dataset.extend({
         });
 
         return next_chunk;
-    }
+    },
 });
 
 export var DatasetCollection = Backbone.Collection.extend({
-    model: Dataset
+    model: Dataset,
 });
 
 /**
@@ -134,7 +134,7 @@ var TabularDatasetChunkedView = Backbone.View.extend({
     /**
      * Initialize view and, importantly, set a scroll element.
      */
-    initialize: function(options) {
+    initialize: function (options) {
         // Row count for rendering.
         this.row_count = 0;
         this.loading_chunk = false;
@@ -142,22 +142,22 @@ var TabularDatasetChunkedView = Backbone.View.extend({
         // load trackster button
         new TabularButtonTracksterView({
             model: options.model,
-            $el: this.$el
+            $el: this.$el,
         });
     },
 
-    expand_to_container: function() {
+    expand_to_container: function () {
         if (this.$el.height() < this.scroll_elt.height()) {
             this.attempt_to_fetch();
         }
     },
 
-    attempt_to_fetch: function(func) {
+    attempt_to_fetch: function (func) {
         var self = this;
         if (!this.loading_chunk && this.scrolled_to_bottom()) {
             this.loading_chunk = true;
             this.loading_indicator.show();
-            $.when(self.model.get_next_chunk()).then(result => {
+            $.when(self.model.get_next_chunk()).then((result) => {
                 if (result) {
                     self._renderChunk(result);
                     self.loading_chunk = false;
@@ -168,7 +168,7 @@ var TabularDatasetChunkedView = Backbone.View.extend({
         }
     },
 
-    render: function() {
+    render: function () {
         // Add loading indicator.
         this.loading_indicator = $("<div/>").attr("id", "loading_indicator");
         this.$el.append(this.loading_indicator);
@@ -176,7 +176,7 @@ var TabularDatasetChunkedView = Backbone.View.extend({
         // Add data table and header.
         var data_table = $("<table/>").attr({
             id: "content_table",
-            cellpadding: 0
+            cellpadding: 0,
         });
         this.$el.append(data_table);
         var column_names = this.model.get_metadata("column_names");
@@ -199,7 +199,7 @@ var TabularDatasetChunkedView = Backbone.View.extend({
             this._renderChunk(first_chunk);
         } else {
             // No bootstrapping, so get first chunk and then render.
-            $.when(self.model.get_next_chunk()).then(result => {
+            $.when(self.model.get_next_chunk()).then((result) => {
                 self._renderChunk(result);
             });
         }
@@ -215,13 +215,13 @@ var TabularDatasetChunkedView = Backbone.View.extend({
     /**
      * Returns true if user has scrolled to the bottom of the view.
      */
-    scrolled_to_bottom: function() {
+    scrolled_to_bottom: function () {
         return false;
     },
 
     // -- Helper functions. --
 
-    _renderCell: function(cell_contents, index, colspan) {
+    _renderCell: function (cell_contents, index, colspan) {
         var $cell = $("<td>").text(cell_contents);
         var column_types = this.model.get_metadata("column_types");
         if (colspan !== undefined) {
@@ -237,7 +237,7 @@ var TabularDatasetChunkedView = Backbone.View.extend({
         return $cell;
     },
 
-    _renderRow: function(line) {
+    _renderRow: function (line) {
         // Check length of cells to ensure this is a complete row.
         var cells = line.split("\t");
 
@@ -251,7 +251,7 @@ var TabularDatasetChunkedView = Backbone.View.extend({
         if (cells.length === num_columns) {
             _.each(
                 cells,
-                function(cell_contents, index) {
+                function (cell_contents, index) {
                     row.append(this._renderCell(cell_contents, index));
                 },
                 this
@@ -260,7 +260,7 @@ var TabularDatasetChunkedView = Backbone.View.extend({
             // SAM file or like format with optional metadata included.
             _.each(
                 cells.slice(0, num_columns - 1),
-                function(cell_contents, index) {
+                function (cell_contents, index) {
                     row.append(this._renderCell(cell_contents, index));
                 },
                 this
@@ -271,7 +271,7 @@ var TabularDatasetChunkedView = Backbone.View.extend({
             if (cells.length === num_columns) {
                 _.each(
                     cells,
-                    function(cell_contents, index) {
+                    function (cell_contents, index) {
                         row.append(this._renderCell(cell_contents, index));
                     },
                     this
@@ -281,7 +281,7 @@ var TabularDatasetChunkedView = Backbone.View.extend({
                 if (cells.length === num_columns) {
                     _.each(
                         cells,
-                        function(cell_contents, index) {
+                        function (cell_contents, index) {
                             row.append(this._renderCell(cell_contents, index));
                         },
                         this
@@ -297,7 +297,7 @@ var TabularDatasetChunkedView = Backbone.View.extend({
             // Could also be a tabular file with a line with missing columns.
             _.each(
                 cells,
-                function(cell_contents, index) {
+                function (cell_contents, index) {
                     row.append(this._renderCell(cell_contents, index));
                 },
                 this
@@ -311,18 +311,18 @@ var TabularDatasetChunkedView = Backbone.View.extend({
         return row;
     },
 
-    _renderChunk: function(chunk) {
+    _renderChunk: function (chunk) {
         var data_table = this.$el.find("table");
         _.each(
             chunk.ck_data.split("\n"),
-            function(line, index) {
+            function (line, index) {
                 if (line !== "") {
                     data_table.append(this._renderRow(line));
                 }
             },
             this
         );
-    }
+    },
 });
 
 /**
@@ -330,11 +330,11 @@ var TabularDatasetChunkedView = Backbone.View.extend({
  * view top-level elements outside of view.
  */
 var TopLevelTabularDatasetChunkedView = TabularDatasetChunkedView.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         TabularDatasetChunkedView.prototype.initialize.call(this, options);
 
         // Scrolling happens in top-level elements.
-        var scroll_elt = _.find(this.$el.parents(), p => $(p).css("overflow") === "auto");
+        var scroll_elt = _.find(this.$el.parents(), (p) => $(p).css("overflow") === "auto");
 
         // If no scrolling element found, use window.
         if (!scroll_elt) {
@@ -348,32 +348,32 @@ var TopLevelTabularDatasetChunkedView = TabularDatasetChunkedView.extend({
     /**
      * Returns true if user has scrolled to the bottom of the view.
      */
-    scrolled_to_bottom: function() {
+    scrolled_to_bottom: function () {
         return this.$el.height() - this.scroll_elt.scrollTop() - this.scroll_elt.height() <= 0;
-    }
+    },
 });
 
 /**
  * Tabular view tnat is embedded in a page. Scrolling occurs in view's el.
  */
 var EmbeddedTabularDatasetChunkedView = TabularDatasetChunkedView.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         TabularDatasetChunkedView.prototype.initialize.call(this, options);
 
         // Because view is embedded, set up div to do scrolling.
         this.scroll_elt = this.$el.css({
             position: "relative",
             overflow: "scroll",
-            height: options.height || "500px"
+            height: options.height || "500px",
         });
     },
 
     /**
      * Returns true if user has scrolled to the bottom of the view.
      */
-    scrolled_to_bottom: function() {
+    scrolled_to_bottom: function () {
         return this.$el.scrollTop() + this.$el.innerHeight() >= this.el.scrollHeight;
-    }
+    },
 });
 
 function search(str, array) {
@@ -387,7 +387,7 @@ var TabularButtonTracksterView = Backbone.View.extend({
     col: {
         chrom: null,
         start: null,
-        end: null
+        end: null,
     },
 
     // url for trackster
@@ -403,7 +403,7 @@ var TabularButtonTracksterView = Backbone.View.extend({
     file_ext: null,
 
     // backbone initialize
-    initialize: function(options) {
+    initialize: function (options) {
         // check if environment is available
         const Galaxy = getGalaxyInstance();
 
@@ -495,8 +495,8 @@ var TabularButtonTracksterView = Backbone.View.extend({
             model: new mod_icon_btn.IconButton({
                 title: _l("Visualize"),
                 icon_class: "chart_curve",
-                id: "btn_viz"
-            })
+                id: "btn_viz",
+            }),
         });
 
         // set element
@@ -512,11 +512,11 @@ var TabularButtonTracksterView = Backbone.View.extend({
     /** Add event handlers */
     events: {
         "mouseover tr": "show",
-        mouseleave: "hide"
+        mouseleave: "hide",
     },
 
     // show button
-    show: function(e) {
+    show: function (e) {
         var self = this;
 
         // is numeric
@@ -531,29 +531,18 @@ var TabularButtonTracksterView = Backbone.View.extend({
         var row = $(e.target).parent();
 
         // verify that location has been found
-        var chrom = row
-            .children()
-            .eq(this.col.chrom)
-            .html();
-        var start = row
-            .children()
-            .eq(this.col.start)
-            .html();
+        var chrom = row.children().eq(this.col.chrom).html();
+        var start = row.children().eq(this.col.start).html();
 
         // end is optional
-        var end = this.col.end
-            ? row
-                  .children()
-                  .eq(this.col.end)
-                  .html()
-            : start;
+        var end = this.col.end ? row.children().eq(this.col.end).html() : start;
 
         // double check location
         if (!chrom.match("^#") && chrom !== "" && is_numeric(start)) {
             // get target gene region
             var btn_viz_pars = {
                 dataset_id: this.dataset_id,
-                gene_region: `${chrom}:${start}-${end}`
+                gene_region: `${chrom}:${start}-${end}`,
             };
 
             // get button position
@@ -565,13 +554,13 @@ var TabularButtonTracksterView = Backbone.View.extend({
             $("#btn_viz").css({
                 position: "fixed",
                 top: `${top}px`,
-                left: `${left}px`
+                left: `${left}px`,
             });
             $("#btn_viz").off("click");
             $("#btn_viz").click(() => {
                 self.frame.add({
                     title: _l("Trackster"),
-                    url: `${self.url_viz}/trackster?${$.param(btn_viz_pars)}`
+                    url: `${self.url_viz}/trackster?${$.param(btn_viz_pars)}`,
                 });
             });
 
@@ -584,16 +573,16 @@ var TabularButtonTracksterView = Backbone.View.extend({
     },
 
     /** hide button */
-    hide: function() {
+    hide: function () {
         this.$("#btn_viz").hide();
-    }
+    },
 });
 
 /**
  * Create a tabular dataset chunked view (and requisite tabular dataset model)
  * and appends to parent_elt.
  */
-export var createTabularDatasetChunkedView = options => {
+export var createTabularDatasetChunkedView = (options) => {
     // If no model, create and set model from dataset config.
     if (!options.model) {
         options.model = new TabularDataset(options.dataset_config);
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-choice.js b/client/galaxy/scripts/mvc/dataset/dataset-choice.js
index 81aeded717a4..387e4ff0f781 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-choice.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-choice.js
@@ -38,7 +38,7 @@ function _filterDatasetJSON(datasetJSON, where, datasetsOnly) {
         return true;
     }
 
-    return datasetJSON.filter(json => {
+    return datasetJSON.filter((json) => {
         console.debug(json);
         return (
             !json.deleted &&
@@ -94,7 +94,7 @@ var DatasetChoiceModal = (datasetJSON, options) => {
         // select more than one dataset?
         multiselect: false,
         // any dataset ids that will display as already selected
-        selected: []
+        selected: [],
     });
     // default title should depend on multiselect
     options.title = options.title || (options.multiselect ? _l("Choose datasets:") : _l("Choose a dataset:"));
@@ -113,7 +113,7 @@ var DatasetChoiceModal = (datasetJSON, options) => {
 
     // resolve the returned promise with the json of the selected datasets
     function resolveWithSelected() {
-        promise.resolve(list.getSelectedModels().map(model => model.toJSON()));
+        promise.resolve(list.getSelectedModels().map((model) => model.toJSON()));
     }
     // if multiselect - add a button for the user to complete the changes
     if (options.multiselect) {
@@ -126,10 +126,10 @@ var DatasetChoiceModal = (datasetJSON, options) => {
         height: "auto",
         buttons: buttons,
         closing_events: true,
-        closing_callback: function() {
+        closing_callback: function () {
             promise.resolve(null);
         },
-        body: ['<div class="list-panel"></div>'].join("")
+        body: ['<div class="list-panel"></div>'].join(""),
     });
     modal.$(".modal-header").remove();
     modal.$(".modal-footer").css("margin-top", "0px");
@@ -143,13 +143,13 @@ var DatasetChoiceModal = (datasetJSON, options) => {
                 [
                     //TODO: as option
                     "Click the checkboxes on the right to select datasets. ",
-                    "Click the datasets names to see their details. "
+                    "Click the datasets names to see their details. ",
                 ].join("")
             ),
         el: modal.$body.find(".list-panel"),
         selecting: true,
         selected: options.selected,
-        collection: new DATASET.DatasetAssociationCollection(datasetJSON)
+        collection: new DATASET.DatasetAssociationCollection(datasetJSON),
     });
 
     // when the list is rendered, show the modal (also add a specifying class for css)
@@ -163,7 +163,7 @@ var DatasetChoiceModal = (datasetJSON, options) => {
             list.$(".list-actions").hide();
         });
         // if single select, immediately resolve on a single selection
-        list.on("view:selected", view => {
+        list.on("view:selected", (view) => {
             promise.resolve([view.model.toJSON()]);
         });
     }
@@ -209,7 +209,7 @@ var DatasetChoice = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
     className: "dataset-choice",
 
     /** set up defaults, options, and listeners */
-    initialize: function(attributes) {
+    initialize: function (attributes) {
         this.debug(`${this}(DatasetChoice).initialize:`, attributes);
 
         this.label = attributes.label !== undefined ? _l(attributes.label) : "";
@@ -223,14 +223,14 @@ var DatasetChoice = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** add any (bbone) listeners */
-    _setUpListeners: function() {
+    _setUpListeners: function () {
         //this.on( 'all', function(){
         //    this.log( this + '', arguments );
         //});
     },
 
     /** render the view */
-    render: function() {
+    render: function () {
         var json = this.toJSON();
         this.$el.html(this._template(json));
         this.$(".selected").replaceWith(this._renderSelected(json));
@@ -238,14 +238,14 @@ var DatasetChoice = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** return plain html for the overall control */
-    _template: function(json) {
+    _template: function (json) {
         return _.template(
             ["<label>", '<span class="prompt"><%- label %></span>', '<div class="selected"></div>', "</label>"].join("")
         )(json);
     },
 
     /** return jQ DOM for the selected dataset (only one) */
-    _renderSelected: function(json) {
+    _renderSelected: function (json) {
         if (json.selected.length) {
             //TODO: break out?
             return $(
@@ -260,7 +260,7 @@ var DatasetChoice = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
                         "<%- selected.file_ext %></i>",
                         "<i><%- selected.misc_info %></i>",
                         "</span>",
-                        "</div>"
+                        "</div>",
                     ].join(""),
                     { variable: "selected" }
                 )(json.selected[0])
@@ -271,25 +271,25 @@ var DatasetChoice = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
 
     //TODO:?? why not just pass in view?
     /** return a plain JSON object with both the view and dataset attributes */
-    toJSON: function() {
+    toJSON: function () {
         var chooser = this;
         return {
             label: chooser.label,
             datasets: chooser.datasetJSON,
             selected: _.compact(
-                _.map(chooser.selected, id =>
+                _.map(chooser.selected, (id) =>
                     _.findWhere(chooser.datasetJSON, {
-                        id: id
+                        id: id,
                     })
                 )
-            )
+            ),
         };
     },
 
     /** event map: when to open the modal */
     events: {
         // the whole thing functions as a button
-        click: "chooseWithModal"
+        click: "chooseWithModal",
     },
 
     //TODO:?? modal to prop of this?
@@ -299,11 +299,11 @@ var DatasetChoice = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
      *  @fires 'cancelled' when the user clicks away/closes the modal (no selection made) - passed this
      *  @fires 'error' if the modal has no selectable datasets based on this.where - passed this and other args
      */
-    chooseWithModal: function() {
+    chooseWithModal: function () {
         var chooser = this;
 
         return this._createModal()
-            .done(json => {
+            .done((json) => {
                 if (json) {
                     chooser.selected = _.pluck(json, "id");
                     chooser.trigger("selected", chooser, json);
@@ -312,32 +312,32 @@ var DatasetChoice = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
                     chooser.trigger("cancelled", chooser);
                 }
             })
-            .fail(function() {
+            .fail(function () {
                 chooser.trigger("error", chooser, arguments);
             });
     },
 
     /** create and return the modal to use for choosing */
-    _createModal: function() {
+    _createModal: function () {
         return new DatasetChoiceModal(this.datasetJSON, this._getModalOptions());
     },
 
     /** return a plain JSON containing the options to pass to the modal */
-    _getModalOptions: function() {
+    _getModalOptions: function () {
         return {
             title: this.label,
             multiselect: false,
             selected: this.selected,
             where: this.where,
-            datasetsOnly: this.datasetsOnly
+            datasetsOnly: this.datasetsOnly,
         };
     },
 
     // ------------------------------------------------------------------------ misc
     /** string rep */
-    toString: function() {
+    toString: function () {
         return `DatasetChoice(${this.selected})`;
-    }
+    },
 });
 
 // ============================================================================
@@ -362,18 +362,18 @@ var MultiDatasetChoice = DatasetChoice.extend({
         file_ext: _l("Format"),
         genome_build: _l("Genome"),
         tags: _l("Tags"),
-        annotation: _l("Annotation")
+        annotation: _l("Annotation"),
     },
 
     /** in this override, add the showHeaders and cells options */
-    initialize: function(attributes) {
+    initialize: function (attributes) {
         this.showHeaders = attributes.showHeaders !== undefined ? attributes.showHeaders : true;
         this.cells = attributes.cells || this.cells;
         DatasetChoice.prototype.initialize.call(this, attributes);
     },
 
     /** in this override, display the selected datasets as a table with optional headers */
-    _renderSelected: function(json) {
+    _renderSelected: function (json) {
         if (json.selected.length) {
             return $(
                 _.template(
@@ -395,7 +395,7 @@ var MultiDatasetChoice = DatasetChoice.extend({
                         "</tr>",
                         "<% }); %>",
                         "</tbody>",
-                        "</table>"
+                        "</table>",
                     ].join(""),
                     { variable: "json" }
                 )(json)
@@ -405,30 +405,30 @@ var MultiDatasetChoice = DatasetChoice.extend({
     },
 
     /** in this override, send the showHeaders and cells options as well */
-    toJSON: function() {
+    toJSON: function () {
         return _.extend(DatasetChoice.prototype.toJSON.call(this), {
             showHeaders: this.showHeaders,
-            cells: this.cells
+            cells: this.cells,
         });
     },
 
     /** in this override, set multiselect to true */
-    _getModalOptions: function() {
+    _getModalOptions: function () {
         return _.extend(DatasetChoice.prototype._getModalOptions.call(this), {
-            multiselect: true
+            multiselect: true,
         });
     },
 
     // ------------------------------------------------------------------------ misc
     /** string rep */
-    toString: function() {
+    toString: function () {
         return `DatasetChoice(${this.selected})`;
-    }
+    },
 });
 
 // ============================================================================
 export default {
     DatasetChoiceModal: DatasetChoiceModal,
     DatasetChoice: DatasetChoice,
-    MultiDatasetChoice: MultiDatasetChoice
+    MultiDatasetChoice: MultiDatasetChoice,
 };
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js b/client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
index 9420974a77dd..7fc314b5b859 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
@@ -11,11 +11,11 @@ import Ui from "mvc/ui/ui-misc";
 import Form from "mvc/form/form-view";
 
 var View = Backbone.View.extend({
-    initialize: function() {
+    initialize: function () {
         const Galaxy = getGalaxyInstance();
         this.setElement("<div/>");
         this.model = new Backbone.Model({
-            dataset_id: Galaxy.params.dataset_id
+            dataset_id: Galaxy.params.dataset_id,
         });
         this.message = new Ui.Message({ persistent: true });
         this.tabs = this._createTabs();
@@ -30,11 +30,11 @@ var View = Backbone.View.extend({
     },
 
     /** fetch data for the selected dataset and build forms */
-    render: function() {
+    render: function () {
         var self = this;
         $.ajax({
             url: `${getAppRoot()}dataset/get_edit?dataset_id=${self.model.get("dataset_id")}`,
-            success: function(response) {
+            success: function (response) {
                 !self.initial_message && self.message.update(response);
                 self.initial_message = true;
                 _.each(self.forms, (form, key) => {
@@ -44,18 +44,18 @@ var View = Backbone.View.extend({
                 });
                 self.$el.show();
             },
-            error: function(response) {
+            error: function (response) {
                 var err_msg = response.responseJSON && response.responseJSON.err_msg;
                 self.message.update({
                     status: "danger",
-                    message: err_msg || "Error occurred while loading the dataset."
+                    message: err_msg || "Error occurred while loading the dataset.",
                 });
-            }
+            },
         });
     },
 
     /** submit data to backend to update attributes */
-    _submit: function(operation, form) {
+    _submit: function (operation, form) {
         var self = this;
         var data = form.data.create();
         data.dataset_id = this.model.get("dataset_id");
@@ -64,28 +64,28 @@ var View = Backbone.View.extend({
             type: "PUT",
             url: `${getAppRoot()}dataset/set_edit`,
             data: data,
-            success: function(response) {
+            success: function (response) {
                 self.message.update(response);
                 self.render();
                 self._reloadHistory();
             },
-            error: function(response) {
+            error: function (response) {
                 var err_msg = response.responseJSON && response.responseJSON.err_msg;
                 self.message.update({
                     status: "danger",
-                    message: err_msg || "Error occurred while editing the dataset attributes."
+                    message: err_msg || "Error occurred while editing the dataset attributes.",
                 });
-            }
+            },
         });
     },
 
     /** create tabs for different dataset attribute categories*/
-    _createTabs: function() {
+    _createTabs: function () {
         this.forms = {
             attribute: this._getAttribute(),
             conversion: this._getConversion(),
             datatype: this._getDatatype(),
-            permission: this._getPermission()
+            permission: this._getPermission(),
         };
         var tabs = new Tabs.View();
         tabs.add({
@@ -93,34 +93,34 @@ var View = Backbone.View.extend({
             title: _l("Attributes"),
             icon: "fa fa-bars",
             tooltip: _l("Edit dataset attributes"),
-            $el: this.forms.attribute.$el
+            $el: this.forms.attribute.$el,
         });
         tabs.add({
             id: "convert",
             title: _l("Convert"),
             icon: "fa-gear",
             tooltip: _l("Convert to new format"),
-            $el: this.forms.conversion.$el
+            $el: this.forms.conversion.$el,
         });
         tabs.add({
             id: "datatype",
             title: _l("Datatypes"),
             icon: "fa-database",
             tooltip: _l("Change data type"),
-            $el: this.forms.datatype.$el
+            $el: this.forms.datatype.$el,
         });
         tabs.add({
             id: "permissions",
             title: _l("Permissions"),
             icon: "fa-user",
             tooltip: _l("Permissions"),
-            $el: this.forms.permission.$el
+            $el: this.forms.permission.$el,
         });
         return tabs;
     },
 
     /** edit main attributes form */
-    _getAttribute: function() {
+    _getAttribute: function () {
         var self = this;
         var form = new Form({
             title: _l("Edit attributes"),
@@ -129,26 +129,26 @@ var View = Backbone.View.extend({
                     tooltip: _l("Save attributes of the dataset."),
                     icon: "fa-floppy-o",
                     title: _l("Save"),
-                    onclick: function() {
+                    onclick: function () {
                         self._submit("attributes", form);
-                    }
+                    },
                 }),
                 submit_autodetect: new Ui.Button({
                     tooltip:
                         "This will inspect the dataset and attempt to correct the values of fields if they are not accurate.",
                     icon: "fa-undo",
                     title: "Auto-detect",
-                    onclick: function() {
+                    onclick: function () {
                         self._submit("autodetect", form);
-                    }
-                })
-            }
+                    },
+                }),
+            },
         });
         return form;
     },
 
     /** datatype conversion form */
-    _getConversion: function() {
+    _getConversion: function () {
         var self = this;
         var form = new Form({
             title: _l("Convert to new format"),
@@ -157,17 +157,17 @@ var View = Backbone.View.extend({
                     tooltip: _l("Convert the datatype to a new format."),
                     title: _l("Convert datatype"),
                     icon: "fa-exchange",
-                    onclick: function() {
+                    onclick: function () {
                         self._submit("conversion", form);
-                    }
-                })
-            }
+                    },
+                }),
+            },
         });
         return form;
     },
 
     /** change datatype form */
-    _getDatatype: function() {
+    _getDatatype: function () {
         var self = this;
         var form = new Form({
             title: _l("Change datatype"),
@@ -176,25 +176,25 @@ var View = Backbone.View.extend({
                     tooltip: _l("Change the datatype to a new type."),
                     title: _l("Change datatype"),
                     icon: "fa-exchange",
-                    onclick: function() {
+                    onclick: function () {
                         self._submit("datatype", form);
-                    }
+                    },
                 }),
                 submit_datatype_detect: new Ui.Button({
                     tooltip: _l("Detect the datatype and change it."),
                     title: _l("Detect datatype"),
                     icon: "fa-undo",
-                    onclick: function() {
+                    onclick: function () {
                         self._submit("datatype_detect", form);
-                    }
-                })
-            }
+                    },
+                }),
+            },
         });
         return form;
     },
 
     /** dataset permissions form */
-    _getPermission: function() {
+    _getPermission: function () {
         var self = this;
         var form = new Form({
             title: _l("Manage dataset permissions"),
@@ -203,24 +203,24 @@ var View = Backbone.View.extend({
                     tooltip: _l("Save permissions."),
                     title: _l("Save permissions"),
                     icon: "fa-floppy-o ",
-                    onclick: function() {
+                    onclick: function () {
                         self._submit("permission", form);
-                    }
-                })
-            }
+                    },
+                }),
+            },
         });
         return form;
     },
 
     /** reload Galaxy's history after updating dataset's attributes */
-    _reloadHistory: function() {
+    _reloadHistory: function () {
         const Galaxy = getGalaxyInstance();
         if (Galaxy) {
             Galaxy.currHistoryPanel.loadCurrentHistory();
         }
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-error.js b/client/galaxy/scripts/mvc/dataset/dataset-error.js
index 175934dec525..627bd0f2be8c 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-error.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-error.js
@@ -10,26 +10,26 @@ import Form from "mvc/form/form-view";
 
 /** Dataset edit attributes view */
 var View = Backbone.View.extend({
-    initialize: function() {
+    initialize: function () {
         const Galaxy = getGalaxyInstance();
         this.setElement("<div/>");
         this.model = new Backbone.Model({
-            dataset_id: Galaxy.params.dataset_id
+            dataset_id: Galaxy.params.dataset_id,
         });
         this.active_tab = "user";
         this.render();
     },
 
     // Fetch data for the selected dataset and
-    render: function() {
+    render: function () {
         var data_url = `${getAppRoot()}api/datasets/${this.model.get("dataset_id")}`;
         Utils.get({
             url: data_url,
-            success: dataset => {
+            success: (dataset) => {
                 var job_url = `${getAppRoot()}api/jobs/${dataset.creating_job}?full=True`;
                 Utils.get({
                     url: job_url,
-                    success: job => {
+                    success: (job) => {
                         this.render_error_page(dataset, job);
                         this.find_common_problems(job);
                     },
@@ -38,10 +38,10 @@ var View = Backbone.View.extend({
                             status: "error",
                             message: "Error occurred while loading the job.",
                             persistent: true,
-                            cls: "errormessage"
+                            cls: "errormessage",
                         };
                         this.display_message(error_response, this.$(".response-message"));
-                    }
+                    },
                 });
             },
             error: () => {
@@ -49,29 +49,29 @@ var View = Backbone.View.extend({
                     status: "error",
                     message: "Error occurred while loading the dataset.",
                     persistent: true,
-                    cls: "errormessage"
+                    cls: "errormessage",
                 };
                 this.display_message(error_response, this.$(".response-message"));
-            }
+            },
         });
     },
 
-    find_common_problems: function(job) {
+    find_common_problems: function (job) {
         var job_url = `${getAppRoot()}api/jobs/${job.id}/common_problems`;
         Utils.get({
             url: job_url,
-            success: common_problems => {
+            success: (common_problems) => {
                 this.render_common_problems(common_problems);
             },
-            error: response => {
+            error: (response) => {
                 console.log("error");
                 console.log(response);
-            }
+            },
         });
         return;
     },
 
-    render_common_problems: function(common_problems) {
+    render_common_problems: function (common_problems) {
         const has_duplicate_inputs = common_problems.has_duplicate_inputs;
         const has_empty_inputs = common_problems.has_empty_inputs;
         if (has_duplicate_inputs || has_empty_inputs) {
@@ -95,7 +95,7 @@ var View = Backbone.View.extend({
     },
 
     /** Render the view */
-    render_error_page: function(dataset, job) {
+    render_error_page: function (dataset, job) {
         this.$el.empty().append(`
             ${this._templateHeader()}
             <h2>Dataset Error Report</h2>
@@ -116,7 +116,7 @@ var View = Backbone.View.extend({
         this.$el.append("<h3>Issue Report</h3>").append(this._getBugFormTemplate(dataset, job));
     },
 
-    job_summary: function(job) {
+    job_summary: function (job) {
         const tool_stderr = job.tool_stderr;
         const job_stderr = job.job_stderr;
         const job_messages = job.job_messages;
@@ -143,7 +143,7 @@ var View = Backbone.View.extend({
     },
 
     /** Display actions messages */
-    display_message: function(response, $el, doNotClear, safe) {
+    display_message: function (response, $el, doNotClear, safe) {
         if (!safe) {
             if (doNotClear) {
                 $el.append(new Ui.Message(response).$el);
@@ -160,12 +160,12 @@ var View = Backbone.View.extend({
     },
 
     /** Main template */
-    _templateHeader: function() {
+    _templateHeader: function () {
         return `<div class="page-container edit-attr"><div class="response-message"></div></div>`;
     },
 
     /** Convert tab template */
-    _getBugFormTemplate: function(dataset, job) {
+    _getBugFormTemplate: function (dataset, job) {
         const Galaxy = getGalaxyInstance();
         const userEmail = Galaxy.user.get("email");
         const form = new Form({
@@ -175,14 +175,14 @@ var View = Backbone.View.extend({
                     hidden: !!userEmail,
                     name: "email",
                     value: userEmail,
-                    label: "Please provide your email:"
+                    label: "Please provide your email:",
                 },
                 {
                     type: "text",
                     area: true,
                     name: "message",
-                    label: "Please provide detailed information on the activities leading to this issue:"
-                }
+                    label: "Please provide detailed information on the activities leading to this issue:",
+                },
             ],
             buttons: {
                 save: new Ui.Button({
@@ -195,30 +195,30 @@ var View = Backbone.View.extend({
                         var url = `${getAppRoot()}api/jobs/${job.id}/error`;
                         form_data.dataset_id = dataset.id;
                         this.submit(form_data, url);
-                    }
-                })
-            }
+                    },
+                }),
+            },
         });
         return form.$el;
     },
 
     /** Make ajax request */
-    submit: function(form_data, url) {
+    submit: function (form_data, url) {
         // Some required metadata
         $.ajax({
             type: "POST",
             url: url,
             data: form_data,
-            success: response => {
+            success: (response) => {
                 // Clear out the div
                 this.$el.empty().append(this._templateHeader());
                 // And display the messages.
-                response.messages.forEach(message => {
+                response.messages.forEach((message) => {
                     this.display_message(
                         {
                             status: message[1],
                             message: message[0],
-                            persistent: true
+                            persistent: true,
                         },
                         this.$(".response-message"),
                         true,
@@ -231,14 +231,14 @@ var View = Backbone.View.extend({
                     status: "error",
                     message: "Error occurred while saving. Please fill all the required fields and try again.",
                     persistent: true,
-                    cls: "errormessage"
+                    cls: "errormessage",
                 };
                 this.display_message(error_response, this.$(".response-message"));
-            }
+            },
         });
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
index 742b2f331704..fc02385a3c68 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
@@ -17,7 +17,7 @@ var _super = DATASET_LI.DatasetListItemView;
 var DatasetListItemEdit = _super.extend(
     /** @lends DatasetListItemEdit.prototype */ {
         /** set up: options */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             _super.prototype.initialize.call(this, attributes);
             this.hasUser = attributes.hasUser;
 
@@ -33,7 +33,7 @@ var DatasetListItemEdit = _super.extend(
 
         // ......................................................................... titlebar actions
         /** In this override, add the other two primary actions: edit and delete */
-        _renderPrimaryActions: function() {
+        _renderPrimaryActions: function () {
             var actions = _super.prototype._renderPrimaryActions.call(this);
             if (this.model.get("state") === STATES.NOT_VIEWABLE) {
                 return actions;
@@ -47,7 +47,7 @@ var DatasetListItemEdit = _super.extend(
         //TODO: move titleButtons into state renderers, remove state checks in the buttons
 
         /** Render icon-button to edit the attributes (format, permissions, etc.) this dataset. */
-        _renderEditButton: function() {
+        _renderEditButton: function () {
             var self = this;
             // don't show edit while uploading, in-accessible
             // DO show if in error (ala previous history panel)
@@ -62,15 +62,15 @@ var DatasetListItemEdit = _super.extend(
                 href: `${getAppRoot()}datasets/edit?dataset_id=${this.model.attributes.id}`,
                 faIcon: "fa-pencil",
                 classes: "edit-btn",
-                onclick: function(ev) {
+                onclick: function (ev) {
                     const Galaxy = getGalaxyInstance();
                     if (Galaxy.router) {
                         ev.preventDefault();
                         Galaxy.router.push("datasets/edit", {
-                            dataset_id: self.model.attributes.id
+                            dataset_id: self.model.attributes.id,
                         });
                     }
-                }
+                },
             };
 
             // disable if purged or deleted and explain why in the tooltip
@@ -91,7 +91,7 @@ var DatasetListItemEdit = _super.extend(
         },
 
         /** Render icon-button to delete this hda. */
-        _renderDeleteButton: function() {
+        _renderDeleteButton: function () {
             // don't show delete if...
             if (!this.model.get("accessible")) {
                 return null;
@@ -104,16 +104,16 @@ var DatasetListItemEdit = _super.extend(
                 disabled: deletedAlready,
                 faIcon: "fa-times",
                 classes: "delete-btn",
-                onclick: function() {
+                onclick: function () {
                     self.$el.find(".icon-btn.delete-btn").tooltip("dispose");
                     self.model["delete"]();
-                }
+                },
             });
         },
 
         // ......................................................................... details
         /** In this override, add tags and annotations controls, make the ? dbkey a link to editing page */
-        _renderDetails: function() {
+        _renderDetails: function () {
             //TODO: generalize to be allow different details for each state
             var $details = _super.prototype._renderDetails.call(this);
 
@@ -136,12 +136,12 @@ var DatasetListItemEdit = _super.extend(
          * Render help button to show tool help text without rerunning the tool.
          * Issue #2100
          */
-        _renderToolHelpButton: function() {
+        _renderToolHelpButton: function () {
             var datasetID = this.model.attributes.dataset_id;
             var jobID = this.model.attributes.creating_job;
             var self = this;
 
-            var parseToolBuild = data => {
+            var parseToolBuild = (data) => {
                 var helpString = `<div id="thdiv-${datasetID}" class="toolhelp">`;
                 if (data.name && data.help) {
                     helpString += `<strong>Tool help for ${data.name}</strong><hr/>`;
@@ -152,11 +152,11 @@ var DatasetListItemEdit = _super.extend(
                 helpString += "</div>";
                 self.$el.find(".details").append($.parseHTML(helpString));
             };
-            var parseToolID = data => {
+            var parseToolID = (data) => {
                 $.ajax({
-                    url: `${getAppRoot()}api/tools/${data.tool_id}/build`
+                    url: `${getAppRoot()}api/tools/${data.tool_id}/build`,
                 })
-                    .done(data => {
+                    .done((data) => {
                         parseToolBuild(data);
                     })
                     .fail(() => {
@@ -174,14 +174,14 @@ var DatasetListItemEdit = _super.extend(
                 classes: "icon-btn",
                 href: "#",
                 faIcon: "fa-question",
-                onclick: function() {
+                onclick: function () {
                     if (self.$el.find(".toolhelp").length > 0) {
                         self.$el.find(".toolhelp").toggle();
                     } else {
                         $.ajax({
-                            url: `${getAppRoot()}api/jobs/${jobID}`
+                            url: `${getAppRoot()}api/jobs/${jobID}`,
                         })
-                            .done(data => {
+                            .done((data) => {
                                 parseToolID(data);
                             })
                             .fail(() => {
@@ -190,13 +190,13 @@ var DatasetListItemEdit = _super.extend(
                                 );
                             });
                     }
-                }
+                },
             });
         },
         //*************************************************************************
 
         /** Add less commonly used actions in the details section based on state */
-        _renderSecondaryActions: function() {
+        _renderSecondaryActions: function () {
             var actions = _super.prototype._renderSecondaryActions.call(this);
             switch (this.model.get("state")) {
                 case STATES.UPLOAD:
@@ -211,34 +211,34 @@ var DatasetListItemEdit = _super.extend(
                     return actions.concat([
                         this._renderRerunButton(),
                         this._renderVisualizationsButton(),
-                        this._renderToolHelpButton()
+                        this._renderToolHelpButton(),
                     ]);
             }
             return actions.concat([this._renderRerunButton(), this._renderToolHelpButton()]);
         },
 
         /** Render icon-button to report an error on this dataset to the galaxy admin. */
-        _renderErrButton: function() {
+        _renderErrButton: function () {
             var self = this;
             return faIconButton({
                 title: _l("View or report this error"),
                 href: `${getAppRoot()}datasets/error?dataset_id=${this.model.attributes.id}`,
                 classes: "report-error-btn",
                 faIcon: "fa-bug",
-                onclick: function(ev) {
+                onclick: function (ev) {
                     const Galaxy = getGalaxyInstance();
                     if (Galaxy.router) {
                         ev.preventDefault();
                         Galaxy.router.push("datasets/error", {
-                            dataset_id: self.model.attributes.id
+                            dataset_id: self.model.attributes.id,
                         });
                     }
-                }
+                },
             });
         },
 
         /** Render icon-button to re-run the job that created this dataset. */
-        _renderRerunButton: function() {
+        _renderRerunButton: function () {
             var creating_job = this.model.get("creating_job");
             if (this.model.get("rerunnable")) {
                 return faIconButton({
@@ -247,21 +247,21 @@ var DatasetListItemEdit = _super.extend(
                     classes: "rerun-btn",
                     target: this.linkTarget,
                     faIcon: "fa-refresh",
-                    onclick: function(ev) {
+                    onclick: function (ev) {
                         const Galaxy = getGalaxyInstance();
                         if (Galaxy.router) {
                             ev.preventDefault();
                             Galaxy.router.push("/", {
-                                job_id: creating_job
+                                job_id: creating_job,
                             });
                         }
-                    }
+                    },
                 });
             }
         },
 
         /** Render an icon-button or popupmenu of links based on the applicable visualizations */
-        _renderVisualizationsButton: function() {
+        _renderVisualizationsButton: function () {
             //TODO: someday - lazyload visualizations
             const Galaxy = getGalaxyInstance();
             const visualizations = this.model.get("visualizations");
@@ -286,24 +286,24 @@ var DatasetListItemEdit = _super.extend(
                     href: url,
                     classes: "visualization-link",
                     faIcon: "fa-bar-chart-o",
-                    onclick: ev => {
+                    onclick: (ev) => {
                         if (Galaxy.frame && Galaxy.frame.active) {
                             ev.preventDefault();
                             Galaxy.frame.add({ url: url, title: "Visualization" });
                         } else if (Galaxy.router) {
                             ev.preventDefault();
                             Galaxy.router.push("visualizations", {
-                                dataset_id: dsid
+                                dataset_id: dsid,
                             });
                             Galaxy.trigger("activate-hda", dsid);
                         }
-                    }
+                    },
                 });
             }
         },
 
         /** Render the tags list/control */
-        _renderTags: function($where) {
+        _renderTags: function ($where) {
             if (!this.hasUser) {
                 return;
             }
@@ -313,7 +313,7 @@ var DatasetListItemEdit = _super.extend(
             const propsData = {
                 model: this.model,
                 disabled: false,
-                context: "dataset-li-edit"
+                context: "dataset-li-edit",
             };
 
             const vm = mountModelTags(propsData, el);
@@ -322,7 +322,7 @@ var DatasetListItemEdit = _super.extend(
             const activator = faIconButton({
                 title: _l("Edit dataset tags"),
                 classes: "tag-btn",
-                faIcon: "fa-tags"
+                faIcon: "fa-tags",
             }).appendTo($where.find(".actions .right"));
 
             const toggleEditor = () => {
@@ -343,7 +343,7 @@ var DatasetListItemEdit = _super.extend(
         },
 
         /** Render the annotation display/control */
-        _renderAnnotation: function($where) {
+        _renderAnnotation: function ($where) {
             if (!this.hasUser) {
                 return;
             }
@@ -351,21 +351,21 @@ var DatasetListItemEdit = _super.extend(
             this.annotationEditor = new ANNOTATIONS.AnnotationEditor({
                 model: this.model,
                 el: $where.find(".annotation-display"),
-                onshowFirstTime: function() {
+                onshowFirstTime: function () {
                     this.render();
                 },
                 // persist state on the hda view (and not the editor) since these are currently re-created each time
-                onshow: function() {
+                onshow: function () {
                     view.annotationEditorShown = true;
                 },
-                onhide: function() {
+                onhide: function () {
                     view.annotationEditorShown = false;
                 },
                 $activator: faIconButton({
                     title: _l("Edit dataset annotation"),
                     classes: "annotate-btn",
-                    faIcon: "fa-comment"
-                }).appendTo($where.find(".actions .right"))
+                    faIcon: "fa-comment",
+                }).appendTo($where.find(".actions .right")),
             });
             if (this.annotationEditorShown) {
                 this.annotationEditor.toggle(true);
@@ -373,7 +373,7 @@ var DatasetListItemEdit = _super.extend(
         },
 
         /** If the format/dbkey/genome_build isn't set, make the display a link to the edit page */
-        _makeDbkeyEditLink: function($details) {
+        _makeDbkeyEditLink: function ($details) {
             // make the dbkey a link to editing
             if (this.model.get("metadata_dbkey") === "?" && !this.model.isDeletedOrPurged()) {
                 var editableDbkey = $('<a class="value">?</a>')
@@ -389,34 +389,34 @@ var DatasetListItemEdit = _super.extend(
             "click .undelete-link": "_clickUndeleteLink",
             "click .purge-link": "_clickPurgeLink",
 
-            "click .edit-btn": function(ev) {
+            "click .edit-btn": function (ev) {
                 this.trigger("edit", this, ev);
             },
-            "click .delete-btn": function(ev) {
+            "click .delete-btn": function (ev) {
                 this.trigger("delete", this, ev);
             },
-            "click .rerun-btn": function(ev) {
+            "click .rerun-btn": function (ev) {
                 this.trigger("rerun", this, ev);
             },
-            "click .report-err-btn": function(ev) {
+            "click .report-err-btn": function (ev) {
                 this.trigger("report-err", this, ev);
             },
-            "click .visualization-btn": function(ev) {
+            "click .visualization-btn": function (ev) {
                 this.trigger("visualize", this, ev);
             },
-            "click .dbkey a": function(ev) {
+            "click .dbkey a": function (ev) {
                 this.trigger("edit", this, ev);
-            }
+            },
         }),
 
         /** listener for item undelete (in the messages section) */
-        _clickUndeleteLink: function(ev) {
+        _clickUndeleteLink: function (ev) {
             this.model.undelete();
             return false;
         },
 
         /** listener for item purge (in the messages section) */
-        _clickPurgeLink: function(ev) {
+        _clickPurgeLink: function (ev) {
             if (window.confirm(_l("This will permanently remove the data in your dataset. Are you sure?"))) {
                 this.model.purge();
             }
@@ -425,10 +425,10 @@ var DatasetListItemEdit = _super.extend(
 
         // ......................................................................... misc
         /** string rep */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `HDAEditView(${modelString})`;
-        }
+        },
     }
 );
 
@@ -446,7 +446,7 @@ DatasetListItemEdit.prototype.templates = (() => {
                 _l("Set it manually or retry auto-detection"),
                 "</a>",
                 "</div>",
-                "<% } %>"
+                "<% } %>",
             ],
             "dataset"
         ),
@@ -467,17 +467,17 @@ DatasetListItemEdit.prototype.templates = (() => {
                 "</a>",
                 "<% } %>",
                 "</div>",
-                "<% } %>"
+                "<% } %>",
             ],
             "dataset"
-        )
+        ),
     });
     return _.extend({}, _super.prototype.templates, {
-        warnings: warnings
+        warnings: warnings,
     });
 })();
 
 //==============================================================================
 export default {
-    DatasetListItemEdit: DatasetListItemEdit
+    DatasetListItemEdit: DatasetListItemEdit,
 };
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li.js b/client/galaxy/scripts/mvc/dataset/dataset-li.js
index 17f2701edbd6..69a0eabd9e36 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-li.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js
@@ -27,12 +27,12 @@ export var DatasetListItemView = _super.extend(
 
         className: `${_super.prototype.className} dataset`,
         //TODO:?? doesn't exactly match an hda's type_id
-        id: function() {
+        id: function () {
             return ["dataset", this.model.get("id")].join("-");
         },
 
         /** Set up: instance vars, options, and event handlers */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             if (attributes.logger) {
                 this.logger = this.model.logger = attributes.logger;
             }
@@ -44,13 +44,13 @@ export var DatasetListItemView = _super.extend(
         },
 
         // mount new vue component for tags
-        render: function() {
+        render: function () {
             const result = _super.prototype.render.apply(this, arguments);
             this._mountVueNametags();
             return result;
         },
 
-        _mountVueNametags: function() {
+        _mountVueNametags: function () {
             const container = this.$(".nametags")[0];
             const { id, model_class, tags } = this.model.attributes;
             const storeKey = `${model_class}-${id}`;
@@ -58,13 +58,13 @@ export var DatasetListItemView = _super.extend(
         },
 
         /** event listeners */
-        _setUpListeners: function() {
+        _setUpListeners: function () {
             _super.prototype._setUpListeners.call(this);
             var self = this;
 
             // re-rendering on any model changes
             return self.listenTo(self.model, {
-                change: function(model) {
+                change: function (model) {
                     // if the model moved into the ready state and is expanded without details, fetch those details now
                     if (
                         self.model.changedAttributes().state &&
@@ -88,7 +88,7 @@ export var DatasetListItemView = _super.extend(
                             self.render();
                         }
                     }
-                }
+                },
             });
         },
 
@@ -96,7 +96,7 @@ export var DatasetListItemView = _super.extend(
         /** In this override, only get details if in the ready state, get rerunnable if in other states.
          *  Note: fetch with no 'change' event triggering to prevent automatic rendering.
          */
-        _fetchModelDetails: function() {
+        _fetchModelDetails: function () {
             var view = this;
             if (view.model.inReadyState() && !view.model.hasDetails()) {
                 return view.model.fetch({ silent: true });
@@ -109,7 +109,7 @@ export var DatasetListItemView = _super.extend(
          *  @param {Number or String} speed jq effect speed
          *  @param {Function} callback      an optional function called when removal is done (scoped to this view)
          */
-        remove: function(speed, callback) {
+        remove: function (speed, callback) {
             var view = this;
             speed = speed || this.fxSpeed;
             this.$el.fadeOut(speed, () => {
@@ -130,7 +130,7 @@ export var DatasetListItemView = _super.extend(
             - but recreating the view during an update...seems wrong
     */
         /** In this override, add the dataset state as a class for use with state-based CSS */
-        _swapNewRender: function($newRender) {
+        _swapNewRender: function ($newRender) {
             _super.prototype._swapNewRender.call(this, $newRender);
             if (this.model.has("state")) {
                 this.$el.addClass(`state-${this.model.get("state")}`);
@@ -140,13 +140,13 @@ export var DatasetListItemView = _super.extend(
 
         // ................................................................................ titlebar
         /** In this override, add the dataset display button. */
-        _renderPrimaryActions: function() {
+        _renderPrimaryActions: function () {
             // render just the display for read-only
             return [this._renderDisplayButton()];
         },
 
         /** Render icon-button to display dataset data */
-        _renderDisplayButton: function() {
+        _renderDisplayButton: function () {
             // don't show display if not viewable or not accessible
             var state = this.model.get("state");
             if (state === STATES.NOT_VIEWABLE || state === STATES.DISCARDED || !this.model.get("accessible")) {
@@ -155,7 +155,7 @@ export var DatasetListItemView = _super.extend(
 
             var displayBtnData = {
                 target: this.linkTarget,
-                classes: "display-btn"
+                classes: "display-btn",
             };
 
             // show a disabled display if the data's been purged
@@ -180,7 +180,7 @@ export var DatasetListItemView = _super.extend(
 
                 // add frame manager option onclick event
                 var self = this;
-                displayBtnData.onclick = ev => {
+                displayBtnData.onclick = (ev) => {
                     const Galaxy = getGalaxyInstance();
                     if (Galaxy.frame && Galaxy.frame.active) {
                         // Add dataset to frames.
@@ -197,7 +197,7 @@ export var DatasetListItemView = _super.extend(
         /** Render the enclosing div of the hda body and, if expanded, the html in the body
          *  @returns {jQuery} rendered DOM
          */
-        _renderDetails: function() {
+        _renderDetails: function () {
             //TODO: generalize to be allow different details for each state
 
             // no access - render nothing but a message
@@ -206,14 +206,8 @@ export var DatasetListItemView = _super.extend(
             }
 
             var $details = _super.prototype._renderDetails.call(this);
-            $details
-                .find(".actions .left")
-                .empty()
-                .append(this._renderSecondaryActions());
-            $details
-                .find(".summary")
-                .html(this._renderSummary())
-                .prepend(this._renderDetailMessages());
+            $details.find(".actions .left").empty().append(this._renderSecondaryActions());
+            $details.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());
             $details.find(".display-applications").html(this._renderDisplayApplications());
 
             this._setUpBehaviors($details);
@@ -221,7 +215,7 @@ export var DatasetListItemView = _super.extend(
         },
 
         /** Defer to the appropo summary rendering fn based on state */
-        _renderSummary: function() {
+        _renderSummary: function () {
             var json = this.model.toJSON();
             var summaryRenderFn = this.templates.summaries[json.state];
             summaryRenderFn = summaryRenderFn || this.templates.summaries.unknown;
@@ -229,32 +223,32 @@ export var DatasetListItemView = _super.extend(
         },
 
         /** Render messages to be displayed only when the details are shown */
-        _renderDetailMessages: function() {
+        _renderDetailMessages: function () {
             var view = this;
             var $warnings = $('<div class="detail-messages"></div>');
             var json = view.model.toJSON();
             //TODO:! unordered (map)
-            _.each(view.templates.detailMessages, templateFn => {
+            _.each(view.templates.detailMessages, (templateFn) => {
                 $warnings.append($(templateFn(json, view)));
             });
             return $warnings;
         },
 
         /** Render the external display application links */
-        _renderDisplayApplications: function() {
+        _renderDisplayApplications: function () {
             if (this.model.isDeletedOrPurged()) {
                 return "";
             }
             // render both old and new display apps using the same template
             return [
                 this.templates.displayApplications(this.model.get("display_apps"), this),
-                this.templates.displayApplications(this.model.get("display_types"), this)
+                this.templates.displayApplications(this.model.get("display_types"), this),
             ].join("");
         },
 
         // ......................................................................... secondary/details actions
         /** A series of links/buttons for less commonly used actions: re-run, info, etc. */
-        _renderSecondaryActions: function() {
+        _renderSecondaryActions: function () {
             this.debug("_renderSecondaryActions");
             switch (this.model.get("state")) {
                 case STATES.NOT_VIEWABLE:
@@ -270,7 +264,7 @@ export var DatasetListItemView = _super.extend(
         /** Render icon-button to show the input and output (stdout/err) for the job that created this.
          *  @returns {jQuery} rendered DOM
          */
-        _renderShowParamsButton: function() {
+        _renderShowParamsButton: function () {
             // gen. safe to show in all cases
             return faIconButton({
                 title: _l("View details"),
@@ -278,24 +272,24 @@ export var DatasetListItemView = _super.extend(
                 href: this.model.urls.show_params,
                 target: this.linkTarget,
                 faIcon: "fa-info-circle",
-                onclick: function(ev) {
+                onclick: function (ev) {
                     const Galaxy = getGalaxyInstance();
                     if (Galaxy.frame && Galaxy.frame.active) {
                         Galaxy.frame.add({
                             title: _l("Dataset details"),
-                            url: this.href
+                            url: this.href,
                         });
                         ev.preventDefault();
                         ev.stopPropagation();
                     }
-                }
+                },
             });
         },
 
         /** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this.
          *  @returns {jQuery} rendered DOM
          */
-        _renderDownloadButton: function() {
+        _renderDownloadButton: function () {
             // don't show anything if the data's been purged
             if (this.model.get("purged") || !this.model.hasData()) {
                 return null;
@@ -314,7 +308,7 @@ export var DatasetListItemView = _super.extend(
         },
 
         /** Render the download button which opens a dropdown with links to download assoc. meta files (indices, etc.) */
-        _renderMetaFileDownloadButton: function() {
+        _renderMetaFileDownloadButton: function () {
             var urls = this.model.urls;
             return $(`
                 <div class="metafile-dropdown dropdown">
@@ -329,7 +323,7 @@ export var DatasetListItemView = _super.extend(
                         </a>
                         ${_.map(
                             this.model.get("meta_files"),
-                            meta_file =>
+                            (meta_file) =>
                                 `<a class="dropdown-item" href="${urls.meta_download + meta_file.file_type}">
                                     ${_l("Download")} ${meta_file.file_type}
                                 </a>`
@@ -340,23 +334,23 @@ export var DatasetListItemView = _super.extend(
 
         // ......................................................................... misc
         events: _.extend(_.clone(_super.prototype.events), {
-            "click .display-btn": function(ev) {
+            "click .display-btn": function (ev) {
                 this.trigger("display", this, ev);
             },
-            "click .params-btn": function(ev) {
+            "click .params-btn": function (ev) {
                 this.trigger("params", this, ev);
             },
-            "click .download-btn": function(ev) {
+            "click .download-btn": function (ev) {
                 this.trigger("download", this, ev);
-            }
+            },
         }),
 
         // ......................................................................... misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `DatasetListItemView(${modelString})`;
-        }
+        },
     }
 );
 
@@ -372,7 +366,7 @@ DatasetListItemView.prototype.templates = (() => {
             '<div class="warningmessagesmall">',
             _l("An error occurred setting the metadata for this dataset"),
             "</div>",
-            "<% } %>"
+            "<% } %>",
         ]),
         error: BASE_MVC.wrapTemplate([
             // error during index fetch - show error on dataset
@@ -381,14 +375,14 @@ DatasetListItemView.prototype.templates = (() => {
             _l("There was an error getting the data for this dataset"),
             ": <%- model.error %>",
             "</div>",
-            "<% } %>"
+            "<% } %>",
         ]),
         purged: BASE_MVC.wrapTemplate([
             "<% if( model.purged ){ %>",
             '<div class="purged-msg warningmessagesmall">',
             _l("This dataset has been deleted and removed from disk"),
             "</div>",
-            "<% } %>"
+            "<% } %>",
         ]),
         deleted: BASE_MVC.wrapTemplate([
             // deleted not purged
@@ -396,8 +390,8 @@ DatasetListItemView.prototype.templates = (() => {
             '<div class="deleted-msg warningmessagesmall">',
             _l("This dataset has been deleted"),
             "</div>",
-            "<% } %>"
-        ])
+            "<% } %>",
+        ]),
 
         //NOTE: hidden warning is only needed for HDAs
     });
@@ -423,7 +417,7 @@ DatasetListItemView.prototype.templates = (() => {
             '<pre class="dataset-peek"><%= dataset.peek %></pre>',
             "<% } %>",
             "<% } %>",
-            "</div>"
+            "</div>",
         ],
         "dataset"
     );
@@ -434,7 +428,7 @@ DatasetListItemView.prototype.templates = (() => {
             '<div class="summary">',
             _l("You do not have permission to view this dataset"),
             "</div>",
-            "</div>"
+            "</div>",
         ],
         "dataset"
     );
@@ -473,7 +467,7 @@ DatasetListItemView.prototype.templates = (() => {
             '<div class="info">',
             '<span class="value"><%- dataset.misc_info %></span>',
             "</div>",
-            "<% } %>"
+            "<% } %>",
         ],
         "dataset"
     );
@@ -510,7 +504,7 @@ DatasetListItemView.prototype.templates = (() => {
             "<div>",
             _l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),
             "</div>",
-            '<div class="info"><%- dataset.misc_info %></div>'
+            '<div class="info"><%- dataset.misc_info %></div>',
         ],
         "dataset"
     );
@@ -522,7 +516,7 @@ DatasetListItemView.prototype.templates = (() => {
             '<span class="help-text">',
             _l("An error occurred with this dataset"),
             ":</span>",
-            '<div class="job-error-text"><%- dataset.misc_info %></div>'
+            '<div class="job-error-text"><%- dataset.misc_info %></div>',
         ],
         "dataset"
     );
@@ -543,8 +537,8 @@ DatasetListItemView.prototype.templates = (() => {
             '<div class="resubmitted-msg infomessagesmall">',
             _l("The job creating this dataset has been resubmitted"),
             "</div>",
-            "<% } %>"
-        ])
+            "<% } %>",
+        ]),
     };
 
     // this is applied to both old and new style display apps
@@ -561,7 +555,7 @@ DatasetListItemView.prototype.templates = (() => {
             "<% }); %>",
             "</span>",
             "</div>",
-            "<% }); %>"
+            "<% }); %>",
         ],
         "apps"
     );
@@ -572,11 +566,11 @@ DatasetListItemView.prototype.templates = (() => {
         noAccess: noAccessTemplate,
         summaries: summaryTemplates,
         detailMessages: detailMessageTemplates,
-        displayApplications: displayApplicationsTemplate
+        displayApplications: displayApplicationsTemplate,
     });
 })();
 
 // ============================================================================
 export default {
-    DatasetListItemView: DatasetListItemView
+    DatasetListItemView: DatasetListItemView,
 };
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-list.js b/client/galaxy/scripts/mvc/dataset/dataset-list.js
index 0ab655798aa2..23a77cfcfde3 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-list.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-list.js
@@ -25,18 +25,18 @@ var DatasetList = _super.extend(
         /** Set up the view, set up storage, bind listeners to HistoryContents events
          *  @param {Object} attributes optional settings for the panel
          */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             _super.prototype.initialize.call(this, attributes);
         },
 
         /** Return a string rep of the history */
-        toString: function() {
+        toString: function () {
             return `DatasetList(${this.collection})`;
-        }
+        },
     }
 );
 
 //==============================================================================
 export default {
-    DatasetList: DatasetList
+    DatasetList: DatasetList,
 };
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-model.js b/client/galaxy/scripts/mvc/dataset/dataset-model.js
index 85a8559bea57..2a302f55f9e2 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-model.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-model.js
@@ -39,14 +39,14 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                 misc_blurb: "",
                 misc_info: "",
 
-                tags: []
+                tags: [],
                 // do NOT default on annotation, as this default is valid and will be passed on 'save'
                 //  which is incorrect behavior when the model is only partially fetched (annos are not passed in summary data)
                 //annotation          : ''
             },
 
             /** instance vars and listeners */
-            initialize: function(attributes, options) {
+            initialize: function (attributes, options) {
                 this.debug(`${this}(Dataset).initialize`, attributes, options);
 
                 //!! this state is not in trans.app.model.Dataset.states - set it here -
@@ -60,12 +60,12 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                 this._setUpListeners();
             },
 
-            _getDatasetId: function() {
+            _getDatasetId: function () {
                 return this.get("id");
             },
 
             /** returns misc. web urls for rendering things like re-run, display, etc. */
-            _generateUrls: function() {
+            _generateUrls: function () {
                 const id = this._getDatasetId();
                 if (!id) {
                     return {};
@@ -79,7 +79,7 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                     rerun: `tool_runner/rerun?id=${id}`,
                     show_params: `datasets/${id}/show_params`,
                     visualization: "visualization",
-                    meta_download: `dataset/get_metadata_file?hda_id=${id}&metadata_name=`
+                    meta_download: `dataset/get_metadata_file?hda_id=${id}&metadata_name=`,
                 };
                 _.each(urls, (value, key) => {
                     urls[key] = getAppRoot() + value;
@@ -88,23 +88,23 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                 return urls;
             },
 
-            _downloadQueryParameters: function() {
+            _downloadQueryParameters: function () {
                 return `?to_ext=${this.get("file_ext")}`;
             },
 
             /** set up any event listeners
              *  event: state:ready  fired when this DA moves into/is already in a ready state
              */
-            _setUpListeners: function() {
+            _setUpListeners: function () {
                 // if the state has changed and the new state is a ready state, fire an event
-                this.on("change:state", function(currModel, newState) {
+                this.on("change:state", function (currModel, newState) {
                     this.log(`${this} has changed state:`, currModel, newState);
                     if (this.inReadyState()) {
                         this.trigger("state:ready", currModel, newState, this.previous("state"));
                         if (newState != "discarded") {
                             if (newState === "ok") {
                                 new Notification(`Job complete: ${this.get("name")}`, {
-                                    icon: "static/favicon.ico"
+                                    icon: "static/favicon.ico",
                                 });
                                 if (TAB_UPDATES.is_hidden()) {
                                     TAB_UPDATES.hidden_count(hiddenupdates);
@@ -112,7 +112,7 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                                 }
                             } else if (newState == "error") {
                                 new Notification(`Job failure: ${this.get("name")}`, {
-                                    icon: "static/erricon.ico"
+                                    icon: "static/erricon.ico",
                                 });
                                 if (TAB_UPDATES.is_hidden() && Notification.permission == "granted") {
                                     TAB_UPDATES.change_favicon("static/erricon.ico");
@@ -122,37 +122,37 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                     }
                 });
                 // the download url (currently) relies on having a correct file extension
-                this.on("change:id change:file_ext", function(currModel) {
+                this.on("change:id change:file_ext", function (currModel) {
                     this._generateUrls();
                 });
             },
 
             // ........................................................................ common queries
             /** override to add urls */
-            toJSON: function() {
+            toJSON: function () {
                 var json = Backbone.Model.prototype.toJSON.call(this);
                 //console.warn( 'returning json?' );
                 //return json;
                 return _.extend(json, {
-                    urls: this.urls
+                    urls: this.urls,
                 });
             },
 
             /** Is this dataset deleted or purged? */
-            isDeletedOrPurged: function() {
+            isDeletedOrPurged: function () {
                 return this.get("deleted") || this.get("purged");
             },
 
             /** Is this dataset in a 'ready' state; where 'Ready' states are states where no
              *      processing (for the ds) is left to do on the server.
              */
-            inReadyState: function() {
+            inReadyState: function () {
                 var ready = _.contains(STATES.READY_STATES, this.get("state"));
                 return this.isDeletedOrPurged() || ready;
             },
 
             /** Does this model already contain detailed data (as opposed to just summary level data)? */
-            hasDetails: function() {
+            hasDetails: function () {
                 // if it's inaccessible assume it has everything it needs
                 if (!this.get("accessible")) {
                     return true;
@@ -161,12 +161,12 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             /** Convenience function to match dataset.has_data. */
-            hasData: function() {
+            hasData: function () {
                 return this.get("file_size") > 0;
             },
 
             // ........................................................................ ajax
-            fetch: function(options) {
+            fetch: function (options) {
                 var dataset = this;
                 return Backbone.Model.prototype.fetch.call(this, options).always(() => {
                     dataset._generateUrls();
@@ -174,7 +174,7 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             /** override to use actual Dates objects for create/update times */
-            parse: function(response, options) {
+            parse: function (response, options) {
                 var parsed = Backbone.Model.prototype.parse.call(this, response, options);
                 if (parsed.create_time) {
                     parsed.create_time = new Date(parsed.create_time);
@@ -186,7 +186,7 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             /** override to wait by default */
-            save: function(attrs, options) {
+            save: function (attrs, options) {
                 options = options || {};
                 options.wait = _.isUndefined(options.wait) ? true : options.wait;
                 return Backbone.Model.prototype.save.call(this, attrs, options);
@@ -194,14 +194,14 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
 
             //NOTE: subclasses of DA's will need to implement url and urlRoot in order to have these work properly
             /** save this dataset, _Mark_ing it as deleted (just a flag) */
-            delete: function(options) {
+            delete: function (options) {
                 if (this.get("deleted")) {
                     return jQuery.when();
                 }
                 return this.save({ deleted: true }, options);
             },
             /** save this dataset, _Mark_ing it as undeleted */
-            undelete: function(options) {
+            undelete: function (options) {
                 if (!this.get("deleted") || this.get("purged")) {
                     return jQuery.when();
                 }
@@ -238,7 +238,7 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                     }
                     xhr.responseText = error;
                     hda.trigger("error", hda, xhr, options, _l(error), {
-                        error: error
+                        error: error,
                     });
                 });
                 return xhr;
@@ -259,18 +259,18 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                 blurb: "misc_blurb",
                 description: "misc_blurb",
                 info: "misc_info",
-                tag: "tags"
+                tag: "tags",
             },
 
             // ........................................................................ misc
             /** String representation */
-            toString: function() {
+            toString: function () {
                 var nameAndId = this.get("id") || "";
                 if (this.get("name")) {
                     nameAndId = `"${this.get("name")}",${nameAndId}`;
                 }
                 return `Dataset(${nameAndId})`;
-            }
+            },
         }
     )
 );
@@ -288,7 +288,7 @@ var DatasetAssociationCollection = Backbone.Collection.extend(BASE_MVC.LoggableM
         urlRoot: `${getAppRoot()}api/datasets`,
 
         /** url fn */
-        url: function() {
+        url: function () {
             return this.urlRoot;
         },
 
@@ -296,25 +296,25 @@ var DatasetAssociationCollection = Backbone.Collection.extend(BASE_MVC.LoggableM
         /** Get the ids of every item in this collection
          *  @returns array of encoded ids
          */
-        ids: function() {
-            return this.map(item => item.get("id"));
+        ids: function () {
+            return this.map((item) => item.get("id"));
         },
 
         /** Get contents that are not ready
          *  @returns array of content models
          */
-        notReady: function() {
-            return this.filter(content => !content.inReadyState());
+        notReady: function () {
+            return this.filter((content) => !content.inReadyState());
         },
 
         /** return true if any datasets don't have details */
-        haveDetails: function() {
-            return this.all(dataset => dataset.hasDetails());
+        haveDetails: function () {
+            return this.all((dataset) => dataset.hasDetails());
         },
 
         // ........................................................................ ajax
         /** using a queue, perform ajaxFn on each of the models in this collection */
-        ajaxQueue: function(ajaxFn, options) {
+        ajaxQueue: function (ajaxFn, options) {
             var deferred = jQuery.Deferred();
             var startingLength = this.length;
             var responses = [];
@@ -330,17 +330,17 @@ var DatasetAssociationCollection = Backbone.Collection.extend(BASE_MVC.LoggableM
                 .map((dataset, i) => () => {
                     var xhr = ajaxFn.call(dataset, options);
                     // if successful, notify using the deferred to allow tracking progress
-                    xhr.done(response => {
+                    xhr.done((response) => {
                         deferred.notify({
                             curr: i,
                             total: startingLength,
                             response: response,
-                            model: dataset
+                            model: dataset,
                         });
                     });
                     // (regardless of previous error or success) if not last ajax call, shift and call the next
                     //  if last fn, resolve deferred
-                    xhr.always(response => {
+                    xhr.always((response) => {
                         responses.push(response);
                         if (ajaxFns.length) {
                             ajaxFns.shift()();
@@ -358,18 +358,18 @@ var DatasetAssociationCollection = Backbone.Collection.extend(BASE_MVC.LoggableM
 
         // ........................................................................ sorting/filtering
         /** return a new collection of datasets whose attributes contain the substring matchesWhat */
-        matches: function(matchesWhat) {
-            return this.filter(dataset => dataset.matches(matchesWhat));
+        matches: function (matchesWhat) {
+            return this.filter((dataset) => dataset.matches(matchesWhat));
         },
 
         /** String representation. */
-        toString: function() {
+        toString: function () {
             return ["DatasetAssociationCollection(", this.length, ")"].join("");
-        }
+        },
     }
 );
 
-window.addEventListener("focus", function() {
+window.addEventListener("focus", function () {
     const testing = document.getElementById("tabicon");
     if (testing && testing.href.search("erricon") != -1) {
         TAB_UPDATES.change_favicon("static/favicon.ico");
@@ -380,5 +380,5 @@ window.addEventListener("focus", function() {
 //==============================================================================
 export default {
     DatasetAssociation: DatasetAssociation,
-    DatasetAssociationCollection: DatasetAssociationCollection
+    DatasetAssociationCollection: DatasetAssociationCollection,
 };
diff --git a/client/galaxy/scripts/mvc/dataset/states.js b/client/galaxy/scripts/mvc/dataset/states.js
index 406c0aeee79f..68722ef9cf0d 100644
--- a/client/galaxy/scripts/mvc/dataset/states.js
+++ b/client/galaxy/scripts/mvc/dataset/states.js
@@ -31,7 +31,7 @@ var STATES = {
     /** deleted while uploading */
     DISCARDED: "discarded",
     /** the tool producing this dataset failed */
-    ERROR: "error"
+    ERROR: "error",
 };
 
 STATES.READY_STATES = [
@@ -41,7 +41,7 @@ STATES.READY_STATES = [
     STATES.FAILED_METADATA,
     STATES.NOT_VIEWABLE,
     STATES.DISCARDED,
-    STATES.ERROR
+    STATES.ERROR,
 ];
 
 STATES.NOT_READY_STATES = [STATES.UPLOAD, STATES.QUEUED, STATES.RUNNING, STATES.SETTING_METADATA, STATES.NEW];
diff --git a/client/galaxy/scripts/mvc/embedded-objects.js b/client/galaxy/scripts/mvc/embedded-objects.js
index 18455634ef35..51343ecf7483 100644
--- a/client/galaxy/scripts/mvc/embedded-objects.js
+++ b/client/galaxy/scripts/mvc/embedded-objects.js
@@ -2,7 +2,7 @@ import $ from "jquery";
 import { make_popup_menus } from "ui/popupmenu";
 
 export function render_embedded_items() {
-    $(".embedded-item").each(function() {
+    $(".embedded-item").each(function () {
         var container = $(this);
         if (container.hasClass("history")) {
             return;
@@ -13,7 +13,7 @@ export function render_embedded_items() {
         //  and add new ones (in embed_in_frame.mako) ...ugh.
 
         // Show embedded item.
-        var show_embedded_item = function() {
+        var show_embedded_item = function () {
             var ajax_url = container.find("input[type=hidden]").val();
             if (!ajax_url) {
                 ajax_url = container.data("item-url");
@@ -24,10 +24,10 @@ export function render_embedded_items() {
                 $.ajax({
                     type: "GET",
                     url: ajax_url,
-                    error: function() {
+                    error: function () {
                         alert("Getting item content failed.");
                     },
-                    success: function(item_content) {
+                    success: function (item_content) {
                         container.find(".summary-content").hide("fast");
                         container.find(".item-content").html(item_content);
                         container.find(".expanded-content").show("fast");
@@ -35,7 +35,7 @@ export function render_embedded_items() {
                         container.find(".toggle").show();
 
                         make_popup_menus();
-                    }
+                    },
                 });
             } else {
                 container.find(".summary-content").hide("fast");
@@ -46,7 +46,7 @@ export function render_embedded_items() {
         };
 
         // Hide embedded item.
-        var hide_embedded_item = function() {
+        var hide_embedded_item = function () {
             container.find(".expanded-content").hide("fast");
             container.find(".summary-content").show("fast");
             container.find(".toggle").hide();
@@ -55,20 +55,20 @@ export function render_embedded_items() {
 
         // Setup toggle expand.
         var toggle_expand = $(this).find(".toggle-expand");
-        toggle_expand.click(function() {
+        toggle_expand.click(function () {
             show_embedded_item();
             return false;
         });
         // Setup toggle contract.
         var toggle_contract = $(this).find(".toggle");
-        toggle_contract.click(function() {
+        toggle_contract.click(function () {
             hide_embedded_item();
             return false;
         });
 
         // Setup toggle embed.
         var toggle_embed = $(this).find(".toggle-embed");
-        toggle_embed.click(function() {
+        toggle_embed.click(function () {
             if (container.find(".expanded-content").is(":visible")) {
                 hide_embedded_item();
             } else {
diff --git a/client/galaxy/scripts/mvc/entrypoints/poll.js b/client/galaxy/scripts/mvc/entrypoints/poll.js
index a141eaddcfe6..b21051f136a9 100644
--- a/client/galaxy/scripts/mvc/entrypoints/poll.js
+++ b/client/galaxy/scripts/mvc/entrypoints/poll.js
@@ -12,7 +12,7 @@ export const pollUntilActive = (onUpdate, onError, params) => {
     const url = getAppRoot() + `api/entry_points`;
     axios
         .get(url, { params: params })
-        .then(response => {
+        .then((response) => {
             const entryPoints = [];
             let allReady = true;
             response.data.forEach((entryPoint, i) => {
diff --git a/client/galaxy/scripts/mvc/entrypoints/view.js b/client/galaxy/scripts/mvc/entrypoints/view.js
index 23b3204b9d57..31a990dab656 100644
--- a/client/galaxy/scripts/mvc/entrypoints/view.js
+++ b/client/galaxy/scripts/mvc/entrypoints/view.js
@@ -3,13 +3,13 @@ import GridView from "mvc/grid/grid-view";
 import { clearPolling, pollUntilActive } from "mvc/entrypoints/poll";
 
 export default GridView.extend({
-    init_grid_elements: function() {
+    init_grid_elements: function () {
         GridView.prototype.init_grid_elements.call(this);
 
         const activated = {};
 
-        const onUpdate = entryPoints => {
-            entryPoints.forEach(entryPoint => {
+        const onUpdate = (entryPoints) => {
+            entryPoints.forEach((entryPoint) => {
                 const entryPointId = entryPoint.id;
                 if (entryPoint.active && !activated[entryPointId]) {
                     const $link = $(`.entry-point-link[entry_point_id='${entryPointId}']`);
@@ -20,14 +20,14 @@ export default GridView.extend({
                 }
             });
         };
-        const onError = e => {
+        const onError = (e) => {
             console.error(e);
         };
         pollUntilActive(onUpdate, onError, { running: true });
     },
-    remove: function() {
+    remove: function () {
         // Your processing code here
         clearPolling();
         GridView.prototype.remove.apply(this, arguments);
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/form/form-data.js b/client/galaxy/scripts/mvc/form/form-data.js
index ddee94761195..61f0778b8f8e 100644
--- a/client/galaxy/scripts/mvc/form/form-data.js
+++ b/client/galaxy/scripts/mvc/form/form-data.js
@@ -5,15 +5,15 @@ import { getGalaxyInstance } from "app";
 
 /* This class maps the form dom to an api compatible javascript dictionary. */
 export var Manager = Backbone.Model.extend({
-    initialize: function(app) {
+    initialize: function (app) {
         this.app = app;
     },
 
     /** Creates a checksum. */
-    checksum: function() {
+    checksum: function () {
         var sum = "";
         var self = this;
-        this.app.section.$el.find(".section-row").each(function() {
+        this.app.section.$el.find(".section-row").each(function () {
             var id = $(this).attr("id");
             var field = self.app.field_list[id];
             if (field) {
@@ -24,7 +24,7 @@ export var Manager = Backbone.Model.extend({
     },
 
     /** Convert dom into a dictionary of flat id/value pairs used e.g. on job submission. */
-    create: function() {
+    create: function () {
         var self = this;
 
         // get raw dictionary from dom
@@ -113,19 +113,19 @@ export var Manager = Backbone.Model.extend({
     /** Matches flat ids to corresponding input element
      * @param{string} flat_id - Flat input id to be looked up.
      */
-    match: function(flat_id) {
+    match: function (flat_id) {
         return this.flat_dict && this.flat_dict[flat_id];
     },
 
     /** Match conditional values to selected cases
      */
-    matchCase: function(input, value) {
+    matchCase: function (input, value) {
         return matchCase(input, value);
     },
 
     /** Matches a new tool model to the current input elements e.g. used to update dynamic options
      */
-    matchModel: function(model, callback) {
+    matchModel: function (model, callback) {
         var self = this;
         visitInputs(model.inputs, (input, name) => {
             if (self.flat_dict[name]) {
@@ -136,7 +136,7 @@ export var Manager = Backbone.Model.extend({
 
     /** Matches identifier from api response to input elements e.g. used to display validation errors
      */
-    matchResponse: function(response) {
+    matchResponse: function (response) {
         var result = {};
         var self = this;
         function search(id, head) {
@@ -165,10 +165,10 @@ export var Manager = Backbone.Model.extend({
 
     /** Map dom tree to dictionary tree with input elements.
      */
-    _iterate: function(parent, dict) {
+    _iterate: function (parent, dict) {
         var self = this;
         var children = $(parent).children();
-        children.each(function() {
+        children.each(function () {
             var child = this;
             var id = $(child).attr("id");
             if ($(child).hasClass("section-row")) {
@@ -179,7 +179,7 @@ export var Manager = Backbone.Model.extend({
                 self._iterate(child, dict);
             }
         });
-    }
+    },
 });
 
 /** Match conditional values to selected cases
@@ -208,7 +208,7 @@ export var matchCase = (input, value) => {
  */
 export var visitInputs = (inputs, callback, prefix, context) => {
     context = $.extend({}, context);
-    _.each(inputs, input => {
+    _.each(inputs, (input) => {
         if (input && input.type && input.name) {
             context[input.name] = input;
         }
@@ -248,5 +248,5 @@ export var visitInputs = (inputs, callback, prefix, context) => {
 
 export default {
     Manager: Manager,
-    visitInputs: visitInputs
+    visitInputs: visitInputs,
 };
diff --git a/client/galaxy/scripts/mvc/form/form-input.js b/client/galaxy/scripts/mvc/form/form-input.js
index 2f1c2274e070..8d337c2ccec0 100644
--- a/client/galaxy/scripts/mvc/form/form-input.js
+++ b/client/galaxy/scripts/mvc/form/form-input.js
@@ -5,7 +5,7 @@ import $ from "jquery";
 import _ from "underscore";
 import Backbone from "backbone";
 export default Backbone.View.extend({
-    initialize: function(app, options) {
+    initialize: function (app, options) {
         this.app = app;
         this.app_options = app.model ? app.model.attributes : {};
         this.field = (options && options.field) || new Backbone.View();
@@ -18,7 +18,7 @@ export default Backbone.View.extend({
                 text_connected_disable: this.app_options.text_connected_disable || "Remove connection from module",
                 cls_enable: this.app_options.cls_enable || "fa fa-caret-square-o-down",
                 cls_disable: this.app_options.cls_disable || "fa fa-caret-square-o-up",
-                always_refresh: this.app_options.always_refresh
+                always_refresh: this.app_options.always_refresh,
             }).set(options);
 
         // set element and link components
@@ -74,7 +74,7 @@ export default Backbone.View.extend({
 
         // add error listener
         if (this.field.model) {
-            this.listenTo(this.field.model, "error", message => {
+            this.listenTo(this.field.model, "error", (message) => {
                 if (message) {
                     this.error(message);
                 } else {
@@ -85,21 +85,21 @@ export default Backbone.View.extend({
     },
 
     /** Set backdrop for input element */
-    backdrop: function() {
+    backdrop: function () {
         this.model.set("backdrop", true);
     },
 
     /** Set error text */
-    error: function(text) {
+    error: function (text) {
         this.model.set("error_text", text);
     },
 
     /** Reset this view */
-    reset: function() {
+    reset: function () {
         !this.model.get("fixed") && this.model.set("error_text", null);
     },
 
-    render: function() {
+    render: function () {
         // render help
         $(".tooltip").hide();
         var help_text = this.model.get("help", "");
@@ -131,7 +131,7 @@ export default Backbone.View.extend({
         this.field.model &&
             this.field.model.set({
                 color: this.model.get("color"),
-                style: this.model.get("style")
+                style: this.model.get("style"),
             });
         // render collapsible options
         const connected = this.field.connected;
@@ -180,7 +180,7 @@ export default Backbone.View.extend({
         this.$field.attr("data-label", this.model.get("label"));
     },
 
-    _template: function() {
+    _template: function () {
         return $("<div/>")
             .addClass("ui-form-element")
             .append(
@@ -208,5 +208,5 @@ export default Backbone.View.extend({
                     .append($("<div/>").addClass("ui-form-backdrop"))
             )
             .append($("<div/>").addClass("ui-form-preview"));
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/form/form-parameters.js b/client/galaxy/scripts/mvc/form/form-parameters.js
index 1afedfec3d64..92d4079d22a6 100644
--- a/client/galaxy/scripts/mvc/form/form-parameters.js
+++ b/client/galaxy/scripts/mvc/form/form-parameters.js
@@ -37,11 +37,11 @@ export default Backbone.Model.extend({
         ftpfile: "_fieldFtp",
         upload: "_fieldUpload",
         rules: "_fieldRulesEdit",
-        data_dialog: "_fieldDialog"
+        data_dialog: "_fieldDialog",
     },
 
     /** Returns an input field for a given field type */
-    create: function(input_def) {
+    create: function (input_def) {
         const Galaxy = getGalaxyInstance();
         var fieldClass = this.types[input_def.type];
         var field = typeof this[fieldClass] === "function" ? this[fieldClass].call(this, input_def) : null;
@@ -57,7 +57,7 @@ export default Backbone.Model.extend({
     },
 
     /** Data input field */
-    _fieldData: function(input_def) {
+    _fieldData: function (input_def) {
         return new SelectContent.View({
             id: `field-${input_def.id}`,
             extensions: input_def.extensions,
@@ -66,12 +66,12 @@ export default Backbone.Model.extend({
             type: input_def.type,
             flavor: input_def.flavor,
             data: input_def.options,
-            onchange: input_def.onchange
+            onchange: input_def.onchange,
         });
     },
 
     /** Select/Checkbox/Radio options field */
-    _fieldSelect: function(input_def) {
+    _fieldSelect: function (input_def) {
         // show text field e.g. in workflow editor
         if (input_def.is_workflow) {
             return this._fieldText(input_def);
@@ -86,7 +86,7 @@ export default Backbone.Model.extend({
         var classes = {
             checkboxes: Ui.Checkbox,
             radio: Ui.Radio,
-            radiobutton: Ui.RadioButton
+            radiobutton: Ui.RadioButton,
         };
         var SelectClass = classes[input_def.display] || Ui.Select;
         // use Select2 fields or regular select fields in workflow launch form?
@@ -115,12 +115,12 @@ export default Backbone.Model.extend({
             individual: input_def.individual,
             searchable: searchable,
             textable: input_def.textable,
-            SelectClass: SelectClass
+            SelectClass: SelectClass,
         });
     },
 
     /** Drill down options field */
-    _fieldDrilldown: function(input_def) {
+    _fieldDrilldown: function (input_def) {
         // show text field e.g. in workflow editor
         if (input_def.is_workflow) {
             return this._fieldText(input_def);
@@ -132,12 +132,12 @@ export default Backbone.Model.extend({
             data: input_def.options,
             display: input_def.display,
             optional: input_def.optional,
-            onchange: input_def.onchange
+            onchange: input_def.onchange,
         });
     },
 
     /** Text input field */
-    _fieldText: function(input_def) {
+    _fieldText: function (input_def) {
         // field replaces e.g. a select field
         if (input_def.model_class === "SelectTagParameter" || (input_def.options && input_def.data)) {
             input_def.area = input_def.multiple;
@@ -165,92 +165,92 @@ export default Backbone.Model.extend({
             readonly: input_def.readonly,
             placeholder: input_def.placeholder,
             datalist: input_def.datalist,
-            onchange: input_def.onchange
+            onchange: input_def.onchange,
         });
     },
 
     /** Slider field */
-    _fieldSlider: function(input_def) {
+    _fieldSlider: function (input_def) {
         return new Ui.Slider.View({
             id: `field-${input_def.id}`,
             precise: input_def.type == "float",
             is_workflow: input_def.is_workflow,
             min: input_def.min,
             max: input_def.max,
-            onchange: input_def.onchange
+            onchange: input_def.onchange,
         });
     },
 
     /** Hidden field */
-    _fieldHidden: function(input_def) {
+    _fieldHidden: function (input_def) {
         return new Ui.Hidden({
             id: `field-${input_def.id}`,
-            info: input_def.info
+            info: input_def.info,
         });
     },
 
     /** Boolean field */
-    _fieldBoolean: function(input_def) {
+    _fieldBoolean: function (input_def) {
         return new Ui.RadioButton.View({
             id: `field-${input_def.id}`,
             data: [
                 { label: "Yes", value: "true" },
-                { label: "No", value: "false" }
+                { label: "No", value: "false" },
             ],
-            onchange: input_def.onchange
+            onchange: input_def.onchange,
         });
     },
 
     /** Color picker field */
-    _fieldColor: function(input_def) {
+    _fieldColor: function (input_def) {
         return new ColorPicker({
             id: `field-${input_def.id}`,
-            onchange: input_def.onchange
+            onchange: input_def.onchange,
         });
     },
 
     /** Data dialog picker field */
-    _fieldDialog: function(input_def) {
+    _fieldDialog: function (input_def) {
         return new DataPicker({
             id: `field-${input_def.id}`,
             multiple: input_def.multiple,
-            onchange: input_def.onchange
+            onchange: input_def.onchange,
         });
     },
 
     /** Library dataset field */
-    _fieldLibrary: function(input_def) {
+    _fieldLibrary: function (input_def) {
         return new SelectLibrary.View({
             id: `field-${input_def.id}`,
             optional: input_def.optional,
             multiple: input_def.multiple,
-            onchange: input_def.onchange
+            onchange: input_def.onchange,
         });
     },
 
     /** FTP file field */
-    _fieldFtp: function(input_def) {
+    _fieldFtp: function (input_def) {
         return new SelectFtp.View({
             id: `field-${input_def.id}`,
             optional: input_def.optional,
             multiple: input_def.multiple,
-            onchange: input_def.onchange
+            onchange: input_def.onchange,
         });
     },
 
-    _fieldRulesEdit: function(input_def) {
+    _fieldRulesEdit: function (input_def) {
         return new RulesEdit.View({
             id: `field-${input_def.id}`,
             onchange: input_def.onchange,
-            target: input_def.target
+            target: input_def.target,
         });
     },
 
     /** Upload file field */
-    _fieldUpload: function(input_def) {
+    _fieldUpload: function (input_def) {
         return new Ui.Upload({
             id: `field-${input_def.id}`,
-            onchange: input_def.onchange
+            onchange: input_def.onchange,
         });
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/form/form-repeat.js b/client/galaxy/scripts/mvc/form/form-repeat.js
index 3adbe7905e40..dbf3077cfac5 100644
--- a/client/galaxy/scripts/mvc/form/form-repeat.js
+++ b/client/galaxy/scripts/mvc/form/form-repeat.js
@@ -9,24 +9,24 @@ import Portlet from "mvc/ui/ui-portlet";
 import Ui from "mvc/ui/ui-misc";
 
 export var View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.list = {};
         this.options = Utils.merge(options, {
             title: _l("Repeat"),
             empty_text: "Not available.",
             max: null,
-            min: null
+            min: null,
         });
         this.button_new = new Ui.Button({
             icon: "fa-plus",
             title: `Insert ${this.options.title}`,
             tooltip: `Add new ${this.options.title} block`,
             cls: "btn btn-secondary float-none form-repeat-add",
-            onclick: function() {
+            onclick: function () {
                 if (options.onnew) {
                     options.onnew();
                 }
-            }
+            },
         });
         this.setElement(
             $("<div/>")
@@ -36,12 +36,12 @@ export var View = Backbone.View.extend({
     },
 
     /** Number of repeat blocks */
-    size: function() {
+    size: function () {
         return _.size(this.list);
     },
 
     /** Add new repeat block */
-    add: function(options) {
+    add: function (options) {
         const Galaxy = getGalaxyInstance();
         if (!options.id || this.list[options.id]) {
             Galaxy.emit.debug("form-repeat::add()", "Duplicate or invalid repeat block id.");
@@ -51,17 +51,17 @@ export var View = Backbone.View.extend({
             icon: "fa-trash-o",
             tooltip: _l("Delete this repeat block"),
             cls: "ui-button-icon-plain form-repeat-delete",
-            onclick: function() {
+            onclick: function () {
                 if (options.ondel) {
                     options.ondel();
                 }
-            }
+            },
         });
         var portlet = new Portlet.View({
             id: options.id,
             title: _l("placeholder"),
             cls: options.cls || "ui-portlet-section",
-            operations: { button_delete: button_delete }
+            operations: { button_delete: button_delete },
         });
         portlet.append(options.$el);
         portlet.$el.addClass("section-row").hide();
@@ -74,7 +74,7 @@ export var View = Backbone.View.extend({
     },
 
     /** Delete repeat block */
-    del: function(id) {
+    del: function (id) {
         const Galaxy = getGalaxyInstance();
         if (!this.list[id]) {
             Galaxy.emit.debug("form-repeat::del()", "Invalid repeat block id.");
@@ -87,38 +87,34 @@ export var View = Backbone.View.extend({
     },
 
     /** Remove all */
-    delAll: function() {
+    delAll: function () {
         for (var id in this.list) {
             this.del(id);
         }
     },
 
     /** Hides add/del options */
-    hideOptions: function() {
+    hideOptions: function () {
         this.button_new.$el.hide();
-        _.each(this.list, portlet => {
+        _.each(this.list, (portlet) => {
             portlet.hideOperation("button_delete");
         });
         if (_.isEmpty(this.list)) {
-            this.$el.append(
-                $("<div/>")
-                    .addClass("form-text text-muted")
-                    .html(this.options.empty_text)
-            );
+            this.$el.append($("<div/>").addClass("form-text text-muted").html(this.options.empty_text));
         }
     },
 
     /** Refresh view */
-    _refresh: function() {
+    _refresh: function () {
         var index = 0;
         for (var id in this.list) {
             var portlet = this.list[id];
             portlet.title(`${++index}: ${this.options.title}`);
             portlet[this.size() > this.options.min ? "showOperation" : "hideOperation"]("button_delete");
         }
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/form/form-section.js b/client/galaxy/scripts/mvc/form/form-section.js
index a8fe83d3f422..728694b26222 100644
--- a/client/galaxy/scripts/mvc/form/form-section.js
+++ b/client/galaxy/scripts/mvc/form/form-section.js
@@ -10,7 +10,7 @@ import Repeat from "mvc/form/form-repeat";
 import InputElement from "mvc/form/form-input";
 import Parameters from "mvc/form/form-parameters";
 var View = Backbone.View.extend({
-    initialize: function(app, options) {
+    initialize: function (app, options) {
         this.app = app;
         this.inputs = options.inputs;
         this.parameters = new Parameters();
@@ -19,16 +19,16 @@ var View = Backbone.View.extend({
     },
 
     /** Render section view */
-    render: function() {
+    render: function () {
         var self = this;
         this.$el.empty();
-        _.each(this.inputs, input => {
+        _.each(this.inputs, (input) => {
             self.add(input);
         });
     },
 
     /** Add a new input element */
-    add: function(input) {
+    add: function (input) {
         var input_def = $.extend({}, input);
         input_def.id = Utils.uid();
         this.app.input_list[input_def.id] = input_def;
@@ -48,7 +48,7 @@ var View = Backbone.View.extend({
     },
 
     /** Add a conditional block */
-    _addConditional: function(input_def) {
+    _addConditional: function (input_def) {
         var self = this;
         input_def.test_param.id = input_def.id;
         input_def.test_param.textable = false;
@@ -59,11 +59,11 @@ var View = Backbone.View.extend({
             // add conditional sub sections
             for (var i in input_def.cases) {
                 var sub_section = new View(this.app, {
-                    inputs: input_def.cases[i].inputs
+                    inputs: input_def.cases[i].inputs,
                 });
                 this._append(sub_section.$el.addClass("ui-portlet-section pl-2"), `${input_def.id}-section-${i}`);
             }
-            field.model.set("onchange", value => {
+            field.model.set("onchange", (value) => {
                 var selectedCase = self.app.data.matchCase(input_def, value);
                 for (var i in input_def.cases) {
                     var case_def = input_def.cases[i];
@@ -89,7 +89,7 @@ var View = Backbone.View.extend({
     },
 
     /** Add a repeat block */
-    _addRepeat: function(input_def) {
+    _addRepeat: function (input_def) {
         var self = this;
         var block_index = 0;
 
@@ -98,10 +98,10 @@ var View = Backbone.View.extend({
             title: input_def.title || "Repeat",
             min: input_def.min,
             max: input_def.max,
-            onnew: function() {
+            onnew: function () {
                 create(input_def.inputs);
                 self.app.trigger("change");
-            }
+            },
         });
 
         // helper function to create new repeat blocks
@@ -111,10 +111,10 @@ var View = Backbone.View.extend({
             repeat.add({
                 id: sub_section_id,
                 $el: sub_section.$el,
-                ondel: function() {
+                ondel: function () {
                     repeat.del(sub_section_id);
                     self.app.trigger("change");
-                }
+                },
             });
         }
 
@@ -133,34 +133,30 @@ var View = Backbone.View.extend({
         var input_element = new InputElement(this.app, {
             label: input_def.title || input_def.name,
             help: input_def.help,
-            field: repeat
+            field: repeat,
         });
         this._append(input_element.$el, input_def.id);
     },
 
     /** Add a customized section */
-    _addSection: function(input_def) {
+    _addSection: function (input_def) {
         var portlet = new Portlet.View({
             title: input_def.title || input_def.name,
             cls: "ui-portlet-section",
             collapsible: true,
             collapsible_button: true,
-            collapsed: !input_def.expanded
+            collapsed: !input_def.expanded,
         });
         portlet.append(new View(this.app, { inputs: input_def.inputs }).$el);
-        portlet.append(
-            $("<div/>")
-                .addClass("form-text text-muted")
-                .html(input_def.help)
-        );
-        this.app.on("expand", input_id => {
+        portlet.append($("<div/>").addClass("form-text text-muted").html(input_def.help));
+        this.app.on("expand", (input_id) => {
             portlet.$(`#${input_id}`).length > 0 && portlet.expand();
         });
         this._append(portlet.$el, input_def.id);
     },
 
     /** Add a single input field element */
-    _addRow: function(input_def) {
+    _addRow: function (input_def) {
         var self = this;
         var id = input_def.id;
         input_def.onchange =
@@ -186,7 +182,7 @@ var View = Backbone.View.extend({
             backdrop: input_def.backdrop,
             hidden: input_def.hidden,
             fixed: input_def.fixed,
-            field: field
+            field: field,
         });
         this.app.element_list[id] = input_element;
         this._append(input_element.$el, input_def.id);
@@ -194,11 +190,11 @@ var View = Backbone.View.extend({
     },
 
     /** Append a new element to the form i.e. input element, repeat block, conditionals etc. */
-    _append: function($el, id) {
+    _append: function ($el, id) {
         this.$el.append($el.addClass("section-row").attr("id", id));
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/form/form-view.js b/client/galaxy/scripts/mvc/form/form-view.js
index 6d2416fc7a3a..9e00bbdda6b5 100644
--- a/client/galaxy/scripts/mvc/form/form-view.js
+++ b/client/galaxy/scripts/mvc/form/form-view.js
@@ -11,7 +11,7 @@ import FormData from "mvc/form/form-data";
 import { getGalaxyInstance } from "app";
 
 export default Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model = new Backbone.Model({
             initial_errors: false,
             cls: "ui-portlet",
@@ -19,14 +19,14 @@ export default Backbone.View.extend({
             always_refresh: true,
             status: "warning",
             hide_operations: false,
-            onchange: function() {}
+            onchange: function () {},
         }).set(options);
         this.setElement("<div/>");
         this.render();
     },
 
     /** Update available options */
-    update: function(new_model) {
+    update: function (new_model) {
         var self = this;
         this.data.matchModel(new_model, (node, input_id) => {
             var field = self.field_list[input_id];
@@ -40,7 +40,7 @@ export default Backbone.View.extend({
     },
 
     /** Set form into wait mode */
-    wait: function(active) {
+    wait: function (active) {
         for (var i in this.input_list) {
             var field = this.field_list[i];
             var input = this.input_list[i];
@@ -51,7 +51,7 @@ export default Backbone.View.extend({
     },
 
     /** Highlight and scroll to input element (currently only used for error notifications) */
-    highlight: function(input_id, message, silent) {
+    highlight: function (input_id, message, silent) {
         var input_element = this.element_list[input_id];
         if (input_element) {
             input_element.error(message || "Please verify this parameter.");
@@ -60,13 +60,13 @@ export default Backbone.View.extend({
             if (!silent) {
                 var $panel = this.$el
                     .parents()
-                    .filter(function() {
+                    .filter(function () {
                         return ["auto", "scroll"].indexOf($(this).css("overflow")) != -1;
                     })
                     .first();
                 $panel.animate(
                     {
-                        scrollTop: $panel.scrollTop() + input_element.$el.offset().top - $panel.position().top - 120
+                        scrollTop: $panel.scrollTop() + input_element.$el.offset().top - $panel.position().top - 120,
                     },
                     500
                 );
@@ -75,7 +75,7 @@ export default Backbone.View.extend({
     },
 
     /** Highlights errors */
-    errors: function(options) {
+    errors: function (options) {
         this.trigger("reset");
         if (options && options.errors) {
             var error_messages = this.data.matchResponse(options.errors);
@@ -88,7 +88,7 @@ export default Backbone.View.extend({
     },
 
     /** Render tool form */
-    render: function() {
+    render: function () {
         var self = this;
         this.off("change");
         this.off("reset");
@@ -107,7 +107,7 @@ export default Backbone.View.extend({
         }
         // add listener which triggers on checksum change, and reset the form input wrappers
         var current_check = this.data.checksum();
-        this.on("change", input_id => {
+        this.on("change", (input_id) => {
             var input = self.input_list[input_id];
             if (!input || input.refresh_on_change || self.model.get("always_refresh")) {
                 var new_check = self.data.checksum();
@@ -118,7 +118,7 @@ export default Backbone.View.extend({
             }
         });
         this.on("reset", () => {
-            _.each(self.element_list, input_element => {
+            _.each(self.element_list, (input_element) => {
                 input_element.reset();
             });
         });
@@ -126,12 +126,12 @@ export default Backbone.View.extend({
     },
 
     /** Renders/appends dom elements of the form */
-    _renderForm: function() {
+    _renderForm: function () {
         $(".tooltip").remove();
         var options = this.model.attributes;
         this.message = new Ui.UnescapedMessage();
         this.section = new FormSection.View(this, {
-            inputs: options.inputs
+            inputs: options.inputs,
         });
         this.portlet = new Portlet.View({
             icon: options.icon,
@@ -142,7 +142,7 @@ export default Backbone.View.extend({
             buttons: options.buttons,
             collapsible: options.collapsible,
             collapsed: options.collapsed,
-            onchange_title: options.onchange_title
+            onchange_title: options.onchange_title,
         });
         this.portlet.append(this.message.$el);
         this.portlet.append(this.section.$el);
@@ -154,10 +154,10 @@ export default Backbone.View.extend({
             this.message.update({
                 persistent: true,
                 status: options.status,
-                message: options.message
+                message: options.message,
             });
         }
         const Galaxy = getGalaxyInstance();
         Galaxy.emit.debug("form-view::initialize()", "Completed");
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/form/form-wrapper.js b/client/galaxy/scripts/mvc/form/form-wrapper.js
index c633de7c786c..0bbf51372d2d 100644
--- a/client/galaxy/scripts/mvc/form/form-wrapper.js
+++ b/client/galaxy/scripts/mvc/form/form-wrapper.js
@@ -6,7 +6,7 @@ import Form from "mvc/form/form-view";
 import Ui from "mvc/ui/ui-misc";
 
 var View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model = new Backbone.Model(options);
         this.url = this.model.get("url");
         this.redirect = this.model.get("redirect");
@@ -17,13 +17,13 @@ var View = Backbone.View.extend({
         this.render();
     },
 
-    render: function() {
+    render: function () {
         var self = this;
         $.ajax({
             url: getAppRoot() + this.url,
-            type: "GET"
+            type: "GET",
         })
-            .done(response => {
+            .done((response) => {
                 var options = $.extend({}, self.model.attributes, response);
                 var form = new Form({
                     title: options.title,
@@ -40,34 +40,34 @@ var View = Backbone.View.extend({
                             title: options.submit_title || "Save",
                             icon: options.submit_icon || "fa-save",
                             cls: "btn btn-primary",
-                            onclick: function() {
+                            onclick: function () {
                                 self._submit(form);
-                            }
-                        })
-                    }
+                            },
+                        }),
+                    },
                 });
                 self.$el.empty().append(form.$el);
             })
-            .fail(response => {
+            .fail((response) => {
                 self.$el.empty().append(
                     new Ui.Message({
                         message: `Failed to load resource ${self.url}.`,
                         status: "danger",
-                        persistent: true
+                        persistent: true,
                     }).$el
                 );
             });
     },
 
-    _submit: function(form) {
+    _submit: function (form) {
         var self = this;
         $.ajax({
             url: getAppRoot() + self.url,
             data: JSON.stringify(form.data.create()),
             type: "PUT",
-            contentType: "application/json"
+            contentType: "application/json",
         })
-            .done(response => {
+            .done((response) => {
                 var params = {};
                 if (response.id) {
                     params.id = response.id;
@@ -75,7 +75,7 @@ var View = Backbone.View.extend({
                     params = {
                         message: response.message,
                         status: "success",
-                        persistent: false
+                        persistent: false,
                     };
                 }
                 if (self.redirect) {
@@ -87,27 +87,27 @@ var View = Backbone.View.extend({
                     self._showMessage(form, response.message);
                 }
             })
-            .fail(response => {
+            .fail((response) => {
                 self._showMessage(form, {
                     message: response.responseJSON.err_msg,
                     status: "danger",
-                    persistent: false
+                    persistent: false,
                 });
             });
     },
 
-    _showMessage: function(form, options) {
+    _showMessage: function (form, options) {
         var $panel = form.$el
             .parents()
-            .filter(function() {
+            .filter(function () {
                 return ["auto", "scroll"].indexOf($(this).css("overflow")) != -1;
             })
             .first();
         $panel.animate({ scrollTop: 0 }, 500);
         form.message.update(options);
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/grid/grid-model.js b/client/galaxy/scripts/mvc/grid/grid-model.js
index 519ce4a67d30..8c94c18a915b 100644
--- a/client/galaxy/scripts/mvc/grid/grid-model.js
+++ b/client/galaxy/scripts/mvc/grid/grid-model.js
@@ -15,13 +15,13 @@ export default Backbone.Model.extend({
         cur_page: 1,
         num_pages: 1,
         operation: undefined,
-        item_ids: undefined
+        item_ids: undefined,
     },
 
     /**
      * Add filtering criterion.
      */
-    add_filter: function(key, value, append) {
+    add_filter: function (key, value, append) {
         // Update URL arg with new condition.
         if (append) {
             // Update or append value.
@@ -57,7 +57,7 @@ export default Backbone.Model.extend({
     /**
      * Remove filtering criterion.
      */
-    remove_filter: function(key, condition) {
+    remove_filter: function (key, condition) {
         var cur_val = this.attributes.filters[key];
         if (cur_val === null || cur_val === undefined) {
             return false;
@@ -78,13 +78,13 @@ export default Backbone.Model.extend({
     /**
      * Returns URL data for obtaining a new grid.
      */
-    get_url_data: function() {
+    get_url_data: function () {
         var url_data = {
             async: this.attributes.async,
             sort: this.attributes.sort_key,
             page: this.attributes.cur_page,
             show_item_checkboxes: this.attributes.show_item_checkboxes,
-            advanced_search: this.attributes.advanced_search
+            advanced_search: this.attributes.advanced_search,
         };
 
         // Add operation, item_ids only if they have values.
@@ -97,14 +97,14 @@ export default Backbone.Model.extend({
 
         // Add filter arguments to data, placing "f-" in front of all arguments.
         var self = this;
-        _.each(_.pairs(self.attributes.filters), k => {
+        _.each(_.pairs(self.attributes.filters), (k) => {
             url_data[`f-${k[0]}`] = k[1];
         });
         return url_data;
     },
 
     // Return URL for obtaining a new grid
-    get_url: function(args) {
+    get_url: function (args) {
         return `${this.get("url_base")}?${$.param(this.get_url_data())}&${$.param(args)}`;
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/grid/grid-shared.js b/client/galaxy/scripts/mvc/grid/grid-shared.js
index d73f06e2697d..322be5dbddb1 100644
--- a/client/galaxy/scripts/mvc/grid/grid-shared.js
+++ b/client/galaxy/scripts/mvc/grid/grid-shared.js
@@ -8,7 +8,7 @@ import GridView from "mvc/grid/grid-view";
 import LoadingIndicator from "ui/loading-indicator";
 
 var View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         var self = this;
         const Galaxy = getGalaxyInstance();
         LoadingIndicator.markViewAsLoading(this);
@@ -20,20 +20,20 @@ var View = Backbone.View.extend({
         }
         $.ajax({
             url: `${getAppRoot() + this.item}/${this.model.get("action_id")}?${$.param(Galaxy.params)}`,
-            success: function(response) {
+            success: function (response) {
                 self.model.set(response);
                 self.render();
-            }
+            },
         });
     },
 
-    render: function() {
+    render: function () {
         var grid = new GridView(this.model.attributes);
         this.$el.empty().append(grid.$el);
         this.$el.append(this._templateShared());
     },
 
-    _templateShared: function() {
+    _templateShared: function () {
         var self = this;
         var $tmpl = $(`<div><br/><h2>${this.model.get("plural")} shared with you by others</h2></div>`);
         var options = this.model.attributes;
@@ -61,9 +61,9 @@ var View = Backbone.View.extend({
             $tmpl.append(`No ${this.model.get("plural").toLowerCase()} have been shared with you.`);
         }
         return $tmpl;
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/grid/grid-template.js b/client/galaxy/scripts/mvc/grid/grid-template.js
index 7ef318ae24bf..9b64b4d2095a 100644
--- a/client/galaxy/scripts/mvc/grid/grid-template.js
+++ b/client/galaxy/scripts/mvc/grid/grid-template.js
@@ -5,7 +5,7 @@ import _ from "underscore";
 // grid view templates
 export default {
     // template
-    grid: function(options) {
+    grid: function (options) {
         let tmpl;
         if (options.embedded) {
             tmpl = this.grid_header(options) + this.grid_table(options);
@@ -38,7 +38,7 @@ export default {
     },
 
     // template
-    grid_table: function() {
+    grid_table: function () {
         return `
             <form method="post" onsubmit="return false;">
                 <table id="grid-table" class="grid">
@@ -50,7 +50,7 @@ export default {
     },
 
     // template
-    grid_header: function(options) {
+    grid_header: function (options) {
         var tmpl = '<div class="grid-header">';
         if (!options.embedded) {
             let id_str = "";
@@ -88,7 +88,7 @@ export default {
     },
 
     // template
-    header: function(options) {
+    header: function (options) {
         // start
         var tmpl = "<tr>";
 
@@ -124,7 +124,7 @@ export default {
     },
 
     // template
-    body: function(options) {
+    body: function (options) {
         // initialize
         var tmpl = "";
         var items_length = options.items.length;
@@ -204,7 +204,7 @@ export default {
     },
 
     // template
-    footer: function(options) {
+    footer: function (options) {
         // create template string
         var tmpl = "";
 
@@ -334,7 +334,7 @@ export default {
     },
 
     // template
-    message: function(options) {
+    message: function (options) {
         var status = options.status;
         if (["success", "ok"].indexOf(status) != -1) {
             status = "done";
@@ -345,7 +345,7 @@ export default {
     },
 
     // template
-    grid_filters: function(options) {
+    grid_filters: function (options) {
         // get filters
         var default_filter_dict = options.default_filter_dict;
         var filters = options.filters;
@@ -419,7 +419,7 @@ export default {
     },
 
     // template
-    grid_column_filter: function(options, column) {
+    grid_column_filter: function (options, column) {
         // collect parameters
         var filters = options.filters;
         var column_label = column.label;
@@ -544,8 +544,8 @@ export default {
     },
 
     // template for filter items
-    filter_element: function(filter_key, filter_value) {
+    filter_element: function (filter_key, filter_value) {
         filter_value = Utils.sanitize(filter_value);
         return `<span class="text-filter-val">${filter_value}<a href="javascript:void(0);" filter_key="${filter_key}" filter_val="${filter_value}"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>`;
-    }
+    },
 };
diff --git a/client/galaxy/scripts/mvc/grid/grid-view.js b/client/galaxy/scripts/mvc/grid/grid-view.js
index 45156d826afa..61d912b704f1 100644
--- a/client/galaxy/scripts/mvc/grid/grid-view.js
+++ b/client/galaxy/scripts/mvc/grid/grid-view.js
@@ -21,7 +21,7 @@ export default Backbone.View.extend({
     grid: null,
 
     // Initialize
-    initialize: function(grid_config) {
+    initialize: function (grid_config) {
         this.grid = new GridModel();
         this.title = grid_config.title;
         this.active_tab = grid_config.active_tab;
@@ -32,8 +32,8 @@ export default Backbone.View.extend({
         // when we rework the grid. This subscription ties this older grid
         // code to the new vue components
         store.watch(
-            state => state.gridSearch.searchTags,
-            newTags => {
+            (state) => state.gridSearch.searchTags,
+            (newTags) => {
                 const tagArray = Array.from(newTags);
                 self.grid.add_filter("tags", tagArray, false);
                 self.openAdvancedSearch();
@@ -51,11 +51,11 @@ export default Backbone.View.extend({
             });
             $.ajax({
                 url: `${grid_config.url_base}?${$.param(url_data)}`,
-                success: function(response) {
+                success: function (response) {
                     response.embedded = grid_config.embedded;
                     response.filters = grid_config.filters || {};
                     self.init_grid(response);
-                }
+                },
             });
         } else {
             // set element
@@ -67,12 +67,12 @@ export default Backbone.View.extend({
         if (grid_config.use_panels) {
             $("#center").css({
                 padding: "10px",
-                overflow: "auto"
+                overflow: "auto",
             });
         }
     },
 
-    openAdvancedSearch: function() {
+    openAdvancedSearch: function () {
         var isOpen = $("#advanced-search").is(":visible");
         if (!isOpen) {
             $("#standard-search").slideToggle("fast");
@@ -81,7 +81,7 @@ export default Backbone.View.extend({
     },
 
     // refresh frames
-    handle_refresh: function(refresh_frames) {
+    handle_refresh: function (refresh_frames) {
         if (refresh_frames) {
             if ($.inArray("history", refresh_frames) > -1) {
                 const Galaxy = getGalaxyInstance();
@@ -93,7 +93,7 @@ export default Backbone.View.extend({
     },
 
     // Initialize
-    init_grid: function(grid_config) {
+    init_grid: function (grid_config) {
         this.grid.set(grid_config);
 
         // get options
@@ -142,44 +142,44 @@ export default Backbone.View.extend({
     },
 
     // Initialize grid controls
-    init_grid_controls: function() {
+    init_grid_controls: function () {
         // link
         var self = this;
 
         // Initialize grid operation button.
-        this.$el.find(".operation-button").each(function() {
+        this.$el.find(".operation-button").each(function () {
             $(this).off();
-            $(this).click(function() {
+            $(this).click(function () {
                 self.submit_operation(this);
                 return false;
             });
         });
 
         // Initialize text filters to select text on click and use normal font when user is typing.
-        this.$el.find("input[type=text]").each(function() {
+        this.$el.find("input[type=text]").each(function () {
             $(this).off();
             $(this)
-                .click(function() {
+                .click(function () {
                     $(this).select();
                 })
-                .keyup(function() {
+                .keyup(function () {
                     $(this).css("font-style", "normal");
                 });
         });
 
         // Initialize sort links.
-        this.$el.find(".sort-link").each(function() {
+        this.$el.find(".sort-link").each(function () {
             $(this).off();
-            $(this).click(function() {
+            $(this).click(function () {
                 self.set_sort_condition($(this).attr("sort_key"));
                 return false;
             });
         });
 
         // Initialize text filters.
-        this.$el.find(".text-filter-form").each(function() {
+        this.$el.find(".text-filter-form").each(function () {
             $(this).off();
-            $(this).submit(function() {
+            $(this).submit(function () {
                 var column_key = $(this).attr("column_key");
                 var text_input_obj = $(`#input-${column_key}-filter`);
                 var text_input = text_input_obj.val();
@@ -190,13 +190,11 @@ export default Backbone.View.extend({
         });
 
         // Initialize categorical filters.
-        this.$el.find(".text-filter-val > a").each(function() {
+        this.$el.find(".text-filter-val > a").each(function () {
             $(this).off();
-            $(this).click(function() {
+            $(this).click(function () {
                 // Remove visible element.
-                $(this)
-                    .parent()
-                    .remove();
+                $(this).parent().remove();
 
                 // Remove filter condition.
                 self.remove_filter_condition($(this).attr("filter_key"), $(this).attr("filter_val"));
@@ -207,16 +205,16 @@ export default Backbone.View.extend({
         });
 
         // Initialize categorical filters.
-        this.$el.find(".categorical-filter > a").each(function() {
+        this.$el.find(".categorical-filter > a").each(function () {
             $(this).off();
-            $(this).click(function() {
+            $(this).click(function () {
                 self.set_categorical_filter($(this).attr("filter_key"), $(this).attr("filter_val"));
                 return false;
             });
         });
 
         // Initialize standard, advanced search toggles.
-        this.$el.find(".advanced-search-toggle").each(function() {
+        this.$el.find(".advanced-search-toggle").each(function () {
             $(this).off();
             $(this).click(() => {
                 self.$el.find("#standard-search").slideToggle("fast");
@@ -233,16 +231,16 @@ export default Backbone.View.extend({
     },
 
     // Initialize grid elements.
-    init_grid_elements: function() {
+    init_grid_elements: function () {
         // Initialize grid selection checkboxes.
-        this.$el.find(".grid").each(function() {
+        this.$el.find(".grid").each(function () {
             var checkboxes = $(this).find("input.grid-row-select-checkbox");
             var check_count = $(this).find("span.grid-selected-count");
             var update_checked = () => {
                 check_count.text($(checkboxes).filter(":checked").length);
             };
 
-            $(checkboxes).each(function() {
+            $(checkboxes).each(function () {
                 $(this).change(update_checked);
             });
             update_checked();
@@ -258,8 +256,8 @@ export default Backbone.View.extend({
         //
         // add page click events
         //
-        this.$el.find(".page-link-grid > a").each(function() {
-            $(this).click(function() {
+        this.$el.find(".page-link-grid > a").each(function () {
+            $(this).click(function () {
                 self.set_page($(this).attr("page_num"));
                 return false;
             });
@@ -268,11 +266,11 @@ export default Backbone.View.extend({
         //
         // add inbound/outbound events
         //
-        this.$el.find(".use-target").each(function() {
-            $(this).click(function() {
+        this.$el.find(".use-target").each(function () {
+            $(this).click(function () {
                 self.execute({
                     href: $(this).attr("href"),
-                    target: $(this).attr("target")
+                    target: $(this).attr("target"),
                 });
                 return false;
             });
@@ -288,14 +286,14 @@ export default Backbone.View.extend({
         _.each(options.items, (item, index) => {
             var button = self.$(`#grid-${item.encode_id}-popup`).off();
             var popup = new PopupMenu(button);
-            _.each(options.operations, operation => {
+            _.each(options.operations, (operation) => {
                 self.add_operation(popup, operation, item);
             });
         });
     },
 
     /** Add an operation to the items menu */
-    add_operation: function(popup, operation, item) {
+    add_operation: function (popup, operation, item) {
         var self = this;
         var settings = item.operation_config[operation.label];
         if (settings.allowed && operation.allow_popup) {
@@ -304,7 +302,7 @@ export default Backbone.View.extend({
                 href: settings.url_args,
                 target: settings.target,
                 confirmation_text: operation.confirm,
-                func: function(e) {
+                func: function (e) {
                     e.preventDefault();
                     var label = $(e.target).html();
                     if (operation.onclick) {
@@ -312,13 +310,13 @@ export default Backbone.View.extend({
                     } else {
                         self.execute(this.findItemByHtml(label));
                     }
-                }
+                },
             });
         }
     },
 
     // Add a condition to the grid filter; this adds the condition and refreshes the grid.
-    add_filter_condition: function(name, value) {
+    add_filter_condition: function (name, value) {
         // Do nothing is value is empty.
         if (value === "") {
             return false;
@@ -334,11 +332,11 @@ export default Backbone.View.extend({
         this.execute();
     },
 
-    render_filter_button: function(name, value) {
+    render_filter_button: function (name, value) {
         // Add button that displays filter and provides a button to delete it.
         var t = $(Templates.filter_element(name, value));
         var self = this;
-        t.click(function() {
+        t.click(function () {
             // Remove visible element.
             $(this).remove();
 
@@ -352,7 +350,7 @@ export default Backbone.View.extend({
     },
 
     // Remove a condition to the grid filter; this adds the condition and refreshes the grid.
-    remove_filter_condition: function(name, value) {
+    remove_filter_condition: function (name, value) {
         // Remove filter condition.
         this.grid.remove_filter(name, value);
 
@@ -367,7 +365,7 @@ export default Backbone.View.extend({
     },
 
     // Set sort condition for grid.
-    set_sort_condition: function(col_key) {
+    set_sort_condition: function (col_key) {
         // Set new sort condition. New sort is col_key if sorting new column; if reversing sort on
         // currently sorted column, sort is reversed.
         var cur_sort = this.grid.get("sort_key");
@@ -396,13 +394,13 @@ export default Backbone.View.extend({
     },
 
     // Set new value for categorical filter.
-    set_categorical_filter: function(name, new_value) {
+    set_categorical_filter: function (name, new_value) {
         // Update filter hyperlinks to reflect new filter value.
         var category_filter = this.grid.get("categorical_filters")[name];
 
         var cur_value = this.grid.get("filters")[name];
         var self = this;
-        this.$el.find(`.${name}-filter`).each(function() {
+        this.$el.find(`.${name}-filter`).each(function () {
             var text = $.trim($(this).text());
             var filter = category_filter[text];
             var filter_value = filter[name];
@@ -432,10 +430,10 @@ export default Backbone.View.extend({
     },
 
     // Set page to view.
-    set_page: function(new_page) {
+    set_page: function (new_page) {
         // Update page hyperlink to reflect new page.
         var self = this;
-        this.$el.find(".page-link").each(function() {
+        this.$el.find(".page-link").each(function () {
             var id = $(this).attr("id");
 
             var // Id has form 'page-link-<page_num>
@@ -446,9 +444,7 @@ export default Backbone.View.extend({
             if (page_num === new_page) {
                 // Remove link to page since grid will be on this page. It is assumed that
                 // this element has a single child, a hyperlink/anchor with text.
-                text = $(this)
-                    .children()
-                    .text();
+                text = $(this).children().text();
                 $(this).empty();
                 $(this).addClass("inactive-link");
                 $(this).text(text);
@@ -475,7 +471,7 @@ export default Backbone.View.extend({
     },
 
     // confirmation/submission of operation request
-    submit_operation: function(operation_button, confirmation_text) {
+    submit_operation: function (operation_button, confirmation_text) {
         // identify operation
         var operation_name = $(operation_button).val();
 
@@ -487,7 +483,7 @@ export default Backbone.View.extend({
 
         // Check to see if there's grid confirmation text for this operation
         var operation = _.findWhere(this.grid.attributes.operations, {
-            label: operation_name
+            label: operation_name,
         });
         if (operation && !confirmation_text) {
             confirmation_text = operation.confirm || "";
@@ -495,7 +491,7 @@ export default Backbone.View.extend({
 
         // collect ids
         var item_ids = [];
-        this.$el.find("input[name=id]:checked").each(function() {
+        this.$el.find("input[name=id]:checked").each(function () {
             item_ids.push($(this).val());
         });
 
@@ -503,29 +499,29 @@ export default Backbone.View.extend({
         var options = {
             operation: operation_name,
             id: item_ids,
-            confirmation_text: confirmation_text
+            confirmation_text: confirmation_text,
         };
         if (operation.target == "top" || operation.target == "center") {
             options = _.extend(options, {
                 href: operation.href,
-                target: operation.target
+                target: operation.target,
             });
         }
         this.execute(options);
         return true;
     },
 
-    check_all_items: function() {
+    check_all_items: function () {
         var check = this.$(".grid-row-select-checkbox");
         var state = this.$("#check_all").prop("checked");
-        _.each(check, c => {
+        _.each(check, (c) => {
             $(c).prop("checked", state);
         });
         this.init_grid_elements();
     },
 
     // Go back to page one; this is useful when a filter is applied.
-    go_page_one: function() {
+    go_page_one: function () {
         // Need to go back to page 1 if not showing all.
         var cur_page = this.grid.get("cur_page");
         if (cur_page !== null && cur_page !== undefined && cur_page !== "all") {
@@ -536,7 +532,7 @@ export default Backbone.View.extend({
     //
     // execute operations and hyperlink requests
     //
-    execute: function(options) {
+    execute: function (options) {
         // get url
         var id = null;
         var href = null;
@@ -591,7 +587,7 @@ export default Backbone.View.extend({
             // Update grid.
             this.grid.set({
                 operation: operation,
-                item_ids: id
+                item_ids: id,
             });
 
             // Do operation. If operation cannot be performed asynchronously, redirect to location.
@@ -621,7 +617,7 @@ export default Backbone.View.extend({
     },
 
     // go to url
-    go_to: function(target, href) {
+    go_to: function (target, href) {
         // get slide status
         var advanced_search = this.$el.find("#advanced-search").is(":visible");
         this.grid.set("advanced_search", advanced_search);
@@ -634,7 +630,7 @@ export default Backbone.View.extend({
         // clear grid of transient request attributes.
         this.grid.set({
             operation: undefined,
-            item_ids: undefined
+            item_ids: undefined,
         });
         switch (target) {
             case "center":
@@ -649,7 +645,7 @@ export default Backbone.View.extend({
     },
 
     // Update grid.
-    update_grid: function() {
+    update_grid: function () {
         // If there's an operation, do POST; otherwise, do GET.
         var method = this.grid.get("operation") ? "POST" : "GET";
 
@@ -660,10 +656,10 @@ export default Backbone.View.extend({
             type: method,
             url: self.grid.get("url_base"),
             data: self.grid.get_url_data(),
-            error: function() {
+            error: function () {
                 alert("Grid refresh failed");
             },
-            success: function(response_text) {
+            success: function (response_text) {
                 // backup
                 var embedded = self.grid.get("embedded");
                 var insert = self.grid.get("insert");
@@ -683,13 +679,13 @@ export default Backbone.View.extend({
                 // Hide loading overlay.
                 self.$el.find(".loading-elt-overlay").hide();
             },
-            complete: function() {
+            complete: function () {
                 // Clear grid of transient request attributes.
                 self.grid.set({
                     operation: undefined,
-                    item_ids: undefined
+                    item_ids: undefined,
                 });
-            }
+            },
         });
     },
 
@@ -698,5 +694,5 @@ export default Backbone.View.extend({
     // instead of acres of if/then statements in javascript
     getRootClassName({ title = "grid" }) {
         return slugify(title).toLowerCase();
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/history/copy-dialog.js b/client/galaxy/scripts/mvc/history/copy-dialog.js
index 7a75b6ef6419..fef26015a997 100644
--- a/client/galaxy/scripts/mvc/history/copy-dialog.js
+++ b/client/galaxy/scripts/mvc/history/copy-dialog.js
@@ -72,18 +72,14 @@ var CopyDialog = {
             '<% if( copyWhat === "copy-all" ){ print( "checked" ); } %>/>',
             '<label for="copy-all"> <%- allLabel %></label>',
             "<% } %>",
-            "</form>"
+            "</form>",
         ].join("")
     ),
 
     // empty modal body and let the user know the copy is happening
     _showAjaxIndicator: function _showAjaxIndicator() {
         var indicator = `<p><span class="fa fa-spinner fa-spin"></span> ${this.progressive}...</p>`;
-        this.modal
-            .$(".modal-body")
-            .empty()
-            .append(indicator)
-            .css({ "margin-top": "8px" });
+        this.modal.$(".modal-body").empty().append(indicator).css({ "margin-top": "8px" });
     },
 
     // (sorta) public interface - display the modal, render the form, and potentially copy the history
@@ -98,7 +94,7 @@ var CopyDialog = {
             defaultCopyNameFn = options.nameFn || this.defaultName;
 
         var defaultCopyName = defaultCopyNameFn({
-            name: history.get("name")
+            name: history.get("name"),
         });
 
         var // TODO: these two might be simpler as one 3 state option (all,active,no-choice)
@@ -123,13 +119,13 @@ var CopyDialog = {
             dialog._showAjaxIndicator();
             history
                 .copy(true, name, copyAllDatasets)
-                .done(response => {
+                .done((response) => {
                     deferred.resolve(response);
                 })
-                .fail(function(xhr, status, message) {
+                .fail(function (xhr, status, message) {
                     var options = {
                         name: name,
-                        copyAllDatasets: copyAllDatasets
+                        copyAllDatasets: copyAllDatasets,
                     };
                     ERROR_MODAL.ajaxErrorModal(history, xhr, options, dialog.errorMessage);
                     deferred.rejectWith(deferred, arguments);
@@ -155,7 +151,7 @@ var CopyDialog = {
                         copyWhat: defaultCopyWhat,
                         activeLabel: this.activeLabel,
                         allLabel: this.allLabel,
-                        anonWarning: this.anonWarning
+                        anonWarning: this.anonWarning,
                     })
                 ),
                 buttons: _.object([
@@ -163,9 +159,9 @@ var CopyDialog = {
                         _l("Cancel"),
                         () => {
                             modal.hide();
-                        }
+                        },
                     ],
-                    [this.submitLabel, checkNameAndCopy]
+                    [this.submitLabel, checkNameAndCopy],
                 ]),
                 height: "auto",
                 closing_events: true,
@@ -176,16 +172,13 @@ var CopyDialog = {
                     if (originalClosingCallback) {
                         originalClosingCallback(cancelled);
                     }
-                }
+                },
             })
         );
 
         // set the default dataset copy, autofocus the title, and set up for a simple return
-        modal
-            .$("#copy-modal-title")
-            .focus()
-            .select();
-        modal.$("#copy-modal-title").on("keydown", ev => {
+        modal.$("#copy-modal-title").focus().select();
+        modal.$("#copy-modal-title").on("keydown", (ev) => {
             if (ev.keyCode === 13) {
                 ev.preventDefault();
                 checkNameAndCopy();
@@ -193,7 +186,7 @@ var CopyDialog = {
         });
 
         return deferred;
-    }
+    },
 };
 
 //==============================================================================
@@ -211,7 +204,7 @@ var ImportDialog = _.extend({}, CopyDialog, {
     allLabel: _l("Import all datasets including deleted ones"),
     anonWarning:
         _l("As an anonymous user, unless you login or register, you will lose your current history ") +
-        _l("after importing this history. ")
+        _l("after importing this history. "),
 });
 
 //==============================================================================
diff --git a/client/galaxy/scripts/mvc/history/hda-li-edit.js b/client/galaxy/scripts/mvc/history/hda-li-edit.js
index ead623951e87..65f3b75e2d58 100644
--- a/client/galaxy/scripts/mvc/history/hda-li-edit.js
+++ b/client/galaxy/scripts/mvc/history/hda-li-edit.js
@@ -16,7 +16,7 @@ var HDAListItemEdit = _super.extend(
         /** In this override, only get details if in the ready state, get rerunnable if in other states.
          *  Note: fetch with no 'change' event triggering to prevent automatic rendering.
          */
-        _fetchModelDetails: function() {
+        _fetchModelDetails: function () {
             var view = this;
             if (view.model.inReadyState() && !view.model.hasDetails()) {
                 return view.model.fetch({ silent: true });
@@ -28,8 +28,8 @@ var HDAListItemEdit = _super.extend(
                     silent: true,
                     data: {
                         // only fetch rerunnable and creating_job to keep overhead down
-                        keys: ["rerunnable", "creating_job"].join(",")
-                    }
+                        keys: ["rerunnable", "creating_job"].join(","),
+                    },
                 });
             }
             return $.when();
@@ -37,17 +37,17 @@ var HDAListItemEdit = _super.extend(
 
         /** event map */
         events: _.extend(_.clone(_super.prototype.events), {
-            "click .unhide-link": function(ev) {
+            "click .unhide-link": function (ev) {
                 this.model.unhide();
                 return false;
-            }
+            },
         }),
 
         /** string rep */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `HDAListItemEdit(${modelString})`;
-        }
+        },
     }
 );
 
@@ -65,20 +65,20 @@ HDAListItemEdit.prototype.templates = (() => {
                 _l("Unhide it"),
                 "</a>",
                 "</div>",
-                "<% } %>"
+                "<% } %>",
             ],
             "dataset"
-        )
+        ),
     });
 
     return _.extend({}, _super.prototype.templates, {
         //NOTE: *steal* the HDAListItemView titleBar
         titleBar: HDA_LI.HDAListItemView.prototype.templates.titleBar,
-        warnings: warnings
+        warnings: warnings,
     });
 })();
 
 //==============================================================================
 export default {
-    HDAListItemEdit: HDAListItemEdit
+    HDAListItemEdit: HDAListItemEdit,
 };
diff --git a/client/galaxy/scripts/mvc/history/hda-li.js b/client/galaxy/scripts/mvc/history/hda-li.js
index b814b452a9e7..d5e13f82810e 100644
--- a/client/galaxy/scripts/mvc/history/hda-li.js
+++ b/client/galaxy/scripts/mvc/history/hda-li.js
@@ -14,23 +14,23 @@ var HDAListItemView = _super.extend(
     /** @lends HDAListItemView.prototype */ {
         className: `${_super.prototype.className} history-content`,
 
-        initialize: function(attributes, options) {
+        initialize: function (attributes, options) {
             _super.prototype.initialize.call(this, attributes, options);
         },
 
         // ......................................................................... misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `HDAListItemView(${modelString})`;
-        }
+        },
     }
 );
 
 // ............................................................................ TEMPLATES
 /** underscore templates */
 HDAListItemView.prototype.templates = (() => {
-    var titleBarTemplate = dataset => `
+    var titleBarTemplate = (dataset) => `
         <div class="title-bar clear" tabindex="0">
             <span class="state-icon"></span>
             <div class="title">
@@ -50,19 +50,19 @@ HDAListItemView.prototype.templates = (() => {
                 '<div class="hidden-msg warningmessagesmall">',
                 _l("This dataset has been hidden"),
                 "</div>",
-                "<% } %>"
+                "<% } %>",
             ],
             "dataset"
-        )
+        ),
     });
 
     return _.extend({}, _super.prototype.templates, {
         titleBar: titleBarTemplate,
-        warnings: warnings
+        warnings: warnings,
     });
 })();
 
 //==============================================================================
 export default {
-    HDAListItemView: HDAListItemView
+    HDAListItemView: HDAListItemView,
 };
diff --git a/client/galaxy/scripts/mvc/history/hda-model.js b/client/galaxy/scripts/mvc/history/hda-model.js
index 60f230b8c3f2..21b4ed161164 100644
--- a/client/galaxy/scripts/mvc/history/hda-model.js
+++ b/client/galaxy/scripts/mvc/history/hda-model.js
@@ -16,13 +16,13 @@ var HistoryDatasetAssociation = _super.extend(
             /** default attributes for a model */
             defaults: _.extend({}, _super.prototype.defaults, hcontentMixin.defaults, {
                 history_content_type: "dataset",
-                model_class: "HistoryDatasetAssociation"
-            })
+                model_class: "HistoryDatasetAssociation",
+            }),
         }
     )
 );
 
 //==============================================================================
 export default {
-    HistoryDatasetAssociation: HistoryDatasetAssociation
+    HistoryDatasetAssociation: HistoryDatasetAssociation,
 };
diff --git a/client/galaxy/scripts/mvc/history/hdca-li-edit.js b/client/galaxy/scripts/mvc/history/hdca-li-edit.js
index 70b017c695d1..9120e7018976 100644
--- a/client/galaxy/scripts/mvc/history/hdca-li-edit.js
+++ b/client/galaxy/scripts/mvc/history/hdca-li-edit.js
@@ -13,7 +13,7 @@ var HDCAListItemEdit = _super.extend(
         /** logger used to record this.log messages, commonly set to console */
         //logger              : console,
         /** set up: options */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             _super.prototype.initialize.call(this, attributes);
 
             /** allow user purge of dataset files? */
@@ -21,19 +21,19 @@ var HDCAListItemEdit = _super.extend(
         },
 
         /** Override to return editable versions of the collection panels */
-        _getFoldoutPanelClass: function() {
+        _getFoldoutPanelClass: function () {
             return DC_VIEW_EDIT.CollectionViewEdit;
         },
 
         // ......................................................................... delete
         /** In this override, add the delete button. */
-        _renderPrimaryActions: function() {
+        _renderPrimaryActions: function () {
             this.log(`${this}._renderPrimaryActions`);
             // render the display, edit attr and delete icon-buttons
             return _super.prototype._renderPrimaryActions.call(this).concat([this._renderDeleteButton()]);
         },
 
-        _renderDeleteButton: function() {
+        _renderDeleteButton: function () {
             return $(`
                 <div class="dropdown">
                     <a class="delete-btn icon-btn" title="${_l("Delete")}" data-toggle="dropdown">
@@ -57,27 +57,27 @@ var HDCAListItemEdit = _super.extend(
 
         // ......................................................................... misc
         events: _.extend(_.clone(_super.prototype.events), {
-            "click .delete-collection": function(ev) {
+            "click .delete-collection": function (ev) {
                 this.model["delete"]();
             },
-            "click .delete-collection-and-datasets": function(ev) {
+            "click .delete-collection-and-datasets": function (ev) {
                 this.model["delete"](true);
             },
-            "click .delete-collection-and-purge-datasets": function(ev) {
+            "click .delete-collection-and-purge-datasets": function (ev) {
                 this.model["delete"](true, true);
-            }
+            },
         }),
 
         // ......................................................................... misc
         /** string rep */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `HDCAListItemEdit(${modelString})`;
-        }
+        },
     }
 );
 
 //==============================================================================
 export default {
-    HDCAListItemEdit: HDCAListItemEdit
+    HDCAListItemEdit: HDCAListItemEdit,
 };
diff --git a/client/galaxy/scripts/mvc/history/hdca-li.js b/client/galaxy/scripts/mvc/history/hdca-li.js
index 0035fad644c9..f5b7aec7c2ce 100644
--- a/client/galaxy/scripts/mvc/history/hdca-li.js
+++ b/client/galaxy/scripts/mvc/history/hdca-li.js
@@ -14,14 +14,14 @@ var HDCAListItemView = _super.extend(
     /** @lends HDCAListItemView.prototype */ {
         className: `${_super.prototype.className} history-content`,
 
-        render: function() {
+        render: function () {
             const result = _super.prototype.render.apply(this, arguments);
             this._mountNametags("initialize");
             return result;
         },
 
         /** event listeners */
-        _setUpListeners: function() {
+        _setUpListeners: function () {
             _super.prototype._setUpListeners.call(this);
             var renderListen = (model, options) => {
                 // We want this to swap immediately without extra animations.
@@ -32,7 +32,7 @@ var HDCAListItemView = _super.extend(
                 this.listenTo(this.model.jobStatesSummary, "change", renderListen);
             }
             this.listenTo(this.model, {
-                "change:tags change:visible change:state": renderListen
+                "change:tags change:visible change:state": renderListen,
             });
         },
 
@@ -46,12 +46,12 @@ var HDCAListItemView = _super.extend(
         },
 
         /** Override to provide the proper collections panels as the foldout */
-        _getFoldoutPanelClass: function() {
+        _getFoldoutPanelClass: function () {
             return DC_VIEW.CollectionView;
         },
 
         /** In this override, add the state as a class for use with state-based CSS */
-        _swapNewRender: function($newRender) {
+        _swapNewRender: function ($newRender) {
             _super.prototype._swapNewRender.call(this, $newRender);
             //TODO: model currently has no state
             var state;
@@ -83,24 +83,24 @@ var HDCAListItemView = _super.extend(
 
         // ......................................................................... misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `HDCAListItemView(${modelString})`;
-        }
+        },
     }
 );
 
 /** underscore templates */
 HDCAListItemView.prototype.templates = (() => {
     var warnings = _.extend({}, _super.prototype.templates.warnings, {
-        hidden: collection => {
+        hidden: (collection) => {
             collection.visible
                 ? ""
                 : `<div class="hidden-msg warningmessagesmall">${_l("This collection has been hidden")}</div>`;
-        }
+        },
     });
 
-    var titleBarTemplate = collection => `
+    var titleBarTemplate = (collection) => `
         <div class="title-bar clear" tabindex="0">
             <span class="state-icon"></span>
             <div class="title">
@@ -115,11 +115,11 @@ HDCAListItemView.prototype.templates = (() => {
 
     return _.extend({}, _super.prototype.templates, {
         warnings: warnings,
-        titleBar: titleBarTemplate
+        titleBar: titleBarTemplate,
     });
 })();
 
 //==============================================================================
 export default {
-    HDCAListItemView: HDCAListItemView
+    HDCAListItemView: HDCAListItemView,
 };
diff --git a/client/galaxy/scripts/mvc/history/hdca-model.js b/client/galaxy/scripts/mvc/history/hdca-model.js
index 0a3a4dcf249c..bf1c5ff179f2 100644
--- a/client/galaxy/scripts/mvc/history/hdca-model.js
+++ b/client/galaxy/scripts/mvc/history/hdca-model.js
@@ -18,12 +18,12 @@ var HistoryDatasetCollection = DC.extend(hcontentMixin).extend(
     /** @lends HistoryDatasetCollection.prototype */ {
         defaults: _.extend(_.clone(DC.prototype.defaults), {
             history_content_type: "dataset_collection",
-            model_class: "HistoryDatasetCollectionAssociation"
+            model_class: "HistoryDatasetCollectionAssociation",
         }),
 
         //==============================================================================
         /** Override to post to contents route w/o id. */
-        save: function(attributes, options) {
+        save: function (attributes, options) {
             if (this.isNew()) {
                 options = options || {};
                 options.url = `${this.urlRoot + this.get("history_id")}/contents`;
@@ -34,13 +34,13 @@ var HistoryDatasetCollection = DC.extend(hcontentMixin).extend(
         },
 
         /** String representation. */
-        toString: function() {
+        toString: function () {
             return `History${DC.prototype.toString.call(this)}`;
-        }
+        },
     }
 );
 
 //==============================================================================
 export default {
-    HistoryDatasetCollection: HistoryDatasetCollection
+    HistoryDatasetCollection: HistoryDatasetCollection,
 };
diff --git a/client/galaxy/scripts/mvc/history/history-content-model.js b/client/galaxy/scripts/mvc/history/history-content-model.js
index f79155fb33a3..74b54efe216d 100644
--- a/client/galaxy/scripts/mvc/history/history-content-model.js
+++ b/client/galaxy/scripts/mvc/history/history-content-model.js
@@ -26,7 +26,7 @@ var HistoryContentMixin = {
         /** indicating when/what order the content was generated in the context of the history */
         hid: null,
         /** whether the user wants the content shown (visible) */
-        visible: true
+        visible: true,
     },
 
     // ........................................................................ mixed content element
@@ -37,7 +37,7 @@ var HistoryContentMixin = {
 
     // ........................................................................ common queries
     /** the more common alias of visible */
-    hidden: function() {
+    hidden: function () {
         return !this.get("visible");
     },
 
@@ -47,7 +47,7 @@ var HistoryContentMixin = {
      *  @param {Boolean} includeDeleted are we showing deleted hdas?
      *  @param {Boolean} includeHidden are we showing hidden hdas?
      */
-    isVisible: function(includeDeleted, includeHidden) {
+    isVisible: function (includeDeleted, includeHidden) {
         var isVisible = true;
         if (!includeDeleted && (this.get("deleted") || this.get("purged"))) {
             isVisible = false;
@@ -64,7 +64,7 @@ var HistoryContentMixin = {
     urlRoot: `${getAppRoot()}api/histories/`,
 
     /** full url spec. for this content */
-    url: function() {
+    url: function () {
         var historyContentType = this.get("history_content_type");
         var historyId = this.get("history_id");
         var historyContentId = this.get("id");
@@ -78,14 +78,14 @@ var HistoryContentMixin = {
     },
 
     /** save this content as not visible */
-    hide: function(options) {
+    hide: function (options) {
         if (!this.get("visible")) {
             return jQuery.when();
         }
         return this.save({ visible: false }, options);
     },
     /** save this content as visible */
-    unhide: function(options) {
+    unhide: function (options) {
         if (this.get("visible")) {
             return jQuery.when();
         }
@@ -93,12 +93,12 @@ var HistoryContentMixin = {
     },
 
     // ........................................................................ misc
-    toString: function() {
+    toString: function () {
         return [this.get("type_id"), this.get("hid"), this.get("name")].join(":");
-    }
+    },
 };
 
 //==============================================================================
 export default {
-    HistoryContentMixin: HistoryContentMixin
+    HistoryContentMixin: HistoryContentMixin,
 };
diff --git a/client/galaxy/scripts/mvc/history/history-contents.js b/client/galaxy/scripts/mvc/history/history-contents.js
index 9a8cbe67bb38..2ac3c253d2bb 100644
--- a/client/galaxy/scripts/mvc/history/history-contents.js
+++ b/client/galaxy/scripts/mvc/history/history-contents.js
@@ -35,14 +35,14 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     order: "hid",
 
     /** complete api url */
-    url: function() {
+    url: function () {
         return `${this.urlRoot}/${this.historyId}/contents`;
     },
 
     /** Set up */
-    initialize: function(models, options) {
+    initialize: function (models, options) {
         this.on({
-            "sync add": this.trackJobStates
+            "sync add": this.trackJobStates,
         });
 
         options = options || {};
@@ -62,8 +62,8 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
         this.model.prototype.idAttribute = "type_id";
     },
 
-    trackJobStates: function() {
-        this.each(historyContent => {
+    trackJobStates: function () {
+        this.each((historyContent) => {
             if (this.jobStateSummariesCollection) {
                 this.jobStateSummariesCollection.trackModel(historyContent);
             }
@@ -72,26 +72,26 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
 
     // ........................................................................ composite collection
     /** since history content is a mix, override model fn into a factory, creating based on history_content_type */
-    model: function(attrs, options) {
+    model: function (attrs, options) {
         if (attrs.history_content_type === "dataset") {
             return new HDA_MODEL.HistoryDatasetAssociation(attrs, options);
         } else if (attrs.history_content_type === "dataset_collection") {
             return new HDCA_MODEL.HistoryDatasetCollection(attrs, options);
         } else {
             return {
-                validationError: `Unknown history_content_type: ${attrs.history_content_type}`
+                validationError: `Unknown history_content_type: ${attrs.history_content_type}`,
             };
         }
     },
 
-    stopPolling: function() {
+    stopPolling: function () {
         if (this.jobStateSummariesCollection) {
             this.jobStateSummariesCollection.active = false;
             this.jobStateSummariesCollection.clearUpdateTimeout();
         }
     },
 
-    setHistoryId: function(newId) {
+    setHistoryId: function (newId) {
         this.stopPolling();
         this.historyId = newId;
         if (newId) {
@@ -106,20 +106,20 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** Set up client side storage. Currently PersistanStorage keyed under 'history:<id>' */
-    _setUpWebStorage: function(initialSettings) {
+    _setUpWebStorage: function (initialSettings) {
         // TODO: use initialSettings
         this.storage = new HISTORY_PREFS.HistoryPrefs({
-            id: HISTORY_PREFS.HistoryPrefs.historyStorageKey(this.historyId)
+            id: HISTORY_PREFS.HistoryPrefs.historyStorageKey(this.historyId),
         });
         this.trigger("new-storage", this.storage, this);
 
         this.on({
-            "include-deleted": function(newVal) {
+            "include-deleted": function (newVal) {
                 this.storage.includeDeleted(newVal);
             },
-            "include-hidden": function(newVal) {
+            "include-hidden": function (newVal) {
                 this.storage.includeHidden(newVal);
-            }
+            },
         });
 
         this.includeDeleted = this.storage.includeDeleted() || false;
@@ -132,21 +132,21 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     comparators: _.extend(_.clone(_super.prototype.comparators), {
         name: BASE_MVC.buildComparator("name", { ascending: true }),
         "name-dsc": BASE_MVC.buildComparator("name", {
-            ascending: false
+            ascending: false,
         }),
         hid: BASE_MVC.buildComparator("hid", { ascending: false }),
-        "hid-asc": BASE_MVC.buildComparator("hid", { ascending: true })
+        "hid-asc": BASE_MVC.buildComparator("hid", { ascending: true }),
     }),
 
     /** Get every model in this collection not in a 'ready' state (running). */
-    running: function() {
-        return this.filter(c => !c.inReadyState());
+    running: function () {
+        return this.filter((c) => !c.inReadyState());
     },
 
     /** return contents that are not ready and not deleted/hidden */
-    runningAndActive: function() {
+    runningAndActive: function () {
         return this.filter(
-            c =>
+            (c) =>
                 !c.inReadyState() &&
                 c.get("visible") &&
                 // TODO: deletedOrPurged?
@@ -158,31 +158,31 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
      *  @param {Int} hid the hid to search for
      *  @returns {HistoryDatasetAssociation} the model with the given hid or undefined if not found
      */
-    getByHid: function(hid) {
+    getByHid: function (hid) {
         // note: there *can* be more than one content with a given hid, this finds the first based on order
         return this.findWhere({ hid: hid });
     },
 
     /** return true if all contents have details */
-    haveDetails: function() {
-        return this.all(c => c.hasDetails());
+    haveDetails: function () {
+        return this.all((c) => c.hasDetails());
     },
 
     // ........................................................................ hidden / deleted
     /** return a new contents collection of only hidden items */
-    hidden: function() {
-        return this.filter(c => c.hidden());
+    hidden: function () {
+        return this.filter((c) => c.hidden());
     },
 
     /** return a new contents collection of only hidden items */
-    deleted: function() {
-        return this.filter(c => c.get("deleted"));
+    deleted: function () {
+        return this.filter((c) => c.get("deleted"));
     },
 
     /** return a new contents collection of only hidden items */
-    visibleAndUndeleted: function() {
+    visibleAndUndeleted: function () {
         return this.filter(
-            c =>
+            (c) =>
                 c.get("visible") &&
                 // TODO: deletedOrPurged?
                 !c.get("deleted")
@@ -190,7 +190,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** create a setter in order to publish the change */
-    setIncludeDeleted: function(setting, options) {
+    setIncludeDeleted: function (setting, options) {
         if (_.isBoolean(setting) && setting !== this.includeDeleted) {
             this.includeDeleted = setting;
             if (_.result(options, "silent")) {
@@ -201,7 +201,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** create a setter in order to publish the change */
-    setIncludeHidden: function(setting, options) {
+    setIncludeHidden: function (setting, options) {
         if (_.isBoolean(setting) && setting !== this.includeHidden) {
             this.includeHidden = setting;
             options = options || {};
@@ -215,7 +215,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     // ........................................................................ ajax
     // ............ controlled fetch collection
     /** override to get expanded ids from sessionStorage and pass to API as details */
-    fetch: function(options) {
+    fetch: function (options) {
         options = options || {};
         if (this.historyId && !options.details) {
             var prefs = HISTORY_PREFS.HistoryPrefs.get(this.historyId).toJSON();
@@ -228,9 +228,9 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
 
     // ............. ControlledFetch stuff
     /** override to include the API versioning flag */
-    _buildFetchData: function(options) {
+    _buildFetchData: function (options) {
         return _.extend(_super.prototype._buildFetchData.call(this, options), {
-            v: "dev"
+            v: "dev",
         });
     },
 
@@ -240,11 +240,11 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
         /** version */
         "v",
         /** dataset ids to get full details of */
-        "details"
+        "details",
     ]),
 
     /** override to add deleted/hidden filters */
-    _buildFetchFilters: function(options) {
+    _buildFetchFilters: function (options) {
         var superFilters = _super.prototype._buildFetchFilters.call(this, options) || {};
         var filters = {};
         if (!this.includeDeleted) {
@@ -258,13 +258,13 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     // ............ paginated collection
-    getTotalItemCount: function() {
+    getTotalItemCount: function () {
         return this.history.contentsShown();
     },
 
     // ............ history contents specific ajax
     /** override to filter requested contents to those updated after the Date 'since' */
-    fetchUpdated: function(since, options) {
+    fetchUpdated: function (since, options) {
         if (since) {
             options = options || { filters: {} };
             options.remove = false;
@@ -273,19 +273,19 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
                 // workflows will produce hidden datasets (non-output datasets) that still
                 // need to be updated in the collection or they'll update forever
                 // we can remove the default visible filter by using an 'empty' value
-                visible: ""
+                visible: "",
             };
         }
         return this.fetch(options);
     },
 
     /** fetch all the deleted==true contents of this collection */
-    fetchDeleted: function(options) {
+    fetchDeleted: function (options) {
         options = options || {};
         options.filters = _.extend(options.filters, {
             // all deleted, purged or not
             deleted: true,
-            purged: undefined
+            purged: undefined,
         });
         options.remove = false;
 
@@ -296,10 +296,10 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** fetch all the visible==false contents of this collection */
-    fetchHidden: function(options) {
+    fetchHidden: function (options) {
         options = options || {};
         options.filters = _.extend(options.filters, {
-            visible: false
+            visible: false,
         });
         options.remove = false;
 
@@ -310,7 +310,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** fetch detailed model data for all contents in this collection */
-    fetchAllDetails: function(options) {
+    fetchAllDetails: function (options) {
         options = options || {};
         var detailsFlag = { details: "all" };
         options.data = _.extend(options.data || {}, detailsFlag);
@@ -320,11 +320,11 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     // ............. quasi-batch ops
     // TODO: to batch
     /** helper that fetches using filterParams then calls save on each fetched using updateWhat as the save params */
-    _filterAndUpdate: function(filterParams, updateWhat) {
+    _filterAndUpdate: function (filterParams, updateWhat) {
         var idAttribute = this.model.prototype.idAttribute;
         var updateArgs = [updateWhat];
 
-        return this.fetch({ filters: filterParams, remove: false }).then(fetched => {
+        return this.fetch({ filters: filterParams, remove: false }).then((fetched) => {
             // convert filtered json array to model array
             fetched = fetched.reduce((modelArray, currJson, i) => {
                 var model = this.get(currJson[idAttribute]);
@@ -335,7 +335,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** using a queue, perform ajaxFn on each of the models in this collection */
-    ajaxQueue: function(ajaxFn, args, collection) {
+    ajaxQueue: function (ajaxFn, args, collection) {
         collection = collection || this.models;
         return new AJAX_QUEUE.AjaxQueue(
             collection
@@ -348,7 +348,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
         ).deferred;
     },
 
-    _recursivelyFetch: function(options, detailKeys, deferred, limit, offset) {
+    _recursivelyFetch: function (options, detailKeys, deferred, limit, offset) {
         offset = offset || 0;
         var _options = _.extend(_.clone(options), {
             view: "summary",
@@ -356,14 +356,14 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
             limit: limit,
             offset: offset,
             reset: offset === 0,
-            remove: false
+            remove: false,
         });
 
         _.defer(() => {
             this.fetch
                 .call(this, _options)
                 .fail(deferred.reject)
-                .done(response => {
+                .done((response) => {
                     deferred.notify(response, limit, offset);
                     if (response.length !== limit) {
                         this.allFetched = true;
@@ -376,7 +376,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** fetch contents' details in batches of limitPerCall - note: only get searchable details here */
-    progressivelyFetchDetails: function(options) {
+    progressivelyFetchDetails: function (options) {
         // TODO: only fetch tags and annotations if specifically requested
         options = options || {};
         const deferred = jQuery.Deferred();
@@ -390,7 +390,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** does some bit of JSON represent something that can be copied into this contents collection */
-    isCopyable: function(contentsJSON) {
+    isCopyable: function (contentsJSON) {
         var copyableModelClasses = ["HistoryDatasetAssociation", "HistoryDatasetCollectionAssociation"];
         return (
             _.isObject(contentsJSON) && contentsJSON.id && _.contains(copyableModelClasses, contentsJSON.model_class)
@@ -398,7 +398,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** copy an existing, accessible hda into this collection */
-    copy: function(json) {
+    copy: function (json) {
         // TODO: somehow showhorn all this into 'save'
         var id;
 
@@ -414,7 +414,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
                 {
                     HistoryDatasetAssociation: "hda",
                     LibraryDatasetDatasetAssociation: "ldda",
-                    HistoryDatasetCollectionAssociation: "hdca"
+                    HistoryDatasetCollectionAssociation: "hdca",
                 }[json.model_class] || "hda";
             type = contentType === "hdca" ? "dataset_collection" : "dataset";
         }
@@ -428,17 +428,17 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
                     content: id,
                     source: contentType,
                     type: type,
-                    copy_elements: true
-                })
+                    copy_elements: true,
+                }),
             })
-            .done(response => {
+            .done((response) => {
                 collection.add([response], { parse: true });
             })
             .fail((error, status, message) => {
                 collection.trigger("error", collection, xhr, {}, "Error copying contents", {
                     type: type,
                     id: id,
-                    source: contentType
+                    source: contentType,
                 });
             });
 
@@ -446,7 +446,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** create a new HDCA in this collection */
-    createHDCA: function(elementIdentifiers, collectionType, name, hideSourceItems, copyElements, options) {
+    createHDCA: function (elementIdentifiers, collectionType, name, hideSourceItems, copyElements, options) {
         // normally collection.create returns the new model, but we need the promise from the ajax, so we fake create
         //precondition: elementIdentifiers is an array of plain js objects
         //  in the proper form to create the collectionType
@@ -463,7 +463,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
             copy_elements: copyElements,
             // should probably be able to just send in a bunch of json here and restruct per class
             // note: element_identifiers is now (incorrectly) an attribute
-            element_identifiers: elementIdentifiers
+            element_identifiers: elementIdentifiers,
             // do not create the model on the client until the ajax returns
         });
         return hdca.save(options);
@@ -471,7 +471,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
 
     // ........................................................................ searching
     /** return true if all contents have the searchable attributes */
-    haveSearchDetails: function() {
+    haveSearchDetails: function () {
         return (
             this.allFetched &&
             this.all((
@@ -485,20 +485,20 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** return a new collection of contents whose attributes contain the substring matchesWhat */
-    matches: function(matchesWhat) {
-        return this.filter(content => content.matches(matchesWhat));
+    matches: function (matchesWhat) {
+        return this.filter((content) => content.matches(matchesWhat));
     },
 
     // ........................................................................ misc
     /** In this override, copy the historyId to the clone */
-    clone: function() {
+    clone: function () {
         var clone = Backbone.Collection.prototype.clone.call(this);
         clone.historyId = this.historyId;
         return clone;
     },
 
     /** String representation. */
-    toString: function() {
+    toString: function () {
         return ["HistoryContents(", [this.historyId, this.length].join(), ")"].join("");
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/history/history-list.js b/client/galaxy/scripts/mvc/history/history-list.js
index 6941d0c4b741..dd46cc1dce04 100644
--- a/client/galaxy/scripts/mvc/history/history-list.js
+++ b/client/galaxy/scripts/mvc/history/history-list.js
@@ -12,12 +12,12 @@ import historyCopyDialog from "mvc/history/copy-dialog";
 import LoadingIndicator from "ui/loading-indicator";
 
 var HistoryGridView = GridView.extend({
-    initialize: function(grid_config) {
+    initialize: function (grid_config) {
         this.ajaxQueue = new AjaxQueue.AjaxQueue();
         GridView.prototype.initialize.call(this, grid_config);
     },
 
-    init_grid_elements: function() {
+    init_grid_elements: function () {
         const ajaxQueue = this.ajaxQueue;
         ajaxQueue.stop();
         GridView.prototype.init_grid_elements.call(this);
@@ -29,7 +29,7 @@ var HistoryGridView = GridView.extend({
                     const options = {};
                     options.url = url;
                     options.type = "GET";
-                    options.success = req => {
+                    options.success = (req) => {
                         const contentsStates = req.contents_states;
                         let stateHtml = "";
                         for (const state of ["ok", "running", "queued", "new", "error"]) {
@@ -54,10 +54,10 @@ var HistoryGridView = GridView.extend({
                 };
             })
         );
-        fetchDetails.forEach(fn => ajaxQueue.add(fn));
+        fetchDetails.forEach((fn) => ajaxQueue.add(fn));
         ajaxQueue.start();
     },
-    _showCopyDialog: function(id) {
+    _showCopyDialog: function (id) {
         var history = new History({ id: id });
         history
             .fetch()
@@ -75,19 +75,19 @@ var HistoryGridView = GridView.extend({
             });
     },
     /** Add an operation to the items menu */
-    add_operation: function(popup, operation, item) {
+    add_operation: function (popup, operation, item) {
         if (operation.label == "Copy") {
-            operation.onclick = id => {
+            operation.onclick = (id) => {
                 this._showCopyDialog(id);
             };
         }
         GridView.prototype.add_operation.call(this, popup, operation, item);
-    }
+    },
 });
 
 var View = Backbone.View.extend({
     title: _l("Histories"),
-    initialize: function(options) {
+    initialize: function (options) {
         const Galaxy = getGalaxyInstance();
         LoadingIndicator.markViewAsLoading(this);
 
@@ -99,19 +99,19 @@ var View = Backbone.View.extend({
         this.model = new Backbone.Model();
         Utils.get({
             url: `${getAppRoot()}history/${options.action_id}?${$.param(Galaxy.params)}`,
-            success: response => {
+            success: (response) => {
                 this.model.set(response);
                 this.render();
-            }
+            },
         });
     },
 
-    render: function() {
+    render: function () {
         var grid = new HistoryGridView(this.model.attributes);
         this.$el.empty().append(grid.$el);
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/history/history-model.js b/client/galaxy/scripts/mvc/history/history-model.js
index bc4f136b46be..ed704a141df1 100644
--- a/client/galaxy/scripts/mvc/history/history-model.js
+++ b/client/galaxy/scripts/mvc/history/history-model.js
@@ -33,7 +33,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
 
                 deleted: false,
                 contents_active: {},
-                contents_states: {}
+                contents_states: {},
             },
 
             contentsClass: HistoryContents,
@@ -44,7 +44,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             /** Adding title and singular tag */
             searchAliases: {
                 title: "name",
-                tag: "tags"
+                tag: "tags",
             },
 
             // ........................................................................ set up/tear down
@@ -52,7 +52,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
              *  @param {Object} historyJSON model data for this History
              *  @param {Object} options     any extra settings including logger
              */
-            initialize: function(historyJSON, options) {
+            initialize: function (historyJSON, options) {
                 options = options || {};
                 this.logger = options.logger || null;
                 this.log(`${this}.initialize:`, historyJSON, options);
@@ -62,7 +62,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                 this.contents = new this.contentsClass([], {
                     history: this,
                     historyId: this.get("id"),
-                    order: options.order
+                    order: options.order,
                 });
 
                 this._setUpListeners();
@@ -75,36 +75,36 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             /** set up any event listeners for this history including those to the contained HDAs
              *  events: error:contents  if an error occurred with the contents collection
              */
-            _setUpListeners: function() {
+            _setUpListeners: function () {
                 // if the model's id changes ('current' or null -> an actual id), update the contents history_id
                 return this.on({
-                    error: function(model, xhr, options, msg, details) {
+                    error: function (model, xhr, options, msg, details) {
                         this.clearUpdateTimeout();
                     },
-                    "change:id": function(model, newId) {
+                    "change:id": function (model, newId) {
                         if (this.contents) {
                             this.contents.historyId = newId;
                         }
-                    }
+                    },
                 });
             },
 
             /** event handlers for the contents submodels */
-            _setUpCollectionListeners: function() {
+            _setUpCollectionListeners: function () {
                 if (!this.contents) {
                     return this;
                 }
                 // bubble up errors
                 return this.listenTo(this.contents, {
-                    error: function() {
+                    error: function () {
                         this.trigger.apply(this, jQuery.makeArray(arguments));
-                    }
+                    },
                 });
             },
 
             // ........................................................................ derived attributes
             /**  */
-            contentsShown: function() {
+            contentsShown: function () {
                 var contentsActive = this.get("contents_active");
                 var shown = contentsActive.active || 0;
                 shown += this.contents.includeDeleted ? contentsActive.deleted : 0;
@@ -113,20 +113,20 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             /** convert size in bytes to a more human readable version */
-            nice_size: function() {
+            nice_size: function () {
                 var size = this.get("size");
                 return size ? UTILS.bytesToString(size, true, 2) : _l("(empty)");
             },
 
             /** override to add nice_size */
-            toJSON: function() {
+            toJSON: function () {
                 return _.extend(Backbone.Model.prototype.toJSON.call(this), {
-                    nice_size: this.nice_size()
+                    nice_size: this.nice_size(),
                 });
             },
 
             /** override to allow getting nice_size */
-            get: function(key) {
+            get: function (key) {
                 if (key === "nice_size") {
                     return this.nice_size();
                 }
@@ -137,7 +137,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             /** T/F is this history owned by the current user (Galaxy.user)
              *      Note: that this will return false for an anon user even if the history is theirs.
              */
-            ownedByCurrUser: function() {
+            ownedByCurrUser: function () {
                 const Galaxy = getGalaxyInstance();
                 // no currUser
                 if (!Galaxy || !Galaxy.user) {
@@ -151,28 +151,28 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             /** Return the number of running jobs assoc with this history (note: unknown === 0) */
-            numOfUnfinishedJobs: function() {
+            numOfUnfinishedJobs: function () {
                 var unfinishedJobIds = this.get("non_ready_jobs");
                 return unfinishedJobIds ? unfinishedJobIds.length : 0;
             },
 
             /** Return the number of running hda/hdcas in this history (note: unknown === 0) */
-            numOfUnfinishedShownContents: function() {
+            numOfUnfinishedShownContents: function () {
                 return this.contents.runningAndActive().length || 0;
             },
 
             // ........................................................................ updates
-            _fetchContentRelatedAttributes: function() {
+            _fetchContentRelatedAttributes: function () {
                 var contentRelatedAttrs = ["size", "non_ready_jobs", "contents_active", "hid_counter"];
                 return this.fetch({
                     data: jQuery.param({
-                        keys: contentRelatedAttrs.join(",")
-                    })
+                        keys: contentRelatedAttrs.join(","),
+                    }),
                 });
             },
 
             /** check for any changes since the last time we updated (or fetch all if ) */
-            refresh: function(options) {
+            refresh: function (options) {
                 // console.log( this + '.refresh' );
                 options = options || {};
 
@@ -198,7 +198,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             /** continuously fetch updated contents every UPDATE_DELAY ms if this history's datasets or jobs are unfinished */
-            checkForUpdates: function(options) {
+            checkForUpdates: function (options) {
                 // console.log( this + '.checkForUpdates' );
                 options = options || {};
                 var delay = this.UPDATE_DELAY;
@@ -223,7 +223,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                     // no datasets are running, but currently runnning jobs may still produce new datasets
                     // see if the history has any running jobs and continue to update if so
                     // (also update the size for the user in either case)
-                    this._fetchContentRelatedAttributes().done(historyData => {
+                    this._fetchContentRelatedAttributes().done((historyData) => {
                         // console.log( 'non_ready_jobs:', historyData.non_ready_jobs );
                         if (this.numOfUnfinishedJobs() > 0) {
                             _delayThenUpdate();
@@ -236,14 +236,14 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             /** clear the timeout and the cached timeout id */
-            clearUpdateTimeout: function() {
+            clearUpdateTimeout: function () {
                 if (this.updateTimeoutId) {
                     clearTimeout(this.updateTimeoutId);
                     this.updateTimeoutId = null;
                 }
             },
 
-            stopPolling: function() {
+            stopPolling: function () {
                 this.clearUpdateTimeout();
                 if (this.contents) {
                     this.contents.stopPolling();
@@ -252,7 +252,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
 
             // ........................................................................ ajax
             /** override to use actual Dates objects for create/update times */
-            parse: function(response, options) {
+            parse: function (response, options) {
                 var parsed = Backbone.Model.prototype.parse.call(this, response, options);
                 if (parsed.create_time) {
                     parsed.create_time = new Date(parsed.create_time);
@@ -264,7 +264,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             /** fetch this histories data (using options) then it's contents (using contentsOptions) */
-            fetchWithContents: function(options, contentsOptions) {
+            fetchWithContents: function (options, contentsOptions) {
                 options = options || {};
                 var self = this;
 
@@ -281,7 +281,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             /** fetch this histories contents, adjusting options based on the stored history preferences */
-            fetchContents: function(options) {
+            fetchContents: function (options) {
                 options = options || {};
 
                 // we're updating, reset the update time
@@ -290,21 +290,21 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             /** save this history, _Mark_ing it as deleted (just a flag) */
-            _delete: function(options) {
+            _delete: function (options) {
                 if (this.get("deleted")) {
                     return jQuery.when();
                 }
                 return this.save({ deleted: true }, options);
             },
             /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */
-            purge: function(options) {
+            purge: function (options) {
                 if (this.get("purged")) {
                     return jQuery.when();
                 }
                 return this.save({ deleted: true, purged: true }, options);
             },
             /** save this history, _Mark_ing it as undeleted */
-            undelete: function(options) {
+            undelete: function (options) {
                 if (!this.get("deleted")) {
                     return jQuery.when();
                 }
@@ -317,7 +317,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
              *  @fires copied               passed this history and the response JSON from the copy
              *  @returns {xhr}
              */
-            copy: function(current, name, allDatasets) {
+            copy: function (current, name, allDatasets) {
                 current = current !== undefined ? current : true;
                 if (!this.id) {
                     throw new Error("You must set the history ID before copying it.");
@@ -339,19 +339,19 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                 var copy = jQuery.post(this.urlRoot, postData);
                 // if current - queue to setAsCurrent before firing 'copied'
                 if (current) {
-                    return copy.then(response => {
+                    return copy.then((response) => {
                         var newHistory = new History(response);
                         return newHistory.setAsCurrent().done(() => {
                             history.trigger("copied", history, response);
                         });
                     });
                 }
-                return copy.done(response => {
+                return copy.done((response) => {
                     history.trigger("copied", history, response);
                 });
             },
 
-            setAsCurrent: function() {
+            setAsCurrent: function () {
                 var history = this;
 
                 var xhr = jQuery.getJSON(`${getAppRoot()}history/set_as_current?id=${this.id}`);
@@ -363,9 +363,9 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             // ........................................................................ misc
-            toString: function() {
+            toString: function () {
                 return `History(${this.get("id")},${this.get("name")})`;
-            }
+            },
         }
     )
 );
@@ -387,7 +387,7 @@ export var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).e
     /** @type {Number} limit used for each subsequent fetch */
     limitPerFetch: 10,
 
-    initialize: function(models, options) {
+    initialize: function (models, options) {
         options = options || {};
         this.log("HistoryCollection.initialize", models, options);
         this.urlRoot = `${getAppRoot()}api/histories`;
@@ -404,7 +404,7 @@ export var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).e
         // the collection *is empty*
     },
 
-    url: function() {
+    url: function () {
         return this.urlRoot;
     },
 
@@ -412,7 +412,7 @@ export var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).e
     setUpListeners: function setUpListeners() {
         return this.on({
             // when a history is deleted, remove it from the collection (if optionally set to do so)
-            "change:deleted": function(history) {
+            "change:deleted": function (history) {
                 // TODO: this becomes complicated when more filters are used
                 this.debug("change:deleted", this.includeDeleted, history.get("deleted"));
                 if (!this.includeDeleted && history.get("deleted")) {
@@ -420,27 +420,27 @@ export var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).e
                 }
             },
             // listen for a history copy, setting it to current
-            copied: function(original, newData) {
+            copied: function (original, newData) {
                 this.setCurrent(new History(newData, []));
             },
             // when a history is made current, track the id in the collection
-            "set-as-current": function(history) {
+            "set-as-current": function (history) {
                 var oldCurrentId = this.currentHistoryId;
                 this.trigger("no-longer-current", oldCurrentId);
                 this.currentHistoryId = history.id;
-            }
+            },
         });
     },
 
     /** override to change view */
-    _buildFetchData: function(options) {
+    _buildFetchData: function (options) {
         return _.extend(_collectionSuper.prototype._buildFetchData.call(this, options), {
-            view: "dev-detailed"
+            view: "dev-detailed",
         });
     },
 
     /** override to filter out deleted and purged */
-    _buildFetchFilters: function(options) {
+    _buildFetchFilters: function (options) {
         var superFilters = _collectionSuper.prototype._buildFetchFilters.call(this, options) || {};
         var filters = {};
         if (this.includeDeleted !== true) {
@@ -455,7 +455,7 @@ export var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).e
     },
 
     /** override to fetch current as well (as it may be outside the first 10, etc.) */
-    fetchFirst: function(options) {
+    fetchFirst: function (options) {
         // TODO: batch?
         var xhr = jQuery.when();
         if (this.currentHistoryId) {
@@ -466,8 +466,8 @@ export var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).e
                     "encoded_id-in": this.currentHistoryId,
                     // without these a deleted current history will return [] here and block the other xhr
                     deleted: null,
-                    purged: ""
-                }
+                    purged: "",
+                },
             });
         }
         return xhr.then(() => {
@@ -480,21 +480,21 @@ export var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).e
     /** @type {Object} map of collection available sorting orders containing comparator fns */
     comparators: _.extend(_.clone(_collectionSuper.prototype.comparators), {
         name: BASE_MVC.buildComparator("name", {
-            ascending: true
+            ascending: true,
         }),
         "name-dsc": BASE_MVC.buildComparator("name", {
-            ascending: false
+            ascending: false,
         }),
         size: BASE_MVC.buildComparator("size", {
-            ascending: false
+            ascending: false,
         }),
         "size-asc": BASE_MVC.buildComparator("size", {
-            ascending: true
-        })
+            ascending: true,
+        }),
     }),
 
     /** override to always have the current history first */
-    sort: function(options) {
+    sort: function (options) {
         options = options || {};
         var silent = options.silent;
         var currentHistory = this.remove(this.get(this.currentHistoryId));
@@ -512,7 +512,7 @@ export var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).e
         var collection = this;
 
         var xhr = jQuery.getJSON(`${getAppRoot()}history/create_new_current`);
-        return xhr.done(newData => {
+        return xhr.done((newData) => {
             collection.setCurrent(new History(newData, [], historyOptions || {}));
         });
     },
@@ -521,7 +521,7 @@ export var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).e
      *  Pass standard bbone options for use in unshift.
      *  @triggers new-current passed history and this collection
      */
-    setCurrent: function(history, options) {
+    setCurrent: function (history, options) {
         options = options || {};
         // new histories go in the front
         this.unshift(history, options);
@@ -534,5 +534,5 @@ export var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).e
 
     toString: function toString() {
         return `HistoryCollection(${this.length},current:${this.currentHistoryId})`;
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/history/history-preferences.js b/client/galaxy/scripts/mvc/history/history-preferences.js
index 0ae63605903b..5ed66037a1a6 100644
--- a/client/galaxy/scripts/mvc/history/history-preferences.js
+++ b/client/galaxy/scripts/mvc/history/history-preferences.js
@@ -10,11 +10,11 @@ var HistoryPrefs = BASE_MVC.SessionStorageModel.extend(
             //TODO:?? expandedIds to array?
             expandedIds: {},
             show_deleted: false,
-            show_hidden: false
+            show_hidden: false,
         },
 
         /** add an hda id to the hash of expanded hdas */
-        addExpanded: function(model) {
+        addExpanded: function (model) {
             //TODO: use type_id and not model
             var current = this.get("expandedIds");
             current[model.id] = model.get("id");
@@ -22,25 +22,25 @@ var HistoryPrefs = BASE_MVC.SessionStorageModel.extend(
         },
 
         /** remove an hda id from the hash of expanded hdas */
-        removeExpanded: function(model) {
+        removeExpanded: function (model) {
             var current = this.get("expandedIds");
             delete current[model.id];
             this.save("expandedIds", current);
         },
 
-        isExpanded: function(contentId) {
+        isExpanded: function (contentId) {
             return _.result(this.get("expandedIds"), contentId, false);
         },
 
-        allExpanded: function() {
+        allExpanded: function () {
             return _.values(this.get("expandedIds"));
         },
 
-        clearExpanded: function() {
+        clearExpanded: function () {
             this.set("expandedIds", {});
         },
 
-        includeDeleted: function(val) {
+        includeDeleted: function (val) {
             // moving the invocation here so other components don't need to know the key
             // TODO: change this key later
             if (!_.isUndefined(val)) {
@@ -49,7 +49,7 @@ var HistoryPrefs = BASE_MVC.SessionStorageModel.extend(
             return this.get("show_deleted");
         },
 
-        includeHidden: function(val) {
+        includeHidden: function (val) {
             // TODO: change this key later
             if (!_.isUndefined(val)) {
                 this.set("show_hidden", val);
@@ -57,9 +57,9 @@ var HistoryPrefs = BASE_MVC.SessionStorageModel.extend(
             return this.get("show_hidden");
         },
 
-        toString: function() {
+        toString: function () {
             return `HistoryPrefs(${this.id})`;
-        }
+        },
     },
     {
         // ........................................................................ class vars
@@ -78,7 +78,7 @@ var HistoryPrefs = BASE_MVC.SessionStorageModel.extend(
         /** return the existing storage for the history with the given id (or create one if it doesn't exist) */
         get: function get(historyId) {
             return new HistoryPrefs({
-                id: HistoryPrefs.historyStorageKey(historyId)
+                id: HistoryPrefs.historyStorageKey(historyId),
             });
         },
 
@@ -89,11 +89,11 @@ var HistoryPrefs = BASE_MVC.SessionStorageModel.extend(
                     sessionStorage.removeItem(key);
                 }
             }
-        }
+        },
     }
 );
 
 //==============================================================================
 export default {
-    HistoryPrefs: HistoryPrefs
+    HistoryPrefs: HistoryPrefs,
 };
diff --git a/client/galaxy/scripts/mvc/history/history-view-annotated.js b/client/galaxy/scripts/mvc/history/history-view-annotated.js
index 3504b1301f89..10fedea132f2 100644
--- a/client/galaxy/scripts/mvc/history/history-view-annotated.js
+++ b/client/galaxy/scripts/mvc/history/history-view-annotated.js
@@ -22,7 +22,7 @@ var AnnotatedHistoryView = _super.extend(
 
         // ------------------------------------------------------------------------ panel rendering
         /** In this override, add the history annotation */
-        _buildNewRender: function() {
+        _buildNewRender: function () {
             //TODO: shouldn't this display regardless (on all non-current panels)?
             var $newRender = _super.prototype._buildNewRender.call(this);
             this.renderHistoryAnnotation($newRender);
@@ -30,7 +30,7 @@ var AnnotatedHistoryView = _super.extend(
         },
 
         /** render the history's annotation as its own field */
-        renderHistoryAnnotation: function($newRender) {
+        renderHistoryAnnotation: function ($newRender) {
             var annotation = this.model.get("annotation");
             if (!annotation) {
                 return;
@@ -39,7 +39,7 @@ var AnnotatedHistoryView = _super.extend(
         },
 
         /** override to add headers to indicate the dataset, annotation columns */
-        renderItems: function($whereTo) {
+        renderItems: function ($whereTo) {
             $whereTo = $whereTo || this.$el;
             _super.prototype.renderItems.call(this, $whereTo);
 
@@ -49,7 +49,7 @@ var AnnotatedHistoryView = _super.extend(
             $('<div class="contents-container headers"/>')
                 .append([
                     $('<div class="history-content header"/>').text(_l("Dataset")),
-                    $('<div class="additional-info header"/>').text(_l("Annotation"))
+                    $('<div class="additional-info header"/>').text(_l("Annotation")),
                 ])
                 .appendTo($controls);
 
@@ -58,24 +58,22 @@ var AnnotatedHistoryView = _super.extend(
 
         // ------------------------------------------------------------------------ sub-views
         /** override to wrap each subview */
-        _renderItemView$el: function(view) {
+        _renderItemView$el: function (view) {
             return $('<div class="contents-container"/>').append([
                 view.render(0).$el,
-                $('<div class="additional-info"/>').text(view.model.get("annotation") || "")
+                $('<div class="additional-info"/>').text(view.model.get("annotation") || ""),
             ]);
         },
 
         // ------------------------------------------------------------------------ panel events
         events: _.extend(_.clone(_super.prototype.events), {
             // clicking on any part of the row will expand the items
-            "click .contents-container": function(ev) {
+            "click .contents-container": function (ev) {
                 ev.stopPropagation();
-                $(ev.currentTarget)
-                    .find(".list-item .title-bar")
-                    .click();
+                $(ev.currentTarget).find(".list-item .title-bar").click();
             },
             // prevent propagation on icon btns so they won't bubble up to tr and toggleBodyVisibility
-            "click .icon-btn": function(ev) {
+            "click .icon-btn": function (ev) {
                 ev.stopPropagation();
                 // stopProp will prevent bootstrap from getting the click needed to open a dropdown
                 //  in the case of metafile download buttons - workaround here
@@ -83,26 +81,23 @@ var AnnotatedHistoryView = _super.extend(
                 if ($currTarget.length && $currTarget.attr("data-toggle") === "dropdown") {
                     $currTarget.dropdown("toggle");
                 }
-            }
+            },
         }),
 
-        _clickSectionLink: function(ev) {
-            var sectionNumber = $(ev.currentTarget)
-                .parent()
-                .parent()
-                .data("section");
+        _clickSectionLink: function (ev) {
+            var sectionNumber = $(ev.currentTarget).parent().parent().data("section");
             this.openSection(sectionNumber);
         },
 
         // ........................................................................ misc
         /** Return a string rep of the history */
-        toString: function() {
+        toString: function () {
             return `AnnotatedHistoryView(${this.model ? this.model.get("name") : ""})`;
-        }
+        },
     }
 );
 
 //==============================================================================
 export default {
-    AnnotatedHistoryView: AnnotatedHistoryView
+    AnnotatedHistoryView: AnnotatedHistoryView,
 };
diff --git a/client/galaxy/scripts/mvc/history/history-view-edit-current.js b/client/galaxy/scripts/mvc/history/history-view-edit-current.js
index ff2f15174d6f..5d63f0ac965c 100644
--- a/client/galaxy/scripts/mvc/history/history-view-edit-current.js
+++ b/client/galaxy/scripts/mvc/history/history-view-edit-current.js
@@ -21,11 +21,11 @@ var HistoryViewPrefs = BASE_MVC.SessionStorageModel.extend(
             // */
             //focusedContentId : null
             /** Current scroll position */
-            scrollPosition: 0
+            scrollPosition: 0,
         },
-        toString: function() {
+        toString: function () {
             return `HistoryViewPrefs(${JSON.stringify(this.toJSON())})`;
-        }
+        },
     }
 );
 
@@ -53,7 +53,7 @@ var CurrentHistoryView = _super.extend(
 
         /** override to use drilldown (and not foldout) for how collections are displayed */
         HDCAViewClass: _super.prototype.HDCAViewClass.extend({
-            foldoutStyle: "drilldown"
+            foldoutStyle: "drilldown",
         }),
 
         emptyMsg: [
@@ -66,12 +66,12 @@ var CurrentHistoryView = _super.extend(
             _l(" or "),
             '<a class="get-data-link" href="javascript:void(0)">',
             _l("get data from an external source"),
-            "</a>"
+            "</a>",
         ].join(""),
 
         // ......................................................................... SET UP
         /** Set up the view, set up storage, bind listeners to HistoryContents events */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             attributes = attributes || {};
 
             // ---- persistent preferences
@@ -79,7 +79,7 @@ var CurrentHistoryView = _super.extend(
             this.preferences = new HistoryViewPrefs(
                 _.extend(
                     {
-                        id: HistoryViewPrefs.storageKey()
+                        id: HistoryViewPrefs.storageKey(),
                     },
                     _.pick(attributes, _.keys(HistoryViewPrefs.prototype.defaults))
                 )
@@ -96,7 +96,7 @@ var CurrentHistoryView = _super.extend(
         },
 
         /** Override to cache the current scroll position with a listener */
-        _setUpListeners: function() {
+        _setUpListeners: function () {
             _super.prototype._setUpListeners.call(this);
 
             var panel = this;
@@ -109,38 +109,38 @@ var CurrentHistoryView = _super.extend(
         // ------------------------------------------------------------------------ loading history/item models
         // TODO: next three more appropriate moved to the app level
         /** (re-)loads the user's current history & contents w/ details */
-        loadCurrentHistory: function() {
+        loadCurrentHistory: function () {
             return this.loadHistory(null, {
-                url: `${getAppRoot()}history/current_history_json`
+                url: `${getAppRoot()}history/current_history_json`,
             });
         },
 
         /** loads a history & contents w/ details and makes them the current history */
-        switchToHistory: function(historyId, attributes) {
+        switchToHistory: function (historyId, attributes) {
             const Galaxy = getGalaxyInstance();
             if (Galaxy.user.isAnonymous()) {
                 this.trigger("error", _l("You must be logged in to switch histories"), _l("Anonymous user"));
                 return $.when();
             }
             return this.loadHistory(historyId, {
-                url: `${getAppRoot()}history/set_as_current?id=${historyId}`
+                url: `${getAppRoot()}history/set_as_current?id=${historyId}`,
             });
         },
 
         /** creates a new history on the server and sets it as the user's current history */
-        createNewHistory: function(attributes) {
+        createNewHistory: function (attributes) {
             const Galaxy = getGalaxyInstance();
             if (Galaxy.user.isAnonymous()) {
                 this.trigger("error", _l("You must be logged in to create histories"), _l("Anonymous user"));
                 return $.when();
             }
             return this.loadHistory(null, {
-                url: `${getAppRoot()}history/create_new_current`
+                url: `${getAppRoot()}history/create_new_current`,
             });
         },
 
         /** release/free/shutdown old models and set up panel for new models */
-        setModel: function(model, attributes, render) {
+        setModel: function (model, attributes, render) {
             _super.prototype.setModel.call(this, model, attributes, render);
             if (this.model && this.model.id) {
                 this.log("checking for updates");
@@ -151,27 +151,27 @@ var CurrentHistoryView = _super.extend(
 
         // ------------------------------------------------------------------------ history/content event listening
         /** listening for history events */
-        _setUpModelListeners: function() {
+        _setUpModelListeners: function () {
             _super.prototype._setUpModelListeners.call(this);
             // re-broadcast any model change events so that listeners don't have to re-bind to each history
             return this.listenTo(this.model, {
-                "change:nice_size change:size": function() {
+                "change:nice_size change:size": function () {
                     this.trigger("history-size-change", this, this.model, arguments);
                 },
-                "change:id": function() {
-                    this.once("loading-done", function() {
+                "change:id": function () {
+                    this.once("loading-done", function () {
                         this.model.checkForUpdates();
                     });
-                }
+                },
             });
         },
 
         /** listening for collection events */
-        _setUpCollectionListeners: function() {
+        _setUpCollectionListeners: function () {
             _super.prototype._setUpCollectionListeners.call(this);
             // if a hidden item is created (gen. by a workflow), moves thru the updater to the ready state,
             //  then: remove it from the collection if the panel is set to NOT show hidden datasets
-            this.listenTo(this.collection, "state:ready", function(model, newState, oldState) {
+            this.listenTo(this.collection, "state:ready", function (model, newState, oldState) {
                 if (!model.get("visible") && !this.collection.storage.includeHidden()) {
                     this.removeItemView(model);
                 }
@@ -180,7 +180,7 @@ var CurrentHistoryView = _super.extend(
 
         // ------------------------------------------------------------------------ panel rendering
         /** override to add a handler to capture the scroll position when the parent scrolls */
-        _setUpBehaviors: function($where) {
+        _setUpBehaviors: function ($where) {
             $where = $where || this.$el;
             // console.log( '_setUpBehaviors', this.$scrollContainer( $where ).get(0), this.$list( $where ) );
             // we need to call this in _setUpBehaviors which is called after render since the $el
@@ -206,7 +206,7 @@ var CurrentHistoryView = _super.extend(
         },
 
         /** In this override, handle null models and move the search input to the top */
-        _buildNewRender: function() {
+        _buildNewRender: function () {
             if (!this.model) {
                 return $();
             }
@@ -217,18 +217,18 @@ var CurrentHistoryView = _super.extend(
         },
 
         /** render the message displayed when a user is over quota and can't run jobs */
-        _renderQuotaMessage: function($whereTo) {
+        _renderQuotaMessage: function ($whereTo) {
             $whereTo = $whereTo || this.$el;
             return $(this.templates.quotaMsg({}, this)).prependTo($whereTo.find(".messages"));
         },
 
         /** In this override, get and set current panel preferences when editor is used */
-        _renderTags: function($where) {
+        _renderTags: function ($where) {
             return _super.prototype._renderTags.call(this, $where);
         },
 
         /** In this override, get and set current panel preferences when editor is used */
-        _renderAnnotation: function($where) {
+        _renderAnnotation: function ($where) {
             var panel = this;
             // render annotation and show/hide based on preferences
             _super.prototype._renderAnnotation.call(panel, $where);
@@ -239,14 +239,14 @@ var CurrentHistoryView = _super.extend(
             panel.listenTo(
                 panel.annotationEditor,
                 "hiddenUntilActivated:shown hiddenUntilActivated:hidden",
-                annotationEditor => {
+                (annotationEditor) => {
                     panel.preferences.set("annotationEditorShown", annotationEditor.hidden);
                 }
             );
         },
 
         /** Override to scroll to cached position (in prefs) after swapping */
-        _swapNewRender: function($newRender) {
+        _swapNewRender: function ($newRender) {
             _super.prototype._swapNewRender.call(this, $newRender);
             var panel = this;
             _.delay(() => {
@@ -262,7 +262,7 @@ var CurrentHistoryView = _super.extend(
 
         // ------------------------------------------------------------------------ sub-views
         /** Override to add the current-content highlight class to currentContentId's view */
-        _attachItems: function($whereTo) {
+        _attachItems: function ($whereTo) {
             _super.prototype._attachItems.call(this, $whereTo);
             var panel = this;
             if (panel.currentContentId) {
@@ -272,7 +272,7 @@ var CurrentHistoryView = _super.extend(
         },
 
         /** Override to remove any drill down panels */
-        addItemView: function(model, collection, options) {
+        addItemView: function (model, collection, options) {
             var view = _super.prototype.addItemView.call(this, model, collection, options);
             if (!view) {
                 return view;
@@ -285,22 +285,22 @@ var CurrentHistoryView = _super.extend(
 
         // ------------------------------------------------------------------------ collection sub-views
         /** In this override, add/remove expanded/collapsed model ids to/from web storage */
-        _setUpItemViewListeners: function(view) {
+        _setUpItemViewListeners: function (view) {
             var panel = this;
             _super.prototype._setUpItemViewListeners.call(panel, view);
             // use pub-sub to: handle drilldown expansion and collapse
             return panel.listenTo(view, {
-                "expanded:drilldown": function(v, drilldown) {
+                "expanded:drilldown": function (v, drilldown) {
                     this._expandDrilldownPanel(drilldown);
                 },
-                "collapsed:drilldown": function(v, drilldown) {
+                "collapsed:drilldown": function (v, drilldown) {
                     this._collapseDrilldownPanel(drilldown);
-                }
+                },
             });
         },
 
         /** display 'current content': add a visible highlight and store the id of a content item */
-        setCurrentContent: function(view) {
+        setCurrentContent: function (view) {
             this.$(".history-content.current-content").removeClass("current-content");
             if (view) {
                 view.$el.addClass("current-content");
@@ -311,57 +311,50 @@ var CurrentHistoryView = _super.extend(
         },
 
         /** find the view with the id and then call setCurrentContent on it */
-        _setCurrentContentById: function(id) {
+        _setCurrentContentById: function (id) {
             var view = this.viewFromModelId(id) || null;
             this.setCurrentContent(view);
         },
 
         /** Handle drill down by hiding this panels list and controls and showing the sub-panel */
-        _expandDrilldownPanel: function(drilldown) {
+        _expandDrilldownPanel: function (drilldown) {
             this.panelStack.push(drilldown);
             // hide this panel's controls and list, set the name for back navigation, and attach to the $el
-            this.$controls()
-                .add(this.$list())
-                .hide();
+            this.$controls().add(this.$list()).hide();
             drilldown.parentName = this.model.get("name");
-            drilldown
-                .delegateEvents()
-                .render()
-                .$el.appendTo(this.$el);
+            drilldown.delegateEvents().render().$el.appendTo(this.$el);
         },
 
         /** Handle drilldown close by freeing the panel and re-rendering this panel */
-        _collapseDrilldownPanel: function(drilldown) {
+        _collapseDrilldownPanel: function (drilldown) {
             this.panelStack.pop();
             //TODO: MEM: free the panel
-            this.$controls()
-                .add(this.$list())
-                .show();
+            this.$controls().add(this.$list()).show();
         },
 
         // ........................................................................ panel events
         /** event map */
         events: _.extend(_.clone(_super.prototype.events), {
             // the two links in the empty message
-            "click .uploader-link": function(ev) {
+            "click .uploader-link": function (ev) {
                 const Galaxy = getGalaxyInstance();
                 Galaxy.upload.show(ev);
             },
-            "click .get-data-link": function(ev) {
+            "click .get-data-link": function (ev) {
                 var $toolMenu = $(".toolMenuContainer");
                 $toolMenu.parent().scrollTop(0);
                 $toolMenu.find('span:contains("Get Data")').click();
-            }
+            },
         }),
 
         // ........................................................................ external objects/MVC
-        listenToGalaxy: function(galaxy) {
+        listenToGalaxy: function (galaxy) {
             this.listenTo(galaxy, {
                 // when the galaxy_main iframe is loaded with a new page,
                 // compare the url to the following list and if there's a match
                 // pull the id from url and indicate in the history view that
                 // the dataset with that id is the 'current'ly active dataset
-                "center-frame:load": function(data) {
+                "center-frame:load": function (data) {
                     var pathToMatch = data.fullpath;
                     var hdaId = null;
                     var useToURLRegexMap = {
@@ -369,7 +362,7 @@ var CurrentHistoryView = _super.extend(
                         edit: /datasets\/([a-f0-9]+)\/edit/,
                         report_error: /dataset\/errors\?id=([a-f0-9]+)/,
                         rerun: /tool_runner\/rerun\?id=([a-f0-9]+)/,
-                        show_params: /datasets\/([a-f0-9]+)\/show_params/
+                        show_params: /datasets\/([a-f0-9]+)\/show_params/,
                         // no great way to do this here? (leave it in the dataset event handlers above?)
                         // 'visualization' : 'visualization',
                     };
@@ -382,7 +375,7 @@ var CurrentHistoryView = _super.extend(
                     this._setCurrentContentById(hdaId ? `dataset-${hdaId}` : null);
                 },
                 // when the center panel is given a new view, clear the current indicator
-                "center-panel:load": function(view) {
+                "center-panel:load": function (view) {
                     try {
                         const hdaId = view.model.attributes.dataset_id || null;
                         if (hdaId === null) {
@@ -393,15 +386,15 @@ var CurrentHistoryView = _super.extend(
                         this._setCurrentContentById();
                     }
                 },
-                "activate-hda": function(hdaId) {
+                "activate-hda": function (hdaId) {
                     this._setCurrentContentById(`dataset-${hdaId}`);
-                }
+                },
             });
         },
 
         //TODO: remove quota meter from panel and remove this
         /** add listeners to an external quota meter (mvc/user/user-quotameter.js) */
-        connectToQuotaMeter: function(quotaMeter) {
+        connectToQuotaMeter: function (quotaMeter) {
             if (!quotaMeter) {
                 return this;
             }
@@ -410,7 +403,7 @@ var CurrentHistoryView = _super.extend(
             this.listenTo(quotaMeter, "quota:under", this.hideQuotaMessage);
 
             // having to add this to handle re-render of hview while overquota (the above do not fire)
-            this.on("rendered rendered:initial", function() {
+            this.on("rendered rendered:initial", function () {
                 if (quotaMeter && quotaMeter.isOverQuota()) {
                     this.showQuotaMessage();
                 }
@@ -419,10 +412,10 @@ var CurrentHistoryView = _super.extend(
         },
 
         /** Override to preserve the quota message */
-        clearMessages: function(ev) {
+        clearMessages: function (ev) {
             var $target = !_.isUndefined(ev) ? $(ev.currentTarget) : this.$messages().children('[class$="message"]');
             $target = $target.not(".quota-message");
-            $target.fadeOut(this.fxSpeed, function() {
+            $target.fadeOut(this.fxSpeed, function () {
                 $(this).remove();
             });
             return this;
@@ -430,7 +423,7 @@ var CurrentHistoryView = _super.extend(
 
         /** Show the over quota message (which happens to be in the history panel).
          */
-        showQuotaMessage: function() {
+        showQuotaMessage: function () {
             var $msg = this.$(".quota-message");
             if ($msg.is(":hidden")) {
                 $msg.slideDown(this.fxSpeed);
@@ -439,7 +432,7 @@ var CurrentHistoryView = _super.extend(
 
         /** Hide the over quota message (which happens to be in the history panel).
          */
-        hideQuotaMessage: function() {
+        hideQuotaMessage: function () {
             var $msg = this.$(".quota-message");
             if (!$msg.is(":hidden")) {
                 $msg.slideUp(this.fxSpeed);
@@ -449,7 +442,7 @@ var CurrentHistoryView = _super.extend(
         // ........................................................................ options menu
         //TODO: remove to batch
         /** unhide any hidden datasets */
-        unhideHidden: function() {
+        unhideHidden: function () {
             var self = this;
             if (window.confirm(_l("Really unhide all hidden datasets?"))) {
                 // get all hidden, regardless of deleted/purged
@@ -466,7 +459,7 @@ var CurrentHistoryView = _super.extend(
         },
 
         /** delete any hidden datasets */
-        deleteHidden: function() {
+        deleteHidden: function () {
             var self = this;
             if (window.confirm(_l("Really delete all hidden datasets?"))) {
                 return self.model.contents._filterAndUpdate(
@@ -480,9 +473,9 @@ var CurrentHistoryView = _super.extend(
         },
 
         /** Return a string rep of the history */
-        toString: function() {
+        toString: function () {
             return `CurrentHistoryView(${this.model ? this.model.get("name") : ""})`;
-        }
+        },
     }
 );
 
@@ -495,16 +488,16 @@ CurrentHistoryView.prototype.templates = (() => {
             ". ",
             _l("Tool execution is on hold until your disk usage drops below your allocated quota"),
             ".",
-            "</div>"
+            "</div>",
         ],
         "history"
     );
     return _.extend(_.clone(_super.prototype.templates), {
-        quotaMsg: quotaMsgTemplate
+        quotaMsg: quotaMsgTemplate,
     });
 })();
 
 //==============================================================================
 export default {
-    CurrentHistoryView: CurrentHistoryView
+    CurrentHistoryView: CurrentHistoryView,
 };
diff --git a/client/galaxy/scripts/mvc/history/history-view-edit.js b/client/galaxy/scripts/mvc/history/history-view-edit.js
index 0084805a96e0..7911709d8ad3 100644
--- a/client/galaxy/scripts/mvc/history/history-view-edit.js
+++ b/client/galaxy/scripts/mvc/history/history-view-edit.js
@@ -42,7 +42,7 @@ var HistoryViewEdit = _super.extend(
         /** Set up the view, set up storage, bind listeners to HistoryContents events
          *  @param {Object} attributes
          */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             attributes = attributes || {};
             _super.prototype.initialize.call(this, attributes);
 
@@ -66,55 +66,55 @@ var HistoryViewEdit = _super.extend(
         },
 
         /** Override to handle history as drag-drop target */
-        _setUpListeners: function() {
+        _setUpListeners: function () {
             _super.prototype._setUpListeners.call(this);
             return this.on({
-                "droptarget:drop": function(ev, data) {
+                "droptarget:drop": function (ev, data) {
                     // process whatever was dropped and re-hide the drop target
                     this.dataDropped(data);
                     this.dropTargetOff();
                 },
-                "view:attached view:removed": function() {
+                "view:attached view:removed": function () {
                     this._renderCounts();
                 },
                 "search:loading-progress": this._renderSearchProgress,
-                "search:searching": this._renderSearchFindings
+                "search:searching": this._renderSearchFindings,
             });
         },
 
         // ------------------------------------------------------------------------ listeners
         /** listening for history and HDA events */
-        _setUpModelListeners: function() {
+        _setUpModelListeners: function () {
             _super.prototype._setUpModelListeners.call(this);
             this.listenTo(this.model, "change:size", this.updateHistoryDiskSize);
             return this;
         },
 
         /** listening for collection events */
-        _setUpCollectionListeners: function() {
+        _setUpCollectionListeners: function () {
             _super.prototype._setUpCollectionListeners.call(this);
             this.listenTo(this.collection, {
                 "change:deleted": this._handleItemDeletedChange,
                 "change:visible": this._handleItemVisibleChange,
-                "change:purged": function(model) {
+                "change:purged": function (model) {
                     // hafta get the new nice-size w/o the purged model
                     this.model.fetch();
                 },
                 // loading indicators for deleted/hidden
-                "fetching-deleted": function(collection) {
+                "fetching-deleted": function (collection) {
                     this.$("> .controls .deleted-count").html(`<i>${_l("loading...")}</i>`);
                 },
-                "fetching-hidden": function(collection) {
+                "fetching-hidden": function (collection) {
                     this.$("> .controls .hidden-count").html(`<i>${_l("loading...")}</i>`);
                 },
-                "fetching-deleted-done fetching-hidden-done": this._renderCounts
+                "fetching-deleted-done fetching-hidden-done": this._renderCounts,
             });
             return this;
         },
 
         // ------------------------------------------------------------------------ panel rendering
         /** In this override, add tag and annotation editors and a btn to toggle the selectors */
-        _buildNewRender: function() {
+        _buildNewRender: function () {
             var Galaxy = getGalaxyInstance();
 
             // create a new render using a skeleton template, render title buttons, render body, and set up events, etc.
@@ -131,12 +131,12 @@ var HistoryViewEdit = _super.extend(
         },
 
         /** Update the history size display (curr. upper right of panel). */
-        updateHistoryDiskSize: function() {
+        updateHistoryDiskSize: function () {
             this.$(".history-size").text(this.model.get("nice_size"));
         },
 
         /** override to render counts when the items are rendered */
-        renderItems: function($whereTo) {
+        renderItems: function ($whereTo) {
             var views = _super.prototype.renderItems.call(this, $whereTo);
             if (!this.searchFor) {
                 this._renderCounts($whereTo);
@@ -147,20 +147,20 @@ var HistoryViewEdit = _super.extend(
         },
 
         /** override to show counts, what's deleted/hidden, and links to toggle those */
-        _renderCounts: function($whereTo) {
+        _renderCounts: function ($whereTo) {
             $whereTo = $whereTo instanceof jQuery ? $whereTo : this.$el;
             var html = this.templates.counts(this.model.toJSON(), this);
             return $whereTo.find("> .controls .subtitle").html(html);
         },
 
         /** render the tags sub-view controller */
-        _renderTags: function($where) {
+        _renderTags: function ($where) {
             const el = $where.find(".controls .tags-display")[0];
 
             const propsData = {
                 model: this.model,
                 disabled: false,
-                context: "history-view-edit"
+                context: "history-view-edit",
             };
 
             const vm = mountModelTags(propsData, el);
@@ -170,7 +170,7 @@ var HistoryViewEdit = _super.extend(
                 title: _l("Edit history tags"),
                 classes: "history-tag-btn",
                 faIcon: "fa-tags",
-                tooltipConfig: { placement: "top" }
+                tooltipConfig: { placement: "top" },
             }).appendTo($where.find(".controls .actions"));
 
             activator.on("click", () => {
@@ -181,34 +181,34 @@ var HistoryViewEdit = _super.extend(
         },
 
         /** render the annotation sub-view controller */
-        _renderAnnotation: function($where) {
+        _renderAnnotation: function ($where) {
             var panel = this;
             this.annotationEditor = new ANNOTATIONS.AnnotationEditor({
                 model: this.model,
                 el: $where.find(".controls .annotation-display"),
-                onshowFirstTime: function() {
+                onshowFirstTime: function () {
                     this.render();
                 },
                 // show hide sub-view view annotation editors when this is shown/hidden
-                onshow: function() {
+                onshow: function () {
                     panel.toggleHDAAnnotationEditors(true, panel.fxSpeed);
                 },
-                onhide: function() {
+                onhide: function () {
                     panel.toggleHDAAnnotationEditors(false, panel.fxSpeed);
                 },
                 $activator: faIconButton({
                     title: _l("Edit history annotation"),
                     classes: "history-annotate-btn",
                     faIcon: "fa-comment",
-                    tooltipConfig: { placement: "top" }
-                }).appendTo($where.find(".controls .actions"))
+                    tooltipConfig: { placement: "top" },
+                }).appendTo($where.find(".controls .actions")),
             });
         },
 
         /** Set up HistoryViewEdit js/widget behaviours
          *  In this override, make the name editable
          */
-        _setUpBehaviors: function($where) {
+        _setUpBehaviors: function ($where) {
             var Galaxy = getGalaxyInstance();
 
             $where = $where || this.$el;
@@ -229,7 +229,7 @@ var HistoryViewEdit = _super.extend(
                 .attr("title", _l("Click to rename history"))
                 .tooltip({ placement: "bottom" })
                 .make_text_editable({
-                    on_finish: function(newName) {
+                    on_finish: function (newName) {
                         var previousName = panel.model.get("name");
                         if (newName && newName !== previousName) {
                             panel.$el.find(nameSelector).text(newName);
@@ -239,14 +239,14 @@ var HistoryViewEdit = _super.extend(
                         } else {
                             panel.$el.find(nameSelector).text(previousName);
                         }
-                    }
+                    },
                 });
         },
 
         /** return a new popup menu for choosing a multi selection action
          *  ajax calls made for multiple datasets are queued
          */
-        multiselectActions: function() {
+        multiselectActions: function () {
             var Galaxy = getGalaxyInstance();
             var panel = this;
 
@@ -254,14 +254,14 @@ var HistoryViewEdit = _super.extend(
                 const actionModels = {};
                 const items = panel
                     .getSelectedModels()
-                    .filter(model => {
+                    .filter((model) => {
                         console.log(model.attributes[key]);
                         return model.attributes[key] != value;
                     })
-                    .map(model => {
+                    .map((model) => {
                         const res = {
                             history_content_type: model.attributes.history_content_type,
-                            id: model.attributes.id
+                            id: model.attributes.id,
                         };
                         actionModels[model.id] = model;
                         // Tried "optimistically" deleting the dataset - but it didn't quite work -
@@ -297,45 +297,45 @@ var HistoryViewEdit = _super.extend(
             var actions = [
                 {
                     html: _l("Hide datasets"),
-                    func: function() {
+                    func: function () {
                         batchUpdate("visible", false);
-                    }
+                    },
                 },
                 {
                     html: _l("Unhide datasets"),
-                    func: function() {
+                    func: function () {
                         batchUpdate("visible", true);
-                    }
+                    },
                 },
                 {
                     html: _l("Delete datasets"),
                     func: () => {
                         batchUpdate("deleted", true);
-                    }
+                    },
                 },
                 {
                     html: _l("Undelete datasets"),
-                    func: function() {
+                    func: function () {
                         batchUpdate("deleted", false);
-                    }
-                }
+                    },
+                },
             ];
 
             if (panel.purgeAllowed) {
                 actions.push({
                     html: _l("Permanently delete datasets"),
-                    func: function() {
+                    func: function () {
                         if (
                             window.confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))
                         ) {
                             var action = HDA_MODEL.HistoryDatasetAssociation.prototype.purge;
                             const historyContents = panel.getSelectedModels();
                             const selectedDatasets = historyContents.filter(
-                                c => c.get("history_content_type") == "dataset"
+                                (c) => c.get("history_content_type") == "dataset"
                             );
                             historyContents.ajaxQueue(action, {}, selectedDatasets);
                         }
-                    }
+                    },
                 });
             }
             actions = actions.concat(panel._collectionActions());
@@ -343,30 +343,30 @@ var HistoryViewEdit = _super.extend(
         },
 
         /**   */
-        _collectionActions: function() {
+        _collectionActions: function () {
             var panel = this;
             return [
                 {
                     html: _l("Build Dataset List"),
-                    func: () => panel.buildCollection("list")
+                    func: () => panel.buildCollection("list"),
                 },
                 // TODO: Only show quick pair if two things selected.
                 {
                     html: _l("Build Dataset Pair"),
-                    func: () => panel.buildCollection("paired")
+                    func: () => panel.buildCollection("paired"),
                 },
                 {
                     html: _l("Build List of Dataset Pairs"),
-                    func: () => panel.buildCollection("list:paired")
+                    func: () => panel.buildCollection("list:paired"),
                 },
                 {
                     html: _l("Build Collection from Rules"),
-                    func: () => panel.buildCollection("rules")
-                }
+                    func: () => panel.buildCollection("rules"),
+                },
             ];
         },
 
-        buildCollection: function(collectionType, selection, hideSourceItems) {
+        buildCollection: function (collectionType, selection, hideSourceItems) {
             var panel = this;
             selection = selection || panel.getSelectedModels();
             hideSourceItems = hideSourceItems || false;
@@ -389,12 +389,12 @@ var HistoryViewEdit = _super.extend(
 
         // ------------------------------------------------------------------------ sub-views
         /** In this override, add purgeAllowed and whether tags/annotation editors should be shown */
-        _getItemViewOptions: function(model) {
+        _getItemViewOptions: function (model) {
             var options = _super.prototype._getItemViewOptions.call(this, model);
             _.extend(options, {
                 purgeAllowed: this.purgeAllowed,
                 tagsEditorShown: this.tagsEditor && !this.tagsEditor.hidden,
-                annotationEditorShown: this.annotationEditor && !this.annotationEditor.hidden
+                annotationEditorShown: this.annotationEditor && !this.annotationEditor.hidden,
             });
             return options;
         },
@@ -402,7 +402,7 @@ var HistoryViewEdit = _super.extend(
         /** If this item is deleted and we're not showing deleted items, remove the view
          *  @param {Model} the item model to check
          */
-        _handleItemDeletedChange: function(itemModel) {
+        _handleItemDeletedChange: function (itemModel) {
             if (itemModel.get("deleted")) {
                 this._handleItemDeletion(itemModel);
             } else {
@@ -411,7 +411,7 @@ var HistoryViewEdit = _super.extend(
             this._renderCounts();
         },
 
-        _handleItemDeletion: function(itemModel) {
+        _handleItemDeletion: function (itemModel) {
             var contentsShown = this.model.get("contents_active");
             contentsShown.deleted += 1;
             contentsShown.active -= 1;
@@ -421,7 +421,7 @@ var HistoryViewEdit = _super.extend(
             this.model.set("contents_active", contentsShown);
         },
 
-        _handleItemUndeletion: function(itemModel) {
+        _handleItemUndeletion: function (itemModel) {
             var contentsShown = this.model.get("contents_active");
             contentsShown.deleted -= 1;
             if (!this.model.contents.includeDeleted) {
@@ -433,7 +433,7 @@ var HistoryViewEdit = _super.extend(
         /** If this item is hidden and we're not showing hidden items, remove the view
          *  @param {Model} the item model to check
          */
-        _handleItemVisibleChange: function(itemModel) {
+        _handleItemVisibleChange: function (itemModel) {
             if (itemModel.hidden()) {
                 this._handleItemHidden(itemModel);
             } else {
@@ -442,7 +442,7 @@ var HistoryViewEdit = _super.extend(
             this._renderCounts();
         },
 
-        _handleItemHidden: function(itemModel) {
+        _handleItemHidden: function (itemModel) {
             var contentsShown = this.model.get("contents_active");
             contentsShown.hidden += 1;
             contentsShown.active -= 1;
@@ -452,7 +452,7 @@ var HistoryViewEdit = _super.extend(
             this.model.set("contents_active", contentsShown);
         },
 
-        _handleItemUnhidden: function(itemModel) {
+        _handleItemUnhidden: function (itemModel) {
             var contentsShown = this.model.get("contents_active");
             contentsShown.hidden -= 1;
             if (!this.model.contents.includeHidden) {
@@ -471,8 +471,8 @@ var HistoryViewEdit = _super.extend(
         // },
 
         /** toggle the visibility of each content's annotationEditor applying all the args sent to this function */
-        toggleHDAAnnotationEditors: function(showOrHide, speed) {
-            _.each(this.views, view => {
+        toggleHDAAnnotationEditors: function (showOrHide, speed) {
+            _.each(this.views, (view) => {
                 if (view.annotationEditor) {
                     view.annotationEditor.toggle(showOrHide, speed);
                 }
@@ -483,16 +483,16 @@ var HistoryViewEdit = _super.extend(
         /** event map */
         events: _.extend(_.clone(_super.prototype.events), {
             "click .show-selectors-btn": "toggleSelectors",
-            "click .toggle-deleted-link": function(ev) {
+            "click .toggle-deleted-link": function (ev) {
                 this.toggleShowDeleted();
             },
-            "click .toggle-hidden-link": function(ev) {
+            "click .toggle-hidden-link": function (ev) {
                 this.toggleShowHidden();
-            }
+            },
         }),
 
         // ------------------------------------------------------------------------ search
-        _renderSearchProgress: function(limit, offset) {
+        _renderSearchProgress: function (limit, offset) {
             var stop = limit + offset;
             return this.$("> .controls .subtitle").html(
                 ["<i>", _l("Searching "), stop, "/", this.model.contentsShown(), "</i>"].join("")
@@ -500,7 +500,7 @@ var HistoryViewEdit = _super.extend(
         },
 
         /** override to display number found in subtitle */
-        _renderSearchFindings: function($whereTo) {
+        _renderSearchFindings: function ($whereTo) {
             $whereTo = $whereTo instanceof jQuery ? $whereTo : this.$el;
             var html = this.templates.found(this.model.toJSON(), this);
             $whereTo.find("> .controls .subtitle").html(html);
@@ -509,7 +509,7 @@ var HistoryViewEdit = _super.extend(
 
         // ------------------------------------------------------------------------ as drop target
         /** turn all the drag and drop handlers on and add some help text above the drop area */
-        dropTargetOn: function() {
+        dropTargetOn: function () {
             if (this.dropTarget) {
                 return this;
             }
@@ -520,7 +520,7 @@ var HistoryViewEdit = _super.extend(
                 dragenter: _.bind(this.dragenter, this),
                 dragover: _.bind(this.dragover, this),
                 dragleave: _.bind(this.dragleave, this),
-                drop: _.bind(this.drop, this)
+                drop: _.bind(this.drop, this),
             };
 
             var $dropTarget = this._renderDropTarget();
@@ -534,13 +534,13 @@ var HistoryViewEdit = _super.extend(
         },
 
         /** render a box to serve as a 'drop here' area on the history */
-        _renderDropTarget: function() {
+        _renderDropTarget: function () {
             this.$(".history-drop-target").remove();
             return $("<div/>").addClass("history-drop-target");
         },
 
         /** tell the user how it works  */
-        _renderDropTargetHelp: function() {
+        _renderDropTargetHelp: function () {
             this.$(".history-drop-target-help").remove();
             return $("<div/>")
                 .addClass("history-drop-target-help")
@@ -548,7 +548,7 @@ var HistoryViewEdit = _super.extend(
         },
 
         /** shut down drag and drop event handlers and remove drop target */
-        dropTargetOff: function() {
+        dropTargetOff: function () {
             if (!this.dropTarget) {
                 return this;
             }
@@ -565,7 +565,7 @@ var HistoryViewEdit = _super.extend(
             return this;
         },
         /** toggle the target on/off */
-        dropTargetToggle: function() {
+        dropTargetToggle: function () {
             if (this.dropTarget) {
                 this.dropTargetOff();
             } else {
@@ -574,24 +574,24 @@ var HistoryViewEdit = _super.extend(
             return this;
         },
 
-        dragenter: function(ev) {
+        dragenter: function (ev) {
             //console.debug( 'dragenter:', this, ev );
             ev.preventDefault();
             ev.stopPropagation();
             this.$(".history-drop-target").css("border", "2px solid black");
         },
-        dragover: function(ev) {
+        dragover: function (ev) {
             ev.preventDefault();
             ev.stopPropagation();
         },
-        dragleave: function(ev) {
+        dragleave: function (ev) {
             //console.debug( 'dragleave:', this, ev );
             ev.preventDefault();
             ev.stopPropagation();
             this.$(".history-drop-target").css("border", "1px dashed black");
         },
         /** when (text) is dropped try to parse as json and trigger an event */
-        drop: function(ev) {
+        drop: function (ev) {
             ev.preventDefault();
             //ev.stopPropagation();
             var dataTransfer = ev.dataTransfer;
@@ -609,7 +609,7 @@ var HistoryViewEdit = _super.extend(
         },
 
         /** handler that copies data into the contents */
-        dataDropped: function(data) {
+        dataDropped: function (data) {
             // HDA: dropping will copy it to the history
             if (_.isObject(data) && data.model_class === "HistoryDatasetAssociation" && data.id) {
                 if (this.contents.currentPage !== 0) {
@@ -622,9 +622,9 @@ var HistoryViewEdit = _super.extend(
 
         // ........................................................................ misc
         /** Return a string rep of the history */
-        toString: function() {
+        toString: function () {
             return `HistoryViewEdit(${this.model ? this.model.get("name") : ""})`;
-        }
+        },
     }
 );
 
@@ -668,7 +668,7 @@ HistoryViewEdit.prototype.templates = (() => {
             "</a>",
             "<% } %>",
             "</span>",
-            "<% } %>"
+            "<% } %>",
         ],
         "history"
     );
@@ -700,18 +700,18 @@ HistoryViewEdit.prototype.templates = (() => {
             _l("show hidden"),
             "</a>",
             "<% } %>",
-            "<% } %>"
+            "<% } %>",
         ],
         "history"
     );
 
     return _.extend(_.clone(_super.prototype.templates), {
         counts: countsTemplate,
-        found: foundTemplate
+        found: foundTemplate,
     });
 })();
 
 //==============================================================================
 export default {
-    HistoryViewEdit: HistoryViewEdit
+    HistoryViewEdit: HistoryViewEdit,
 };
diff --git a/client/galaxy/scripts/mvc/history/history-view.js b/client/galaxy/scripts/mvc/history/history-view.js
index 35c42388cf9f..cf74acde814d 100644
--- a/client/galaxy/scripts/mvc/history/history-view.js
+++ b/client/galaxy/scripts/mvc/history/history-view.js
@@ -56,7 +56,7 @@ var HistoryView = _super.extend(
         /** Set up the view, bind listeners.
          *  @param {Object} attributes optional settings for the panel
          */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             _super.prototype.initialize.call(this, attributes);
             // ---- instance vars
             // control contents/behavior based on where (and in what context) the panel is being used
@@ -65,15 +65,15 @@ var HistoryView = _super.extend(
         },
 
         /** create and return a collection for when none is initially passed */
-        _createDefaultCollection: function() {
+        _createDefaultCollection: function () {
             // override
             return new this.collectionClass([], {
-                history: this.model
+                history: this.model,
             });
         },
 
         /** In this override, clear the update timer on the model */
-        freeModel: function() {
+        freeModel: function () {
             _super.prototype.freeModel.call(this);
             if (this.model) {
                 this.model.stopPolling();
@@ -85,25 +85,25 @@ var HistoryView = _super.extend(
          *  @fires: rendered:initial    on the first render
          *  @fires: empty-history       when switching to a history with no contents or creating a new history
          */
-        _setUpListeners: function() {
+        _setUpListeners: function () {
             _super.prototype._setUpListeners.call(this);
             this.on({
-                error: function(model, xhr, options, msg, details) {
+                error: function (model, xhr, options, msg, details) {
                     this.errorHandler(model, xhr, options, msg, details);
                 },
-                "views:ready view:attached view:removed": function(view) {
+                "views:ready view:attached view:removed": function (view) {
                     this._renderSelectButton();
                 },
-                "view:attached": function(view) {
+                "view:attached": function (view) {
                     this.scrollTo(0);
-                }
+                },
             });
             // this.on( 'all', function(){ console.debug( arguments ); });
         },
 
         // ------------------------------------------------------------------------ loading history/hda models
         /** load the history with the given id then it's contents, sending ajax options to both */
-        loadHistory: function(historyId, options, contentsOptions) {
+        loadHistory: function (historyId, options, contentsOptions) {
             contentsOptions = _.extend(contentsOptions || { silent: true });
             this.info("loadHistory:", historyId, options, contentsOptions);
             this.setModel(new History({ id: historyId }));
@@ -117,7 +117,7 @@ var HistoryView = _super.extend(
         },
 
         /** convenience alias to the model. Updates the item list only (not the history) */
-        refreshContents: function(options) {
+        refreshContents: function (options) {
             if (this.model) {
                 return this.model.refresh(options);
             }
@@ -126,44 +126,44 @@ var HistoryView = _super.extend(
         },
 
         /** Override to reset web storage when the id changes (since it needs the id) */
-        _setUpCollectionListeners: function() {
+        _setUpCollectionListeners: function () {
             _super.prototype._setUpCollectionListeners.call(this);
             return this.listenTo(this.collection, {
                 // 'all' : function(){ console.log( this.collection + ':', arguments ); },
-                "fetching-more": function() {
+                "fetching-more": function () {
                     this._toggleContentsLoadingIndicator(true);
                     this.$emptyMessage().hide();
                 },
-                "fetching-more-done": function() {
+                "fetching-more-done": function () {
                     this._toggleContentsLoadingIndicator(false);
-                }
+                },
             });
         },
 
         // ------------------------------------------------------------------------ panel rendering
         /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */
-        _showLoadingIndicator: function(msg, speed, callback) {
+        _showLoadingIndicator: function (msg, speed, callback) {
             var $indicator = $('<div class="loading-indicator"/>');
             this.$el.html($indicator.text(msg).slideDown(!_.isUndefined(speed) ? speed : this.fxSpeed));
         },
 
         /** hide the loading indicator */
-        _hideLoadingIndicator: function(speed) {
+        _hideLoadingIndicator: function (speed) {
             // make speed a bit slower to compensate for slow rendering of up to 500 contents
-            this.$(".loading-indicator").slideUp(!_.isUndefined(speed) ? speed : this.fxSpeed + 200, function() {
+            this.$(".loading-indicator").slideUp(!_.isUndefined(speed) ? speed : this.fxSpeed + 200, function () {
                 $(this).remove();
             });
         },
 
         /** In this override, add a btn to toggle the selectors */
-        _buildNewRender: function() {
+        _buildNewRender: function () {
             var $newRender = _super.prototype._buildNewRender.call(this);
             this._renderSelectButton($newRender);
             return $newRender;
         },
 
         /** button for starting select mode */
-        _renderSelectButton: function($where) {
+        _renderSelectButton: function ($where) {
             $where = $where || this.$el;
             // do not render selector option if no actions
             if (!this.multiselectActions().length) {
@@ -185,41 +185,33 @@ var HistoryView = _super.extend(
                 title: _l("Operations on multiple datasets"),
                 classes: "show-selectors-btn",
                 faIcon: "fa-check-square-o",
-                tooltipConfig: { placement: "top" }
+                tooltipConfig: { placement: "top" },
             }).prependTo($where.find(".controls .actions"));
         },
 
         /** override to avoid showing intial empty message using contents_active */
-        _renderEmptyMessage: function($whereTo) {
+        _renderEmptyMessage: function ($whereTo) {
             var $emptyMsg = this.$emptyMessage($whereTo);
             var empty = this.model.get("contents_active").active <= 0;
             if (empty) {
-                return $emptyMsg
-                    .empty()
-                    .append(this.emptyMsg)
-                    .show();
+                return $emptyMsg.empty().append(this.emptyMsg).show();
             } else if (this.searchFor && this.model.contents.haveSearchDetails() && !this.views.length) {
-                return $emptyMsg
-                    .empty()
-                    .append(this.noneFoundMsg)
-                    .show();
+                return $emptyMsg.empty().append(this.noneFoundMsg).show();
             }
             $emptyMsg.hide();
             return $();
         },
 
         /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */
-        $scrollContainer: function($where) {
+        $scrollContainer: function ($where) {
             // override or set via attributes.$scrollContainer
             return this.$list($where);
         },
 
         // ------------------------------------------------------------------------ subviews
-        _toggleContentsLoadingIndicator: function(show) {
+        _toggleContentsLoadingIndicator: function (show) {
             if (!show) {
-                this.$list()
-                    .find(".contents-loading-indicator")
-                    .remove();
+                this.$list().find(".contents-loading-indicator").remove();
             } else {
                 this.$list().html(
                     '<div class="contents-loading-indicator">' + '<span class="fa fa-2x fa-spinner fa-spin"/></div>'
@@ -228,7 +220,7 @@ var HistoryView = _super.extend(
         },
 
         /** override to render pagination also */
-        renderItems: function($whereTo) {
+        renderItems: function ($whereTo) {
             // console.log( this + '.renderItems-----------------', new Date() );
             $whereTo = $whereTo || this.$el;
             var $list = this.$list($whereTo);
@@ -254,7 +246,7 @@ var HistoryView = _super.extend(
         },
 
         /** render pagination controls if not searching and contents says we're paginating */
-        _renderPagination: function($whereTo) {
+        _renderPagination: function ($whereTo) {
             var $paginationControls = $whereTo.find("> .controls .list-pagination");
             if (this.searchFor || !this.model.contents.shouldPaginate()) return $paginationControls.empty();
 
@@ -263,7 +255,7 @@ var HistoryView = _super.extend(
                     {
                         // pagination is 1-based for the user
                         current: this.model.contents.currentPage + 1,
-                        last: this.model.contents.getLastPage() + 1
+                        last: this.model.contents.getLastPage() + 1,
                     },
                     this
                 )
@@ -273,10 +265,10 @@ var HistoryView = _super.extend(
         },
 
         /** render a subset of the entire collection (client-side pagination) */
-        _renderSomeItems: function(models, $list) {
+        _renderSomeItems: function (models, $list) {
             var views = [];
             $list.append(
-                models.map(m => {
+                models.map((m) => {
                     var view = this._createItemView(m);
                     views.push(view);
                     return this._renderItemView$el(view);
@@ -287,7 +279,7 @@ var HistoryView = _super.extend(
 
         // ------------------------------------------------------------------------ sub-views
         /** in this override, check if the contents would also display based on includeDeleted/hidden */
-        _filterItem: function(model) {
+        _filterItem: function (model) {
             var contents = this.model.contents;
             return (
                 (contents.includeHidden || !model.hidden()) &&
@@ -299,7 +291,7 @@ var HistoryView = _super.extend(
         /** In this override, since history contents are mixed,
          *      get the appropo view class based on history_content_type
          */
-        _getItemViewClass: function(model) {
+        _getItemViewClass: function (model) {
             var contentType = model.get("history_content_type");
             switch (contentType) {
                 case "dataset":
@@ -311,40 +303,40 @@ var HistoryView = _super.extend(
         },
 
         /** in this override, add a linktarget, and expand if id is in web storage */
-        _getItemViewOptions: function(model) {
+        _getItemViewOptions: function (model) {
             var options = _super.prototype._getItemViewOptions.call(this, model);
             return _.extend(options, {
                 linkTarget: this.linkTarget,
                 expanded: this.model.contents.storage.isExpanded(model.id),
-                hasUser: this.model.ownedByCurrUser()
+                hasUser: this.model.ownedByCurrUser(),
             });
         },
 
         /** In this override, add/remove expanded/collapsed model ids to/from web storage */
-        _setUpItemViewListeners: function(view) {
+        _setUpItemViewListeners: function (view) {
             var panel = this;
             _super.prototype._setUpItemViewListeners.call(panel, view);
             //TODO: send from content view: this.model.collection.storage.addExpanded
             // maintain a list of items whose bodies are expanded
             return panel.listenTo(view, {
-                expanded: function(v) {
+                expanded: function (v) {
                     panel.model.contents.storage.addExpanded(v.model);
                 },
-                collapsed: function(v) {
+                collapsed: function (v) {
                     panel.model.contents.storage.removeExpanded(v.model);
-                }
+                },
             });
         },
 
         /** override to remove expandedIds from webstorage */
-        collapseAll: function() {
+        collapseAll: function () {
             this.model.contents.storage.clearExpanded();
             _super.prototype.collapseAll.call(this);
         },
 
         // ------------------------------------------------------------------------ selection
         /** Override to correctly set the historyId of the new collection */
-        getSelectedModels: function() {
+        getSelectedModels: function () {
             var collection = _super.prototype.getSelectedModels.call(this);
             collection.historyId = this.collection.historyId;
             return collection;
@@ -358,20 +350,20 @@ var HistoryView = _super.extend(
             "click > .controls .next": "_clickNextPage",
             "change > .controls .pages": "_changePageSelect",
             // allow (error) messages to be clicked away
-            "click .messages [class$=message]": "clearMessages"
+            "click .messages [class$=message]": "clearMessages",
         }),
 
-        _clickPrevPage: function(ev) {
+        _clickPrevPage: function (ev) {
             this.model.stopPolling();
             this.model.contents.fetchPrevPage();
         },
 
-        _clickNextPage: function(ev) {
+        _clickNextPage: function (ev) {
             this.model.stopPolling();
             this.model.contents.fetchNextPage();
         },
 
-        _changePageSelect: function(ev) {
+        _changePageSelect: function (ev) {
             this.model.stopPolling();
             var page = $(ev.currentTarget).val();
             this.model.contents.fetchPage(page);
@@ -380,7 +372,7 @@ var HistoryView = _super.extend(
         /** Toggle and store the deleted visibility and re-render items
          * @returns {Boolean} new setting
          */
-        toggleShowDeleted: function(show, options) {
+        toggleShowDeleted: function (show, options) {
             show = show !== undefined ? show : !this.model.contents.includeDeleted;
             var contents = this.model.contents;
             contents.setIncludeDeleted(show, options);
@@ -393,7 +385,7 @@ var HistoryView = _super.extend(
         /** Toggle and store whether to render explicity hidden contents
          * @returns {Boolean} new setting
          */
-        toggleShowHidden: function(show, store, options) {
+        toggleShowHidden: function (show, store, options) {
             // console.log( 'toggleShowHidden', show, store );
             show = show !== undefined ? show : !this.model.contents.includeHidden;
             var contents = this.model.contents;
@@ -405,7 +397,7 @@ var HistoryView = _super.extend(
         },
 
         /** On the first search, if there are no details - load them, then search */
-        _firstSearch: function(searchFor) {
+        _firstSearch: function (searchFor) {
             var inputSelector = "> .controls .search-input";
             this.log("onFirstSearch", searchFor);
 
@@ -434,7 +426,7 @@ var HistoryView = _super.extend(
         },
 
         /** clear the search filters and show all views that are normally shown */
-        clearSearch: function(searchFor) {
+        clearSearch: function (searchFor) {
             if (!this.searchFor) return this;
             //this.log( 'onSearchClear', this );
             this.searchFor = "";
@@ -455,7 +447,7 @@ var HistoryView = _super.extend(
          *  @param {XMLHTTPRequest} xhr     any ajax obj. assoc. with the error
          *  @param {Object} options         the options map commonly used with bbone ajax
          */
-        errorHandler: function(model, xhr, options) {
+        errorHandler: function (model, xhr, options) {
             //TODO: to mixin or base model
             // interrupted ajax or no connection
             if (xhr && xhr.status === 0 && xhr.readyState === 0) {
@@ -480,9 +472,9 @@ var HistoryView = _super.extend(
         },
 
         /** Remove all messages from the panel. */
-        clearMessages: function(ev) {
+        clearMessages: function (ev) {
             var $target = !_.isUndefined(ev) ? $(ev.currentTarget) : this.$messages().children('[class$="message"]');
-            $target.fadeOut(this.fxSpeed, function() {
+            $target.fadeOut(this.fxSpeed, function () {
                 $(this).remove();
             });
             return this;
@@ -493,13 +485,13 @@ var HistoryView = _super.extend(
          *  @param {Integer} hid    the hid of item to scroll into view
          *  @returns {HistoryView} the panel
          */
-        scrollToHid: function(hid) {
+        scrollToHid: function (hid) {
             return this.scrollToItem(_.first(this.viewsWhereModel({ hid: hid })));
         },
 
         // ........................................................................ misc
         /** utility for adding -st, -nd, -rd, -th to numbers */
-        ordinalIndicator: function(number) {
+        ordinalIndicator: function (number) {
             var numStr = `${number}`;
             switch (numStr.charAt(numStr.length - 1)) {
                 case "1":
@@ -514,9 +506,9 @@ var HistoryView = _super.extend(
         },
 
         /** Return a string rep of the history */
-        toString: function() {
+        toString: function () {
             return `HistoryView(${this.model ? this.model.get("name") : ""})`;
-        }
+        },
     }
 );
 
@@ -586,7 +578,7 @@ HistoryView.prototype.templates = (() => {
             "</div>",
             "</div>",
             '<div class="list-pagination form-inline"></div>',
-            "</div>"
+            "</div>",
         ],
         "history"
     );
@@ -604,7 +596,7 @@ HistoryView.prototype.templates = (() => {
             "</option>",
             "<% }); %>",
             "</select>",
-            '<button class="next" <%- pages.current === pages.last ? "disabled" : "" %>>next</button>'
+            '<button class="next" <%- pages.current === pages.last ? "disabled" : "" %>>next</button>',
         ],
         "pages"
     );
@@ -612,7 +604,7 @@ HistoryView.prototype.templates = (() => {
     return _.extend(_.clone(_super.prototype.templates), {
         el: mainTemplate,
         controls: controlsTemplate,
-        pagination: paginationTemplate
+        pagination: paginationTemplate,
     });
 })();
 
@@ -621,17 +613,17 @@ export function historyEntry(options) {
         initialMode: options.initialModeDeleted,
         modes: [
             { mode: "showing_deleted", html: _l("Exclude deleted") },
-            { mode: "not_showing_deleted", html: _l("Include deleted") }
-        ]
+            { mode: "not_showing_deleted", html: _l("Include deleted") },
+        ],
     });
     $("#toggle-hidden").modeButton({
         initialMode: options.initialModeHidden,
         modes: [
             { mode: "showing_hidden", html: _l("Exclude hidden") },
-            { mode: "not_showing_hidden", html: _l("Include hidden") }
-        ]
+            { mode: "not_showing_hidden", html: _l("Include hidden") },
+        ],
     });
-    $("#switch").click(function() {
+    $("#switch").click(function () {
         //##HACK:ity hack hack
         //##TODO: remove when out of iframe
         const Galaxy = getGalaxyInstance();
@@ -652,13 +644,13 @@ export function historyEntry(options) {
     const history = new History(options.historyJSON);
 
     // attach the copy dialog to the import button now that we have a history
-    $("#import").click(function() {
+    $("#import").click(function () {
         const Galaxy = getGalaxyInstance();
         HistoryCopyDialog(history, {
             useImport: true,
             // use default datasets option to match the toggle-deleted button
-            allDatasets: $("#toggle-deleted").modeButton("getMode").mode === "showing_deleted"
-        }).done(function() {
+            allDatasets: $("#toggle-deleted").modeButton("getMode").mode === "showing_deleted",
+        }).done(function () {
             if (window === window.parent) {
                 window.location = getAppRoot();
             } else if (Galaxy.currHistoryPanel) {
@@ -671,29 +663,29 @@ export function historyEntry(options) {
         el: $("#history-" + options.historyJSON.id),
         className: viewClass.prototype.className + " wide",
         $scrollContainer: options.hasMasthead
-            ? function() {
+            ? function () {
                   return this.$el.parent();
               }
             : undefined,
         model: history,
         show_deleted: options.showDeletedJson,
         show_hidden: options.showHiddenJson,
-        purgeAllowed: options.allow_user_dataset_purge
+        purgeAllowed: options.allow_user_dataset_purge,
     });
     historyView.trigger("loading");
     history
         .fetchContents({ silent: true })
-        .fail(function() {
+        .fail(function () {
             alert("Galaxy history failed to load");
         })
-        .done(function() {
+        .done(function () {
             historyView.trigger("loading-done");
             historyView.render();
         });
-    $("#toggle-deleted").on("click", function() {
+    $("#toggle-deleted").on("click", function () {
         historyView.toggleShowDeleted();
     });
-    $("#toggle-hidden").on("click", function() {
+    $("#toggle-hidden").on("click", function () {
         historyView.toggleShowHidden();
     });
 }
@@ -701,5 +693,5 @@ export function historyEntry(options) {
 //==============================================================================
 export default {
     HistoryView: HistoryView,
-    historyEntry: historyEntry
+    historyEntry: historyEntry,
 };
diff --git a/client/galaxy/scripts/mvc/history/job-dag.js b/client/galaxy/scripts/mvc/history/job-dag.js
index d6eb32d1855c..e102c2726709 100644
--- a/client/galaxy/scripts/mvc/history/job-dag.js
+++ b/client/galaxy/scripts/mvc/history/job-dag.js
@@ -8,7 +8,7 @@ var _super = GRAPH.Graph;
  *      Reads in job json, filters and process that json, and builds a graph
  *      using the connections between job inputs and outputs.
  */
-var JobDAG = function(options) {
+var JobDAG = function (options) {
     options = options || {};
     var self = this;
     //this.logger = console;
@@ -45,7 +45,7 @@ JobDAG.prototype.init = function _init(options) {
 
     var self = this;
     self.options = _.defaults(options, {
-        excludeSetMetadata: false
+        excludeSetMetadata: false,
     });
     self.filters = self._initFilters();
 
@@ -137,7 +137,7 @@ JobDAG.prototype.preprocessJobs = function _preprocessJobs(jobs) {
     var self = this;
     self._outputIdToJobMap = {};
 
-    self._jobsData = self.sort(jobs).map(job => self.preprocessJob(_.clone(job)));
+    self._jobsData = self.sort(jobs).map((job) => self.preprocessJob(_.clone(job)));
     //console.debug( JSON.stringify( self._jobsData, null, '    ' ) );
     //console.debug( JSON.stringify( self._outputIdToJobMap, null, '    ' ) );
     return self;
@@ -256,12 +256,12 @@ JobDAG.prototype.createGraph = function _createGraph(jobsData) {
     self.debug("connections:");
     //console.debug( jobsData );
 
-    _.each(jobsData, jobData => {
+    _.each(jobsData, (jobData) => {
         var id = jobData.job.id;
         self.debug("\t", id, jobData);
         self.createVertex(id, jobData);
     });
-    _.each(jobsData, jobData => {
+    _.each(jobsData, (jobData) => {
         var targetId = jobData.job.id;
         _.each(jobData.inputs, (input, inputId) => {
             //console.debug( '\t\t target input:', inputId, input );
@@ -275,7 +275,7 @@ JobDAG.prototype.createGraph = function _createGraph(jobsData) {
             //console.debug( '\t\t creating edge, source:', sourceId, self.vertices[ sourceId ] );
             //console.debug( '\t\t creating edge, target:', targetId, self.vertices[ targetId ] );
             self.createEdge(sourceId, targetId, self.directed, {
-                dataset: inputId
+                dataset: inputId,
             });
         });
     });
@@ -296,9 +296,9 @@ JobDAG.prototype.createJobLessVertex = function _createJobLessVertex(contentId)
 };
 
 /** Override to re-sort (ugh) jobs in each component by update time */
-JobDAG.prototype.weakComponentGraphArray = function() {
+JobDAG.prototype.weakComponentGraphArray = function () {
     var dag = this;
-    return this.weakComponents().map(component => {
+    return this.weakComponents().map((component) => {
         //TODO: this seems to belong above (in sort) - why isn't it preserved?
         // note: using create_time (as opposed to update_time)
         //  since update_time for jobless/copied datasets is changes more often
@@ -319,9 +319,9 @@ JobDAG.prototype.weakComponentGraphArray = function() {
     });
 };
 
-JobDAG.prototype._jobsDataMap = function() {
+JobDAG.prototype._jobsDataMap = function () {
     var jobsDataMap = {};
-    this._jobsData.forEach(jobData => {
+    this._jobsData.forEach((jobData) => {
         jobsDataMap[jobData.job.id] = jobData;
     });
     return jobsDataMap;
diff --git a/client/galaxy/scripts/mvc/history/job-states-model.js b/client/galaxy/scripts/mvc/history/job-states-model.js
index b03577359c37..788242d27a38 100644
--- a/client/galaxy/scripts/mvc/history/job-states-model.js
+++ b/client/galaxy/scripts/mvc/history/job-states-model.js
@@ -11,33 +11,33 @@ var FETCH_STATE_ON_ADD = false;
 var BATCH_FETCH_STATE = true;
 
 var JobStatesSummary = Backbone.Model.extend({
-    url: function() {
+    url: function () {
         return `${getAppRoot()}api/histories/${this.attributes.history_id}/contents/dataset_collections/${
             this.attributes.collection_id
         }/jobs_summary`;
     },
 
-    hasDetails: function() {
+    hasDetails: function () {
         return this.has("populated_state");
     },
 
-    new: function() {
+    new: function () {
         return !this.hasDetails() || this.get("populated_state") == "new";
     },
 
-    errored: function() {
+    errored: function () {
         return this.get("populated_state") === "error" || this.anyWithStates(ERROR_STATES);
     },
 
-    states: function() {
+    states: function () {
         return this.get("states") || {};
     },
 
-    anyWithState: function(queryState) {
+    anyWithState: function (queryState) {
         return (this.states()[queryState] || 0) > 0;
     },
 
-    anyWithStates: function(queryStates) {
+    anyWithStates: function (queryStates) {
         var states = this.states();
         for (var index in queryStates) {
             if ((states[queryStates[index]] || 0) > 0) {
@@ -47,7 +47,7 @@ var JobStatesSummary = Backbone.Model.extend({
         return false;
     },
 
-    numWithStates: function(queryStates) {
+    numWithStates: function (queryStates) {
         var states = this.states();
         var count = 0;
         for (var index in queryStates) {
@@ -56,15 +56,15 @@ var JobStatesSummary = Backbone.Model.extend({
         return count;
     },
 
-    numInError: function() {
+    numInError: function () {
         return this.numWithStates(ERROR_STATES);
     },
 
-    running: function() {
+    running: function () {
         return this.anyWithState("running");
     },
 
-    terminal: function() {
+    terminal: function () {
         if (this.new()) {
             return false;
         } else {
@@ -73,7 +73,7 @@ var JobStatesSummary = Backbone.Model.extend({
         }
     },
 
-    jobCount: function() {
+    jobCount: function () {
         var states = this.states();
         var count = 0;
         for (var index in states) {
@@ -82,15 +82,15 @@ var JobStatesSummary = Backbone.Model.extend({
         return count;
     },
 
-    toString: function() {
+    toString: function () {
         return `JobStatesSummary(id=${this.get("id")})`;
-    }
+    },
 });
 
 var JobStatesSummaryCollection = Backbone.Collection.extend({
     model: JobStatesSummary,
 
-    initialize: function() {
+    initialize: function () {
         /* By default we wait for a polling update to do model fetch because
            FETCH_STATE_ON_ADD is false to load the application and target components
            as quickly as possible. that said if the polling is turned off
@@ -100,15 +100,15 @@ var JobStatesSummaryCollection = Backbone.Collection.extend({
         */
         if (FETCH_STATE_ON_ADD) {
             this.on({
-                add: model => model.fetch()
+                add: (model) => model.fetch(),
             });
         } else {
             this.on({
-                add: model => {
+                add: (model) => {
                     if (!this.active) {
                         model.fetch();
                     }
-                }
+                },
             });
         }
 
@@ -118,7 +118,7 @@ var JobStatesSummaryCollection = Backbone.Collection.extend({
         this.active = true;
     },
 
-    trackModel: function(historyContent) {
+    trackModel: function (historyContent) {
         if (historyContent.has("job_states_summary")) {
             // already tracked...
             return;
@@ -133,31 +133,31 @@ var JobStatesSummaryCollection = Backbone.Collection.extend({
                     id: jobSourceId,
                     model: jobSourceType,
                     history_id: historyId,
-                    collection_id: historyContent.attributes.id
+                    collection_id: historyContent.attributes.id,
                 });
                 historyContent.jobStatesSummary = this.get(jobSourceId);
             }
         }
     },
 
-    url: function() {
-        var nonTerminalModels = this.models.filter(model => {
+    url: function () {
+        var nonTerminalModels = this.models.filter((model) => {
             return !model.terminal();
         });
         var ids = nonTerminalModels
-            .map(summary => {
+            .map((summary) => {
                 return summary.get("id");
             })
             .join(",");
         var types = nonTerminalModels
-            .map(summary => {
+            .map((summary) => {
                 return summary.get("model");
             })
             .join(",");
         return `${getAppRoot()}api/histories/${this.historyId}/jobs_summary?ids=${ids}&types=${types}`;
     },
 
-    monitor: function() {
+    monitor: function () {
         this.clearUpdateTimeout();
         if (!this.active) {
             return;
@@ -169,13 +169,13 @@ var JobStatesSummaryCollection = Backbone.Collection.extend({
             }, UPDATE_DELAY);
         };
 
-        var nonTerminalModels = this.models.filter(model => {
+        var nonTerminalModels = this.models.filter((model) => {
             return !model.terminal();
         });
 
         if (nonTerminalModels.length > 0 && !BATCH_FETCH_STATE) {
             // Allow models to fetch their own details.
-            var updateFunctions = nonTerminalModels.map(summary => {
+            var updateFunctions = nonTerminalModels.map((summary) => {
                 return () => {
                     return summary.fetch();
                 };
@@ -191,16 +191,16 @@ var JobStatesSummaryCollection = Backbone.Collection.extend({
     },
 
     /** clear the timeout and the cached timeout id */
-    clearUpdateTimeout: function() {
+    clearUpdateTimeout: function () {
         if (this.updateTimeoutId) {
             clearTimeout(this.updateTimeoutId);
             this.updateTimeoutId = null;
         }
     },
 
-    toString: function() {
+    toString: function () {
         return `JobStatesSummaryCollection()`;
-    }
+    },
 });
 
 export default { JobStatesSummary, JobStatesSummaryCollection, FETCH_STATE_ON_ADD, NON_TERMINAL_STATES, ERROR_STATES };
diff --git a/client/galaxy/scripts/mvc/history/multi-panel.js b/client/galaxy/scripts/mvc/history/multi-panel.js
index e7d9d47770bd..4b9643c2a9e3 100644
--- a/client/galaxy/scripts/mvc/history/multi-panel.js
+++ b/client/galaxy/scripts/mvc/history/multi-panel.js
@@ -49,9 +49,9 @@ var HistoryViewColumn = Backbone.View.extend(baseMVC.LoggableMixin).extend({
                 // non-current panels should set their hdas to draggable
                 purgeAllowed: this.purgeAllowed,
                 dragItems: true,
-                $scrollContainer: function() {
+                $scrollContainer: function () {
                     return this.$el;
-                }
+                },
             })
         );
     },
@@ -79,16 +79,16 @@ var HistoryViewColumn = Backbone.View.extend(baseMVC.LoggableMixin).extend({
                 // when a panel's view expands turn off the click handler on the rerun button so that it uses it's href
                 // this allows the button to open the tool rerun form in a new tab (instead of erroring)
                 // TODO: hack
-                "view:expanded view:rendered": function(view) {
+                "view:expanded view:rendered": function (view) {
                     view.$(".rerun-btn").off();
-                }
+                },
             },
             this
         );
     },
 
     /** do the dimensions of this column overlap the given (horizontal) browser coords? */
-    inView: function(viewLeft, viewRight) {
+    inView: function (viewLeft, viewRight) {
         var columnLeft = this.$el.offset().left;
         var columnRight = columnLeft + this.$el.width();
         if (columnRight < viewLeft) {
@@ -130,7 +130,7 @@ var HistoryViewColumn = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     /** column body template with inner div for panel based on data (model json) */
     template: function template(data) {
         data = _.extend(data || {}, {
-            isCurrentHistory: this.currentHistory
+            isCurrentHistory: this.currentHistory,
         });
         return $(`
             <div class="panel-controls mb-1">
@@ -158,29 +158,29 @@ var HistoryViewColumn = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     /** event map */
     events: {
         // will make this the current history
-        "click .switch-to.btn": function() {
+        "click .switch-to.btn": function () {
             this.model.setAsCurrent();
         },
         //TODO: remove boiler plate from next 3
-        "click .delete-history": function() {
-            this.model._delete().done(data => {
+        "click .delete-history": function () {
+            this.model._delete().done((data) => {
                 this.render();
             });
         },
-        "click .undelete-history": function() {
-            this.model.undelete().done(data => {
+        "click .undelete-history": function () {
+            this.model.undelete().done((data) => {
                 this.render();
             });
         },
-        "click .purge-history": function() {
+        "click .purge-history": function () {
             if (window.confirm(_l("This will permanently remove the data. Are you sure?"))) {
-                this.model.purge().done(data => {
+                this.model.purge().done((data) => {
                     this.render();
                 });
             }
         },
         // will copy this history and make the copy the current history
-        "click .copy-history": "copy"
+        "click .copy-history": "copy",
     },
 
     // ------------------------------------------------------------------------ non-current controls
@@ -246,9 +246,9 @@ var HistoryViewColumn = Backbone.View.extend(baseMVC.LoggableMixin).extend({
 
     // ------------------------------------------------------------------------ misc
     /** String rep */
-    toString: function() {
+    toString: function () {
         return `HistoryViewColumn(${this.panel ? this.panel : ""})`;
-    }
+    },
 });
 
 //==============================================================================
@@ -276,7 +276,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
             columnGap: 8,
             headerHeight: 29,
             footerHeight: 0,
-            controlsHeight: 20
+            controlsHeight: 20,
         };
 
         /** how many histories to get when fetching a new batch/page */
@@ -335,7 +335,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         // console.log( 'addModels:', models, collection, options );
         options = options || {};
         models = _.isArray(models) ? models : [models];
-        models.forEach(model => {
+        models.forEach((model) => {
             this.addColumn(model, false);
             // if this is from a fetch, sort will be called and it will call render
         });
@@ -343,7 +343,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     },
 
     /** Set up listeners for the collection - handling: added histories, change of current, deletion, and sorting */
-    setUpCollectionListeners: function() {
+    setUpCollectionListeners: function () {
         this.listenTo(this.collection, {
             // handle ajax errors from the collection
             error: this.errorHandler,
@@ -358,13 +358,13 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
             // handle deleting a history (depends on whether panels is including deleted or not)
             "change:deleted change:purged": this.handleDeletedHistory,
             // re-render columns after a sort
-            sort: function() {
+            sort: function () {
                 this.renderColumns(0);
-            }
+            },
         });
     },
 
-    _postFetchAll: function(fetchData) {
+    _postFetchAll: function (fetchData) {
         // console.log( '_postFetchAll' );
         this.$(".histories-loading-indicator").remove();
         // when new histories is fetched and the indicator is not required,
@@ -380,7 +380,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     setCurrentHistory: function setCurrentHistory(history) {
         this.log("setCurrentHistory:", history);
         var oldCurrentColumn = _.findWhere(this.columnMap, {
-            currentHistory: true
+            currentHistory: true,
         });
         if (oldCurrentColumn) {
             oldCurrentColumn.currentHistory = false;
@@ -426,7 +426,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
      *  @param {XMLHTTPRequest} xhr     any ajax obj. assoc. with the error
      *  @param {Object} options         the options map commonly used with bbone ajax
      */
-    errorHandler: function(model, xhr, options) {
+    errorHandler: function (model, xhr, options) {
         // interrupted ajax or no connection
         if (xhr && xhr.status === 0 && xhr.readyState === 0) {
             // return ERROR_MODAL.offlineErrorModal();
@@ -450,12 +450,12 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     },
 
     /** If Galaxy object is available handle error there, otherwise, locally (and crudely) */
-    _ajaxErrorHandler: function() {
+    _ajaxErrorHandler: function () {
         ERROR_MODAL.ajaxErrorModal.apply(null, _.toArray(arguments));
     },
 
     /** create a new history and set it to current */
-    create: function(ev) {
+    create: function (ev) {
         return this.collection.create({ current: true });
     },
 
@@ -477,7 +477,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         // options passed can be re-used, so extend them before adding the model to prevent pollution for the next
         options = _.extend({}, options, {
             model: history,
-            purgeAllowed: Galaxy.config.allow_user_dataset_purge
+            purgeAllowed: Galaxy.config.allow_user_dataset_purge,
         });
         var column = new HistoryViewColumn(options);
         if (history.id === this.collection.currentHistoryId) {
@@ -540,7 +540,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     setUpColumnListeners: function setUpColumnListeners(column) {
         this.listenTo(column, {
             //'all': function(){ console.info( 'column ' + column + ':', arguments ) },
-            "in-view": this.queueHdaFetch
+            "in-view": this.queueHdaFetch,
         });
 
         this.listenTo(column.panel, {
@@ -556,56 +556,56 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
             },
             "droptarget:drop": (ev, data, panel) => {
                 //note: bad copy sources fail silently
-                var toCopy = this._dropData.filter(json => panel.model.contents.isCopyable(json));
+                var toCopy = this._dropData.filter((json) => panel.model.contents.isCopyable(json));
                 this._dropData = null;
 
                 var queue = new ajaxQueue.NamedAjaxQueue();
                 if (panel.model.contents.currentPage !== 0) {
                     queue.add({
                         name: "fetch-front-page",
-                        fn: function() {
+                        fn: function () {
                             return panel.model.contents.fetchPage(0);
-                        }
+                        },
                     });
                 }
                 // need to reverse to better match expected order
                 // TODO: reconsider order in list-view._setUpItemViewListeners, dragstart (instead of here)
-                toCopy.reverse().forEach(content => {
+                toCopy.reverse().forEach((content) => {
                     queue.add({
                         name: `copy-${content.id}`,
-                        fn: function() {
+                        fn: function () {
                             return panel.model.contents.copy(content);
-                        }
+                        },
                     });
                 });
                 queue.start();
-                queue.done(responses => {
+                queue.done((responses) => {
                     panel.model.fetch();
                 });
-            }
+            },
         });
     },
 
     /** conv. fn to count the columns in columnMap */
-    columnMapLength: function() {
+    columnMapLength: function () {
         return Object.keys(this.columnMap).length;
     },
 
     /** return array of Columns filtered by filters and sorted to match the collection
      *  @param: filters Function[] array of filter fns
      */
-    sortedFilteredColumns: function(filters) {
+    sortedFilteredColumns: function (filters) {
         filters = filters || this.filters;
         if (!filters || !filters.length) {
             return this.sortedColumns();
         }
         return this.sortedColumns().filter((column, index) => {
-            return column.currentHistory || _.every(filters.map(filter => filter.call(column)));
+            return column.currentHistory || _.every(filters.map((filter) => filter.call(column)));
         });
     },
 
     /** return array of Columns sorted to match the collection */
-    sortedColumns: function() {
+    sortedColumns: function () {
         return this.collection.map((history, index) => this.columnMap[history.id]);
     },
 
@@ -651,7 +651,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         return sortedAndFiltered;
     },
 
-    _addColumns: function(columns, speed) {
+    _addColumns: function (columns, speed) {
         speed = _.isNumber(speed) ? speed : this.fxSpeed;
         var $middle = this.$(".middle");
 
@@ -659,14 +659,11 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         $middle.width(this._calcMiddleWidth(columns.length + numExisting));
 
         columns.forEach((column, i) => {
-            column
-                .delegateEvents()
-                .render(speed)
-                .$el.appendTo($middle);
+            column.delegateEvents().render(speed).$el.appendTo($middle);
         });
     },
 
-    _calcMiddleWidth: function(numColumns) {
+    _calcMiddleWidth: function (numColumns) {
         var preventStackWidthAdj = 16;
         return (
             numColumns * (this.options.columnWidth + this.options.columnGap) +
@@ -697,7 +694,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
             // this uses a 'named' queue so that duplicate requests are ignored
             this.hdaQueue.add({
                 name: column.model.id,
-                fn: function() {
+                fn: function () {
                     return contents
                         .fetchCurrentPage(fetchOptions)
                         .done(() => {
@@ -708,7 +705,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
                                 contents.jobStateSummariesCollection.fetch();
                             }
                         });
-                }
+                },
             });
             // the queue is re-used, so if it's not processing requests - start it again
             if (!this.hdaQueue.running) {
@@ -718,18 +715,18 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     },
 
     /** Get the *detailed* json for *all* of a column's history's contents - req'd for searching */
-    queueHdaFetchDetails: function(column) {
+    queueHdaFetchDetails: function (column) {
         var contents = column.model.contents;
         var needsContentsLoaded = contents.length === 0 && column.model.contentsShown();
         if (needsContentsLoaded || !contents.haveDetails()) {
             // this uses a 'named' queue so that duplicate requests are ignored
             this.hdaQueue.add({
                 name: column.model.id,
-                fn: function() {
+                fn: function () {
                     return contents.progressivelyFetchDetails().done(() => {
                         column.panel._renderEmptyMessage();
                     });
-                }
+                },
             });
             // the queue is re-used, so if it's not processing requests - start it again
             if (!this.hdaQueue.running) {
@@ -739,7 +736,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     },
 
     /** put a text msg in the header */
-    renderInfo: function(msg) {
+    renderInfo: function (msg) {
         return this.$(".header .header-info").text(msg);
     },
 
@@ -753,21 +750,21 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         // these change the collection and column sort order
         "click .order .set-order": "_chooseOrder",
         "click #toggle-deleted": "_clickToggleDeletedDatasets",
-        "click #toggle-hidden": "_clickToggleHiddenDatasets"
+        "click #toggle-hidden": "_clickToggleHiddenDatasets",
     },
 
-    close: function(ev) {
+    close: function (ev) {
         //TODO: switch to pushState/router
         window.location = getAppRoot();
     },
 
-    _clickToggleDeletedHistories: function(ev) {
+    _clickToggleDeletedHistories: function (ev) {
         this.toggleDeletedHistories($(ev.currentTarget).is(":checked"));
         this.toggleOptionsPopover();
     },
 
     /** Include deleted histories in the collection */
-    toggleDeletedHistories: function(show) {
+    toggleDeletedHistories: function (show) {
         if (show) {
             window.location = `${getAppRoot()}history/view_multiple?include_deleted_histories=True`;
         } else {
@@ -775,11 +772,11 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         }
     },
 
-    _clickToggleDeletedDatasets: function(ev) {
+    _clickToggleDeletedDatasets: function (ev) {
         this.toggleDeletedDatasets($(ev.currentTarget).is(":checked"));
         this.toggleOptionsPopover();
     },
-    toggleDeletedDatasets: function(show) {
+    toggleDeletedDatasets: function (show) {
         show = show !== undefined ? show : false;
         this.sortedFilteredColumns().forEach((column, i) => {
             _.delay(() => {
@@ -788,11 +785,11 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         });
     },
 
-    _clickToggleHiddenDatasets: function(ev) {
+    _clickToggleHiddenDatasets: function (ev) {
         this.toggleHiddenDatasets($(ev.currentTarget).is(":checked"));
         this.toggleOptionsPopover();
     },
-    toggleHiddenDatasets: function(show) {
+    toggleHiddenDatasets: function (show) {
         show = show !== undefined ? show : false;
         this.sortedFilteredColumns().forEach((column, i) => {
             _.delay(() => {
@@ -802,7 +799,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     },
 
     /** change the collection order and re-fetch when the drop down in the options menu is changed */
-    _chooseOrder: function(ev) {
+    _chooseOrder: function (ev) {
         var collection = this.collection;
         var orderKey = $(ev.currentTarget).data("order");
         // set the sort order text also
@@ -813,7 +810,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         var currentHistoryModel = collection.slice(0, 1);
         collection.fetchFirst().done(() => {
             collection.unshift(currentHistoryModel, {
-                silent: true
+                silent: true,
             });
             this.createColumns();
             // need to clear this or previously fetched contents won't refetch now (bc of named queue)
@@ -825,24 +822,24 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     },
 
     /** scroll the column container right or left */
-    _scrollLeft: function(val) {
+    _scrollLeft: function (val) {
         val = _.isNumber(val) ? val : 0;
         this.$(".outer-middle").scrollLeft(val);
     },
 
     /** Set up any view plugins */
-    setUpBehaviors: function() {
+    setUpBehaviors: function () {
         this._moreOptionsPopover();
-        const searchHistories = searchFor => {
+        const searchHistories = (searchFor) => {
             const multipanel = this;
             this.historySearch = searchFor;
             this.filters = [
-                function() {
+                function () {
                     // This is intentionally a function where 'this' gets
                     // bound, applying the filter to the model of the
                     // caller.
                     return this.model.matchesAll(multipanel.historySearch);
-                }
+                },
             ];
             this.renderColumns(0);
         };
@@ -851,7 +848,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
             name: "search-histories",
             placeholder: _l("search histories"),
 
-            onfirstsearch: searchFor => {
+            onfirstsearch: (searchFor) => {
                 this.$("#search-histories").searchInput("toggle-loading");
                 this.renderInfo(_l("loading all histories for search"));
                 this.collection.fetchAll().done(() => {
@@ -862,12 +859,12 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
             },
 
             onsearch: searchHistories,
-            onclear: searchFor => {
+            onclear: (searchFor) => {
                 this.historySearch = null;
                 //TODO: remove specifically not just reset
                 this.filters = [];
                 this.renderColumns(0);
-            }
+            },
         });
 
         // input to search datasets
@@ -875,16 +872,16 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
             name: "search-datasets",
             placeholder: _l("search all datasets"),
 
-            onfirstsearch: searchFor => {
+            onfirstsearch: (searchFor) => {
                 this.hdaQueue.clear();
                 this.$("#search-datasets").searchInput("toggle-loading");
                 this.datasetSearch = searchFor;
-                this.sortedFilteredColumns().forEach(column => {
+                this.sortedFilteredColumns().forEach((column) => {
                     column.panel.searchItems(searchFor);
                     // load details for them that need
                     this.queueHdaFetchDetails(column);
                 });
-                this.hdaQueue.progress(progress => {
+                this.hdaQueue.progress((progress) => {
                     this.renderInfo([_l("searching"), progress.curr + 1, _l("of"), progress.total].join(" "));
                 });
                 this.hdaQueue.deferred.done(() => {
@@ -892,18 +889,18 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
                     this.$("#search-datasets").searchInput("toggle-loading");
                 });
             },
-            onsearch: searchFor => {
+            onsearch: (searchFor) => {
                 this.datasetSearch = searchFor;
-                this.sortedFilteredColumns().forEach(column => {
+                this.sortedFilteredColumns().forEach((column) => {
                     column.panel.searchItems(searchFor);
                 });
             },
-            onclear: searchFor => {
+            onclear: (searchFor) => {
                 this.datasetSearch = null;
-                this.sortedFilteredColumns().forEach(column => {
+                this.sortedFilteredColumns().forEach((column) => {
                     column.panel.clearSearch();
                 });
-            }
+            },
         });
 
         // resize first (fixed position) column on page resize
@@ -918,29 +915,27 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
             this.checkColumnsInView(viewport);
             this.checkForEndOfScroll(viewport);
         }, 100);
-        this.$(".middle")
-            .parent()
-            .scroll(debouncedInView);
+        this.$(".middle").parent().scroll(debouncedInView);
     },
 
     /** create the options popover */
-    _moreOptionsPopover: function() {
+    _moreOptionsPopover: function () {
         return this.$(".open-more-options.btn").popover({
             container: ".header",
             placement: "bottom",
             html: true,
-            content: $(this.optionsPopoverTemplate(this))
+            content: $(this.optionsPopoverTemplate(this)),
         });
     },
 
     /** change the collection order and re-fetch when the drop down in the options menu is changed */
-    toggleOptionsPopover: function(ev) {
+    toggleOptionsPopover: function (ev) {
         // hide seems broken in our version
         this.$(".open-more-options.btn").popover("toggle");
     },
 
     /** Adjust the height of the first, current column since flex-boxes won't work with fixed postiion elements */
-    _recalcFirstColumnHeight: function() {
+    _recalcFirstColumnHeight: function () {
         var $firstColumn = this.$(".history-column").first();
         var middleHeight = this.$(".middle").height();
         var controlHeight = $firstColumn.find(".panel-controls").height();
@@ -951,35 +946,37 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     },
 
     /** Get the left and right pixel coords of the middle element */
-    _viewport: function() {
+    _viewport: function () {
         var $outerMiddle = this.$(".middle").parent();
         var viewLeft = $outerMiddle.offset().left;
         var width = $outerMiddle.width();
         return {
             left: viewLeft,
-            right: viewLeft + width
+            right: viewLeft + width,
         };
     },
 
     /** returns the columns currently in the viewport */
-    columnsInView: function(viewport) {
+    columnsInView: function (viewport) {
         //TODO: uses offset which is render intensive
         //TODO: 2N - could use arg filter (sortedFilteredColumns( filter )) instead
         var vp = viewport || this._viewport();
-        return this.sortedFilteredColumns().filter(column => column.currentHistory || column.inView(vp.left, vp.right));
+        return this.sortedFilteredColumns().filter(
+            (column) => column.currentHistory || column.inView(vp.left, vp.right)
+        );
     },
 
     //TODO: sortByInView - return cols in view, then others
     /** trigger in-view from columns in-view */
-    checkColumnsInView: function() {
+    checkColumnsInView: function () {
         //TODO: assbackward - don't fire from the column, fire from here and listen from here
-        this.columnsInView().forEach(column => {
+        this.columnsInView().forEach((column) => {
             column.trigger("in-view", column);
         });
     },
 
     /** is the middle, horizontally scrolling section scrolled fully to the right? */
-    checkForEndOfScroll: function(viewport) {
+    checkForEndOfScroll: function (viewport) {
         viewport = viewport || this._viewport();
         var END_PADDING = 16;
         var $middle = this.$(".middle");
@@ -990,18 +987,18 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     },
 
     /** Show and enable the current columns drop target */
-    currentColumnDropTargetOn: function() {
+    currentColumnDropTargetOn: function () {
         var currentColumn = this.columnMap[this.collection.currentHistoryId];
         if (!currentColumn) {
             return;
         }
         //TODO: fix this - shouldn't need monkeypatch
-        currentColumn.panel.dataDropped = data => {};
+        currentColumn.panel.dataDropped = (data) => {};
         currentColumn.panel.dropTargetOn();
     },
 
     /** Hide and disable the current columns drop target */
-    currentColumnDropTargetOff: function() {
+    currentColumnDropTargetOff: function () {
         var currentColumn = this.columnMap[this.collection.currentHistoryId];
         if (!currentColumn) {
             return;
@@ -1014,7 +1011,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
 
     // ------------------------------------------------------------------------ misc
     /** String rep */
-    toString: function() {
+    toString: function () {
         return `MultiPanelColumns(${this.columns ? this.columns.length : 0})`;
     },
 
@@ -1055,7 +1052,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         name: _l("name, a to z"),
         "name-dsc": _l("name, z to a"),
         size: _l("size, large to small"),
-        "size-asc": _l("size, small to large")
+        "size-asc": _l("size, small to large"),
     },
 
     optionsPopoverTemplate: _.template(
@@ -1094,10 +1091,10 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
             </div>
         </div>`,
         { variable: "view" }
-    )
+    ),
 });
 
 //==============================================================================
 export default {
-    MultiPanelColumns: MultiPanelColumns
+    MultiPanelColumns: MultiPanelColumns,
 };
diff --git a/client/galaxy/scripts/mvc/history/options-menu.js b/client/galaxy/scripts/mvc/history/options-menu.js
index 411d4a6d2cb1..890228a2f43b 100644
--- a/client/galaxy/scripts/mvc/history/options-menu.js
+++ b/client/galaxy/scripts/mvc/history/options-menu.js
@@ -12,53 +12,53 @@ var menu = [
     {
         html: _l("History Actions"),
         header: true,
-        anon: true
+        anon: true,
     },
     {
         html: _l("Copy"),
-        func: function() {
+        func: function () {
             const Galaxy = getGalaxyInstance();
             historyCopyDialog(Galaxy.currHistoryPanel.model).done(() => {
                 Galaxy.currHistoryPanel.loadCurrentHistory();
             });
-        }
+        },
     },
     {
         html: _l("Share or Publish"),
-        func: function() {
+        func: function () {
             const Galaxy = getGalaxyInstance();
             if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
                 Galaxy.router.push(`/histories/sharing?id=${Galaxy.currHistoryPanel.model.id}`);
             }
-        }
+        },
     },
     {
         html: _l("Show Structure"),
         anon: true,
-        func: function() {
+        func: function () {
             const Galaxy = getGalaxyInstance();
             if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
                 Galaxy.router.push("/histories/show_structure");
             }
-        }
+        },
     },
     {
         html: _l("Extract Workflow"),
-        href: "workflow/build_from_current_history"
+        href: "workflow/build_from_current_history",
     },
     {
         html: _l("Set Permissions"),
-        func: function() {
+        func: function () {
             const Galaxy = getGalaxyInstance();
             if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
                 Galaxy.router.push(`/histories/permissions?id=${Galaxy.currHistoryPanel.model.id}`);
             }
-        }
+        },
     },
     {
         html: _l("Make Private"),
         anon: true,
-        func: function() {
+        func: function () {
             const Galaxy = getGalaxyInstance();
             if (
                 Galaxy &&
@@ -73,35 +73,35 @@ var menu = [
                     Galaxy.currHistoryPanel.loadCurrentHistory();
                 });
             }
-        }
+        },
     },
     {
         html: _l("Resume Paused Jobs"),
         href: "history/resume_paused_jobs?current=True",
-        anon: true
+        anon: true,
     },
     {
         html: _l("Dataset Actions"),
         header: true,
-        anon: true
+        anon: true,
     },
     {
         html: _l("Copy Datasets"),
-        href: "dataset/copy_datasets"
+        href: "dataset/copy_datasets",
     },
     {
         html: _l("Collapse Expanded Datasets"),
-        func: function() {
+        func: function () {
             const Galaxy = getGalaxyInstance();
             if (Galaxy && Galaxy.currHistoryPanel) {
                 Galaxy.currHistoryPanel.collapseAll();
             }
-        }
+        },
     },
     {
         html: _l("Unhide Hidden Datasets"),
         anon: true,
-        func: function() {
+        func: function () {
             const Galaxy = getGalaxyInstance();
             // TODO: Deprecate this functionality and replace with group dataset selector and action combination
             if (Galaxy && Galaxy.currHistoryPanel && confirm(_l("Really unhide all hidden datasets?"))) {
@@ -109,12 +109,12 @@ var menu = [
                     Galaxy.currHistoryPanel.loadCurrentHistory();
                 });
             }
-        }
+        },
     },
     {
         html: _l("Delete Hidden Datasets"),
         anon: true,
-        func: function() {
+        func: function () {
             const Galaxy = getGalaxyInstance();
             // TODO: Deprecate this functionality and replace with group dataset selector and action combination
             if (Galaxy && Galaxy.currHistoryPanel && confirm(_l("Really delete all hidden datasets?"))) {
@@ -122,51 +122,51 @@ var menu = [
                     Galaxy.currHistoryPanel.loadCurrentHistory();
                 });
             }
-        }
+        },
     },
     {
         html: _l("Purge Deleted Datasets"),
         confirm: _l("Really delete all deleted datasets permanently? This cannot be undone."),
         href: "history/purge_deleted_datasets",
         purge: true,
-        anon: true
+        anon: true,
     },
 
     {
         html: _l("Downloads"),
-        header: true
+        header: true,
     },
     {
         html: _l("Export Tool Citations"),
         anon: true,
-        func: function() {
+        func: function () {
             const Galaxy = getGalaxyInstance();
             if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
                 Galaxy.router.push(`/histories/citations?id=${Galaxy.currHistoryPanel.model.id}`);
             }
-        }
+        },
     },
     {
         html: _l("Export History to File"),
         href: "history/export_archive?preview=True",
-        anon: true
-    }
+        anon: true,
+    },
 ];
 
 // Webhooks
 Webhooks.load({
     type: "history-menu",
     async: false, // (hypothetically) slows down the performance
-    callback: function(webhooks) {
+    callback: function (webhooks) {
         var webhooks_menu = [];
 
-        webhooks.each(model => {
+        webhooks.each((model) => {
             var webhook = model.toJSON();
             if (webhook.activate) {
                 webhooks_menu.push({
                     html: _l(webhook.config.title),
                     // func: function() {},
-                    anon: true
+                    anon: true,
                 });
             }
         });
@@ -174,15 +174,15 @@ Webhooks.load({
         if (webhooks_menu.length > 0) {
             webhooks_menu.unshift({
                 html: _l("Webhooks"),
-                header: true
+                header: true,
             });
             $.merge(menu, webhooks_menu);
         }
-    }
+    },
 });
 
 function buildMenu(isAnon, purgeAllowed, urlRoot) {
-    return _.clone(menu).filter(menuOption => {
+    return _.clone(menu).filter((menuOption) => {
         if (isAnon && !menuOption.anon) {
             return false;
         }
diff --git a/client/galaxy/scripts/mvc/job/job-li.js b/client/galaxy/scripts/mvc/job/job-li.js
index b502226dadfb..787a7ae7706d 100644
--- a/client/galaxy/scripts/mvc/job/job-li.js
+++ b/client/galaxy/scripts/mvc/job/job-li.js
@@ -14,14 +14,14 @@ var JobListItemView = _super.extend(
         //logger              : console,
 
         className: `${_super.prototype.className} job`,
-        id: function() {
+        id: function () {
             return ["job", this.model.get("id")].join("-");
         },
 
         foldoutPanelClass: DATASET_LIST.DatasetList,
 
         /** Set up: instance vars, options, and event handlers */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             if (attributes.logger) {
                 this.logger = this.model.logger = attributes.logger;
             }
@@ -36,7 +36,7 @@ var JobListItemView = _super.extend(
         },
 
         /** In this override, add the state as a class for use with state-based CSS */
-        _swapNewRender: function($newRender) {
+        _swapNewRender: function ($newRender) {
             _super.prototype._swapNewRender.call(this, $newRender);
             if (this.model.has("state")) {
                 this.$el.addClass(`state-${this.model.get("state")}`);
@@ -45,11 +45,11 @@ var JobListItemView = _super.extend(
         },
 
         /** Stub to return proper foldout panel options */
-        _getFoldoutPanelOptions: function() {
+        _getFoldoutPanelOptions: function () {
             var options = _super.prototype._getFoldoutPanelOptions.call(this);
             return _.extend(options, {
                 collection: this.model.outputCollection,
-                selecting: false
+                selecting: false,
             });
         },
 
@@ -58,12 +58,12 @@ var JobListItemView = _super.extend(
         //  or something similar in order to remove some of the complexity here
 
         /** Return tool.inputs that should/can be safely displayed */
-        _labelParamMap: function() {
+        _labelParamMap: function () {
             //ADAPTER
             var params = this.model.get("params");
 
             var labelParamMap = {};
-            _.each(this.tool.inputs, i => {
+            _.each(this.tool.inputs, (i) => {
                 //console.debug( i.label, i.model_class );
                 if (i.label && i.model_class !== "DataToolParameter") {
                     labelParamMap[i.label] = params[i.name];
@@ -72,12 +72,12 @@ var JobListItemView = _super.extend(
             return labelParamMap;
         },
 
-        _labelInputMap: function() {
+        _labelInputMap: function () {
             //ADAPTER
             var view = this;
 
             var labelInputMap = {};
-            _.each(this.jobData.inputs, input => {
+            _.each(this.jobData.inputs, (input) => {
                 var toolInput = view._findToolInput(input.name);
                 if (toolInput) {
                     labelInputMap[toolInput.label] = input;
@@ -87,7 +87,7 @@ var JobListItemView = _super.extend(
         },
 
         /** Return a tool.inputs object that matches (or partially matches) the given (job input) name */
-        _findToolInput: function(name) {
+        _findToolInput: function (name) {
             //ADAPTER
             var toolInputs = this.tool.inputs;
 
@@ -99,22 +99,22 @@ var JobListItemView = _super.extend(
         },
 
         /** Return a tool.inputs object that partially matches the given (job input) name (for repeat dataset inputs)*/
-        _findRepeatToolInput: function(name, toolInputs) {
+        _findRepeatToolInput: function (name, toolInputs) {
             //ADAPTER
             toolInputs = toolInputs || this.tool.inputs;
-            var partialMatch = _.find(toolInputs, i => name.indexOf(i.name) === 0);
+            var partialMatch = _.find(toolInputs, (i) => name.indexOf(i.name) === 0);
             if (!partialMatch) {
                 return undefined;
             }
 
-            return _.find(partialMatch.inputs, i => name.indexOf(i.name) !== -1);
+            return _.find(partialMatch.inputs, (i) => name.indexOf(i.name) !== -1);
         },
 
         // ........................................................................ misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             return `JobListItemView(${this.model})`;
-        }
+        },
     }
 );
 
@@ -141,7 +141,7 @@ JobListItemView.prototype.templates = (() => {
 
         // expandable area for more details
         '<div class="details"></div>',
-        "</div>"
+        "</div>",
     ]);
 
     var titleBarTemplate = BASE_MVC.wrapTemplate(
@@ -160,7 +160,7 @@ JobListItemView.prototype.templates = (() => {
             ": <%= new Date( job.create_time ).toString() %>, ",
             "</span",
             "</div>",
-            "</div>"
+            "</div>",
         ],
         "job"
     );
@@ -175,7 +175,7 @@ JobListItemView.prototype.templates = (() => {
             //'<span class="version">',
             //    ' (', _l( 'version' ), ': <%- view.tool.version %>)',
             //'</span',
-            "</div>"
+            "</div>",
         ],
         "job"
     );
@@ -202,7 +202,7 @@ JobListItemView.prototype.templates = (() => {
             "</div>",
             "<% }) %>",
             "</div>",
-            "</div>"
+            "</div>",
         ],
         "job"
     );
@@ -211,11 +211,11 @@ JobListItemView.prototype.templates = (() => {
         //el          : elTemplate,
         titleBar: titleBarTemplate,
         subtitle: subtitleTemplate,
-        details: detailsTemplate
+        details: detailsTemplate,
     });
 })();
 
 //=============================================================================
 export default {
-    JobListItemView: JobListItemView
+    JobListItemView: JobListItemView,
 };
diff --git a/client/galaxy/scripts/mvc/job/job-model.js b/client/galaxy/scripts/mvc/job/job-model.js
index 5cfb39076c75..b221fd20cae0 100644
--- a/client/galaxy/scripts/mvc/job/job-model.js
+++ b/client/galaxy/scripts/mvc/job/job-model.js
@@ -31,17 +31,17 @@ var Job = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
 
                 create_time: null,
                 update_time: null,
-                state: STATES.NEW
+                state: STATES.NEW,
             },
 
             /** override to parse params on incomming */
-            parse: function(response, options) {
+            parse: function (response, options) {
                 response.params = this.parseParams(response.params);
                 return response;
             },
 
             /** override to treat param values as json */
-            parseParams: function(params) {
+            parseParams: function (params) {
                 var newParams = {};
                 _.each(params, (value, key) => {
                     newParams[key] = JSON.parse(value);
@@ -50,11 +50,11 @@ var Job = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             /** instance vars and listeners */
-            initialize: function(attributes, options) {
+            initialize: function (attributes, options) {
                 this.debug(`${this}(Job).initialize`, attributes, options);
 
                 this.set("params", this.parseParams(this.get("params")), {
-                    silent: true
+                    silent: true,
                 });
 
                 this.outputCollection = attributes.outputCollection || new HISTORY_CONTENTS.HistoryContents([]);
@@ -64,9 +64,9 @@ var Job = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             /** set up any event listeners
              *  event: state:ready  fired when this DA moves into/is already in a ready state
              */
-            _setUpListeners: function() {
+            _setUpListeners: function () {
                 // if the state has changed and the new state is a ready state, fire an event
-                this.on("change:state", function(currModel, newState) {
+                this.on("change:state", function (currModel, newState) {
                     this.log(`${this} has changed state:`, currModel, newState);
                     if (this.inReadyState()) {
                         this.trigger("state:ready", currModel, newState, this.previous("state"));
@@ -78,12 +78,12 @@ var Job = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             /** Is this job in a 'ready' state; where 'Ready' states are states where no
              *      processing is left to do on the server.
              */
-            inReadyState: function() {
+            inReadyState: function () {
                 return _.contains(STATES.READY_STATES, this.get("state"));
             },
 
             /** Does this model already contain detailed data (as opposed to just summary level data)? */
-            hasDetails: function() {
+            hasDetails: function () {
                 //?? this may not be reliable
                 return !_.isEmpty(this.get("outputs"));
             },
@@ -102,9 +102,9 @@ var Job = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
 
             // ........................................................................ misc
             /** String representation */
-            toString: function() {
+            toString: function () {
                 return ["Job(", this.get("id"), ":", this.get("tool_id"), ")"].join("");
-            }
+            },
         }
     )
 );
@@ -120,11 +120,11 @@ var JobCollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(
 
         /** root api url */
         urlRoot: `${getAppRoot()}api/jobs`,
-        url: function() {
+        url: function () {
             return this.urlRoot;
         },
 
-        intialize: function(models, options) {
+        intialize: function (models, options) {
             console.debug(models, options);
         },
 
@@ -132,28 +132,28 @@ var JobCollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(
         /** Get the ids of every item in this collection
          *  @returns array of encoded ids
          */
-        ids: function() {
-            return this.map(item => item.get("id"));
+        ids: function () {
+            return this.map((item) => item.get("id"));
         },
 
         /** Get jobs that are not ready
          *  @returns array of content models
          */
-        notReady: function() {
-            return this.filter(job => !job.inReadyState());
+        notReady: function () {
+            return this.filter((job) => !job.inReadyState());
         },
 
         /** return true if any jobs don't have details */
-        haveDetails: function() {
-            return this.all(job => job.hasDetails());
+        haveDetails: function () {
+            return this.all((job) => job.hasDetails());
         },
 
         // ........................................................................ ajax
         /** fetches all details for each job in the collection using a queue */
-        queueDetailFetching: function() {
+        queueDetailFetching: function () {
             var collection = this;
 
-            var queue = new AJAX_QUEUE.AjaxQueue(this.map(job => () => job.fetch({ silent: true })));
+            var queue = new AJAX_QUEUE.AjaxQueue(this.map((job) => () => job.fetch({ silent: true })));
 
             queue.done(() => {
                 collection.trigger("details-loaded");
@@ -167,21 +167,21 @@ var JobCollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(
 
         // ........................................................................ sorting/filtering
         /** return a new collection of jobs whose attributes contain the substring matchesWhat */
-        matches: function(matchesWhat) {
-            return this.filter(job => job.matches(matchesWhat));
+        matches: function (matchesWhat) {
+            return this.filter((job) => job.matches(matchesWhat));
         },
 
         // ........................................................................ misc
         /** String representation. */
-        toString: function() {
+        toString: function () {
             return ["JobCollection(", this.length, ")"].join("");
-        }
+        },
 
         //----------------------------------------------------------------------------- class vars
     },
     {
         /** class level fn for fetching the job details for all jobs in a history */
-        fromHistory: function(historyId) {
+        fromHistory: function (historyId) {
             console.debug(this);
             var Collection = this;
             var collection = new Collection([]);
@@ -189,12 +189,12 @@ var JobCollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(
                 window.queue = collection.queueDetailFetching();
             });
             return collection;
-        }
+        },
     }
 );
 
 //=============================================================================
 export default {
     Job: Job,
-    JobCollection: JobCollection
+    JobCollection: JobCollection,
 };
diff --git a/client/galaxy/scripts/mvc/lazy/lazy-limited.js b/client/galaxy/scripts/mvc/lazy/lazy-limited.js
index 03b5c2249de1..76385e420a9c 100644
--- a/client/galaxy/scripts/mvc/lazy/lazy-limited.js
+++ b/client/galaxy/scripts/mvc/lazy/lazy-limited.js
@@ -4,7 +4,7 @@ import _ from "underscore";
 import Backbone from "backbone";
 
 export default Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.$container = options.$container;
         this.collection = options.collection;
         this.new_content = options.new_content;
@@ -21,15 +21,15 @@ export default Backbone.View.extend({
     },
 
     /** Checks if the limit has been reached */
-    _done: function() {
+    _done: function () {
         var done = _.size(this.content_list) >= this.max;
         this.$message[done ? "show" : "hide"]();
         return done;
     },
 
     /** Remove all content */
-    _reset: function() {
-        _.each(this.content_list, content => {
+    _reset: function () {
+        _.each(this.content_list, (content) => {
             content.remove();
         });
         this.content_list = {};
@@ -37,7 +37,7 @@ export default Backbone.View.extend({
     },
 
     /** Remove content */
-    _remove: function(model) {
+    _remove: function (model) {
         var model_id = model.id;
         var content = this.content_list[model_id];
         if (content) {
@@ -48,7 +48,7 @@ export default Backbone.View.extend({
     },
 
     /** Refreshes container content by adding new views if visible */
-    _refresh: function() {
+    _refresh: function () {
         if (!this._done()) {
             for (var i in this.collection.models) {
                 var model = this.collection.models[i];
@@ -62,5 +62,5 @@ export default Backbone.View.extend({
                 }
             }
         }
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/library/library-dataset-view.js b/client/galaxy/scripts/mvc/library/library-dataset-view.js
index 58d6edb26f50..f066e00ace8e 100644
--- a/client/galaxy/scripts/mvc/library/library-dataset-view.js
+++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js
@@ -18,7 +18,7 @@ var LibraryDatasetView = Backbone.View.extend({
     options: {},
 
     defaults: {
-        edit_mode: false
+        edit_mode: false,
     },
 
     events: {
@@ -31,7 +31,7 @@ var LibraryDatasetView = Backbone.View.extend({
         "click .remove-restrictions": "removeDatasetRestrictions",
         "click .toolbtn_save_permissions": "savePermissions",
         "click .toolbtn_save_modifications": "saveModifications",
-        "click .toolbtn_detect_datatype": "detectDatatype"
+        "click .toolbtn_detect_datatype": "detectDatatype",
     },
 
     // genome select
@@ -53,13 +53,13 @@ var LibraryDatasetView = Backbone.View.extend({
             " it most likely means that it has some format problems (e.g., different" +
             " number of columns on different rows). You can still coerce the system" +
             " to set your data to the format you think it should be." +
-            " You can also upload compressed files, which will automatically be decompressed."
+            " You can also upload compressed files, which will automatically be decompressed.",
     },
 
     // genomes
     list_genomes: [],
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = _.extend(this.options, options);
         this.fetchExtAndGenomes();
         if (this.options.id) {
@@ -67,15 +67,15 @@ var LibraryDatasetView = Backbone.View.extend({
         }
     },
 
-    fetchDataset: function(options) {
+    fetchDataset: function (options) {
         const Galaxy = getGalaxyInstance();
         this.options = _.extend(this.options, options);
         this.model = new mod_library_model.Item({
-            id: this.options.id
+            id: this.options.id,
         });
         var self = this;
         this.model.fetch({
-            success: function() {
+            success: function () {
                 if (self.options.show_permissions) {
                     self.showPermissions();
                 } else if (self.options.show_version) {
@@ -84,25 +84,25 @@ var LibraryDatasetView = Backbone.View.extend({
                     self.render();
                 }
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(`${response.responseJSON.err_msg} Click this to go back.`, "", {
-                        onclick: function() {
+                        onclick: function () {
                             Galaxy.libraries.library_router.back();
-                        }
+                        },
                     });
                 } else {
                     Toast.error("An error occurred. Click this to go back.", "", {
-                        onclick: function() {
+                        onclick: function () {
                             Galaxy.libraries.library_router.back();
-                        }
+                        },
                     });
                 }
-            }
+            },
         });
     },
 
-    render: function(options) {
+    render: function (options) {
         this.options = _.extend(this.options, options);
         $(".tooltip").remove();
         var template = this.templateDataset();
@@ -125,7 +125,7 @@ var LibraryDatasetView = Backbone.View.extend({
         }
     },
 
-    fetchVersion: function(options) {
+    fetchVersion: function (options) {
         this.options = _.extend(this.options, options);
         var self = this;
         if (!this.options.ldda_id) {
@@ -133,58 +133,58 @@ var LibraryDatasetView = Backbone.View.extend({
             Toast.error("Library dataset version requested but no id provided.");
         } else {
             this.ldda = new mod_library_model.Ldda({
-                id: this.options.ldda_id
+                id: this.options.ldda_id,
             });
             this.ldda.url = `${this.ldda.urlRoot + this.model.id}/versions/${this.ldda.id}`;
             this.ldda.fetch({
-                success: function() {
+                success: function () {
                     self.renderVersion();
                 },
-                error: function(model, response) {
+                error: function (model, response) {
                     if (typeof response.responseJSON !== "undefined") {
                         Toast.error(response.responseJSON.err_msg);
                     } else {
                         Toast.error("An error occurred.");
                     }
-                }
+                },
             });
         }
     },
 
-    renderVersion: function() {
+    renderVersion: function () {
         $(".tooltip").remove();
         var template = this.templateVersion();
         this.$el.html(template({ item: this.model, ldda: this.ldda }));
         $(".peek").html(this.ldda.get("peek"));
     },
 
-    enableModification: function() {
+    enableModification: function () {
         $(".tooltip").remove();
         var template = this.templateModifyDataset();
         this.$el.html(template({ item: this.model }));
         this.renderSelectBoxes({
             genome_build: this.model.get("genome_build"),
-            file_ext: this.model.get("file_ext")
+            file_ext: this.model.get("file_ext"),
         });
         $(".peek").html(this.model.get("peek"));
         $('#center [data-toggle="tooltip"]').tooltip({ trigger: "hover" });
         this._mountNametags("listener");
     },
 
-    downloadDataset: function() {
+    downloadDataset: function () {
         var url = `${getAppRoot()}api/libraries/datasets/download/uncompressed`;
         var data = { ld_ids: this.id };
         this.processDownload(url, data);
     },
 
-    processDownload: function(url, data, method) {
+    processDownload: function (url, data, method) {
         //url and data options required
         if (url && data) {
             //data can be string of parameters or array/object
             data = typeof data == "string" ? data : $.param(data);
             //split params into form inputs
             var inputs = "";
-            $.each(data.split("&"), function() {
+            $.each(data.split("&"), function () {
                 var pair = this.split("=");
                 inputs += `<input type="hidden" name="${pair[0]}" value="${pair[1]}" />`;
             });
@@ -198,8 +198,8 @@ var LibraryDatasetView = Backbone.View.extend({
         }
     },
 
-    importIntoHistory: function() {
-        this.refreshUserHistoriesList(self => {
+    importIntoHistory: function () {
+        this.refreshUserHistoriesList((self) => {
             const Galaxy = getGalaxyInstance();
             var template = self.templateBulkImportInModal();
             self.modal = Galaxy.modal;
@@ -208,51 +208,51 @@ var LibraryDatasetView = Backbone.View.extend({
                 title: _l("Import into History"),
                 body: template({ histories: self.histories.models }),
                 buttons: {
-                    Import: function() {
+                    Import: function () {
                         self.importCurrentIntoHistory();
                     },
-                    Close: function() {
+                    Close: function () {
                         Galaxy.modal.hide();
-                    }
-                }
+                    },
+                },
             });
         });
     },
 
-    refreshUserHistoriesList: function(callback) {
+    refreshUserHistoriesList: function (callback) {
         var self = this;
         this.histories = new mod_library_model.GalaxyHistories();
         this.histories.fetch({
-            success: function(histories) {
+            success: function (histories) {
                 if (histories.length === 0) {
                     Toast.warning("You have to create history first. Click this to do so.", "", {
-                        onclick: function() {
+                        onclick: function () {
                             window.location = getAppRoot();
-                        }
+                        },
                     });
                 } else {
                     callback(self);
                 }
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(response.responseJSON.err_msg);
                 } else {
                     Toast.error("An error occurred.");
                 }
-            }
+            },
         });
     },
 
-    importCurrentIntoHistory: function() {
+    importCurrentIntoHistory: function () {
         this.modal.disableButton("Import");
         var new_history_name = this.modal.$("input[name=history_name]").val();
         var self = this;
         if (new_history_name !== "") {
             $.post(`${getAppRoot()}api/histories`, {
-                name: new_history_name
+                name: new_history_name,
             })
-                .done(new_history => {
+                .done((new_history) => {
                     self.processImportToHistory(new_history.id);
                 })
                 .fail((xhr, status, error) => {
@@ -262,15 +262,13 @@ var LibraryDatasetView = Backbone.View.extend({
                     self.modal.enableButton("Import");
                 });
         } else {
-            var history_id = $(this.modal.$el)
-                .find("select[name=dataset_import_single] option:selected")
-                .val();
+            var history_id = $(this.modal.$el).find("select[name=dataset_import_single] option:selected").val();
             this.processImportToHistory(history_id);
             this.modal.enableButton("Import");
         }
     },
 
-    processImportToHistory: function(history_id) {
+    processImportToHistory: function (history_id) {
         const Galaxy = getGalaxyInstance();
         var historyItem = new mod_library_model.HistoryItem();
         historyItem.url = `${historyItem.urlRoot + history_id}/contents`;
@@ -281,26 +279,26 @@ var LibraryDatasetView = Backbone.View.extend({
         historyItem.save(
             { content: this.id, source: "library" },
             {
-                success: function() {
+                success: function () {
                     Galaxy.modal.hide();
                     Toast.success("Dataset imported. Click this to start analyzing it.", "", {
-                        onclick: function() {
+                        onclick: function () {
                             window.location = getAppRoot();
-                        }
+                        },
                     });
                 },
-                error: function(model, response) {
+                error: function (model, response) {
                     if (typeof response.responseJSON !== "undefined") {
                         Toast.error(`Dataset not imported. ${response.responseJSON.err_msg}`);
                     } else {
                         Toast.error("An error occurred. Dataset not imported. Please try again.");
                     }
-                }
+                },
             }
         );
     },
 
-    showPermissions: function(options) {
+    showPermissions: function (options) {
         const Galaxy = getGalaxyInstance();
         var template = this.templateDatasetPermissions();
         var self = this;
@@ -316,14 +314,14 @@ var LibraryDatasetView = Backbone.View.extend({
         this.$el.html(
             template({
                 item: this.model,
-                is_admin: Galaxy.config.is_admin_user
+                is_admin: Galaxy.config.is_admin_user,
             })
         );
         $.get(`${getAppRoot()}api/libraries/datasets/${self.id}/permissions?scope=current`)
-            .done(fetched_permissions => {
+            .done((fetched_permissions) => {
                 self.prepareSelectBoxes({
                     fetched_permissions: fetched_permissions,
-                    is_admin: Galaxy.config.is_admin_user
+                    is_admin: Galaxy.config.is_admin_user,
                 });
             })
             .fail(() => {
@@ -333,7 +331,7 @@ var LibraryDatasetView = Backbone.View.extend({
         $("#center").css("overflow", "auto");
     },
 
-    _serializeRoles: function(role_list) {
+    _serializeRoles: function (role_list) {
         var selected_roles = [];
         for (var i = 0; i < role_list.length; i++) {
             // Replace the : and , in role's name since these are select2 separators for initialData
@@ -342,29 +340,29 @@ var LibraryDatasetView = Backbone.View.extend({
         return selected_roles;
     },
 
-    prepareSelectBoxes: function(options) {
+    prepareSelectBoxes: function (options) {
         this.options = _.extend(this.options, options);
         this.accessSelectObject = new mod_select.View(
             this._generate_select_options({
                 selector: "access_perm",
-                initialData: this._serializeRoles(this.options.fetched_permissions.access_dataset_roles)
+                initialData: this._serializeRoles(this.options.fetched_permissions.access_dataset_roles),
             })
         );
         this.modifySelectObject = new mod_select.View(
             this._generate_select_options({
                 selector: "modify_perm",
-                initialData: this._serializeRoles(this.options.fetched_permissions.modify_item_roles)
+                initialData: this._serializeRoles(this.options.fetched_permissions.modify_item_roles),
             })
         );
         this.manageSelectObject = new mod_select.View(
             this._generate_select_options({
                 selector: "manage_perm",
-                initialData: this._serializeRoles(this.options.fetched_permissions.manage_dataset_roles)
+                initialData: this._serializeRoles(this.options.fetched_permissions.manage_dataset_roles),
             })
         );
     },
 
-    _generate_select_options: function(options) {
+    _generate_select_options: function (options) {
         var select_options = {
             minimumInputLength: 0,
             multiple: true,
@@ -375,21 +373,21 @@ var LibraryDatasetView = Backbone.View.extend({
             formatSelection: function roleFormatSelection(role) {
                 return role.name;
             },
-            initSelection: function(element, callback) {
+            initSelection: function (element, callback) {
                 // the input tag has a value attribute preloaded that points to a preselected role's id
                 // this function resolves that id attribute to an object that select2 can render
                 // using its formatResult renderer - that way the role name is shown preselected
                 var data = [];
-                $(element.val().split(",")).each(function() {
+                $(element.val().split(",")).each(function () {
                     var item = this.split(":");
                     data.push({
                         id: item[0],
-                        name: item[1]
+                        name: item[1],
                     });
                 });
                 callback(data);
             },
-            dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller
+            dropdownCssClass: "bigdrop", // apply css that makes the dropdown taller
         };
         select_options.container = this.$el.find(`#${options.selector}`);
         select_options.css = options.selector;
@@ -398,24 +396,24 @@ var LibraryDatasetView = Backbone.View.extend({
             url: `${getAppRoot()}api/libraries/datasets/${this.id}/permissions?scope=available`,
             dataType: "json",
             quietMillis: 100,
-            data: function(term, page) {
+            data: function (term, page) {
                 // page is the one-based page number tracked by Select2
                 return {
                     q: term, //search term
                     page_limit: 10, // page size, should be same as used in 'more' variable below
-                    page: page // page number
+                    page: page, // page number
                 };
             },
-            results: function(data, page) {
+            results: function (data, page) {
                 var more = page * 10 < data.total; // whether or not there are more results available
                 // notice we return the value of more so Select2 knows if more results can be loaded
                 return { results: data.roles, more: more };
-            }
+            },
         };
         return select_options;
     },
 
-    detectDatatype: function(options) {
+    detectDatatype: function (options) {
         const ld = this.model;
         ld.set("file_ext", "auto");
         this._submitModification(ld);
@@ -424,7 +422,7 @@ var LibraryDatasetView = Backbone.View.extend({
     /**
      * Save the changes made to the library dataset.
      */
-    saveModifications: function(options) {
+    saveModifications: function (options) {
         var is_changed = false;
         var ld = this.model;
         var new_name = this.$el.find(".input_dataset_name").val();
@@ -468,21 +466,21 @@ var LibraryDatasetView = Backbone.View.extend({
     _submitModification(library_dataset) {
         library_dataset.save(null, {
             patch: true,
-            success: library_dataset => {
+            success: (library_dataset) => {
                 this.render();
                 Toast.success("Changes to library dataset saved.");
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(response.responseJSON.err_msg);
                 } else {
                     Toast.error("An error occurred while attempting to update the library dataset.");
                 }
-            }
+            },
         });
     },
 
-    copyToClipboard: function(e) {
+    copyToClipboard: function (e) {
         e.preventDefault();
         var href = Backbone.history.location.href;
         if (href.lastIndexOf("/permissions") !== -1) {
@@ -491,13 +489,13 @@ var LibraryDatasetView = Backbone.View.extend({
         window.prompt("Copy to clipboard: Ctrl+C, Enter", href);
     },
 
-    makeDatasetPrivate: function() {
+    makeDatasetPrivate: function () {
         var self = this;
         $.post(`${getAppRoot()}api/libraries/datasets/${self.id}/permissions?action=make_private`)
-            .done(fetched_permissions => {
+            .done((fetched_permissions) => {
                 self.model.set({ is_unrestricted: false });
                 self.showPermissions({
-                    fetched_permissions: fetched_permissions
+                    fetched_permissions: fetched_permissions,
                 });
                 Toast.success("The dataset is now private to you.");
             })
@@ -506,13 +504,13 @@ var LibraryDatasetView = Backbone.View.extend({
             });
     },
 
-    removeDatasetRestrictions: function() {
+    removeDatasetRestrictions: function () {
         var self = this;
         $.post(`${getAppRoot()}api/libraries/datasets/${self.id}/permissions?action=remove_restrictions`)
-            .done(fetched_permissions => {
+            .done((fetched_permissions) => {
                 self.model.set({ is_unrestricted: true });
                 self.showPermissions({
-                    fetched_permissions: fetched_permissions
+                    fetched_permissions: fetched_permissions,
                 });
                 Toast.success("Access to this dataset is now unrestricted.");
             })
@@ -524,7 +522,7 @@ var LibraryDatasetView = Backbone.View.extend({
     /**
      * Extract the role ids from Select2 elements's 'data'
      */
-    _extractIds: function(roles_list) {
+    _extractIds: function (roles_list) {
         var ids_list = [];
         for (var i = roles_list.length - 1; i >= 0; i--) {
             ids_list.push(roles_list[i].id);
@@ -535,7 +533,7 @@ var LibraryDatasetView = Backbone.View.extend({
     /**
      * Save the permissions for roles entered in the select boxes.
      */
-    savePermissions: function(event) {
+    savePermissions: function (event) {
         var self = this;
         var access_ids = this._extractIds(this.accessSelectObject.$el.select2("data"));
         var manage_ids = this._extractIds(this.manageSelectObject.$el.select2("data"));
@@ -543,11 +541,11 @@ var LibraryDatasetView = Backbone.View.extend({
         $.post(`${getAppRoot()}api/libraries/datasets/${self.id}/permissions?action=set_permissions`, {
             "access_ids[]": access_ids,
             "manage_ids[]": manage_ids,
-            "modify_ids[]": modify_ids
+            "modify_ids[]": modify_ids,
         })
-            .done(fetched_permissions => {
+            .done((fetched_permissions) => {
                 self.showPermissions({
-                    fetched_permissions: fetched_permissions
+                    fetched_permissions: fetched_permissions,
                 });
                 Toast.success("Permissions saved.");
             })
@@ -560,42 +558,42 @@ var LibraryDatasetView = Backbone.View.extend({
      * If needed request all extensions and/or genomes from Galaxy
      * and save them in sorted arrays.
      */
-    fetchExtAndGenomes: function() {
+    fetchExtAndGenomes: function () {
         var self = this;
         if (this.list_genomes.length == 0) {
             mod_utils.get({
                 url: `${getAppRoot()}api/datatypes?extension_only=False`,
-                success: function(datatypes) {
+                success: function (datatypes) {
                     for (var key in datatypes) {
                         self.list_extensions.push({
                             id: datatypes[key].extension,
                             text: datatypes[key].extension,
                             description: datatypes[key].description,
-                            description_url: datatypes[key].description_url
+                            description_url: datatypes[key].description_url,
                         });
                     }
                     self.list_extensions.sort((a, b) => (a.id > b.id ? 1 : a.id < b.id ? -1 : 0));
                     self.list_extensions.unshift(self.auto);
-                }
+                },
             });
         }
         if (this.list_extensions.length == 0) {
             mod_utils.get({
                 url: `${getAppRoot()}api/genomes`,
-                success: function(genomes) {
+                success: function (genomes) {
                     for (var key in genomes) {
                         self.list_genomes.push({
                             id: genomes[key][1],
-                            text: genomes[key][0]
+                            text: genomes[key][0],
                         });
                     }
                     self.list_genomes.sort((a, b) => (a.id > b.id ? 1 : a.id < b.id ? -1 : 0));
-                }
+                },
             });
         }
     },
 
-    renderSelectBoxes: function(options) {
+    renderSelectBoxes: function (options) {
         // This won't work properly unlesss we already have the data fetched.
         // See this.fetchExtAndGenomes()
         // TODO switch to common resources:
@@ -615,17 +613,17 @@ var LibraryDatasetView = Backbone.View.extend({
             css: "dataset-genome-select",
             data: self.list_genomes,
             container: self.$el.find("#dataset_genome_select"),
-            value: current_genome
+            value: current_genome,
         });
         this.select_extension = new mod_select.View({
             css: "dataset-extension-select",
             data: self.list_extensions,
             container: self.$el.find("#dataset_extension_select"),
-            value: current_ext
+            value: current_ext,
         });
     },
 
-    templateDataset: function() {
+    templateDataset: function () {
         return _.template(
             `<!-- CONTAINER START -->
             <div class="library_style_container">
@@ -838,7 +836,7 @@ var LibraryDatasetView = Backbone.View.extend({
         );
     },
 
-    templateVersion: function() {
+    templateVersion: function () {
         return _.template(
             `<!-- CONTAINER START -->
             <div class="library_style_container">
@@ -980,7 +978,7 @@ var LibraryDatasetView = Backbone.View.extend({
         );
     },
 
-    templateModifyDataset: function() {
+    templateModifyDataset: function () {
         return _.template(
             `<!-- CONTAINER START -->
             <div class="library_style_container">
@@ -1112,7 +1110,7 @@ var LibraryDatasetView = Backbone.View.extend({
         );
     },
 
-    templateDatasetPermissions: function() {
+    templateDatasetPermissions: function () {
         return _.template(
             `<!-- CONTAINER START -->
             <div class="library_style_container">
@@ -1206,7 +1204,7 @@ var LibraryDatasetView = Backbone.View.extend({
         );
     },
 
-    templateBulkImportInModal: function() {
+    templateBulkImportInModal: function () {
         return _.template(
             `<div>
                 <div class="library-modal-item">
@@ -1226,9 +1224,9 @@ var LibraryDatasetView = Backbone.View.extend({
                 </div>
             </div>`
         );
-    }
+    },
 });
 
 export default {
-    LibraryDatasetView: LibraryDatasetView
+    LibraryDatasetView: LibraryDatasetView,
 };
diff --git a/client/galaxy/scripts/mvc/library/library-folder-view.js b/client/galaxy/scripts/mvc/library/library-folder-view.js
index d94239dd9a9e..82464f44d5a4 100644
--- a/client/galaxy/scripts/mvc/library/library-folder-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folder-view.js
@@ -15,48 +15,48 @@ var FolderView = Backbone.View.extend({
     options: {},
 
     events: {
-        "click .toolbtn_save_permissions": "savePermissions"
+        "click .toolbtn_save_permissions": "savePermissions",
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = _.extend(this.options, options);
         if (this.options.id) {
             this.fetchFolder();
         }
     },
 
-    fetchFolder: function(options) {
+    fetchFolder: function (options) {
         const Galaxy = getGalaxyInstance();
         this.options = _.extend(this.options, options);
         this.model = new mod_library_model.FolderAsModel({
-            id: this.options.id
+            id: this.options.id,
         });
         var that = this;
         this.model.fetch({
-            success: function() {
+            success: function () {
                 if (that.options.show_permissions) {
                     that.showPermissions();
                 }
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(`${response.responseJSON.err_msg} Click this to go back.`, "", {
-                        onclick: function() {
+                        onclick: function () {
                             Galaxy.libraries.library_router.back();
-                        }
+                        },
                     });
                 } else {
                     Toast.error("An error occurred. Click this to go back.", "", {
-                        onclick: function() {
+                        onclick: function () {
                             Galaxy.libraries.library_router.back();
-                        }
+                        },
                     });
                 }
-            }
+            },
         });
     },
 
-    showPermissions: function(options) {
+    showPermissions: function (options) {
         const Galaxy = getGalaxyInstance();
         this.options = _.extend(this.options, options);
         $(".tooltip").remove();
@@ -70,9 +70,9 @@ var FolderView = Backbone.View.extend({
 
         var self = this;
         $.get(`${getAppRoot()}api/folders/${self.id}/permissions?scope=current`)
-            .done(fetched_permissions => {
+            .done((fetched_permissions) => {
                 self.prepareSelectBoxes({
-                    fetched_permissions: fetched_permissions
+                    fetched_permissions: fetched_permissions,
                 });
             })
             .fail(() => {
@@ -84,7 +84,7 @@ var FolderView = Backbone.View.extend({
         $("#center").css("overflow", "auto");
     },
 
-    _serializeRoles: function(role_list) {
+    _serializeRoles: function (role_list) {
         var selected_roles = [];
         for (var i = 0; i < role_list.length; i++) {
             selected_roles.push(`${role_list[i][1]}:${role_list[i][0]}`);
@@ -92,7 +92,7 @@ var FolderView = Backbone.View.extend({
         return selected_roles;
     },
 
-    prepareSelectBoxes: function(options) {
+    prepareSelectBoxes: function (options) {
         this.options = _.extend(this.options, options);
         var fetched_permissions = this.options.fetched_permissions;
         var self = this;
@@ -112,7 +112,7 @@ var FolderView = Backbone.View.extend({
         );
     },
 
-    _createSelectOptions: function(self, id, init_data) {
+    _createSelectOptions: function (self, id, init_data) {
         var select_options = {
             minimumInputLength: 0,
             css: id,
@@ -123,19 +123,19 @@ var FolderView = Backbone.View.extend({
                 url: `${getAppRoot()}api/folders/${self.id}/permissions?scope=available`,
                 dataType: "json",
                 quietMillis: 100,
-                data: function(term, page) {
+                data: function (term, page) {
                     // page is the one-based page number tracked by Select2
                     return {
                         q: term, //search term
                         page_limit: 10, // page size
-                        page: page // page number
+                        page: page, // page number
                     };
                 },
-                results: function(data, page) {
+                results: function (data, page) {
                     var more = page * 10 < data.total; // whether or not there are more results available
                     // notice we return the value of more so Select2 knows if more results can be loaded
                     return { results: data.roles, more: more };
-                }
+                },
             },
             formatResult: function roleFormatResult(role) {
                 return `${role.name} type: ${role.type}`;
@@ -144,22 +144,22 @@ var FolderView = Backbone.View.extend({
             formatSelection: function roleFormatSelection(role) {
                 return role.name;
             },
-            initSelection: function(element, callback) {
+            initSelection: function (element, callback) {
                 // the input tag has a value attribute preloaded that points to a preselected role's id
                 // this function resolves that id attribute to an object that select2 can render
                 // using its formatResult renderer - that way the role name is shown preselected
                 var data = [];
-                $(element.val().split(",")).each(function() {
+                $(element.val().split(",")).each(function () {
                     var item = this.split(":");
                     data.push({
                         id: item[0],
-                        name: item[1]
+                        name: item[1],
                     });
                 });
                 callback(data);
             },
             initialData: init_data.join(","),
-            dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller
+            dropdownCssClass: "bigdrop", // apply css that makes the dropdown taller
         };
 
         return select_options;
@@ -168,7 +168,7 @@ var FolderView = Backbone.View.extend({
     /**
      * Extract the role ids from Select2 elements's 'data'
      */
-    _extractIds: function(roles_list) {
+    _extractIds: function (roles_list) {
         var ids_list = [];
         for (var i = roles_list.length - 1; i >= 0; i--) {
             ids_list.push(roles_list[i].id);
@@ -179,7 +179,7 @@ var FolderView = Backbone.View.extend({
     /**
      * Save the permissions for roles entered in the select boxes.
      */
-    savePermissions: function(event) {
+    savePermissions: function (event) {
         var self = this;
         var add_ids = this._extractIds(this.addSelectObject.$el.select2("data"));
         var manage_ids = this._extractIds(this.manageSelectObject.$el.select2("data"));
@@ -187,11 +187,11 @@ var FolderView = Backbone.View.extend({
         $.post(`${getAppRoot()}api/folders/${self.id}/permissions?action=set_permissions`, {
             "add_ids[]": add_ids,
             "manage_ids[]": manage_ids,
-            "modify_ids[]": modify_ids
+            "modify_ids[]": modify_ids,
         })
-            .done(fetched_permissions => {
+            .done((fetched_permissions) => {
                 self.showPermissions({
-                    fetched_permissions: fetched_permissions
+                    fetched_permissions: fetched_permissions,
                 });
                 Toast.success("Permissions saved.");
             })
@@ -200,7 +200,7 @@ var FolderView = Backbone.View.extend({
             });
     },
 
-    templateFolderPermissions: function() {
+    templateFolderPermissions: function () {
         return _.template(
             `<div class="library_style_container">
                 <div>
@@ -255,9 +255,9 @@ var FolderView = Backbone.View.extend({
                 </div>
             </div>`
         );
-    }
+    },
 });
 
 export default {
-    FolderView: FolderView
+    FolderView: FolderView,
 };
diff --git a/client/galaxy/scripts/mvc/library/library-folderlist-view.js b/client/galaxy/scripts/mvc/library/library-folderlist-view.js
index 0513c94c3991..481c68bdf0cd 100644
--- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js
@@ -28,7 +28,7 @@ var FolderListView = Backbone.View.extend({
         "click .sort-folder-message": "sortColumnClicked",
         "click .sort-folder-update_time": "sortColumnClicked",
         "click .sort-folder-raw_size": "sortColumnClicked",
-        "click .sort-folder-state": "sortColumnClicked"
+        "click .sort-folder-state": "sortColumnClicked",
     },
 
     collection: null,
@@ -36,14 +36,14 @@ var FolderListView = Backbone.View.extend({
     defaults: {
         include_deleted: false,
         page_count: null,
-        show_page: null
+        show_page: null,
     },
 
     /**
      * Initialize and fetch the folder from the server.
      * @param  {object} options an object with options
      */
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = _.defaults(this.options || {}, this.defaults, options);
         this.modal = null;
         // map of folder item ids to item views = cache
@@ -60,12 +60,12 @@ var FolderListView = Backbone.View.extend({
         this.fetchFolder();
     },
 
-    fetchFolder: function(options = {}) {
+    fetchFolder: function (options = {}) {
         this.options.include_deleted = options.include_deleted;
         var self = this;
 
         this.folderContainer = new mod_library_model.FolderContainer({
-            id: this.options.id
+            id: this.options.id,
         });
         this.folderContainer.url = `${this.folderContainer.attributes.urlRoot + this.options.id}/contents`;
 
@@ -73,30 +73,30 @@ var FolderListView = Backbone.View.extend({
             this.folderContainer.url = `${this.folderContainer.url}?include_deleted=true`;
         }
         this.folderContainer.fetch({
-            success: function(folder_container) {
+            success: function (folder_container) {
                 self.folder_container = folder_container;
                 self.render();
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 const Galaxy = getGalaxyInstance();
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(`${response.responseJSON.err_msg} Click this to go back.`, "", {
-                        onclick: function() {
+                        onclick: function () {
                             Galaxy.libraries.library_router.back();
-                        }
+                        },
                     });
                 } else {
                     Toast.error("An error occurred. Click this to go back.", "", {
-                        onclick: function() {
+                        onclick: function () {
                             Galaxy.libraries.library_router.back();
-                        }
+                        },
                     });
                 }
-            }
+            },
         });
     },
 
-    render: function(options) {
+    render: function (options) {
         this.options = _.extend(this.options, options);
         var template = this.templateFolder();
         $(".tooltip").hide();
@@ -117,14 +117,14 @@ var FolderListView = Backbone.View.extend({
                 parent_library_id: this.folderContainer.attributes.metadata.parent_library_id,
                 id: this.options.id,
                 upper_folder_id: upper_folder_id,
-                order: this.current_sort_order
+                order: this.current_sort_order,
             })
         );
 
         // when dataset_id is present render its details too
         if (this.options.dataset_id) {
             var row = _.findWhere(self.rowViews, {
-                id: this.options.dataset_id
+                id: this.options.dataset_id,
             });
             if (row) {
                 row.showDatasetDetails();
@@ -141,7 +141,7 @@ var FolderListView = Backbone.View.extend({
         $("#center").css("overflow", "auto");
     },
 
-    paginate: function(options) {
+    paginate: function (options) {
         const Galaxy = getGalaxyInstance();
         this.options = _.extend(this.options, options);
 
@@ -169,7 +169,7 @@ var FolderListView = Backbone.View.extend({
         this.collection.reset(items_to_render);
     },
 
-    rePaint: function(options) {
+    rePaint: function (options) {
         this.options = _.extend(this.options, options);
         this.removeAllRows();
         this.renderAll();
@@ -181,11 +181,11 @@ var FolderListView = Backbone.View.extend({
      * @param {array of Item or FolderAsModel} array of models that should
      *  be added to the view's collection.
      */
-    addAll: function(models) {
+    addAll: function (models) {
         const Galaxy = getGalaxyInstance();
-        _.each(models, model => {
+        _.each(models, (model) => {
             Galaxy.libraries.folderListView.collection.add(model, {
-                current_sort_order: false
+                current_sort_order: false,
             });
         });
         $('#center [data-toggle="tooltip"]').tooltip({ trigger: "hover" });
@@ -198,7 +198,7 @@ var FolderListView = Backbone.View.extend({
      * to ensure that the folder toolbar will show proper options
      * and that event will be bound on all subviews.
      */
-    postRender: function() {
+    postRender: function () {
         const Galaxy = getGalaxyInstance();
         var fetched_metadata = this.folderContainer.attributes.metadata;
         fetched_metadata.contains_file_or_folder =
@@ -211,9 +211,9 @@ var FolderListView = Backbone.View.extend({
      * Iterates this view's collection and calls the render
      * function for each. Also binds the hover behavior.
      */
-    renderAll: function() {
+    renderAll: function () {
         var self = this;
-        _.each(this.collection.models.reverse(), model => {
+        _.each(this.collection.models.reverse(), (model) => {
             self.renderOne(model);
         });
         this.postRender();
@@ -223,14 +223,14 @@ var FolderListView = Backbone.View.extend({
      * Creates a view for the given model and adds it to the folder view.
      * @param {Item or FolderAsModel} model of the view that will be rendered
      */
-    renderOne: function(model) {
+    renderOne: function (model) {
         this.options.contains_file_or_folder = true;
         //if (model.get('type') !== 'folder'){
         // model.set('readable_size', this.size_to_string(model.get('file_size')));
         //}
         model.set("folder_id", this.id);
         var rowView = new mod_library_folderrow_view.FolderRowView({
-            model: model
+            model: model,
         });
 
         // save new rowView to cache
@@ -243,10 +243,10 @@ var FolderListView = Backbone.View.extend({
      * Remove the view of the given model from the DOM.
      * @param {Item or FolderAsModel} model of the view that will be removed
      */
-    removeOne: function(model) {
+    removeOne: function (model) {
         this.$el
             .find("tr")
-            .filter(function() {
+            .filter(function () {
                 return $(this).data("id") && $(this).data("id") === model.id;
             })
             .remove();
@@ -255,12 +255,12 @@ var FolderListView = Backbone.View.extend({
     /**
      * Remove all dataset and folder row elements from the DOM.
      */
-    removeAllRows: function() {
+    removeAllRows: function () {
         $(".library-row").remove();
     },
 
     /** Checks whether the list is empty and adds/removes the message */
-    checkEmptiness: function() {
+    checkEmptiness: function () {
         if (this.$el.find(".dataset_row").length === 0 && this.$el.find(".folder_row").length === 0) {
             this.$el.find(".empty-folder-message").show();
         } else {
@@ -268,7 +268,7 @@ var FolderListView = Backbone.View.extend({
         }
     },
 
-    sortColumnClicked: function(event) {
+    sortColumnClicked: function (event) {
         event.preventDefault();
         this.current_sort_order = this.current_sort_order === "asc" ? "desc" : "asc";
         this.current_sort_key = event.currentTarget.className.replace("sort-folder-", "");
@@ -282,7 +282,7 @@ var FolderListView = Backbone.View.extend({
      * the result. Render all visible folder items otherwise.
      * @param  {string} search_term string to search for
      */
-    searchFolder: function(search_term) {
+    searchFolder: function (search_term) {
         const trimmed_term = $.trim(search_term);
         if (trimmed_term !== "") {
             const result_collection = this.folder_container.search(search_term);
@@ -296,11 +296,11 @@ var FolderListView = Backbone.View.extend({
      * User clicked the checkbox in the table heading
      * @param  {context} event
      */
-    selectAll: function(event) {
+    selectAll: function (event) {
         var selected = event.target.checked;
         var self = this;
         // Iterate each checkbox
-        $(":checkbox", "#folder_list_body").each(function() {
+        $(":checkbox", "#folder_list_body").each(function () {
             this.checked = selected;
             var $row = $(this).closest("tr");
             // Change color of selected/unselected
@@ -316,7 +316,7 @@ var FolderListView = Backbone.View.extend({
      * Check checkbox if user clicks on the whole row or
      *  on the checkbox itself
      */
-    selectClickedRow: function(event) {
+    selectClickedRow: function (event) {
         var checkbox = "";
         var $row;
         var source;
@@ -345,18 +345,16 @@ var FolderListView = Backbone.View.extend({
         }
     },
 
-    makeDarkRow: function($row) {
+    makeDarkRow: function ($row) {
         $row.addClass("table-primary");
     },
 
-    makeWhiteRow: function($row) {
+    makeWhiteRow: function ($row) {
         $row.removeClass("table-primary");
     },
 
-    renderSortIcon: function() {
-        $('[class*="sort-icon"]')
-            .removeClass("fa-sort-alpha-desc")
-            .removeClass("fa-sort-alpha-asc");
+    renderSortIcon: function () {
+        $('[class*="sort-icon"]').removeClass("fa-sort-alpha-desc").removeClass("fa-sort-alpha-asc");
 
         if (this.current_sort_order === "asc") {
             $(`.sort-icon-${this.current_sort_key}`).addClass("fa-sort-alpha-asc");
@@ -368,7 +366,7 @@ var FolderListView = Backbone.View.extend({
     /**
      * Create the new folder inline
      */
-    createFolderInline: function() {
+    createFolderInline: function () {
         if (this.$el.find("tr.new-row").length) {
             this.$el.find("tr.new-row textarea")[0].focus();
         } else {
@@ -393,11 +391,11 @@ var FolderListView = Backbone.View.extend({
     /**
      * Create the new library using the API asynchronously.
      */
-    createNewFolder: function(name, description) {
+    createNewFolder: function (name, description) {
         const Galaxy = getGalaxyInstance();
         const folderDetails = {
             name,
-            description
+            description,
         };
         if (folderDetails.name !== "") {
             var folder = new mod_library_model.FolderAsModel();
@@ -411,7 +409,7 @@ var FolderListView = Backbone.View.extend({
             folder.url = folder.urlRoot + current_folder_id;
 
             folder.save(folderDetails, {
-                success: folder => {
+                success: (folder) => {
                     Toast.success("Folder created.");
                     folder.set({ type: "folder" });
                     this.$el.find("tr.new-row").remove();
@@ -419,7 +417,7 @@ var FolderListView = Backbone.View.extend({
 
                     $(`tr[data-id="${folder.attributes.id}"`)
                         .addClass("table-success")
-                        .on("mouseover click", function() {
+                        .on("mouseover click", function () {
                             $(this).removeClass("table-success");
                         });
                 },
@@ -430,7 +428,7 @@ var FolderListView = Backbone.View.extend({
                     } else {
                         Toast.error("An error occurred.");
                     }
-                }
+                },
             });
         } else {
             Toast.error("Folder's name is missing.");
@@ -438,7 +436,7 @@ var FolderListView = Backbone.View.extend({
         return false;
     },
 
-    templateNewFolder: function() {
+    templateNewFolder: function () {
         return _.template(
             `<tr class="new-row">
                 <td class="mid">
@@ -469,7 +467,7 @@ var FolderListView = Backbone.View.extend({
         );
     },
 
-    templateFolder: function() {
+    templateFolder: function () {
         return _.template(
             `<ol class="breadcrumb">
                 <li class="breadcrumb-item">
@@ -554,9 +552,9 @@ var FolderListView = Backbone.View.extend({
                 </a>.
             </div>`
         );
-    }
+    },
 });
 
 export default {
-    FolderListView: FolderListView
+    FolderListView: FolderListView,
 };
diff --git a/client/galaxy/scripts/mvc/library/library-folderrow-view.js b/client/galaxy/scripts/mvc/library/library-folderrow-view.js
index 2b4a734d4d64..31bea665da9b 100644
--- a/client/galaxy/scripts/mvc/library/library-folderrow-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folderrow-view.js
@@ -14,7 +14,7 @@ var FolderRowView = Backbone.View.extend({
         "click .undelete_folder_btn": "undeleteFolder",
         "click .edit_folder_btn": "startModifications",
         "click .cancel_folder_btn": "cancelModifications",
-        "click .save_folder_btn": "saveModifications"
+        "click .save_folder_btn": "saveModifications",
     },
 
     defaults: {
@@ -23,17 +23,17 @@ var FolderRowView = Backbone.View.extend({
             edit_folder_btn: false,
             save_folder_btn: false,
             cancel_folder_btn: false,
-            permission_folder_btn: false
+            permission_folder_btn: false,
         },
-        edit_mode: false
+        edit_mode: false,
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = _.defaults(options || {}, this.defaults);
         this.render(this.options);
     },
 
-    render: function(options) {
+    render: function (options) {
         this.options = _.extend(this.options, options);
         var folder_item = this.options.model;
         var template = null;
@@ -66,7 +66,7 @@ var FolderRowView = Backbone.View.extend({
             template({
                 content_item: folder_item,
                 edit_mode: this.options.edit_mode,
-                button_config: this.options.visibility_config
+                button_config: this.options.visibility_config,
             })
         );
         this.$el.show();
@@ -93,7 +93,7 @@ var FolderRowView = Backbone.View.extend({
      * Modify the visibility of buttons for
      * the filling of the row template of a given folder.
      */
-    prepareButtons: function(folder) {
+    prepareButtons: function (folder) {
         var vis_config = this.options.visibility_config;
         if (this.options.edit_mode === false) {
             vis_config.save_folder_btn = false;
@@ -121,84 +121,80 @@ var FolderRowView = Backbone.View.extend({
     },
 
     /* Show the page with dataset details. */
-    showDatasetDetails: function() {
+    showDatasetDetails: function () {
         const Galaxy = getGalaxyInstance();
         Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({ id: this.id });
     },
 
     /* Undelete the dataset on server and render the row again. */
-    undeleteDataset: function(event) {
+    undeleteDataset: function (event) {
         $(".tooltip").hide();
         const Galaxy = getGalaxyInstance();
         var that = this;
-        var dataset_id = $(event.target)
-            .closest("tr")
-            .data("id");
+        var dataset_id = $(event.target).closest("tr").data("id");
         var dataset = Galaxy.libraries.folderListView.collection.get(dataset_id);
         dataset.url = `${dataset.urlRoot + dataset.id}?undelete=true`;
         dataset.destroy({
-            success: function(model, response) {
+            success: function (model, response) {
                 Galaxy.libraries.folderListView.collection.remove(dataset_id);
                 var updated_dataset = new mod_library_model.Item(response);
                 Galaxy.libraries.folderListView.collection.add(updated_dataset);
                 Galaxy.libraries.folderListView.collection.sortFolder("name", "asc");
                 Toast.success("Dataset undeleted. Click this to see it.", "", {
-                    onclick: function() {
+                    onclick: function () {
                         var folder_id = that.model.get("folder_id");
                         window.location = `${getAppRoot()}library/list#folders/${folder_id}/datasets/${that.id}`;
-                    }
+                    },
                 });
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(`Dataset was not undeleted. ${response.responseJSON.err_msg}`);
                 } else {
                     Toast.error("An error occurred! Dataset was not undeleted. Please try again.");
                 }
-            }
+            },
         });
     },
 
     /* Undelete the folder on server and render the row again. */
-    undeleteFolder: function(event) {
+    undeleteFolder: function (event) {
         const Galaxy = getGalaxyInstance();
         $(".tooltip").hide();
-        var folder_id = $(event.target)
-            .closest("tr")
-            .data("id");
+        var folder_id = $(event.target).closest("tr").data("id");
         var folder = Galaxy.libraries.folderListView.collection.get(folder_id);
         folder.url = `${folder.urlRoot + folder.id}?undelete=true`;
         folder.destroy({
-            success: function(model, response) {
+            success: function (model, response) {
                 Galaxy.libraries.folderListView.collection.remove(folder_id);
                 var updated_folder = new mod_library_model.FolderAsModel(response);
                 Galaxy.libraries.folderListView.collection.add(updated_folder);
                 Galaxy.libraries.folderListView.collection.sortFolder("name", "asc");
                 Toast.success("Folder undeleted.");
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(`Folder was not undeleted. ${response.responseJSON.err_msg}`);
                 } else {
                     Toast.error("An error occurred! Folder was not undeleted. Please try again.");
                 }
-            }
+            },
         });
     },
 
     /* User clicked the 'edit' button on row so render the row as editable. */
-    startModifications: function() {
+    startModifications: function () {
         this.options.edit_mode = true;
         this.repaint();
     },
 
     /* User clicked the 'cancel' button so render normal row */
-    cancelModifications: function() {
+    cancelModifications: function () {
         this.options.edit_mode = false;
         this.repaint();
     },
 
-    saveModifications: function() {
+    saveModifications: function () {
         const Galaxy = getGalaxyInstance();
         var folder = Galaxy.libraries.folderListView.collection.get(this.$el.data("id"));
         var is_changed = false;
@@ -221,18 +217,18 @@ var FolderRowView = Backbone.View.extend({
             var row_view = this;
             folder.save(null, {
                 patch: true,
-                success: function(folder) {
+                success: function (folder) {
                     row_view.options.edit_mode = false;
                     row_view.repaint(folder);
                     Toast.success("Changes to folder saved.");
                 },
-                error: function(model, response) {
+                error: function (model, response) {
                     if (typeof response.responseJSON !== "undefined") {
                         Toast.error(response.responseJSON.err_msg);
                     } else {
                         Toast.error("An error occurred while attempting to update the folder.");
                     }
-                }
+                },
             });
         } else {
             this.options.edit_mode = false;
@@ -241,7 +237,7 @@ var FolderRowView = Backbone.View.extend({
         }
     },
 
-    repaint: function() {
+    repaint: function () {
         /* need to hide manually because of the element removal in setElement
     invoked in render() */
         $(".tooltip").hide();
@@ -256,7 +252,7 @@ var FolderRowView = Backbone.View.extend({
         this.$el.find('[data-toggle="tooltip"]').tooltip({ trigger: "hover" });
     },
 
-    templateRowFolder: function() {
+    templateRowFolder: function () {
         return _.template(
             `<tr class="folder_row library-row" data-id="<%- content_item.id %>">
                 <td class="mid">
@@ -327,7 +323,7 @@ var FolderRowView = Backbone.View.extend({
         );
     },
 
-    templateRowFile: function() {
+    templateRowFile: function () {
         return _.template(
             `<tr class="dataset_row library-row" data-id="<%- content_item.id %>">
                 <td class="mid">
@@ -388,7 +384,7 @@ var FolderRowView = Backbone.View.extend({
         );
     },
 
-    templateRowDeletedFile: function() {
+    templateRowDeletedFile: function () {
         return _.template(
             `<tr class="active deleted_dataset library-row" data-id="<%- content_item.id %>">
                 <td class="mid">
@@ -431,7 +427,7 @@ var FolderRowView = Backbone.View.extend({
         );
     },
 
-    templateRowDeletedFolder: function() {
+    templateRowDeletedFolder: function () {
         return _.template(
             `<tr class="active deleted_folder library-row" data-id="<%- content_item.id %>">
                 <td class="mid">
@@ -473,9 +469,9 @@ var FolderRowView = Backbone.View.extend({
                 </td>
             </tr>`
         );
-    }
+    },
 });
 
 export default {
-    FolderRowView: FolderRowView
+    FolderRowView: FolderRowView,
 };
diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
index 1d9efb799058..3955e91c03f2 100644
--- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
@@ -26,7 +26,7 @@ var FolderToolbarView = Backbone.View.extend({
         "keydown .page_size": "changePageSize",
         "blur .page_size": "changePageSize",
         "click .toolbtn-collection-import": "showCollectionSelect",
-        "keyup .folder-search-input": "searchFolder"
+        "keyup .folder-search-input": "searchFolder",
     },
 
     defaults: {
@@ -34,9 +34,9 @@ var FolderToolbarView = Backbone.View.extend({
         contains_file_or_folder: false,
         chain_call_control: {
             total_number: 0,
-            failed_number: 0
+            failed_number: 0,
         },
-        disabled_jstree_element: "folders"
+        disabled_jstree_element: "folders",
     },
 
     modal: null,
@@ -66,19 +66,19 @@ var FolderToolbarView = Backbone.View.extend({
             " it most likely means that it has some format problems (e.g., different" +
             " number of columns on different rows). You can still coerce the system" +
             " to set your data to the format you think it should be." +
-            " You can also upload compressed files, which will automatically be decompressed."
+            " You can also upload compressed files, which will automatically be decompressed.",
     },
 
     // genomes
     list_genomes: [],
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = _.defaults(options || {}, this.defaults);
         this.fetchExtAndGenomes();
         this.render();
     },
 
-    render: function(options) {
+    render: function (options) {
         this.options = _.extend(this.options, options);
         const Galaxy = getGalaxyInstance();
         var toolbar_template = this.templateToolBar();
@@ -88,7 +88,7 @@ var FolderToolbarView = Backbone.View.extend({
             is_anonym: true,
             multiple_add_dataset_options: false,
             Galaxy: Galaxy,
-            folder_page_size: Galaxy.libraries.preferences.get("folder_page_size")
+            folder_page_size: Galaxy.libraries.preferences.get("folder_page_size"),
         };
         if (Galaxy.user) {
             template_defaults.is_admin = Galaxy.user.isAdmin();
@@ -108,7 +108,7 @@ var FolderToolbarView = Backbone.View.extend({
      * Called from FolderListView when needed.
      * @param  {object} options common options
      */
-    renderPaginator: function(options) {
+    renderPaginator: function (options) {
         this.options = _.extend(this.options, options);
         const Galaxy = getGalaxyInstance();
         var paginator_template = this.templatePaginator();
@@ -122,7 +122,7 @@ var FolderToolbarView = Backbone.View.extend({
                     page_count: parseInt(this.options.page_count),
                     total_items_count: this.options.total_items_count,
                     items_shown: this.options.items_shown,
-                    folder_page_size: Galaxy.libraries.preferences.get("folder_page_size")
+                    folder_page_size: Galaxy.libraries.preferences.get("folder_page_size"),
                 })
             );
         $("body")
@@ -134,12 +134,12 @@ var FolderToolbarView = Backbone.View.extend({
                     page_count: parseInt(this.options.page_count),
                     total_items_count: this.options.total_items_count,
                     items_shown: this.options.items_shown,
-                    folder_page_size: Galaxy.libraries.preferences.get("folder_page_size")
+                    folder_page_size: Galaxy.libraries.preferences.get("folder_page_size"),
                 })
             );
     },
 
-    configureElements: function(options) {
+    configureElements: function (options) {
         this.options = _.extend(this.options, options);
         const Galaxy = getGalaxyInstance();
 
@@ -168,12 +168,12 @@ var FolderToolbarView = Backbone.View.extend({
         this.$el.find('[data-toggle="tooltip"]').tooltip({ trigger: "hover" });
     },
 
-    createFolderInline: function() {
+    createFolderInline: function () {
         const Galaxy = getGalaxyInstance();
         Galaxy.libraries.folderListView.createFolderInline();
     },
 
-    importToHistoryModal: function(e) {
+    importToHistoryModal: function (e) {
         e.preventDefault();
         const Galaxy = getGalaxyInstance();
         var $checkedValues = this.findCheckedRows();
@@ -189,7 +189,7 @@ var FolderToolbarView = Backbone.View.extend({
                         closing_events: true,
                         title: _l("Import into History"),
                         body: template({
-                            histories: this.histories.models
+                            histories: this.histories.models,
                         }),
                         buttons: {
                             Import: () => {
@@ -197,8 +197,8 @@ var FolderToolbarView = Backbone.View.extend({
                             },
                             Close: () => {
                                 Galaxy.modal.hide();
-                            }
-                        }
+                            },
+                        },
                     });
                 })
                 .fail((model, response) => {
@@ -214,17 +214,17 @@ var FolderToolbarView = Backbone.View.extend({
     /**
      * This function returns a promise
      */
-    fetchUserHistories: function() {
+    fetchUserHistories: function () {
         this.histories = new mod_library_model.GalaxyHistories();
         return this.histories.fetch();
     },
 
-    importAllIntoHistory: function() {
+    importAllIntoHistory: function () {
         this.modal.disableButton("Import");
         var new_history_name = this.modal.$("input[name=history_name]").val();
         if (new_history_name !== "") {
             this.createNewHistory(new_history_name)
-                .done(new_history => {
+                .done((new_history) => {
                     this.processImportToHistory(new_history.id, new_history.name);
                 })
                 .fail((xhr, status, error) => {
@@ -244,11 +244,11 @@ var FolderToolbarView = Backbone.View.extend({
     /**
      * This function returns a promise
      */
-    createNewHistory: function(new_history_name) {
+    createNewHistory: function (new_history_name) {
         return $.post(`${getAppRoot()}api/histories`, { name: new_history_name });
     },
 
-    processImportToHistory: function(history_id, history_name) {
+    processImportToHistory: function (history_id, history_name) {
         var checked_items = this.findCheckedItems();
         var items_to_import = [];
         // prepare the dataset objects to be imported
@@ -272,7 +272,7 @@ var FolderToolbarView = Backbone.View.extend({
         this.initChainCallControl({
             length: items_to_import.length,
             action: "to_history",
-            history_name: history_name
+            history_name: history_name,
         });
         // set the used history as current so user will see the last one
         // that he imported into in the history panel on the 'analysis' page
@@ -283,7 +283,7 @@ var FolderToolbarView = Backbone.View.extend({
     /**
      * Update progress bar in modal.
      */
-    updateProgress: function() {
+    updateProgress: function () {
         this.progress += this.progressStep;
         $(".progress-bar-import").width(`${Math.round(this.progress)}%`);
         var txt_representation = `${Math.round(this.progress)}% Complete`;
@@ -294,7 +294,7 @@ var FolderToolbarView = Backbone.View.extend({
      * Download selected datasets. Called from the router.
      * @param  {str} format    requested archive format
      */
-    download: function(format) {
+    download: function (format) {
         var checked_items = this.findCheckedItems();
         var url = `${getAppRoot()}api/libraries/datasets/download/${format}`;
         var data = { ld_ids: checked_items.dataset_ids, folder_ids: checked_items.folder_ids };
@@ -308,13 +308,13 @@ var FolderToolbarView = Backbone.View.extend({
      * @param  {obj} data   data to include in the request
      * @param  {str} method method of the request
      */
-    processDownload: function(url, data, method) {
+    processDownload: function (url, data, method) {
         if (url && data) {
             // data can be string of parameters or array/object
             data = typeof data === "string" ? data : $.param(data);
             // split params into form inputs
             var inputs = "";
-            $.each(data.split("&"), function() {
+            $.each(data.split("&"), function () {
                 var pair = this.split("=");
                 inputs += `<input type="hidden" name="${pair[0]}" value="${pair[1]}" />`;
             });
@@ -329,7 +329,7 @@ var FolderToolbarView = Backbone.View.extend({
         }
     },
 
-    addFilesFromHistoryModal: function() {
+    addFilesFromHistoryModal: function () {
         const Galaxy = getGalaxyInstance();
         this.histories = new mod_library_model.GalaxyHistories();
         this.histories
@@ -341,7 +341,7 @@ var FolderToolbarView = Backbone.View.extend({
                     closing_events: true,
                     title: _l("Adding datasets from your history"),
                     body: template_modal({
-                        histories: this.histories.models
+                        histories: this.histories.models,
                     }),
                     buttons: {
                         Add: () => {
@@ -349,14 +349,14 @@ var FolderToolbarView = Backbone.View.extend({
                         },
                         Close: () => {
                             Galaxy.modal.hide();
-                        }
+                        },
                     },
                     closing_callback: () => {
                         Galaxy.libraries.library_router.navigate(`folders/${this.id}`, { trigger: true });
-                    }
+                    },
                 });
                 this.fetchAndDisplayHistoryContents(this.histories.models[0].id);
-                $("#dataset_add_bulk").change(event => {
+                $("#dataset_add_bulk").change((event) => {
                     this.fetchAndDisplayHistoryContents(event.target.value);
                 });
             })
@@ -372,7 +372,7 @@ var FolderToolbarView = Backbone.View.extend({
     /**
      * Create modal for importing from Galaxy path.
      */
-    importFilesFromPathModal: function() {
+    importFilesFromPathModal: function () {
         const Galaxy = getGalaxyInstance();
         this.modal = Galaxy.modal;
         var template_modal = this.templateImportPathModal();
@@ -386,14 +386,14 @@ var FolderToolbarView = Backbone.View.extend({
                 },
                 Close: () => {
                     Galaxy.modal.hide();
-                }
+                },
             },
             closing_callback: () => {
                 //  TODO: should not trigger routes outside of the router
                 Galaxy.libraries.library_router.navigate(`folders/${this.id}`, {
-                    trigger: true
+                    trigger: true,
                 });
-            }
+            },
         });
         this.renderSelectBoxes();
     },
@@ -402,41 +402,41 @@ var FolderToolbarView = Backbone.View.extend({
      * Request all extensions and genomes from Galaxy
      * and save them in sorted arrays.
      */
-    fetchExtAndGenomes: function() {
+    fetchExtAndGenomes: function () {
         mod_utils.get({
             url: `${getAppRoot()}api/datatypes?extension_only=False`,
-            success: datatypes => {
+            success: (datatypes) => {
                 this.list_extensions = [];
                 for (const key in datatypes) {
                     this.list_extensions.push({
                         id: datatypes[key].extension,
                         text: datatypes[key].extension,
                         description: datatypes[key].description,
-                        description_url: datatypes[key].description_url
+                        description_url: datatypes[key].description_url,
                     });
                 }
                 this.list_extensions.sort((a, b) => (a.id > b.id ? 1 : a.id < b.id ? -1 : 0));
                 this.list_extensions.unshift(this.auto);
             },
-            cache: true
+            cache: true,
         });
         mod_utils.get({
             url: `${getAppRoot()}api/genomes`,
-            success: genomes => {
+            success: (genomes) => {
                 this.list_genomes = [];
                 for (const key in genomes) {
                     this.list_genomes.push({
                         id: genomes[key][1],
-                        text: genomes[key][0]
+                        text: genomes[key][0],
                     });
                 }
                 this.list_genomes.sort((a, b) => (a.id > b.id ? 1 : a.id < b.id ? -1 : 0));
             },
-            cache: true
+            cache: true,
         });
     },
 
-    renderSelectBoxes: function() {
+    renderSelectBoxes: function () {
         const Galaxy = getGalaxyInstance();
         // This won't work properly unlesss we already have the data fetched.
         // See this.fetchExtAndGenomes()
@@ -444,13 +444,13 @@ var FolderToolbarView = Backbone.View.extend({
             css: "library-genome-select",
             data: this.list_genomes,
             container: Galaxy.modal.$el.find("#library_genome_select"),
-            value: "?"
+            value: "?",
         });
         this.select_extension = new mod_select.View({
             css: "library-extension-select",
             data: this.list_extensions,
             container: Galaxy.modal.$el.find("#library_extension_select"),
-            value: "auto"
+            value: "auto",
         });
     },
 
@@ -458,7 +458,7 @@ var FolderToolbarView = Backbone.View.extend({
      * Create modal for importing from given directory
      * on Galaxy. Bind jQuery events.
      */
-    importFilesFromGalaxyFolderModal: function(options) {
+    importFilesFromGalaxyFolderModal: function (options) {
         var template_modal = this.templateBrowserModal();
         const Galaxy = getGalaxyInstance();
         this.modal = Galaxy.modal;
@@ -472,14 +472,14 @@ var FolderToolbarView = Backbone.View.extend({
                 },
                 Close: () => {
                     Galaxy.modal.hide();
-                }
+                },
             },
             closing_callback: () => {
                 //  TODO: should not trigger routes outside of the router
                 Galaxy.libraries.library_router.navigate(`folders/${this.id}`, {
-                    trigger: true
+                    trigger: true,
                 });
-            }
+            },
         });
 
         $(".libimport-select-all").bind("click", () => {
@@ -493,7 +493,7 @@ var FolderToolbarView = Backbone.View.extend({
         options.disabled_jstree_element = "folders";
         this.renderJstree(options);
 
-        $("input[type=radio]").change(event => {
+        $("input[type=radio]").change((event) => {
             if (event.target.value === "jstree-disable-folders") {
                 options.disabled_jstree_element = "folders";
                 this.renderJstree(options);
@@ -516,7 +516,7 @@ var FolderToolbarView = Backbone.View.extend({
      * data.
      * @param  {[type]} options [description]
      */
-    renderJstree: function(options) {
+    renderJstree: function (options) {
         this.options = _.extend(this.options, options);
         var target = options.source || "userdir";
         var disabled_jstree_element = this.options.disabled_jstree_element;
@@ -527,20 +527,20 @@ var FolderToolbarView = Backbone.View.extend({
                 $("#jstree_browser").jstree("destroy");
                 $("#jstree_browser").jstree({
                     core: {
-                        data: model
+                        data: model,
                     },
                     plugins: ["types", "checkbox"],
                     types: {
                         folder: {
-                            icon: "jstree-folder"
+                            icon: "jstree-folder",
                         },
                         file: {
-                            icon: "jstree-file"
-                        }
+                            icon: "jstree-file",
+                        },
                     },
                     checkbox: {
-                        three_state: false
-                    }
+                        three_state: false,
+                    },
                 });
             },
             error: (model, response) => {
@@ -553,7 +553,7 @@ var FolderToolbarView = Backbone.View.extend({
                 } else {
                     Toast.error("An error occurred.");
                 }
-            }
+            },
         });
     },
 
@@ -562,7 +562,7 @@ var FolderToolbarView = Backbone.View.extend({
      * a request queue and call a function that starts sending
      * one by one to be imported on the server.
      */
-    importFromPathsClicked: function() {
+    importFromPathsClicked: function () {
         var preserve_dirs = this.modal.$el.find(".preserve-checkbox").is(":checked");
         var link_data = this.modal.$el.find(".link-checkbox").is(":checked");
         var space_to_tab = this.modal.$el.find(".spacetab-checkbox").is(":checked");
@@ -585,7 +585,7 @@ var FolderToolbarView = Backbone.View.extend({
             }
             this.initChainCallControl({
                 length: valid_paths.length,
-                action: "adding_datasets"
+                action: "adding_datasets",
             });
             this.chainCallImportingFolders({
                 paths: valid_paths,
@@ -596,7 +596,7 @@ var FolderToolbarView = Backbone.View.extend({
                 source: "admin_path",
                 file_type: file_type,
                 tag_using_filenames: tag_using_filenames,
-                dbkey: dbkey
+                dbkey: dbkey,
             });
         }
     },
@@ -606,7 +606,7 @@ var FolderToolbarView = Backbone.View.extend({
      * in the current modal.
      * @param {int} length The number of items in the chain call.
      */
-    initChainCallControl: function(options) {
+    initChainCallControl: function (options) {
         const Galaxy = getGalaxyInstance();
         var template;
         switch (options.action) {
@@ -614,7 +614,7 @@ var FolderToolbarView = Backbone.View.extend({
                 template = this.templateAddingDatasetsProgressBar();
                 this.modal.$el.find(".modal-body").html(
                     template({
-                        folder_name: this.options.folder_name
+                        folder_name: this.options.folder_name,
                     })
                 );
                 break;
@@ -647,12 +647,10 @@ var FolderToolbarView = Backbone.View.extend({
      * jstree.js has to be loaded before
      * @see renderJstree
      */
-    importFromJstreePath: function(that, options) {
-        var all_nodes = $("#jstree_browser")
-            .jstree()
-            .get_selected(true);
+    importFromJstreePath: function (that, options) {
+        var all_nodes = $("#jstree_browser").jstree().get_selected(true);
         // remove the disabled elements that could have been trigerred with the 'select all'
-        var selected_nodes = _.filter(all_nodes, node => node.state.disabled == false);
+        var selected_nodes = _.filter(all_nodes, (node) => node.state.disabled == false);
         var preserve_dirs = this.modal.$el.find(".preserve-checkbox").is(":checked");
         var link_data = this.modal.$el.find(".link-checkbox").is(":checked");
         var space_to_tab = this.modal.$el.find(".spacetab-checkbox").is(":checked");
@@ -673,7 +671,7 @@ var FolderToolbarView = Backbone.View.extend({
             }
             this.initChainCallControl({
                 length: paths.length,
-                action: "adding_datasets"
+                action: "adding_datasets",
             });
             if (selection_type === "folder") {
                 const full_source = `${options.source}_folder`;
@@ -686,7 +684,7 @@ var FolderToolbarView = Backbone.View.extend({
                     source: full_source,
                     file_type: file_type,
                     dbkey: dbkey,
-                    tag_using_filenames: tag_using_filenames
+                    tag_using_filenames: tag_using_filenames,
                 });
             } else if (selection_type === "file") {
                 const full_source = `${options.source}_file`;
@@ -698,25 +696,25 @@ var FolderToolbarView = Backbone.View.extend({
                     space_to_tab: space_to_tab,
                     to_posix_lines: to_posix_lines,
                     source: full_source,
-                    tag_using_filenames: tag_using_filenames
+                    tag_using_filenames: tag_using_filenames,
                 });
             }
         }
     },
 
-    fetchAndDisplayHistoryContents: function(history_id) {
+    fetchAndDisplayHistoryContents: function (history_id) {
         var history_contents = new mod_library_model.HistoryContents({
-            id: history_id
+            id: history_id,
         });
         history_contents.fetch({
-            success: history_contents => {
+            success: (history_contents) => {
                 var history_contents_template = this.templateHistoryContents();
 
                 if (history_contents.length > 0) {
                     this.histories.get(history_id).set({ contents: history_contents });
                     this.modal.$el.find(".library_selected_history_content").html(
                         history_contents_template({
-                            history_contents: history_contents.models.reverse()
+                            history_contents: history_contents.models.reverse(),
                         })
                     );
                     this.modal.$el.find(".history-import-select-all").bind("click", () => {
@@ -726,11 +724,11 @@ var FolderToolbarView = Backbone.View.extend({
                         $(".library_selected_history_content [type=checkbox]").prop("checked", false);
                     });
 
-                    this.modal.$el.find(".history-import-toggle-all").bind("click", e => {
+                    this.modal.$el.find(".history-import-toggle-all").bind("click", (e) => {
                         this.selectAll(e);
                     });
 
-                    this.modal.$el.find(".dataset_row").bind("click", e => {
+                    this.modal.$el.find(".dataset_row").bind("click", (e) => {
                         this.selectClickedRow(e);
                     });
                 } else {
@@ -743,14 +741,14 @@ var FolderToolbarView = Backbone.View.extend({
                 } else {
                     Toast.error("An error occurred.");
                 }
-            }
+            },
         });
     },
 
     /**
      * Import all selected datasets from history into the current folder.
      */
-    addAllDatasetsFromHistory: function() {
+    addAllDatasetsFromHistory: function () {
         var checked_hdas = this.modal.$el.find(".library_selected_history_content").find(":checked");
         var history_item_ids = []; // can be hda or hdca
         var history_item_types = [];
@@ -759,14 +757,10 @@ var FolderToolbarView = Backbone.View.extend({
             Toast.info("You must select some datasets first.");
         } else {
             this.modal.disableButton("Add");
-            checked_hdas.each(function() {
-                var hid = $(this)
-                    .closest("tr")
-                    .data("id");
+            checked_hdas.each(function () {
+                var hid = $(this).closest("tr").data("id");
                 if (hid) {
-                    var item_type = $(this)
-                        .closest("tr")
-                        .data("name");
+                    var item_type = $(this).closest("tr").data("name");
                     history_item_ids.push(hid);
                     history_item_types.push(item_type);
                 }
@@ -784,7 +778,7 @@ var FolderToolbarView = Backbone.View.extend({
             }
             this.initChainCallControl({
                 length: items_to_add.length,
-                action: "adding_datasets"
+                action: "adding_datasets",
             });
             this.chainCallAddingHdas(items_to_add);
         }
@@ -794,11 +788,11 @@ var FolderToolbarView = Backbone.View.extend({
      * User clicked the checkbox in the table heading
      * @param  {context} event
      */
-    selectAll: function(event) {
+    selectAll: function (event) {
         var selected = event.target.checked;
         var self = this;
         // Iterate each checkbox
-        $(":checkbox", "#dataset_list tbody").each(function() {
+        $(":checkbox", "#dataset_list tbody").each(function () {
             this.checked = selected;
             var $row = $(this).closest("tr");
             // Change color of selected/unselected
@@ -814,7 +808,7 @@ var FolderToolbarView = Backbone.View.extend({
      * Check checkbox if user clicks on the whole row or
      *  on the checkbox itself
      */
-    selectClickedRow: function(event) {
+    selectClickedRow: function (event) {
         var checkbox = "";
         var $row;
         var source;
@@ -843,11 +837,11 @@ var FolderToolbarView = Backbone.View.extend({
         }
     },
 
-    makeDarkRow: function($row) {
+    makeDarkRow: function ($row) {
         $row.addClass("table-primary");
     },
 
-    makeWhiteRow: function($row) {
+    makeWhiteRow: function ($row) {
         $row.removeClass("table-primary");
     },
 
@@ -857,7 +851,7 @@ var FolderToolbarView = Backbone.View.extend({
      * @param  {array} history_item_set array of empty history items
      * @param  {str} history_name     name of the history to import to
      */
-    chainCallImportingIntoHistory: function(history_item_set, history_name) {
+    chainCallImportingIntoHistory: function (history_item_set, history_name) {
         const Galaxy = getGalaxyInstance();
         var popped_item = history_item_set.pop();
         if (typeof popped_item == "undefined") {
@@ -865,7 +859,7 @@ var FolderToolbarView = Backbone.View.extend({
                 Toast.success("Selected datasets imported into history. Click this to start analyzing it.", "", {
                     onclick: () => {
                         window.location = getAppRoot();
-                    }
+                    },
                 });
             } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number) {
                 Toast.error("There was an error and no datasets were imported into history.");
@@ -876,7 +870,7 @@ var FolderToolbarView = Backbone.View.extend({
                     {
                         onclick: () => {
                             window.location = getAppRoot();
-                        }
+                        },
                     }
                 );
             }
@@ -886,7 +880,7 @@ var FolderToolbarView = Backbone.View.extend({
         var promise = $.when(
             popped_item.save({
                 content: popped_item.content,
-                source: popped_item.source
+                source: popped_item.source,
             })
         );
 
@@ -908,7 +902,7 @@ var FolderToolbarView = Backbone.View.extend({
      * @param  {array} paths                    paths relative to user folder on Galaxy
      * @param  {boolean} tag_using_filenames    add tags to datasets using names of files
      */
-    chainCallImportingUserdirFiles: function(options) {
+    chainCallImportingUserdirFiles: function (options) {
         const Galaxy = getGalaxyInstance();
         const popped_item = options.paths.pop();
         if (typeof popped_item === "undefined") {
@@ -930,11 +924,11 @@ var FolderToolbarView = Backbone.View.extend({
             space_to_tab: options.space_to_tab,
             to_posix_lines: options.to_posix_lines,
             dbkey: options.dbkey,
-            tag_using_filenames: options.tag_using_filenames
+            tag_using_filenames: options.tag_using_filenames,
         };
         const promise = $.when($.post(post_url, post_data));
         promise
-            .done(response => {
+            .done((response) => {
                 this.updateProgress();
                 this.chainCallImportingUserdirFiles(options);
             })
@@ -957,7 +951,7 @@ var FolderToolbarView = Backbone.View.extend({
      *                                          is the source of import
      * @param  {boolean} tag_using_filenames    add tags to datasets using names of files
      */
-    chainCallImportingFolders: function(options) {
+    chainCallImportingFolders: function (options) {
         const Galaxy = getGalaxyInstance();
         // TODO need to check which paths to call
         const popped_item = options.paths.pop();
@@ -982,11 +976,11 @@ var FolderToolbarView = Backbone.View.extend({
             space_to_tab: options.space_to_tab,
             file_type: options.file_type,
             dbkey: options.dbkey,
-            tag_using_filenames: options.tag_using_filenames
+            tag_using_filenames: options.tag_using_filenames,
         };
         const promise = $.when($.post(post_url, post_data));
         promise
-            .done(response => {
+            .done((response) => {
                 this.updateProgress();
                 this.chainCallImportingFolders(options);
             })
@@ -1002,7 +996,7 @@ var FolderToolbarView = Backbone.View.extend({
      * Call them in chain and update progress bar in between each.
      * @param  {array} hdas_set array of empty hda objects
      */
-    chainCallAddingHdas: function(hdas_set) {
+    chainCallAddingHdas: function (hdas_set) {
         const Galaxy = getGalaxyInstance();
         this.added_hdas = new mod_library_model.Folder();
         var popped_item = hdas_set.pop();
@@ -1019,12 +1013,12 @@ var FolderToolbarView = Backbone.View.extend({
         }
         var promise = $.when(
             popped_item.save({
-                from_hda_id: popped_item.get("from_hda_id")
+                from_hda_id: popped_item.get("from_hda_id"),
             })
         );
 
         promise
-            .done(model => {
+            .done((model) => {
                 Galaxy.libraries.folderListView.collection.add(model);
                 this.updateProgress();
                 this.chainCallAddingHdas(hdas_set);
@@ -1041,7 +1035,7 @@ var FolderToolbarView = Backbone.View.extend({
      * call them in chain. Update progress bar in between each.
      * @param  {array} lddas_set array of lddas to delete
      */
-    chainCallDeletingItems: function(items_to_delete) {
+    chainCallDeletingItems: function (items_to_delete) {
         const Galaxy = getGalaxyInstance();
         this.deleted_items = new mod_library_model.Folder();
         var item_to_delete = items_to_delete.pop();
@@ -1062,7 +1056,7 @@ var FolderToolbarView = Backbone.View.extend({
         }
         item_to_delete
             .destroy()
-            .done(item => {
+            .done((item) => {
                 Galaxy.libraries.folderListView.collection.remove(item_to_delete.id);
                 this.updateProgress();
                 // add the deleted item to collection, triggers rendering
@@ -1090,15 +1084,15 @@ var FolderToolbarView = Backbone.View.extend({
     /**
      * Handles the click on 'show deleted' checkbox
      */
-    checkIncludeDeleted: function(event) {
+    checkIncludeDeleted: function (event) {
         const Galaxy = getGalaxyInstance();
         if (event.target.checked) {
             Galaxy.libraries.folderListView.fetchFolder({
-                include_deleted: true
+                include_deleted: true,
             });
         } else {
             Galaxy.libraries.folderListView.fetchFolder({
-                include_deleted: false
+                include_deleted: false,
             });
         }
     },
@@ -1106,7 +1100,7 @@ var FolderToolbarView = Backbone.View.extend({
     /**
      * Delete the selected items. Atomic. One by one.
      */
-    deleteSelectedItems: function() {
+    deleteSelectedItems: function () {
         const Galaxy = getGalaxyInstance();
         var dataset_ids = [];
         var folder_ids = [];
@@ -1123,17 +1117,14 @@ var FolderToolbarView = Backbone.View.extend({
                 buttons: {
                     Close: () => {
                         Galaxy.modal.hide();
-                    }
-                }
+                    },
+                },
             });
             // init the control counters
             this.options.chain_call_control.total_number = 0;
             this.options.chain_call_control.failed_number = 0;
-            $checkedValues.each(function() {
-                var row_id = $(this)
-                    .closest("tr")
-                    .data("id")
-                    .toString();
+            $checkedValues.each(function () {
+                var row_id = $(this).closest("tr").data("id").toString();
                 if (row_id !== undefined) {
                     if (row_id.substring(0, 1) == "F") {
                         folder_ids.push(row_id);
@@ -1151,13 +1142,13 @@ var FolderToolbarView = Backbone.View.extend({
             var items_to_delete = [];
             for (let i = dataset_ids.length - 1; i >= 0; i--) {
                 var dataset = new mod_library_model.Item({
-                    id: dataset_ids[i]
+                    id: dataset_ids[i],
                 });
                 items_to_delete.push(dataset);
             }
             for (let i = folder_ids.length - 1; i >= 0; i--) {
                 var folder = new mod_library_model.FolderAsModel({
-                    id: folder_ids[i]
+                    id: folder_ids[i],
                 });
                 items_to_delete.push(folder);
             }
@@ -1168,7 +1159,7 @@ var FolderToolbarView = Backbone.View.extend({
         }
     },
 
-    showLocInfo: function() {
+    showLocInfo: function () {
         const Galaxy = getGalaxyInstance();
         var library = null;
         if (Galaxy.libraries.libraryListView !== null) {
@@ -1176,24 +1167,24 @@ var FolderToolbarView = Backbone.View.extend({
             this.showLocInfoModal(library);
         } else {
             library = new mod_library_model.Library({
-                id: this.options.parent_library_id
+                id: this.options.parent_library_id,
             });
             library.fetch({
                 success: () => {
                     this.showLocInfoModal(library);
                 },
-                error: function(model, response) {
+                error: function (model, response) {
                     if (typeof response.responseJSON !== "undefined") {
                         Toast.error(response.responseJSON.err_msg);
                     } else {
                         Toast.error("An error occurred.");
                     }
-                }
+                },
             });
         }
     },
 
-    showLocInfoModal: function(library) {
+    showLocInfoModal: function (library) {
         const Galaxy = getGalaxyInstance();
         var template = this.templateLocInfoInModal();
         this.modal = Galaxy.modal;
@@ -1204,12 +1195,12 @@ var FolderToolbarView = Backbone.View.extend({
             buttons: {
                 Close: () => {
                     Galaxy.modal.hide();
-                }
-            }
+                },
+            },
         });
     },
 
-    showImportModal: function(options) {
+    showImportModal: function (options) {
         const Galaxy = getGalaxyInstance();
         switch (options.source) {
             case "history":
@@ -1217,7 +1208,7 @@ var FolderToolbarView = Backbone.View.extend({
                 break;
             case "importdir":
                 this.importFilesFromGalaxyFolderModal({
-                    source: "importdir"
+                    source: "importdir",
                 });
                 break;
             case "path":
@@ -1225,7 +1216,7 @@ var FolderToolbarView = Backbone.View.extend({
                 break;
             case "userdir":
                 this.importFilesFromGalaxyFolderModal({
-                    source: "userdir"
+                    source: "userdir",
                 });
                 break;
             default:
@@ -1238,32 +1229,29 @@ var FolderToolbarView = Backbone.View.extend({
     /**
      * Change the number of libs shown on page.
      */
-    changePageSize: function(e) {
+    changePageSize: function (e) {
         if (e.type === "focusout" || (e.type === "keydown" && e.keyCode === 13)) {
             e.preventDefault();
             const Galaxy = getGalaxyInstance();
             Galaxy.libraries.preferences.set({
-                folder_page_size: parseInt(e.target.value)
+                folder_page_size: parseInt(e.target.value),
             });
             Galaxy.libraries.folderListView.render({
                 id: this.options.id,
-                show_page: 1
+                show_page: 1,
             });
         }
     },
 
-    findCheckedRows: function() {
+    findCheckedRows: function () {
         return $("#folder_list_body").find(":checked");
     },
 
-    findCheckedItems: function() {
+    findCheckedItems: function () {
         var folder_ids = [];
         var dataset_ids = [];
-        this.findCheckedRows().each(function() {
-            var row_id = $(this)
-                .closest("tr")
-                .data("id")
-                .toString();
+        this.findCheckedRows().each(function () {
+            var row_id = $(this).closest("tr").data("id").toString();
             if (row_id.substring(0, 1) == "F") {
                 folder_ids.push(row_id);
             } else {
@@ -1273,7 +1261,7 @@ var FolderToolbarView = Backbone.View.extend({
         return { folder_ids: folder_ids, dataset_ids: dataset_ids };
     },
 
-    showCollectionSelect: function(e) {
+    showCollectionSelect: function (e) {
         e.preventDefault();
         const Galaxy = getGalaxyInstance();
         var checked_items = this.findCheckedItems();
@@ -1288,7 +1276,7 @@ var FolderToolbarView = Backbone.View.extend({
                     title: "Create History Collection from Datasets",
                     body: template({
                         selected_datasets: checked_items.dataset_ids.length,
-                        histories: this.histories.models
+                        histories: this.histories.models,
                     }),
                     buttons: {
                         Continue: () => {
@@ -1296,8 +1284,8 @@ var FolderToolbarView = Backbone.View.extend({
                         },
                         Close: () => {
                             Galaxy.modal.hide();
-                        }
-                    }
+                        },
+                    },
                 });
             })
             .fail((model, response) => {
@@ -1314,7 +1302,7 @@ var FolderToolbarView = Backbone.View.extend({
      * in the collection_elements array but we operate on ld_ids in libraries.
      * The code below overwrites the id with ldda_id for this reason.
      */
-    showCollectionBuilder: function(checked_items) {
+    showCollectionBuilder: function (checked_items) {
         const Galaxy = getGalaxyInstance();
         let collection_elements = [];
         const elements_source = this.modal.$('input[type="radio"]:checked').val();
@@ -1338,7 +1326,7 @@ var FolderToolbarView = Backbone.View.extend({
         const new_history_name = this.modal.$("input[name=history_name]").val();
         if (new_history_name !== "") {
             this.createNewHistory(new_history_name)
-                .done(new_history => {
+                .done((new_history) => {
                     Toast.success("History created");
                     this.collectionImport(collection_elements, new_history.id, new_history.name);
                 })
@@ -1353,7 +1341,7 @@ var FolderToolbarView = Backbone.View.extend({
         }
     },
 
-    collectionImport: function(collection_elements, history_id, history_name) {
+    collectionImport: function (collection_elements, history_id, history_name) {
         const modal_title = `Creating Collection in ${history_name}`;
         let creator_class;
         let creationFn;
@@ -1361,10 +1349,10 @@ var FolderToolbarView = Backbone.View.extend({
         if (this.collectionType === "list") {
             creator_class = LIST_CREATOR.ListCollectionCreator;
             creationFn = (elements, name, hideSourceItems) => {
-                elements = elements.map(element => ({
+                elements = elements.map((element) => ({
                     id: element.id,
                     name: element.name,
-                    src: "ldda"
+                    src: "ldda",
                 }));
                 return this.createHDCA(elements, this.collectionType, name, hideSourceItems, history_id);
             };
@@ -1378,7 +1366,7 @@ var FolderToolbarView = Backbone.View.extend({
             creationFn = (elements, name, hideSourceItems) => {
                 elements = [
                     { name: "forward", src: "ldda", id: elements[0].id },
-                    { name: "reverse", src: "ldda", id: elements[1].id }
+                    { name: "reverse", src: "ldda", id: elements[1].id },
                 ];
                 return this.createHDCA(elements, this.collectionType, name, hideSourceItems, history_id);
             };
@@ -1388,15 +1376,15 @@ var FolderToolbarView = Backbone.View.extend({
                 creator_class
             );
         } else if (this.collectionType === "list:paired") {
-            const elements = collection_elements.map(element => ({
+            const elements = collection_elements.map((element) => ({
                 id: element.id,
                 name: element.name,
-                src: "ldda"
+                src: "ldda",
             }));
             PAIRED_CREATOR.pairedCollectionCreatorModal(elements, {
                 historyId: history_id,
                 title: modal_title,
-                defaultHideSourceItems: true
+                defaultHideSourceItems: true,
             });
         } else if (this.collectionType === "rules") {
             const creationFn = (elements, collectionType, name, hideSourceItems) => {
@@ -1404,19 +1392,19 @@ var FolderToolbarView = Backbone.View.extend({
             };
             LIST_CREATOR.ruleBasedCollectionCreatorModal(collection_elements, "library_datasets", "collections", {
                 creationFn: creationFn,
-                defaultHideSourceItems: true
+                defaultHideSourceItems: true,
             });
         }
     },
 
-    createHDCA: function(elementIdentifiers, collectionType, name, hideSourceItems, history_id, options) {
+    createHDCA: function (elementIdentifiers, collectionType, name, hideSourceItems, history_id, options) {
         const hdca = new HDCA_MODEL.HistoryDatasetCollection({
             history_content_type: "dataset_collection",
             collection_type: collectionType,
             history_id: history_id,
             name: name,
             hide_source_items: hideSourceItems || false,
-            element_identifiers: elementIdentifiers
+            element_identifiers: elementIdentifiers,
         });
         return hdca.save(options);
     },
@@ -1425,14 +1413,14 @@ var FolderToolbarView = Backbone.View.extend({
      * Take the contents of the search field and send it to the list view
      * to query the collection of folder items.
      */
-    searchFolder: function(event) {
+    searchFolder: function (event) {
         const Galaxy = getGalaxyInstance();
         const search_term = $(".folder-search-input").val();
         this.options.search_term = search_term;
         Galaxy.libraries.folderListView.searchFolder(search_term);
     },
 
-    templateToolBar: function() {
+    templateToolBar: function () {
         return _.template(
             `<div class="library_style_container">
                 <div class="d-flex align-items-center mb-2">
@@ -1538,7 +1526,7 @@ var FolderToolbarView = Backbone.View.extend({
         );
     },
 
-    templateLocInfoInModal: function() {
+    templateLocInfoInModal: function () {
         return _.template(
             `<div>
                 <table class="grid table table-sm">
@@ -1605,7 +1593,7 @@ var FolderToolbarView = Backbone.View.extend({
         );
     },
 
-    templateImportIntoHistoryModal: function() {
+    templateImportIntoHistoryModal: function () {
         return _.template(
             `<div>
                 <div class="library-modal-item">
@@ -1627,7 +1615,7 @@ var FolderToolbarView = Backbone.View.extend({
         );
     },
 
-    templateImportIntoHistoryProgressBar: function() {
+    templateImportIntoHistoryProgressBar: function () {
         return _.template(
             `<div class="import_text">
                 Importing selected items to history <b><%= _.escape(history_name) %></b>
@@ -1641,7 +1629,7 @@ var FolderToolbarView = Backbone.View.extend({
         );
     },
 
-    templateAddingDatasetsProgressBar: function() {
+    templateAddingDatasetsProgressBar: function () {
         return _.template(
             `<div class="import_text">
                 Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>
@@ -1655,7 +1643,7 @@ var FolderToolbarView = Backbone.View.extend({
         );
     },
 
-    templateDeletingItemsProgressBar: function() {
+    templateDeletingItemsProgressBar: function () {
         return _.template(
             `<div class="import_text">
             </div>
@@ -1668,7 +1656,7 @@ var FolderToolbarView = Backbone.View.extend({
         );
     },
 
-    templateBrowserModal: function() {
+    templateBrowserModal: function () {
         return _.template(
             `<div id="file_browser_modal">
                     <div style="margin-bottom:1em;">
@@ -1731,7 +1719,7 @@ var FolderToolbarView = Backbone.View.extend({
         );
     },
 
-    templateImportPathModal: function() {
+    templateImportPathModal: function () {
         return _.template(
             `<div id="file_browser_modal">
                 <div class="alert alert-info jstree-folders-message">
@@ -1775,7 +1763,7 @@ var FolderToolbarView = Backbone.View.extend({
         );
     },
 
-    templateAddFilesFromHistory: function() {
+    templateAddFilesFromHistory: function () {
         return _.template(
             `<div id="add_files_modal">
                 <div class="form-group">
@@ -1794,7 +1782,7 @@ var FolderToolbarView = Backbone.View.extend({
         );
     },
 
-    templateHistoryContents: function() {
+    templateHistoryContents: function () {
         return _.template(
             `<div class="form-group">
                 <label>2. Choose the datasets to import:</label>
@@ -1854,7 +1842,7 @@ var FolderToolbarView = Backbone.View.extend({
         );
     },
 
-    templatePaginator: function() {
+    templatePaginator: function () {
         return _.template(
             `
                 <% if ( ( show_page - 1 ) > 0 ) { %>
@@ -1925,12 +1913,12 @@ var FolderToolbarView = Backbone.View.extend({
         );
     },
 
-    templatePaginatorText: function() {
+    templatePaginatorText: function () {
         return _.template(`per page,
             <%- total_items_count %> total`);
     },
 
-    templateCollectionSelectModal: function() {
+    templateCollectionSelectModal: function () {
         return _.template(
             `<div> <!-- elements selection -->
                 <div class="library-modal-item">
@@ -1995,9 +1983,9 @@ var FolderToolbarView = Backbone.View.extend({
                 </div>
             </div>`
         );
-    }
+    },
 });
 
 export default {
-    FolderToolbarView: FolderToolbarView
+    FolderToolbarView: FolderToolbarView,
 };
diff --git a/client/galaxy/scripts/mvc/library/library-library-view.js b/client/galaxy/scripts/mvc/library/library-library-view.js
index af02f41dc1ad..8a2218502afe 100644
--- a/client/galaxy/scripts/mvc/library/library-library-view.js
+++ b/client/galaxy/scripts/mvc/library/library-library-view.js
@@ -15,48 +15,48 @@ var LibraryView = Backbone.View.extend({
     options: {},
 
     events: {
-        "click .toolbtn_save_permissions": "savePermissions"
+        "click .toolbtn_save_permissions": "savePermissions",
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = _.extend(this.options, options);
         if (this.options.id) {
             this.fetchLibrary();
         }
     },
 
-    fetchLibrary: function(options) {
+    fetchLibrary: function (options) {
         this.options = _.extend(this.options, options);
         this.model = new mod_library_model.Library({
-            id: this.options.id
+            id: this.options.id,
         });
         var that = this;
         this.model.fetch({
-            success: function() {
+            success: function () {
                 if (that.options.show_permissions) {
                     that.showPermissions();
                 }
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 const Galaxy = getGalaxyInstance();
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(`${response.responseJSON.err_msg} Click this to go back.`, "", {
-                        onclick: function() {
+                        onclick: function () {
                             Galaxy.libraries.library_router.back();
-                        }
+                        },
                     });
                 } else {
                     Toast.error("An error occurred. Click this to go back.", "", {
-                        onclick: function() {
+                        onclick: function () {
                             Galaxy.libraries.library_router.back();
-                        }
+                        },
                     });
                 }
-            }
+            },
         });
     },
 
-    showPermissions: function(options) {
+    showPermissions: function (options) {
         this.options = _.extend(this.options, options);
         $(".tooltip").remove();
 
@@ -77,9 +77,9 @@ var LibraryView = Backbone.View.extend({
 
         var self = this;
         $.get(`${getAppRoot()}api/libraries/${self.id}/permissions?scope=current`)
-            .done(fetched_permissions => {
+            .done((fetched_permissions) => {
                 self.prepareSelectBoxes({
-                    fetched_permissions: fetched_permissions
+                    fetched_permissions: fetched_permissions,
                 });
             })
             .fail(() => {
@@ -91,7 +91,7 @@ var LibraryView = Backbone.View.extend({
         $("#center").css("overflow", "auto");
     },
 
-    _serializeRoles: function(role_list) {
+    _serializeRoles: function (role_list) {
         var selected_roles = [];
         for (var i = 0; i < role_list.length; i++) {
             selected_roles.push(`${role_list[i][1]}:${role_list[i][0]}`);
@@ -99,7 +99,7 @@ var LibraryView = Backbone.View.extend({
         return selected_roles;
     },
 
-    prepareSelectBoxes: function(options) {
+    prepareSelectBoxes: function (options) {
         this.options = _.extend(this.options, options);
         var fetched_permissions = this.options.fetched_permissions;
         var self = this;
@@ -123,7 +123,7 @@ var LibraryView = Backbone.View.extend({
         );
     },
 
-    _createSelectOptions: function(self, id, init_data, is_library_access) {
+    _createSelectOptions: function (self, id, init_data, is_library_access) {
         is_library_access = is_library_access === true ? is_library_access : false;
         var select_options = {
             minimumInputLength: 0,
@@ -137,19 +137,19 @@ var LibraryView = Backbone.View.extend({
                 }/permissions?scope=available&is_library_access=${is_library_access}`,
                 dataType: "json",
                 quietMillis: 100,
-                data: function(term, page) {
+                data: function (term, page) {
                     // page is the one-based page number tracked by Select2
                     return {
                         q: term, //search term
                         page_limit: 10, // page size
-                        page: page // page number
+                        page: page, // page number
                     };
                 },
-                results: function(data, page) {
+                results: function (data, page) {
                     var more = page * 10 < data.total; // whether or not there are more results available
                     // notice we return the value of more so Select2 knows if more results can be loaded
                     return { results: data.roles, more: more };
-                }
+                },
             },
             formatResult: function roleFormatResult(role) {
                 return `${role.name} type: ${role.type}`;
@@ -158,35 +158,35 @@ var LibraryView = Backbone.View.extend({
             formatSelection: function roleFormatSelection(role) {
                 return role.name;
             },
-            initSelection: function(element, callback) {
+            initSelection: function (element, callback) {
                 // the input tag has a value attribute preloaded that points to a preselected role's id
                 // this function resolves that id attribute to an object that select2 can render
                 // using its formatResult renderer - that way the role name is shown preselected
                 var data = [];
-                $(element.val().split(",")).each(function() {
+                $(element.val().split(",")).each(function () {
                     var item = this.split(":");
                     data.push({
                         id: item[0],
-                        name: item[1]
+                        name: item[1],
                     });
                 });
                 callback(data);
             },
             // initialData: init_data.join(','),
             initialData: init_data,
-            dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller
+            dropdownCssClass: "bigdrop", // apply css that makes the dropdown taller
         };
 
         return select_options;
     },
 
-    makeDatasetPrivate: function() {
+    makeDatasetPrivate: function () {
         var self = this;
         $.post(`${getAppRoot()}api/libraries/datasets/${self.id}/permissions?action=make_private`)
-            .done(fetched_permissions => {
+            .done((fetched_permissions) => {
                 self.model.set({ is_unrestricted: false });
                 self.showPermissions({
-                    fetched_permissions: fetched_permissions
+                    fetched_permissions: fetched_permissions,
                 });
                 Toast.success("The dataset is now private to you.");
             })
@@ -195,13 +195,13 @@ var LibraryView = Backbone.View.extend({
             });
     },
 
-    removeDatasetRestrictions: function() {
+    removeDatasetRestrictions: function () {
         var self = this;
         $.post(`${getAppRoot()}api/libraries/datasets/${self.id}/permissions?action=remove_restrictions`)
-            .done(fetched_permissions => {
+            .done((fetched_permissions) => {
                 self.model.set({ is_unrestricted: true });
                 self.showPermissions({
-                    fetched_permissions: fetched_permissions
+                    fetched_permissions: fetched_permissions,
                 });
                 Toast.success("Access to this dataset is now unrestricted.");
             })
@@ -210,14 +210,14 @@ var LibraryView = Backbone.View.extend({
             });
     },
 
-    _extractIds: function(roles_list) {
+    _extractIds: function (roles_list) {
         var ids_list = [];
         for (var i = roles_list.length - 1; i >= 0; i--) {
             ids_list.push(roles_list[i].id);
         }
         return ids_list;
     },
-    savePermissions: function(event) {
+    savePermissions: function (event) {
         var self = this;
 
         var access_ids = this._extractIds(this.accessSelectObject.$el.select2("data"));
@@ -229,12 +229,12 @@ var LibraryView = Backbone.View.extend({
             "access_ids[]": access_ids,
             "add_ids[]": add_ids,
             "manage_ids[]": manage_ids,
-            "modify_ids[]": modify_ids
+            "modify_ids[]": modify_ids,
         })
-            .done(fetched_permissions => {
+            .done((fetched_permissions) => {
                 //fetch dataset again
                 self.showPermissions({
-                    fetched_permissions: fetched_permissions
+                    fetched_permissions: fetched_permissions,
                 });
                 Toast.success("Permissions saved.");
             })
@@ -243,7 +243,7 @@ var LibraryView = Backbone.View.extend({
             });
     },
 
-    templateLibraryPermissions: function() {
+    templateLibraryPermissions: function () {
         return _.template(
             `<div class="library_style_container">
                 <div>
@@ -298,9 +298,9 @@ var LibraryView = Backbone.View.extend({
                 </div>
             </div>`
         );
-    }
+    },
 });
 
 export default {
-    LibraryView: LibraryView
+    LibraryView: LibraryView,
 };
diff --git a/client/galaxy/scripts/mvc/library/library-librarylist-view.js b/client/galaxy/scripts/mvc/library/library-librarylist-view.js
index 967671b8eb8e..d2078ae7c680 100644
--- a/client/galaxy/scripts/mvc/library/library-librarylist-view.js
+++ b/client/galaxy/scripts/mvc/library/library-librarylist-view.js
@@ -10,13 +10,13 @@ var LibraryListView = Backbone.View.extend({
     el: "#libraries_element",
 
     events: {
-        "click .sort-libraries-link": "sort_clicked"
+        "click .sort-libraries-link": "sort_clicked",
     },
 
     defaults: {
         page_count: null,
         show_page: null,
-        all_fetched: false
+        all_fetched: false,
     },
 
     /**
@@ -24,7 +24,7 @@ var LibraryListView = Backbone.View.extend({
      * Async render afterwards.
      * @param  {object} options an object with options
      */
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = _.defaults(this.options || {}, options, this.defaults);
         var that = this;
         this.modal = null;
@@ -32,16 +32,16 @@ var LibraryListView = Backbone.View.extend({
         this.collection = new mod_library_model.Libraries();
         this.collection.url = `${this.collection.urlRoot}?deleted=false`;
         this.collection.fetch({
-            success: function() {
+            success: function () {
                 that.render();
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(response.responseJSON.err_msg);
                 } else {
                     Toast.error("An error occurred.");
                 }
-            }
+            },
         });
     },
 
@@ -50,14 +50,14 @@ var LibraryListView = Backbone.View.extend({
      * or from a given array of library models,
      * or render an empty list in case no data is given.
      */
-    render: function(options) {
+    render: function (options) {
         const Galaxy = getGalaxyInstance();
         this.options = _.extend(this.options, options);
         this.setElement("#libraries_element");
         var template = this.templateLibraryList();
         var libraries_to_render = null;
         var models = null;
-        var is_public = model => model.get("public") === true;
+        var is_public = (model) => model.get("public") === true;
         $(".tooltip").hide();
         if (typeof options !== "undefined") {
             models = typeof options.models !== "undefined" ? options.models : null;
@@ -68,7 +68,7 @@ var LibraryListView = Backbone.View.extend({
                 libraries_to_render = this.collection.models;
             } else {
                 libraries_to_render = this.collection.where({
-                    deleted: false
+                    deleted: false,
                 });
             }
             if (Galaxy.libraries.preferences.get("without_restricted")) {
@@ -78,7 +78,7 @@ var LibraryListView = Backbone.View.extend({
             if (Galaxy.libraries.preferences.get("with_deleted")) {
                 libraries_to_render = models;
             } else {
-                var is_deleted = model => model.get("deleted") === false;
+                var is_deleted = (model) => model.get("deleted") === false;
                 libraries_to_render = _.filter(models, is_deleted);
             }
             if (Galaxy.libraries.preferences.get("without_restricted")) {
@@ -114,7 +114,7 @@ var LibraryListView = Backbone.View.extend({
                 template({
                     length: 1,
                     order: Galaxy.libraries.preferences.get("sort_order"),
-                    search_term: Galaxy.libraries.libraryToolbarView.options.search_term
+                    search_term: Galaxy.libraries.libraryToolbarView.options.search_term,
                 })
             );
             Galaxy.libraries.libraryToolbarView.renderPaginator(this.options);
@@ -124,7 +124,7 @@ var LibraryListView = Backbone.View.extend({
                 template({
                     length: 0,
                     order: Galaxy.libraries.preferences.get("sort_order"),
-                    search_term: Galaxy.libraries.libraryToolbarView.options.search_term
+                    search_term: Galaxy.libraries.libraryToolbarView.options.search_term,
                 })
             );
             Galaxy.libraries.libraryToolbarView.renderPaginator(this.options);
@@ -133,7 +133,7 @@ var LibraryListView = Backbone.View.extend({
         $("#center").css("overflow", "auto");
     },
 
-    fetchDeleted: function() {
+    fetchDeleted: function () {
         if (this.options.all_fetched) {
             this.render();
         } else {
@@ -141,17 +141,17 @@ var LibraryListView = Backbone.View.extend({
             this.collection.url = `${this.collection.urlRoot}?deleted=true`;
             this.collection.fetch({
                 remove: false,
-                success: function() {
+                success: function () {
                     that.options.all_fetched = true;
                     that.render();
                 },
-                error: function(model, response) {
+                error: function (model, response) {
                     if (typeof response.responseJSON !== "undefined") {
                         Toast.error(response.responseJSON.err_msg);
                     } else {
                         Toast.error("An error occurred.");
                     }
-                }
+                },
             });
         }
     },
@@ -160,7 +160,7 @@ var LibraryListView = Backbone.View.extend({
      * Render all given models as rows in the library list
      * @param  {array} libraries_to_render array of library models to render
      */
-    renderRows: function(libraries_to_render) {
+    renderRows: function (libraries_to_render) {
         for (var i = 0; i < libraries_to_render.length; i++) {
             var library = libraries_to_render[i];
             this.renderOne({ library: library });
@@ -171,7 +171,7 @@ var LibraryListView = Backbone.View.extend({
      * Create a view for the given model and add it to the libraries view.
      * @param {Library} model of the view that will be rendered
      */
-    renderOne: function(options) {
+    renderOne: function (options) {
         var library = options.library;
         var rowView = new mod_library_libraryrow_view.LibraryRowView(library);
         this.$el.find("#library_list_body").append(rowView.el);
@@ -181,7 +181,7 @@ var LibraryListView = Backbone.View.extend({
      * Table heading was clicked, update sorting preferences and re-render.
      * @return {[type]} [description]
      */
-    sort_clicked: function() {
+    sort_clicked: function () {
         const Galaxy = getGalaxyInstance();
         if (Galaxy.libraries.preferences.get("sort_order") === "asc") {
             Galaxy.libraries.preferences.set({ sort_order: "desc" });
@@ -195,7 +195,7 @@ var LibraryListView = Backbone.View.extend({
      * Sort the underlying collection according to the parameters received.
      * Currently supports only sorting by name.
      */
-    sortLibraries: function() {
+    sortLibraries: function () {
         const Galaxy = getGalaxyInstance();
         if (Galaxy.libraries.preferences.get("sort_by") === "name") {
             if (Galaxy.libraries.preferences.get("sort_order") === "asc") {
@@ -211,7 +211,7 @@ var LibraryListView = Backbone.View.extend({
      * the result. Render all visible libraries otherwise.
      * @param  {string} search_term string to search for
      */
-    searchLibraries: function(search_term) {
+    searchLibraries: function (search_term) {
         var trimmed_term = $.trim(search_term);
         if (trimmed_term !== "") {
             var results = null;
@@ -227,15 +227,12 @@ var LibraryListView = Backbone.View.extend({
     /**
      * Create the new library inline
      */
-    createLibraryInline: function() {
+    createLibraryInline: function () {
         if (this.$el.find("tr.new-row").length) {
             this.$el.find("tr.new-row textarea")[0].focus();
         } else {
             const template = this.templateNewRow();
-            this.$el
-                .find("#library_list_body")
-                .closest("table")
-                .show();
+            this.$el.find("#library_list_body").closest("table").show();
             this.$el.find("#library_list_body").prepend(template);
 
             this.$el.find("tr.new-row textarea")[0].focus();
@@ -257,24 +254,24 @@ var LibraryListView = Backbone.View.extend({
     /**
      * Create the new library using the API asynchronously.
      */
-    createNewLibrary: function(name, description, synopsis) {
+    createNewLibrary: function (name, description, synopsis) {
         const Galaxy = getGalaxyInstance();
         const libraryDetails = {
             name,
             description,
-            synopsis
+            synopsis,
         };
         if (libraryDetails.name !== "") {
             var library = new mod_library_model.Library();
             library.save(libraryDetails, {
-                success: library => {
+                success: (library) => {
                     Galaxy.libraries.libraryListView.collection.add(library);
                     this.$el.find("tr.new-row").remove();
                     Galaxy.libraries.libraryListView.render();
 
                     $(`tr[data-id="${library.attributes.id}"`)
                         .addClass("table-success")
-                        .on("mouseover click", function() {
+                        .on("mouseover click", function () {
                             $(this).removeClass("table-success");
                         });
 
@@ -286,7 +283,7 @@ var LibraryListView = Backbone.View.extend({
                     } else {
                         Toast.error("An error occurred.");
                     }
-                }
+                },
             });
         } else {
             Toast.error("Library's name is missing.");
@@ -298,7 +295,7 @@ var LibraryListView = Backbone.View.extend({
     // === TEMPLATES ====
     // MMMMMMMMMMMMMMMMMM
 
-    templateNewRow: function() {
+    templateNewRow: function () {
         return _.template(
             `<tr class="new-row">
                     <td>
@@ -324,7 +321,7 @@ var LibraryListView = Backbone.View.extend({
         );
     },
 
-    templateLibraryList: function() {
+    templateLibraryList: function () {
         return _.template(
             `<div class="library_container table-responsive">
                 <table class="grid table table-sm"
@@ -359,9 +356,9 @@ var LibraryListView = Backbone.View.extend({
                 <% }%>
             </div>`
         );
-    }
+    },
 });
 
 export default {
-    LibraryListView: LibraryListView
+    LibraryListView: LibraryListView,
 };
diff --git a/client/galaxy/scripts/mvc/library/library-libraryrow-view.js b/client/galaxy/scripts/mvc/library/library-libraryrow-view.js
index c673a85c17eb..97833b988b22 100644
--- a/client/galaxy/scripts/mvc/library/library-libraryrow-view.js
+++ b/client/galaxy/scripts/mvc/library/library-libraryrow-view.js
@@ -11,7 +11,7 @@ var LibraryRowView = Backbone.View.extend({
         "click .cancel_library_btn": "cancel_library_modification",
         "click .save_library_btn": "save_library_modification",
         "click .delete_library_btn": "delete_library",
-        "click .undelete_library_btn": "undelete_library"
+        "click .undelete_library_btn": "undelete_library",
     },
 
     edit_mode: false,
@@ -23,14 +23,14 @@ var LibraryRowView = Backbone.View.extend({
         save_library_btn: false,
         cancel_library_btn: false,
         delete_library_btn: false,
-        undelete_library_btn: false
+        undelete_library_btn: false,
     },
 
-    initialize: function(library) {
+    initialize: function (library) {
         this.render(library);
     },
 
-    render: function(library) {
+    render: function (library) {
         if (typeof library === "undefined") {
             const Galaxy = getGalaxyInstance();
             library = Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));
@@ -42,14 +42,14 @@ var LibraryRowView = Backbone.View.extend({
             tmpl({
                 library: library,
                 button_config: this.element_visibility_config,
-                edit_mode: this.edit_mode
+                edit_mode: this.edit_mode,
             })
         );
         this.$el.show();
         return this;
     },
 
-    repaint: function(library) {
+    repaint: function (library) {
         /* need to dispose manually because of the element removal in setElement
     invoked in render() */
         this.$el.find('[data-toggle="tooltip"]').tooltip("dispose");
@@ -68,7 +68,7 @@ var LibraryRowView = Backbone.View.extend({
      * Function modifies the visibility of buttons for
      * the filling of the row template of given library.
      */
-    prepareButtons: function(library) {
+    prepareButtons: function (library) {
         var vis_config = this.element_visibility_config;
 
         if (this.edit_mode === false) {
@@ -109,19 +109,19 @@ var LibraryRowView = Backbone.View.extend({
 
     /* User clicked the 'edit' button on row so we render a new row
     that allows editing */
-    edit_button_clicked: function() {
+    edit_button_clicked: function () {
         this.edit_mode = true;
         this.repaint();
     },
 
     /* User clicked the 'cancel' button so we render normal rowView */
-    cancel_library_modification: function() {
+    cancel_library_modification: function () {
         // Toast.info('Modifications canceled');
         this.edit_mode = false;
         this.repaint();
     },
 
-    save_library_modification: function() {
+    save_library_modification: function () {
         const Galaxy = getGalaxyInstance();
         var library = Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));
         var is_changed = false;
@@ -153,18 +153,18 @@ var LibraryRowView = Backbone.View.extend({
             var row_view = this;
             library.save(null, {
                 patch: true,
-                success: function(library) {
+                success: function (library) {
                     row_view.edit_mode = false;
                     row_view.repaint(library);
                     Toast.success("Changes to library saved.");
                 },
-                error: function(model, response) {
+                error: function (model, response) {
                     if (typeof response.responseJSON !== "undefined") {
                         Toast.error(response.responseJSON.err_msg);
                     } else {
                         Toast.error("An error occurred while attempting to update the library.");
                     }
-                }
+                },
             });
         } else {
             this.edit_mode = false;
@@ -173,13 +173,13 @@ var LibraryRowView = Backbone.View.extend({
         }
     },
 
-    delete_library: function() {
+    delete_library: function () {
         const Galaxy = getGalaxyInstance();
         var library = Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));
         var row_view = this;
         // mark the library deleted
         library.destroy({
-            success: function(library) {
+            success: function (library) {
                 library.set("deleted", true);
                 // add the new deleted library back to the collection (Galaxy specialty)
                 Galaxy.libraries.libraryListView.collection.add(library);
@@ -193,17 +193,17 @@ var LibraryRowView = Backbone.View.extend({
                 }
                 Toast.success("Library has been marked deleted.");
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(response.responseJSON.err_msg);
                 } else {
                     Toast.error("An error occurred during deleting the library.");
                 }
-            }
+            },
         });
     },
 
-    undelete_library: function() {
+    undelete_library: function () {
         const Galaxy = getGalaxyInstance();
         var library = Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));
         var row_view = this;
@@ -211,7 +211,7 @@ var LibraryRowView = Backbone.View.extend({
         // mark the library undeleted
         library.url = `${library.urlRoot + library.id}?undelete=true`;
         library.destroy({
-            success: function(library) {
+            success: function (library) {
                 // add the newly undeleted library back to the collection
                 // backbone does not accept changes through destroy, so update it too
                 library.set("deleted", false);
@@ -220,17 +220,17 @@ var LibraryRowView = Backbone.View.extend({
                 row_view.repaint(library);
                 Toast.success("Library has been undeleted.");
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(response.responseJSON.err_msg);
                 } else {
                     Toast.error("An error occurred while undeleting the library.");
                 }
-            }
+            },
         });
     },
 
-    templateRow: function() {
+    templateRow: function () {
         return _.template(
             `<tr class="<% if(library.get("deleted") === true) { print("active") } %>"
                 style="display:none;" data-id="<%- library.get("id") %>">
@@ -323,9 +323,9 @@ var LibraryRowView = Backbone.View.extend({
                 </td>
             </tr>`
         );
-    }
+    },
 });
 
 export default {
-    LibraryRowView: LibraryRowView
+    LibraryRowView: LibraryRowView,
 };
diff --git a/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js b/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
index f419375d16a6..fda5d681c1a9 100644
--- a/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
@@ -11,7 +11,7 @@ var LibraryToolbarView = Backbone.View.extend({
     el: "#center",
 
     defaults: {
-        search_term: ""
+        search_term: "",
     },
 
     events: {
@@ -20,15 +20,15 @@ var LibraryToolbarView = Backbone.View.extend({
         "click #exclude_restricted_chk": "excludeRestrictedChecked",
         "keydown .page_size": "changePageSize",
         "blur .page_size": "changePageSize",
-        "keyup .library-search-input": "searchLibraries"
+        "keyup .library-search-input": "searchLibraries",
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = _.defaults(this.options || {}, options, this.defaults);
         this.render();
     },
 
-    render: function() {
+    render: function () {
         const Galaxy = getGalaxyInstance();
         var toolbar_template = this.templateToolBar();
         var is_admin = false;
@@ -41,7 +41,7 @@ var LibraryToolbarView = Backbone.View.extend({
             toolbar_template({
                 admin_user: is_admin,
                 anon_user: is_anonym,
-                library_page_size: Galaxy.libraries.preferences.get("library_page_size")
+                library_page_size: Galaxy.libraries.preferences.get("library_page_size"),
             })
         );
         if (is_admin) {
@@ -55,7 +55,7 @@ var LibraryToolbarView = Backbone.View.extend({
     /**
      * Renders the element that shows pages into its div within the toolbar.
      */
-    renderPaginator: function(options) {
+    renderPaginator: function (options) {
         const Galaxy = getGalaxyInstance();
         this.options = _.extend(this.options, options);
         var paginator_template = this.templatePaginator();
@@ -66,7 +66,7 @@ var LibraryToolbarView = Backbone.View.extend({
                 page_count: parseInt(this.options.page_count),
                 total_libraries_count: this.options.total_libraries_count,
                 libraries_shown: this.options.libraries_shown,
-                library_page_size: Galaxy.libraries.preferences.get("library_page_size")
+                library_page_size: Galaxy.libraries.preferences.get("library_page_size"),
             })
         );
         this.$el.find(".library-paginator > .paginator-text").html(
@@ -75,7 +75,7 @@ var LibraryToolbarView = Backbone.View.extend({
                 page_count: parseInt(this.options.page_count),
                 total_libraries_count: this.options.total_libraries_count,
                 libraries_shown: this.options.libraries_shown,
-                library_page_size: Galaxy.libraries.preferences.get("library_page_size")
+                library_page_size: Galaxy.libraries.preferences.get("library_page_size"),
             })
         );
     },
@@ -83,7 +83,7 @@ var LibraryToolbarView = Backbone.View.extend({
     /**
      * Crreate the new library inline
      */
-    createLibraryInline: function() {
+    createLibraryInline: function () {
         const Galaxy = getGalaxyInstance();
         Galaxy.libraries.libraryListView.createLibraryInline();
     },
@@ -91,12 +91,12 @@ var LibraryToolbarView = Backbone.View.extend({
     /**
      * Change the number of libs shown on page.
      */
-    changePageSize: function(e) {
+    changePageSize: function (e) {
         if (e.type === "focusout" || (e.type === "keydown" && e.keyCode === 13)) {
             e.preventDefault();
             const Galaxy = getGalaxyInstance();
             Galaxy.libraries.preferences.set({
-                library_page_size: parseInt(e.target.value)
+                library_page_size: parseInt(e.target.value),
             });
             Galaxy.libraries.libraryListView.render({ show_page: 1 });
         }
@@ -105,7 +105,7 @@ var LibraryToolbarView = Backbone.View.extend({
     /**
      * Include or exclude deleted libraries in the view.
      */
-    includeDeletedChecked: function(event) {
+    includeDeletedChecked: function (event) {
         const Galaxy = getGalaxyInstance();
         if (event.target.checked) {
             Galaxy.libraries.preferences.set({ with_deleted: true });
@@ -119,7 +119,7 @@ var LibraryToolbarView = Backbone.View.extend({
     /**
      * Include or exclude restricted libraries in the view.
      */
-    excludeRestrictedChecked: function(event) {
+    excludeRestrictedChecked: function (event) {
         const Galaxy = getGalaxyInstance();
         if (event.target.checked) {
             Galaxy.libraries.preferences.set({ without_restricted: true });
@@ -133,14 +133,14 @@ var LibraryToolbarView = Backbone.View.extend({
      * Take the contents of the search field and send it to the list view
      * to query the collection of libraries.
      */
-    searchLibraries: function(event) {
+    searchLibraries: function (event) {
         const Galaxy = getGalaxyInstance();
         var search_term = $(".library-search-input").val();
         this.options.search_term = search_term;
         Galaxy.libraries.libraryListView.searchLibraries(search_term);
     },
 
-    templateToolBar: function() {
+    templateToolBar: function () {
         return _.template(
             `<div class="library_style_container">
                 <div class="d-flex align-items-center mb-2 library-toolbar">
@@ -178,7 +178,7 @@ var LibraryToolbarView = Backbone.View.extend({
         );
     },
 
-    templatePaginator: function() {
+    templatePaginator: function () {
         return _.template(
             `
                         <% if ( ( show_page - 1 ) > 0 ) { %>
@@ -248,11 +248,11 @@ var LibraryToolbarView = Backbone.View.extend({
                 `
         );
     },
-    templatePaginatorText: function() {
+    templatePaginatorText: function () {
         return _.template(`per page, <%- total_libraries_count %> total`);
-    }
+    },
 });
 
 export default {
-    LibraryToolbarView: LibraryToolbarView
+    LibraryToolbarView: LibraryToolbarView,
 };
diff --git a/client/galaxy/scripts/mvc/library/library-model.js b/client/galaxy/scripts/mvc/library/library-model.js
index b8b0a4ea24b5..d9cccef37128 100644
--- a/client/galaxy/scripts/mvc/library/library-model.js
+++ b/client/galaxy/scripts/mvc/library/library-model.js
@@ -12,13 +12,13 @@ var Library = Backbone.Model.extend({
     /** based on show_deleted would this lib show in the list of lib's?
      *  @param {Boolean} show_deleted are we including deleted libraries?
      */
-    isVisible: function(show_deleted) {
+    isVisible: function (show_deleted) {
         var isVisible = true;
         if (!show_deleted && this.get("deleted")) {
             isVisible = false;
         }
         return isVisible;
-    }
+    },
 });
 
 var Libraries = Backbone.Collection.extend({
@@ -26,11 +26,11 @@ var Libraries = Backbone.Collection.extend({
 
     model: Library,
 
-    initialize: function(options) {
+    initialize: function (options) {
         options = options || {};
     },
 
-    search: function(search_term) {
+    search: function (search_term) {
         /**
          * Search the collection and return only the models that have
          * the search term in their names.
@@ -39,7 +39,7 @@ var Libraries = Backbone.Collection.extend({
          */
         if (search_term == "") return this;
         var lowercase_term = search_term.toLowerCase();
-        return this.filter(data => {
+        return this.filter((data) => {
             var lowercase_name = data.get("name").toLowerCase();
             return lowercase_name.indexOf(lowercase_term) !== -1;
         });
@@ -49,15 +49,15 @@ var Libraries = Backbone.Collection.extend({
      *  @param {Boolean} show_deleted are we including deleted libraries?
      *  @returns array of library models
      */
-    getVisible: function(show_deleted, filters) {
+    getVisible: function (show_deleted, filters) {
         filters = filters || [];
-        return new Libraries(this.filter(item => item.isVisible(show_deleted)));
+        return new Libraries(this.filter((item) => item.isVisible(show_deleted)));
     },
 
-    sortLibraries: function(sort_key, sort_order) {
+    sortLibraries: function (sort_key, sort_order) {
         this.comparator = mod_util.generateComparator(sort_key, sort_order);
         this.sort();
-    }
+    },
 });
 
 // ============================================================================
@@ -66,22 +66,22 @@ var Libraries = Backbone.Collection.extend({
 var LibraryItem = Backbone.Model.extend({});
 
 var Ldda = LibraryItem.extend({
-    urlRoot: `${getAppRoot()}api/libraries/datasets/`
+    urlRoot: `${getAppRoot()}api/libraries/datasets/`,
 });
 
 var FolderAsModel = LibraryItem.extend({
-    urlRoot: `${getAppRoot()}api/folders/`
+    urlRoot: `${getAppRoot()}api/folders/`,
 });
 
 var Folder = Backbone.Collection.extend({
-    model: LibraryItem
+    model: LibraryItem,
 });
 
 var FolderContainer = Backbone.Model.extend({
     defaults: {
         folder: new Folder(),
         urlRoot: `${getAppRoot()}api/folders/`,
-        id: "unknown"
+        id: "unknown",
     },
 
     /**
@@ -90,22 +90,22 @@ var FolderContainer = Backbone.Model.extend({
      * [the term to search]
      * @type {string}
      */
-    search: function(search_term) {
+    search: function (search_term) {
         if (search_term == "") return this;
         const lowercase_term = search_term.toLowerCase();
-        return this.get("folder").filter(data => {
+        return this.get("folder").filter((data) => {
             const lowercase_name = data.get("name").toLowerCase();
             return lowercase_name.indexOf(lowercase_term) !== -1;
         });
     },
 
-    sortFolder: function(sort_key, sort_order) {
+    sortFolder: function (sort_key, sort_order) {
         this.get("folder").comparator = mod_util.generateComparator(sort_key, sort_order);
         this.get("folder").sort();
         return this.get("folder");
     },
 
-    parse: function(obj) {
+    parse: function (obj) {
         const Galaxy = getGalaxyInstance();
         // empty the collection
         this.get("folder").reset();
@@ -123,7 +123,7 @@ var FolderContainer = Backbone.Model.extend({
             }
         }
         return obj;
-    }
+    },
 });
 
 // ============================================================================
@@ -131,27 +131,27 @@ var FolderContainer = Backbone.Model.extend({
 // TODO UNITE
 
 var HistoryItem = Backbone.Model.extend({
-    urlRoot: `${getAppRoot()}api/histories/`
+    urlRoot: `${getAppRoot()}api/histories/`,
 });
 
 var HistoryContents = Backbone.Collection.extend({
     urlRoot: `${getAppRoot()}api/histories/`,
-    initialize: function(options) {
+    initialize: function (options) {
         this.id = options.id;
     },
-    url: function() {
+    url: function () {
         return `${this.urlRoot + this.id}/contents`;
     },
-    model: HistoryItem
+    model: HistoryItem,
 });
 
 var GalaxyHistory = Backbone.Model.extend({
-    urlRoot: `${getAppRoot()}api/histories/`
+    urlRoot: `${getAppRoot()}api/histories/`,
 });
 
 var GalaxyHistories = Backbone.Collection.extend({
     url: `${getAppRoot()}api/histories`,
-    model: GalaxyHistory
+    model: GalaxyHistory,
 });
 
 // ============================================================================
@@ -161,7 +161,7 @@ var GalaxyHistories = Backbone.Collection.extend({
  */
 
 var Jstree = Backbone.Model.extend({
-    urlRoot: `${getAppRoot()}api/remote_files`
+    urlRoot: `${getAppRoot()}api/remote_files`,
 });
 
 export default {
@@ -176,5 +176,5 @@ export default {
     HistoryContents: HistoryContents,
     GalaxyHistory: GalaxyHistory,
     GalaxyHistories: GalaxyHistories,
-    Jstree: Jstree
+    Jstree: Jstree,
 };
diff --git a/client/galaxy/scripts/mvc/library/library-util.js b/client/galaxy/scripts/mvc/library/library-util.js
index ab330d9925db..7b1a8ff66aad 100644
--- a/client/galaxy/scripts/mvc/library/library-util.js
+++ b/client/galaxy/scripts/mvc/library/library-util.js
@@ -33,5 +33,5 @@ var generateComparator = (sort_key, sort_order) => (itemA, itemB) => {
     return 0; // equal
 };
 export default {
-    generateComparator: generateComparator
+    generateComparator: generateComparator,
 };
diff --git a/client/galaxy/scripts/mvc/list/list-item.js b/client/galaxy/scripts/mvc/list/list-item.js
index f4e1791c8640..72f24a8cdc6c 100644
--- a/client/galaxy/scripts/mvc/list/list-item.js
+++ b/client/galaxy/scripts/mvc/list/list-item.js
@@ -16,7 +16,7 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
     //PRECONDITION: model must have method hasDetails
     //PRECONDITION: subclasses must have templates.el and templates.details
 
-    initialize: function(attributes) {
+    initialize: function (attributes) {
         /** are the details of this view expanded/shown or not? */
         this.expanded = attributes.expanded || false;
         this.log("\t expanded:", this.expanded);
@@ -30,7 +30,7 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
     /** Render this content, set up ui.
      *  @param {Number or String} speed   the speed of the render
      */
-    render: function(speed) {
+    render: function (speed) {
         var $newRender = this._buildNewRender();
         this._setUpBehaviors($newRender);
         this._queueNewRender($newRender, speed);
@@ -40,7 +40,7 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
     /** Build a temp div containing the new children for the view's $el.
      *      If the view is already expanded, build the details as well.
      */
-    _buildNewRender: function() {
+    _buildNewRender: function () {
         // create a new render using a skeleton template, render title buttons, render body, and set up events, etc.
         var $newRender = $(this.templates.el(this.model.toJSON(), this));
         if (this.expanded) {
@@ -53,7 +53,7 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
      *  @param {Number or String} speed   jq speed to use for rendering effects
      *  @fires rendered when rendered
      */
-    _queueNewRender: function($newRender, speed) {
+    _queueNewRender: function ($newRender, speed) {
         speed = speed === undefined ? this.fxSpeed : speed;
         var view = this;
 
@@ -62,26 +62,26 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
             view.trigger("rendered", view);
         } else {
             $(view).queue("fx", [
-                next => {
+                (next) => {
                     view.$el.fadeOut(speed, next);
                 },
-                next => {
+                (next) => {
                     view._swapNewRender($newRender);
                     next();
                 },
-                next => {
+                (next) => {
                     view.$el.fadeIn(speed, next);
                 },
-                next => {
+                (next) => {
                     view.trigger("rendered", view);
                     next();
-                }
+                },
             ]);
         }
     },
 
     /** empty out the current el, move the $newRender's children in */
-    _swapNewRender: function($newRender) {
+    _swapNewRender: function ($newRender) {
         return this.$el
             .empty()
             .attr("class", _.isFunction(this.className) ? this.className() : this.className)
@@ -91,7 +91,7 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
     /** set up js behaviors, event handlers for elements within the given container
      *  @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el)
      */
-    _setUpBehaviors: function($where) {
+    _setUpBehaviors: function ($where) {
         $where = $where || this.$el;
         // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.)
         //make_popup_menus( $where );
@@ -100,13 +100,13 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
 
     // ......................................................................... details
     /** shortcut to details DOM (as jQ) */
-    $details: function($where) {
+    $details: function ($where) {
         $where = $where || this.$el;
         return $where.find("> .details");
     },
 
     /** build the DOM for the details and set up behaviors on it */
-    _renderDetails: function() {
+    _renderDetails: function () {
         var $newDetails = $(this.templates.details(this.model.toJSON(), this));
         this._setUpBehaviors($newDetails);
         return $newDetails;
@@ -116,7 +116,7 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
     /** Show or hide the details
      *  @param {Boolean} expand if true, expand; if false, collapse
      */
-    toggleExpanded: function(expand) {
+    toggleExpanded: function (expand) {
         expand = expand === undefined ? !this.expanded : expand;
         if (expand) {
             this.expand();
@@ -130,7 +130,7 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
      *      note: if the model does not have detailed data, fetch that data before showing the body
      *  @fires expanded when a body has been expanded
      */
-    expand: function() {
+    expand: function () {
         var view = this;
         return view._fetchModelDetails().always(() => {
             view._expand();
@@ -140,7 +140,7 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
     /** Check for model details and, if none, fetch them.
      *  @returns {jQuery.promise} the model.fetch.xhr if details are being fetched, an empty promise if not
      */
-    _fetchModelDetails: function() {
+    _fetchModelDetails: function () {
         if (!this.model.hasDetails()) {
             return this.model.fetch();
         }
@@ -148,7 +148,7 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
     },
 
     /** Inner fn called when expand (public) has fetched the details */
-    _expand: function() {
+    _expand: function () {
         var view = this;
         var $newDetails = view._renderDetails();
         view.$details().replaceWith($newDetails);
@@ -162,14 +162,14 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
     /** Hide the body/details of an HDA.
      *  @fires collapsed when a body has been collapsed
      */
-    collapse: function() {
+    collapse: function () {
         this.debug(`${this}(ExpandableView).collapse`);
         var view = this;
         view.expanded = false;
         this.$details().slideUp(view.fxSpeed, () => {
             view.trigger("collapsed", view);
         });
-    }
+    },
 });
 
 //==============================================================================
@@ -190,7 +190,7 @@ export var ListItemView = ExpandableView.extend(
         className: "list-item",
 
         /** Set up the base class and all mixins */
-        initialize: function(attributes) {
+        initialize: function (attributes) {
             ExpandableView.prototype.initialize.call(this, attributes);
             BASE_MVC.SelectableViewMixin.initialize.call(this, attributes);
             BASE_MVC.DraggableViewMixin.initialize.call(this, attributes);
@@ -198,11 +198,11 @@ export var ListItemView = ExpandableView.extend(
         },
 
         /** event listeners */
-        _setUpListeners: function() {
+        _setUpListeners: function () {
             // hide the primary actions in the title bar when selectable and narrow
             this.on(
                 "selectable",
-                function(isSelectable) {
+                function (isSelectable) {
                     if (isSelectable) {
                         this.$(".primary-actions").hide();
                     } else {
@@ -216,7 +216,7 @@ export var ListItemView = ExpandableView.extend(
 
         // ........................................................................ rendering
         /** In this override, call methods to build warnings, titlebar and primary actions */
-        _buildNewRender: function() {
+        _buildNewRender: function () {
             var $newRender = ExpandableView.prototype._buildNewRender.call(this);
             $newRender.children(".warnings").replaceWith(this._renderWarnings());
             $newRender.children(".title-bar").replaceWith(this._renderTitleBar());
@@ -226,7 +226,7 @@ export var ListItemView = ExpandableView.extend(
         },
 
         /** In this override, render the selector controls and set up dragging before the swap */
-        _swapNewRender: function($newRender) {
+        _swapNewRender: function ($newRender) {
             ExpandableView.prototype._swapNewRender.call(this, $newRender);
             if (this.selectable) {
                 this.showSelector(0);
@@ -238,30 +238,30 @@ export var ListItemView = ExpandableView.extend(
         },
 
         /** Render any warnings the item may need to show (e.g. "I'm deleted") */
-        _renderWarnings: function() {
+        _renderWarnings: function () {
             var view = this;
             var $warnings = $('<div class="warnings"></div>');
             var json = view.model.toJSON();
             //TODO:! unordered (map)
-            _.each(view.templates.warnings, templateFn => {
+            _.each(view.templates.warnings, (templateFn) => {
                 $warnings.append($(templateFn(json, view)));
             });
             return $warnings;
         },
 
         /** Render the title bar (the main/exposed SUMMARY dom element) */
-        _renderTitleBar: function() {
+        _renderTitleBar: function () {
             return $(this.templates.titleBar(this.model.toJSON(), this));
         },
 
         /** Return an array of jQ objects containing common/easily-accessible item controls */
-        _renderPrimaryActions: function() {
+        _renderPrimaryActions: function () {
             // override this
             return [];
         },
 
         /** Render the title bar (the main/exposed SUMMARY dom element) */
-        _renderSubtitle: function() {
+        _renderSubtitle: function () {
             return $(this.templates.subtitle(this.model.toJSON(), this));
         },
 
@@ -271,11 +271,11 @@ export var ListItemView = ExpandableView.extend(
             // expand the body when the title is clicked or when in focus and space or enter is pressed
             "click .title-bar": "_clickTitleBar",
             "keydown .title-bar": "_keyDownTitleBar",
-            "click .selector": "toggleSelect"
+            "click .selector": "toggleSelect",
         },
 
         /** expand when the title bar is clicked */
-        _clickTitleBar: function(event) {
+        _clickTitleBar: function (event) {
             event.stopPropagation();
             if (event.altKey) {
                 this.toggleSelect(event);
@@ -288,7 +288,7 @@ export var ListItemView = ExpandableView.extend(
         },
 
         /** expand when the title bar is in focus and enter or space is pressed */
-        _keyDownTitleBar: function(event) {
+        _keyDownTitleBar: function (event) {
             // bail (with propagation) if keydown and not space or enter
             var KEYCODE_SPACE = 32;
 
@@ -307,10 +307,10 @@ export var ListItemView = ExpandableView.extend(
 
         // ......................................................................... misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             var modelString = this.model ? `${this.model}` : "(no model)";
             return `ListItemView(${modelString})`;
-        }
+        },
     })
 );
 
@@ -332,7 +332,7 @@ ListItemView.prototype.templates = (() => {
 
         // expandable area for more details
         '<div class="details"></div>',
-        "</div>"
+        "</div>",
     ]);
 
     var warnings = {};
@@ -347,19 +347,19 @@ ListItemView.prototype.templates = (() => {
             '<span class="name"><%- element.name %></span>',
             "</div>",
             '<div class="subtitle"></div>',
-            "</div>"
+            "</div>",
         ],
         "element"
     );
 
     var subtitleTemplate = BASE_MVC.wrapTemplate([
         // override this
-        '<div class="subtitle"></div>'
+        '<div class="subtitle"></div>',
     ]);
 
     var detailsTemplate = BASE_MVC.wrapTemplate([
         // override this
-        '<div class="details"></div>'
+        '<div class="details"></div>',
     ]);
 
     return {
@@ -367,7 +367,7 @@ ListItemView.prototype.templates = (() => {
         warnings: warnings,
         titleBar: titleBarTemplate,
         subtitle: subtitleTemplate,
-        details: detailsTemplate
+        details: detailsTemplate,
     };
 })();
 
@@ -395,7 +395,7 @@ export var FoldoutListItemView = ListItemView.extend({
      *      add attributes foldoutStyle and foldoutPanelClass for config poly
      *      disrespect attributes.expanded if drilldown
      */
-    initialize: function(attributes) {
+    initialize: function (attributes) {
         if (this.foldoutStyle === "drilldown") {
             this.expanded = false;
         }
@@ -407,7 +407,7 @@ export var FoldoutListItemView = ListItemView.extend({
     },
 
     /** in this override, attach the foldout panel when rendering details */
-    _renderDetails: function() {
+    _renderDetails: function () {
         if (this.foldoutStyle === "drilldown") {
             return $();
         }
@@ -416,35 +416,35 @@ export var FoldoutListItemView = ListItemView.extend({
     },
 
     /** In this override, handle collection expansion. */
-    _createFoldoutPanel: function() {
+    _createFoldoutPanel: function () {
         var model = this.model;
         var FoldoutClass = this._getFoldoutPanelClass(model);
         var options = this._getFoldoutPanelOptions(model);
 
         return new FoldoutClass(
             _.extend(options, {
-                model: model
+                model: model,
             })
         );
     },
 
     /** Stub to return proper foldout panel class */
-    _getFoldoutPanelClass: function() {
+    _getFoldoutPanelClass: function () {
         // override
         return this.foldoutPanelClass;
     },
 
     /** Stub to return proper foldout panel options */
-    _getFoldoutPanelOptions: function() {
+    _getFoldoutPanelOptions: function () {
         return {
             // propagate foldout style down
             foldoutStyle: this.foldoutStyle,
-            fxSpeed: this.fxSpeed
+            fxSpeed: this.fxSpeed,
         };
     },
 
     /** Render the foldout panel inside the view, hiding controls */
-    _attachFoldout: function(foldout, $whereTo) {
+    _attachFoldout: function (foldout, $whereTo) {
         $whereTo = $whereTo || this.$("> .details");
         this.foldout = foldout.render(0);
         foldout.$("> .controls").hide();
@@ -452,7 +452,7 @@ export var FoldoutListItemView = ListItemView.extend({
     },
 
     /** In this override, branch on foldoutStyle to show expanded */
-    expand: function() {
+    expand: function () {
         var view = this;
         return view._fetchModelDetails().always(() => {
             if (view.foldoutStyle === "foldout") {
@@ -467,14 +467,14 @@ export var FoldoutListItemView = ListItemView.extend({
      *      containing views can listen to this and handle other things
      *      (like hiding themselves) by listening for expanded/collapsed:drilldown
      */
-    _expandByDrilldown: function() {
+    _expandByDrilldown: function () {
         var view = this;
         // attachment and rendering done by listener
         view.listenTo(view.foldout, "close", () => {
             view.trigger("collapsed:drilldown", view, view.foldout);
         });
         view.trigger("expanded:drilldown", view, view.foldout);
-    }
+    },
 });
 
 // ............................................................................ TEMPLATES
@@ -484,13 +484,13 @@ FoldoutListItemView.prototype.templates = (() => {
         [
             '<div class="details">',
             // override with more info (that goes above the panel)
-            "</div>"
+            "</div>",
         ],
         "collection"
     );
 
     return _.extend({}, ListItemView.prototype.templates, {
-        details: detailsTemplate
+        details: detailsTemplate,
     });
 })();
 
@@ -498,5 +498,5 @@ FoldoutListItemView.prototype.templates = (() => {
 export default {
     ExpandableView: ExpandableView,
     ListItemView: ListItemView,
-    FoldoutListItemView: FoldoutListItemView
+    FoldoutListItemView: FoldoutListItemView,
 };
diff --git a/client/galaxy/scripts/mvc/list/list-view.js b/client/galaxy/scripts/mvc/list/list-view.js
index eabe0dc817ff..7329927644be 100644
--- a/client/galaxy/scripts/mvc/list/list-view.js
+++ b/client/galaxy/scripts/mvc/list/list-view.js
@@ -51,7 +51,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         /** Set up the view, set up storage, bind listeners to HistoryContents events
          *  @param {Object} attributes optional settings for the list
          */
-        initialize: function(attributes, options) {
+        initialize: function (attributes, options) {
             attributes = attributes || {};
             // set the logger if requested
             if (attributes.logger) {
@@ -107,27 +107,27 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
 
         // ------------------------------------------------------------------------ listeners
         /** create any event listeners for the list */
-        _setUpListeners: function() {
+        _setUpListeners: function () {
             this.off();
 
             //TODO: move errorHandler down into list-view from history-view or
             //  pass to global error handler (Galaxy)
             this.on({
-                error: function(model, xhr, options, msg, details) {
+                error: function (model, xhr, options, msg, details) {
                     //this.errorHandler( model, xhr, options, msg, details );
                     console.error(model, xhr, options, msg, details);
                 },
                 // show hide the loading indicator
-                loading: function() {
+                loading: function () {
                     this._showLoadingIndicator("loading...", 40);
                 },
-                "loading-done": function() {
+                "loading-done": function () {
                     this._hideLoadingIndicator(40);
-                }
+                },
             });
 
             // throw the first render up as a diff namespace using once (for outside consumption)
-            this.once("rendered", function() {
+            this.once("rendered", function () {
                 this.trigger("rendered:initial", this);
             });
 
@@ -137,22 +137,22 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** create and return a collection for when none is initially passed */
-        _createDefaultCollection: function() {
+        _createDefaultCollection: function () {
             // override
             return new this.collectionClass([]);
         },
 
         /** listening for collection events */
-        _setUpCollectionListeners: function() {
+        _setUpCollectionListeners: function () {
             this.log(`${this}._setUpCollectionListeners`, this.collection);
             this.stopListening(this.collection);
 
             // bubble up error events
             this.listenTo(this.collection, {
-                error: function(model, xhr, options, msg, details) {
+                error: function (model, xhr, options, msg, details) {
                     this.trigger("error", model, xhr, options, msg, details);
                 },
-                update: function(collection, options) {
+                update: function (collection, options) {
                     var changes = options.changes;
                     // console.info( collection + ', update:', changes, '\noptions:', options );
                     // more than one: render everything
@@ -166,18 +166,18 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
                     if (changes.removed.length === 1) {
                         return this.removeItemView(_.first(changes.removed), collection, options);
                     }
-                }
+                },
             });
             return this;
         },
 
         /** listening for sub-view events that bubble up with the 'view:' prefix */
-        _setUpViewListeners: function() {
+        _setUpViewListeners: function () {
             this.log(`${this}._setUpViewListeners`);
 
             // shift to select a range
             this.on({
-                "view:selected": function(view, ev) {
+                "view:selected": function (view, ev) {
                     if (ev && ev.shiftKey && this.lastSelected) {
                         var lastSelectedView = this.viewFromModelId(this.lastSelected);
                         if (lastSelectedView) {
@@ -190,9 +190,9 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
                     this.lastSelected = view.model.id;
                 },
 
-                "view:de-selected": function(view, ev) {
+                "view:de-selected": function (view, ev) {
                     this.selected = _.without(this.selected, view.model.id);
-                }
+                },
             });
         },
 
@@ -200,7 +200,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         /** Render this content, set up ui.
          *  @param {Number or String} speed   the speed of the render
          */
-        render: function(speed) {
+        render: function (speed) {
             this.log(`${this}.render`, speed);
             var $newRender = this._buildNewRender();
             this._setUpBehaviors($newRender);
@@ -209,7 +209,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** Build a temp div containing the new children for the view's $el. */
-        _buildNewRender: function() {
+        _buildNewRender: function () {
             this.debug(`${this}(ListPanel)._buildNewRender`);
             var $newRender = $(this.templates.el({}, this));
             this._renderControls($newRender);
@@ -221,7 +221,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** Build a temp div containing the new children for the view's $el. */
-        _renderControls: function($newRender) {
+        _renderControls: function ($newRender) {
             this.debug(`${this}(ListPanel)._renderControls`);
             var $controls = $(this.templates.controls({}, this));
             $newRender.find(".controls").replaceWith($controls);
@@ -229,13 +229,13 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** return a jQuery object containing the title DOM */
-        _renderTitle: function($where) {
+        _renderTitle: function ($where) {
             //$where = $where || this.$el;
             //$where.find( '.title' ).replaceWith( ... )
         },
 
         /** return a jQuery object containing the subtitle DOM (if any) */
-        _renderSubtitle: function($where) {
+        _renderSubtitle: function ($where) {
             //$where = $where || this.$el;
             //$where.find( '.title' ).replaceWith( ... )
         },
@@ -244,35 +244,32 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
          *  @param {Number or String} speed   jq speed to use for rendering effects
          *  @fires rendered when rendered
          */
-        _queueNewRender: function($newRender, speed) {
+        _queueNewRender: function ($newRender, speed) {
             speed = speed === undefined ? this.fxSpeed : speed;
             var panel = this;
             panel.log("_queueNewRender:", $newRender, speed);
 
             $(panel).queue("fx", [
-                next => {
+                (next) => {
                     panel.$el.fadeOut(speed, next);
                 },
-                next => {
+                (next) => {
                     panel._swapNewRender($newRender);
                     next();
                 },
-                next => {
+                (next) => {
                     panel.$el.fadeIn(speed, next);
                 },
-                next => {
+                (next) => {
                     panel.trigger("rendered", panel);
                     next();
-                }
+                },
             ]);
         },
 
         /** empty out the current el, move the $newRender's children in */
-        _swapNewRender: function($newRender) {
-            this.$el
-                .empty()
-                .attr("class", this.className)
-                .append($newRender.children());
+        _swapNewRender: function ($newRender) {
+            this.$el.empty().attr("class", this.className).append($newRender.children());
             if (this.selecting) {
                 this.showSelectors(0);
             }
@@ -282,18 +279,16 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         /** Set up any behaviors, handlers (ep. plugins) that need to be called when the entire view has been built but
          *  not attached to the page yet.
          */
-        _setUpBehaviors: function($where) {
+        _setUpBehaviors: function ($where) {
             $where = $where || this.$el;
-            this.$controls($where)
-                .find("[title]")
-                .tooltip();
+            this.$controls($where).find("[title]").tooltip();
             // set up the pupup for actions available when multi selecting
             this._renderMultiselectActionMenu($where);
             return this;
         },
 
         /** render a menu containing the actions available to sets of selected items */
-        _renderMultiselectActionMenu: function($where) {
+        _renderMultiselectActionMenu: function ($where) {
             $where = $where || this.$el;
             var $menu = $where.find(".list-action-menu");
             var actions = this.multiselectActions();
@@ -308,9 +303,9 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
                     <div class="dropdown-menu float-right" role="menu"/>
                 </div>`
             );
-            var $actions = actions.map(action => {
+            var $actions = actions.map((action) => {
                 var html = `<a class="dropdown-item" href="javascript:void(0);">${action.html}</a>`;
-                return $(html).click(ev => {
+                return $(html).click((ev) => {
                     ev.preventDefault();
                     return action.func(ev);
                 });
@@ -324,37 +319,37 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
          *      html: an html string used as the anchor contents
          *      func: a function called when the anchor is clicked (passed the click event)
          */
-        multiselectActions: function() {
+        multiselectActions: function () {
             return [];
         },
 
         // ------------------------------------------------------------------------ sub-$element shortcuts
         /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */
-        $scrollContainer: function($where) {
+        $scrollContainer: function ($where) {
             // override or set via attributes.$scrollContainer
             return ($where || this.$el).parent().parent();
         },
         /** convenience selector for the section that displays the list controls */
-        $controls: function($where) {
+        $controls: function ($where) {
             return ($where || this.$el).find("> .controls");
         },
         /** list-items: where the subviews are contained in the view's dom */
-        $list: function($where) {
+        $list: function ($where) {
             return ($where || this.$el).find("> .list-items");
         },
         /** container where list messages are attached */
-        $messages: function($where) {
+        $messages: function ($where) {
             //TODO: controls isn't really correct here (only for ModelListPanel)
             return ($where || this.$el).find("> .controls .messages");
         },
         /** the message displayed when no views can be shown (no views, none matching search) */
-        $emptyMessage: function($where) {
+        $emptyMessage: function ($where) {
             return ($where || this.$el).find("> .empty-message");
         },
 
         // ------------------------------------------------------------------------ hda sub-views
         /** render the subviews for the list's collection */
-        renderItems: function($whereTo) {
+        renderItems: function ($whereTo) {
             $whereTo = $whereTo || this.$el;
             var panel = this;
             panel.log(`${this}.renderItems`, $whereTo);
@@ -366,7 +361,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
             var shownModels = panel._filterCollection();
             // console.log( 'models filtered:', shownModels );
 
-            panel.views = shownModels.map(itemModel => {
+            panel.views = shownModels.map((itemModel) => {
                 return panel._createItemView(itemModel);
             });
 
@@ -384,7 +379,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** Filter the collection to only those models that should be currently viewed */
-        _filterCollection: function() {
+        _filterCollection: function () {
             // override this
             var panel = this;
             return panel.collection.filter(_.bind(panel._filterItem, panel));
@@ -393,20 +388,20 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         /** Should the model be viewable in the current state?
          *     Checks against this.filters and this.searchFor
          */
-        _filterItem: function(model) {
+        _filterItem: function (model) {
             // override this
             var panel = this;
             return (
-                _.every(panel.filters.map(fn => fn.call(model))) &&
+                _.every(panel.filters.map((fn) => fn.call(model))) &&
                 (!panel.searchFor || model.matchesAll(panel.searchFor))
             );
         },
 
         /** Create a view for a model and set up it's listeners */
-        _createItemView: function(model) {
+        _createItemView: function (model) {
             var ViewClass = this._getItemViewClass(model);
             var options = _.extend(this._getItemViewOptions(model), {
-                model: model
+                model: model,
             });
             var view = new ViewClass(options);
             this._setUpItemViewListeners(view);
@@ -414,14 +409,14 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** Free a view for a model. Note: does not remove it from the DOM */
-        _destroyItemView: function(view) {
+        _destroyItemView: function (view) {
             this.stopListening(view);
             this.views = _.without(this.views, view);
         },
 
-        _destroyItemViews: function(view) {
+        _destroyItemViews: function (view) {
             var self = this;
-            self.views.forEach(v => {
+            self.views.forEach((v) => {
                 self.stopListening(v);
             });
             self.views = [];
@@ -429,18 +424,18 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** free any sub-views the list has */
-        freeViews: function() {
+        freeViews: function () {
             return this._destroyItemViews();
         },
 
         /** Get the bbone view class based on the model */
-        _getItemViewClass: function(model) {
+        _getItemViewClass: function (model) {
             // override this
             return this.viewClass;
         },
 
         /** Get the options passed to the new view based on the model */
-        _getItemViewOptions: function(model) {
+        _getItemViewOptions: function (model) {
             // override this
             return {
                 //logger      : this.logger,
@@ -448,15 +443,15 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
                 expanded: false,
                 selectable: this.selecting,
                 selected: _.contains(this.selected, model.id),
-                draggable: this.dragItems
+                draggable: this.dragItems,
             };
         },
 
         /** Set up listeners for new models */
-        _setUpItemViewListeners: function(view) {
+        _setUpItemViewListeners: function (view) {
             var panel = this;
             // send all events to the panel, re-namspaceing them with the view prefix
-            this.listenTo(view, "all", function() {
+            this.listenTo(view, "all", function () {
                 var args = Array.prototype.slice.call(arguments, 0);
                 args[0] = `view:${args[0]}`;
                 panel.trigger.apply(panel, args);
@@ -466,7 +461,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
             this.listenTo(
                 view,
                 "draggable:dragstart",
-                function(ev, v) {
+                function (ev, v) {
                     //TODO: set multiple drag data here
                     var json = {};
 
@@ -486,44 +481,44 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** Attach views in this.views to the model based on $whereTo */
-        _attachItems: function($whereTo) {
+        _attachItems: function ($whereTo) {
             var self = this;
             // console.log( '_attachItems:', $whereTo, this.$list( $whereTo ) );
             //ASSUMES: $list has been emptied
-            this.$list($whereTo).append(this.views.map(view => self._renderItemView$el(view)));
+            this.$list($whereTo).append(this.views.map((view) => self._renderItemView$el(view)));
             return this;
         },
 
         /** get a given subview's $el (or whatever may wrap it) and return it */
-        _renderItemView$el: function(view) {
+        _renderItemView$el: function (view) {
             // useful to wrap and override
             return view.render(0).$el;
         },
 
         /** render the empty/none-found message */
-        _renderEmptyMessage: function($whereTo) {
+        _renderEmptyMessage: function ($whereTo) {
             this.debug("_renderEmptyMessage", $whereTo, this.searchFor);
             var text = this.searchFor ? this.noneFoundMsg : this.emptyMsg;
             return this.$emptyMessage($whereTo).text(text);
         },
 
         /** expand all item views */
-        expandAll: function() {
-            _.each(this.views, view => {
+        expandAll: function () {
+            _.each(this.views, (view) => {
                 view.expand();
             });
         },
 
         /** collapse all item views */
-        collapseAll: function() {
-            _.each(this.views, view => {
+        collapseAll: function () {
+            _.each(this.views, (view) => {
                 view.collapse();
             });
         },
 
         // ------------------------------------------------------------------------ collection/views syncing
         /** Add a view (if the model should be viewable) to the panel */
-        addItemView: function(model, collection, options) {
+        addItemView: function (model, collection, options) {
             // console.log( this + '.addItemView:', model );
             var panel = this;
             // get the index of the model in the list of filtered models shown by this list
@@ -537,7 +532,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
             // console.log( 'adding and rendering:', modelIndex, view.toString() );
 
             $(view).queue("fx", [
-                next => {
+                (next) => {
                     // hide the empty message first if only view
                     if (panel.$emptyMessage().is(":visible")) {
                         panel.$emptyMessage().fadeOut(panel.fxSpeed, next);
@@ -545,16 +540,16 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
                         next();
                     }
                 },
-                next => {
+                (next) => {
                     panel._attachView(view, modelIndex);
                     next();
-                }
+                },
             ]);
             return view;
         },
 
         /** internal fn to add view (to both panel.views and panel.$list) */
-        _attachView: function(view, modelIndex, useFx) {
+        _attachView: function (view, modelIndex, useFx) {
             // console.log( this + '._attachView:', view, modelIndex, useFx );
             useFx = _.isUndefined(useFx) ? true : useFx;
             modelIndex = modelIndex || 0;
@@ -577,7 +572,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** insert a jq object as a child of list-items at the specified *DOM index* */
-        _insertIntoListAt: function(index, $what) {
+        _insertIntoListAt: function (index, $what) {
             // console.log( this + '._insertIntoListAt:', index, $what );
             var $list = this.$list();
             if (index === 0) {
@@ -592,9 +587,9 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** Remove a view from the panel (if found) */
-        removeItemView: function(model, collection, options) {
+        removeItemView: function (model, collection, options) {
             var panel = this;
-            var view = _.find(panel.views, v => v.model === model);
+            var view = _.find(panel.views, (v) => v.model === model);
             if (!view) {
                 return undefined;
             }
@@ -604,10 +599,10 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
             // potentially show the empty message if no views left
             // use anonymous queue here - since remove can happen multiple times
             $({}).queue("fx", [
-                next => {
+                (next) => {
                     view.$el.fadeOut(panel.fxSpeed, next);
                 },
-                next => {
+                (next) => {
                     view.remove();
                     panel.trigger("view:removed:rendered");
                     if (!panel.views.length) {
@@ -615,28 +610,28 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
                     } else {
                         next();
                     }
-                }
+                },
             ]);
             return view;
         },
 
         /** get views based on model.id */
-        viewFromModelId: function(id) {
-            return _.find(this.views, v => v.model.id === id);
+        viewFromModelId: function (id) {
+            return _.find(this.views, (v) => v.model.id === id);
         },
 
         /** get views based on model */
-        viewFromModel: function(model) {
+        viewFromModel: function (model) {
             return model ? this.viewFromModelId(model.id) : undefined;
         },
 
         /** get views based on model properties */
-        viewsWhereModel: function(properties) {
-            return this.views.filter(view => _.isMatch(view.model.attributes, properties));
+        viewsWhereModel: function (properties) {
+            return this.views.filter((view) => _.isMatch(view.model.attributes, properties));
         },
 
         /** A range of views between (and including) viewA and viewB */
-        viewRange: function(viewA, viewB) {
+        viewRange: function (viewA, viewB) {
             if (viewA === viewB) {
                 return viewA ? [viewA] : [];
             }
@@ -664,26 +659,26 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
          *      clicking the clear button will clear the search
          *      uses searchInput in ui.js
          */
-        _renderSearch: function($where) {
+        _renderSearch: function ($where) {
             $where.find(".controls .search-input").searchInput({
                 placeholder: this.searchPlaceholder,
                 initialVal: this.searchFor,
                 onfirstsearch: _.bind(this._firstSearch, this),
                 onsearch: _.bind(this.searchItems, this),
-                onclear: _.bind(this.clearSearch, this)
+                onclear: _.bind(this.clearSearch, this),
             });
             return $where;
         },
 
         /** What to do on the first search entered */
-        _firstSearch: function(searchFor) {
+        _firstSearch: function (searchFor) {
             // override to load model details if necc.
             this.log("onFirstSearch", searchFor);
             return this.searchItems(searchFor);
         },
 
         /** filter view list to those that contain the searchFor terms */
-        searchItems: function(searchFor, force) {
+        searchItems: function (searchFor, force) {
             this.log("searchItems", searchFor, this.searchFor, force);
             if (!force && this.searchFor === searchFor) {
                 return this;
@@ -699,7 +694,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** clear the search filters and show all views that are normally shown */
-        clearSearch: function(searchFor) {
+        clearSearch: function (searchFor) {
             //this.log( 'onSearchClear', this );
             this.searchFor = "";
             this.trigger("search:clear", this);
@@ -713,12 +708,12 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         THROTTLE_SELECTOR_FX_AT: 20,
 
         /** show selectors on all visible itemViews and associated controls */
-        showSelectors: function(speed) {
+        showSelectors: function (speed) {
             speed = speed !== undefined ? speed : this.fxSpeed;
             this.selecting = true;
             this.$(".list-actions").slideDown(speed);
             speed = this.views.length >= this.THROTTLE_SELECTOR_FX_AT ? 0 : speed;
-            _.each(this.views, view => {
+            _.each(this.views, (view) => {
                 view.showSelector(speed);
             });
             //this.selected = [];
@@ -726,12 +721,12 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** hide selectors on all visible itemViews and associated controls */
-        hideSelectors: function(speed) {
+        hideSelectors: function (speed) {
             speed = speed !== undefined ? speed : this.fxSpeed;
             this.selecting = false;
             this.$(".list-actions").slideUp(speed);
             speed = this.views.length >= this.THROTTLE_SELECTOR_FX_AT ? 0 : speed;
-            _.each(this.views, view => {
+            _.each(this.views, (view) => {
                 view.hideSelector(speed);
             });
             this.selected = [];
@@ -739,7 +734,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** show or hide selectors on all visible itemViews and associated controls */
-        toggleSelectors: function() {
+        toggleSelectors: function () {
             if (!this.selecting) {
                 this.showSelectors();
             } else {
@@ -748,43 +743,43 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** select all visible items */
-        selectAll: function(event) {
-            _.each(this.views, view => {
+        selectAll: function (event) {
+            _.each(this.views, (view) => {
                 view.select(event);
             });
         },
 
         /** deselect all visible items */
-        deselectAll: function(event) {
+        deselectAll: function (event) {
             this.lastSelected = null;
-            _.each(this.views, view => {
+            _.each(this.views, (view) => {
                 view.deselect(event);
             });
         },
 
         /** select a range of datasets between A and B */
-        selectRange: function(viewA, viewB) {
+        selectRange: function (viewA, viewB) {
             var range = this.viewRange(viewA, viewB);
-            _.each(range, view => {
+            _.each(range, (view) => {
                 view.select();
             });
             return range;
         },
 
         /** return an array of all currently selected itemViews */
-        getSelectedViews: function() {
-            return _.filter(this.views, v => v.selected);
+        getSelectedViews: function () {
+            return _.filter(this.views, (v) => v.selected);
         },
 
         /** return a collection of the models of all currenly selected items */
-        getSelectedModels: function() {
+        getSelectedModels: function () {
             // console.log( '(getSelectedModels)' );
-            return new this.collection.constructor(_.map(this.getSelectedViews(), view => view.model));
+            return new this.collection.constructor(_.map(this.getSelectedViews(), (view) => view.model));
         },
 
         // ------------------------------------------------------------------------ loading indicator
         /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */
-        _showLoadingIndicator: function(msg, speed, callback) {
+        _showLoadingIndicator: function (msg, speed, callback) {
             this.debug("_showLoadingIndicator", this.indicator, msg, speed, callback);
             speed = speed !== undefined ? speed : this.fxSpeed;
             if (!this.indicator) {
@@ -800,7 +795,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** hide the loading indicator */
-        _hideLoadingIndicator: function(speed, callback) {
+        _hideLoadingIndicator: function (speed, callback) {
             this.debug("_hideLoadingIndicator", this.indicator, speed, callback);
             speed = speed !== undefined ? speed : this.fxSpeed;
             if (this.indicator) {
@@ -810,24 +805,24 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
 
         // ------------------------------------------------------------------------ scrolling
         /** get the current scroll position of the panel in its parent */
-        scrollPosition: function() {
+        scrollPosition: function () {
             return this.$scrollContainer().scrollTop();
         },
 
         /** set the current scroll position of the panel in its parent */
-        scrollTo: function(pos, speed) {
+        scrollTo: function (pos, speed) {
             speed = speed || 0;
             this.$scrollContainer().animate({ scrollTop: pos }, speed);
             return this;
         },
 
         /** Scrolls the panel to the top. */
-        scrollToTop: function(speed) {
+        scrollToTop: function (speed) {
             return this.scrollTo(0, speed);
         },
 
         /** scroll to the given view in list-items */
-        scrollToItem: function(view, speed) {
+        scrollToItem: function (view, speed) {
             if (!view) {
                 return this;
             }
@@ -835,7 +830,7 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         },
 
         /** Scrolls the panel to show the content with the given id. */
-        scrollToId: function(id, speed) {
+        scrollToId: function (id, speed) {
             return this.scrollToItem(this.viewFromModelId(id), speed);
         },
 
@@ -843,14 +838,14 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         /** event map */
         events: {
             "click .select-all": "selectAll",
-            "click .deselect-all": "deselectAll"
+            "click .deselect-all": "deselectAll",
         },
 
         // ------------------------------------------------------------------------ misc
         /** Return a string rep of the panel */
-        toString: function() {
+        toString: function () {
             return `ListPanel(${this.collection})`;
-        }
+        },
     }
 );
 
@@ -863,7 +858,7 @@ ListPanel.prototype.templates = (() => {
         '<div class="controls"></div>',
         '<div class="list-items"></div>',
         '<div class="empty-message infomessagesmall"></div>',
-        "</div>"
+        "</div>",
     ]);
 
     var controlsTemplate = BASE_MVC.wrapTemplate([
@@ -896,12 +891,12 @@ ListPanel.prototype.templates = (() => {
         '<div class="list-action-menu btn-group">',
         "</div>",
         "</div>",
-        "</div>"
+        "</div>",
     ]);
 
     return {
         el: elTemplate,
-        controls: controlsTemplate
+        controls: controlsTemplate,
     };
 })();
 
@@ -916,7 +911,7 @@ var ModelListPanel = ListPanel.extend({
     /** key of attribute in model to assign to this.collection */
     modelCollectionKey: "contents",
 
-    initialize: function(attributes) {
+    initialize: function (attributes) {
         ListPanel.prototype.initialize.call(this, attributes);
         this.selecting = attributes.selecting !== undefined ? attributes.selecting : false;
 
@@ -926,7 +921,7 @@ var ModelListPanel = ListPanel.extend({
     /** release/free/shutdown old models and set up panel for new models
      *  @fires new-model with the panel as parameter
      */
-    setModel: function(model, attributes) {
+    setModel: function (model, attributes) {
         attributes = attributes || {};
         this.debug(`${this}.setModel:`, model, attributes);
 
@@ -959,7 +954,7 @@ var ModelListPanel = ListPanel.extend({
     },
 
     /** free the current model and all listeners for it, free any views for the model */
-    freeModel: function() {
+    freeModel: function () {
         // stop/release the previous model, and clear cache to sub-views
         if (this.model) {
             this.stopListening(this.model);
@@ -972,14 +967,14 @@ var ModelListPanel = ListPanel.extend({
 
     // ------------------------------------------------------------------------ listening
     /** listening for model events */
-    _setUpModelListeners: function() {
+    _setUpModelListeners: function () {
         // override
         this.log(`${this}._setUpModelListeners`, this.model);
         // bounce model errors up to the panel
         this.listenTo(
             this.model,
             "error",
-            function() {
+            function () {
                 var args = Array.prototype.slice.call(arguments, 0);
                 //args.unshift( 'model:error' );
                 args.unshift("error");
@@ -990,7 +985,7 @@ var ModelListPanel = ListPanel.extend({
 
         // debugging
         if (this.logger) {
-            this.listenTo(this.model, "all", function(event) {
+            this.listenTo(this.model, "all", function (event) {
                 this.info(`${this}(model)`, event, arguments);
             });
         }
@@ -999,7 +994,7 @@ var ModelListPanel = ListPanel.extend({
 
     /** Build a temp div containing the new children for the view's $el.
      */
-    _renderControls: function($newRender) {
+    _renderControls: function ($newRender) {
         this.debug(`${this}(ModelListPanel)._renderControls`);
         var json = this.model ? this.model.toJSON() : {};
         var $controls = $(this.templates.controls(json, this));
@@ -1009,9 +1004,9 @@ var ModelListPanel = ListPanel.extend({
 
     // ------------------------------------------------------------------------ misc
     /** Return a string rep of the panel */
-    toString: function() {
+    toString: function () {
         return `ModelListPanel(${this.model})`;
-    }
+    },
 });
 
 // ............................................................................ TEMPLATES
@@ -1045,16 +1040,16 @@ ModelListPanel.prototype.templates = (() => {
         '<div class="list-action-menu btn-group">',
         "</div>",
         "</div>",
-        "</div>"
+        "</div>",
     ]);
 
     return _.extend(_.clone(ListPanel.prototype.templates), {
-        controls: controlsTemplate
+        controls: controlsTemplate,
     });
 })();
 
 //=============================================================================
 export default {
     ListPanel: ListPanel,
-    ModelListPanel: ModelListPanel
+    ModelListPanel: ModelListPanel,
 };
diff --git a/client/galaxy/scripts/mvc/rules/rule-definitions.js b/client/galaxy/scripts/mvc/rules/rule-definitions.js
index bbd294dfdf92..aac362155492 100644
--- a/client/galaxy/scripts/mvc/rules/rule-definitions.js
+++ b/client/galaxy/scripts/mvc/rules/rule-definitions.js
@@ -4,19 +4,19 @@ import pyre from "pyre-to-regexp";
 
 const NEW_COLUMN = "new";
 
-const multiColumnsToString = function(targetColumns, colHeaders) {
+const multiColumnsToString = function (targetColumns, colHeaders) {
     if (targetColumns.length == 0) {
         return `no columns`;
     } else if (targetColumns.length == 1) {
         return `column ${colHeaders[targetColumns[0]]}`;
     } else {
-        const targetHeaders = targetColumns.map(el => colHeaders[el]);
+        const targetHeaders = targetColumns.map((el) => colHeaders[el]);
         // https://stackoverflow.com/questions/16251822/array-to-comma-separated-string-and-for-last-tag-use-the-and-instead-of-comma
         return `columns ${[targetHeaders.slice(0, -1).join(", "), targetHeaders.slice(-1)[0]].join(" and ")}`;
     }
 };
 
-const removeColumns = function(columns, targetColumns) {
+const removeColumns = function (columns, targetColumns) {
     const newColumns = [];
     for (const index in columns) {
         if (targetColumns.indexOf(index) === -1) {
@@ -26,7 +26,7 @@ const removeColumns = function(columns, targetColumns) {
     return newColumns;
 };
 
-const applyRegex = function(regex, target, data, replacement, groupCount) {
+const applyRegex = function (regex, target, data, replacement, groupCount) {
     let regExp;
     try {
         regExp = pyre(String(regex));
@@ -93,7 +93,7 @@ const RULES = {
             columns.push(NEW_COLUMN);
             rval.columns = columns;
             return rval;
-        }
+        },
     },
     add_column_rownum: {
         title: _l("Row Number"),
@@ -121,7 +121,7 @@ const RULES = {
             data = data.map(newRow);
             columns.push(NEW_COLUMN);
             return { data, columns };
-        }
+        },
     },
     add_column_value: {
         title: _l("Fixed Value"),
@@ -148,7 +148,7 @@ const RULES = {
             data = data.map(newRow);
             columns.push(NEW_COLUMN);
             return { data, columns };
-        }
+        },
     },
     add_column_metadata: {
         title: _l("Add Column from Metadata"),
@@ -195,7 +195,7 @@ const RULES = {
             data = data.map(newRow);
             columns.push(NEW_COLUMN);
             return { data, columns };
-        }
+        },
     },
     add_column_group_tag_value: {
         title: _l("Add Column from Group Tag Value"),
@@ -236,7 +236,7 @@ const RULES = {
             data = data.map(newRow);
             columns.push(NEW_COLUMN);
             return { data, columns };
-        }
+        },
     },
     add_column_regex: {
         title: _l("Using a Regular Expression"),
@@ -279,7 +279,7 @@ const RULES = {
             columns.push(NEW_COLUMN);
             rval.columns = columns;
             return rval;
-        }
+        },
     },
     add_column_concatenate: {
         title: _l("Concatenate Columns"),
@@ -312,7 +312,7 @@ const RULES = {
             data = data.map(newRow);
             columns.push(NEW_COLUMN);
             return { data, columns };
-        }
+        },
     },
     add_column_substr: {
         title: _l("Keep or Trim Prefix or Suffix"),
@@ -380,7 +380,7 @@ const RULES = {
             data = data.map(newRow);
             columns.push(NEW_COLUMN);
             return { data };
-        }
+        },
     },
     remove_columns: {
         title: _l("Remove Column(s)"),
@@ -412,7 +412,7 @@ const RULES = {
             data = data.map(newRow);
             columns = removeColumns(columns, targets);
             return { data, columns };
-        }
+        },
     },
     add_filter_regex: {
         title: _l("Using a Regular Expression"),
@@ -447,14 +447,14 @@ const RULES = {
             }
             const target = rule.target_column;
             const invert = rule.invert;
-            const filterFunction = function(el, index) {
+            const filterFunction = function (el, index) {
                 const row = data[parseInt(index, 10)];
                 return regExp.exec(row[target]) ? !invert : invert;
             };
             sources = sources.filter(filterFunction);
             data = data.filter(filterFunction);
             return { data, sources };
-        }
+        },
     },
     add_filter_count: {
         title: _l("First or Last N Rows"),
@@ -492,7 +492,7 @@ const RULES = {
             const invert = rule.invert;
             const which = rule.which;
             const dataLength = data.length;
-            const filterFunction = function(el, index) {
+            const filterFunction = function (el, index) {
                 let matches;
                 if (which == "first") {
                     matches = index >= count;
@@ -504,7 +504,7 @@ const RULES = {
             sources = sources.filter(filterFunction);
             data = data.filter(filterFunction);
             return { data, sources };
-        }
+        },
     },
     add_filter_empty: {
         title: _l("On Emptiness"),
@@ -527,14 +527,14 @@ const RULES = {
         apply: (rule, data, sources, columns) => {
             const target = rule.target_column;
             const invert = rule.invert;
-            const filterFunction = function(el, index) {
+            const filterFunction = function (el, index) {
                 const row = data[parseInt(index, 10)];
                 return row[target].length ? !invert : invert;
             };
             sources = sources.filter(filterFunction);
             data = data.filter(filterFunction);
             return { data, sources };
-        }
+        },
     },
     add_filter_matches: {
         title: _l("Matching a Supplied Value"),
@@ -561,14 +561,14 @@ const RULES = {
             const target = rule.target_column;
             const invert = rule.invert;
             const value = rule.value;
-            const filterFunction = function(el, index) {
+            const filterFunction = function (el, index) {
                 const row = data[parseInt(index, 10)];
                 return row[target] == value ? !invert : invert;
             };
             sources = sources.filter(filterFunction);
             data = data.filter(filterFunction);
             return { data, sources };
-        }
+        },
     },
     add_filter_compare: {
         title: _l("By Comparing to a Numeric Value"),
@@ -597,7 +597,7 @@ const RULES = {
             const target = rule.target_column;
             const compare_type = rule.compare_type;
             const value = rule.value;
-            const filterFunction = function(el, index) {
+            const filterFunction = function (el, index) {
                 const row = data[parseInt(index, 10)];
                 const targetValue = parseFloat(row[target]);
                 let matches;
@@ -615,7 +615,7 @@ const RULES = {
             sources = sources.filter(filterFunction);
             data = data.filter(filterFunction);
             return { data, sources };
-        }
+        },
     },
     sort: {
         title: _l("Sort"),
@@ -662,13 +662,13 @@ const RULES = {
             const newData = [];
             const newSources = [];
 
-            sortable.map(zipped => {
+            sortable.map((zipped) => {
                 newData.push(zipped[0]);
                 newSources.push(zipped[1]);
             });
 
             return { data: newData, sources: newSources };
-        }
+        },
     },
     swap_columns: {
         title: _l("Swap Column(s)"),
@@ -702,7 +702,7 @@ const RULES = {
             columns[target0] = columns[target1];
             columns[target1] = tempColumn;
             return { data, columns };
-        }
+        },
     },
     split_columns: {
         title: _l("Split Column(s)"),
@@ -726,7 +726,7 @@ const RULES = {
             const targets0 = rule.target_columns_0;
             const targets1 = rule.target_columns_1;
 
-            const splitRow = function(row) {
+            const splitRow = function (row) {
                 const newRow0 = [];
                 const newRow1 = [];
                 for (let index in row) {
@@ -743,11 +743,11 @@ const RULES = {
                 return [newRow0, newRow1];
             };
             data = flatMap(splitRow, data);
-            sources = flatMap(src => [src, src], sources);
+            sources = flatMap((src) => [src, src], sources);
             columns = removeColumns(columns, targets0);
             return { data, sources, columns };
-        }
-    }
+        },
+    },
 };
 
 const MAPPING_TARGETS = {
@@ -758,7 +758,7 @@ const MAPPING_TARGETS = {
         help: _l(
             "This should be a short description of the replicate, sample name, condition, etc... that describes each level of the list structure."
         ),
-        importType: "collections"
+        importType: "collections",
     },
     paired_identifier: {
         label: _l("Paired-end Indicator"),
@@ -766,7 +766,7 @@ const MAPPING_TARGETS = {
         help: _l(
             "This should be set to '1', 'R1', 'forward', 'f', or 'F' to indicate forward reads, and '2', 'r', 'reverse', 'R2', 'R', or 'R2' to indicate reverse reads."
         ),
-        importType: "collections"
+        importType: "collections",
     },
     collection_name: {
         label: _l("Collection Name"),
@@ -774,13 +774,13 @@ const MAPPING_TARGETS = {
             "If this is set, all rows with the same collection name will be joined into a collection and it is possible to create multiple collections at once."
         ),
         modes: ["raw", "ftp", "datasets", "library_datasets"],
-        importType: "collections"
+        importType: "collections",
     },
     name_tag: {
         label: _l("Name Tag"),
         help: _l("Add a name tag or hash tag based on the specified column value for imported datasets."),
         importType: "datasets",
-        modes: ["raw", "ftp"]
+        modes: ["raw", "ftp"],
     },
     tags: {
         multiple: true,
@@ -788,7 +788,7 @@ const MAPPING_TARGETS = {
         help: _l(
             "Add a general purpose tag based on the specified column value, use : to separate key-value pairs if desired. These tags are not propagated to derived datasets the way name and group tags are."
         ),
-        modes: ["raw", "ftp", "datasets", "library_datasets"]
+        modes: ["raw", "ftp", "datasets", "library_datasets"],
     },
     group_tags: {
         multiple: true,
@@ -796,32 +796,32 @@ const MAPPING_TARGETS = {
         help: _l(
             "Add a group tag based on the specified column value, use : to separate key-value pairs. These tags are propagated to derived datasets and may be useful for factorial experiments."
         ),
-        modes: ["raw", "ftp", "datasets", "library_datasets"]
+        modes: ["raw", "ftp", "datasets", "library_datasets"],
     },
     name: {
         label: _l("Name"),
-        importType: "datasets"
+        importType: "datasets",
     },
     dbkey: {
         label: _l("Genome"),
-        modes: ["raw", "ftp"]
+        modes: ["raw", "ftp"],
     },
     file_type: {
         label: _l("Type"),
         modes: ["raw", "ftp"],
-        help: _l("This should be the Galaxy file type corresponding to this file.")
+        help: _l("This should be the Galaxy file type corresponding to this file."),
     },
     url: {
         label: _l("URL"),
         modes: ["raw"],
-        help: _l("This should be a URL the file can be downloaded from.")
+        help: _l("This should be a URL the file can be downloaded from."),
     },
     info: {
         label: _l("Info"),
         help: _l(
             "Unstructured text associated with the dataset that shows up in the history panel, this is optional and can be whatever you would like."
         ),
-        modes: ["raw", "ftp"]
+        modes: ["raw", "ftp"],
     },
     ftp_path: {
         label: _l("FTP Path"),
@@ -829,14 +829,14 @@ const MAPPING_TARGETS = {
         help: _l(
             "This should be the path to the target file to include relative to your FTP directory on the Galaxy server"
         ),
-        requiresFtp: true
-    }
+        requiresFtp: true,
+    },
 };
 
-const columnDisplay = function(columns, colHeaders) {
+const columnDisplay = function (columns, colHeaders) {
     let columnNames;
     if (typeof columns == "object") {
-        columnNames = columns.map(idx => colHeaders[idx]);
+        columnNames = columns.map((idx) => colHeaders[idx]);
     } else {
         columnNames = [colHeaders[columns]];
     }
@@ -849,7 +849,7 @@ const columnDisplay = function(columns, colHeaders) {
     }
 };
 
-const colHeadersFor = function(data, columns) {
+const colHeadersFor = function (data, columns) {
     if (data.length == 0) {
         if (columns) {
             return columns.map((el, i) => String.fromCharCode(65 + i));
@@ -861,7 +861,7 @@ const colHeadersFor = function(data, columns) {
     }
 };
 
-const applyRules = function(data, sources, columns, rules, headersPerRule = []) {
+const applyRules = function (data, sources, columns, rules, headersPerRule = []) {
     const colHeadersPerRule = Array.from(headersPerRule);
     let hasRuleError = false;
     for (var ruleIndex in rules) {
@@ -896,5 +896,5 @@ export default {
     columnDisplay: columnDisplay,
     colHeadersFor: colHeadersFor,
     RULES: RULES,
-    MAPPING_TARGETS: MAPPING_TARGETS
+    MAPPING_TARGETS: MAPPING_TARGETS,
 };
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js
index a9de6ed3d555..084484ee74df 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-base.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js
@@ -17,7 +17,7 @@ import Vue from "vue";
 import axios from "axios";
 
 export default FormBase.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         const Galaxy = getGalaxyInstance();
         var self = this;
         this.deferred = new Deferred();
@@ -39,12 +39,12 @@ export default FormBase.extend({
     },
 
     /** Allows tool form variation to update tool model */
-    _update: function(callback) {
+    _update: function (callback) {
         var self = this;
         callback = callback || this.model.get("buildmodel");
         if (callback) {
             this.deferred.reset();
-            this.deferred.execute(process => {
+            this.deferred.execute((process) => {
                 callback(process, self);
                 process.then(() => {
                     self._render();
@@ -56,7 +56,7 @@ export default FormBase.extend({
     },
 
     /** Wait for deferred build processes before removal */
-    _destroy: function() {
+    _destroy: function () {
         var self = this;
         this.$el.off().hide();
         this.deferred.execute(() => {
@@ -67,7 +67,7 @@ export default FormBase.extend({
     },
 
     /** Build form */
-    _render: function() {
+    _render: function () {
         var self = this;
         var options = this.model.attributes;
         this.model.set({
@@ -75,38 +75,34 @@ export default FormBase.extend({
                 options.fixed_title ||
                 `<b>${options.name}</b> ${options.description} (Galaxy Version ${options.version})`,
             operations: !options.hide_operations && this._operations(),
-            onchange: function() {
+            onchange: function () {
                 self.deferred.reset();
-                self.deferred.execute(process => {
+                self.deferred.execute((process) => {
                     self.model.get("postchange")(process, self);
                 });
-            }
+            },
         });
         this.render();
         if (!this.model.get("collapsible")) {
-            this.$el.append(
-                $("<div/>")
-                    .addClass("mt-2")
-                    .append(this._footer())
-            );
+            this.$el.append($("<div/>").addClass("mt-2").append(this._footer()));
         }
         options.tool_errors &&
             this.message.update({
                 status: "danger",
                 message: options.tool_errors,
-                persistent: true
+                persistent: true,
             });
         this.show_message &&
             this.message.update({
                 status: "success",
                 message: `Now you are using '${options.name}' version ${options.version}, id '${options.id}'.`,
-                persistent: false
+                persistent: false,
             });
         this.show_message = true;
     },
 
     /** Create tool operation menu */
-    _operations: function() {
+    _operations: function () {
         var self = this;
         var options = this.model.attributes;
         const Galaxy = getGalaxyInstance();
@@ -121,13 +117,13 @@ export default FormBase.extend({
             onclick: () => {
                 axios
                     .put(`${Galaxy.root}api/users/${Galaxy.user.id}/favorites/tools`, { object_id: options.id })
-                    .then(response => {
+                    .then((response) => {
                         favorite_button.hide();
                         remove_favorite_button.show();
                         Galaxy.user.updateFavorites("tools", response.data);
                         ariaAlert("added to favorites");
                     });
-            }
+            },
         });
 
         var remove_favorite_button = new Ui.Button({
@@ -140,20 +136,20 @@ export default FormBase.extend({
                     .delete(
                         `${Galaxy.root}api/users/${Galaxy.user.id}/favorites/tools/${encodeURIComponent(options.id)}`
                     )
-                    .then(response => {
+                    .then((response) => {
                         remove_favorite_button.hide();
                         favorite_button.show();
                         Galaxy.user.updateFavorites("tools", response.data);
                         ariaAlert("removed from favorites");
                     });
-            }
+            },
         });
 
         // button for version selection
         var versions_button = new Ui.ButtonMenu({
             icon: "fa-cubes",
             title: options.narrow ? null : "Versions",
-            tooltip: "Select another tool version"
+            tooltip: "Select another tool version",
         });
 
         if (!options.sustain_version && options.versions && options.versions.length > 1) {
@@ -164,12 +160,12 @@ export default FormBase.extend({
                         title: `Switch to ${version}`,
                         version: version,
                         icon: "fa-cube",
-                        onclick: function() {
+                        onclick: function () {
                             // here we update the tool version (some tools encode the version also in the id)
                             self.model.set("id", options.id.replace(options.version, this.version));
                             self.model.set("version", this.version);
                             self._update();
-                        }
+                        },
                     });
                 }
             }
@@ -182,17 +178,17 @@ export default FormBase.extend({
             id: "options",
             icon: "fa-caret-down",
             title: options.narrow ? null : "Options",
-            tooltip: "View available options"
+            tooltip: "View available options",
         });
         menu_button.addMenu({
             icon: "fa-share",
             title: _l("Share"),
-            onclick: function() {
+            onclick: function () {
                 prompt(
                     "Copy to clipboard: Ctrl+C, Enter",
                     `${window.location.origin + getAppRoot()}root?tool_id=${options.id}`
                 );
-            }
+            },
         });
 
         // add admin operations
@@ -200,9 +196,9 @@ export default FormBase.extend({
             menu_button.addMenu({
                 icon: "fa-download",
                 title: _l("Download"),
-                onclick: function() {
+                onclick: function () {
                     window.location.href = `${getAppRoot()}api/tools/${options.id}/download`;
-                }
+                },
             });
         }
 
@@ -211,20 +207,20 @@ export default FormBase.extend({
             menu_button.addMenu({
                 icon: "fa-info-circle",
                 title: _l("Requirements"),
-                onclick: function() {
+                onclick: function () {
                     if (!this.requirements_visible || self.portlet.collapsed) {
                         this.requirements_visible = true;
                         self.portlet.expand();
                         self.message.update({
                             persistent: true,
                             message: self._templateRequirements(options),
-                            status: "info"
+                            status: "info",
                         });
                     } else {
                         this.requirements_visible = false;
                         self.message.update({ message: "" });
                     }
-                }
+                },
             });
         }
 
@@ -233,42 +229,42 @@ export default FormBase.extend({
             menu_button.addMenu({
                 icon: "fa-external-link",
                 title: _l("See in Tool Shed"),
-                onclick: function() {
+                onclick: function () {
                     window.open(options.sharable_url);
-                }
+                },
             });
         }
 
         // add tool menu webhooks
         Webhooks.load({
             type: "tool-menu",
-            callback: function(webhooks) {
-                webhooks.each(model => {
+            callback: function (webhooks) {
+                webhooks.each((model) => {
                     var webhook = model.toJSON();
                     if (webhook.activate && webhook.config.function) {
                         menu_button.addMenu({
                             icon: webhook.config.icon,
                             title: webhook.config.title,
-                            onclick: function() {
+                            onclick: function () {
                                 var func = new Function("options", webhook.config.function);
                                 func(options);
-                            }
+                            },
                         });
                     }
                 });
-            }
+            },
         });
 
         return {
             menu: menu_button,
             versions: versions_button,
             favorite: favorite_button,
-            remove_favorite: remove_favorite_button
+            remove_favorite: remove_favorite_button,
         };
     },
 
     /** Create footer */
-    _footer: function() {
+    _footer: function () {
         var options = this.model.attributes;
         var $el = $("<div/>").append(this._templateHelp(options));
         if (options.citations) {
@@ -278,8 +274,8 @@ export default FormBase.extend({
             new citationInstance({
                 propsData: {
                     id: options.id,
-                    source: "tools"
-                }
+                    source: "tools",
+                },
             }).$mount(vm);
         }
         if (options.xrefs && options.xrefs.length) {
@@ -289,20 +285,18 @@ export default FormBase.extend({
             new xrefInstance({
                 propsData: {
                     id: options.id,
-                    source: "tools"
-                }
+                    source: "tools",
+                },
             }).$mount(vm);
         }
         return $el;
     },
 
     /** Templates */
-    _templateHelp: function(options) {
-        var $tmpl = $("<div/>")
-            .addClass("form-help form-text mt-4")
-            .append(options.help);
+    _templateHelp: function (options) {
+        var $tmpl = $("<div/>").addClass("form-help form-text mt-4").append(options.help);
         $tmpl.find("a").attr("target", "_blank");
-        $tmpl.find("img").each(function() {
+        $tmpl.find("img").each(function () {
             var img_src = $(this).attr("src");
             if (img_src.indexOf("admin_toolshed") !== -1) {
                 $(this).attr("src", getAppRoot() + img_src);
@@ -311,7 +305,7 @@ export default FormBase.extend({
         return $tmpl;
     },
 
-    _templateRequirements: function(options) {
+    _templateRequirements: function (options) {
         var nreq = options.requirements.length;
         if (nreq > 0) {
             var requirements_message = "This tool requires ";
@@ -331,5 +325,5 @@ export default FormBase.extend({
                 .append(" for more information.");
         }
         return "No requirements found.";
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
index ce80873c1235..2540c48786b2 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
@@ -14,7 +14,7 @@ import Modal from "mvc/ui/ui-modal";
 import WorkflowIcons from "components/Workflow/icons";
 
 var View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         const Galaxy = getGalaxyInstance();
         this.modal = Galaxy.modal || new Modal.View();
         this.model = (options && options.model) || new Backbone.Model(options);
@@ -30,7 +30,7 @@ var View = Backbone.View.extend({
     },
 
     /** Configures form/step options for each workflow step */
-    _configure: function() {
+    _configure: function () {
         var self = this;
         const Galaxy = getGalaxyInstance();
         this.forms = [];
@@ -69,7 +69,7 @@ var View = Backbone.View.extend({
                     cls: "ui-portlet-section",
                     hide_operations: true,
                     needs_refresh: false,
-                    always_refresh: step.step_type != "tool"
+                    always_refresh: step.step_type != "tool",
                 },
                 step
             );
@@ -87,7 +87,7 @@ var View = Backbone.View.extend({
 
         // iterate through data input modules and collect linked sub steps
         _.each(this.steps, (step, i) => {
-            _.each(step.output_connections, output_connection => {
+            _.each(step.output_connections, (output_connection) => {
                 _.each(self.steps, (sub_step, j) => {
                     if (sub_step.step_index === output_connection.input_step_index) {
                         self.links[i].push(sub_step);
@@ -101,7 +101,7 @@ var View = Backbone.View.extend({
         _.each(this.steps, (step, i) => {
             _.each(self.steps, (sub_step, j) => {
                 var connections_by_name = {};
-                _.each(step.output_connections, connection => {
+                _.each(step.output_connections, (connection) => {
                     if (sub_step.step_index === connection.input_step_index) {
                         connections_by_name[connection.input_name] = connection;
                     }
@@ -130,7 +130,7 @@ var View = Backbone.View.extend({
                 type: "text",
                 color: `hsl( ${++wp_count * 100}, 70%, 30% )`,
                 style: "ui-form-wp-source",
-                links: []
+                links: [],
             });
         }
 
@@ -144,7 +144,7 @@ var View = Backbone.View.extend({
         }
         _.each(this.steps, (step, i) => {
             _.each(self.parms[i], (input, name) => {
-                _handleWorkflowParameter(input.value, wp_input => {
+                _handleWorkflowParameter(input.value, (wp_input) => {
                     wp_input.links.push(step);
                     input.wp_linked = true;
                     input.type = "text";
@@ -152,7 +152,7 @@ var View = Backbone.View.extend({
                     input.style = "ui-form-wp-target";
                 });
             });
-            _.each(step.replacement_parameters, wp_name => {
+            _.each(step.replacement_parameters, (wp_name) => {
                 _ensureWorkflowParameter(wp_name);
             });
         });
@@ -197,20 +197,20 @@ var View = Backbone.View.extend({
         });
     },
 
-    render: function() {
+    render: function () {
         var self = this;
         this.deferred.reset();
         this._renderParameters();
         this._renderHistory();
         this._renderUseCachedJob();
         this._renderResourceParameters();
-        _.each(this.steps, step => {
+        _.each(this.steps, (step) => {
             self._renderStep(step);
         });
     },
 
     /** Render workflow parameters */
-    _renderParameters: function() {
+    _renderParameters: function () {
         var self = this;
         this.wp_form = null;
         if (!_.isEmpty(this.wp_inputs)) {
@@ -218,20 +218,20 @@ var View = Backbone.View.extend({
                 title: "<b>Workflow Parameters</b>",
                 inputs: this.wp_inputs,
                 cls: "ui-portlet-section",
-                onchange: function() {
+                onchange: function () {
                     _.each(self.wp_form.input_list, (input_def, i) => {
-                        _.each(input_def.links, step => {
+                        _.each(input_def.links, (step) => {
                             self._refreshStep(step);
                         });
                     });
-                }
+                },
             });
             this._append(this.$el.empty(), this.wp_form.$el);
         }
     },
 
     /** Render workflow parameters */
-    _renderHistory: function() {
+    _renderHistory: function () {
         this.history_form = new Form({
             cls: "ui-portlet-section",
             title: "<b>History Options</b>",
@@ -244,7 +244,7 @@ var View = Backbone.View.extend({
                         label: "Send results to a new history",
                         type: "boolean",
                         value: "false",
-                        help: ""
+                        help: "",
                     },
                     cases: [
                         {
@@ -254,32 +254,32 @@ var View = Backbone.View.extend({
                                     name: "name",
                                     label: "History name",
                                     type: "text",
-                                    value: this.model.get("name")
-                                }
-                            ]
-                        }
-                    ]
-                }
-            ]
+                                    value: this.model.get("name"),
+                                },
+                            ],
+                        },
+                    ],
+                },
+            ],
         });
         this._append(this.$el, this.history_form.$el);
     },
 
     /** Render Workflow Options */
-    _renderResourceParameters: function() {
+    _renderResourceParameters: function () {
         this.workflow_resource_parameters_form = null;
         if (!_.isEmpty(this.model.get("workflow_resource_parameters"))) {
             this.workflow_resource_parameters_form = new Form({
                 cls: "ui-portlet-section",
                 title: "<b>Workflow Resource Options</b>",
-                inputs: this.model.get("workflow_resource_parameters")
+                inputs: this.model.get("workflow_resource_parameters"),
             });
             this._append(this.$el, this.workflow_resource_parameters_form.$el);
         }
     },
 
     /** Render job caching option */
-    _renderUseCachedJob: function() {
+    _renderUseCachedJob: function () {
         const Galaxy = getGalaxyInstance();
         var extra_user_preferences = {};
         if (Galaxy.user.attributes.preferences && "extra_user_preferences" in Galaxy.user.attributes.preferences) {
@@ -303,28 +303,28 @@ var View = Backbone.View.extend({
                             label: "BETA: Attempt to reuse jobs with identical parameters?",
                             type: "boolean",
                             value: "false",
-                            help: "This may skip executing jobs that you have already run."
-                        }
-                    }
-                ]
+                            help: "This may skip executing jobs that you have already run.",
+                        },
+                    },
+                ],
             });
             this._append(this.$el, this.job_options_form.$el);
         }
     },
 
     /** Render step */
-    _renderStep: function(step) {
+    _renderStep: function (step) {
         const Galaxy = getGalaxyInstance();
         var self = this;
         var form = null;
-        this.deferred.execute(promise => {
+        this.deferred.execute((promise) => {
             self.$el.addClass("ui-steps");
             if (step.step_type == "tool") {
-                step.postchange = function(process, form) {
+                step.postchange = function (process, form) {
                     var current_state = {
                         tool_id: step.id,
                         tool_version: step.version,
-                        inputs: $.extend(true, {}, form.data.create())
+                        inputs: $.extend(true, {}, form.data.create()),
                     };
                     form.wait(true);
                     Galaxy.emit.debug("tool-form-composite::postchange()", "Sending current state.", current_state);
@@ -332,16 +332,16 @@ var View = Backbone.View.extend({
                         type: "POST",
                         url: `${getAppRoot()}api/tools/${step.id}/build`,
                         data: current_state,
-                        success: function(data) {
+                        success: function (data) {
                             form.update(data);
                             form.wait(false);
                             Galaxy.emit.debug("tool-form-composite::postchange()", "Received new model.", data);
                             process.resolve();
                         },
-                        error: function(response) {
+                        error: function (response) {
                             Galaxy.emit.debug("tool-form-composite::postchange()", "Refresh request failed.", response);
                             process.reject();
-                        }
+                        },
                     });
                 };
                 form = new ToolFormBase(step);
@@ -349,11 +349,7 @@ var View = Backbone.View.extend({
                     form.portlet.append(
                         $("<div/>")
                             .addClass("ui-form-element-disabled")
-                            .append(
-                                $("<div/>")
-                                    .addClass("ui-form-title")
-                                    .html("<b>Job Post Actions</b>")
-                            )
+                            .append($("<div/>").addClass("ui-form-title").html("<b>Job Post Actions</b>"))
                             .append(
                                 $("<div/>")
                                     .addClass("ui-form-preview")
@@ -369,7 +365,7 @@ var View = Backbone.View.extend({
                 }
             } else {
                 var is_simple_input = ["data_input", "data_collection_input"].indexOf(step.step_type) != -1;
-                _.each(step.inputs, input => {
+                _.each(step.inputs, (input) => {
                     input.flavor = "module";
                     input.hide_label = is_simple_input;
                 });
@@ -377,8 +373,8 @@ var View = Backbone.View.extend({
                     Utils.merge(
                         {
                             title: step.fixed_title,
-                            onchange: function() {
-                                _.each(self.links[step.index], link => {
+                            onchange: function () {
+                                _.each(self.links[step.index], (link) => {
                                     self._refreshStep(link);
                                 });
                             },
@@ -389,9 +385,9 @@ var View = Backbone.View.extend({
                                           {
                                               type: "hidden",
                                               name: "No options available.",
-                                              ignore: null
-                                          }
-                                      ]
+                                              ignore: null,
+                                          },
+                                      ],
                         },
                         step
                     )
@@ -418,7 +414,7 @@ var View = Backbone.View.extend({
     },
 
     /** Refreshes step values from source step values */
-    _refreshStep: function(step) {
+    _refreshStep: function (step) {
         var self = this;
         var form = this.forms[step.index];
         if (form) {
@@ -429,11 +425,11 @@ var View = Backbone.View.extend({
                         var new_value;
                         if (input.step_linked) {
                             new_value = { values: [] };
-                            _.each(input.step_linked, source_step => {
+                            _.each(input.step_linked, (source_step) => {
                                 if (self._isDataStep(source_step)) {
                                     var value = self.forms[source_step.index].data.create().input;
                                     if (value) {
-                                        _.each(value.values, v => {
+                                        _.each(value.values, (v) => {
                                             new_value.values.push(v);
                                         });
                                     }
@@ -441,7 +437,7 @@ var View = Backbone.View.extend({
                             });
                             if (!input.multiple && new_value.values.length > 0) {
                                 new_value = {
-                                    values: [new_value.values[0]]
+                                    values: [new_value.values[0]],
                                 };
                             }
                         } else if (input.wp_linked) {
@@ -469,10 +465,10 @@ var View = Backbone.View.extend({
     },
 
     /** Build remaining steps */
-    execute: function() {
+    execute: function () {
         this.show_progress = true;
         this._enabled(false);
-        this.deferred.execute(promise => {
+        this.deferred.execute((promise) => {
             window.setTimeout(() => {
                 promise.resolve();
                 this._submit();
@@ -481,7 +477,7 @@ var View = Backbone.View.extend({
     },
 
     /** Validate and submit workflow */
-    _submit: function() {
+    _submit: function () {
         const Galaxy = getGalaxyInstance();
         var self = this;
         var history_form_data = this.history_form.data.create();
@@ -499,7 +495,7 @@ var View = Backbone.View.extend({
             parameters_normalized: true,
             // Tool form always wants a list of invocations back
             // so that inputs can be batched.
-            batch: true
+            batch: true,
         };
         if (this.display_use_cached_job_checkbox) {
             job_def.use_cached_job = this.job_options_form.data.create()["use_cached_job|check"] === "true";
@@ -548,7 +544,7 @@ var View = Backbone.View.extend({
                 type: "POST",
                 url: `${getAppRoot()}api/workflows/${this.model.id}/invocations`,
                 data: job_def,
-                success: response => {
+                success: (response) => {
                     Galaxy.emit.debug("tool-form-composite::submit", "Submission successful.", response);
                     if ($.isArray(response) && response.length > 0) {
                         this.handleInvocations(response);
@@ -556,7 +552,7 @@ var View = Backbone.View.extend({
                         this.submissionErrorModal(job_def, response);
                     }
                 },
-                error: response => {
+                error: (response) => {
                     Galaxy.emit.debug("tool-form-composite::submit", "Submission failed.", response);
                     var input_found = false;
                     if (response && response.err_data) {
@@ -577,20 +573,20 @@ var View = Backbone.View.extend({
                         this.submissionErrorModal(job_def, response);
                     }
                 },
-                complete: function() {
+                complete: function () {
                     self._enabled(true);
-                }
+                },
             });
         }
     },
 
     /** Append new dom to body */
-    _append: function($container, $el) {
+    _append: function ($container, $el) {
         $container.append("<p/>").append($el);
     },
 
     /** Set enabled/disabled state */
-    _enabled: function(enabled) {
+    _enabled: function (enabled) {
         this.setRunButtonStatus(enabled, "Sending...", -1);
         if (this.wp_form) {
             this.wp_form.portlet[enabled ? "enable" : "disable"]();
@@ -598,7 +594,7 @@ var View = Backbone.View.extend({
         if (this.history_form) {
             this.history_form.portlet[enabled ? "enable" : "disable"]();
         }
-        _.each(this.forms, form => {
+        _.each(this.forms, (form) => {
             if (form) {
                 form.portlet[enabled ? "enable" : "disable"]();
             }
@@ -606,7 +602,7 @@ var View = Backbone.View.extend({
     },
 
     /** Is data input module/step */
-    _isDataStep: function(steps) {
+    _isDataStep: function (steps) {
         var lst = $.isArray(steps) ? steps : [steps];
         for (var i = 0; i < lst.length; i++) {
             var step = lst[i];
@@ -617,32 +613,32 @@ var View = Backbone.View.extend({
         return true;
     },
 
-    submissionErrorModal: function(job_def, response) {
+    submissionErrorModal: function (job_def, response) {
         this.modal.show({
             title: _l("Workflow submission failed"),
             body: this._templateError(job_def, response && response.err_msg),
             buttons: {
                 Close: () => {
                     this.modal.hide();
-                }
-            }
+                },
+            },
         });
     },
 
     /** Templates */
-    _templateError: function(response, err_msg) {
+    _templateError: function (response, err_msg) {
         return $("<div/>")
             .addClass("errormessagelarge")
             .append(
                 $("<p/>").text(
-                    `The server could not complete the request. Please contact the Galaxy Team if this error persists. ${JSON.stringify(
-                        err_msg
-                    ) || ""}`
+                    `The server could not complete the request. Please contact the Galaxy Team if this error persists. ${
+                        JSON.stringify(err_msg) || ""
+                    }`
                 )
             )
             .append($("<pre/>").text(JSON.stringify(response, null, 4)));
-    }
+    },
 });
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index 59ced2add5ea..815b42db4fb4 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -16,7 +16,7 @@ import ToolEntryPoints from "components/ToolEntryPoints/ToolEntryPoints";
 import ToolRecommendation from "components/ToolRecommendation";
 
 const View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         const Galaxy = getGalaxyInstance();
         this.modal = Galaxy.modal || new Modal.View();
         this.form = new ToolFormBase(
@@ -44,7 +44,7 @@ const View = Backbone.View.extend({
                         Utils.get({
                             url: build_url,
                             data: build_data,
-                            success: data => {
+                            success: (data) => {
                                 if (!data.display) {
                                     window.location = getAppRoot();
                                     return;
@@ -58,14 +58,14 @@ const View = Backbone.View.extend({
                                 const error_message = (response && response.err_msg) || "Uncaught error.";
                                 if (status == 401) {
                                     window.location = `${getAppRoot()}user/login?${$.param({
-                                        redirect: `${getAppRoot()}?tool_id=${options.id}`
+                                        redirect: `${getAppRoot()}?tool_id=${options.id}`,
                                     })}`;
                                 } else if (form.$el.is(":empty")) {
                                     form.$el.prepend(
                                         new Ui.Message({
                                             message: error_message,
                                             status: "danger",
-                                            persistent: true
+                                            persistent: true,
                                         }).$el
                                     );
                                 } else {
@@ -76,8 +76,8 @@ const View = Backbone.View.extend({
                                             buttons: {
                                                 Close: () => {
                                                     Galaxy.modal.hide();
-                                                }
-                                            }
+                                                },
+                                            },
                                         });
                                 }
                                 Galaxy.emit.debug(
@@ -86,14 +86,14 @@ const View = Backbone.View.extend({
                                     response
                                 );
                                 process.reject();
-                            }
+                            },
                         });
                     },
                     postchange: (process, form) => {
                         const current_state = {
                             tool_id: form.model.get("id"),
                             tool_version: form.model.get("version"),
-                            inputs: $.extend(true, {}, form.data.create())
+                            inputs: $.extend(true, {}, form.data.create()),
                         };
                         form.wait(true);
                         Galaxy.emit.debug("tool-form::postchange()", "Sending current state.", current_state);
@@ -101,18 +101,18 @@ const View = Backbone.View.extend({
                             type: "POST",
                             url: `${getAppRoot()}api/tools/${form.model.get("id")}/build`,
                             data: current_state,
-                            success: data => {
+                            success: (data) => {
                                 form.update(data);
                                 form.wait(false);
                                 Galaxy.emit.debug("tool-form::postchange()", "Received new model.", data);
                                 process.resolve();
                             },
-                            error: response => {
+                            error: (response) => {
                                 Galaxy.emit.debug("tool-form::postchange()", "Refresh request failed.", response);
                                 process.reject();
-                            }
+                            },
                         });
-                    }
+                    },
                 },
                 options
             )
@@ -122,7 +122,7 @@ const View = Backbone.View.extend({
         this.$el.append(this.form.$el);
     },
 
-    _customize: function(form) {
+    _customize: function (form) {
         const Galaxy = getGalaxyInstance();
         const options = form.model.attributes;
         var inputs = options.inputs;
@@ -136,7 +136,7 @@ const View = Backbone.View.extend({
                 type: "boolean",
                 value: "false",
                 ignore: "false",
-                help: _l("Send an email notification when the job completes.")
+                help: _l("Send an email notification when the job completes."),
             });
         }
 
@@ -154,7 +154,7 @@ const View = Backbone.View.extend({
                     execute_button.unwait();
                     form.portlet.enable();
                 });
-            }
+            },
         });
         options.buttons = { execute: execute_button };
 
@@ -180,9 +180,9 @@ const View = Backbone.View.extend({
                 value: "__ignore__",
                 options: [
                     ["Yes", options.job_id],
-                    ["No", "__ignore__"]
+                    ["No", "__ignore__"],
                 ],
-                help: help
+                help: help,
             });
         }
 
@@ -206,8 +206,8 @@ const View = Backbone.View.extend({
                 value: "__ignore__",
                 options: [
                     ["No", false],
-                    ["Yes", true]
-                ]
+                    ["Yes", true],
+                ],
             });
         }
     },
@@ -216,14 +216,14 @@ const View = Backbone.View.extend({
      * @param{dict}     options   - Specifies tool id and version
      * @param{function} callback  - Called when request has completed
      */
-    submit: function(options, callback) {
+    submit: function (options, callback) {
         const Galaxy = getGalaxyInstance();
         const history_id = Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model.id;
         const job_def = {
             history_id: history_id,
             tool_id: options.id,
             tool_version: options.version,
-            inputs: this.form.data.create()
+            inputs: this.form.data.create(),
         };
         this.form.trigger("reset");
         if (!this.validate(job_def)) {
@@ -235,15 +235,12 @@ const View = Backbone.View.extend({
             const $f = $("<form/>").attr({
                 action: options.action,
                 method: options.method,
-                enctype: options.enctype
+                enctype: options.enctype,
             });
             _.each(job_def.inputs, (value, key) => {
                 $f.append($("<input/>").attr({ name: key, value: value }));
             });
-            $f.hide()
-                .appendTo("body")
-                .submit()
-                .remove();
+            $f.hide().appendTo("body").submit().remove();
             callback && callback();
             return;
         }
@@ -252,7 +249,7 @@ const View = Backbone.View.extend({
             type: "POST",
             url: `${getAppRoot()}api/tools`,
             data: job_def,
-            success: response => {
+            success: (response) => {
                 callback && callback();
                 this.$el.children().hide();
                 if (response.produces_entry_points) {
@@ -262,8 +259,8 @@ const View = Backbone.View.extend({
                         this.$el.append(vm);
                         const instance = new toolEntryPointsInstance({
                             propsData: {
-                                jobId: job.id
-                            }
+                                jobId: job.id,
+                            },
                         });
                         instance.$mount(vm);
                     }
@@ -277,8 +274,8 @@ const View = Backbone.View.extend({
                     this.$el.append(vm);
                     const instance = new ToolRecommendationInstance({
                         propsData: {
-                            toolId: job_def.tool_id
-                        }
+                            toolId: job_def.tool_id,
+                        },
                     });
                     instance.$mount(vm);
                 }
@@ -288,7 +285,7 @@ const View = Backbone.View.extend({
                     this.$el.append($("<div/>", { id: "webhook-view" }));
                     new Webhooks.WebhookView({
                         type: "tool",
-                        toolId: job_def.tool_id
+                        toolId: job_def.tool_id,
                     });
                 }
                 if (Galaxy.currHistoryPanel) {
@@ -296,7 +293,7 @@ const View = Backbone.View.extend({
                     Galaxy.currHistoryPanel.refreshContents();
                 }
             },
-            error: response => {
+            error: (response) => {
                 callback && callback();
                 Galaxy.emit.debug("tool-form::submit", "Submission failed.", response);
                 let input_found = false;
@@ -315,18 +312,18 @@ const View = Backbone.View.extend({
                         buttons: {
                             Close: () => {
                                 this.modal.hide();
-                            }
-                        }
+                            },
+                        },
                     });
                 }
-            }
+            },
         });
     },
 
     /** Validate job dictionary.
      * @param{dict}     job_def   - Job execution dictionary
      */
-    validate: function(job_def) {
+    validate: function (job_def) {
         const Galaxy = getGalaxyInstance();
         const job_inputs = job_def.inputs;
         let batch_n = -1;
@@ -379,7 +376,7 @@ const View = Backbone.View.extend({
         return true;
     },
 
-    _getInputs: function(job_def) {
+    _getInputs: function (job_def) {
         const inputs = [];
         const index = {};
         for (const i in job_def.inputs) {
@@ -396,7 +393,7 @@ const View = Backbone.View.extend({
         return inputs;
     },
 
-    _templateRow: function(list, title) {
+    _templateRow: function (list, title) {
         let blurb = "";
         if (list.length > 0) {
             blurb += `<p>${title}:</p>`;
@@ -413,7 +410,7 @@ const View = Backbone.View.extend({
         return blurb;
     },
 
-    _templateSuccess: function(response, job_def) {
+    _templateSuccess: function (response, job_def) {
         const njobs = response && response.jobs ? response.jobs.length : 0;
         if (njobs > 0) {
             const inputs = this._getInputs(job_def);
@@ -438,19 +435,20 @@ const View = Backbone.View.extend({
         }
     },
 
-    _templateError: function(response, err_msg) {
+    _templateError: function (response, err_msg) {
         return $("<div/>")
             .addClass("errormessagelarge")
             .append(
                 $("<p/>").text(
-                    `The server could not complete the request. Please contact the Galaxy Team if this error persists. ${err_msg ||
-                        ""}`
+                    `The server could not complete the request. Please contact the Galaxy Team if this error persists. ${
+                        err_msg || ""
+                    }`
                 )
             )
             .append($("<pre/>").text(JSON.stringify(response, null, 4)));
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/tours.js b/client/galaxy/scripts/mvc/tours.js
index eaca3c05fce5..672db26184de 100644
--- a/client/galaxy/scripts/mvc/tours.js
+++ b/client/galaxy/scripts/mvc/tours.js
@@ -57,18 +57,18 @@ const TOURPAGE_TEMPLATE = `
 
 var tour_opts = {
     storage: window.sessionStorage,
-    onEnd: function() {
+    onEnd: function () {
         window.sessionStorage.removeItem("activeGalaxyTour");
     },
     delay: 150, // Attempts to make it look natural
-    orphan: true
+    orphan: true,
 };
 
-var hooked_tour_from_data = data => {
-    _.each(data.steps, step => {
+var hooked_tour_from_data = (data) => {
+    _.each(data.steps, (step) => {
         if (step.preclick) {
             step.onShow = () => {
-                _.each(step.preclick, preclick => {
+                _.each(step.preclick, (preclick) => {
                     // TODO: click delay between clicks
                     $(preclick).click();
                 });
@@ -76,7 +76,7 @@ var hooked_tour_from_data = data => {
         }
         if (step.postclick) {
             step.onHide = () => {
-                _.each(step.postclick, postclick => {
+                _.each(step.postclick, (postclick) => {
                     // TODO: click delay between clicks
                     $(postclick).click();
                 });
@@ -87,9 +87,7 @@ var hooked_tour_from_data = data => {
             // elements which have additional logic, like the
             // upload input box
             step.onShown = () => {
-                $(step.element)
-                    .val(step.textinsert)
-                    .trigger("change");
+                $(step.element).val(step.textinsert).trigger("change");
             };
         }
         if (step.path) {
@@ -107,36 +105,36 @@ var hooked_tour_from_data = data => {
 };
 
 var TourItem = Backbone.Model.extend({
-    urlRoot: `${gxy_root}api/tours`
+    urlRoot: `${gxy_root}api/tours`,
 });
 
 var Tours = Backbone.Collection.extend({
     url: `${gxy_root}api/tours`,
-    model: TourItem
+    model: TourItem,
 });
 
 export var ToursView = Backbone.View.extend({
     title: _l("Tours"),
-    initialize: function() {
+    initialize: function () {
         var self = this;
         this.setElement("<div/>");
         this.model = new Tours();
         this.model.fetch({
-            success: function() {
+            success: function () {
                 self.render();
             },
-            error: function() {
+            error: function () {
                 // Do something.
                 console.error("Failed to fetch tours.");
-            }
+            },
         });
     },
 
-    render: function() {
+    render: function () {
         var tpl = _.template(TOURPAGE_TEMPLATE);
 
         var tourtags = {};
-        _.each(this.model.models, tour => {
+        _.each(this.model.models, (tour) => {
             tour.attributes.tags_lc = [];
             if (tour.attributes.tags === null) {
                 if (tourtags.Untagged === undefined) {
@@ -144,7 +142,7 @@ export var ToursView = Backbone.View.extend({
                 }
                 tourtags.Untagged.tours.push(tour);
             } else {
-                _.each(tour.attributes.tags, otag => {
+                _.each(tour.attributes.tags, (otag) => {
                     var tag = otag.charAt(0).toUpperCase() + otag.slice(1);
                     if (tourtags[tag] === undefined) {
                         tourtags[tag] = { name: tag, tours: [] };
@@ -156,7 +154,7 @@ export var ToursView = Backbone.View.extend({
         });
         //var tourtagorder = Object.keys(tourtags).sort();
         var tourtagorder = [];
-        Object.keys(tourtags).forEach(function(tag, index) {
+        Object.keys(tourtags).forEach(function (tag, index) {
             tourtagorder.push({ name: tag, key: tag.toLowerCase() });
         });
 
@@ -165,14 +163,14 @@ export var ToursView = Backbone.View.extend({
                 tpl({
                     tours: this.model.models,
                     tourtags: tourtags,
-                    tourtagorder: tourtagorder
+                    tourtagorder: tourtagorder,
                 })
             )
-            .on("click", ".tourItem", function(e) {
+            .on("click", ".tourItem", function (e) {
                 e.preventDefault();
                 giveTourById($(this).data("tour.id"));
             })
-            .on("click", ".tag-selector-button", e => {
+            .on("click", ".tag-selector-button", (e) => {
                 var elem = $(e.target);
                 var active_tags = [];
 
@@ -181,20 +179,20 @@ export var ToursView = Backbone.View.extend({
                 elem.toggleClass("btn-secondary");
 
                 // Get all non-disabled tags
-                $(`.tag-selector-button.btn-primary`).each(function() {
+                $(`.tag-selector-button.btn-primary`).each(function () {
                     active_tags.push($(this).attr("tag-selector-button"));
                 });
 
                 // Loop over all list items, subsequently determine these are
                 // only the tours (tags should be unique). Then use the non-disabled tags to
                 // determien whether or not to display this specific tour.
-                $(`li.list-group-item`).each(function() {
+                $(`li.list-group-item`).each(function () {
                     if ($(this).attr("tags")) {
                         var tour_tags = [];
                         var tour_tags_html = $(this).attr("tags");
 
                         tour_tags = tour_tags_html.split(",");
-                        var fil_tour_tags = tour_tags.filter(function(tag) {
+                        var fil_tour_tags = tour_tags.filter(function (tag) {
                             return active_tags.indexOf(tag.toLowerCase()) > -1;
                         });
 
@@ -202,7 +200,7 @@ export var ToursView = Backbone.View.extend({
                     }
                 });
             });
-    }
+    },
 });
 
 export function giveTourWithData(data) {
@@ -219,7 +217,7 @@ export function giveTourWithData(data) {
 
 export function giveTourById(tour_id) {
     var url = `${gxy_root}api/tours/${tour_id}`;
-    $.getJSON(url, data => {
+    $.getJSON(url, (data) => {
         giveTourWithData(data);
     });
 }
@@ -237,7 +235,7 @@ export function activeGalaxyTourRunner() {
                 var tour = new Tour(
                     _.extend(
                         {
-                            steps: et.steps
+                            steps: et.steps,
                         },
                         tour_opts
                     )
@@ -253,5 +251,5 @@ export default {
     ToursView: ToursView,
     giveTourWithData: giveTourWithData,
     giveTourById: giveTourById,
-    activeGalaxyTourRunner: activeGalaxyTourRunner
+    activeGalaxyTourRunner: activeGalaxyTourRunner,
 };
diff --git a/client/galaxy/scripts/mvc/ui/error-modal.js b/client/galaxy/scripts/mvc/ui/error-modal.js
index f38414683ac9..525e97122cb5 100644
--- a/client/galaxy/scripts/mvc/ui/error-modal.js
+++ b/client/galaxy/scripts/mvc/ui/error-modal.js
@@ -42,18 +42,15 @@ function _errorModal(message, title, details) {
         body: message,
         closing_events: true,
         buttons: {
-            Ok: function() {
+            Ok: function () {
                 Galaxy.modal.hide();
-            }
-        }
+            },
+        },
     });
     Galaxy.modal.$el.addClass("error-modal");
 
     if (details) {
-        Galaxy.modal
-            .$(".error-details")
-            .add(Galaxy.modal.$('button:contains("Details")'))
-            .remove();
+        Galaxy.modal.$(".error-details").add(Galaxy.modal.$('button:contains("Details")')).remove();
         $("<div/>")
             .addClass("error-details")
             .hide()
@@ -127,7 +124,7 @@ function _ajaxDetails(model, xhr, options) {
         data: _.result(Galaxy.lastAjax, "data"),
         // backbone stuff (auto-redacting email for user)
         model: _.result(model, "toJSON", `${model}`),
-        user: _.omit(_.result(Galaxy.user, "toJSON"), "email")
+        user: _.omit(_.result(Galaxy.user, "toJSON"), "email"),
     };
 }
 
@@ -136,5 +133,5 @@ export default {
     errorModal: errorModal,
     offlineErrorModal: offlineErrorModal,
     badGatewayErrorModal: badGatewayErrorModal,
-    ajaxErrorModal: ajaxErrorModal
+    ajaxErrorModal: ajaxErrorModal,
 };
diff --git a/client/galaxy/scripts/mvc/ui/icon-button.js b/client/galaxy/scripts/mvc/ui/icon-button.js
index d742aebad571..534937ebf63a 100644
--- a/client/galaxy/scripts/mvc/ui/icon-button.js
+++ b/client/galaxy/scripts/mvc/ui/icon-button.js
@@ -19,21 +19,21 @@ var IconButton = Backbone.Model.extend({
         target: null,
         enabled: true,
         visible: true,
-        tooltip_config: {}
-    }
+        tooltip_config: {},
+    },
 });
 
 /**
  *  backbone view for icon buttons
  */
 var IconButtonView = Backbone.View.extend({
-    initialize: function() {
+    initialize: function () {
         // better rendering this way
         this.model.attributes.tooltip_config = { placement: "bottom" };
         this.model.bind("change", this.render, this);
     },
 
-    render: function() {
+    render: function () {
         // hide tooltip
         this.$el.tooltip("hide");
 
@@ -46,10 +46,10 @@ var IconButtonView = Backbone.View.extend({
     },
 
     events: {
-        click: "click"
+        click: "click",
     },
 
-    click: function(event) {
+    click: function (event) {
         // if on_click pass to that function
         if (_.isFunction(this.model.get("on_click"))) {
             this.model.get("on_click")(event);
@@ -60,7 +60,7 @@ var IconButtonView = Backbone.View.extend({
     },
 
     // generate html element
-    template: function(options) {
+    template: function (options) {
         var buffer = `title="${options.title}" class="icon-button`;
 
         if (options.is_menu_button) {
@@ -99,12 +99,12 @@ var IconButtonView = Backbone.View.extend({
 
         // return element
         return $(buffer);
-    }
+    },
 });
 
 // define collection
 var IconButtonCollection = Backbone.Collection.extend({
-    model: IconButton
+    model: IconButton,
 });
 
 /**
@@ -114,14 +114,14 @@ var IconButtonCollection = Backbone.Collection.extend({
 var IconButtonMenuView = Backbone.View.extend({
     tagName: "div",
 
-    initialize: function() {
+    initialize: function () {
         this.render();
     },
 
-    render: function() {
+    render: function () {
         // initialize icon buttons
         var self = this;
-        this.collection.each(button => {
+        this.collection.each((button) => {
             // create and add icon button to menu
             var elt = $("<a/>")
                 .attr("href", "javascript:void(0)")
@@ -145,7 +145,7 @@ var IconButtonMenuView = Backbone.View.extend({
 
         // return
         return this;
-    }
+    },
 });
 
 /**
@@ -160,7 +160,7 @@ var create_icon_buttons_menu = (config, global_config) => {
 
     // create and initialize menu
     var buttons = new IconButtonCollection(
-        _.map(config, button_config => new IconButton(_.extend(button_config, global_config)))
+        _.map(config, (button_config) => new IconButton(_.extend(button_config, global_config)))
     );
 
     // return menu
@@ -173,5 +173,5 @@ export default {
     IconButtonView: IconButtonView,
     IconButtonCollection: IconButtonCollection,
     IconButtonMenuView: IconButtonMenuView,
-    create_icon_buttons_menu: create_icon_buttons_menu
+    create_icon_buttons_menu: create_icon_buttons_menu,
 };
diff --git a/client/galaxy/scripts/mvc/ui/popup-menu.js b/client/galaxy/scripts/mvc/ui/popup-menu.js
index 6166a6e078ee..cd3e23760479 100644
--- a/client/galaxy/scripts/mvc/ui/popup-menu.js
+++ b/client/galaxy/scripts/mvc/ui/popup-menu.js
@@ -10,7 +10,7 @@ const PopupMenu = Backbone.View.extend({
     /** Cache the desired button element and options, set up the button click handler
      *  NOTE: attaches this view as HTML/jQ data on the button for later use.
      */
-    initialize: function($button, options) {
+    initialize: function ($button, options) {
         // default settings
         this.$button = $button;
         if (!this.$button.length) {
@@ -20,7 +20,7 @@ const PopupMenu = Backbone.View.extend({
         this.$button.data("popupmenu", this);
 
         // set up button click -> open menu behavior
-        this.$button.click(event => {
+        this.$button.click((event) => {
             // if there's already a menu open, remove it
             $(".popmenu-wrapper").remove();
             this._renderAndShow(event);
@@ -29,18 +29,15 @@ const PopupMenu = Backbone.View.extend({
     },
 
     // render the menu, append to the page body at the click position, and set up the 'click-away' handlers, show
-    _renderAndShow: function(clickEvent) {
+    _renderAndShow: function (clickEvent) {
         this.render();
-        this.$el
-            .appendTo("body")
-            .css(this._getShownPosition(clickEvent))
-            .show();
+        this.$el.appendTo("body").css(this._getShownPosition(clickEvent)).show();
         this._setUpCloseBehavior();
     },
 
     // render the menu
     // this menu doesn't attach itself to the DOM ( see _renderAndShow )
-    render: function() {
+    render: function () {
         // render the menu body absolute and hidden, fill with template
         this.$el
             .addClass("popmenu-wrapper")
@@ -54,7 +51,7 @@ const PopupMenu = Backbone.View.extend({
                 const option = this.options[i];
                 // if the option has 'func', call that function when the anchor is clicked
                 if (option.func) {
-                    $(el).click(event => {
+                    $(el).click((event) => {
                         option.func.call(this, event, option);
                         // We must preventDefault otherwise clicking "cancel"
                         // on a purge or something still navigates and causes
@@ -68,17 +65,17 @@ const PopupMenu = Backbone.View.extend({
         return this;
     },
 
-    template: function(id, options) {
+    template: function (id, options) {
         return `<div id="${id}-menu" class="dropdown-menu">
                     ${this._templateOptions(options)}
                 </div>`;
     },
 
-    _templateOptions: function(options) {
+    _templateOptions: function (options) {
         if (!options.length) {
             return '<div class="dropdown-header">(no options)</div>';
         }
-        return _.map(options, option => {
+        return _.map(options, (option) => {
             if (option.divider) {
                 return '<div class="popupmenu-option dropdown-divider"/>';
             } else if (option.header) {
@@ -92,7 +89,7 @@ const PopupMenu = Backbone.View.extend({
     },
 
     // get the absolute position/offset for the menu
-    _getShownPosition: function(clickEvent) {
+    _getShownPosition: function (clickEvent) {
         // display menu horiz. centered on click...
         const menuWidth = this.$el.width();
         let x = clickEvent.pageX - menuWidth / 2;
@@ -102,17 +99,17 @@ const PopupMenu = Backbone.View.extend({
         x = Math.max(x, $(document).scrollLeft() + 5);
         return {
             top: clickEvent.pageY,
-            left: x
+            left: x,
         };
     },
 
     // bind an event handler to all available frames so that when anything is clicked
     // the menu is removed from the DOM and the event handler unbinds itself
-    _setUpCloseBehavior: function() {
+    _setUpCloseBehavior: function () {
         //TODO: alternately: focus hack, blocking overlay, jquery.blockui
 
         // function to close popup and unbind itself
-        const closePopup = event => {
+        const closePopup = (event) => {
             //do nothing if header item is clicked
             if (event.target.classList.contains("dropdown-header")) {
                 return;
@@ -122,9 +119,7 @@ const PopupMenu = Backbone.View.extend({
                 if (window && window.parent !== window) {
                     $(window.parent.document).off("click.close_popup");
                 } else {
-                    $("iframe#galaxy_main")
-                        .contents()
-                        .off("click.close_popup");
+                    $("iframe#galaxy_main").contents().off("click.close_popup");
                 }
             } catch (err) {
                 if (err instanceof DOMException) {
@@ -141,13 +136,9 @@ const PopupMenu = Backbone.View.extend({
         $("html").on("click.close_popup", closePopup);
         try {
             if (window && window.parent !== window) {
-                $(window.parent.document)
-                    .find("html")
-                    .on("click.close_popup", closePopup);
+                $(window.parent.document).find("html").on("click.close_popup", closePopup);
             } else {
-                $("iframe#galaxy_main")
-                    .contents()
-                    .on("click.close_popup", closePopup);
+                $("iframe#galaxy_main").contents().on("click.close_popup", closePopup);
             }
         } catch (err) {
             if (err instanceof DOMException) {
@@ -161,7 +152,7 @@ const PopupMenu = Backbone.View.extend({
     },
 
     // add a menu option/item at the given index
-    addItem: function(item, index) {
+    addItem: function (item, index) {
         // append to end if no index
         index = index >= 0 ? index : this.options.length;
         this.options.splice(index, 0, item);
@@ -169,7 +160,7 @@ const PopupMenu = Backbone.View.extend({
     },
 
     // remove a menu option/item at the given index
-    removeItem: function(index) {
+    removeItem: function (index) {
         if (index >= 0) {
             this.options.splice(index, 1);
         }
@@ -177,7 +168,7 @@ const PopupMenu = Backbone.View.extend({
     },
 
     // search for a menu option by its html
-    findIndexByHtml: function(html) {
+    findIndexByHtml: function (html) {
         for (let i = 0; i < this.options.length; i++) {
             if (_.has(this.options[i], "html") && this.options[i].html === html) {
                 return i;
@@ -187,14 +178,14 @@ const PopupMenu = Backbone.View.extend({
     },
 
     // search for a menu option by its html
-    findItemByHtml: function(html) {
+    findItemByHtml: function (html) {
         return this.options[this.findIndexByHtml(html)];
     },
 
     // string representation
-    toString: function() {
+    toString: function () {
         return "PopupMenu";
-    }
+    },
 });
 /** shortcut to new for when you don't need to preserve the ref */
 PopupMenu.create = function _create($button, options) {
diff --git a/client/galaxy/scripts/mvc/ui/ui-buttons.js b/client/galaxy/scripts/mvc/ui/ui-buttons.js
index 512d6a3ec52b..6c30dd47642c 100644
--- a/client/galaxy/scripts/mvc/ui/ui-buttons.js
+++ b/client/galaxy/scripts/mvc/ui/ui-buttons.js
@@ -5,7 +5,7 @@ import Backbone from "backbone";
 
 /** This renders the default button which is used e.g. at the bottom of the upload modal. */
 var Button = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model =
             (options && options.model) ||
             new Backbone.Model({
@@ -18,7 +18,7 @@ var Button = Backbone.View.extend({
                 wait_cls: "btn btn-info",
                 disabled: false,
                 percentage: -1,
-                visible: true
+                visible: true,
             }).set(options);
         this.setElement(
             $("<button/>")
@@ -31,7 +31,7 @@ var Button = Backbone.View.extend({
         this.render();
     },
 
-    render: function() {
+    render: function () {
         var options = this.model.attributes;
         this.$el
             .removeClass()
@@ -67,44 +67,44 @@ var Button = Backbone.View.extend({
     },
 
     /** Show button */
-    show: function() {
+    show: function () {
         this.model.set("visible", true);
     },
 
     /** Hide button */
-    hide: function() {
+    hide: function () {
         this.model.set("visible", false);
     },
 
     /** Disable button */
-    disable: function() {
+    disable: function () {
         this.model.set("disabled", true);
     },
 
     /** Enable button */
-    enable: function() {
+    enable: function () {
         this.model.set("disabled", false);
     },
 
     /** Show spinner to indicate that the button is not ready to be clicked */
-    wait: function() {
+    wait: function () {
         this.model.set("wait", true);
     },
 
     /** Hide spinner to indicate that the button is ready to be clicked */
-    unwait: function() {
+    unwait: function () {
         this.model.set("wait", false);
     },
 
     /** Change icon */
-    setIcon: function(icon) {
+    setIcon: function (icon) {
         this.model.set("icon", icon);
-    }
+    },
 });
 
 /** This button allows the right-click/open-in-new-tab feature, its used e.g. for panel buttons. */
 var ButtonLink = Button.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model =
             (options && options.model) ||
             new Backbone.Model({
@@ -112,14 +112,14 @@ var ButtonLink = Button.extend({
                 visible: true,
                 title: "",
                 icon: "",
-                cls: ""
+                cls: "",
             }).set(options);
         this.setElement($("<a/>").append((this.$icon = $("<span/>"))));
         this.listenTo(this.model, "change", this.render, this);
         this.render();
     },
 
-    render: function() {
+    render: function () {
         var options = this.model.attributes;
         this.$el
             .removeClass()
@@ -129,7 +129,7 @@ var ButtonLink = Button.extend({
                 href: options.href || "javascript:void(0)",
                 title: options.title,
                 target: options.target || "_top",
-                disabled: options.disabled
+                disabled: options.disabled,
             })
             .css("display", options.visible ? "inline-block" : "none")
             .tooltip({ placement: "bottom" })
@@ -138,12 +138,12 @@ var ButtonLink = Button.extend({
                 options.onclick && !options.disabled && options.onclick();
             });
         this.$icon.removeClass().addClass(options.icon);
-    }
+    },
 });
 
 /** The check button is used in the tool form and allows to distinguish between multiple states e.g. all, partially and nothing selected. */
 var ButtonCheck = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model =
             (options && options.model) ||
             new Backbone.Model({
@@ -152,7 +152,7 @@ var ButtonCheck = Backbone.View.extend({
                 icons: ["fa-square-o", "fa-minus-square-o", "fa-check-square-o"],
                 value: 0,
                 visible: true,
-                onchange: function() {}
+                onchange: function () {},
             }).set(options);
         this.setElement(
             $("<div/>")
@@ -164,7 +164,7 @@ var ButtonCheck = Backbone.View.extend({
         this.render();
     },
 
-    render: function(options) {
+    render: function (options) {
         options = this.model.attributes;
         this.$el
             .addClass("ui-button-check")
@@ -175,10 +175,7 @@ var ButtonCheck = Backbone.View.extend({
                 options.onclick && options.onclick();
             });
         this.$title.html(options.title);
-        this.$icon
-            .removeClass()
-            .addClass("icon fa mr-1")
-            .addClass(options.icons[options.value]);
+        this.$icon.removeClass().addClass("icon fa mr-1").addClass(options.icons[options.value]);
     },
 
     /* Sets a new value and/or returns the value.
@@ -187,7 +184,7 @@ var ButtonCheck = Backbone.View.extend({
      * @param{Integer}   new_val - Number of selected options.
      * @param{Integer}   total   - Total number of available options.
      */
-    value: function(new_val, total) {
+    value: function (new_val, total) {
         if (new_val !== undefined) {
             if (total && new_val !== 0) {
                 new_val = (new_val !== total && 1) || 2;
@@ -196,13 +193,13 @@ var ButtonCheck = Backbone.View.extend({
             this.model.get("onchange")(this.model.get("value"));
         }
         return this.model.get("value");
-    }
+    },
 });
 
 /** This class creates a button with dropdown menu. */
 var ButtonMenu = Backbone.View.extend({
     $menu: null,
-    initialize: function(options) {
+    initialize: function (options) {
         this.model =
             (options && options.model) ||
             new Backbone.Model({
@@ -217,7 +214,7 @@ var ButtonMenu = Backbone.View.extend({
                 href: "",
                 onunload: null,
                 visible: true,
-                tag: ""
+                tag: "",
             }).set(options);
         this.collection = new Backbone.Collection();
         this.setElement(
@@ -232,34 +229,27 @@ var ButtonMenu = Backbone.View.extend({
         this.render();
     },
 
-    render: function() {
+    render: function () {
         var options = this.model.attributes;
         this.$el
             .removeClass()
             .addClass("dropdown")
             .attr("id", options.id)
             .css({
-                display: options.visible && this.collection.where({ visible: true }).length > 0 ? "block" : "none"
+                display: options.visible && this.collection.where({ visible: true }).length > 0 ? "block" : "none",
             });
         this.$root
             .addClass(options.cls)
             .attr("data-toggle", "dropdown")
             .tooltip({ title: options.tooltip || "", placement: "bottom" })
             .off("click")
-            .on("click", e => {
+            .on("click", (e) => {
                 $(".tooltip").hide();
                 e.preventDefault();
                 options.onclick && options.onclick();
             });
-        this.$icon
-            .removeClass()
-            .addClass("icon fa")
-            .addClass(options.icon);
-        options.title &&
-            this.$title
-                .removeClass()
-                .addClass("title ml-1")
-                .html(options.title);
+        this.$icon.removeClass().addClass("icon fa").addClass(options.icon);
+        options.title && this.$title.removeClass().addClass("title ml-1").html(options.title);
         this.$menu && this.$menu.remove();
         if (this.collection.length > 0) {
             this.$menu = $("<div/>")
@@ -268,14 +258,14 @@ var ButtonMenu = Backbone.View.extend({
                 .attr("role", "menu");
             this.$el.append(this.$menu);
         }
-        this.collection.each(submodel => {
+        this.collection.each((submodel) => {
             var suboptions = submodel.attributes;
             if (suboptions.visible) {
                 var $link = $("<a/>")
                     .addClass("dropdown-item")
                     .attr({
                         href: suboptions.href,
-                        target: suboptions.target
+                        target: suboptions.target,
                     })
                     .append(
                         $("<i/>")
@@ -284,7 +274,7 @@ var ButtonMenu = Backbone.View.extend({
                             .css("display", suboptions.icon ? "inline-block" : "none")
                     )
                     .append(suboptions.title)
-                    .on("click", e => {
+                    .on("click", (e) => {
                         if (suboptions.onclick) {
                             e.preventDefault();
                             suboptions.onclick();
@@ -297,7 +287,7 @@ var ButtonMenu = Backbone.View.extend({
     },
 
     /** Add a new menu item */
-    addMenu: function(options) {
+    addMenu: function (options) {
         this.collection.add(
             Utils.merge(options, {
                 title: "",
@@ -307,15 +297,15 @@ var ButtonMenu = Backbone.View.extend({
                 divider: false,
                 visible: true,
                 icon: null,
-                cls: "button-menu btn-group"
+                cls: "button-menu btn-group",
             })
         );
-    }
+    },
 });
 
 export default {
     Button: Button,
     ButtonLink: ButtonLink,
     ButtonCheck: ButtonCheck,
-    ButtonMenu: ButtonMenu
+    ButtonMenu: ButtonMenu,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-color-picker.js b/client/galaxy/scripts/mvc/ui/ui-color-picker.js
index 8621b6d58cbd..e862d974f265 100644
--- a/client/galaxy/scripts/mvc/ui/ui-color-picker.js
+++ b/client/galaxy/scripts/mvc/ui/ui-color-picker.js
@@ -16,11 +16,11 @@ export default Backbone.View.extend({
             ["d8d8d8", "595959", "c4bd97", "8db3e2", "b8cce4", "e5b9b7", "d7e3bc", "ccc1d9", "b7dde8", "fbd5b5"],
             ["bfbfbf", "3f3f3f", "938953", "548dd4", "95b3d7", "d99694", "c3d69b", "b2a2c7", "92cddc", "fac08f"],
             ["a5a5a5", "262626", "494429", "17365d", "366092", "953734", "76923c", "5f497a", "31859b", "e36c09"],
-            ["7f7f7e", "0c0c0c", "1d1b10", "0f243e", "244061", "632423", "4f6128", "3f3151", "205867", "974806"]
-        ]
+            ["7f7f7e", "0c0c0c", "1d1b10", "0f243e", "244061", "632423", "4f6128", "3f3151", "205867", "974806"],
+        ],
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = Utils.merge(options, {});
         this.setElement(this._template());
         this.$panel = this.$(".ui-color-picker-panel");
@@ -32,7 +32,7 @@ export default Backbone.View.extend({
         this.value(this.options.value);
         this.$boxes = this.$(".ui-color-picker-box");
         var self = this;
-        this.$boxes.on("click", function() {
+        this.$boxes.on("click", function () {
             self.value($(this).css("background-color"));
             self.$header.trigger("click");
         });
@@ -47,7 +47,7 @@ export default Backbone.View.extend({
     },
 
     /** Get/set value */
-    value: function(new_val) {
+    value: function (new_val) {
         if (new_val !== undefined && new_val !== null) {
             this.$value.css("background-color", new_val);
             this.$(".ui-color-picker-box").empty();
@@ -58,7 +58,7 @@ export default Backbone.View.extend({
     },
 
     /** Get value from dom */
-    _getValue: function() {
+    _getValue: function () {
         var rgb = this.$value.css("background-color");
         rgb = rgb.match(/^rgb\((\d+),\s*(\d+),\s*(\d+)\)$/);
         if (rgb) {
@@ -69,7 +69,7 @@ export default Backbone.View.extend({
     },
 
     /** Build color panel */
-    _build: function() {
+    _build: function () {
         this._content({ colors: this.colors.base });
         for (var i in this.colors.theme) {
             var line_def = {};
@@ -88,7 +88,7 @@ export default Backbone.View.extend({
     },
 
     /** Create content */
-    _content: function(options) {
+    _content: function (options) {
         var colors = options.colors;
         var $content = $(this._templateContent());
         var $line = $content.find(".line");
@@ -111,22 +111,22 @@ export default Backbone.View.extend({
     },
 
     /** Check icon */
-    _templateCheck: function() {
+    _templateCheck: function () {
         return '<div class="ui-color-picker-check fa fa-check"/>';
     },
 
     /** Content template */
-    _templateContent: function() {
+    _templateContent: function () {
         return '<div class="ui-color-picker-content"><div class="line"/></div>';
     },
 
     /** Box template */
-    _templateBox: function(color) {
+    _templateBox: function (color) {
         return `<div id="${color}" class="ui-color-picker-box" style="background-color: #${color};"/>`;
     },
 
     /** Main template */
-    _template: function() {
+    _template: function () {
         return `
             <div class="ui-color-picker">
                 <div class="ui-color-picker-header">
@@ -138,5 +138,5 @@ export default Backbone.View.extend({
                 </div>
             </div>
             `;
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/ui/ui-data-picker.js b/client/galaxy/scripts/mvc/ui/ui-data-picker.js
index c5f65b6b13a2..6689fd8c7530 100644
--- a/client/galaxy/scripts/mvc/ui/ui-data-picker.js
+++ b/client/galaxy/scripts/mvc/ui/ui-data-picker.js
@@ -14,35 +14,30 @@ export default Backbone.View.extend({
             cls: "btn btn-secondary float-left mr-2",
             onclick: () => {
                 Galaxy.data.dialog(
-                    response => {
+                    (response) => {
                         this.model.set("value", response);
                         if (this.model.get("onchange")) {
                             this.model.get("onchange")(response);
                         }
                     },
                     {
-                        multiple: Boolean(this.model.get("multiple"))
+                        multiple: Boolean(this.model.get("multiple")),
                     }
                 );
-            }
+            },
         });
         this.$info = $("<input disabled/>").addClass("ui-input float-left");
-        this.setElement(
-            $("<div/>")
-                .addClass("d-flex")
-                .append(this.button_dialog.$el)
-                .append(this.$info)
-        );
+        this.setElement($("<div/>").addClass("d-flex").append(this.button_dialog.$el).append(this.$info));
         this.listenTo(this.model, "change", this.render, this);
         this.render();
     },
-    value: function(new_val) {
+    value: function (new_val) {
         if (new_val !== undefined) {
             this.model.set("value", new_val);
         }
         return this.model.get("value");
     },
-    render: function() {
+    render: function () {
         this.$el.attr("id", this.model.id);
         let label = this.model.get("value");
         if (label && this.model.get("multiple")) {
@@ -50,5 +45,5 @@ export default Backbone.View.extend({
         }
         this.$info.val(label || "Empty");
         return this;
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/ui/ui-drilldown.js b/client/galaxy/scripts/mvc/ui/ui-drilldown.js
index 03aaed057958..8f09c53fd5b6 100644
--- a/client/galaxy/scripts/mvc/ui/ui-drilldown.js
+++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js
@@ -4,26 +4,26 @@ import _ from "underscore";
 import Utils from "utils/utils";
 import Options from "mvc/ui/ui-options";
 var View = Options.BaseIcons.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         options.type = options.display || "checkbox";
         options.multiple = options.type == "checkbox";
         Options.BaseIcons.prototype.initialize.call(this, options);
     },
 
     /** Update available options */
-    update: function(input_def) {
+    update: function (input_def) {
         this.model.set("data", input_def.options);
     },
 
     /** Set states for selected values */
-    _setValue: function(new_value) {
+    _setValue: function (new_value) {
         Options.BaseIcons.prototype._setValue.call(this, new_value);
         if (new_value !== undefined && new_value !== null && this.header_index) {
             var self = this;
             var values = $.isArray(new_value) ? new_value : [new_value];
-            _.each(values, v => {
+            _.each(values, (v) => {
                 var list = self.header_index[v];
-                _.each(list, element => {
+                _.each(list, (element) => {
                     self._setState(element, true);
                 });
             });
@@ -31,7 +31,7 @@ var View = Options.BaseIcons.extend({
     },
 
     /** Expand/collapse a sub group */
-    _setState: function(header_id, is_expanded) {
+    _setState: function (header_id, is_expanded) {
         var $button = this.$(`.button-${header_id}`);
         var $subgroup = this.$(`.subgroup-${header_id}`);
         $button.data("is_expanded", is_expanded);
@@ -45,7 +45,7 @@ var View = Options.BaseIcons.extend({
     },
 
     /** Template to create options tree */
-    _templateOptions: function() {
+    _templateOptions: function () {
         var self = this;
         this.header_index = {};
 
@@ -71,16 +71,14 @@ var View = Options.BaseIcons.extend({
                     var $button = $("<span/>")
                         .addClass(`button-${header_id}`)
                         .addClass("ui-drilldown-button fa fa-plus-square");
-                    var $subgroup = $("<div/>")
-                        .addClass(`subgroup-${header_id}`)
-                        .addClass("ui-drilldown-subgroup");
+                    var $subgroup = $("<div/>").addClass(`subgroup-${header_id}`).addClass("ui-drilldown-subgroup");
                     $group.append(
                         $("<div/>")
                             .append($button)
                             .append(
                                 self._templateOption({
                                     label: level.name,
-                                    value: level.value
+                                    value: level.value,
                                 })
                             )
                     );
@@ -92,7 +90,7 @@ var View = Options.BaseIcons.extend({
                     $group.append(
                         self._templateOption({
                             label: level.name,
-                            value: level.value
+                            value: level.value,
                         })
                     );
                 }
@@ -107,13 +105,11 @@ var View = Options.BaseIcons.extend({
     },
 
     /** Template for drill down view */
-    _template: function() {
-        return $("<div/>")
-            .addClass("ui-options-list drilldown-container")
-            .attr("id", this.model.id);
-    }
+    _template: function () {
+        return $("<div/>").addClass("ui-options-list drilldown-container").attr("id", this.model.id);
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-frames.js b/client/galaxy/scripts/mvc/ui/ui-frames.js
index 86ba1e7795d2..866ca8150a38 100644
--- a/client/galaxy/scripts/mvc/ui/ui-frames.js
+++ b/client/galaxy/scripts/mvc/ui/ui-frames.js
@@ -6,7 +6,7 @@ import _l from "utils/localization";
 import { getGalaxyInstance } from "app";
 
 var FrameView = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model = (options && options.model) || new Backbone.Model(options);
         this.setElement($("<div/>").addClass("corner frame"));
         this.$el
@@ -19,16 +19,12 @@ var FrameView = Backbone.View.extend({
                             .addClass("f-icon f-close fa fa-close")
                             .tooltip({
                                 title: _l("Close"),
-                                placement: "bottom"
+                                placement: "bottom",
                             })
                     )
             )
             .append($("<div/>").addClass("f-content"))
-            .append(
-                $("<div/>")
-                    .addClass("f-resize f-icon corner fa fa-expand")
-                    .tooltip({ title: "Resize" })
-            )
+            .append($("<div/>").addClass("f-resize f-icon corner fa fa-expand").tooltip({ title: "Resize" }))
             .append($("<div/>").addClass("f-cover"));
         this.$header = this.$(".f-header");
         this.$title = this.$(".f-title");
@@ -37,15 +33,13 @@ var FrameView = Backbone.View.extend({
         this.listenTo(this.model, "change", this.render, this);
     },
 
-    render: function() {
+    render: function () {
         var self = this;
         var options = this.model.attributes;
         this.$title.html(_.escape(options.title) || "");
         this.$header.find(".f-icon-left").remove();
-        _.each(options.menu, option => {
-            var $option = $("<div/>")
-                .addClass("f-icon-left")
-                .addClass(option.icon);
+        _.each(options.menu, (option) => {
+            var $option = $("<div/>").addClass("f-icon-left").addClass(option.icon);
             if (_.isFunction(option.disabled) && option.disabled()) {
                 $option.attr("disabled", true);
             } else {
@@ -55,7 +49,7 @@ var FrameView = Backbone.View.extend({
                     })
                     .tooltip({
                         title: option.tooltip || "",
-                        placement: "bottom"
+                        placement: "bottom",
                     });
             }
             self.$header.append($option);
@@ -74,7 +68,7 @@ var FrameView = Backbone.View.extend({
                 self.$content.html(options.content);
             }
         }
-    }
+    },
 });
 
 /** Scratchbook viewer */
@@ -83,7 +77,7 @@ var View = Backbone.View.extend({
         frame: {
             // default frame size in cells
             cols: 6,
-            rows: 3
+            rows: 3,
         },
         rows: 1000, // maximum number of rows
         cell: 130, // cell size in px
@@ -91,7 +85,7 @@ var View = Backbone.View.extend({
         scroll: 5, // scroll speed
         top_min: 40, // top margin
         frame_max: 9, // maximum number of frames
-        visible: true // initial visibility
+        visible: true, // initial visibility
     },
 
     cols: 0, // number of columns
@@ -105,7 +99,7 @@ var View = Backbone.View.extend({
     visible: false, // flag indicating if scratchbook viewer is visible or not
     event: {}, // dictionary keeping track of current event
 
-    initialize: function(options) {
+    initialize: function (options) {
         var self = this;
         this.options = _.defaults(options || {}, this.defaultOptions);
         this.visible = this.options.visible;
@@ -120,7 +114,7 @@ var View = Backbone.View.extend({
 
         // initialize shadow to guiding drag/resize events
         this.frame_shadow = new Backbone.View({
-            el: $("<div/>").addClass("corner frame-shadow")
+            el: $("<div/>").addClass("corner frame-shadow"),
         });
         this.$el.append(this.frame_shadow.$el);
         this._frameInit(this.frame_shadow, "#frame-shadow");
@@ -142,7 +136,7 @@ var View = Backbone.View.extend({
     },
 
     /** Render */
-    render: function() {
+    render: function () {
         this.$(".frame-scroll-up")[(this.top != this.options.top_min && "show") || "hide"]();
         this.$(".frame-scroll-down")[(this.top != this.top_max && "show") || "hide"]();
     },
@@ -155,17 +149,17 @@ var View = Backbone.View.extend({
      *  content : content is treated as a function or raw HTML, function is passed a single
      *              argument that is the frame's content DOM element
      */
-    add: function(options) {
+    add: function (options) {
         const Galaxy = getGalaxyInstance();
         if (this.frame_counter >= this.options.frame_max) {
             Galaxy.modal.show({
                 title: _l("Warning"),
                 body: `You have reached the maximum number of allowed frames (${this.options.frame_max}).`,
                 buttons: {
-                    Close: function() {
+                    Close: function () {
                         Galaxy.modal.hide();
-                    }
-                }
+                    },
+                },
             });
         } else {
             var frame_id = `#frame-${this.frame_uid++}`;
@@ -174,10 +168,10 @@ var View = Backbone.View.extend({
                     title: _l("Error"),
                     body: "This frame already exists. This page might contain multiple frame managers.",
                     buttons: {
-                        Close: function() {
+                        Close: function () {
                             Galaxy.modal.hide();
-                        }
-                    }
+                        },
+                    },
                 });
             } else {
                 // initialize new frame elements
@@ -196,7 +190,7 @@ var View = Backbone.View.extend({
                 this._frameInit(frame, frame_id);
                 this._frameResize(frame, {
                     width: options.width,
-                    height: options.height
+                    height: options.height,
                 });
                 this._frameInsert(frame, { top: 0, left: 0 }, true);
                 if (!this.visible) {
@@ -208,7 +202,7 @@ var View = Backbone.View.extend({
     },
 
     /** Remove a frame */
-    del: function(frame) {
+    del: function (frame) {
         var self = this;
         var $frame = frame.$el;
         $frame.fadeOut("fast", () => {
@@ -222,17 +216,17 @@ var View = Backbone.View.extend({
     },
 
     /** Show panel */
-    show: function() {
+    show: function () {
         this.visible = true;
         this.$el.fadeIn("fast");
         this.trigger("show");
     },
 
     /** Hide panel */
-    hide: function() {
+    hide: function () {
         if (!this.event.type) {
             this.visible = false;
-            this.$el.fadeOut("fast", function() {
+            this.$el.fadeOut("fast", function () {
                 $(this).hide();
             });
             this.trigger("hide");
@@ -240,7 +234,7 @@ var View = Backbone.View.extend({
     },
 
     /** Returns the number of frames */
-    length: function() {
+    length: function () {
         return this.frame_counter;
     },
 
@@ -260,11 +254,11 @@ var View = Backbone.View.extend({
         "mousedown .frame-background": "_eventHide",
         "mousedown .frame-scroll-up": "_eventPanelScroll_up",
         "mousedown .frame-scroll-down": "_eventPanelScroll_down",
-        "mousedown .f-close": "_eventFrameClose"
+        "mousedown .f-close": "_eventFrameClose",
     },
 
     /** Start drag/resize event */
-    _eventFrameMouseDown: function(e) {
+    _eventFrameMouseDown: function (e) {
         $(".tooltip").hide();
         if (!this.event.type) {
             if ($(e.target).hasClass("f-header") || $(e.target).hasClass("f-title")) {
@@ -278,7 +272,7 @@ var View = Backbone.View.extend({
                 this.event.target = this._frameIdentify(e.target);
                 this.event.xy = {
                     x: e.originalEvent.pageX,
-                    y: e.originalEvent.pageY
+                    y: e.originalEvent.pageY,
                 };
                 this._frameDragStart(this.event.target);
             }
@@ -286,16 +280,16 @@ var View = Backbone.View.extend({
     },
 
     /** Processes drag/resize events */
-    _eventFrameMouseMove: function(e) {
+    _eventFrameMouseMove: function (e) {
         if (this.event.type) {
             // get mouse motion and delta
             var event_xy_new = {
                 x: e.originalEvent.pageX,
-                y: e.originalEvent.pageY
+                y: e.originalEvent.pageY,
             };
             var event_xy_delta = {
                 x: event_xy_new.x - this.event.xy.x,
-                y: event_xy_new.y - this.event.xy.y
+                y: event_xy_new.y - this.event.xy.y,
             };
             this.event.xy = event_xy_new;
 
@@ -317,7 +311,7 @@ var View = Backbone.View.extend({
                 this._frameResize(this.frame_shadow, p);
                 this._frameInsert(this.frame_shadow, {
                     top: this._toGridCoord("top", p.top),
-                    left: this._toGridCoord("left", p.left)
+                    left: this._toGridCoord("left", p.left),
                 });
             } else if (this.event.type == "drag") {
                 p.left += event_xy_delta.x;
@@ -325,7 +319,7 @@ var View = Backbone.View.extend({
                 this._frameOffset(this.event.target, p);
                 var l = {
                     top: this._toGridCoord("top", p.top),
-                    left: this._toGridCoord("left", p.left)
+                    left: this._toGridCoord("left", p.left),
                 };
                 if (l.left !== 0) {
                     l.left++;
@@ -336,7 +330,7 @@ var View = Backbone.View.extend({
     },
 
     /** Stop drag/resize events */
-    _eventFrameMouseUp: function(e) {
+    _eventFrameMouseUp: function (e) {
         if (this.event.type) {
             this._frameDragStop(this.event.target);
             this.event.type = null;
@@ -344,7 +338,7 @@ var View = Backbone.View.extend({
     },
 
     /** Destroy a frame */
-    _eventFrameClose: function(e) {
+    _eventFrameClose: function (e) {
         if (!this.event.type) {
             e.preventDefault();
             this.del(this._frameIdentify(e.target));
@@ -352,14 +346,14 @@ var View = Backbone.View.extend({
     },
 
     /** Hide all frames */
-    _eventHide: function(e) {
+    _eventHide: function (e) {
         if (!this.event.type) {
             this.hide();
         }
     },
 
     /** Fired when scrolling occurs on panel */
-    _eventPanelScroll: function(e) {
+    _eventPanelScroll: function (e) {
         if (!this.event.type && this.visible) {
             // Stop propagation if scrolling is happening inside a frame.
             // TODO: could propagate scrolling if at top/bottom of frame.
@@ -374,7 +368,7 @@ var View = Backbone.View.extend({
     },
 
     /** Handle scroll up event */
-    _eventPanelScroll_up: function(e) {
+    _eventPanelScroll_up: function (e) {
         if (!this.event.type) {
             e.preventDefault();
             this._panelScroll(-this.options.scroll);
@@ -382,7 +376,7 @@ var View = Backbone.View.extend({
     },
 
     /** Handle scroll down */
-    _eventPanelScroll_down: function(e) {
+    _eventPanelScroll_down: function (e) {
         if (!this.event.type) {
             e.preventDefault();
             this._panelScroll(this.options.scroll);
@@ -394,16 +388,12 @@ var View = Backbone.View.extend({
     */
 
     /** Identify the target frame */
-    _frameIdentify: function(target) {
-        return this.frame_list[
-            `#${$(target)
-                .closest(".frame")
-                .attr("id")}`
-        ];
+    _frameIdentify: function (target) {
+        return this.frame_list[`#${$(target).closest(".frame").attr("id")}`];
     },
 
     /** Provides drag support */
-    _frameDragStart: function(frame) {
+    _frameDragStart: function (frame) {
         this._frameFocus(frame, true);
         var p = this._frameScreen(frame);
         this._frameResize(this.frame_shadow, p);
@@ -414,7 +404,7 @@ var View = Backbone.View.extend({
     },
 
     /** Removes drag support */
-    _frameDragStop: function(frame) {
+    _frameDragStop: function (frame) {
         this._frameFocus(frame, false);
         var p = this._frameScreen(this.frame_shadow);
         this._frameResize(frame, p);
@@ -430,7 +420,7 @@ var View = Backbone.View.extend({
     */
 
     /** Converts a pixel to a grid dimension */
-    _toGridCoord: function(type, px) {
+    _toGridCoord: function (type, px) {
         var sign = type == "width" || type == "height" ? 1 : -1;
         if (type == "top") {
             px -= this.top;
@@ -439,7 +429,7 @@ var View = Backbone.View.extend({
     },
 
     /** Converts a grid to a pixels dimension */
-    _toPixelCoord: function(type, g) {
+    _toPixelCoord: function (type, g) {
         var sign = type == "width" || type == "height" ? 1 : -1;
         var px = g * this.options.cell - sign * this.options.margin;
         if (type == "top") {
@@ -449,22 +439,22 @@ var View = Backbone.View.extend({
     },
 
     /** Converts a pixel to a grid coordinate set */
-    _toGrid: function(px) {
+    _toGrid: function (px) {
         return {
             top: this._toGridCoord("top", px.top),
             left: this._toGridCoord("left", px.left),
             width: this._toGridCoord("width", px.width),
-            height: this._toGridCoord("height", px.height)
+            height: this._toGridCoord("height", px.height),
         };
     },
 
     /** Converts a pixel to a grid coordinate set */
-    _toPixel: function(g) {
+    _toPixel: function (g) {
         return {
             top: this._toPixelCoord("top", g.top),
             left: this._toPixelCoord("left", g.left),
             width: this._toPixelCoord("width", g.width),
-            height: this._toPixelCoord("height", g.height)
+            height: this._toPixelCoord("height", g.height),
         };
     },
 
@@ -473,7 +463,7 @@ var View = Backbone.View.extend({
     */
 
     /** Check collisions for a grid coordinate set */
-    _isCollision: function(g) {
+    _isCollision: function (g) {
         function is_collision_pair(a, b) {
             return !(
                 a.left > b.left + b.width - 1 ||
@@ -492,7 +482,7 @@ var View = Backbone.View.extend({
     },
 
     /** Return location/grid rank */
-    _locationRank: function(loc) {
+    _locationRank: function (loc) {
         return loc.top * this.cols + loc.left;
     },
 
@@ -501,13 +491,13 @@ var View = Backbone.View.extend({
     */
 
     /** Refresh panel */
-    _panelRefresh: function(animate) {
+    _panelRefresh: function (animate) {
         this.cols = parseInt($(window).width() / this.options.cell, 10) + 1;
         this._frameInsert(null, null, animate);
     },
 
     /** Complete panel animation / frames not moving */
-    _panelAnimationComplete: function() {
+    _panelAnimationComplete: function () {
         var self = this;
         $(".frame")
             .promise()
@@ -517,7 +507,7 @@ var View = Backbone.View.extend({
     },
 
     /** Scroll panel */
-    _panelScroll: function(delta, animate) {
+    _panelScroll: function (delta, animate) {
         var top_new = this.top - this.options.scroll * delta;
         top_new = Math.max(top_new, this.top_max);
         top_new = Math.min(top_new, this.options.top_min);
@@ -527,7 +517,7 @@ var View = Backbone.View.extend({
                 if (frame.grid_location !== null) {
                     var screen_location = {
                         top: frame.screen_location.top - (this.top - top_new),
-                        left: frame.screen_location.left
+                        left: frame.screen_location.left,
                     };
                     this._frameOffset(frame, screen_location, animate);
                 }
@@ -542,7 +532,7 @@ var View = Backbone.View.extend({
     */
 
     /** Initialize a new frame */
-    _frameInit: function(frame, id) {
+    _frameInit: function (frame, id) {
         frame.id = id;
         frame.screen_location = {};
         frame.grid_location = {};
@@ -551,25 +541,25 @@ var View = Backbone.View.extend({
     },
 
     /** Insert frame at given location */
-    _frameInsert: function(frame, new_loc, animate) {
+    _frameInsert: function (frame, new_loc, animate) {
         var self = this;
         var place_list = [];
         if (frame) {
             frame.grid_location = null;
             place_list.push([frame, this._locationRank(new_loc)]);
         }
-        _.each(this.frame_list, f => {
+        _.each(this.frame_list, (f) => {
             if (f.grid_location !== null) {
                 f.grid_location = null;
                 place_list.push([f, f.grid_rank]);
             }
         });
         place_list.sort((a, b) => (a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0));
-        _.each(place_list, place => {
+        _.each(place_list, (place) => {
             self._framePlace(place[0], animate);
         });
         this.top_max = 0;
-        _.each(this.frame_list, f => {
+        _.each(this.frame_list, (f) => {
             if (f.grid_location !== null) {
                 self.top_max = Math.max(self.top_max, f.grid_location.top + f.grid_location.height);
             }
@@ -580,7 +570,7 @@ var View = Backbone.View.extend({
     },
 
     /** Naive frame placement */
-    _framePlace: function(frame, animate) {
+    _framePlace: function (frame, animate) {
         frame.grid_location = null;
         var g = this._toGrid(this._frameScreen(frame));
         var done = false;
@@ -605,12 +595,12 @@ var View = Backbone.View.extend({
     },
 
     /** Handle frame focussing */
-    _frameFocus: function(frame, has_focus) {
+    _frameFocus: function (frame, has_focus) {
         frame.$el.css("z-index", this.frame_z + (has_focus ? 1 : 0));
     },
 
     /** New left/top position frame */
-    _frameOffset: function(frame, p, animate) {
+    _frameOffset: function (frame, p, animate) {
         frame.screen_location.left = p.left;
         frame.screen_location.top = p.top;
         if (animate) {
@@ -625,31 +615,31 @@ var View = Backbone.View.extend({
     },
 
     /** Resize frame */
-    _frameResize: function(frame, p) {
+    _frameResize: function (frame, p) {
         frame.$el.css({ width: p.width, height: p.height });
         frame.screen_location.width = p.width;
         frame.screen_location.height = p.height;
     },
 
     /** Push frame to new grid location */
-    _frameGrid: function(frame, l, animate) {
+    _frameGrid: function (frame, l, animate) {
         frame.grid_location = l;
         this._frameOffset(frame, this._toPixel(l), animate);
         frame.grid_rank = this._locationRank(l);
     },
 
     /** Get frame dimensions */
-    _frameScreen: function(frame) {
+    _frameScreen: function (frame) {
         var p = frame.screen_location;
         return {
             top: p.top,
             left: p.left,
             width: p.width,
-            height: p.height
+            height: p.height,
         };
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-list.js b/client/galaxy/scripts/mvc/ui/ui-list.js
index 1fb56b0c6df0..3b114429f32d 100644
--- a/client/galaxy/scripts/mvc/ui/ui-list.js
+++ b/client/galaxy/scripts/mvc/ui/ui-list.js
@@ -3,7 +3,7 @@ import Backbone from "backbone";
 import Utils from "utils/utils";
 import Ui from "mvc/ui/ui-misc";
 var View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = options;
         this.name = options.name || "element";
         this.multiple = options.multiple || false;
@@ -22,7 +22,7 @@ var View = Backbone.View.extend({
         this.$button.on("click", () => {
             this.add({
                 id: this.select.value(),
-                name: this.select.text()
+                name: this.select.text(),
             });
         });
 
@@ -35,7 +35,7 @@ var View = Backbone.View.extend({
     },
 
     /** Return/Set currently selected list elements */
-    value: function(val) {
+    value: function (val) {
         // set new value
         if (val !== undefined) {
             this.selections.empty();
@@ -53,7 +53,7 @@ var View = Backbone.View.extend({
                     if (v_id != null) {
                         this.add({
                             id: v_id,
-                            name: v_name
+                            name: v_name,
                         });
                     }
                 }
@@ -62,12 +62,10 @@ var View = Backbone.View.extend({
         }
         // get current value
         var lst = [];
-        this.$(".ui-list-id").each(function() {
+        this.$(".ui-list-id").each(function () {
             lst.push({
                 id: $(this).prop("id"),
-                name: $(this)
-                    .find(".ui-list-name")
-                    .html()
+                name: $(this).find(".ui-list-name").html(),
             });
         });
         if (lst.length == 0) {
@@ -77,14 +75,14 @@ var View = Backbone.View.extend({
     },
 
     /** Add row */
-    add: function(options) {
+    add: function (options) {
         var self = this;
         if (this.$(`[id="${options.id}"]`).length === 0) {
             if (!Utils.isEmpty(options.id)) {
                 var $el = $(
                     this._templateRow({
                         id: options.id,
-                        name: options.name
+                        name: options.name,
                     })
                 );
                 $el.find("button").on("click", () => {
@@ -96,23 +94,23 @@ var View = Backbone.View.extend({
             } else {
                 this.message.update({
                     message: `Please select a valid ${this.name}.`,
-                    status: "danger"
+                    status: "danger",
                 });
             }
         } else {
             this.message.update({
-                message: `This ${this.name} is already in the list.`
+                message: `This ${this.name} is already in the list.`,
             });
         }
     },
 
     /** Update available options */
-    update: function(input_def) {
+    update: function (input_def) {
         this.select.update(input_def);
     },
 
     /** Refresh view */
-    _refresh: function() {
+    _refresh: function () {
         if (this.$(".ui-list-id").length > 0) {
             !this.multiple && this.$button.attr("disabled", true);
         } else {
@@ -122,7 +120,7 @@ var View = Backbone.View.extend({
     },
 
     /** Main Template */
-    _template: function(options) {
+    _template: function (options) {
         return `<div class="ui-list container">
                     <div class="row">
                         <div class="col-1 pl-0 mb-2">
@@ -136,14 +134,14 @@ var View = Backbone.View.extend({
     },
 
     /** Row Template */
-    _templateRow: function(options) {
+    _templateRow: function (options) {
         return `<div id="${options.id}" class="ui-list-id row mt-2">
                     <button class="ui-list-delete fa fa-trash mr-3"/>
                     <div class="ui-list-name">${options.name}</span>
                 </div>`;
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-misc.js b/client/galaxy/scripts/mvc/ui/ui-misc.js
index 45727ff342f5..79452c6b139b 100644
--- a/client/galaxy/scripts/mvc/ui/ui-misc.js
+++ b/client/galaxy/scripts/mvc/ui/ui-misc.js
@@ -13,7 +13,7 @@ import Modal from "mvc/ui/ui-modal";
 
 /** Displays messages used e.g. in the tool form */
 export var Message = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model =
             (options && options.model) ||
             new Backbone.Model({
@@ -21,7 +21,7 @@ export var Message = Backbone.View.extend({
                 status: "info",
                 cls: "",
                 persistent: false,
-                fade: true
+                fade: true,
             }).set(options);
         this.listenTo(this.model, "change", this.render, this);
         if (options && options.active_tab) {
@@ -29,15 +29,12 @@ export var Message = Backbone.View.extend({
         }
         this.render();
     },
-    update: function(options) {
+    update: function (options) {
         this.model.set(options);
     },
-    render: function() {
+    render: function () {
         var status = this.model.get("status");
-        this.$el
-            .removeClass()
-            .addClass(`alert alert-${status} mt-2`)
-            .addClass(this.model.get("cls"));
+        this.$el.removeClass().addClass(`alert alert-${status} mt-2`).addClass(this.model.get("cls"));
         if (this.model.get("message")) {
             this.$el.html(this.messageForDisplay());
             this.$el[this.model.get("fade") ? "fadeIn" : "show"]();
@@ -53,20 +50,20 @@ export var Message = Backbone.View.extend({
         }
         return this;
     },
-    messageForDisplay: function() {
+    messageForDisplay: function () {
         return _.escape(this.model.get("message"));
-    }
+    },
 });
 
 export var UnescapedMessage = Message.extend({
-    messageForDisplay: function() {
+    messageForDisplay: function () {
         return this.model.get("message");
-    }
+    },
 });
 
 /** Renders an input element used e.g. in the tool form */
 export var Input = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model =
             (options && options.model) ||
             new Backbone.Model({
@@ -78,7 +75,7 @@ export var Input = Backbone.View.extend({
                 cls: "",
                 area: false,
                 color: null,
-                style: null
+                style: null,
             }).set(options);
         this.tagName = this.model.get("area") ? "textarea" : "input";
         this.setElement($(`<${this.tagName}/>`));
@@ -86,13 +83,13 @@ export var Input = Backbone.View.extend({
         this.render();
     },
     events: {
-        input: "_onchange"
+        input: "_onchange",
     },
-    value: function(new_val) {
+    value: function (new_val) {
         new_val !== undefined && this.model.set("value", typeof new_val === "string" ? new_val : "");
         return this.model.get("value");
     },
-    render: function() {
+    render: function () {
         var self = this;
         this.$el
             .removeClass()
@@ -107,32 +104,32 @@ export var Input = Backbone.View.extend({
         var datalist = this.model.get("datalist");
         if ($.isArray(datalist) && datalist.length > 0) {
             this.$el.autocomplete({
-                source: function(request, response) {
+                source: function (request, response) {
                     response(self.model.get("datalist"));
                 },
-                change: function() {
+                change: function () {
                     self._onchange();
-                }
+                },
             });
         }
         if (this.model.get("value") !== this.$el.val()) {
             this.$el.val(this.model.get("value"));
         }
-        _.each(["readonly", "disabled"], attr_name => {
+        _.each(["readonly", "disabled"], (attr_name) => {
             self.model.get(attr_name) ? self.$el.attr(attr_name, true) : self.$el.removeAttr(attr_name);
         });
         this.$el[this.model.get("visible") ? "show" : "hide"]();
         return this;
     },
-    _onchange: function() {
+    _onchange: function () {
         this.value(this.$el.val());
         this.model.get("onchange") && this.model.get("onchange")(this.model.get("value"));
-    }
+    },
 });
 
 /** Creates a hidden element input field used e.g. in the tool form */
 export var Hidden = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model = (options && options.model) || new Backbone.Model(options);
         this.setElement(
             $("<div/>")
@@ -142,53 +139,49 @@ export var Hidden = Backbone.View.extend({
         this.listenTo(this.model, "change", this.render, this);
         this.render();
     },
-    value: function(new_val) {
+    value: function (new_val) {
         new_val !== undefined && this.model.set("value", new_val);
         return this.model.get("value");
     },
-    render: function() {
+    render: function () {
         this.$el.attr("id", this.model.id);
         this.$hidden.val(this.model.get("value"));
         this.model.get("info") ? this.$info.show().text(this.model.get("info")) : this.$info.hide();
         return this;
-    }
+    },
 });
 
 /** Creates an input element which switches between select and text field */
 export var TextSelect = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.select = new options.SelectClass.View(options);
         this.model = this.select.model;
         this.text = new Input({
-            onchange: this.model.get("onchange")
+            onchange: this.model.get("onchange"),
         });
         this.on("change", () => {
             if (this.model.get("onchange")) {
                 this.model.get("onchange")(this.value());
             }
         });
-        this.setElement(
-            $("<div/>")
-                .append(this.select.$el)
-                .append(this.text.$el)
-        );
+        this.setElement($("<div/>").append(this.select.$el).append(this.text.$el));
         this.update(options);
     },
-    wait: function() {
+    wait: function () {
         this.select.wait();
     },
-    unwait: function() {
+    unwait: function () {
         this.select.unwait();
     },
-    value: function(new_val) {
+    value: function (new_val) {
         var element = this.textmode ? this.text : this.select;
         return element.value(new_val);
     },
-    update: function(input_def) {
+    update: function (input_def) {
         var data = input_def.data;
         if (!data) {
             data = [];
-            _.each(input_def.options, option => {
+            _.each(input_def.options, (option) => {
                 data.push({ label: option[0], value: option[1] });
             });
         }
@@ -198,58 +191,50 @@ export var TextSelect = Backbone.View.extend({
         this.select.$el[this.textmode ? "hide" : "show"]();
         this.select.update({ data: data });
         this.value(v);
-    }
+    },
 });
 
 /** Creates a upload element input field */
 export var Upload = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         var self = this;
         this.model = (options && options.model) || new Backbone.Model(options);
         this.setElement(
             $("<div/>")
                 .append((this.$info = $("<div/>")))
-                .append(
-                    (this.$file = $("<input/>")
-                        .attr("type", "file")
-                        .addClass("mb-1"))
-                )
-                .append(
-                    (this.$text = $("<textarea/>")
-                        .addClass("ui-textarea")
-                        .attr("disabled", true))
-                )
+                .append((this.$file = $("<input/>").attr("type", "file").addClass("mb-1")))
+                .append((this.$text = $("<textarea/>").addClass("ui-textarea").attr("disabled", true)))
                 .append((this.$wait = $("<i/>").addClass("fa fa-spinner fa-spin")))
         );
         this.listenTo(this.model, "change", this.render, this);
-        this.$file.on("change", e => {
+        this.$file.on("change", (e) => {
             self._readFile(e);
         });
         this.render();
     },
-    value: function(new_val) {
+    value: function (new_val) {
         new_val !== undefined && this.model.set("value", new_val);
         return this.model.get("value");
     },
-    render: function() {
+    render: function () {
         this.$el.attr("id", this.model.id);
         this.model.get("info") ? this.$info.show().text(this.model.get("info")) : this.$info.hide();
         this.model.get("value") ? this.$text.text(this.model.get("value")).show() : this.$text.hide();
         this.model.get("wait") ? this.$wait.show() : this.$wait.hide();
         return this;
     },
-    _readFile: function(e) {
+    _readFile: function (e) {
         var self = this;
         var file = e.target.files && e.target.files[0];
         if (file) {
             var reader = new FileReader();
-            reader.onload = function() {
+            reader.onload = function () {
                 self.model.set({ wait: false, value: this.result });
             };
             this.model.set({ wait: true, value: null });
             reader.readAsText(file);
         }
-    }
+    },
 });
 
 /* Make more Ui stuff directly available at this namespace (for backwards
@@ -283,5 +268,5 @@ export default {
     TextSelect: TextSelect,
     Hidden: Hidden,
     Slider: Slider,
-    Drilldown: Drilldown
+    Drilldown: Drilldown,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-modal.js b/client/galaxy/scripts/mvc/ui/ui-modal.js
index 25dc0aa76792..e36f52e199d4 100644
--- a/client/galaxy/scripts/mvc/ui/ui-modal.js
+++ b/client/galaxy/scripts/mvc/ui/ui-modal.js
@@ -17,14 +17,14 @@ export var View = Backbone.View.extend({
         xlarge: false /* BS4 max-width already expanded in Galaxy, expand even more if true. */,
         closing_events: false,
         closing_callback: null,
-        title_separator: true
+        title_separator: true,
     },
 
     // button list
     buttonList: {},
 
     // initialize
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = _.defaults(options || {}, this.optionsDefault);
         $(this.options.container).prepend(this.el);
         // optional render
@@ -36,7 +36,7 @@ export var View = Backbone.View.extend({
     /**
      * Displays modal
      */
-    show: function(options) {
+    show: function (options) {
         if (options) {
             this.options = _.defaults(options, this.optionsDefault);
             this.render();
@@ -46,7 +46,7 @@ export var View = Backbone.View.extend({
             this.$el.fadeIn("fast");
         }
         if (this.options.closing_events) {
-            $(document).on("keyup.ui-modal", e => {
+            $(document).on("keyup.ui-modal", (e) => {
                 if (e.keyCode == 27) {
                     this.hide(true);
                 }
@@ -61,7 +61,7 @@ export var View = Backbone.View.extend({
     /**
      * Hide modal
      */
-    hide: function(canceled) {
+    hide: function (canceled) {
         this.visible = false;
         this.$el.fadeOut("fast");
         if (this.options.closing_callback) {
@@ -74,7 +74,7 @@ export var View = Backbone.View.extend({
     /**
      * Render modal
      */
-    render: function() {
+    render: function () {
         var self = this;
         this.$el.html(this._template());
 
@@ -98,10 +98,7 @@ export var View = Backbone.View.extend({
         }
 
         // fix main content
-        this.$el
-            .removeClass()
-            .addClass("modal")
-            .addClass(this.options.cls);
+        this.$el.removeClass().addClass("modal").addClass(this.options.cls);
         this.$header.find(".title").html(this.options.title);
         this.$body.html(this.options.body);
 
@@ -147,7 +144,7 @@ export var View = Backbone.View.extend({
      * Returns the button dom
      * @param{String}   name    - Button name/title
      */
-    getButton: function(name) {
+    getButton: function (name) {
         return this.buttonList[name];
     },
 
@@ -155,7 +152,7 @@ export var View = Backbone.View.extend({
      * Enables a button
      * @param{String}   name    - Button name/title
      */
-    enableButton: function(name) {
+    enableButton: function (name) {
         this.getButton(name).prop("disabled", false);
     },
 
@@ -163,7 +160,7 @@ export var View = Backbone.View.extend({
      * Disables a button
      * @param{String}   name    - Button name/title
      */
-    disableButton: function(name) {
+    disableButton: function (name) {
         this.getButton(name).prop("disabled", true);
     },
 
@@ -171,7 +168,7 @@ export var View = Backbone.View.extend({
      * Show a button
      * @param{String}   name    - Button name/title
      */
-    showButton: function(name) {
+    showButton: function (name) {
         this.getButton(name).show();
     },
 
@@ -179,21 +176,21 @@ export var View = Backbone.View.extend({
      * Hide a button
      * @param{String}   name    - Button name/title
      */
-    hideButton: function(name) {
+    hideButton: function (name) {
         this.getButton(name).hide();
     },
 
     /**
      * Returns scroll top for body element
      */
-    scrollTop: function() {
+    scrollTop: function () {
         return this.$body.scrollTop();
     },
 
     /**
      * Returns the modal template
      */
-    _template: function() {
+    _template: function () {
         return (
             '<div class="modal-backdrop fade"/>' +
             '<div class="modal-dialog">' +
@@ -208,9 +205,9 @@ export var View = Backbone.View.extend({
             "</div>" +
             "</div>"
         );
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-options.js b/client/galaxy/scripts/mvc/ui/ui-options.js
index 8f3a93fd5f2f..9fb40e03b388 100644
--- a/client/galaxy/scripts/mvc/ui/ui-options.js
+++ b/client/galaxy/scripts/mvc/ui/ui-options.js
@@ -6,7 +6,7 @@ import Utils from "utils/utils";
 import Buttons from "mvc/ui/ui-buttons";
 
 var Base = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         var self = this;
         this.model =
             (options && options.model) ||
@@ -19,7 +19,7 @@ var Base = Backbone.View.extend({
                 wait_text: "Please wait...",
                 multiple: false,
                 optional: false,
-                onchange: function() {}
+                onchange: function () {},
             }).set(options);
         this.listenTo(this.model, "change:value", this._changeValue, this);
         this.listenTo(this.model, "change:wait", this._changeWait, this);
@@ -31,7 +31,7 @@ var Base = Backbone.View.extend({
         this.render();
     },
 
-    render: function() {
+    render: function () {
         var self = this;
         this.$el
             .empty()
@@ -46,11 +46,11 @@ var Base = Backbone.View.extend({
         this.all_button = null;
         if (this.model.get("multiple")) {
             this.all_button = new Buttons.ButtonCheck({
-                onclick: function() {
+                onclick: function () {
                     self.$("input").prop("checked", self.all_button.value() !== 0);
                     self.value(self._getValue());
                     self.trigger("change");
-                }
+                },
             });
             this.$menu.append(this.all_button.$el);
         }
@@ -62,25 +62,25 @@ var Base = Backbone.View.extend({
     },
 
     /** Update available options */
-    update: function(input_def) {
+    update: function (input_def) {
         if (input_def.data) {
             this.model.set("data", input_def.data);
         }
     },
 
-    _changeData: function() {
+    _changeData: function () {
         var self = this;
         this.$options.empty();
         if (this._templateOptions) {
             this.$options.append(this._templateOptions(this.model.get("data")));
         } else {
-            _.each(this.model.get("data"), option => {
+            _.each(this.model.get("data"), (option) => {
                 self.$options.append(
                     $(self._templateOption(option))
                         .addClass("ui-option")
                         .tooltip({
                             title: option.tooltip || "",
-                            placement: "bottom"
+                            placement: "bottom",
                         })
                 );
             });
@@ -93,11 +93,11 @@ var Base = Backbone.View.extend({
         this._changeWait();
     },
 
-    _changeVisible: function() {
+    _changeVisible: function () {
         this.$el[this.model.get("visible") ? "show" : "hide"]();
     },
 
-    _changeWait: function() {
+    _changeWait: function () {
         if (this.model.get("wait")) {
             if (this.length() === 0) {
                 this._messageShow(this.model.get("wait_text"), "info");
@@ -117,7 +117,7 @@ var Base = Backbone.View.extend({
         }
     },
 
-    _changeValue: function() {
+    _changeValue: function () {
         this._setValue(this.model.get("value"));
         if (this._getValue() === null && !this.model.get("multiple") && !this.model.get("optional")) {
             this._setValue(this.first());
@@ -128,7 +128,7 @@ var Base = Backbone.View.extend({
     },
 
     /** Return/Set current selection */
-    value: function(new_value) {
+    value: function (new_value) {
         if (new_value !== undefined) {
             this.model.set("value", new_value);
         }
@@ -136,56 +136,54 @@ var Base = Backbone.View.extend({
     },
 
     /** Return first available option */
-    first: function() {
+    first: function () {
         var options = this.$("input").first();
         return options.length > 0 ? options.val() : null;
     },
 
     /** Show a spinner indicating that the select options are currently loaded */
-    wait: function() {
+    wait: function () {
         this.model.set("wait", true);
     },
 
     /** Hide spinner indicating that the request has been completed */
-    unwait: function() {
+    unwait: function () {
         this.model.set("wait", false);
     },
 
     /** Returns the number of options */
-    length: function() {
+    length: function () {
         return this.$(".ui-option").length;
     },
 
     /** Shows the options */
-    show: function() {
+    show: function () {
         this.model.set("visible", true);
     },
 
     /** Hides the options */
-    hide: function() {
+    hide: function () {
         this.model.set("visible", false);
     },
 
     /** Set value to dom */
-    _setValue: function(new_value) {
+    _setValue: function (new_value) {
         var self = this;
         if (new_value !== undefined) {
             this.$("input").prop("checked", false);
             if (new_value !== null) {
                 var values = $.isArray(new_value) ? new_value : [new_value];
-                _.each(values, v => {
-                    self.$(`input[value="${v}"]`)
-                        .first()
-                        .prop("checked", true);
+                _.each(values, (v) => {
+                    self.$(`input[value="${v}"]`).first().prop("checked", true);
                 });
             }
         }
     },
 
     /** Return current selection */
-    _getValue: function() {
+    _getValue: function () {
         var selected = [];
-        this.$(":checked").each(function() {
+        this.$(":checked").each(function () {
             selected.push($(this).val());
         });
         if (Utils.isEmpty(selected)) {
@@ -195,23 +193,19 @@ var Base = Backbone.View.extend({
     },
 
     /** Show message instead if options */
-    _messageShow: function(text, status) {
-        this.$message
-            .show()
-            .removeClass()
-            .addClass(`alert alert-${status}`)
-            .html(text);
+    _messageShow: function (text, status) {
+        this.$message.show().removeClass().addClass(`alert alert-${status}`).html(text);
     },
 
     /** Main template function */
-    _template: function() {
+    _template: function () {
         return $("<div/>").addClass("ui-options-list");
-    }
+    },
 });
 
 /** Iconized **/
 var BaseIcons = Base.extend({
-    _templateOption: function(pair) {
+    _templateOption: function (pair) {
         var id = Utils.uid();
         return $("<div/>")
             .addClass("ui-option")
@@ -220,61 +214,51 @@ var BaseIcons = Base.extend({
                     id: id,
                     type: this.model.get("type"),
                     name: this.model.id,
-                    value: pair.value
+                    value: pair.value,
                 })
             )
-            .append(
-                $("<label/>")
-                    .addClass("ui-options-label")
-                    .attr("for", id)
-                    .html(pair.label)
-            );
-    }
+            .append($("<label/>").addClass("ui-options-label").attr("for", id).html(pair.label));
+    },
 });
 
 /** Radio button field **/
 var Radio = {};
 Radio.View = BaseIcons.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         options.type = "radio";
         BaseIcons.prototype.initialize.call(this, options);
-    }
+    },
 });
 
 /** Checkbox options field **/
 var Checkbox = {};
 Checkbox.View = BaseIcons.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         options.type = "checkbox";
         options.multiple = true;
         BaseIcons.prototype.initialize.call(this, options);
-    }
+    },
 });
 
 /** Radio button options field styled as classic buttons **/
 var RadioButton = {};
 RadioButton.View = Base.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         Base.prototype.initialize.call(this, options);
     },
 
     /** Set current value */
-    _setValue: function(new_value) {
+    _setValue: function (new_value) {
         if (new_value !== undefined) {
             this.$("input").prop("checked", false);
             this.$("label").removeClass("active");
-            this.$(`[value="${new_value}"]`)
-                .prop("checked", true)
-                .closest("label")
-                .addClass("active");
+            this.$(`[value="${new_value}"]`).prop("checked", true).closest("label").addClass("active");
         }
     },
 
     /** Template for a single option */
-    _templateOption: function(pair) {
-        var $el = $("<label/>")
-            .addClass("btn btn-secondary m-0")
-            .attr("role", "button");
+    _templateOption: function (pair) {
+        var $el = $("<label/>").addClass("btn btn-secondary m-0").attr("role", "button");
         if (pair.icon) {
             $el.append(
                 $("<i/>")
@@ -288,7 +272,7 @@ RadioButton.View = Base.extend({
                 .attr({
                     type: "radio",
                     name: this.model.id,
-                    value: pair.value
+                    value: pair.value,
                 })
                 .hide()
         );
@@ -299,9 +283,9 @@ RadioButton.View = Base.extend({
     },
 
     /** Main template function */
-    _template: function() {
+    _template: function () {
         return $("<div/>").addClass("btn-group ui-radiobutton");
-    }
+    },
 });
 
 export default {
@@ -309,5 +293,5 @@ export default {
     BaseIcons: BaseIcons,
     Radio: Radio,
     RadioButton: RadioButton,
-    Checkbox: Checkbox
+    Checkbox: Checkbox,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-popover.js b/client/galaxy/scripts/mvc/ui/ui-popover.js
index 009360982a9e..a97fced01142 100644
--- a/client/galaxy/scripts/mvc/ui/ui-popover.js
+++ b/client/galaxy/scripts/mvc/ui/ui-popover.js
@@ -7,11 +7,11 @@ import _ from "underscore";
 import Utils from "utils/utils";
 
 export default Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = _.defaults(options || {}, {
             title: null,
             placement: "top",
-            container: "body"
+            container: "body",
         });
         this.uid = Utils.uid();
         this.$target = this.options.container;
@@ -20,14 +20,14 @@ export default Backbone.View.extend({
     /**
      * Show popover
      */
-    show: function($content) {
+    show: function ($content) {
         const btn = "<i class='fa fa-times-circle'/>";
         $(this.$target).popover({
             title: `${this.options.title} ${btn}`,
             placement: this.options.placement,
             content: $content,
             html: true,
-            trigger: "manual"
+            trigger: "manual",
         });
         $(this.$target).popover("show");
 
@@ -35,7 +35,7 @@ export default Backbone.View.extend({
         var self = this;
         const $popover = $(this.$target.data("bs.popover").tip);
         $popover.find(".popover-header > i").on("click", () => this.hide());
-        $("body").on(`mousedown.${this.uid}`, e => {
+        $("body").on(`mousedown.${this.uid}`, (e) => {
             if (!$($popover).is(e.target) && $($popover).has(e.target).length === 0) {
                 self.hide();
             }
@@ -45,8 +45,8 @@ export default Backbone.View.extend({
     /**
      * Hide popover
      */
-    hide: function() {
+    hide: function () {
         $(this.$target).popover("dispose");
         $("body").off(`mousedown.${this.uid}`);
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/ui/ui-portlet.js b/client/galaxy/scripts/mvc/ui/ui-portlet.js
index 433d16d5700b..b0646c645635 100644
--- a/client/galaxy/scripts/mvc/ui/ui-portlet.js
+++ b/client/galaxy/scripts/mvc/ui/ui-portlet.js
@@ -5,7 +5,7 @@ import Ui from "mvc/ui/ui-misc";
 
 export var View = Backbone.View.extend({
     visible: false,
-    initialize: function(options) {
+    initialize: function (options) {
         var self = this;
         this.model =
             (options && options.model) ||
@@ -21,7 +21,7 @@ export var View = Backbone.View.extend({
                 collapsible: false,
                 collapsible_button: true,
                 collapsed: false,
-                onchange_title: null
+                onchange_title: null,
             }).set(options);
         this.setElement(this._template());
 
@@ -44,20 +44,17 @@ export var View = Backbone.View.extend({
             icon: "fa-eye",
             tooltip: "Collapse/Expand",
             cls: "ui-button-icon-plain",
-            onclick: function() {
+            onclick: function () {
                 self[self.collapsed ? "expand" : "collapse"]();
-            }
+            },
         });
         this.render();
     },
 
-    render: function() {
+    render: function () {
         var self = this;
         var options = this.model.attributes;
-        this.$el
-            .removeClass()
-            .addClass(options.cls)
-            .attr("id", options.id);
+        this.$el.removeClass().addClass(options.cls).attr("id", options.id);
         this.$header[options.title ? "show" : "hide"]();
         this.$title_text.html(options.title);
         if (options.title_id) {
@@ -66,11 +63,7 @@ export var View = Backbone.View.extend({
 
         // render title icon
         if (options.icon) {
-            this.$title_icon
-                .removeClass()
-                .addClass("portlet-title-icon fa mr-1")
-                .addClass(options.icon)
-                .show();
+            this.$title_icon.removeClass().addClass("portlet-title-icon fa mr-1").addClass(options.icon).show();
         } else {
             this.$title_icon.hide();
         }
@@ -88,9 +81,9 @@ export var View = Backbone.View.extend({
         this.$title_text.prop("disabled", !options.onchange_title);
         options.onchange_title &&
             this.$title_text.make_text_editable({
-                on_finish: function(new_title) {
+                on_finish: function (new_title) {
                     options.onchange_title(new_title);
-                }
+                },
             });
 
         // render buttons
@@ -119,96 +112,93 @@ export var View = Backbone.View.extend({
     },
 
     /** Append new doms to body */
-    append: function($el) {
+    append: function ($el) {
         this.$body.append($el);
     },
 
     /** Remove all content */
-    empty: function() {
+    empty: function () {
         this.$body.empty();
     },
 
     /** Return header element */
-    header: function() {
+    header: function () {
         return this.$header;
     },
 
     /** Return body element */
-    body: function() {
+    body: function () {
         return this.$body;
     },
 
     /** Show portlet */
-    show: function() {
+    show: function () {
         this.visible = true;
         this.$el.fadeIn("fast");
     },
 
     /** Hide portlet */
-    hide: function() {
+    hide: function () {
         this.visible = false;
         this.$el.hide();
     },
 
     /** Enable a particular button */
-    enableButton: function(id) {
+    enableButton: function (id) {
         this.$buttons.find(`#${id}`).prop("disabled", false);
     },
 
     /** Disable a particular button */
-    disableButton: function(id) {
+    disableButton: function (id) {
         this.$buttons.find(`#${id}`).prop("disabled", true);
     },
 
     /** Hide a particular operation */
-    hideOperation: function(id) {
+    hideOperation: function (id) {
         this.$operations.find(`#${id}`).hide();
     },
 
     /** Show a particular operation */
-    showOperation: function(id) {
+    showOperation: function (id) {
         this.$operations.find(`#${id}`).show();
     },
 
     /** Replaces the event callback of an existing operation */
-    setOperation: function(id, callback) {
-        this.$operations
-            .find(`#${id}`)
-            .off("click")
-            .on("click", callback);
+    setOperation: function (id, callback) {
+        this.$operations.find(`#${id}`).off("click").on("click", callback);
     },
 
     /** Change title */
-    title: function(new_title) {
+    title: function (new_title) {
         new_title && this.$title_text.html(new_title);
         return this.$title_text.html();
     },
 
     /** Collapse portlet */
-    collapse: function() {
+    collapse: function () {
         this.collapsed = true;
         this.$content.hide();
         this.collapsible_button.setIcon("fa-eye-slash");
     },
 
     /** Expand portlet */
-    expand: function() {
+    expand: function () {
         this.collapsed = false;
         this.$content.show();
         this.collapsible_button.setIcon("fa-eye");
     },
 
     /** Disable content access */
-    disable: function() {
+    disable: function () {
         this.$backdrop.show();
     },
 
     /** Enable content access */
-    enable: function() {
+    enable: function () {
         this.$backdrop.hide();
     },
 
-    _template: function() {
+    _template: function () {
         return $("<div/>")
             .append(
                 $("<div/>")
@@ -228,8 +218,8 @@ export var View = Backbone.View.extend({
                     .append($("<div/>").addClass("portlet-buttons mt-3 mb-3"))
             )
             .append($("<div/>").addClass("portlet-backdrop"));
-    }
+    },
 });
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-rules-edit.js b/client/galaxy/scripts/mvc/ui/ui-rules-edit.js
index a48e9092ae2e..566a61047124 100644
--- a/client/galaxy/scripts/mvc/ui/ui-rules-edit.js
+++ b/client/galaxy/scripts/mvc/ui/ui-rules-edit.js
@@ -11,7 +11,7 @@ import RulesDisplay from "components/RulesDisplay.vue";
  * Bridge rule based builder and the tool form.
  */
 var View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model = new Backbone.Model();
         this.target = options.target;
         const view = this;
@@ -27,7 +27,7 @@ var View = Backbone.View.extend({
                 } else {
                     view._showRuleEditor(null);
                 }
-            }
+            },
         });
 
         // add change event. fires on trigger
@@ -47,35 +47,35 @@ var View = Backbone.View.extend({
             propsData: {
                 initialRules: {
                     rules: [],
-                    mapping: []
-                }
-            }
+                    mapping: [],
+                },
+            },
         });
         this.instance.$mount(vm);
         this.collapsible_disabled = true;
     },
 
-    _fetcCollectionAndEdit: function() {
+    _fetcCollectionAndEdit: function () {
         const view = this;
         const url = `${getAppRoot()}api/dataset_collections/${view.target.id}?instance_type=history`;
         axios
             .get(url)
-            .then(response => this._showCollection(response))
+            .then((response) => this._showCollection(response))
             .catch(view._renderFetchError);
     },
 
-    _showCollection: function(response) {
+    _showCollection: function (response) {
         const elements = response.data;
         this._showRuleEditor(elements);
     },
 
-    _showRuleEditor: function(elements) {
+    _showRuleEditor: function (elements) {
         const elementsType = "collection_contents";
         const importType = "collections";
         const value = this._value;
         const options = {
-            saveRulesFn: rules => this._handleRulesSave(rules),
-            initialRules: value
+            saveRulesFn: (rules) => this._handleRulesSave(rules),
+            initialRules: value,
         };
         ListCollectionCreator.ruleBasedCollectionCreatorModal(
             elements,
@@ -85,17 +85,17 @@ var View = Backbone.View.extend({
         ).done(() => {});
     },
 
-    _handleRulesSave: function(rules) {
+    _handleRulesSave: function (rules) {
         this._setValue(rules);
     },
 
-    _renderFetchError: function(e) {
+    _renderFetchError: function (e) {
         console.log(e);
         console.log("problem fetching collection");
     },
 
     /** Main Template */
-    _template: function(options) {
+    _template: function (options) {
         return `
             <div class="ui-rules-edit clearfix">
                 <span class="ui-rules-preview" />
@@ -105,7 +105,7 @@ var View = Backbone.View.extend({
     },
 
     /** Return/Set current value */
-    value: function(new_value) {
+    value: function (new_value) {
         if (new_value !== undefined) {
             this._setValue(new_value);
         } else {
@@ -114,17 +114,17 @@ var View = Backbone.View.extend({
     },
 
     /** Update input element options */
-    update: function(input_def) {
+    update: function (input_def) {
         this.target = input_def.target;
     },
 
     /** Returns current value */
-    _getValue: function() {
+    _getValue: function () {
         return this._value;
     },
 
     /** Sets current value */
-    _setValue: function(new_value) {
+    _setValue: function (new_value) {
         if (new_value) {
             if (typeof new_value == "string") {
                 new_value = JSON.parse(new_value);
@@ -137,7 +137,7 @@ var View = Backbone.View.extend({
     },
 
     /** Validate input element value */
-    validate: function() {
+    validate: function () {
         const value = this._value;
         let message = null;
         if (!value || value.rules.length === 0) {
@@ -153,9 +153,9 @@ var View = Backbone.View.extend({
             }
         }
         return message;
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-select-content.js b/client/galaxy/scripts/mvc/ui/ui-select-content.js
index 27f5de24554c..8e037348d2e9 100644
--- a/client/galaxy/scripts/mvc/ui/ui-select-content.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-content.js
@@ -19,22 +19,22 @@ const Configurations = {
             tooltip: _l("Single dataset"),
             library: true,
             multiple: false,
-            batch: Batch.DISABLED
+            batch: Batch.DISABLED,
         },
         {
             src: "hda",
             icon: "fa-files-o",
             tooltip: _l("Multiple datasets"),
             multiple: true,
-            batch: Batch.LINKED
+            batch: Batch.LINKED,
         },
         {
             src: "hdca",
             icon: "fa-folder-o",
             tooltip: _l("Dataset collection"),
             multiple: false,
-            batch: Batch.LINKED
-        }
+            batch: Batch.LINKED,
+        },
     ],
     data_multiple: [
         {
@@ -42,15 +42,15 @@ const Configurations = {
             icon: "fa-files-o",
             tooltip: _l("Multiple datasets"),
             multiple: true,
-            batch: Batch.DISABLED
+            batch: Batch.DISABLED,
         },
         {
             src: "hdca",
             icon: "fa-folder-o",
             tooltip: _l("Dataset collections"),
             multiple: true,
-            batch: Batch.DISABLED
-        }
+            batch: Batch.DISABLED,
+        },
     ],
     data_collection: [
         {
@@ -58,8 +58,8 @@ const Configurations = {
             icon: "fa-folder-o",
             tooltip: _l("Dataset collection"),
             multiple: false,
-            batch: Batch.DISABLED
-        }
+            batch: Batch.DISABLED,
+        },
     ],
     workflow_data: [
         {
@@ -67,8 +67,8 @@ const Configurations = {
             icon: "fa-file-o",
             tooltip: _l("Single dataset"),
             multiple: false,
-            batch: Batch.DISABLED
-        }
+            batch: Batch.DISABLED,
+        },
     ],
     workflow_data_multiple: [
         {
@@ -76,8 +76,8 @@ const Configurations = {
             icon: "fa-files-o",
             tooltip: _l("Multiple datasets"),
             multiple: true,
-            batch: Batch.DISABLED
-        }
+            batch: Batch.DISABLED,
+        },
     ],
     workflow_data_collection: [
         {
@@ -85,8 +85,8 @@ const Configurations = {
             icon: "fa-folder-o",
             tooltip: _l("Dataset collection"),
             multiple: false,
-            batch: Batch.DISABLED
-        }
+            batch: Batch.DISABLED,
+        },
     ],
     module_data: [
         {
@@ -94,15 +94,15 @@ const Configurations = {
             icon: "fa-file-o",
             tooltip: _l("Single dataset"),
             multiple: false,
-            batch: Batch.DISABLED
+            batch: Batch.DISABLED,
         },
         {
             src: "hda",
             icon: "fa-files-o",
             tooltip: _l("Multiple datasets"),
             multiple: true,
-            batch: Batch.ENABLED
-        }
+            batch: Batch.ENABLED,
+        },
     ],
     module_data_collection: [
         {
@@ -110,28 +110,28 @@ const Configurations = {
             icon: "fa-folder-o",
             tooltip: _l("Dataset collection"),
             multiple: false,
-            batch: Batch.DISABLED
+            batch: Batch.DISABLED,
         },
         {
             src: "hdca",
             icon: "fa-folder",
             tooltip: _l("Multiple collections"),
             multiple: true,
-            batch: Batch.ENABLED
-        }
-    ]
+            batch: Batch.ENABLED,
+        },
+    ],
 };
 
 /** View for hda and hdca content selector ui elements */
 const View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         const self = this;
         this.model =
             (options && options.model) ||
             new Backbone.Model({
                 src_labels: { hda: "dataset", hdca: "dataset collection" },
                 pagelimit: 100,
-                statustimer: 1000
+                statustimer: 1000,
             }).set(options);
         this.setElement($("<div/>").addClass("ui-select-content"));
         this.button_product = new Ui.RadioButton.View({
@@ -141,35 +141,33 @@ const View = Backbone.View.extend({
                     icon: "fa fa-chain",
                     value: "false",
                     tooltip:
-                        "Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."
+                        "Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads.",
                 },
                 {
                     icon: "fa fa-chain-broken",
                     value: "true",
-                    tooltip: "Unlinked dataset inputs will be run against *all* other inputs."
-                }
-            ]
+                    tooltip: "Unlinked dataset inputs will be run against *all* other inputs.",
+                },
+            ],
         });
         this.$batch = {
             linked: $(this._templateBatch()).clone(),
-            enabled: $(this._templateBatch())
-                .clone()
-                .append(this.button_product.$el)
+            enabled: $(this._templateBatch()).clone().append(this.button_product.$el),
         };
 
         // add drag-drop event handlers
         const element = this.$el.get(0);
-        element.addEventListener("dragenter", e => {
+        element.addEventListener("dragenter", (e) => {
             this.lastenter = e.target;
             self.$el.addClass("ui-dragover");
         });
-        element.addEventListener("dragover", e => {
+        element.addEventListener("dragover", (e) => {
             e.preventDefault();
         });
-        element.addEventListener("dragleave", e => {
+        element.addEventListener("dragleave", (e) => {
             this.lastenter === e.target && self.$el.removeClass("ui-dragover");
         });
-        element.addEventListener("drop", e => {
+        element.addEventListener("drop", (e) => {
             e.preventDefault();
             try {
                 const drop_data = JSON.parse(e.dataTransfer.getData("text"))[0];
@@ -201,29 +199,29 @@ const View = Backbone.View.extend({
         });
     },
 
-    render: function() {
+    render: function () {
         this._changeType();
         this._changeValue();
         this._changeWait();
     },
 
     /** Indicate that select fields are being updated */
-    wait: function() {
+    wait: function () {
         this.model.set("wait", true);
     },
 
     /** Indicate that the options update has been completed */
-    unwait: function() {
+    unwait: function () {
         this.model.set("wait", false);
     },
 
     /** Update data representing selectable options */
-    update: function(input_def) {
+    update: function (input_def) {
         this.model.set("data", input_def.options);
     },
 
     /** Return the currently selected dataset values */
-    value: function(new_value) {
+    value: function (new_value) {
         const galaxy = getGalaxyInstance();
         new_value !== undefined && this.model.set("value", new_value);
         const current = this.model.get("current");
@@ -257,7 +255,7 @@ const View = Backbone.View.extend({
     },
 
     /** Change of current select field */
-    _changeCurrent: function() {
+    _changeCurrent: function () {
         const self = this;
         _.each(this.fields, (field, i) => {
             const cnf = self.config[i];
@@ -288,7 +286,7 @@ const View = Backbone.View.extend({
     },
 
     /** Change of type */
-    _changeType: function() {
+    _changeType: function () {
         const self = this;
         const galaxy = getGalaxyInstance();
 
@@ -316,7 +314,7 @@ const View = Backbone.View.extend({
             self.button_data.push({
                 value: i,
                 icon: c.icon,
-                tooltip: c.tooltip
+                tooltip: c.tooltip,
             });
             self.fields.push(
                 new Select.View({
@@ -326,9 +324,9 @@ const View = Backbone.View.extend({
                         !c.multiple || (data && data[c.src] && data[c.src].length > self.model.get("pagelimit")),
                     individual: true,
                     error_text: `No ${extensions ? `${extensions} ` : ""}${src_labels[c.src] || "content"} available.`,
-                    onchange: function() {
+                    onchange: function () {
                         self.trigger("change");
-                    }
+                    },
                 })
             );
         });
@@ -336,10 +334,10 @@ const View = Backbone.View.extend({
             value: this.model.get("current"),
             data: this.button_data,
             cls: "pr-lg-2",
-            onchange: function(value) {
+            onchange: function (value) {
                 self.model.set("current", value);
                 self.trigger("change");
-            }
+            },
         });
 
         // build data dialog button
@@ -350,16 +348,16 @@ const View = Backbone.View.extend({
                 const current = this.model.get("current");
                 const cnf = this.config[current];
                 galaxy.data.dialog(
-                    response => {
+                    (response) => {
                         this._handleDropValues(response, false);
                     },
                     {
                         multiple: cnf.multiple,
                         library: !!cnf.library,
-                        format: null
+                        format: null,
                     }
                 );
-            }
+            },
         });
 
         // append views
@@ -370,7 +368,7 @@ const View = Backbone.View.extend({
             .append($("<div/>").append(this.button_type.$el))
             .append($fields)
             .append($("<div/>").append(this.button_dialog.$el));
-        _.each(this.fields, field => {
+        _.each(this.fields, (field) => {
             $fields.append(field.$el);
         });
         _.each(this.$batch, ($batchfield, batchmode) => {
@@ -382,28 +380,28 @@ const View = Backbone.View.extend({
     },
 
     /** Change of wait flag */
-    _changeWait: function() {
+    _changeWait: function () {
         const self = this;
-        _.each(this.fields, field => {
+        _.each(this.fields, (field) => {
             field[self.model.get("wait") ? "wait" : "unwait"]();
         });
     },
 
     /** Change of available options */
-    _changeData: function() {
+    _changeData: function () {
         const options = this.model.get("data");
         const self = this;
         const select_options = {};
         _.each(options, (items, src) => {
             select_options[src] = [];
-            _.each(items, item => {
+            _.each(items, (item) => {
                 select_options[src].push({
                     hid: item.hid,
                     keep: item.keep,
                     label: `${item.hid}: ${item.name}`,
                     value: item.id,
                     origin: item.origin,
-                    tags: item.tags
+                    tags: item.tags,
                 });
                 self.cache[`${item.id}_${src}`] = item;
             });
@@ -414,12 +412,12 @@ const View = Backbone.View.extend({
     },
 
     /** Change of incoming value */
-    _changeValue: function() {
+    _changeValue: function () {
         const new_value = this.model.get("value");
         if (new_value && new_value.values && new_value.values.length > 0) {
             // create list with content ids
             const list = [];
-            _.each(new_value.values, value => {
+            _.each(new_value.values, (value) => {
                 list.push(value.id);
             });
             // sniff first suitable field type from config list
@@ -435,19 +433,19 @@ const View = Backbone.View.extend({
                 }
             }
         } else {
-            _.each(this.fields, field => {
+            _.each(this.fields, (field) => {
                 field.value(null);
             });
         }
     },
 
     /** Source helper matches history_content_types to source types */
-    _getSource: function(v) {
+    _getSource: function (v) {
         return v.history_content_type == "dataset_collection" ? "hdca" : "hda";
     },
 
     /** Library datasets are displayed and selected together with history datasets **/
-    _patchValue: function(v) {
+    _patchValue: function (v) {
         if (v.src == "ldda") {
             v.src = "hda";
             v.origin = "ldda";
@@ -456,7 +454,7 @@ const View = Backbone.View.extend({
     },
 
     /** Restores original value e.g. after patching library datasets **/
-    _unpatchValue: function(v) {
+    _unpatchValue: function (v) {
         if (v.origin) {
             const d = Object.assign({}, v);
             d.id = d.id.substr(d.origin.length);
@@ -467,7 +465,7 @@ const View = Backbone.View.extend({
     },
 
     /** Add values from drag/drop */
-    _handleDropValues: function(drop_data, drop_partial = true) {
+    _handleDropValues: function (drop_data, drop_partial = true) {
         const self = this;
         const data = this.model.get("data");
         const current = this.model.get("current");
@@ -477,7 +475,7 @@ const View = Backbone.View.extend({
             const values = $.isArray(drop_data) ? drop_data : [drop_data];
             if (values.length > 0) {
                 let data_changed = false;
-                _.each(values, v => {
+                _.each(values, (v) => {
                     self._patchValue(v);
                     const new_id = v.id;
                     const new_src = (v.src = this._getSource(v));
@@ -491,7 +489,7 @@ const View = Backbone.View.extend({
                             name: v.name ? v.name : new_id,
                             origin: v.origin,
                             keep: true,
-                            tags: []
+                            tags: [],
                         });
                     }
                 });
@@ -503,7 +501,7 @@ const View = Backbone.View.extend({
                 if (config.src == first_src && drop_partial) {
                     let current_value = field.value();
                     if (current_value && config.multiple) {
-                        _.each(values, v => {
+                        _.each(values, (v) => {
                             if (current_value.indexOf(v.id) == -1) {
                                 current_value.push(v.id);
                             }
@@ -523,7 +521,7 @@ const View = Backbone.View.extend({
     },
 
     /** Highlight drag result */
-    _handleDropStatus: function(status) {
+    _handleDropStatus: function (status) {
         const self = this;
         this.$el.removeClass("ui-dragover").addClass(`ui-dragover-${status}`);
         setTimeout(() => {
@@ -532,7 +530,7 @@ const View = Backbone.View.extend({
     },
 
     /** Assists in identifying the batch mode */
-    _batch: function(result) {
+    _batch: function (result) {
         result["batch"] = false;
         const current = this.model.get("current");
         const config = this.config[current];
@@ -552,16 +550,16 @@ const View = Backbone.View.extend({
     },
 
     /** Template for batch mode execution options */
-    _templateBatch: function() {
+    _templateBatch: function () {
         return `<div class="form-text text-muted" style="clear: both;">
                     <i class="fa fa-sitemap"/>
                     <span>
                         This is a batch mode input field. Separate jobs will be triggered for each dataset selection.
                     </span>
                 </div>`;
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-select-default.js b/client/galaxy/scripts/mvc/ui/ui-select-default.js
index 0627eadaeb3e..9ac2dcba2e0f 100644
--- a/client/galaxy/scripts/mvc/ui/ui-select-default.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js
@@ -8,7 +8,7 @@ import Utils from "utils/utils";
 import { keyedColorScheme } from "utils/color";
 import Buttons from "mvc/ui/ui-buttons";
 var View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.data = [];
         this.data2 = [];
         this.model =
@@ -25,10 +25,10 @@ var View = Backbone.View.extend({
                 optional: false,
                 disabled: false,
                 readonly: false,
-                onchange: function() {},
+                onchange: function () {},
                 value: null,
                 individual: false,
-                pagesize: 20
+                pagesize: 20,
             }).set(options);
         this.on("change", () => {
             if (this.model.get("onchange")) {
@@ -44,7 +44,7 @@ var View = Backbone.View.extend({
         this.render();
     },
 
-    render: function() {
+    render: function () {
         if (this.model.get("searchable")) {
             this._renderSearchable();
         } else {
@@ -67,7 +67,7 @@ var View = Backbone.View.extend({
     },
 
     /** Renders the classic selection field */
-    _renderClassic: function() {
+    _renderClassic: function () {
         this.$el
             .addClass(this.model.get("multiple") ? "ui-select-multiple" : "ui-select")
             .append((this.$select = $("<select/>")))
@@ -81,19 +81,17 @@ var View = Backbone.View.extend({
                 .addClass("icon-resize")
                 .show()
                 .off("mousedown")
-                .on("mousedown", event => {
+                .on("mousedown", (event) => {
                     var currentY = event.pageY;
                     var currentHeight = this.$select.height();
                     this.minHeight = this.minHeight || currentHeight;
                     $("#dd-helper")
                         .show()
-                        .on("mousemove", event => {
+                        .on("mousemove", (event) => {
                             this.$select.height(Math.max(currentHeight + (event.pageY - currentY), this.minHeight));
                         })
                         .on("mouseup mouseleave", () => {
-                            $("#dd-helper")
-                                .hide()
-                                .off();
+                            $("#dd-helper").hide().off();
                         });
                 });
         } else {
@@ -104,7 +102,7 @@ var View = Backbone.View.extend({
     },
 
     /** Renders the default select2 field */
-    _renderSearchable: function() {
+    _renderSearchable: function () {
         this.$el.append((this.$select = $("<div/>"))).append((this.$dropdown = $("<div/>")));
         this.$dropdown.hide();
         if (!this.model.get("multiple")) {
@@ -120,45 +118,39 @@ var View = Backbone.View.extend({
                 onclick: () => {
                     var new_value = [];
                     if (this.all_button.value() !== 0) {
-                        _.each(this.model.get("data"), option => {
+                        _.each(this.model.get("data"), (option) => {
                             new_value.push(option.value);
                         });
                     }
                     this.value(new_value);
                     this.trigger("change");
-                }
+                },
             });
             this.$el.prepend(this.all_button.$el);
         }
     },
 
     /** Matches a search term with a given text */
-    _match: function(term, text) {
-        return (
-            !term ||
-            term === "" ||
-            String(text)
-                .toUpperCase()
-                .indexOf(term.toUpperCase()) >= 0
-        );
+    _match: function (term, text) {
+        return !term || term === "" || String(text).toUpperCase().indexOf(term.toUpperCase()) >= 0;
     },
 
     /** Updates the selection options */
-    _changeData: function() {
+    _changeData: function () {
         this.data = [];
         if (!this.model.get("multiple") && this.model.get("optional")) {
             this.data.push({
                 value: "__null__",
-                label: this.model.get("empty_text")
+                label: this.model.get("empty_text"),
             });
         }
-        _.each(this.model.get("data"), option => {
+        _.each(this.model.get("data"), (option) => {
             this.data.push(option);
         });
         if (this.length() === 0) {
             this.data.push({
                 value: "__null__",
-                label: this.model.get("error_text")
+                label: this.model.get("error_text"),
             });
         }
         if (this.model.get("searchable")) {
@@ -169,7 +161,7 @@ var View = Backbone.View.extend({
                     order: index,
                     id: option.value,
                     text: option.label,
-                    tags: option.tags
+                    tags: option.tags,
                 };
                 this.data2.push(d);
                 this.data2index[d.id] = d;
@@ -182,12 +174,12 @@ var View = Backbone.View.extend({
                 data: this.data2,
                 closeOnSelect: !this.model.get("multiple"),
                 multiple: this.model.get("multiple"),
-                query: q => {
+                query: (q) => {
                     this.matched_tags = {};
                     var pagesize = this.model.get("pagesize");
-                    var results = _.filter(this.data2, e => {
+                    var results = _.filter(this.data2, (e) => {
                         var found = false;
-                        _.each(e.tags, tag => {
+                        _.each(e.tags, (tag) => {
                             if (this._match(q.term, tag)) {
                                 found = this.matched_tags[tag] = true;
                             }
@@ -196,17 +188,18 @@ var View = Backbone.View.extend({
                     });
                     q.callback({
                         results: results.slice((q.page - 1) * pagesize, q.page * pagesize),
-                        more: results.length >= q.page * pagesize
+                        more: results.length >= q.page * pagesize,
                     });
                 },
-                formatResult: result => {
+                formatResult: (result) => {
                     let extraTagWarning = "";
-                    const filteredTags = _.filter(result.tags, t =>
+                    const filteredTags = _.filter(result.tags, (t) =>
                         Object.prototype.hasOwnProperty.call(this.matched_tags, t)
                     );
                     if (filteredTags.length > 5) {
-                        extraTagWarning = `&nbsp;<div class="label label-warning">${filteredTags.length -
-                            5} more tags</div>`;
+                        extraTagWarning = `&nbsp;<div class="label label-warning">${
+                            filteredTags.length - 5
+                        } more tags</div>`;
                     }
                     return `
                     ${_.escape(result.text)}
@@ -224,17 +217,13 @@ var View = Backbone.View.extend({
                         }, "")}
                         ${extraTagWarning}
                    </div>`;
-                }
+                },
             });
             this.$(".select2-container .select2-search input").off("blur");
         } else {
             this.$select.find("option").remove();
-            _.each(this.data, option => {
-                this.$select.append(
-                    $("<option/>")
-                        .attr("value", option.value)
-                        .html(_.escape(option.label))
-                );
+            _.each(this.data, (option) => {
+                this.$select.append($("<option/>").attr("value", option.value).html(_.escape(option.label)));
             });
         }
         this.model.set("disabled", this.model.get("readonly") || this.length() === 0);
@@ -242,7 +231,7 @@ var View = Backbone.View.extend({
     },
 
     /** Handles field enabling/disabling, usually used when no options are available */
-    _changeDisabled: function() {
+    _changeDisabled: function () {
         if (this.model.get("searchable")) {
             this.$select.select2(this.model.get("disabled") ? "disable" : "enable");
         } else {
@@ -251,7 +240,7 @@ var View = Backbone.View.extend({
     },
 
     /** Searchable fields may display a spinner e.g. while waiting for a server response */
-    _changeWait: function() {
+    _changeWait: function () {
         this.$dropdown
             .removeClass()
             .addClass("icon-dropdown fa")
@@ -259,13 +248,13 @@ var View = Backbone.View.extend({
     },
 
     /** Handles field visibility */
-    _changeVisible: function() {
+    _changeVisible: function () {
         this.$el[this.model.get("visible") ? "show" : "hide"]();
         this.$select[this.model.get("visible") ? "show" : "hide"]();
     },
 
     /** Synchronizes the model value with the actually selected field value */
-    _changeValue: function() {
+    _changeValue: function () {
         this._setValue(this.model.get("value"));
         if (this.model.get("multiple")) {
             if (this.all_button) {
@@ -278,7 +267,7 @@ var View = Backbone.View.extend({
     },
 
     /** Return/Set current selection */
-    value: function(new_value) {
+    value: function (new_value) {
         if (new_value !== undefined) {
             this.model.set("value", new_value);
         }
@@ -286,60 +275,60 @@ var View = Backbone.View.extend({
     },
 
     /** Return the first select option */
-    first: function() {
+    first: function () {
         return this.data.length > 0 ? this.data[0].value : null;
     },
 
     /** Check if a value is an existing option */
-    exists: function(value) {
+    exists: function (value) {
         return _.findWhere(this.data, { value: value });
     },
 
     /** Return the label/text of the current selection */
-    text: function() {
+    text: function () {
         var v = this._getValue();
         var d = this.exists($.isArray(v) ? v[0] : v);
         return d ? d.label : "";
     },
 
     /** Show the select field */
-    show: function() {
+    show: function () {
         this.model.set("visible", true);
     },
 
     /** Hide the select field */
-    hide: function() {
+    hide: function () {
         this.model.set("visible", false);
     },
 
     /** Show a spinner indicating that the select options are currently loaded */
-    wait: function() {
+    wait: function () {
         this.model.set("wait", true);
     },
 
     /** Hide spinner indicating that the request has been completed */
-    unwait: function() {
+    unwait: function () {
         this.model.set("wait", false);
     },
 
     /** Returns true if the field is disabled */
-    disabled: function() {
+    disabled: function () {
         return this.model.get("disabled");
     },
 
     /** Enable the select field */
-    enable: function() {
+    enable: function () {
         this.model.set("disabled", false);
     },
 
     /** Disable the select field */
-    disable: function() {
+    disable: function () {
         this.model.set("disabled", true);
     },
 
     /** Update all available options at once */
-    add: function(options, sorter) {
-        _.each(this.model.get("data"), v => {
+    add: function (options, sorter) {
+        _.each(this.model.get("data"), (v) => {
             if (v.keep && !_.findWhere(options, { value: v.value })) {
                 options.push(v);
             }
@@ -351,22 +340,22 @@ var View = Backbone.View.extend({
     },
 
     /** Update available options */
-    update: function(input_def) {
+    update: function (input_def) {
         this.model.set("data", input_def.data);
     },
 
     /** Set the custom onchange callback function */
-    setOnChange: function(callback) {
+    setOnChange: function (callback) {
         this.model.set("onchange", callback);
     },
 
     /** Number of available options */
-    length: function() {
+    length: function () {
         return $.isArray(this.model.get("data")) ? this.model.get("data").length : 0;
     },
 
     /** Set value to dom */
-    _setValue: function(new_value) {
+    _setValue: function (new_value) {
         if (new_value === null || new_value === undefined) {
             new_value = "__null__";
         }
@@ -382,7 +371,7 @@ var View = Backbone.View.extend({
         if (this.model.get("searchable")) {
             if ($.isArray(new_value)) {
                 var val = [];
-                _.each(new_value, v => {
+                _.each(new_value, (v) => {
                     var d = this.data2index[v];
                     if (d) {
                         val.push(d);
@@ -399,7 +388,7 @@ var View = Backbone.View.extend({
     },
 
     /** Get value from dom */
-    _getValue: function() {
+    _getValue: function () {
         var val = null;
         if (this.model.get("searchable")) {
             var selected = this.$select.select2("data");
@@ -407,7 +396,7 @@ var View = Backbone.View.extend({
                 if ($.isArray(selected)) {
                     val = [];
                     selected.sort((a, b) => a.order - b.order);
-                    _.each(selected, v => {
+                    _.each(selected, (v) => {
                         val.push(v.id);
                     });
                 } else {
@@ -418,9 +407,9 @@ var View = Backbone.View.extend({
             val = this.$select.val();
         }
         return Utils.isEmpty(val) ? null : val;
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-select-ftp.js b/client/galaxy/scripts/mvc/ui/ui-select-ftp.js
index b62136579e9b..06e4ef469586 100644
--- a/client/galaxy/scripts/mvc/ui/ui-select-ftp.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-ftp.js
@@ -8,7 +8,7 @@ import List from "mvc/ui/ui-list";
  */
 var View = Backbone.View.extend({
     // initialize
-    initialize: function(options) {
+    initialize: function (options) {
         // link this
         var self = this;
 
@@ -17,9 +17,9 @@ var View = Backbone.View.extend({
             name: "file",
             optional: options.optional,
             multiple: options.multiple,
-            onchange: function() {
+            onchange: function () {
                 options.onchange && options.onchange(self.value());
-            }
+            },
         });
 
         // create elements
@@ -28,25 +28,25 @@ var View = Backbone.View.extend({
         // initial fetch of ftps
         Utils.get({
             url: `${getAppRoot()}api/remote_files`,
-            success: function(response) {
+            success: function (response) {
                 var data = [];
                 for (var i in response) {
                     data.push({
                         value: response[i]["path"],
-                        label: response[i]["path"]
+                        label: response[i]["path"],
                     });
                 }
                 self.ftpfile_list.update(data);
-            }
+            },
         });
     },
 
     /** Return/Set currently selected ftp datasets */
-    value: function(val) {
+    value: function (val) {
         return this.ftpfile_list.value(val);
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-select-library.js b/client/galaxy/scripts/mvc/ui/ui-select-library.js
index 77b265937c35..7da44eb4bb25 100644
--- a/client/galaxy/scripts/mvc/ui/ui-select-library.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-library.js
@@ -6,27 +6,27 @@ import { getAppRoot } from "onload/loadConfig";
 
 // collection of libraries
 var Libraries = Backbone.Collection.extend({
-    url: `${getAppRoot()}api/libraries?deleted=false`
+    url: `${getAppRoot()}api/libraries?deleted=false`,
 });
 
 // collection of dataset
 var LibraryDatasets = Backbone.Collection.extend({
-    initialize: function() {
+    initialize: function () {
         var self = this;
         this.config = new Backbone.Model({ library_id: null });
         this.config.on("change", () => {
             self.fetch({ reset: true });
         });
     },
-    url: function() {
+    url: function () {
         return `${getAppRoot()}api/libraries/${this.config.get("library_id")}/contents`;
-    }
+    },
 });
 
 // hda/hdca content selector ui element
 var View = Backbone.View.extend({
     // initialize
-    initialize: function(options) {
+    initialize: function (options) {
         // link this
         var self = this;
 
@@ -40,9 +40,9 @@ var View = Backbone.View.extend({
         // select field for the library
         // TODO: Remove this once the library API supports searching for library datasets
         this.library_select = new Ui.Select.View({
-            onchange: function(value) {
+            onchange: function (value) {
                 self.datasets.config.set("library_id", value);
-            }
+            },
         });
 
         // create ui-list view to keep track of selected data libraries
@@ -50,18 +50,18 @@ var View = Backbone.View.extend({
             name: "dataset",
             optional: options.optional,
             multiple: options.multiple,
-            onchange: function() {
+            onchange: function () {
                 self.trigger("change");
-            }
+            },
         });
 
         // add reset handler for fetched libraries
         this.libraries.on("reset", () => {
             var data = [];
-            self.libraries.each(model => {
+            self.libraries.each((model) => {
                 data.push({
                     value: model.id,
-                    label: model.get("name")
+                    label: model.get("name"),
                 });
             });
             self.library_select.update({ data: data });
@@ -72,11 +72,11 @@ var View = Backbone.View.extend({
             var data = [];
             var library_current = self.library_select.text();
             if (library_current !== null) {
-                self.datasets.each(model => {
+                self.datasets.each((model) => {
                     if (model.get("type") === "file") {
                         data.push({
                             value: model.id,
-                            label: model.get("name")
+                            label: model.get("name"),
                         });
                     }
                 });
@@ -99,28 +99,28 @@ var View = Backbone.View.extend({
         // initial fetch of libraries
         this.libraries.fetch({
             reset: true,
-            success: function() {
+            success: function () {
                 self.library_select.trigger("change");
                 if (self.options.value !== undefined) {
                     self.value(self.options.value);
                 }
-            }
+            },
         });
     },
 
     /** Return/Set currently selected library datasets */
-    value: function(val) {
+    value: function (val) {
         return this.dataset_list.value(val);
     },
 
     /** Template */
-    _template: function() {
+    _template: function () {
         return `<div class="ui-select-library">
                     <div class="library-select mb-2"/>
                 </div>`;
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-select.js b/client/galaxy/scripts/mvc/ui/ui-select.js
index ead66ad4df5e..4a72b8ac1a89 100644
--- a/client/galaxy/scripts/mvc/ui/ui-select.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select.js
@@ -18,11 +18,11 @@ var View = Backbone.View.extend({
         minimumInputLength: 0,
         maximumTextLength: 100,
         // example format of initial data: "id:name,55:anotherrole@role.com,27:role@role.com"
-        initialData: ""
+        initialData: "",
     },
 
     // initialize
-    initialize: function(options) {
+    initialize: function (options) {
         // configure options
         this.options = Utils.merge(options, this.optionsDefault);
 
@@ -61,7 +61,7 @@ var View = Backbone.View.extend({
     },
 
     // value
-    value: function(new_value) {
+    value: function (new_value) {
         // get current id/value
         var before = this._getValue();
 
@@ -83,31 +83,31 @@ var View = Backbone.View.extend({
     },
 
     // label
-    text: function() {
+    text: function () {
         return this.$el.select2("data").text;
     },
 
     // disabled
-    disabled: function() {
+    disabled: function () {
         return !this.$el.select2("enable");
     },
 
     // enable
-    enable: function() {
+    enable: function () {
         this.$el.select2("enable", true);
     },
 
     // disable
-    disable: function() {
+    disable: function () {
         this.$el.select2("enable", false);
     },
 
     // add
-    add: function(options) {
+    add: function (options) {
         // add options
         this.select_data.push({
             id: options.id,
-            text: options.text
+            text: options.text,
         });
 
         // refresh
@@ -115,7 +115,7 @@ var View = Backbone.View.extend({
     },
 
     // remove
-    del: function(id) {
+    del: function (id) {
         // search option
         var index = this._getIndex(id);
 
@@ -130,12 +130,12 @@ var View = Backbone.View.extend({
     },
 
     // remove
-    remove: function() {
+    remove: function () {
         this.$el.select2("destroy");
     },
 
     // update
-    update: function(options) {
+    update: function (options) {
         // copy options
         this.select_data = [];
         for (var key in options.data) {
@@ -147,12 +147,12 @@ var View = Backbone.View.extend({
     },
 
     // refresh
-    _refresh: function() {
+    _refresh: function () {
         let select_opt;
         // add select2 data based on type of input
         if (!this.options.multiple) {
             if (this.select_data) {
-                this.select_data.map(value => {
+                this.select_data.map((value) => {
                     const mx = this.options.maximumTextLength + 3;
                     if (value.text && value.text.length > mx) {
                         let pos = value.text.indexOf(`(${value.id})`);
@@ -167,7 +167,7 @@ var View = Backbone.View.extend({
                 data: this.select_data,
                 containerCssClass: this.options.css,
                 placeholder: this.options.placeholder,
-                dropdownAutoWidth: true
+                dropdownAutoWidth: true,
             };
             this.$el.select2(select_opt);
             // select previous value (if exists)
@@ -184,25 +184,25 @@ var View = Backbone.View.extend({
                 formatResult: this.options.formatResult,
                 formatSelection: this.options.formatSelection,
                 initSelection: this.options.initSelection,
-                initialData: this.options.initialData
+                initialData: this.options.initialData,
             };
             this.$el.select2(select_opt);
         }
     },
 
     // get index
-    _getIndex: function(value) {
+    _getIndex: function (value) {
         // returns the index of the searched value
         _.findIndex(this.select_data, { id: value });
     },
 
     // get value
-    _getValue: function() {
+    _getValue: function () {
         return this.$el.select2("val");
     },
 
     // set value
-    _setValue: function(new_value) {
+    _setValue: function (new_value) {
         var index = this._getIndex(new_value);
         if (index == -1) {
             if (this.select_data.length > 0) {
@@ -213,11 +213,11 @@ var View = Backbone.View.extend({
     },
 
     // element
-    _template: function(options) {
+    _template: function (options) {
         return `<input type="hidden" value="${this.options.initialData}"/>`;
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-slider.js b/client/galaxy/scripts/mvc/ui/ui-slider.js
index b60d956725ba..1a78ec045f39 100644
--- a/client/galaxy/scripts/mvc/ui/ui-slider.js
+++ b/client/galaxy/scripts/mvc/ui/ui-slider.js
@@ -4,7 +4,7 @@ import IMask from "imask";
 import Utils from "utils/utils";
 
 const View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model =
             (options && options.model) ||
             new Backbone.Model({
@@ -15,7 +15,7 @@ const View = Backbone.View.extend({
                 precise: false,
                 split: 10000,
                 value: null,
-                onchange: function() {}
+                onchange: function () {},
             }).set(options);
 
         // create new element
@@ -25,7 +25,7 @@ const View = Backbone.View.extend({
         this.$slider = this.$(".ui-form-slider-element");
 
         IMask(this.$text[0], {
-            mask: value => {
+            mask: (value) => {
                 if (this._isParameter(value)) {
                     return true;
                 }
@@ -35,10 +35,10 @@ const View = Backbone.View.extend({
                     }
                 }
                 return value == value.replace(/[^0-9eE.-]/g, "");
-            }
+            },
         });
 
-        this.$text[0].addEventListener("change", e => {
+        this.$text[0].addEventListener("change", (e) => {
             this.value(e.currentTarget.value);
         });
 
@@ -64,7 +64,7 @@ const View = Backbone.View.extend({
         this.render();
     },
 
-    render: function() {
+    render: function () {
         const value = this.model.get("value");
         if (this.has_slider) {
             this.$slider.slider("value", value);
@@ -80,7 +80,7 @@ const View = Backbone.View.extend({
     },
 
     /** Set and return the current value */
-    value: function(new_val) {
+    value: function (new_val) {
         if (new_val !== undefined) {
             const options = this.model.attributes;
             const original_val = new_val;
@@ -110,21 +110,21 @@ const View = Backbone.View.extend({
     },
 
     /** Return true if the field contains a workflow parameter i.e. $('name') */
-    _isParameter: function(value) {
+    _isParameter: function (value) {
         return this.model.get("is_workflow") && String(value).substring(0, 1) === "$";
     },
 
     /** Slider template */
-    _template: function() {
+    _template: function () {
         return `<div class="ui-form-slider container-fluid">
                     <div class="row">
                         <input class="ui-input ui-form-slider-text" type="text"/>
                         <div class="ui-form-slider-element col mt-1"/>
                     </div>
                 </div>`;
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-table.js b/client/galaxy/scripts/mvc/ui/ui-table.js
index 15e38203657e..ebe63ad32fa0 100644
--- a/client/galaxy/scripts/mvc/ui/ui-table.js
+++ b/client/galaxy/scripts/mvc/ui/ui-table.js
@@ -3,14 +3,14 @@ import $ from "jquery";
 import Backbone from "backbone";
 import Utils from "utils/utils";
 var View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = Utils.merge(options, {
             content: "No content available.",
             onchange: null,
             ondblclick: null,
             onconfirm: null,
             cls: "grid",
-            selectable: true
+            selectable: true,
         });
         this.setElement(this._template());
         this.$thead = this.$("thead");
@@ -22,22 +22,22 @@ var View = Backbone.View.extend({
 
     events: {
         click: "_onclick",
-        dblclick: "_ondblclick"
+        dblclick: "_ondblclick",
     },
 
     /** Add cell to header row */
-    addHeader: function($el) {
+    addHeader: function ($el) {
         this.row.append($("<th/>").append($el));
     },
 
     /** Append header row to table */
-    appendHeader: function() {
+    appendHeader: function () {
         this.$thead.append(this.row);
         this.row = $("<tr/>");
     },
 
     /** Add cell to row */
-    add: function($el, width, align) {
+    add: function ($el, width, align) {
         var wrapper = $("<td/>");
         if (width) {
             wrapper.css("width", width);
@@ -49,22 +49,22 @@ var View = Backbone.View.extend({
     },
 
     /** Append row to table */
-    append: function(id, fade) {
+    append: function (id, fade) {
         this._commit(id, fade, false);
     },
 
     /** Prepend row to table */
-    prepend: function(id, fade) {
+    prepend: function (id, fade) {
         this._commit(id, fade, true);
     },
 
     /** Helper to get row element */
-    get: function(id) {
+    get: function (id) {
         return this.$(`#${id}`);
     },
 
     /** Delete row by id */
-    del: function(id) {
+    del: function (id) {
         var item = this.$tbody.find(`#${id}`);
         if (item.length > 0) {
             item.remove();
@@ -74,14 +74,14 @@ var View = Backbone.View.extend({
     },
 
     /** Delete all rows */
-    delAll: function() {
+    delAll: function () {
         this.$tbody.empty();
         this.row_count = 0;
         this._refresh();
     },
 
     /** Set a value i.e. selects/highlights a particular row by id */
-    value: function(new_value) {
+    value: function (new_value) {
         if (this.options.selectable) {
             this.before = this.$tbody.find(".current").attr("id");
             if (new_value !== undefined) {
@@ -103,12 +103,12 @@ var View = Backbone.View.extend({
     },
 
     /** Return the number of rows */
-    size: function() {
+    size: function () {
         return this.$tbody.find("tr").length;
     },
 
     /** Helper to append rows */
-    _commit: function(id, fade, prepend) {
+    _commit: function (id, fade, prepend) {
         this.del(id);
         this.row.attr("id", id);
         if (prepend) {
@@ -126,11 +126,9 @@ var View = Backbone.View.extend({
     },
 
     /** Handles onclick events */
-    _onclick: function(e) {
+    _onclick: function (e) {
         var old_value = this.value();
-        var new_value = $(e.target)
-            .closest("tr")
-            .attr("id");
+        var new_value = $(e.target).closest("tr").attr("id");
         if (new_value != "") {
             if (new_value && old_value != new_value) {
                 if (this.options.onconfirm) {
@@ -143,7 +141,7 @@ var View = Backbone.View.extend({
     },
 
     /** Handles ondblclick events */
-    _ondblclick: function(e) {
+    _ondblclick: function (e) {
         var value = this.value();
         if (value && this.options.ondblclick) {
             this.options.ondblclick(value);
@@ -151,7 +149,7 @@ var View = Backbone.View.extend({
     },
 
     /** Refresh helper */
-    _refresh: function() {
+    _refresh: function () {
         if (this.row_count == 0) {
             this.$tmessage.show();
         } else {
@@ -160,11 +158,11 @@ var View = Backbone.View.extend({
     },
 
     /** Template */
-    _template: function() {
+    _template: function () {
         return `<div><table class="${this.options.cls}"><thead/><tbody/></table><tmessage>${this.options.content}</tmessage><div>`;
-    }
+    },
 });
 
 export default {
-    View: View
+    View: View,
 };
diff --git a/client/galaxy/scripts/mvc/ui/ui-tabs.js b/client/galaxy/scripts/mvc/ui/ui-tabs.js
index c188ca7521c6..431c7db786a9 100644
--- a/client/galaxy/scripts/mvc/ui/ui-tabs.js
+++ b/client/galaxy/scripts/mvc/ui/ui-tabs.js
@@ -5,13 +5,13 @@ import $ from "jquery";
 import Backbone from "backbone";
 
 export var View = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.collection = new Backbone.Collection();
         this.model =
             (options && options.model) ||
             new Backbone.Model({
                 onchange: null,
-                visible: true
+                visible: true,
             }).set(options);
         this.setElement($(this._template()));
         this.$nav = this.$(".tab-navigation");
@@ -28,7 +28,7 @@ export var View = Backbone.View.extend({
         this.listenTo(this.collection, "add remove reset", this.render, this);
     },
 
-    render: function() {
+    render: function () {
         var id = this.model.get("current");
         id = this.$(`#${id}`).length > 0 ? id : this.first();
         if (id) {
@@ -42,12 +42,12 @@ export var View = Backbone.View.extend({
     },
 
     /** Returns tab id for currently shown tab */
-    current: function() {
+    current: function () {
         return this.model.get("current");
     },
 
     /** Show tab view and highlight a tab by id */
-    show: function(id) {
+    show: function (id) {
         if (id) {
             this.model.set({ current: id, visible: true });
             this.model.get("onchange") && this.model.get("onchange")(id);
@@ -55,65 +55,60 @@ export var View = Backbone.View.extend({
     },
 
     /** Hide tab view */
-    hide: function() {
+    hide: function () {
         this.model.set("visible", false);
     },
 
     /** Returns first tab */
-    first: function() {
+    first: function () {
         var model = this.collection.first();
         return model && model.id;
     },
 
     /** Returns current number of tabs */
-    size: function() {
+    size: function () {
         return this.collection.length;
     },
 
     /** Adds a new tab */
-    add: function(options) {
+    add: function (options) {
         this.collection.add(options);
     },
 
     /** Delete tab */
-    del: function(id) {
+    del: function (id) {
         this.collection.remove(id);
     },
 
     /** Delete all tabs */
-    delAll: function() {
+    delAll: function () {
         this.collection.reset();
     },
 
     /** Show tab */
-    showTab: function(id) {
+    showTab: function (id) {
         this.collection.get(id).set("hidden", false);
     },
 
     /** Hide tab */
-    hideTab: function(id) {
+    hideTab: function (id) {
         this.collection.get(id).set("hidden", true);
     },
 
     /** Adds a new tab */
-    _add: function(tab_model) {
+    _add: function (tab_model) {
         var self = this;
         var options = tab_model.attributes;
-        this.$content.append(
-            $("<div/>")
-                .attr("id", options.id)
-                .addClass("tab-pane")
-                .append(options.$el)
-        );
+        this.$content.append($("<div/>").attr("id", options.id).addClass("tab-pane").append(options.$el));
         this.$nav.append(
             $(this._template_tab(options))
                 .show()
                 .tooltip({
                     title: options.tooltip || "",
                     placement: "bottom",
-                    container: self.$el
+                    container: self.$el,
                 })
-                .on("click", e => {
+                .on("click", (e) => {
                     e.preventDefault();
                     self.show(options.id);
                 })
@@ -124,36 +119,32 @@ export var View = Backbone.View.extend({
     },
 
     /** Delete tab */
-    _remove: function(tab_model) {
+    _remove: function (tab_model) {
         this.$(`#tab-${tab_model.id}`).remove();
         this.$(`#${tab_model.id}`).remove();
     },
 
     /** Reset collection */
-    _reset: function() {
+    _reset: function () {
         this.$nav.empty();
         this.$content.empty();
     },
 
     /** Change tab */
-    _change: function(tab_model) {
+    _change: function (tab_model) {
         this.$(`#tab-${tab_model.id}`)[tab_model.get("hidden") ? "hide" : "show"]();
     },
 
     /** Main template */
-    _template: function() {
+    _template: function () {
         return $("<div/>")
             .addClass("tabbable tabs-left")
-            .append(
-                $("<ul/>")
-                    .attr("style", "display: flex")
-                    .addClass("tab-navigation nav nav-tabs")
-            )
+            .append($("<ul/>").attr("style", "display: flex").addClass("tab-navigation nav nav-tabs"))
             .append($("<div/>").addClass("tab-content"));
     },
 
     /** Tab template */
-    _template_tab: function(options) {
+    _template_tab: function (options) {
         var $tmpl = $("<li/>")
             .addClass("nav-item")
             .attr("id", `tab-${options.id}`)
@@ -164,12 +155,7 @@ export var View = Backbone.View.extend({
                     .attr("href", "javascript:void(0);")
             );
         var $href = $tmpl.find("a");
-        options.icon &&
-            $href.append(
-                $("<i/>")
-                    .addClass("fa")
-                    .addClass(options.icon)
-            );
+        options.icon && $href.append($("<i/>").addClass("fa").addClass(options.icon));
         options.title &&
             $href.append(
                 $("<span/>")
@@ -178,7 +164,7 @@ export var View = Backbone.View.extend({
                     .append(options.title)
             );
         return $tmpl;
-    }
+    },
 });
 
 export default { View: View };
diff --git a/client/galaxy/scripts/mvc/upload/collection/collection-row.js b/client/galaxy/scripts/mvc/upload/collection/collection-row.js
index c151906f96c5..2116548b6d13 100644
--- a/client/galaxy/scripts/mvc/upload/collection/collection-row.js
+++ b/client/galaxy/scripts/mvc/upload/collection/collection-row.js
@@ -4,7 +4,7 @@ import _ from "underscore";
 import Utils from "utils/utils";
 import UploadBoxRow from "mvc/upload/uploadbox-row";
 export default UploadBoxRow.extend({
-    initialize: function(app, options) {
+    initialize: function (app, options) {
         var self = this;
         this.app = app;
         this.model = options.model;
@@ -28,10 +28,10 @@ export default UploadBoxRow.extend({
         });
 
         // handle text editing event
-        this.$text_content.on("change input", e => {
+        this.$text_content.on("change input", (e) => {
             self.model.set({
                 url_paste: $(e.target).val(),
-                file_size: $(e.target).val().length
+                file_size: $(e.target).val().length,
             });
         });
 
@@ -45,19 +45,16 @@ export default UploadBoxRow.extend({
         });
     },
 
-    render: function() {
+    render: function () {
         var options = this.model.attributes;
         this.$title.html(_.escape(options.file_name));
         this.$size.html(Utils.bytesToString(options.file_size));
-        this.$mode
-            .removeClass()
-            .addClass("upload-mode")
-            .addClass("text-primary");
+        this.$mode.removeClass().addClass("upload-mode").addClass("text-primary");
         if (options.file_mode == "new") {
             this.$text
                 .css({
                     width: `${this.$el.width() - 16}px`,
-                    top: `${this.$el.height() - 8}px`
+                    top: `${this.$el.height() - 8}px`,
                 })
                 .show();
             this.$el.height(this.$el.height() - 8 + this.$text.height() + 16);
@@ -70,12 +67,9 @@ export default UploadBoxRow.extend({
     },
 
     /** Refresh status */
-    _refreshStatus: function() {
+    _refreshStatus: function () {
         var status = this.model.get("status");
-        this.$symbol
-            .removeClass()
-            .addClass("upload-symbol")
-            .addClass(this.status_classes[status]);
+        this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[status]);
         this.model.set("enabled", status == "init");
         var enabled = this.model.get("enabled");
         this.$text_content.attr("disabled", !enabled);
@@ -83,7 +77,7 @@ export default UploadBoxRow.extend({
     },
 
     /** View template */
-    _template: function(options) {
+    _template: function (options) {
         return `<tr id="upload-row-${options.id}" class="upload-row"><td><div class="upload-text-column"><div class="upload-mode"/><div class="upload-title-extended"/><div class="upload-text"><div class="upload-text-info">Download data from the web by entering URLs (one per line) or directly paste content.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-size"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td><td><div class="upload-symbol ${this.status_classes.init}"/></td></tr>`;
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/upload/composite/composite-row.js b/client/galaxy/scripts/mvc/upload/composite/composite-row.js
index 41f380517df2..64227e7739b1 100644
--- a/client/galaxy/scripts/mvc/upload/composite/composite-row.js
+++ b/client/galaxy/scripts/mvc/upload/composite/composite-row.js
@@ -16,10 +16,10 @@ export default Backbone.View.extend({
         ready: "upload-mode fa fa-check text-success",
         running: "upload-mode fa fa-spinner fa-spin",
         success: "upload-mode fa fa-check",
-        error: "upload-mode fa fa-exclamation-triangle"
+        error: "upload-mode fa fa-exclamation-triangle",
     },
 
-    initialize: function(app, options) {
+    initialize: function (app, options) {
         var self = this;
         this.app = app;
         this.model = options.model;
@@ -39,88 +39,88 @@ export default Backbone.View.extend({
 
         // build upload functions
         this.uploadinput = this.$el.uploadinput({
-            ondragover: function() {
+            ondragover: function () {
                 self.model.get("enabled") && self.$el.addClass("alert-success");
             },
-            ondragleave: function() {
+            ondragleave: function () {
                 self.$el.removeClass("alert-success");
             },
-            onchange: function(files) {
+            onchange: function (files) {
                 if (self.model.get("status") != "running" && files && files.length > 0) {
                     self.model.reset({
                         file_data: files[0],
                         file_name: files[0].name,
                         file_size: files[0].size,
-                        file_mode: files[0].mode || "local"
+                        file_mode: files[0].mode || "local",
                     });
                     self._refreshReady();
                 }
-            }
+            },
         });
 
         // source selection popup
         this.button_menu = new Ui.ButtonMenu({
             icon: "fa-caret-down",
             title: _l("Select"),
-            pull: "left"
+            pull: "left",
         });
         this.$source.append(this.button_menu.$el);
         this.button_menu.addMenu({
             icon: "fa-laptop",
             title: _l("Choose local file"),
-            onclick: function() {
+            onclick: function () {
                 self.uploadinput.dialog();
-            }
+            },
         });
         if (this.app.ftpUploadSite) {
             this.button_menu.addMenu({
                 icon: "fa-folder-open-o",
                 title: _l("Choose FTP file"),
-                onclick: function() {
+                onclick: function () {
                     self._showFtp();
-                }
+                },
             });
         }
         this.button_menu.addMenu({
             icon: "fa-edit",
             title: "Paste/Fetch data",
-            onclick: function() {
+            onclick: function () {
                 self.model.reset({
                     file_mode: "new",
-                    file_name: "New File"
+                    file_name: "New File",
                 });
-            }
+            },
         });
 
         // add ftp file viewer
         this.ftp = new Popover({
             title: "Select a file",
             container: this.$source.find(".dropdown"),
-            placement: "right"
+            placement: "right",
         });
 
         // append popup to settings icon
         this.settings = new Popover({
             title: _l("Upload configuration"),
             container: this.$settings,
-            placement: "bottom"
+            placement: "bottom",
         });
 
         // handle text editing event
-        this.$text_content.on("change input", e => {
+        this.$text_content.on("change input", (e) => {
             self.model.set({
                 url_paste: $(e.target).val(),
-                file_size: $(e.target).val().length
+                file_size: $(e.target).val().length,
             });
             self._refreshReady();
         });
 
         // handle settings popover
         this.$settings
-            .on("click", e => {
+            .on("click", (e) => {
                 self._showSettings();
             })
-            .on("mousedown", e => {
+            .on("mousedown", (e) => {
                 e.preventDefault();
             });
 
@@ -151,7 +151,7 @@ export default Backbone.View.extend({
         });
     },
 
-    render: function() {
+    render: function () {
         this.$el.attr("id", `upload-row-${this.model.id}`);
         this.$file_name.html(_.escape(this.model.get("file_name") || "-"));
         this.$file_desc.html(this.model.get("file_desc") || "Unavailable");
@@ -160,7 +160,7 @@ export default Backbone.View.extend({
     },
 
     /** Remove view */
-    remove: function() {
+    remove: function () {
         // call the base class remove method
         Backbone.View.prototype.remove.apply(this);
     },
@@ -170,21 +170,21 @@ export default Backbone.View.extend({
     //
 
     /** Refresh ready or not states */
-    _refreshReady: function() {
-        this.app.collection.each(model => {
+    _refreshReady: function () {
+        this.app.collection.each((model) => {
             model.set("status", (model.get("file_size") > 0 && "ready") || "init");
         });
     },
 
     /** Refresh mode and e.g. show/hide textarea field */
-    _refreshMode: function() {
+    _refreshMode: function () {
         var file_mode = this.model.get("file_mode");
         if (file_mode == "new") {
             this.height = this.$el.height();
             this.$text
                 .css({
                     width: `${this.$el.width() - 16}px`,
-                    top: `${this.$el.height() - 8}px`
+                    top: `${this.$el.height() - 8}px`,
                 })
                 .show();
             this.$el.height(this.$el.height() - 8 + this.$text.height() + 16);
@@ -196,7 +196,7 @@ export default Backbone.View.extend({
     },
 
     /** Refresh information */
-    _refreshInfo: function() {
+    _refreshInfo: function () {
         var info = this.model.get("info");
         if (info) {
             this.$info_text.html(`<strong>Failed: </strong>${info}`).show();
@@ -206,7 +206,7 @@ export default Backbone.View.extend({
     },
 
     /** Refresh percentage */
-    _refreshPercentage: function() {
+    _refreshPercentage: function () {
         var percentage = parseInt(this.model.get("percentage"));
         if (percentage != 0) {
             this.$progress_bar.css({ width: `${percentage}%` });
@@ -220,7 +220,7 @@ export default Backbone.View.extend({
     },
 
     /** Refresh status */
-    _refreshStatus: function() {
+    _refreshStatus: function () {
         var status = this.model.get("status");
         this.$status.removeClass().addClass(this.status_classes[status]);
         this.model.set("enabled", status != "running");
@@ -247,44 +247,44 @@ export default Backbone.View.extend({
     },
 
     /** File name */
-    _refreshFileName: function() {
+    _refreshFileName: function () {
         this.$file_name.html(this.model.get("file_name") || "-");
     },
 
     /** File size */
-    _refreshFileSize: function() {
+    _refreshFileSize: function () {
         this.$file_size.html(Utils.bytesToString(this.model.get("file_size")));
     },
 
     /** Show/hide ftp popup */
-    _showFtp: function() {
+    _showFtp: function () {
         var self = this;
         this.ftp.show(
             new UploadFtp({
                 ftp_upload_site: this.app.ftpUploadSite,
-                onchange: function(ftp_file) {
+                onchange: function (ftp_file) {
                     self.ftp.hide();
                     if (self.model.get("status") != "running" && ftp_file) {
                         self.model.reset({
                             file_mode: "ftp",
                             file_name: ftp_file.path,
                             file_size: ftp_file.size,
-                            file_path: ftp_file.path
+                            file_path: ftp_file.path,
                         });
                         self._refreshReady();
                     }
-                }
+                },
             }).$el
         );
     },
 
     /** Show/hide settings popup */
-    _showSettings: function() {
+    _showSettings: function () {
         this.settings.show(new UploadSettings(this).$el);
     },
 
     /** Template */
-    _template: function() {
+    _template: function () {
         return `<tr class="upload-row">
                 <td>
                     <div class="upload-source"/>
@@ -320,5 +320,5 @@ export default Backbone.View.extend({
                     </div>
                 </td>
             </tr>`;
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/upload/default/default-row.js b/client/galaxy/scripts/mvc/upload/default/default-row.js
index e5fb350102ee..f0b4f2a3cb3b 100644
--- a/client/galaxy/scripts/mvc/upload/default/default-row.js
+++ b/client/galaxy/scripts/mvc/upload/default/default-row.js
@@ -7,7 +7,7 @@ import UploadExtension from "mvc/upload/upload-extension";
 import UploadBoxRow from "mvc/upload/uploadbox-row";
 import Select from "mvc/ui/ui-select";
 export default UploadBoxRow.extend({
-    initialize: function(app, options) {
+    initialize: function (app, options) {
         var self = this;
         this.app = app;
         this.list_extensions = app.listExtensions;
@@ -37,9 +37,9 @@ export default UploadBoxRow.extend({
             data: self.app.listGenomes,
             container: this.$(".upload-genome"),
             value: default_genome,
-            onchange: function(genome) {
+            onchange: function (genome) {
                 self.model.set("genome", genome);
-            }
+            },
         });
 
         // create select extension
@@ -48,15 +48,15 @@ export default UploadBoxRow.extend({
             data: self.app.extensions,
             container: this.$(".upload-extension"),
             value: default_extension,
-            onchange: function(extension) {
+            onchange: function (extension) {
                 self.model.set("extension", extension);
-            }
+            },
         });
 
         // initialize genome and extension values
         this.model.set({
             genome: default_genome,
-            extension: default_extension
+            extension: default_extension,
         });
 
         // handle click event
@@ -66,7 +66,7 @@ export default UploadBoxRow.extend({
 
         // handle extension info popover
         this.$(".upload-extension-info")
-            .on("click", e => {
+            .on("click", (e) => {
                 const upload_ext = this.upload_extension;
                 if (upload_ext) {
                     if (upload_ext.extension_popup.visible) {
@@ -79,29 +79,29 @@ export default UploadBoxRow.extend({
                     this._makeUploadExtensionsPopover(e);
                 }
             })
-            .on("mousedown", e => {
+            .on("mousedown", (e) => {
                 e.preventDefault();
             });
 
         // handle settings popover
         this.$settings
-            .on("click", e => {
+            .on("click", (e) => {
                 self._showSettings();
             })
-            .on("mousedown", e => {
+            .on("mousedown", (e) => {
                 e.preventDefault();
             });
 
         // handle text editing event
-        this.$text_content.on("change input", e => {
+        this.$text_content.on("change input", (e) => {
             self.model.set({
                 url_paste: $(e.target).val(),
-                file_size: $(e.target).val().length
+                file_size: $(e.target).val().length,
             });
         });
 
         // handle text editing event
-        this.$title.on("change input", e => {
+        this.$title.on("change input", (e) => {
             self.model.set({ file_name: $(e.target).val() });
         });
 
@@ -115,7 +115,7 @@ export default UploadBoxRow.extend({
         });
     },
 
-    render: function() {
+    render: function () {
         this._refreshType();
         this._refreshPercentage();
         this._refreshStatus();
@@ -126,26 +126,23 @@ export default UploadBoxRow.extend({
     },
 
     /** Remove view */
-    remove: function() {
+    remove: function () {
         this.select_genome.remove();
         this.select_extension.remove();
         Backbone.View.prototype.remove.apply(this);
     },
 
     /** Render type */
-    _refreshType: function() {
+    _refreshType: function () {
         var options = this.model.attributes;
         this.$title.val(_.escape(options.file_name));
         this.$size.html(Utils.bytesToString(options.file_size));
-        this.$mode
-            .removeClass()
-            .addClass("upload-mode")
-            .addClass("text-primary");
+        this.$mode.removeClass().addClass("upload-mode").addClass("text-primary");
         if (options.file_mode == "new") {
             this.$text
                 .css({
                     width: `${this.$el.width() - 16}px`,
-                    top: `${this.$el.height() - 8}px`
+                    top: `${this.$el.height() - 8}px`,
                 })
                 .show();
             this.$el.height(this.$el.height() - 8 + this.$text.height() + 16);
@@ -158,22 +155,19 @@ export default UploadBoxRow.extend({
     },
 
     /** Update extension */
-    _refreshExtension: function() {
+    _refreshExtension: function () {
         this.select_extension.value(this.model.get("extension"));
     },
 
     /** Update genome */
-    _refreshGenome: function() {
+    _refreshGenome: function () {
         this.select_genome.value(this.model.get("genome"));
     },
 
     /** Refresh status */
-    _refreshStatus: function() {
+    _refreshStatus: function () {
         var status = this.model.get("status");
-        this.$symbol
-            .removeClass()
-            .addClass("upload-symbol")
-            .addClass(this.status_classes[status]);
+        this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[status]);
         this.model.set("enabled", status == "init");
         var enabled = this.model.get("enabled");
         this.$text_content.attr("disabled", !enabled);
@@ -191,17 +185,17 @@ export default UploadBoxRow.extend({
     },
 
     /** Make extension popover */
-    _makeUploadExtensionsPopover: function(e) {
+    _makeUploadExtensionsPopover: function (e) {
         this.upload_extension = new UploadExtension({
             $el: $(e.target),
             title: this.select_extension.text(),
             extension: this.select_extension.value(),
-            list: this.list_extensions
+            list: this.list_extensions,
         });
     },
 
     /** View template */
-    _template: function(options) {
+    _template: function (options) {
         return `<tr id="upload-row-${options.id}" class="upload-row">
                     <td>
                         <div class="upload-text-column">
@@ -241,5 +235,5 @@ export default UploadBoxRow.extend({
                         <div class="upload-symbol ${this.status_classes.init}"/>
                     </td>
                 </tr>`;
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/upload/upload-extension.js b/client/galaxy/scripts/mvc/upload/upload-extension.js
index 766e1dfd1329..c1ec08298a03 100644
--- a/client/galaxy/scripts/mvc/upload/upload-extension.js
+++ b/client/galaxy/scripts/mvc/upload/upload-extension.js
@@ -3,28 +3,28 @@ import _ from "underscore";
 import Backbone from "backbone";
 import Popover from "mvc/ui/ui-popover";
 export default Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model = new Backbone.Model(options);
         this.setElement("<div/>");
         this.render();
     },
 
-    render: function() {
+    render: function () {
         var options = this.model.attributes;
         var description = _.findWhere(options.list, {
-            id: options.extension
+            id: options.extension,
         });
         this.extension_popup && this.extension_popup.remove();
         this.extension_popup = new Popover({
             title: options.title,
             placement: options.placement || "bottom",
-            container: options.$el
+            container: options.$el,
         });
         this.extension_popup.show(this._templateDescription(description));
     },
 
     /** Template for extensions description */
-    _templateDescription: function(options) {
+    _templateDescription: function (options) {
         if (options.description) {
             var tmpl = options.description;
             if (options.description_url) {
@@ -34,5 +34,5 @@ export default Backbone.View.extend({
         } else {
             return "There is no description available for this file extension.";
         }
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/upload/upload-ftp.js b/client/galaxy/scripts/mvc/upload/upload-ftp.js
index 3ce9c0e1f05a..9efabd8a1fcd 100644
--- a/client/galaxy/scripts/mvc/upload/upload-ftp.js
+++ b/client/galaxy/scripts/mvc/upload/upload-ftp.js
@@ -7,7 +7,7 @@ import Utils from "utils/utils";
 import UploadUtils from "mvc/upload/upload-utils";
 
 export default Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model = new Backbone.Model({
             cls: "upload-ftp",
             class_add: "upload-icon-button fa fa-square-o",
@@ -18,9 +18,9 @@ export default Backbone.View.extend({
             help_text: `This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>${options.ftp_upload_site}</strong> using your Galaxy credentials.
             For help visit the <a href="https://galaxyproject.org/ftp-upload/" target="_blank">tutorial</a>.`,
             collection: null,
-            onchange: function() {},
-            onadd: function() {},
-            onremove: function() {}
+            onchange: function () {},
+            onadd: function () {},
+            onremove: function () {},
         }).set(options);
 
         this.collection = this.model.get("collection");
@@ -40,33 +40,33 @@ export default Backbone.View.extend({
         this.render();
     },
 
-    render: function() {
+    render: function () {
         var self = this;
         this.$wait.show();
         this.$content.hide();
         this.$warning.hide();
         this.$help.hide();
         UploadUtils.getRemoteFiles(
-            function(ftp_files) {
+            function (ftp_files) {
                 self.model.set("ftp_files", ftp_files);
                 self._index();
                 self._renderTable();
             },
-            function() {
+            function () {
                 self._renderTable();
             }
         );
     },
 
     /** Fill table with ftp entries */
-    _renderTable: function() {
+    _renderTable: function () {
         var self = this;
         var ftp_files = this.model.get("ftp_files");
         this.rows = [];
         if (ftp_files && ftp_files.length > 0) {
             this.$body.empty();
             var size = 0;
-            _.each(ftp_files, ftp_file => {
+            _.each(ftp_files, (ftp_file) => {
                 self.rows.push(self._renderRow(ftp_file));
                 size += ftp_file.size;
             });
@@ -91,7 +91,7 @@ export default Backbone.View.extend({
     },
 
     /** Add row */
-    _renderRow: function(ftp_file) {
+    _renderRow: function (ftp_file) {
         var self = this;
         var options = this.model.attributes;
         var $it = $(this._templateRow(ftp_file));
@@ -113,11 +113,11 @@ export default Backbone.View.extend({
     },
 
     /** Create ftp index */
-    _index: function() {
+    _index: function () {
         var self = this;
         this.ftp_index = {};
         this.collection &&
-            this.collection.each(model => {
+            this.collection.each((model) => {
                 if (model.get("file_mode") == "ftp") {
                     self.ftp_index[model.get("file_path")] = model.id;
                 }
@@ -125,7 +125,7 @@ export default Backbone.View.extend({
     },
 
     /** Select all event handler */
-    _all: function() {
+    _all: function () {
         var options = this.model.attributes;
         var ftp_files = this.model.get("ftp_files");
         var add = this.$select.hasClass(options.class_add);
@@ -140,7 +140,7 @@ export default Backbone.View.extend({
     },
 
     /** Handle collection changes */
-    _switch: function($icon, ftp_file) {
+    _switch: function ($icon, ftp_file) {
         $icon.removeClass();
         var options = this.model.attributes;
         var model_index = this.ftp_index[ftp_file.path];
@@ -156,7 +156,7 @@ export default Backbone.View.extend({
     },
 
     /** Refresh select all button state */
-    _refresh: function() {
+    _refresh: function () {
         var counts = _.reduce(
             this.ftp_index,
             (memo, element) => {
@@ -176,7 +176,7 @@ export default Backbone.View.extend({
     },
 
     /** Template of row */
-    _templateRow: function(options) {
+    _templateRow: function (options) {
         return `<tr class="upload-ftp-row">
                     <td class="_has_collection" style="display: none;">
                         <div class="icon"/>
@@ -188,7 +188,7 @@ export default Backbone.View.extend({
     },
 
     /** Template of main view */
-    _template: function() {
+    _template: function () {
         return `<div class="${this.model.get("cls")}">
                     <div class="upload-ftp-wait fa fa-spinner fa-spin"/>
                     <div class="upload-ftp-help">${this.model.get("help_text")}</div>
@@ -216,5 +216,5 @@ export default Backbone.View.extend({
                     </div>
                     <div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>
                 </div>`;
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/upload/upload-model.js b/client/galaxy/scripts/mvc/upload/upload-model.js
index 356670d7d12d..51876ccf91ec 100644
--- a/client/galaxy/scripts/mvc/upload/upload-model.js
+++ b/client/galaxy/scripts/mvc/upload/upload-model.js
@@ -16,13 +16,11 @@ var Model = Backbone.Model.extend({
         percentage: 0,
         space_to_tab: false,
         to_posix_lines: true,
-        enabled: true
+        enabled: true,
+    },
+    reset: function (attr) {
+        this.clear().set(this.defaults).set(attr);
     },
-    reset: function(attr) {
-        this.clear()
-            .set(this.defaults)
-            .set(attr);
-    }
 });
 var Collection = Backbone.Collection.extend({ model: Model });
 export default { Model: Model, Collection: Collection };
diff --git a/client/galaxy/scripts/mvc/upload/upload-settings.js b/client/galaxy/scripts/mvc/upload/upload-settings.js
index 6923b0d98637..b4fc0b1251c6 100644
--- a/client/galaxy/scripts/mvc/upload/upload-settings.js
+++ b/client/galaxy/scripts/mvc/upload/upload-settings.js
@@ -9,34 +9,30 @@ export default Backbone.View.extend({
         parameters: [
             {
                 id: "space_to_tab",
-                title: "Convert spaces to tabs"
+                title: "Convert spaces to tabs",
             },
             {
                 id: "to_posix_lines",
-                title: "Use POSIX standard"
-            }
-        ]
+                title: "Use POSIX standard",
+            },
+        ],
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.model = options.model;
         this.setElement($("<div/>").addClass("upload-settings"));
         this.$el.append($("<div/>").addClass("upload-settings-cover"));
-        this.$el.append(
-            $("<table/>")
-                .addClass("upload-settings-table grid")
-                .append("<tbody/>")
-        );
+        this.$el.append($("<table/>").addClass("upload-settings-table grid").append("<tbody/>"));
         this.$cover = this.$(".upload-settings-cover");
         this.$table = this.$(".upload-settings-table > tbody");
         this.listenTo(this.model, "change", this.render, this);
         this.model.trigger("change");
     },
 
-    render: function() {
+    render: function () {
         var self = this;
         this.$table.empty();
-        _.each(this.options.parameters, parameter => {
+        _.each(this.options.parameters, (parameter) => {
             var $checkbox = $("<div/>")
                 .addClass(`upload-${parameter.id} fa`)
                 .addClass((self.model.get(parameter.id) && self.options.class_check) || self.options.class_uncheck);
@@ -49,5 +45,5 @@ export default Backbone.View.extend({
             self.$table.append($row);
         });
         this.$cover[(this.model.get("enabled") && "hide") || "show"]();
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/upload/upload-utils.js b/client/galaxy/scripts/mvc/upload/upload-utils.js
index 0a2da7282dcd..33e26b1f110f 100644
--- a/client/galaxy/scripts/mvc/upload/upload-utils.js
+++ b/client/galaxy/scripts/mvc/upload/upload-utils.js
@@ -6,7 +6,7 @@ const AUTO_EXTENSION = {
     id: "auto",
     text: "Auto-detect",
     description:
-        "This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be.  You can also upload compressed files, which will automatically be decompressed."
+        "This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be.  You can also upload compressed files, which will automatically be decompressed.",
 };
 const DEFAULT_GENOME = "?";
 const DEFAULT_EXTENSION = "auto";
@@ -15,7 +15,7 @@ function getUploadDatatypes(callback, datatypesDisableAuto, auto) {
     const url = `${getAppRoot()}api/datatypes?extension_only=False`;
     axios
         .get(url)
-        .then(response => {
+        .then((response) => {
             const datatypes = response.data;
             const listExtensions = [];
             for (var key in datatypes) {
@@ -24,7 +24,7 @@ function getUploadDatatypes(callback, datatypesDisableAuto, auto) {
                     text: datatypes[key].extension,
                     description: datatypes[key].description,
                     description_url: datatypes[key].description_url,
-                    composite_files: datatypes[key].composite_files
+                    composite_files: datatypes[key].composite_files,
                 });
             }
             listExtensions.sort((a, b) => {
@@ -37,7 +37,7 @@ function getUploadDatatypes(callback, datatypesDisableAuto, auto) {
             }
             callback(listExtensions);
         })
-        .catch(errorMessage => {
+        .catch((errorMessage) => {
             console.log(errorMessage);
         });
 }
@@ -46,14 +46,14 @@ function getUploadGenomes(callback, defaultGenome) {
     const url = `${getAppRoot()}api/genomes`;
     axios
         .get(url)
-        .then(response => {
+        .then((response) => {
             const genomes = response.data;
             const listGenomes = [];
 
             for (var key in genomes) {
                 listGenomes.push({
                     id: genomes[key][1],
-                    text: genomes[key][0]
+                    text: genomes[key][0],
                 });
             }
             listGenomes.sort((a, b) => {
@@ -67,7 +67,7 @@ function getUploadGenomes(callback, defaultGenome) {
             });
             callback(listGenomes);
         })
-        .catch(errorMessage => {
+        .catch((errorMessage) => {
             console.log(errorMessage);
         });
 }
@@ -77,7 +77,7 @@ function getRemoteFiles(success, error) {
         url: `${getAppRoot()}api/remote_files`,
         method: "GET",
         success: success,
-        error: error
+        error: error,
     });
 }
 
@@ -87,5 +87,5 @@ export default {
     DEFAULT_EXTENSION,
     getRemoteFiles,
     getUploadDatatypes,
-    getUploadGenomes
+    getUploadGenomes,
 };
diff --git a/client/galaxy/scripts/mvc/upload/uploadbox-row.js b/client/galaxy/scripts/mvc/upload/uploadbox-row.js
index 4f2dc1568bd3..abacc06493c6 100644
--- a/client/galaxy/scripts/mvc/upload/uploadbox-row.js
+++ b/client/galaxy/scripts/mvc/upload/uploadbox-row.js
@@ -13,19 +13,19 @@ export default Backbone.View.extend({
         queued: "upload-icon fa fa-spinner fa-spin",
         running: "upload-icon fa fa-spinner fa-spin",
         success: "upload-icon-button fa fa-check",
-        error: "upload-icon-button fa fa-exclamation-triangle"
+        error: "upload-icon-button fa fa-exclamation-triangle",
     },
 
-    _setupSettings: function() {
+    _setupSettings: function () {
         // append popup to settings icon
         this.settings = new Popover({
             title: _l("Upload configuration"),
             container: this.$(".upload-settings"),
-            placement: "bottom"
+            placement: "bottom",
         });
     },
 
-    _renderStatusType: function(status) {
+    _renderStatusType: function (status) {
         if (status == "success") {
             this.$el.addClass("table-success");
             this.$percentage.html("100%");
@@ -38,7 +38,7 @@ export default Backbone.View.extend({
         }
     },
 
-    _setupUploadBoxListeners: function() {
+    _setupUploadBoxListeners: function () {
         this.listenTo(this.model, "change:percentage", () => {
             this._refreshPercentage();
         });
@@ -53,7 +53,7 @@ export default Backbone.View.extend({
         });
     },
 
-    _refreshInfo: function() {
+    _refreshInfo: function () {
         var info = this.model.get("info");
         if (info) {
             this.$info_text.html(`<strong>Warning: </strong>${info}`).show();
@@ -62,23 +62,23 @@ export default Backbone.View.extend({
         }
     },
 
-    _refreshPercentage: function() {
+    _refreshPercentage: function () {
         var percentage = parseInt(this.model.get("percentage"));
         this.$progress_bar.css({ width: `${percentage}%` });
         this.$percentage.html(percentage != 100 ? `${percentage}%` : "Adding to history...");
     },
 
-    _refreshFileSize: function() {
+    _refreshFileSize: function () {
         this.$size.html(Utils.bytesToString(this.model.get("file_size")));
     },
 
-    _removeRow: function() {
+    _removeRow: function () {
         if (["init", "success", "error"].indexOf(this.model.get("status")) !== -1) {
             this.app.collection.remove(this.model);
         }
     },
 
-    _showSettings: function() {
+    _showSettings: function () {
         this.settings.show(new UploadSettings(this).$el);
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/user/tab-updates.js b/client/galaxy/scripts/mvc/user/tab-updates.js
index 5b32f63d7eab..d1e269f334db 100644
--- a/client/galaxy/scripts/mvc/user/tab-updates.js
+++ b/client/galaxy/scripts/mvc/user/tab-updates.js
@@ -47,5 +47,5 @@ export default {
     change_favicon: change_favicon,
     hidden_permit: hidden_permit,
     is_hidden: is_hidden,
-    hidden_count: hidden_count
+    hidden_count: hidden_count,
 };
diff --git a/client/galaxy/scripts/mvc/user/user-model.js b/client/galaxy/scripts/mvc/user/user-model.js
index afea7d350dca..3ae4aec5ced0 100644
--- a/client/galaxy/scripts/mvc/user/user-model.js
+++ b/client/galaxy/scripts/mvc/user/user-model.js
@@ -13,7 +13,7 @@ var User = Backbone.Model.extend(baseMVC.LoggableMixin).extend(
         _logNamespace: logNamespace,
 
         /** API location for this resource */
-        urlRoot: function() {
+        urlRoot: function () {
             return `${getAppRoot()}api/users`;
         },
 
@@ -29,49 +29,49 @@ var User = Backbone.Model.extend(baseMVC.LoggableMixin).extend(
             nice_total_disk_usage: "",
             quota_percent: null,
             is_admin: false,
-            preferences: {}
+            preferences: {},
         },
 
         /** Set up and bind events
          *  @param {Object} data Initial model data.
          */
-        initialize: function(data) {
+        initialize: function (data) {
             this.log("User.initialize:", data);
 
-            this.on("loaded", function(model, resp) {
+            this.on("loaded", function (model, resp) {
                 this.log(`${this} has loaded:`, model, resp);
             });
-            this.on("change", function(model, data) {
+            this.on("change", function (model, data) {
                 this.log(`${this} has changed:`, model, data.changes);
             });
         },
 
-        isAnonymous: function() {
+        isAnonymous: function () {
             return !this.get("email");
         },
 
-        isAdmin: function() {
+        isAdmin: function () {
             return this.get("is_admin");
         },
 
-        updatePreferences: function(name, new_value) {
+        updatePreferences: function (name, new_value) {
             const preferences = this.get("preferences");
             preferences[name] = JSON.stringify(new_value);
             this.preferences = preferences;
         },
 
-        getFavorites: function() {
+        getFavorites: function () {
             const preferences = this.get("preferences");
             if (preferences && preferences.favorites) {
                 return JSON.parse(preferences.favorites);
             } else {
                 return {
-                    tools: []
+                    tools: [],
                 };
             }
         },
 
-        updateFavorites: function(object_type, new_favorites) {
+        updateFavorites: function (object_type, new_favorites) {
             const favorites = this.getFavorites();
             favorites[object_type] = new_favorites[object_type];
             this.updatePreferences("favorites", favorites);
@@ -84,7 +84,7 @@ var User = Backbone.Model.extend(baseMVC.LoggableMixin).extend(
          *  @param {Object} options hash to pass to Backbone.Model.fetch. Can contain success, error fns.
          *  @fires loaded when the model has been loaded from the API, passing the newModel and AJAX response.
          */
-        loadFromApi: function(idOrCurrent, options) {
+        loadFromApi: function (idOrCurrent, options) {
             idOrCurrent = idOrCurrent || User.CURRENT_ID_STR;
 
             options = options || {};
@@ -108,7 +108,7 @@ var User = Backbone.Model.extend(baseMVC.LoggableMixin).extend(
 
         /** Clears all data from the sessionStorage.
          */
-        clearSessionStorage: function() {
+        clearSessionStorage: function () {
             for (var key in sessionStorage) {
                 //TODO: store these under the user key so we don't have to do this
                 // currently only history
@@ -121,14 +121,14 @@ var User = Backbone.Model.extend(baseMVC.LoggableMixin).extend(
         },
 
         /** string representation */
-        toString: function() {
+        toString: function () {
             var userInfo = [this.get("username")];
             if (this.get("id")) {
                 userInfo.unshift(this.get("id"));
                 userInfo.push(this.get("email"));
             }
             return `User(${userInfo.join(":")})`;
-        }
+        },
     }
 );
 
@@ -136,7 +136,7 @@ var User = Backbone.Model.extend(baseMVC.LoggableMixin).extend(
 User.CURRENT_ID_STR = "current";
 
 // class method to load the current user via the api and return that model
-User.getCurrentUserFromApi = options => {
+User.getCurrentUserFromApi = (options) => {
     var currentUser = new User();
     currentUser.loadFromApi(User.CURRENT_ID_STR, options);
     return currentUser;
@@ -153,5 +153,5 @@ User.getCurrentUserFromApi = options => {
 
 //==============================================================================
 export default {
-    User: User
+    User: User,
 };
diff --git a/client/galaxy/scripts/mvc/user/user-quotameter.js b/client/galaxy/scripts/mvc/user/user-quotameter.js
index a0c0b47803e5..fb42aa71293e 100644
--- a/client/galaxy/scripts/mvc/user/user-quotameter.js
+++ b/client/galaxy/scripts/mvc/user/user-quotameter.js
@@ -19,11 +19,11 @@ var UserQuotaMeter = Backbone.View.extend(baseMVC.LoggableMixin).extend(
         /** Defaults for optional settings passed to initialize */
         options: {
             warnAtPercent: 85,
-            errorAtPercent: 100
+            errorAtPercent: 100,
         },
 
         /** Set up, accept options, and bind events */
-        initialize: function(options) {
+        initialize: function (options) {
             this.log(`${this}.initialize:`, options);
             _.extend(this.options, options);
 
@@ -32,7 +32,7 @@ var UserQuotaMeter = Backbone.View.extend(baseMVC.LoggableMixin).extend(
         },
 
         /** Re-load user model data from the api */
-        update: function(options) {
+        update: function (options) {
             this.log(`${this} updating user data...`, options);
             this.model.loadFromApi(this.model.get("id"), options);
             return this;
@@ -41,7 +41,7 @@ var UserQuotaMeter = Backbone.View.extend(baseMVC.LoggableMixin).extend(
         /** Is the user over their quota (if there is one)?
          * @returns {Boolean} true if over quota, false if no quota or under quota
          */
-        isOverQuota: function() {
+        isOverQuota: function () {
             return (
                 this.model.get("quota_percent") !== null &&
                 this.model.get("quota_percent") >= this.options.errorAtPercent
@@ -56,7 +56,7 @@ var UserQuotaMeter = Backbone.View.extend(baseMVC.LoggableMixin).extend(
          *  @fires quota:under:ok when user is below this.warnAtPercent
          *  @returns {jQuery} the rendered meter
          */
-        _render_quota: function() {
+        _render_quota: function () {
             var modelJson = this.model.toJSON();
 
             var //prevPercent = this.model.previous( 'quota_percent' ),
@@ -96,7 +96,7 @@ var UserQuotaMeter = Backbone.View.extend(baseMVC.LoggableMixin).extend(
          *      showing the human readable sum storage their data is using.
          *  @returns {jQuery} the rendered text
          */
-        _render_usage: function() {
+        _render_usage: function () {
             //var usage = $( UserQuotaMeter.templates.usage( this.model.toJSON() ) );
             var usage = $(this._templateUsage(this.model.toJSON()));
             this.log(`${this}.rendering usage:`, usage);
@@ -107,7 +107,7 @@ var UserQuotaMeter = Backbone.View.extend(baseMVC.LoggableMixin).extend(
          *      depending on whether the user model has quota info (quota_percent === null -> no quota)
          *  @returns {Object} this UserQuotaMeter
          */
-        render: function() {
+        render: function () {
             //this.log( this + '.rendering' );
             var meterHtml = null;
 
@@ -128,7 +128,7 @@ var UserQuotaMeter = Backbone.View.extend(baseMVC.LoggableMixin).extend(
             return this;
         },
 
-        _templateQuotaMeter: function(data) {
+        _templateQuotaMeter: function (data) {
             return [
                 '<div id="quota-meter" class="quota-meter progress">',
                 '<div class="progress-bar" style="width: ',
@@ -143,27 +143,27 @@ var UserQuotaMeter = Backbone.View.extend(baseMVC.LoggableMixin).extend(
                 "%",
                 "</a>",
                 "</div>",
-                "</div>"
+                "</div>",
             ].join("");
         },
 
-        _templateUsage: function(data) {
+        _templateUsage: function (data) {
             return [
                 '<div id="quota-meter" class="quota-meter" style="background-color: transparent">',
                 '<div class="quota-meter-text" data-placement="left" data-original-title="This value is recalculated when you log out." style="top: 6px; color: white">',
                 data.nice_total_disk_usage ? _l("Using ") + data.nice_total_disk_usage : "",
                 "</div>",
-                "</div>"
+                "</div>",
             ].join("");
         },
 
-        toString: function() {
+        toString: function () {
             return `UserQuotaMeter(${this.model})`;
-        }
+        },
     }
 );
 
 //==============================================================================
 export default {
-    UserQuotaMeter: UserQuotaMeter
+    UserQuotaMeter: UserQuotaMeter,
 };
diff --git a/client/galaxy/scripts/mvc/visualization/chart/chart-client.js b/client/galaxy/scripts/mvc/visualization/chart/chart-client.js
index 47d6a4d7158b..c13d88da4907 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/chart-client.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/chart-client.js
@@ -11,7 +11,7 @@ import Viewer from "mvc/visualization/chart/views/viewer";
 import Menu from "mvc/visualization/chart/views/menu";
 
 export default Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         const Galaxy = getGalaxyInstance();
         this.modal = Galaxy && Galaxy.modal ? Galaxy.modal : new Modal.View();
         this.setElement(
@@ -37,16 +37,16 @@ export default Backbone.View.extend({
         this.$right.append(this.message.$el).append(this.editor.$el);
         this.$buttons.append(this.menu.$el);
         $.ajax({
-            url: `${getAppRoot()}api/datasets/${options.dataset_id}`
+            url: `${getAppRoot()}api/datasets/${options.dataset_id}`,
         })
-            .done(dataset => {
+            .done((dataset) => {
                 this.dataset = dataset;
                 this.chart.load();
                 this.chart.trigger("redraw");
             })
-            .fail(response => {
+            .fail((response) => {
                 const message = response.responseJSON && response.responseJSON.err_msg;
                 this.errormessage = message || "Import failed for unkown reason.";
             });
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/visualization/chart/components/model.js b/client/galaxy/scripts/mvc/visualization/chart/components/model.js
index 43e7e1269208..e838980da48b 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/components/model.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/components/model.js
@@ -10,10 +10,10 @@ export default Backbone.Model.extend({
         state_info: "",
         modified: true,
         dataset_id: "",
-        dataset_id_job: null
+        dataset_id_job: null,
     },
 
-    initialize: function(options, viz_options) {
+    initialize: function (options, viz_options) {
         this.groups = new Backbone.Collection();
         this.settings = new Backbone.Model();
         this.visualization_id = viz_options.visualization_id;
@@ -24,37 +24,37 @@ export default Backbone.Model.extend({
         console.debug(viz_options);
     },
 
-    reset: function() {
+    reset: function () {
         this.clear().set({
             title: "New Chart",
-            dataset_id: this.dataset_id
+            dataset_id: this.dataset_id,
         });
         this.settings.clear();
         this.groups.reset();
         this.groups.add({ id: Utils.uid() });
     },
 
-    state: function(value, info) {
+    state: function (value, info) {
         this.set({ state: value, state_info: info });
         this.trigger("set:state");
         console.debug("model::state() - " + info + " (" + value + ")");
     },
 
     /** Create chart dictionary */
-    serialize: function() {
+    serialize: function () {
         var d = {
             attributes: this.attributes,
             settings: this.settings.attributes,
-            groups: []
+            groups: [],
         };
-        this.groups.each(function(group) {
+        this.groups.each(function (group) {
             d.groups.push(group.attributes);
         });
         return d;
     },
 
     /** Pack and save nested chart model */
-    save: function(options) {
+    save: function (options) {
         var self = this;
         options = options || {};
         this.chart_dict = this.serialize();
@@ -64,11 +64,11 @@ export default Backbone.Model.extend({
             title: this.get("title") || "",
             config: {
                 dataset_id: this.dataset_id,
-                chart_dict: this.chart_dict
-            }
+                chart_dict: this.chart_dict,
+            },
         });
         viz.save()
-            .then(function(response) {
+            .then(function (response) {
                 if (response && response.id) {
                     self.visualization_id = response.id;
                     if (options.success) {
@@ -82,7 +82,7 @@ export default Backbone.Model.extend({
                     console.debug("model::save() - Unrecognized response. Saving may have failed.");
                 }
             })
-            .fail(function(response) {
+            .fail(function (response) {
                 if (options.error) {
                     options.error();
                 }
@@ -92,7 +92,7 @@ export default Backbone.Model.extend({
     },
 
     /** Load nested models/collections from packed dictionary */
-    load: function(chart_parsed) {
+    load: function (chart_parsed) {
         var d = chart_parsed || this.chart_dict;
         if (d) {
             console.debug("model::load() - Attempting to load with configuration:");
@@ -115,5 +115,5 @@ export default Backbone.Model.extend({
             console.debug("model::load() - Visualization attributes unavailable.");
             return false;
         }
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js b/client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js
index 78547e418306..506982d1f0b7 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js
@@ -37,7 +37,7 @@ function _toImage($el, x_offset, y_offset, newContext) {
         parseInt($el.css("borderTopWidth"), 10) +
         parseInt($el.css("paddingTop"), 10);
     if (tagname == "div" || tagname == "span") {
-        $el.children().each(function() {
+        $el.children().each(function () {
             _toImage($(this), left, top);
         });
     } else if (tagname == "canvas") {
@@ -61,7 +61,7 @@ function _canvas2png(options) {
             newContext.translate(0, 0);
             newContext.textAlign = "left";
             newContext.textBaseline = "top";
-            $canvas.children().each(function() {
+            $canvas.children().each(function () {
                 _toImage($(this), 0, 0, newContext);
             });
             const imgData = newCanvas.toDataURL("image/png");
@@ -89,7 +89,7 @@ function _svg2png(options) {
     canvas.width = xml.width * scale;
     canvas.height = xml.height * scale;
     source.src = "data:image/svg+xml;base64," + window.btoa(xml.string);
-    source.onload = function() {
+    source.onload = function () {
         context.drawImage(source, 0, 0, canvas.width, canvas.height);
         const imageData = canvas.toDataURL("image/png");
         _downloadPNGData(imageData, options.title);
@@ -113,7 +113,7 @@ function createPDF(options) {
         height: xml.height,
         width: xml.width,
         scale: 2,
-        svg: xml.string
+        svg: xml.string,
     };
     var $el = $("body");
     var form = $el.find("#viewer-form");
@@ -122,7 +122,7 @@ function createPDF(options) {
             id: "viewer-form",
             method: "post",
             action: "http://export.highcharts.com/",
-            display: "none"
+            display: "none",
         });
         $el.append(form);
     }
@@ -131,7 +131,7 @@ function createPDF(options) {
         var input = $("<input/>", {
             type: "hidden",
             name: name,
-            value: data[name]
+            value: data[name],
         });
         form.append(input);
     }
@@ -159,10 +159,10 @@ function toXML(options) {
         version: "1.1",
         xmlns: "http://www.w3.org/2000/svg",
         width: width * nsvgs,
-        height: height
+        height: height,
     });
     var offsetX = 0;
-    $svg.each(function() {
+    $svg.each(function () {
         var $svg = $(this).clone();
         _inline($svg);
         var $g = $('<g transform="translate(' + offsetX + ', 0)">').attr("xmlns", "http://www.w3.org/2000/svg");
@@ -173,7 +173,7 @@ function toXML(options) {
     return {
         string: serializer.serializeToString($composite[0]),
         height: height,
-        width: width
+        width: width,
     };
 }
 
@@ -185,7 +185,7 @@ function _inline($target) {
         if (rules) {
             for (var idx = 0, len = rules.length; idx < len; idx++) {
                 try {
-                    $target.find(rules[idx].selectorText).each(function(i, elem) {
+                    $target.find(rules[idx].selectorText).each(function (i, elem) {
                         elem.style.cssText += rules[idx].style.cssText;
                     });
                 } catch (err) {
@@ -199,5 +199,5 @@ function _inline($target) {
 export default {
     createPNG: createPNG,
     createSVG: createSVG,
-    createPDF: createPDF
+    createPDF: createPDF,
 };
diff --git a/client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js b/client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
index 6c61f1b7a979..08a96b247105 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
@@ -4,7 +4,7 @@ import { getAppRoot } from "onload/loadConfig";
 import Utils from "utils/utils";
 
 /** Assists in assigning the viewport panels */
-var requestPanels = function(options) {
+var requestPanels = function (options) {
     var process = options.process;
     var chart = options.chart;
     var render = options.render;
@@ -15,7 +15,7 @@ var requestPanels = function(options) {
         chart: chart,
         dataset_id: dataset_id,
         dataset_groups: dataset_groups,
-        success: function(result) {
+        success: function (result) {
             try {
                 if (targets.length == result.length) {
                     var valid = true;
@@ -42,19 +42,19 @@ var requestPanels = function(options) {
                 chart.state("failed", err);
                 process.reject();
             }
-        }
+        },
     });
 };
 
 /** Fills request dictionary with data from cache/response */
 var _cache = {};
-var request = function(options) {
+var request = function (options) {
     var groups = options.dataset_groups;
     var dataset_id = options.dataset_id;
     // identify columns needed to fulfill request
     var column_list = [];
-    groups.each(function(group) {
-        _.each(group.get("__data_columns"), function(column_def, column_name) {
+    groups.each(function (group) {
+        _.each(group.get("__data_columns"), function (column_def, column_name) {
             var column = group.get(column_name);
             var block_id = _block_id(dataset_id, column);
             if (
@@ -78,9 +78,9 @@ var request = function(options) {
         data: {
             data_type: "raw_data",
             provider: "dataset-column",
-            indeces: column_list.toString()
+            indeces: column_list.toString(),
         },
-        success: function(response) {
+        success: function (response) {
             var column_length = column_list.length;
             var results = new Array(column_length);
             for (let i = 0; i < results.length; i++) {
@@ -102,18 +102,18 @@ var request = function(options) {
                 _cache[block_id] = results[i];
             }
             _fillFromCache(options);
-        }
+        },
     });
 };
 
 /** Fill data from cache */
-var _fillFromCache = function(options) {
+var _fillFromCache = function (options) {
     var groups = options.dataset_groups;
     var dataset_id = options.dataset_id;
     console.debug("tabular-datasets::_fillFromCache() - Filling request from cache.");
     var limit = 0;
-    groups.each(function(group) {
-        _.each(group.get("__data_columns"), function(column_def, column_name) {
+    groups.each(function (group) {
+        _.each(group.get("__data_columns"), function (column_def, column_name) {
             var column = group.get(column_name);
             var block_id = _block_id(dataset_id, column);
             var column_data = _cache[block_id];
@@ -129,16 +129,16 @@ var _fillFromCache = function(options) {
         }
     }
     var results = [];
-    groups.each(function(group, group_index) {
+    groups.each(function (group, group_index) {
         var dict = Utils.merge({ key: group_index + ":" + group.get("key"), values: [] }, group.attributes);
         for (let j = 0; j < limit; j++) {
             dict.values[j] = { x: parseInt(j) };
         }
         results.push(dict);
     });
-    groups.each(function(group, group_index) {
+    groups.each(function (group, group_index) {
         var values = results[group_index].values;
-        _.each(group.get("__data_columns"), function(column_def, column_name) {
+        _.each(group.get("__data_columns"), function (column_def, column_name) {
             var column = group.get(column_name);
             switch (column) {
                 case "auto":
@@ -169,7 +169,7 @@ var _fillFromCache = function(options) {
 };
 
 /** Get block id */
-var _block_id = function(dataset_id, column) {
+var _block_id = function (dataset_id, column) {
     return dataset_id + "_" + "_" + column;
 };
 
diff --git a/client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js b/client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
index f2ba42f2324a..3b9dce7aaf34 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
@@ -8,7 +8,7 @@ import { getGalaxyInstance } from "app";
 const WAITTIME = 1000;
 
 /** build job dictionary */
-var requestCharts = function(chart, module) {
+var requestCharts = function (chart, module) {
     var settings_string = "";
     var columns_string = "";
     var group_index = 0;
@@ -18,18 +18,18 @@ var requestCharts = function(chart, module) {
             [
                 [" ", "&#32;"],
                 [",", "&#44;"],
-                [":", "&#58;"]
+                [":", "&#58;"],
             ],
-            function(pair) {
+            function (pair) {
                 settings_value = settings_value.replace(new RegExp(pair[0], "g"), pair[1]);
             }
         );
         settings_string += key + ":" + settings_value + ", ";
     }
     settings_string = settings_string.substring(0, settings_string.length - 2);
-    chart.groups.each(function(group) {
+    chart.groups.each(function (group) {
         group_index++;
-        _.each(group.get("__data_columns"), function(data_columns, name) {
+        _.each(group.get("__data_columns"), function (data_columns, name) {
             columns_string += name + "_" + group_index + ":" + (parseInt(group.get(name)) + 1) + ", ";
         });
     });
@@ -39,17 +39,17 @@ var requestCharts = function(chart, module) {
         inputs: {
             input: {
                 id: chart.get("dataset_id"),
-                src: "hda"
+                src: "hda",
             },
             module: module,
             columns: columns_string,
-            settings: settings_string
-        }
+            settings: settings_string,
+        },
     };
 };
 
 /** Submit job request to charts tool */
-var request = function(chart, parameters, success, error) {
+var request = function (chart, parameters, success, error) {
     chart.state("wait", "Requesting job results...");
     if (chart.get("modified") && chart.get("dataset_id_job")) {
         Utils.request({
@@ -58,7 +58,7 @@ var request = function(chart, parameters, success, error) {
             data: { deleted: true },
             success: () => {
                 refreshHdas();
-            }
+            },
         });
         chart.set("dataset_id_job", null);
         chart.set("modified", false);
@@ -71,7 +71,7 @@ var request = function(chart, parameters, success, error) {
             type: "POST",
             url: getAppRoot() + "api/tools",
             data: parameters,
-            success: function(response) {
+            success: function (response) {
                 if (!response.outputs || response.outputs.length === 0) {
                     chart.state("failed", "Job submission failed. No response.");
                     if (error) {
@@ -89,7 +89,7 @@ var request = function(chart, parameters, success, error) {
                     wait(chart, success, error);
                 }
             },
-            error: function(response) {
+            error: function (response) {
                 var message = "";
                 if (response && response.message && response.message.data && response.message.data.input) {
                     message = response.message.data.input + ".";
@@ -104,18 +104,18 @@ var request = function(chart, parameters, success, error) {
                 if (error) {
                     error();
                 }
-            }
+            },
         });
     }
 };
 
 /** Request job details */
-var wait = function(chart, success, error) {
+var wait = function (chart, success, error) {
     Utils.request({
         type: "GET",
         url: getAppRoot() + "api/datasets/" + chart.get("dataset_id_job"),
         data: {},
-        success: function(dataset) {
+        success: function (dataset) {
             var ready = false;
             switch (dataset.state) {
                 case "ok":
@@ -139,16 +139,16 @@ var wait = function(chart, success, error) {
                     );
             }
             if (!ready) {
-                window.setTimeout(function() {
+                window.setTimeout(function () {
                     wait(chart, success, error);
                 }, WAITTIME);
             }
-        }
+        },
     });
 };
 
 /** Refresh history panel */
-var refreshHdas = function() {
+var refreshHdas = function () {
     const Galaxy = getGalaxyInstance();
     if (Galaxy && Galaxy.currHistoryPanel) {
         Galaxy.currHistoryPanel.refreshContents();
diff --git a/client/galaxy/scripts/mvc/visualization/chart/utilities/series.js b/client/galaxy/scripts/mvc/visualization/chart/utilities/series.js
index 1f335089f25b..bd505ba8c6ae 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/utilities/series.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/utilities/series.js
@@ -6,7 +6,7 @@ function getDomains(groups, keys) {
     function _apply(operator, key) {
         let value;
         for (const group_index in groups) {
-            const value_sub = d3[operator](groups[group_index].values, function(d) {
+            const value_sub = d3[operator](groups[group_index].values, function (d) {
                 return d[key];
             });
             value = value === undefined ? value_sub : Math[operator](value, value_sub);
@@ -18,7 +18,7 @@ function getDomains(groups, keys) {
         var key = keys[index];
         result[key] = {
             min: _apply("min", key),
-            max: _apply("max", key)
+            max: _apply("max", key),
         };
     }
     return result;
@@ -53,13 +53,13 @@ function makeSeries(groups, keys) {
 function makeCategories(groups, column_keys) {
     var array = {};
     var data_columns = groups[0].__data_columns;
-    _.each(column_keys, function(key) {
+    _.each(column_keys, function (key) {
         if (data_columns[key].is_label) {
             array[key] = [];
         }
     });
     if (groups && groups[0]) {
-        _.each(groups[0].values, function(value_dict) {
+        _.each(groups[0].values, function (value_dict) {
             for (var key in array) {
                 array[key].push(String(value_dict[key]));
             }
@@ -71,8 +71,8 @@ function makeCategories(groups, column_keys) {
 
 /** Apply default mapping index all values contained in label columns (for all groups) */
 function mapCategories(array, groups) {
-    _.each(groups, function(group) {
-        _.each(group.values, function(value_dict, i) {
+    _.each(groups, function (group) {
+        _.each(group.values, function (value_dict, i) {
             for (var key in array) {
                 value_dict[key] = parseInt(i);
             }
@@ -86,7 +86,7 @@ function makeUniqueCategories(groups, with_index) {
     var array = {};
     var counter = {};
     var data_columns = groups[0].__data_columns;
-    _.each(data_columns, function(column_def, key) {
+    _.each(data_columns, function (column_def, key) {
         if (column_def.is_label) {
             categories[key] = {};
             array[key] = [];
@@ -122,7 +122,7 @@ function makeUniqueCategories(groups, with_index) {
     return {
         categories: categories,
         array: array,
-        counter: counter
+        counter: counter,
     };
 }
 
@@ -133,17 +133,17 @@ function makeTickFormat(options) {
     var categories = options.categories;
     var formatter = options.formatter;
     if (type == "hide") {
-        formatter(function() {
+        formatter(function () {
             return "";
         });
     } else if (type == "auto") {
         if (categories) {
-            formatter(function(value) {
+            formatter(function (value) {
                 return categories[value] || "";
             });
         }
     } else {
-        var d3format = function(d) {
+        var d3format = function (d) {
             switch (type) {
                 case "s":
                     var prefix = d3.formatPrefix(d);
@@ -153,7 +153,7 @@ function makeTickFormat(options) {
             }
         };
         if (categories) {
-            formatter(function(value) {
+            formatter(function (value) {
                 var label = categories[value];
                 if (label) {
                     if (isNaN(label)) {
@@ -170,7 +170,7 @@ function makeTickFormat(options) {
                 }
             });
         } else {
-            formatter(function(value) {
+            formatter(function (value) {
                 return d3format(value);
             });
         }
@@ -210,11 +210,7 @@ function addZoom(options) {
         d3zoom.scale(1);
         d3zoom.translate([0, 0]);
     }
-    d3zoom
-        .x(xScale)
-        .y(yScale)
-        .scaleExtent([1, scaleExtent])
-        .on("zoom", zoomed);
+    d3zoom.x(xScale).y(yScale).scaleExtent([1, scaleExtent]).on("zoom", zoomed);
     svg.call(d3zoom).on("dblclick.zoom", unzoomed);
     return d3zoom;
 }
@@ -226,5 +222,5 @@ export default {
     getDomains: getDomains,
     mapCategories: mapCategories,
     makeTickFormat: makeTickFormat,
-    addZoom: addZoom
+    addZoom: addZoom,
 };
diff --git a/client/galaxy/scripts/mvc/visualization/chart/views/description.js b/client/galaxy/scripts/mvc/visualization/chart/views/description.js
index 6362a6cd18e6..d3472203f3e2 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/views/description.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/views/description.js
@@ -5,7 +5,7 @@ import { getAppRoot } from "onload/loadConfig";
 import Utils from "utils/utils";
 
 export default Backbone.View.extend({
-    initialize: function(app) {
+    initialize: function (app) {
         this.plugin = app.chart.plugin;
         this.setElement(this._template());
         this.$title = this.$(".charts-description-title");
@@ -13,7 +13,7 @@ export default Backbone.View.extend({
         this.$text = this.$(".charts-description-text");
         this.render();
     },
-    render: function() {
+    render: function () {
         if (this.plugin.logo) {
             this.$image.attr("src", getAppRoot() + this.plugin.logo);
             this.$title.html(this.plugin.html || "Unavailable");
@@ -23,7 +23,7 @@ export default Backbone.View.extend({
             this.$el.hide();
         }
     },
-    _template: function() {
+    _template: function () {
         return `<div class="charts-description">
                     <table>
                     <tr>
@@ -37,5 +37,5 @@ export default Backbone.View.extend({
                     </table>
                     <div class="charts-description-text"/>
                 </div>`;
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/visualization/chart/views/editor.js b/client/galaxy/scripts/mvc/visualization/chart/views/editor.js
index 4fac5d23ade1..876cae19b5dc 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/views/editor.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/views/editor.js
@@ -11,14 +11,14 @@ import Settings from "mvc/visualization/chart/views/settings";
 import Description from "mvc/visualization/chart/views/description";
 
 export default Backbone.View.extend({
-    initialize: function(app, options) {
+    initialize: function (app, options) {
         this.app = app;
         this.chart = this.app.chart;
         this.description = new Description(this.app);
         this.title = new Ui.Input({
             onchange: () => {
                 this.chart.set("title", this.title.value());
-            }
+            },
         });
         this.tabs = new Tabs.View({});
         this.tabs.add({
@@ -33,14 +33,14 @@ export default Backbone.View.extend({
                         .addClass("form-text text-muted")
                         .html("This title will appear in the list of 'Saved Visualizations'.")
                 )
-                .append(new Settings(this.app).$el)
+                .append(new Settings(this.app).$el),
         });
         if (this.chart.plugin.groups) {
             this.tabs.add({
                 id: "groups",
                 icon: "fa-database",
                 tooltip: "Select data.",
-                $el: new Groups(this.app).$el
+                $el: new Groups(this.app).$el,
             });
         }
         this.setElement("<div class='charts-editor'/>");
@@ -49,5 +49,5 @@ export default Backbone.View.extend({
         this.listenTo(this.chart, "load", () => {
             this.title.value(this.chart.get("title"));
         });
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/visualization/chart/views/groups.js b/client/galaxy/scripts/mvc/visualization/chart/views/groups.js
index 0d4c6f31d014..18651df6096b 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/views/groups.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/views/groups.js
@@ -10,30 +10,30 @@ import Repeat from "mvc/form/form-repeat";
 import FormData from "mvc/form/form-data";
 
 var GroupView = Backbone.View.extend({
-    initialize: function(app, options) {
+    initialize: function (app, options) {
         var self = this;
         this.deferred = app.deferred;
         this.chart = app.chart;
         this.group = options.group;
         this.setElement($("<div/>"));
-        this.listenTo(this.chart, "change:dataset_id", function() {
+        this.listenTo(this.chart, "change:dataset_id", function () {
             self.render();
         });
         this.render();
     },
-    render: function() {
+    render: function () {
         var self = this;
         var inputs = Utils.clone(this.chart.plugin.groups) || [];
         var dataset_id = this.chart.get("dataset_id");
         if (dataset_id) {
             this.chart.state("wait", "Loading metadata...");
-            this.deferred.execute(function(process) {
+            this.deferred.execute(function (process) {
                 Utils.get({
                     url: getAppRoot() + "api/datasets/" + dataset_id,
                     cache: true,
-                    success: function(dataset) {
+                    success: function (dataset) {
                         var data_columns = {};
-                        FormData.visitInputs(inputs, function(input, prefixed) {
+                        FormData.visitInputs(inputs, function (input, prefixed) {
                             if (input.type == "data_column") {
                                 data_columns[prefixed] = Utils.clone(input);
                                 var columns = [];
@@ -63,30 +63,30 @@ var GroupView = Backbone.View.extend({
                             name: "__data_columns",
                             type: "hidden",
                             hidden: true,
-                            value: data_columns
+                            value: data_columns,
                         });
                         self.chart.state("ok", "Metadata initialized...");
                         self.form = new Form({
                             inputs: inputs,
-                            onchange: function() {
+                            onchange: function () {
                                 self.group.set(self.form.data.create());
                                 self.chart.set("modified", true);
                                 self.chart.trigger("redraw");
-                            }
+                            },
                         });
                         self.group.set(self.form.data.create());
                         self.$el.empty().append(self.form.$el);
                         process.resolve();
                         self.chart.trigger("redraw");
-                    }
+                    },
                 });
             });
         }
-    }
+    },
 });
 
 export default Backbone.View.extend({
-    initialize: function(app) {
+    initialize: function (app) {
         var self = this;
         this.app = app;
         this.chart = app.chart;
@@ -94,33 +94,33 @@ export default Backbone.View.extend({
             title: "Data series",
             title_new: "Data series",
             min: 1,
-            onnew: function() {
+            onnew: function () {
                 self.chart.groups.add({ id: Utils.uid() });
-            }
+            },
         });
         this.setElement($("<div/>").append(this.repeat.$el));
-        this.listenTo(this.chart.groups, "remove", function(group) {
+        this.listenTo(this.chart.groups, "remove", function (group) {
             self.repeat.del(group.id);
             self.chart.trigger("redraw");
         });
-        this.listenTo(this.chart.groups, "reset", function() {
+        this.listenTo(this.chart.groups, "reset", function () {
             self.repeat.delAll();
         });
-        this.listenTo(this.chart.groups, "add", function(group) {
+        this.listenTo(this.chart.groups, "add", function (group) {
             self.repeat.add({
                 id: group.id,
                 $el: new GroupView(self.app, { group: group }).$el,
-                ondel: function() {
+                ondel: function () {
                     self.chart.groups.remove(group);
-                }
+                },
             });
         });
     },
-    render: function() {
+    render: function () {
         if (_.size(this.chart.plugin.groups) > 0) {
             this.repeat.$el.show();
         } else {
             this.repeat.$el.hide();
         }
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/visualization/chart/views/menu.js b/client/galaxy/scripts/mvc/visualization/chart/views/menu.js
index b5b2914a1294..931bfdc0b477 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/views/menu.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/views/menu.js
@@ -4,7 +4,7 @@ import Ui from "mvc/ui/ui-misc";
 import Screenshot from "mvc/visualization/chart/components/screenshot";
 
 export default Backbone.View.extend({
-    initialize: function(app) {
+    initialize: function (app) {
         this.app = app;
         this.model = new Backbone.Model({ visible: true });
         this.execute_button = new Ui.Button({
@@ -12,11 +12,11 @@ export default Backbone.View.extend({
             tooltip: "Confirm",
             onclick: () => {
                 app.chart.trigger("redraw", true);
-            }
+            },
         });
         this.export_button = new Ui.ButtonMenu({
             icon: "fa-camera",
-            tooltip: "Export"
+            tooltip: "Export",
         });
         this.export_button.addMenu({
             key: "png",
@@ -27,12 +27,12 @@ export default Backbone.View.extend({
                     Screenshot.createPNG({
                         $el: app.viewer.$el,
                         title: app.chart.get("title"),
-                        error: err => {
+                        error: (err) => {
                             app.message.update({ message: err, status: "danger" });
-                        }
+                        },
                     });
                 });
-            }
+            },
         });
         this.export_button.addMenu({
             key: "svg",
@@ -43,12 +43,12 @@ export default Backbone.View.extend({
                     Screenshot.createSVG({
                         $el: app.viewer.$el,
                         title: app.chart.get("title"),
-                        error: err => {
+                        error: (err) => {
                             app.message.update({ message: err, status: "danger" });
-                        }
+                        },
                     });
                 });
-            }
+            },
         });
         this.export_button.addMenu({
             key: "pdf",
@@ -69,15 +69,15 @@ export default Backbone.View.extend({
                                 Screenshot.createPDF({
                                     $el: app.viewer.$el,
                                     title: app.chart.get("title"),
-                                    error: err => {
+                                    error: (err) => {
                                         app.message.update({ message: err, status: "danger" });
-                                    }
+                                    },
                                 });
                             });
-                        }
-                    }
+                        },
+                    },
                 });
-            }
+            },
         });
         this.left_button = new Ui.Button({
             icon: "fa-angle-double-left",
@@ -85,7 +85,7 @@ export default Backbone.View.extend({
             onclick: () => {
                 this.model.set("visible", true);
                 window.dispatchEvent(new Event("resize"));
-            }
+            },
         });
         this.right_button = new Ui.Button({
             icon: "fa-angle-double-right",
@@ -93,7 +93,7 @@ export default Backbone.View.extend({
             onclick: () => {
                 this.model.set("visible", false);
                 window.dispatchEvent(new Event("resize"));
-            }
+            },
         });
         this.save_button = new Ui.Button({
             icon: "fa-save",
@@ -104,23 +104,23 @@ export default Backbone.View.extend({
                         message: `Saving '${app.chart.get(
                             "title"
                         )}'. It will appear in the list of 'Saved Visualizations'.`,
-                        status: "success"
+                        status: "success",
                     });
                     app.chart.save({
                         error: () => {
                             app.message.update({
                                 message: "Could not save visualization.",
-                                status: "danger"
+                                status: "danger",
                             });
-                        }
+                        },
                     });
                 } else {
                     app.message.update({
                         message: "Please provide a name.",
-                        status: "danger"
+                        status: "danger",
                     });
                 }
-            }
+            },
         });
         this.buttons = [this.left_button, this.right_button, this.execute_button, this.export_button, this.save_button];
         this.setElement("<div/>");
@@ -131,7 +131,7 @@ export default Backbone.View.extend({
         this.render();
     },
 
-    render: function() {
+    render: function () {
         var visible = this.model.get("visible");
         this.app.$el[visible ? "removeClass" : "addClass"]("charts-fullscreen");
         this.execute_button.model.set("visible", visible && !!this.app.chart.plugin.specs.confirm);
@@ -140,18 +140,18 @@ export default Backbone.View.extend({
         this.right_button.model.set("visible", visible);
         this.left_button.model.set("visible", !visible);
         var exports = this.app.chart.plugin.specs.exports || [];
-        this.export_button.collection.each(model => {
+        this.export_button.collection.each((model) => {
             model.set("visible", exports.indexOf(model.get("key")) !== -1);
         });
     },
 
-    _wait: function(chart, callback) {
+    _wait: function (chart, callback) {
         if (this.app.deferred.ready()) {
             callback();
         } else {
             this.app.message.update({
-                message: "Your visualization is currently being processed. Please wait and try again."
+                message: "Your visualization is currently being processed. Please wait and try again.",
             });
         }
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/visualization/chart/views/settings.js b/client/galaxy/scripts/mvc/visualization/chart/views/settings.js
index 073ef4d83a91..5f1ea40ca6d3 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/views/settings.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/views/settings.js
@@ -6,15 +6,15 @@ import Form from "mvc/form/form-view";
 import FormData from "mvc/form/form-data";
 
 export default Backbone.View.extend({
-    initialize: function(app, options) {
+    initialize: function (app, options) {
         var self = this;
         this.chart = app.chart;
         this.setElement("<div/>");
-        this.listenTo(this.chart, "load", function() {
+        this.listenTo(this.chart, "load", function () {
             self.render();
         });
     },
-    render: function() {
+    render: function () {
         var self = this;
         var inputs = Utils.clone(this.chart.plugin.settings) || [];
         var panel_option = this.chart.plugin.specs.use_panels;
@@ -23,14 +23,14 @@ export default Backbone.View.extend({
                 name: "__use_panels",
                 type: "boolean",
                 label: "Use multi-panels",
-                help: "Would you like to separate your data into individual panels?"
+                help: "Would you like to separate your data into individual panels?",
             });
         } else {
             this.chart.settings.set("__use_panels", panel_option == "yes" ? "true" : "false");
         }
         this.$el.empty();
         if (_.size(inputs) > 0) {
-            FormData.visitInputs(inputs, function(input, name) {
+            FormData.visitInputs(inputs, function (input, name) {
                 var model_value = self.chart.settings.get(name);
                 if (model_value !== undefined && !input.hidden) {
                     input.value = model_value;
@@ -38,13 +38,13 @@ export default Backbone.View.extend({
             });
             this.form = new Form({
                 inputs: inputs,
-                onchange: function() {
+                onchange: function () {
                     self.chart.settings.set(self.form.data.create());
                     self.chart.trigger("redraw");
-                }
+                },
             });
             this.chart.settings.set(this.form.data.create());
             this.$el.append(this.form.$el);
         }
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/visualization/chart/views/viewer.js b/client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
index 7c7ac58b9f9c..4c7e2817d126 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
@@ -7,7 +7,7 @@ import Backbone from "backbone";
 import Utils from "utils/utils";
 
 export default Backbone.View.extend({
-    initialize: function(app, options) {
+    initialize: function (app, options) {
         var self = this;
         this.app = app;
         this.chart = this.app.chart;
@@ -27,9 +27,9 @@ export default Backbone.View.extend({
         this.$text = this.$(".text");
         this._fullscreen(this.$el, 20);
         this._createContainer("div");
-        this.chart.on("redraw", function(confirmed) {
+        this.chart.on("redraw", function (confirmed) {
             if (!self.chart.get("modified") || !self.chart.plugin.specs.confirm || confirmed) {
-                self.app.deferred.execute(function(process) {
+                self.app.deferred.execute(function (process) {
                     console.debug("viewer:redraw() - Redrawing...");
                     self._draw(process, self.chart);
                 });
@@ -37,7 +37,7 @@ export default Backbone.View.extend({
                 self.chart.state("info", "Please confirm the settings before rendering the results.");
             }
         });
-        this.chart.on("set:state", function() {
+        this.chart.on("set:state", function () {
             var $container = self.$(".charts-viewer-container");
             var $info = self.$info;
             var $icon = self.$icon;
@@ -67,15 +67,15 @@ export default Backbone.View.extend({
     },
 
     /** Force resize to fullscreen */
-    _fullscreen: function($el, margin) {
+    _fullscreen: function ($el, margin) {
         $el.css("height", $(window).height() - margin);
-        $(window).resize(function() {
+        $(window).resize(function () {
             $el.css("height", $(window).height() - margin);
         });
     },
 
     /** A chart may contain multiple sub charts/containers which are created here */
-    _createContainer: function(tag, n) {
+    _createContainer: function (tag, n) {
         tag = tag || "div";
         n = n || 1;
         this.$(".charts-viewer-container").remove();
@@ -92,11 +92,11 @@ export default Backbone.View.extend({
     },
 
     /** Draws a new chart by loading and executing the corresponding chart wrapper */
-    _draw: function(process, chart) {
+    _draw: function (process, chart) {
         var n_panels = chart.settings.get("__use_panels") == "true" ? chart.groups.length : 1;
         this._createContainer(chart.plugin.specs.tag, n_panels);
         chart.set("date", Utils.time());
         chart.state("wait", "Please wait...");
         this.app.chart_load({ process: process, chart: chart, dataset: this.app.dataset, targets: this.targets });
-    }
+    },
 });
diff --git a/client/galaxy/scripts/mvc/visualization/visualization-model.js b/client/galaxy/scripts/mvc/visualization/visualization-model.js
index 3188471b7294..4de04f2b102d 100644
--- a/client/galaxy/scripts/mvc/visualization/visualization-model.js
+++ b/client/galaxy/scripts/mvc/visualization/visualization-model.js
@@ -16,11 +16,11 @@ export var Visualization = Backbone.Model.extend(
 
         /** default attributes for a model */
         defaults: {
-            config: {}
+            config: {},
         },
 
         /** override urlRoot to handle prefix */
-        urlRoot: function() {
+        urlRoot: function () {
             var apiUrl = "api/visualizations";
             return getAppRoot() + apiUrl;
         },
@@ -28,7 +28,7 @@ export var Visualization = Backbone.Model.extend(
         /** Set up the model, determine if accessible, bind listeners
          *  @see Backbone.Model#initialize
          */
-        initialize: function(data) {
+        initialize: function (data) {
             //this.log( this + '.initialize', data, this.attributes );
 
             // munge config sub-object here since bbone won't handle defaults with this
@@ -41,7 +41,7 @@ export var Visualization = Backbone.Model.extend(
 
         /** set up any event listeners
          */
-        _setUpListeners: function() {
+        _setUpListeners: function () {
             //this.on( 'change', function(){
             //    console.info( 'change:', arguments );
             //});
@@ -49,7 +49,7 @@ export var Visualization = Backbone.Model.extend(
 
         // ........................................................................ config
         /** override set to properly allow update and trigger change when setting the sub-obj 'config' */
-        set: function(key, val) {
+        set: function (key, val) {
             //TODO: validate config is object
             if (key === "config") {
                 var oldConfig = this.get("config");
@@ -65,13 +65,13 @@ export var Visualization = Backbone.Model.extend(
 
         // ........................................................................ misc
         /** String representation */
-        toString: function() {
+        toString: function () {
             var idAndTitle = this.get("id") || "";
             if (this.get("title")) {
                 idAndTitle += `:${this.get("title")}`;
             }
             return `Visualization(${idAndTitle})`;
-        }
+        },
     }
 );
 
@@ -88,14 +88,14 @@ export var VisualizationCollection = Backbone.Collection.extend(
         //// comment this out to suppress log output
         //logger              : console,
 
-        url: function() {
+        url: function () {
             return `${getAppRoot()}api/visualizations`;
         },
 
         /** Set up.
          *  @see Backbone.Collection#initialize
          */
-        initialize: function(models, options) {
+        initialize: function (models, options) {
             options = options || {};
             //this._setUpListeners();
         },
@@ -106,14 +106,14 @@ export var VisualizationCollection = Backbone.Collection.extend(
         // ........................................................................ common queries
         // ........................................................................ ajax
         // ........................................................................ misc
-        set: function(models, options) {
+        set: function (models, options) {
             // arrrrrrrrrrrrrrrrrg...
             // override to get a correct/smarter merge when incoming data is partial (e.g. stupid backbone)
             //  w/o this partial models from the server will fill in missing data with model defaults
             //  and overwrite existing data on the client
             // see Backbone.Collection.set and _prepareModel
             var collection = this;
-            models = _.map(models, model => {
+            models = _.map(models, (model) => {
                 var existing = collection.get(model.id);
                 if (!existing) {
                     return model;
@@ -129,8 +129,8 @@ export var VisualizationCollection = Backbone.Collection.extend(
         },
 
         /** String representation. */
-        toString: function() {
+        toString: function () {
             return ["VisualizationCollection(", [this.historyId, this.length].join(), ")"].join("");
-        }
+        },
     }
 );
diff --git a/client/galaxy/scripts/mvc/webhooks.js b/client/galaxy/scripts/mvc/webhooks.js
index b5713de87af3..30e0ee69822a 100644
--- a/client/galaxy/scripts/mvc/webhooks.js
+++ b/client/galaxy/scripts/mvc/webhooks.js
@@ -3,15 +3,15 @@ import { getAppRoot } from "onload/loadConfig";
 import Utils from "utils/utils";
 
 const Webhooks = Backbone.Collection.extend({
-    url: function() {
+    url: function () {
         return `${getAppRoot()}api/webhooks`;
-    }
+    },
 });
 
 const WebhookView = Backbone.View.extend({
     el: "#webhook-view",
 
-    initialize: function(options) {
+    initialize: function (options) {
         const toolId = options.toolId || "";
         const toolVersion = options.toolVersion || "";
 
@@ -20,40 +20,40 @@ const WebhookView = Backbone.View.extend({
 
         const webhooks = new Webhooks();
         webhooks.fetch({
-            success: data => {
+            success: (data) => {
                 if (options.type) {
                     data.reset(filterType(data, options.type));
                 }
                 if (data.length > 0) {
                     this.render(weightedRandomPick(data));
                 }
-            }
+            },
         });
     },
 
-    render: function(model) {
+    render: function (model) {
         const webhook = model.toJSON();
         this.$el.html(`<div id="${webhook.id}"></div>`);
         Utils.appendScriptStyle(webhook);
         return this;
-    }
+    },
 });
 
-const load = options => {
+const load = (options) => {
     const webhooks = new Webhooks();
     webhooks.fetch({
         async: options.async !== undefined ? options.async : true,
-        success: data => {
+        success: (data) => {
             if (options.type) {
                 data.reset(filterType(data, options.type));
             }
             options.callback(data);
-        }
+        },
     });
 };
 
 function filterType(data, type) {
-    return data.models.filter(item => {
+    return data.models.filter((item) => {
         const itype = item.get("type");
         if (itype) {
             return itype.indexOf(type) !== -1;
@@ -84,5 +84,5 @@ function weightedRandomPick(data) {
 
 export default {
     WebhookView: WebhookView,
-    load: load
+    load: load,
 };
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-canvas.js b/client/galaxy/scripts/mvc/workflow/workflow-canvas.js
index 7e0b59e27612..bc62fbaaabd0 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-canvas.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-canvas.js
@@ -122,25 +122,25 @@ class CanvasManager {
             y = Math.max(y, -self.cc.height() + self.cv.height() / 2);
             self.cc.css({
                 left: x,
-                top: y
+                top: y,
             });
             self.cv.css({
                 "background-position-x": x,
-                "background-position-y": y
+                "background-position-y": y,
             });
             self.update_viewport_overlay();
         };
         // Dragging within canvas background
-        this.cc.each(function() {
+        this.cc.each(function () {
             this.scroll_panel = new ScrollPanel(this);
         });
         var x_adjust;
         var y_adjust;
         this.cv
-            .bind("click", function() {
+            .bind("click", function () {
                 document.activeElement.blur();
             })
-            .bind("dragstart", function() {
+            .bind("dragstart", function () {
                 var o = $(this).offset();
                 var p = self.cc.position();
                 y_adjust = p.top - o.top;
@@ -153,7 +153,7 @@ class CanvasManager {
                 self.app.fit_canvas_to_nodes();
                 self.draw_overview();
             });
-        this.overview.click(e => {
+        this.overview.click((e) => {
             if (self.overview.hasClass("blockaclick")) {
                 self.overview.removeClass("blockaclick");
             } else {
@@ -185,13 +185,13 @@ class CanvasManager {
                 self.draw_overview();
             });
         // Dragging for overview border (resize)
-        $(".workflow-overview").bind("drag", function(e, d) {
+        $(".workflow-overview").bind("drag", function (e, d) {
             var op = $(this).offsetParent();
             var opo = op.offset();
             var new_size = Math.max(op.width() - (d.offsetX - opo.left), op.height() - (d.offsetY - opo.top));
             $(this).css({
                 width: new_size,
-                height: new_size
+                height: new_size,
             });
             self.draw_overview();
         });
@@ -200,7 +200,7 @@ class CanvasManager {
         $(".workflow-overview div").bind("drag", () => {});
     }
     init_copy_paste() {
-        document.addEventListener("copy", e => {
+        document.addEventListener("copy", (e) => {
             // If it appears that the user is trying to copy/paste text, we
             // pass that through.
             if (window.getSelection().toString() === "") {
@@ -208,7 +208,7 @@ class CanvasManager {
                     e.clipboardData.setData(
                         "application/json",
                         JSON.stringify({
-                            nodeId: this.app.active_node.id
+                            nodeId: this.app.active_node.id,
                         })
                     );
                 }
@@ -216,7 +216,7 @@ class CanvasManager {
             }
         });
 
-        document.addEventListener("paste", e => {
+        document.addEventListener("paste", (e) => {
             // If it appears that the user is trying to paste into a text box,
             // pass that through and skip the workflow copy/paste logic.
             if (
@@ -252,15 +252,12 @@ class CanvasManager {
             top: -((cc_pos.top / in_h) * o_h),
             // Subtract 2 to account for borders (maybe just change box sizing style instead?)
             width: (cv.width() / in_w) * o_w - 2,
-            height: (cv.height() / in_h) * o_h - 2
+            height: (cv.height() / in_h) * o_h - 2,
         });
     }
     draw_overview() {
         var canvas_el = $("#overview-canvas");
-        var size = canvas_el
-            .parent()
-            .parent()
-            .width();
+        var size = canvas_el.parent().parent().width();
 
         var c = canvas_el.get(0).getContext("2d");
         var in_w = $("#canvas-container").width();
@@ -295,7 +292,7 @@ class CanvasManager {
             left: shift_w,
             top: shift_h,
             width: o_w,
-            height: o_h
+            height: o_h,
         });
         canvas_el.attr("width", o_w);
         canvas_el.attr("height", o_h);
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-connector.js b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
index 728eebd1cafa..7f9b4a63ba0c 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-connector.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
@@ -82,8 +82,8 @@ class Connector {
             "handle2-id",
             handle2 && handle2.element.getAttribute ? handle2.element.getAttribute("id") : ""
         );
-        const relativeLeft = e => ($(e).offset().left - canvas_container.offset().left) / canvasZoom;
-        const relativeTop = e => ($(e).offset().top - canvas_container.offset().top) / canvasZoom;
+        const relativeLeft = (e) => ($(e).offset().left - canvas_container.offset().left) / canvasZoom;
+        const relativeTop = (e) => ($(e).offset().top - canvas_container.offset().top) / canvasZoom;
         if (!handle1 || !handle2) {
             return;
         }
@@ -170,14 +170,14 @@ class Connector {
             { x: start_x, y: start_y + offset_start },
             { x: start_x + cp_shift, y: start_y + offset_start },
             { x: end_x - cp_shift, y: end_y + offset_end },
-            { x: end_x, y: end_y + offset_end }
+            { x: end_x, y: end_y + offset_end },
         ];
         const lineFunction = d3.svg
             .line()
-            .x(function(d) {
+            .x(function (d) {
                 return d.x;
             })
-            .y(function(d) {
+            .y(function (d) {
                 return d.y;
             })
             .interpolate("basis");
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
index d9268134851b..c83d7f0dc645 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
@@ -13,7 +13,7 @@ export class DefaultForm {
         var node = options.node;
         this.form = new Form(
             Utils.merge(options, {
-                onchange: function() {
+                onchange: function () {
                     Utils.request({
                         type: "POST",
                         url: `${getAppRoot()}api/workflows/build_module`,
@@ -21,13 +21,13 @@ export class DefaultForm {
                             id: node.id,
                             type: node.type,
                             content_id: node.content_id,
-                            inputs: self.form.data.create()
+                            inputs: self.form.data.create(),
                         },
-                        success: function(data) {
+                        success: function (data) {
                             node.update_field_data(data);
-                        }
+                        },
                     });
-                }
+                },
             })
         );
         _addLabelAnnotation(this.form);
@@ -47,28 +47,28 @@ export class ToolForm {
                 narrow: true,
                 initial_errors: true,
                 cls: "ui-portlet-section",
-                initialmodel: function(process, form) {
+                initialmodel: function (process, form) {
                     self._customize(form);
                     process.resolve();
                 },
-                buildmodel: function(process, form) {
+                buildmodel: function (process, form) {
                     form.model.get("postchange")(process, form);
                 },
-                postchange: function(process, form) {
+                postchange: function (process, form) {
                     const Galaxy = getGalaxyInstance();
                     var options = form.model.attributes;
                     var current_state = {
                         tool_id: options.id,
                         tool_version: options.version,
                         type: "tool",
-                        inputs: $.extend(true, {}, form.data.create())
+                        inputs: $.extend(true, {}, form.data.create()),
                     };
                     Galaxy.emit.debug("tool-form-workflow::postchange()", "Sending current state.", current_state);
                     Utils.request({
                         type: "POST",
                         url: `${getAppRoot()}api/workflows/build_module`,
                         data: current_state,
-                        success: function(data) {
+                        success: function (data) {
                             form.model.set(data.config_form);
                             self._customize(form);
                             form.update(data.config_form);
@@ -81,18 +81,18 @@ export class ToolForm {
                             Galaxy.emit.debug("tool-form-workflow::postchange()", "Received new model.", data);
                             process.resolve();
                         },
-                        error: function(response) {
+                        error: function (response) {
                             Galaxy.emit.debug("tool-form-workflow::postchange()", "Refresh request failed.", response);
                             process.reject();
-                        }
+                        },
                     });
-                }
+                },
             })
         );
     }
     _customize(form) {
         var options = form.model.attributes;
-        Utils.deepeach(options.inputs, input => {
+        Utils.deepeach(options.inputs, (input) => {
             if (input.type) {
                 input.connectable = true;
                 if (["data", "data_collection"].indexOf(input.type) != -1) {
@@ -101,14 +101,14 @@ export class ToolForm {
                     input.value = { __class__: "RuntimeValue" };
                 } else if (!input.fixed) {
                     input.collapsible_value = {
-                        __class__: "RuntimeValue"
+                        __class__: "RuntimeValue",
                     };
                     input.is_workflow =
                         (input.options && input.options.length === 0) || ["integer", "float"].indexOf(input.type) != -1;
                 }
             }
         });
-        Utils.deepeach(options.inputs, input => {
+        Utils.deepeach(options.inputs, (input) => {
             if (input.type === "conditional") {
                 input.connectable = false;
                 input.test_param.collapsible_value = undefined;
@@ -131,7 +131,7 @@ function _addLabelAnnotation(form) {
         fixed: true,
         value: node.annotation,
         area: true,
-        help: "Add an annotation or notes to this step. Annotations are available when a workflow is viewed."
+        help: "Add an annotation or notes to this step. Annotations are available when a workflow is viewed.",
     });
     options.inputs.unshift({
         type: "text",
@@ -140,7 +140,7 @@ function _addLabelAnnotation(form) {
         value: node.label,
         help: _l("Add a step label."),
         fixed: true,
-        onchange: function(new_label) {
+        onchange: function (new_label) {
             var duplicate = false;
             for (var i in workflow.nodes) {
                 var n = workflow.nodes[i];
@@ -156,7 +156,7 @@ function _addLabelAnnotation(form) {
                 duplicate && "Duplicate label. Please fix this before saving the workflow."
             );
             form.trigger("change");
-        }
+        },
     });
 }
 
@@ -203,7 +203,7 @@ function _makeRenameHelp(name_labels) {
         <ul>
             ${name_labels
                 .map(
-                    name_label => `<li><strong>${name_label.name.replace(/\|/g, ".")}</strong>
+                    (name_label) => `<li><strong>${name_label.name.replace(/\|/g, ".")}</strong>
                                                          ${name_label.label ? `(${name_label.label})` : ""}
                                              </li>`
                 )
@@ -232,15 +232,15 @@ function _makeSection(output_id, label, options) {
     extensions.sort((a, b) => (a.label > b.label ? 1 : a.label < b.label ? -1 : 0));
     extensions.unshift({
         0: "Sequences",
-        1: "Sequences"
+        1: "Sequences",
     });
     extensions.unshift({
         0: "Roadmaps",
-        1: "Roadmaps"
+        1: "Roadmaps",
     });
     extensions.unshift({
         0: "Leave unchanged",
-        1: "__empty__"
+        1: "__empty__",
     });
     var output;
     var input_config = {
@@ -253,9 +253,9 @@ function _makeSection(output_id, label, options) {
                 type: "text",
                 value: ((output = node.getWorkflowOutput(output_id)) && output.label) || "",
                 help: "This will provide a short name to describe the output - this must be unique across workflows.",
-                onchange: function(new_value) {
+                onchange: function (new_value) {
                     workflow.attemptUpdateOutputLabel(node, output_id, new_value);
-                }
+                },
             },
             {
                 action: "RenameDatasetAction",
@@ -264,7 +264,7 @@ function _makeSection(output_id, label, options) {
                 type: "text",
                 value: "",
                 ignore: "",
-                help: rename_help
+                help: rename_help,
             },
             {
                 action: "ChangeDatatypeAction",
@@ -275,12 +275,12 @@ function _makeSection(output_id, label, options) {
                 value: "__empty__",
                 options: extensions,
                 help: "This action will change the datatype of the output to the indicated datatype.",
-                onchange: function(new_value) {
+                onchange: function (new_value) {
                     if (new_value === "__empty__") {
                         new_value = null;
                     }
                     workflow.updateDatatype(node, output_id, new_value);
-                }
+                },
             },
             {
                 action: "TagDatasetAction",
@@ -289,7 +289,7 @@ function _makeSection(output_id, label, options) {
                 type: "text",
                 value: "",
                 ignore: "",
-                help: "This action will set tags for the dataset."
+                help: "This action will set tags for the dataset.",
             },
             {
                 action: "RemoveTagDatasetAction",
@@ -298,7 +298,7 @@ function _makeSection(output_id, label, options) {
                 type: "text",
                 value: "",
                 ignore: "",
-                help: "This action will remove tags for the dataset."
+                help: "This action will remove tags for the dataset.",
             },
             {
                 title: _l("Assign columns"),
@@ -311,7 +311,7 @@ function _makeSection(output_id, label, options) {
                         label: "Chrom column",
                         type: "integer",
                         value: "",
-                        ignore: ""
+                        ignore: "",
                     },
                     {
                         action: "ColumnSetAction",
@@ -319,7 +319,7 @@ function _makeSection(output_id, label, options) {
                         label: "Start column",
                         type: "integer",
                         value: "",
-                        ignore: ""
+                        ignore: "",
                     },
                     {
                         action: "ColumnSetAction",
@@ -327,7 +327,7 @@ function _makeSection(output_id, label, options) {
                         label: "End column",
                         type: "integer",
                         value: "",
-                        ignore: ""
+                        ignore: "",
                     },
                     {
                         action: "ColumnSetAction",
@@ -335,7 +335,7 @@ function _makeSection(output_id, label, options) {
                         label: "Strand column",
                         type: "integer",
                         value: "",
-                        ignore: ""
+                        ignore: "",
                     },
                     {
                         action: "ColumnSetAction",
@@ -343,12 +343,12 @@ function _makeSection(output_id, label, options) {
                         label: "Name column",
                         type: "integer",
                         value: "",
-                        ignore: ""
-                    }
+                        ignore: "",
+                    },
                 ],
-                help: "This action will set column assignments in the output dataset. Blank fields are ignored."
-            }
-        ]
+                help: "This action will set column assignments in the output dataset. Blank fields are ignored.",
+            },
+        ],
     };
     _visit(input_config, [], output_id, options);
     return input_config;
@@ -371,8 +371,8 @@ function _addSections(form) {
             ignore: "false",
             help: _l("An email notification will be sent when the job has completed."),
             payload: {
-                host: window.location.host
-            }
+                host: window.location.host,
+            },
         });
         inputs.push({
             name: `pja__${output_id}__DeleteIntermediatesAction`,
@@ -381,7 +381,7 @@ function _addSections(form) {
             value: String(Boolean(post_job_actions[`DeleteIntermediatesAction${output_id}`])),
             ignore: "false",
             help:
-                "Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."
+                "Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs.",
         });
         for (const output_id in node.output_terminals) {
             const label = node.output_terminals[output_id].label || output_id;
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index 490d92bbae89..0fdf0b5b2d8b 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -27,12 +27,12 @@ class Workflow extends EventEmitter {
         if (overview_size !== undefined) {
             $(".workflow-overview").css({
                 width: overview_size,
-                height: overview_size
+                height: overview_size,
             });
         }
 
         // Stores the size of the overview into local storage when it's resized
-        $(".workflow-overview").bind("dragend", function(e, d) {
+        $(".workflow-overview").bind("dragend", function (e, d) {
             var op = $(this).offsetParent();
             var opo = op.offset();
             var new_size = Math.max(op.width() - (d.offsetX - opo.left), op.height() - (d.offsetY - opo.top));
@@ -141,7 +141,7 @@ class Workflow extends EventEmitter {
             id: content_id,
             type: type,
             title: title_text,
-            node: node
+            node: node,
         });
 
         // Set initial scroll position
@@ -155,13 +155,13 @@ class Workflow extends EventEmitter {
         var height = $f.height();
         $f.css({
             left: -o.left + p.width() / 2 - width / 2,
-            top: -o.top + p.height() / 2 - height / 2
+            top: -o.top + p.height() / 2 - height / 2,
         });
         $f.css("width", width);
         $f.bind("dragstart", () => {
             self.activate_node(node);
         })
-            .bind("dragend", function() {
+            .bind("dragend", function () {
                 self.node_changed(node);
                 self.fit_canvas_to_nodes();
                 self.canvas_manager.draw_overview();
@@ -169,11 +169,9 @@ class Workflow extends EventEmitter {
             .bind("dragclickonly", () => {
                 self.activate_node(node);
             })
-            .bind("drag", function(e, d) {
+            .bind("drag", function (e, d) {
                 // Move
-                var po = $(this)
-                    .offsetParent()
-                    .offset();
+                var po = $(this).offsetParent().offset();
                 // Find relative offset and scale by zoom
                 var x = (d.offsetX - po.left) / self.canvas_manager.canvasZoom;
                 var y = (d.offsetY - po.top) / self.canvas_manager.canvasZoom;
@@ -181,7 +179,7 @@ class Workflow extends EventEmitter {
                 // Redraw
                 $(this)
                     .find(".terminal")
-                    .each(function() {
+                    .each(function () {
                         this.terminal.redraw();
                     });
             });
@@ -244,7 +242,7 @@ class Workflow extends EventEmitter {
                             var pja = {
                                 action_type: "HideDatasetAction",
                                 output_name: ot.name,
-                                action_arguments: {}
+                                action_arguments: {},
                             };
                             node.post_job_actions[`HideDatasetAction${ot.name}`] = null;
                             node.post_job_actions[`HideDatasetAction${ot.name}`] = pja;
@@ -271,7 +269,7 @@ class Workflow extends EventEmitter {
                     if (c.handle1) {
                         var con_dict = {
                             id: c.handle1.node.id,
-                            output_name: c.handle1.name
+                            output_name: c.handle1.name,
                         };
                         var input_subworkflow_step_id = t.attributes.input.input_subworkflow_step_id;
                         if (input_subworkflow_step_id !== undefined) {
@@ -288,7 +286,7 @@ class Workflow extends EventEmitter {
                     var pja = {
                         action_type: act.action_type,
                         output_name: act.output_name,
-                        action_arguments: act.action_arguments
+                        action_arguments: act.action_arguments,
                     };
                     post_job_actions[act.action_type + act.output_name] = null;
                     post_job_actions[act.action_type + act.output_name] = pja;
@@ -311,7 +309,7 @@ class Workflow extends EventEmitter {
                 post_job_actions: node.post_job_actions,
                 uuid: node.uuid,
                 label: node.label,
-                workflow_outputs: node.workflow_outputs
+                workflow_outputs: node.workflow_outputs,
             };
             nodes[node.id] = node_data;
         });
@@ -346,7 +344,7 @@ class Workflow extends EventEmitter {
             if (step.position) {
                 node.element.css({
                     top: step.position.top,
-                    left: step.position.left
+                    left: step.position.left,
                 });
             }
             node.id = parseInt(step.id) + offset;
@@ -579,10 +577,10 @@ class Workflow extends EventEmitter {
             left: left / canvasZoom,
             top: top / canvasZoom,
             width: width,
-            height: height
+            height: height,
         });
         // Move elements back if needed
-        this.canvas_container.children().each(function() {
+        this.canvas_container.children().each(function () {
             var p = $(this).position();
             $(this).css("left", (p.left + xmin_delta) / canvasZoom);
             $(this).css("top", (p.top + ymin_delta) / canvasZoom);
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js
index 1eb79015fbaa..fcdc22080e9d 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js
@@ -15,7 +15,7 @@ export class Node {
     }
     getWorkflowOutput(outputName) {
         return _.findWhere(this.workflow_outputs, {
-            output_name: outputName
+            output_name: outputName,
         });
     }
     isWorkflowOutput(outputName) {
@@ -69,7 +69,7 @@ export class Node {
             this.post_job_actions["ChangeDatatypeAction" + outputName] = {
                 action_arguments: { newtype: datatype },
                 action_type: "ChangeDatatypeAction",
-                output_name: outputName
+                output_name: outputName,
             };
         } else {
             delete this.post_job_actions["ChangeDatatypeAction" + outputName];
@@ -140,7 +140,7 @@ export class Node {
     }
     hasMappedOverInputTerminals() {
         var found = false;
-        _.each(this.input_terminals, t => {
+        _.each(this.input_terminals, (t) => {
             var mapOver = t.mapOver;
             if (mapOver.isCollection) {
                 found = true;
@@ -161,7 +161,7 @@ export class Node {
             name: this.name,
             label: this.label,
             annotation: this.annotation,
-            post_job_actions: this.post_job_actions
+            post_job_actions: this.post_job_actions,
         };
         var node = this.app.create_node(this.type, this.name, this.content_id);
         Utils.request({
@@ -170,14 +170,14 @@ export class Node {
             data: {
                 type: this.type,
                 tool_id: this.content_id,
-                tool_state: this.tool_state
+                tool_state: this.tool_state,
             },
-            success: data => {
+            success: (data) => {
                 var newData = Object.assign({}, data, copiedData);
                 node.init_field_data(newData);
                 node.update_field_data(newData);
                 this.app.activate_node(node);
-            }
+            },
         });
     }
     destroy() {
@@ -197,7 +197,7 @@ export class Node {
         // Keep inactive nodes stacked from most to least recently active
         // by moving element to the end of parent's node list
         var element = this.element.get(0);
-        (p => {
+        ((p) => {
             p.removeChild(element);
             p.appendChild(element);
         })(element.parentNode);
@@ -229,7 +229,7 @@ export class Node {
         var node = this;
         var nodeView = new NodeView(this.app, {
             $el: this.element,
-            node: node
+            node: node,
         });
         node.nodeView = nodeView;
         $.each(data.inputs, (i, input) => {
@@ -258,7 +258,7 @@ export class Node {
             var cur_name = output_view.output.name;
             var data_names = data.outputs;
             var cur_name_in_data_outputs = false;
-            _.each(data_names, data_name => {
+            _.each(data_names, (data_name) => {
                 if (data_name.name == cur_name) {
                     cur_name_in_data_outputs = true;
                 }
@@ -268,8 +268,8 @@ export class Node {
             }
         });
         // Remove the unused outputs
-        _.each(unused_outputs, unused_output => {
-            _.each(nodeView.outputViews[unused_output].terminalElement.terminal.connectors, x => {
+        _.each(unused_outputs, (unused_output) => {
+            _.each(nodeView.outputViews[unused_output].terminalElement.terminal.connectors, (x) => {
                 if (x) {
                     x.destroy(); // Removes the noodle connectors
                 }
@@ -314,11 +314,11 @@ export class Node {
         var old_body = nodeView.$el.find("div.inputs");
         var new_body = nodeView.newInputsDiv();
         var newTerminalViews = {};
-        _.each(data.inputs, input => {
+        _.each(data.inputs, (input) => {
             newTerminalViews[input.name] = node.nodeView.addDataInput(input, new_body);
         });
         // Cleanup any leftover terminals
-        _.each(_.difference(_.values(nodeView.terminalViews), _.values(newTerminalViews)), unusedView => {
+        _.each(_.difference(_.values(nodeView.terminalViews), _.values(newTerminalViews)), (unusedView) => {
             unusedView.terminal.destroy();
         });
         nodeView.terminalViews = newTerminalViews;
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
index a91dee984c51..8f472cb3355a 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
@@ -15,44 +15,44 @@ function ConnectionAcceptable(canAccept, reason) {
 
 var NULL_COLLECTION_TYPE_DESCRIPTION = {
     isCollection: false,
-    canMatch: function() {
+    canMatch: function () {
         return false;
     },
-    canMapOver: function() {
+    canMapOver: function () {
         return false;
     },
-    toString: function() {
+    toString: function () {
         return "NullCollectionType[]";
     },
-    append: function(otherCollectionType) {
+    append: function (otherCollectionType) {
         return otherCollectionType;
     },
-    equal: function(other) {
+    equal: function (other) {
         return other === this;
-    }
+    },
 };
 
 var ANY_COLLECTION_TYPE_DESCRIPTION = {
     isCollection: true,
-    canMatch: function(other) {
+    canMatch: function (other) {
         return NULL_COLLECTION_TYPE_DESCRIPTION !== other;
     },
-    canMapOver: function() {
+    canMapOver: function () {
         return false;
     },
-    toString: function() {
+    toString: function () {
         return "AnyCollectionType[]";
     },
-    append: function() {
+    append: function () {
         return ANY_COLLECTION_TYPE_DESCRIPTION;
     },
-    equal: function(other) {
+    equal: function (other) {
         return other === this;
-    }
+    },
 };
 
 $.extend(CollectionTypeDescription.prototype, {
-    append: function(otherCollectionTypeDescription) {
+    append: function (otherCollectionTypeDescription) {
         if (otherCollectionTypeDescription === NULL_COLLECTION_TYPE_DESCRIPTION) {
             return this;
         }
@@ -61,7 +61,7 @@ $.extend(CollectionTypeDescription.prototype, {
         }
         return new CollectionTypeDescription(`${this.collectionType}:${otherCollectionTypeDescription.collectionType}`);
     },
-    canMatch: function(otherCollectionTypeDescription) {
+    canMatch: function (otherCollectionTypeDescription) {
         if (otherCollectionTypeDescription === NULL_COLLECTION_TYPE_DESCRIPTION) {
             return false;
         }
@@ -70,7 +70,7 @@ $.extend(CollectionTypeDescription.prototype, {
         }
         return otherCollectionTypeDescription.collectionType == this.collectionType;
     },
-    canMapOver: function(otherCollectionTypeDescription) {
+    canMapOver: function (otherCollectionTypeDescription) {
         if (otherCollectionTypeDescription === NULL_COLLECTION_TYPE_DESCRIPTION) {
             return false;
         }
@@ -84,7 +84,7 @@ $.extend(CollectionTypeDescription.prototype, {
         var requiredSuffix = otherCollectionTypeDescription.collectionType;
         return this._endsWith(this.collectionType, requiredSuffix);
     },
-    effectiveMapOver: function(otherCollectionTypeDescription) {
+    effectiveMapOver: function (otherCollectionTypeDescription) {
         var otherCollectionType = otherCollectionTypeDescription.collectionType;
         var effectiveCollectionType = this.collectionType.substring(
             0,
@@ -92,15 +92,15 @@ $.extend(CollectionTypeDescription.prototype, {
         );
         return new CollectionTypeDescription(effectiveCollectionType);
     },
-    equal: function(otherCollectionTypeDescription) {
+    equal: function (otherCollectionTypeDescription) {
         return otherCollectionTypeDescription.collectionType == this.collectionType;
     },
-    toString: function() {
+    toString: function () {
         return `CollectionType[${this.collectionType}]`;
     },
-    _endsWith: function(str, suffix) {
+    _endsWith: function (str, suffix) {
         return str.indexOf(suffix, str.length - suffix.length) !== -1;
-    }
+    },
 });
 
 class Terminal extends EventEmitter {
@@ -140,7 +140,7 @@ class Terminal extends EventEmitter {
         this.emit("change");
     }
     destroyInvalidConnections() {
-        _.each(this.connectors, connector => {
+        _.each(this.connectors, (connector) => {
             if (connector) {
                 connector.destroyIfInvalid();
             }
@@ -160,7 +160,7 @@ class Terminal extends EventEmitter {
         }
         if (!this.mapOver.equal(val)) {
             this.mapOver = val;
-            _.each(this.node.output_terminals, outputTerminal => {
+            _.each(this.node.output_terminals, (outputTerminal) => {
                 outputTerminal.setMapOver(output_val);
             });
         }
@@ -175,7 +175,7 @@ class Terminal extends EventEmitter {
     }
     resetCollectionTypeSource() {
         const node = this.node;
-        _.each(node.output_terminals, function(output_terminal) {
+        _.each(node.output_terminals, function (output_terminal) {
             const type_source = output_terminal.attributes.collection_type_source;
             if (type_source && output_terminal.attributes.collection_type) {
                 output_terminal.attributes.collection_type = null;
@@ -205,7 +205,7 @@ class OutputTerminal extends Terminal {
         // If inputs were only mapped over to preserve
         // an output just disconnected reset these...
         if (!this.node.hasConnectedOutputTerminals() && !this.node.hasConnectedMappedInputTerminals()) {
-            _.each(this.node.mappedInputTerminals(), mappedInput => {
+            _.each(this.node.mappedInputTerminals(), (mappedInput) => {
                 mappedInput.resetMappingIfNeeded();
             });
         }
@@ -217,7 +217,7 @@ class OutputTerminal extends Terminal {
     }
     resetMapping() {
         super.resetMapping();
-        _.each(this.connectors, connector => {
+        _.each(this.connectors, (connector) => {
             var connectedInput = connector.handle2;
             if (connectedInput) {
                 // Not exactly right because this is still connected.
@@ -262,7 +262,7 @@ class BaseInputTerminal extends Terminal {
     resetMapping() {
         super.resetMapping();
         if (!this.node.hasMappedOverInputTerminals()) {
-            _.each(this.node.output_terminals, terminal => {
+            _.each(this.node.output_terminals, (terminal) => {
                 // This shouldn't be called if there are mapped over
                 // outputs.
                 terminal.resetMapping();
@@ -320,7 +320,7 @@ class BaseInputTerminal extends Terminal {
 
         var constraints = [];
         if (!this.node.hasConnectedOutputTerminals()) {
-            _.each(this.node.connectedMappedInputTerminals(), inputTerminal => {
+            _.each(this.node.connectedMappedInputTerminals(), (inputTerminal) => {
                 constraints.push(inputTerminal.mapOver);
             });
         } else {
@@ -478,7 +478,7 @@ class InputCollectionTerminal extends BaseInputTerminal {
         this.optional = input.optional;
         var collectionTypes = [];
         if (input.collection_types) {
-            _.each(input.collection_types, collectionType => {
+            _.each(input.collection_types, (collectionType) => {
                 collectionTypes.push(new CollectionTypeDescription(collectionType));
             });
         } else {
@@ -493,7 +493,7 @@ class InputCollectionTerminal extends BaseInputTerminal {
             return;
         } else {
             const node = this.node;
-            _.each(node.output_terminals, function(output_terminal) {
+            _.each(node.output_terminals, function (output_terminal) {
                 if (output_terminal.attributes.collection_type_source && !connector.dragging) {
                     if (other.isMappedOver()) {
                         if (other.isCollection) {
@@ -517,7 +517,7 @@ class InputCollectionTerminal extends BaseInputTerminal {
     _effectiveMapOver(other) {
         var collectionTypes = this.collectionTypes;
         var otherCollectionType = this._otherCollectionType(other);
-        var canMatch = _.some(collectionTypes, collectionType => collectionType.canMatch(otherCollectionType));
+        var canMatch = _.some(collectionTypes, (collectionType) => collectionType.canMatch(otherCollectionType));
 
         if (!canMatch) {
             for (var collectionTypeIndex in collectionTypes) {
@@ -534,14 +534,14 @@ class InputCollectionTerminal extends BaseInputTerminal {
     }
     _effectiveCollectionTypes() {
         var mapOver = this.mapOver;
-        return _.map(this.collectionTypes, t => mapOver.append(t));
+        return _.map(this.collectionTypes, (t) => mapOver.append(t));
     }
     attachable(other) {
         var otherCollectionType = this._otherCollectionType(other);
         if (otherCollectionType.isCollection) {
             var effectiveCollectionTypes = this._effectiveCollectionTypes();
             var mapOver = this.mapOver;
-            var canMatch = _.some(effectiveCollectionTypes, effectiveCollectionType =>
+            var canMatch = _.some(effectiveCollectionTypes, (effectiveCollectionType) =>
                 effectiveCollectionType.canMatch(otherCollectionType)
             );
             if (canMatch) {
@@ -561,7 +561,9 @@ class InputCollectionTerminal extends BaseInputTerminal {
                         "Can't map over this input with output collection type - this step has outputs defined constraining the mapping of this tool. Disconnect outputs and retry."
                     );
                 }
-            } else if (_.some(this.collectionTypes, collectionType => otherCollectionType.canMapOver(collectionType))) {
+            } else if (
+                _.some(this.collectionTypes, (collectionType) => otherCollectionType.canMapOver(collectionType))
+            ) {
                 // we're not mapped over - but hey maybe we could be... lets check.
                 var effectiveMapOver = this._effectiveMapOver(other);
                 if (!effectiveMapOver.isCollection) {
@@ -569,7 +571,7 @@ class InputCollectionTerminal extends BaseInputTerminal {
                 }
                 //  Need to check if this would break constraints...
                 var mappingConstraints = this._mappingConstraints();
-                if (mappingConstraints.every(d => effectiveMapOver.canMatch(d))) {
+                if (mappingConstraints.every((d) => effectiveMapOver.canMatch(d))) {
                     return this._producesAcceptableDatatypeAndOptionalness(other);
                 } else {
                     if (this.node.hasConnectedMappedInputTerminals()) {
@@ -628,7 +630,7 @@ class OutputCollectionTerminal extends Terminal {
         // we need to iterate over a copy, as we slice this.connectors in the process of destroying connections
         var connectors = this.connectors.slice(0);
         if (newCollectionType.collectionType != oldCollectionType.collectionType) {
-            _.each(connectors, connector => {
+            _.each(connectors, (connector) => {
                 connector.destroyIfInvalid(true);
             });
         }
@@ -648,5 +650,5 @@ export default {
     // test export
     CollectionTypeDescription: CollectionTypeDescription,
     NULL_COLLECTION_TYPE_DESCRIPTION: NULL_COLLECTION_TYPE_DESCRIPTION,
-    ANY_COLLECTION_TYPE_DESCRIPTION: ANY_COLLECTION_TYPE_DESCRIPTION
+    ANY_COLLECTION_TYPE_DESCRIPTION: ANY_COLLECTION_TYPE_DESCRIPTION,
 };
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
index 8dca75014b21..a28b7f112593 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
@@ -12,7 +12,7 @@ export class DataInputView {
                 position: "absolute",
                 left: -1000,
                 top: -1000,
-                display: "none"
+                display: "none",
             });
             $("body").append(this.el);
             this.nodeView.updateMaxWidth(this.$el.outerWidth());
@@ -20,7 +20,7 @@ export class DataInputView {
                 position: "",
                 left: "",
                 top: "",
-                display: ""
+                display: "",
             });
             this.$el.remove();
         }
@@ -47,7 +47,7 @@ export class DataOutputView {
             const calloutView = new OutputCalloutView(app, {
                 label: label,
                 output: output,
-                node: node
+                node: node,
             });
             this.calloutView = calloutView;
             this.$el.prepend(calloutView.$el);
@@ -56,7 +56,7 @@ export class DataOutputView {
             position: "absolute",
             left: -1000,
             top: -1000,
-            display: "none"
+            display: "none",
         });
         $("body").append(this.el);
         this.nodeView.updateMaxWidth(this.$el.outerWidth() + 17);
@@ -65,7 +65,7 @@ export class DataOutputView {
                 position: "",
                 left: "",
                 top: "",
-                display: ""
+                display: "",
             })
             .detach();
     }
@@ -91,7 +91,7 @@ export class ParameterOutputView {
             const calloutView = new OutputCalloutView(app, {
                 label: label,
                 output: output,
-                node: node
+                node: node,
             });
             this.calloutView = calloutView;
             this.$el.append(calloutView.$el);
@@ -100,7 +100,7 @@ export class ParameterOutputView {
             position: "absolute",
             left: -1000,
             top: -1000,
-            display: "none"
+            display: "none",
         });
         $("body").append(this.el);
         this.nodeView.updateMaxWidth(this.$el.outerWidth() + 17);
@@ -109,7 +109,7 @@ export class ParameterOutputView {
                 position: "",
                 left: "",
                 top: "",
-                display: ""
+                display: "",
             })
             .detach();
     }
@@ -146,7 +146,7 @@ export class OutputCalloutView {
             )
             .tooltip({
                 delay: 500,
-                title: "Unchecked output datasets will be hidden."
+                title: "Unchecked output datasets will be hidden.",
             });
         this.render();
     }
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
index 01e38c6787bf..0f1857f359c3 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
@@ -70,7 +70,7 @@ export class NodeView {
         if (!terminalView) {
             terminalView = new terminalViewClass(this.app, {
                 node: this.node,
-                input: input
+                input: input,
             });
         } else {
             var terminal = terminalView.terminal;
@@ -83,7 +83,7 @@ export class NodeView {
             terminalElement: terminalElement,
             input: input,
             nodeView: this,
-            skipResize: skipResize
+            skipResize: skipResize,
         });
         var ib = inputView.$el;
         body.append(ib.prepend(terminalView.el));
@@ -99,7 +99,7 @@ export class NodeView {
         }
         return new terminalViewClass(this.app, {
             node: this.node,
-            output: output
+            output: output,
         });
     }
 
@@ -108,7 +108,7 @@ export class NodeView {
         return new outputViewClass(this.app, {
             output: output,
             terminalElement: terminalView.el,
-            nodeView: this
+            nodeView: this,
         });
     }
 
@@ -120,7 +120,7 @@ export class NodeView {
     }
 
     redrawWorkflowOutputs() {
-        _.each(this.outputViews, outputView => {
+        _.each(this.outputViews, (outputView) => {
             outputView.redrawWorkflowOutput();
         });
     }
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index 5697fc976f0c..7808eeea9bae 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -104,9 +104,7 @@ class BaseInputTerminalView {
                 .on("mouseleave", () => {
                     t.remove();
                 });
-            $(this.el)
-                .parent()
-                .append(t);
+            $(this.el).parent().append(t);
         }
     }
 }
@@ -119,7 +117,7 @@ export class InputTerminalView extends BaseInputTerminalView {
         return new Terminals.InputTerminal({
             app: this.app,
             element: this.el,
-            input: input
+            input: input,
         });
     }
 }
@@ -132,7 +130,7 @@ export class InputParameterTerminalView extends BaseInputTerminalView {
         return new Terminals.InputParameterTerminal({
             app: this.app,
             element: this.el,
-            input: input
+            input: input,
         });
     }
 }
@@ -145,7 +143,7 @@ export class InputCollectionTerminalView extends BaseInputTerminalView {
         return new Terminals.InputCollectionTerminal({
             app: this.app,
             element: this.el,
-            input: input
+            input: input,
         });
     }
 }
@@ -180,7 +178,7 @@ export class BaseOutputTerminalView {
         this.$el.on("drag", (d, e) => self.onDrag(d, e));
         this.$el.on("dragstart", (d, e) => self.onDragStart(d, e));
         this.$el.on("dragend", (d, e) => self.onDragEnd(d, e));
-        this.$el.on("keydown", e => self.screenReaderSelectOutputNode(e));
+        this.$el.on("keydown", (e) => self.screenReaderSelectOutputNode(e));
         this.terminal.on("change", this.render.bind(this));
     }
     render() {
@@ -191,7 +189,7 @@ export class BaseOutputTerminalView {
         }
     }
     screenReaderSelectOutputNode(e) {
-        const inputChoiceKeyDown = e => {
+        const inputChoiceKeyDown = (e) => {
             e.stopPropagation();
             const currentItem = e.currentTarget;
             const previousItem = currentItem.previousSibling;
@@ -232,7 +230,7 @@ export class BaseOutputTerminalView {
                             .addClass("delete-terminal")
                             .attr("tabindex", "0")
                             .attr("aria-label", "delete terminal")
-                            .on("keydown click", e => {
+                            .on("keydown click", (e) => {
                                 if (e.keyCode === 32 || e.type === "click") {
                                     //Space or Click
                                     $.each(inputTerminal.connectors, (_, x) => {
@@ -244,16 +242,14 @@ export class BaseOutputTerminalView {
                                     t.remove();
                                 }
                             });
-                        $(currentItem.input)
-                            .parent()
-                            .append(t);
+                        $(currentItem.input).parent().append(t);
                     }
                     break;
             }
         };
         const buildInputChoicesMenu = () => {
             const inputChoicesMenu = document.createElement("ul");
-            $(inputChoicesMenu).focusout(e => {
+            $(inputChoicesMenu).focusout((e) => {
                 /* focus is still inside child element of menu so don't hide */
                 if (inputChoicesMenu.contains(e.relatedTarget)) {
                     return;
@@ -297,9 +293,7 @@ export class BaseOutputTerminalView {
     onDrag(e, d = {}) {
         var onmove = () => {
             var canvasZoom = this.app.canvas_manager.canvasZoom;
-            var po = $(d.proxy)
-                .offsetParent()
-                .offset();
+            var po = $(d.proxy).offsetParent().offset();
 
             var x = d.offsetX - po.left;
             var y = d.offsetY - po.top;
@@ -308,22 +302,18 @@ export class BaseOutputTerminalView {
             this.app.canvas_manager.update_viewport_overlay();
         };
         onmove();
-        $("#canvas-container")
-            .get(0)
-            .scroll_panel.test(e, onmove);
+        $("#canvas-container").get(0).scroll_panel.test(e, onmove);
     }
     onDragStart(e, d = {}) {
         $(d.available).addClass("input-terminal-active");
         // Drag proxy div
-        var h = $("<div class='drag-terminal'/>")
-            .appendTo("#canvas-container")
-            .get(0);
+        var h = $("<div class='drag-terminal'/>").appendTo("#canvas-container").get(0);
         h.dropTooltip = "";
         // Terminal and connection to display noodle while dragging
         $(h).tooltip({
-            title: function() {
+            title: function () {
                 return h.dropTooltip || "";
-            }
+            },
         });
         h.terminal = new Terminals.OutputTerminal({ element: h });
         const c = new Connector(this.app.canvas_manager);
@@ -339,9 +329,7 @@ export class BaseOutputTerminalView {
         $(d.proxy).tooltip("dispose");
         $(d.proxy).remove();
         $(d.available).removeClass("input-terminal-active");
-        $("#canvas-container")
-            .get(0)
-            .scroll_panel.stop();
+        $("#canvas-container").get(0).scroll_panel.stop();
     }
 }
 
@@ -355,7 +343,7 @@ export class OutputTerminalView extends BaseOutputTerminalView {
             element: this.el,
             datatypes: type,
             force_datatype: output.force_datatype,
-            optional: output.optional
+            optional: output.optional,
         });
     }
 }
@@ -373,7 +361,7 @@ export class OutputCollectionTerminalView extends BaseOutputTerminalView {
             collection_type_source: collection_type_source,
             datatypes: output.extensions,
             force_datatype: output.force_datatype,
-            optional: output.optional
+            optional: output.optional,
         });
     }
 }
@@ -386,7 +374,7 @@ export class OutputParameterTerminalView extends BaseOutputTerminalView {
         return new Terminals.OutputParameterTerminal({
             element: this.el,
             type: output.type,
-            optional: output.optional
+            optional: output.optional,
         });
     }
 }
@@ -397,5 +385,5 @@ export default {
     InputCollectionTerminalView: InputCollectionTerminalView,
     OutputTerminalView: OutputTerminalView,
     OutputParameterTerminalView: OutputParameterTerminalView,
-    OutputCollectionTerminalView: OutputCollectionTerminalView
+    OutputCollectionTerminalView: OutputCollectionTerminalView,
 };
diff --git a/client/galaxy/scripts/nls/de/locale.js b/client/galaxy/scripts/nls/de/locale.js
index 3cd06c399e7c..0edc1baa8e75 100644
--- a/client/galaxy/scripts/nls/de/locale.js
+++ b/client/galaxy/scripts/nls/de/locale.js
@@ -202,5 +202,5 @@ define({
     "Edit dataset annotation": "Datensatz-Annotation bearbeiten",
     // ---------------------------------------------------------------------------- misc. MVC
     Tags: "Variablen",
-    "Edit annotation": "Anmerkung bearbeiten"
+    "Edit annotation": "Anmerkung bearbeiten",
 });
diff --git a/client/galaxy/scripts/nls/es/locale.js b/client/galaxy/scripts/nls/es/locale.js
index 3ef2def0ee63..7c373b4f943a 100644
--- a/client/galaxy/scripts/nls/es/locale.js
+++ b/client/galaxy/scripts/nls/es/locale.js
@@ -202,5 +202,5 @@ define({
     "Edit dataset annotation": "Editar anotación del conjunto de datos",
     // ---------------------------------------------------------------------------- misc. MVC
     Tags: "Tags",
-    "Edit annotation": "Editar anotación"
+    "Edit annotation": "Editar anotación",
 });
diff --git a/client/galaxy/scripts/nls/fr/locale.js b/client/galaxy/scripts/nls/fr/locale.js
index df0eb2a39fb5..2b436e2f4f77 100644
--- a/client/galaxy/scripts/nls/fr/locale.js
+++ b/client/galaxy/scripts/nls/fr/locale.js
@@ -454,6 +454,6 @@ define({
     // ---------------------------------------------------------------------------- upload-button
     "Download from URL or upload files from disk": false,
     // ---------------------------------------------------------------------------- workflow_editor_tests
-    "tool tooltip": false
+    "tool tooltip": false,
     // ----------------------------------------------------------------------------
 });
diff --git a/client/galaxy/scripts/nls/ja/locale.js b/client/galaxy/scripts/nls/ja/locale.js
index fefd137dd05a..1ad18569de98 100644
--- a/client/galaxy/scripts/nls/ja/locale.js
+++ b/client/galaxy/scripts/nls/ja/locale.js
@@ -277,5 +277,5 @@ define({
     //false,
     //"Edit annotation" :
     //false,
-    "Your workflows": "����ワークフロー"
+    "Your workflows": "����ワークフロー",
 });
diff --git a/client/galaxy/scripts/nls/locale.js b/client/galaxy/scripts/nls/locale.js
index afb604e5a03e..e4ec208c99e9 100644
--- a/client/galaxy/scripts/nls/locale.js
+++ b/client/galaxy/scripts/nls/locale.js
@@ -454,10 +454,10 @@ define({
         // ---------------------------------------------------------------------------- upload-button
         "Download from URL or upload files from disk": false,
         // ---------------------------------------------------------------------------- workflow_editor_tests
-        "tool tooltip": false
+        "tool tooltip": false,
         // ----------------------------------------------------------------------------
     },
     ja: true,
     fr: true,
-    zh: true
+    zh: true,
 });
diff --git a/client/galaxy/scripts/nls/zh/locale.js b/client/galaxy/scripts/nls/zh/locale.js
index d06132b28a5d..1688182c17e0 100644
--- a/client/galaxy/scripts/nls/zh/locale.js
+++ b/client/galaxy/scripts/nls/zh/locale.js
@@ -241,5 +241,5 @@ define({
 
     ja: true,
     fr: true,
-    zh: true
+    zh: true,
 });
diff --git a/client/galaxy/scripts/onload/defaultAppFactory.js b/client/galaxy/scripts/onload/defaultAppFactory.js
index 778a95412f67..c8f3ed3684e2 100644
--- a/client/galaxy/scripts/onload/defaultAppFactory.js
+++ b/client/galaxy/scripts/onload/defaultAppFactory.js
@@ -8,7 +8,7 @@ import { setGalaxyInstance } from "app";
  * configuration and returns a galaxy instance.
  */
 export const defaultAppFactory = (config, label = "Galaxy") => {
-    return setGalaxyInstance(GalaxyApp => {
+    return setGalaxyInstance((GalaxyApp) => {
         const { options, bootstrapped } = config;
         const app = new GalaxyApp(options, bootstrapped);
         app.debug(`${label} app`);
diff --git a/client/galaxy/scripts/onload/defaultConfigs.js b/client/galaxy/scripts/onload/defaultConfigs.js
index 740cae1d73bd..b220830ba8db 100644
--- a/client/galaxy/scripts/onload/defaultConfigs.js
+++ b/client/galaxy/scripts/onload/defaultConfigs.js
@@ -2,9 +2,9 @@ import { getRootFromIndexLink } from "./getRootFromIndexLink";
 
 export const defaultConfigs = {
     options: {
-        root: getRootFromIndexLink()
+        root: getRootFromIndexLink(),
     },
     bootstrapped: {},
     form_input_auto_focus: false,
-    sentry: {}
+    sentry: {},
 };
diff --git a/client/galaxy/scripts/onload/getRootFromIndexLink.js b/client/galaxy/scripts/onload/getRootFromIndexLink.js
index e0e6cc881422..0bf9d9ef581a 100644
--- a/client/galaxy/scripts/onload/getRootFromIndexLink.js
+++ b/client/galaxy/scripts/onload/getRootFromIndexLink.js
@@ -6,6 +6,6 @@ import { serverPath } from "utils/serverPath";
 
 export function getRootFromIndexLink(defaultRoot = "/") {
     const links = document.getElementsByTagName("link");
-    const indexLink = Array.from(links).find(link => link.rel == "index");
+    const indexLink = Array.from(links).find((link) => link.rel == "index");
     return indexLink && indexLink.href ? serverPath(indexLink.href) : defaultRoot;
 }
diff --git a/client/galaxy/scripts/onload/globalInits/iframesAreTerrible.js b/client/galaxy/scripts/onload/globalInits/iframesAreTerrible.js
index bffd4678ba9b..fab7547d4de0 100644
--- a/client/galaxy/scripts/onload/globalInits/iframesAreTerrible.js
+++ b/client/galaxy/scripts/onload/globalInits/iframesAreTerrible.js
@@ -5,7 +5,7 @@ import $ from "jquery";
 export function adjustIframeLinks() {
     console.log("adjustIframeLinks");
 
-    $("a").click(function() {
+    $("a").click(function () {
         var anchor = $(this);
         var galaxy_main_exists = window.parent.frames && window.parent.frames.galaxy_main;
         if (anchor.attr("target") == "galaxy_main" && !galaxy_main_exists) {
diff --git a/client/galaxy/scripts/onload/globalInits/init_refresh_on_change.js b/client/galaxy/scripts/onload/globalInits/init_refresh_on_change.js
index 84aacc8904a9..9f8a8c43a556 100644
--- a/client/galaxy/scripts/onload/globalInits/init_refresh_on_change.js
+++ b/client/galaxy/scripts/onload/globalInits/init_refresh_on_change.js
@@ -5,7 +5,7 @@ export function init_refresh_on_change() {
 
     $("select[refresh_on_change='true']")
         .off("change")
-        .change(function() {
+        .change(function () {
             var select_field = $(this);
             var select_val = select_field.val();
             var ref_on_change_vals = select_field.attr("refresh_on_change_values");
@@ -27,7 +27,7 @@ export function init_refresh_on_change() {
     // checkboxes refresh on change
     $(":checkbox[refresh_on_change='true']")
         .off("click")
-        .click(function() {
+        .click(function () {
             var select_field = $(this);
             var select_val = select_field.val();
             var ref_on_change_vals = select_field.attr("refresh_on_change_values");
@@ -48,7 +48,7 @@ export function init_refresh_on_change() {
     // Links with confirmation
     $("a[confirm]")
         .off("click")
-        .click(function() {
+        .click(function () {
             return confirm($(this).attr("confirm"));
         });
 }
diff --git a/client/galaxy/scripts/onload/globalInits/onloadWebhooks.js b/client/galaxy/scripts/onload/globalInits/onloadWebhooks.js
index 588277e77bbb..ed19ad84351d 100644
--- a/client/galaxy/scripts/onload/globalInits/onloadWebhooks.js
+++ b/client/galaxy/scripts/onload/globalInits/onloadWebhooks.js
@@ -7,14 +7,14 @@ export function onloadWebhooks(Galaxy) {
     if (Galaxy.config.enable_webhooks) {
         Webhooks.load({
             type: "onload",
-            callback: function(webhooks) {
-                webhooks.each(model => {
+            callback: function (webhooks) {
+                webhooks.each((model) => {
                     var webhook = model.toJSON();
                     if (webhook.activate && webhook.script) {
                         Utils.appendScriptStyle(webhook);
                     }
                 });
-            }
+            },
         });
     }
 }
diff --git a/client/galaxy/scripts/onload/globalInits/panelManagement.js b/client/galaxy/scripts/onload/globalInits/panelManagement.js
index 39c51254cafe..dbb3e9e11027 100644
--- a/client/galaxy/scripts/onload/globalInits/panelManagement.js
+++ b/client/galaxy/scripts/onload/globalInits/panelManagement.js
@@ -12,9 +12,9 @@ export function panelManagement(panelConfig) {
 
     if (left_panel) {
         var lp = new window.bundleEntries.panels.LeftPanel({
-            el: leftPanelSelector
+            el: leftPanelSelector,
         });
-        window.force_left_panel = function(x) {
+        window.force_left_panel = function (x) {
             console.log("window.force_left_panel fired");
             lp.force_panel(x);
         };
@@ -22,13 +22,13 @@ export function panelManagement(panelConfig) {
 
     if (right_panel) {
         var rp = new window.bundleEntries.panels.RightPanel({
-            el: rightPanelSelector
+            el: rightPanelSelector,
         });
-        window.handle_minwidth_hint = function(x) {
+        window.handle_minwidth_hint = function (x) {
             console.log("window.handle_minwidth_hint", x);
             rp.handle_minwidth_hint(x);
         };
-        window.force_right_panel = function(x) {
+        window.force_right_panel = function (x) {
             console.log("window.force_right_panel", x);
             rp.force_panel(x);
         };
diff --git a/client/galaxy/scripts/onload/globalInits/replace_big_select_inputs.js b/client/galaxy/scripts/onload/globalInits/replace_big_select_inputs.js
index f6ba4d89140a..9275b44a2351 100644
--- a/client/galaxy/scripts/onload/globalInits/replace_big_select_inputs.js
+++ b/client/galaxy/scripts/onload/globalInits/replace_big_select_inputs.js
@@ -8,7 +8,7 @@ function refresh_select2(element) {
         placeholder: "Click to select",
         closeOnSelect: !select_elt.is("[MULTIPLE]"),
         dropdownAutoWidth: true,
-        containerCssClass: "select2-minwidth"
+        containerCssClass: "select2-minwidth",
     };
     return element.select2(options);
 }
@@ -33,7 +33,7 @@ export function replace_big_select_inputs(min_length, max_length, select_elts) {
 
     select_elts = select_elts || $("select");
 
-    select_elts.each(function() {
+    select_elts.each(function () {
         var select_elt = $(this).not("[multiple]");
         // Make sure that options is within range.
         var num_options = select_elt.find("option").length;
diff --git a/client/galaxy/scripts/onload/initQueue.js b/client/galaxy/scripts/onload/initQueue.js
index cc2caeebe79e..cc8c05066501 100644
--- a/client/galaxy/scripts/onload/initQueue.js
+++ b/client/galaxy/scripts/onload/initQueue.js
@@ -20,7 +20,7 @@ import { filter } from "rxjs/operators";
 const queue = new BehaviorSubject([]);
 
 // don't emit unless there are things to initialize
-export const initializations$ = queue.pipe(filter(list => list.length > 0));
+export const initializations$ = queue.pipe(filter((list) => list.length > 0));
 
 export const addInitialization = (...fns) => {
     const nextInits = [...queue.getValue(), ...fns];
diff --git a/client/galaxy/scripts/onload/loadConfig.js b/client/galaxy/scripts/onload/loadConfig.js
index bc57603b3d25..e19504669f81 100644
--- a/client/galaxy/scripts/onload/loadConfig.js
+++ b/client/galaxy/scripts/onload/loadConfig.js
@@ -33,7 +33,7 @@ export { addInitialization } from "./initQueue";
 // Process incoming config.set valls
 const input = new Subject();
 const mergedConfigs = input.pipe(
-    filter(fragment => fragment instanceof Object),
+    filter((fragment) => fragment instanceof Object),
     scan((config, fragment) => {
         return Object.assign({}, config, fragment);
     }, defaultConfigs)
@@ -51,7 +51,7 @@ export const config$ = currentConfig$.asObservable().pipe(filter(Boolean), debou
  * @param  {...objects} fragments Config objects to be merged into the global config
  */
 export function set(...fragments) {
-    fragments.forEach(fragment => input.next(fragment));
+    fragments.forEach((fragment) => input.next(fragment));
 }
 
 /**
diff --git a/client/galaxy/scripts/onload/standardInit.js b/client/galaxy/scripts/onload/standardInit.js
index dc128718e064..9339af223d35 100644
--- a/client/galaxy/scripts/onload/standardInit.js
+++ b/client/galaxy/scripts/onload/standardInit.js
@@ -37,7 +37,7 @@ export function standardInit(label = "Galaxy", appFactory = defaultAppFactory) {
     globalInits();
 
     // waits for configs to stop changing then instantiates Galaxy
-    const galaxy$ = config$.pipe(map(cfg => appFactory(cfg, label)));
+    const galaxy$ = config$.pipe(map((cfg) => appFactory(cfg, label)));
 
     // once config, app and initialization observables have a value then run all
     // the initialization functions, this will keep running new initialization
@@ -46,7 +46,7 @@ export function standardInit(label = "Galaxy", appFactory = defaultAppFactory) {
     // the new batch of freshly registered init functions
     combineLatest(config$, galaxy$, initializations$).subscribe(([config, galaxy, inits]) => {
         console.groupCollapsed(`runInitializations`, label, serverPath());
-        inits.forEach(fn => fn(galaxy, config));
+        inits.forEach((fn) => fn(galaxy, config));
         clearInitQueue();
         console.groupEnd();
     });
diff --git a/client/galaxy/scripts/polyfills.js b/client/galaxy/scripts/polyfills.js
index 0ea674d30ab9..9b518cb754f4 100644
--- a/client/galaxy/scripts/polyfills.js
+++ b/client/galaxy/scripts/polyfills.js
@@ -17,12 +17,12 @@ import _ from "underscore";
     // ------------------------------------------------------------------ polyfills
     // console protection needed in some versions of IE (at this point (IE>=9), shouldn't be needed)
     window.console = window.console || {
-        log: function() {},
-        debug: function() {},
-        info: function() {},
-        warn: function() {},
-        error: function() {},
-        assert: function() {}
+        log: function () {},
+        debug: function () {},
+        info: function () {},
+        warn: function () {},
+        error: function () {},
+        assert: function () {},
     };
 
     console.debug("Polyfills are running");
@@ -50,7 +50,7 @@ import _ from "underscore";
         };
 
     if (!window.cancelAnimationFrame)
-        window.cancelAnimationFrame = id => {
+        window.cancelAnimationFrame = (id) => {
             window.clearTimeout(id);
         };
 
@@ -58,24 +58,24 @@ import _ from "underscore";
     var features = [
         {
             name: "canvas",
-            compatible: function() {
+            compatible: function () {
                 return window.CanvasRenderingContext2D;
-            }
+            },
         },
         {
             name: "sessionStorage",
-            compatible: function() {
+            compatible: function () {
                 try {
                     return window.sessionStorage.length >= 0;
                 } catch (err) {
                     console.debug(err);
                 }
                 return false;
-            }
-        }
+            },
+        },
     ];
     // build a list of feature names for features that were not found
-    var incompatibilities = features.filter(feature => !feature.compatible()).map(feature => feature.name);
+    var incompatibilities = features.filter((feature) => !feature.compatible()).map((feature) => feature.name);
 
     // if there are needed features missing, follow the index link to the static incompat warning
     if (incompatibilities.length) {
diff --git a/client/galaxy/scripts/qunit/test-app.js b/client/galaxy/scripts/qunit/test-app.js
index 6ca391741c67..6b4e9ac9fc29 100644
--- a/client/galaxy/scripts/qunit/test-app.js
+++ b/client/galaxy/scripts/qunit/test-app.js
@@ -15,16 +15,16 @@ import "./assets/base.css";
 
 export function setupTestGalaxy(galaxyOptions_ = null) {
     galaxyOptions_ = galaxyOptions_ || galaxyOptions;
-    setGalaxyInstance(GalaxyApp => {
+    setGalaxyInstance((GalaxyApp) => {
         let galaxy = new GalaxyApp(galaxyOptions_);
         galaxy.currHistoryPanel = {
-            model: new Backbone.Model()
+            model: new Backbone.Model(),
         };
         galaxy.emit = {
-            debug: function() {},
-            error: function(v) {
+            debug: function () {},
+            error: function (v) {
                 window.console.error(v);
-            }
+            },
         };
         return galaxy;
     });
@@ -39,7 +39,7 @@ export default {
             window.fakeserver.respondWith("GET", getAppRoot() + route, [
                 200,
                 { "Content-Type": "application/json" },
-                serverdata[route].data
+                serverdata[route].data,
             ]);
         }
     },
@@ -49,5 +49,5 @@ export default {
             window.fakeserver.restore();
             delete window.fakeserver;
         }
-    }
+    },
 };
diff --git a/client/galaxy/scripts/qunit/test-data/bootstrapped.js b/client/galaxy/scripts/qunit/test-data/bootstrapped.js
index b31c561a744e..a57216a20207 100644
--- a/client/galaxy/scripts/qunit/test-data/bootstrapped.js
+++ b/client/galaxy/scripts/qunit/test-data/bootstrapped.js
@@ -11,7 +11,7 @@ export default {
         terms_url: null,
         library_import_dir: null,
         logo_url: null,
-        enable_unique_workflow_defaults: false
+        enable_unique_workflow_defaults: false,
     },
     user: {
         username: "test",
@@ -21,6 +21,6 @@ export default {
         email: "test@test.test",
         tags_used: ["test"],
         model_class: "User",
-        id: "f2db41e1fa331b3e"
-    }
+        id: "f2db41e1fa331b3e",
+    },
 };
diff --git a/client/galaxy/scripts/qunit/test-data/fakeserver.js b/client/galaxy/scripts/qunit/test-data/fakeserver.js
index 6f9640003a7e..904b6fb86975 100644
--- a/client/galaxy/scripts/qunit/test-data/fakeserver.js
+++ b/client/galaxy/scripts/qunit/test-data/fakeserver.js
@@ -4,12 +4,12 @@ import toolsTestBuild from "./json/tools.test.build";
 
 export default {
     "api/datatypes/mapping": {
-        data: JSON.stringify(dataTypesMapping)
+        data: JSON.stringify(dataTypesMapping),
     },
     "api/datatypes": {
-        data: JSON.stringify(dataTypes)
+        data: JSON.stringify(dataTypes),
     },
     "api/tools/test/build": {
-        data: JSON.stringify(toolsTestBuild)
-    }
+        data: JSON.stringify(toolsTestBuild),
+    },
 };
diff --git a/client/galaxy/scripts/qunit/test-data/job-dag-1.js b/client/galaxy/scripts/qunit/test-data/job-dag-1.js
index 1e61806f1126..f2a6596eded1 100644
--- a/client/galaxy/scripts/qunit/test-data/job-dag-1.js
+++ b/client/galaxy/scripts/qunit/test-data/job-dag-1.js
@@ -5,7 +5,7 @@ var tools = {
     "Show tail1": {},
     random_lines1: {},
     __SET_METADATA__: {},
-    cat1: {}
+    cat1: {},
 };
 
 // ============================================================================
@@ -18,8 +18,8 @@ var jobs1 = [
         outputs: {
             output0: {
                 src: "hda",
-                id: "8c959c9304a2bc4b"
-            }
+                id: "8c959c9304a2bc4b",
+            },
         },
         exit_code: 0,
         state: "ok",
@@ -29,7 +29,7 @@ var jobs1 = [
         },
         model_class: "Job",
         id: "8a81cf6f989c4467",
-        tool: null
+        tool: null,
     },
     {
         tool_id: "Show beginning1",
@@ -37,14 +37,14 @@ var jobs1 = [
         inputs: {
             input: {
                 src: "hda",
-                id: "8c959c9304a2bc4b"
-            }
+                id: "8c959c9304a2bc4b",
+            },
         },
         outputs: {
             out_file1: {
                 src: "hda",
-                id: "132016f833b57406"
-            }
+                id: "132016f833b57406",
+            },
         },
         exit_code: 0,
         state: "ok",
@@ -54,7 +54,7 @@ var jobs1 = [
         },
         model_class: "Job",
         id: "6505e875ddb66fd2",
-        tool: null
+        tool: null,
     },
     {
         tool_id: "Show tail1",
@@ -62,14 +62,14 @@ var jobs1 = [
         inputs: {
             input: {
                 src: "hda",
-                id: "132016f833b57406"
-            }
+                id: "132016f833b57406",
+            },
         },
         outputs: {
             out_file1: {
                 src: "hda",
-                id: "846fb0a2a64137c0"
-            }
+                id: "846fb0a2a64137c0",
+            },
         },
         exit_code: 0,
         state: "ok",
@@ -79,8 +79,8 @@ var jobs1 = [
         },
         model_class: "Job",
         id: "77f74776fd03cbc5",
-        tool: null
-    }
+        tool: null,
+    },
 ];
 
 var historyContents1 = [
@@ -97,7 +97,7 @@ var historyContents1 = [
         state: "ok",
         type: "file",
         url: "/api/histories/911dde3ddb677bcd/contents/datasets/8c959c9304a2bc4b",
-        visible: true
+        visible: true,
     },
     {
         deleted: false,
@@ -112,7 +112,7 @@ var historyContents1 = [
         state: "ok",
         type: "file",
         url: "/api/histories/911dde3ddb677bcd/contents/datasets/132016f833b57406",
-        visible: true
+        visible: true,
     },
     {
         deleted: false,
@@ -127,8 +127,8 @@ var historyContents1 = [
         state: "ok",
         type: "file",
         url: "/api/histories/911dde3ddb677bcd/contents/datasets/846fb0a2a64137c0",
-        visible: true
-    }
+        visible: true,
+    },
 ];
 
 // ============================================================================
@@ -141,8 +141,8 @@ var jobs2 = [
         outputs: {
             output0: {
                 src: "hda",
-                id: "eca0af6fb47bf90c"
-            }
+                id: "eca0af6fb47bf90c",
+            },
         },
         exit_code: 0,
         state: "ok",
@@ -152,7 +152,7 @@ var jobs2 = [
         },
         model_class: "Job",
         id: "bf60fd5f5f7f44bf",
-        tool: null
+        tool: null,
     },
     {
         tool_id: "random_lines1",
@@ -160,14 +160,14 @@ var jobs2 = [
         inputs: {
             input: {
                 src: "hda",
-                id: "eca0af6fb47bf90c"
-            }
+                id: "eca0af6fb47bf90c",
+            },
         },
         outputs: {
             out_file1: {
                 src: "hda",
-                id: "6fc9fbb81c497f69"
-            }
+                id: "6fc9fbb81c497f69",
+            },
         },
         exit_code: 0,
         state: "ok",
@@ -177,7 +177,7 @@ var jobs2 = [
         },
         model_class: "Job",
         id: "90240358ebde1489",
-        tool: null
+        tool: null,
     },
     {
         tool_id: "__SET_METADATA__",
@@ -185,8 +185,8 @@ var jobs2 = [
         inputs: {
             input1: {
                 src: "hda",
-                id: "eca0af6fb47bf90c"
-            }
+                id: "eca0af6fb47bf90c",
+            },
         },
         outputs: {},
         exit_code: 0,
@@ -197,8 +197,8 @@ var jobs2 = [
         },
         model_class: "Job",
         id: "86cf1d3beeec9f1c",
-        tool: null
-    }
+        tool: null,
+    },
 ];
 
 var historyContents2 = [
@@ -215,7 +215,7 @@ var historyContents2 = [
         state: "ok",
         type: "file",
         url: "/api/histories/ff5476bcf6c921fa/contents/datasets/eca0af6fb47bf90c",
-        visible: true
+        visible: true,
     },
     {
         deleted: false,
@@ -230,8 +230,8 @@ var historyContents2 = [
         state: "ok",
         type: "file",
         url: "/api/histories/ff5476bcf6c921fa/contents/datasets/6fc9fbb81c497f69",
-        visible: true
-    }
+        visible: true,
+    },
 ];
 
 var jobs3 = [
@@ -242,8 +242,8 @@ var jobs3 = [
         outputs: {
             output0: {
                 src: "hda",
-                id: "6fb17d0cc6e8fae5"
-            }
+                id: "6fb17d0cc6e8fae5",
+            },
         },
         exit_code: 0,
         state: "ok",
@@ -253,7 +253,7 @@ var jobs3 = [
         },
         model_class: "Job",
         id: "8c959c9304a2bc4b",
-        tool: null
+        tool: null,
     },
     {
         tool_id: "upload1",
@@ -262,8 +262,8 @@ var jobs3 = [
         outputs: {
             output0: {
                 src: "hda",
-                id: "5114a2a207b7caff"
-            }
+                id: "5114a2a207b7caff",
+            },
         },
         exit_code: 0,
         state: "ok",
@@ -273,7 +273,7 @@ var jobs3 = [
         },
         model_class: "Job",
         id: "132016f833b57406",
-        tool: null
+        tool: null,
     },
     {
         tool_id: "Show beginning1",
@@ -281,14 +281,14 @@ var jobs3 = [
         inputs: {
             input: {
                 src: "hda",
-                id: "6fb17d0cc6e8fae5"
-            }
+                id: "6fb17d0cc6e8fae5",
+            },
         },
         outputs: {
             out_file1: {
                 src: "hda",
-                id: "06ec17aefa2d49dd"
-            }
+                id: "06ec17aefa2d49dd",
+            },
         },
         exit_code: 0,
         state: "ok",
@@ -298,7 +298,7 @@ var jobs3 = [
         },
         model_class: "Job",
         id: "846fb0a2a64137c0",
-        tool: null
+        tool: null,
     },
     {
         tool_id: "Show beginning1",
@@ -306,14 +306,14 @@ var jobs3 = [
         inputs: {
             input: {
                 src: "hda",
-                id: "5114a2a207b7caff"
-            }
+                id: "5114a2a207b7caff",
+            },
         },
         outputs: {
             out_file1: {
                 src: "hda",
-                id: "b8a0d6158b9961df"
-            }
+                id: "b8a0d6158b9961df",
+            },
         },
         exit_code: 0,
         state: "ok",
@@ -323,7 +323,7 @@ var jobs3 = [
         },
         model_class: "Job",
         id: "eca0af6fb47bf90c",
-        tool: null
+        tool: null,
     },
     {
         tool_id: "Show tail1",
@@ -331,14 +331,14 @@ var jobs3 = [
         inputs: {
             input: {
                 src: "hda",
-                id: "b8a0d6158b9961df"
-            }
+                id: "b8a0d6158b9961df",
+            },
         },
         outputs: {
             out_file1: {
                 src: "hda",
-                id: "24d84bcf64116fe7"
-            }
+                id: "24d84bcf64116fe7",
+            },
         },
         exit_code: 0,
         state: "ok",
@@ -348,8 +348,8 @@ var jobs3 = [
         },
         model_class: "Job",
         id: "6fc9fbb81c497f69",
-        tool: null
-    }
+        tool: null,
+    },
 ];
 
 var historyContents3 = [
@@ -366,7 +366,7 @@ var historyContents3 = [
         state: "ok",
         type: "file",
         url: "/api/histories/5564089c81cf7fe8/contents/datasets/6fb17d0cc6e8fae5",
-        visible: true
+        visible: true,
     },
     {
         deleted: false,
@@ -381,7 +381,7 @@ var historyContents3 = [
         state: "ok",
         type: "file",
         url: "/api/histories/5564089c81cf7fe8/contents/datasets/5114a2a207b7caff",
-        visible: true
+        visible: true,
     },
     {
         deleted: false,
@@ -396,7 +396,7 @@ var historyContents3 = [
         state: "ok",
         type: "file",
         url: "/api/histories/5564089c81cf7fe8/contents/datasets/06ec17aefa2d49dd",
-        visible: true
+        visible: true,
     },
     {
         deleted: false,
@@ -411,7 +411,7 @@ var historyContents3 = [
         state: "ok",
         type: "file",
         url: "/api/histories/5564089c81cf7fe8/contents/datasets/b8a0d6158b9961df",
-        visible: true
+        visible: true,
     },
     {
         deleted: false,
@@ -426,8 +426,8 @@ var historyContents3 = [
         state: "ok",
         type: "file",
         url: "/api/histories/5564089c81cf7fe8/contents/datasets/24d84bcf64116fe7",
-        visible: true
-    }
+        visible: true,
+    },
 ];
 
 var jobs4 = [
@@ -438,20 +438,20 @@ var jobs4 = [
             input1: {
                 src: "hda",
                 id: "422eef6b1b545329",
-                name: "input1"
+                name: "input1",
             },
             "queries_0|input2": {
                 src: "hda",
                 id: "c86c1b73aa7102dd",
-                name: "queries_0|input2"
-            }
+                name: "queries_0|input2",
+            },
         },
         outputs: {
             out_file1: {
                 src: "hda",
                 id: "52d6bdfafedbb5e5",
-                name: "out_file1"
-            }
+                name: "out_file1",
+            },
         },
         exit_code: 0,
         state: "ok",
@@ -460,8 +460,8 @@ var jobs4 = [
             // ...
         },
         model_class: "Job",
-        id: "92b83968e0b52980"
-    }
+        id: "92b83968e0b52980",
+    },
 ];
 
 var historyContents4 = [
@@ -479,7 +479,7 @@ var historyContents4 = [
         state: "ok",
         type: "file",
         url: "/api/histories/c24141d7e4e77705/contents/datasets/422eef6b1b545329",
-        visible: true
+        visible: true,
     },
     {
         dataset_id: 56,
@@ -495,7 +495,7 @@ var historyContents4 = [
         state: "ok",
         type: "file",
         url: "/api/histories/c24141d7e4e77705/contents/datasets/c86c1b73aa7102dd",
-        visible: true
+        visible: true,
     },
     {
         dataset_id: 131,
@@ -511,8 +511,8 @@ var historyContents4 = [
         state: "ok",
         type: "file",
         url: "/api/histories/c24141d7e4e77705/contents/datasets/52d6bdfafedbb5e5",
-        visible: true
-    }
+        visible: true,
+    },
 ];
 
 // ============================================================================
@@ -525,5 +525,5 @@ export default {
     jobs3: jobs3,
     historyContents3: historyContents3,
     jobs4: jobs4,
-    historyContents4: historyContents4
+    historyContents4: historyContents4,
 };
diff --git a/client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js b/client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js
index 9897a38d26f1..5a4a2d42a30b 100644
--- a/client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js
+++ b/client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js
@@ -14,7 +14,7 @@ var datasets1 = [
     { name: "SET1-06_1.fastq" },
     { name: "SET1-06_2.fastq" },
     { name: "SET1-07_1.fastq" },
-    { name: "SET1-07_2.fastq" }
+    { name: "SET1-07_2.fastq" },
 ];
 
 var datasets1CreateRequestJSON = {
@@ -31,14 +31,14 @@ var datasets1CreateRequestJSON = {
                 {
                     name: "forward",
                     id: "2",
-                    src: "hda"
+                    src: "hda",
                 },
                 {
                     name: "reverse",
                     id: "3",
-                    src: "hda"
-                }
-            ]
+                    src: "hda",
+                },
+            ],
         },
         {
             collection_type: "paired",
@@ -48,14 +48,14 @@ var datasets1CreateRequestJSON = {
                 {
                     name: "forward",
                     id: "4",
-                    src: "hda"
+                    src: "hda",
                 },
                 {
                     name: "reverse",
                     id: "5",
-                    src: "hda"
-                }
-            ]
+                    src: "hda",
+                },
+            ],
         },
         {
             collection_type: "paired",
@@ -65,14 +65,14 @@ var datasets1CreateRequestJSON = {
                 {
                     name: "forward",
                     id: "6",
-                    src: "hda"
+                    src: "hda",
                 },
                 {
                     name: "reverse",
                     id: "7",
-                    src: "hda"
-                }
-            ]
+                    src: "hda",
+                },
+            ],
         },
         {
             collection_type: "paired",
@@ -82,14 +82,14 @@ var datasets1CreateRequestJSON = {
                 {
                     name: "forward",
                     id: "8",
-                    src: "hda"
+                    src: "hda",
                 },
                 {
                     name: "reverse",
                     id: "9",
-                    src: "hda"
-                }
-            ]
+                    src: "hda",
+                },
+            ],
         },
         {
             collection_type: "paired",
@@ -99,14 +99,14 @@ var datasets1CreateRequestJSON = {
                 {
                     name: "forward",
                     id: "10",
-                    src: "hda"
+                    src: "hda",
                 },
                 {
                     name: "reverse",
                     id: "11",
-                    src: "hda"
-                }
-            ]
+                    src: "hda",
+                },
+            ],
         },
         {
             collection_type: "paired",
@@ -116,14 +116,14 @@ var datasets1CreateRequestJSON = {
                 {
                     name: "forward",
                     id: "12",
-                    src: "hda"
+                    src: "hda",
                 },
                 {
                     name: "reverse",
                     id: "13",
-                    src: "hda"
-                }
-            ]
+                    src: "hda",
+                },
+            ],
         },
         {
             collection_type: "paired",
@@ -133,20 +133,20 @@ var datasets1CreateRequestJSON = {
                 {
                     name: "forward",
                     id: "14",
-                    src: "hda"
+                    src: "hda",
                 },
                 {
                     name: "reverse",
                     id: "15",
-                    src: "hda"
-                }
-            ]
-        }
-    ]
+                    src: "hda",
+                },
+            ],
+        },
+    ],
 };
 
 // ============================================================================
 export default {
     _1: datasets1,
-    _1requestJSON: datasets1CreateRequestJSON
+    _1requestJSON: datasets1CreateRequestJSON,
 };
diff --git a/client/galaxy/scripts/qunit/tests/form_tests.js b/client/galaxy/scripts/qunit/tests/form_tests.js
index f6e1266f5ceb..e6ace9ef4aee 100644
--- a/client/galaxy/scripts/qunit/tests/form_tests.js
+++ b/client/galaxy/scripts/qunit/tests/form_tests.js
@@ -13,17 +13,17 @@ import Utils from "utils/utils";
 import { getAppRoot } from "onload/loadConfig";
 
 QUnit.module("Form test", {
-    beforeEach: function() {
+    beforeEach: function () {
         testApp.create();
         $.fx.off = true;
     },
-    afterEach: function() {
+    afterEach: function () {
         testApp.destroy();
         $.fx.off = false;
-    }
+    },
 });
 
-QUnit.test("tool-form", function(assert) {
+QUnit.test("tool-form", function (assert) {
     var toolform = new ToolForm.View({ id: "test" });
     $("body").prepend(toolform.$el);
     window.fakeserver.respond();
@@ -38,7 +38,7 @@ QUnit.test("tool-form", function(assert) {
         "Title correct"
     );
     var tour_ids = [];
-    $("[tour_id]").each(function() {
+    $("[tour_id]").each(function () {
         tour_ids.push($(this).attr("tour_id"));
     });
     assert.ok(
@@ -51,7 +51,7 @@ QUnit.test("tool-form", function(assert) {
         "Created data correct"
     );
     var mapped_ids = [];
-    form.data.matchModel(form.model.attributes, function(input, id) {
+    form.data.matchModel(form.model.attributes, function (input, id) {
         mapped_ids.push($("#" + id).attr("tour_id"));
     });
     assert.ok(
@@ -60,10 +60,7 @@ QUnit.test("tool-form", function(assert) {
     );
     var dropdown = form.$("#menu > .dropdown-menu");
     assert.ok(dropdown.children().length == 2, "Found two menu items");
-    dropdown
-        .find(".fa-info-circle")
-        .parent()
-        .click();
+    dropdown.find(".fa-info-circle").parent().click();
     assert.ok(
         form.$(".alert").html() ===
             '<span>This tool requires req_name_a (Version req_version_a) and req_name_b (Version req_version_b). Click <a target="_blank" href="https://galaxyproject.org/tools/requirements/">here</a> for more information.</span>',
@@ -74,7 +71,7 @@ QUnit.test("tool-form", function(assert) {
     assert.ok(!$add.attr("disabled"), "Adding new repeat possible");
     $add.click();
     assert.ok($add.attr("disabled"), "Adding new repeat has been disabled");
-    form.$(".form-repeat-delete").each(function(i, d) {
+    form.$(".form-repeat-delete").each(function (i, d) {
         assert.ok($(d).css("display") == "block", "Delete buttons " + i + " enabled");
     });
     assert.ok(
@@ -91,15 +88,15 @@ QUnit.test("tool-form", function(assert) {
     );
 });
 
-QUnit.test("data", function(assert) {
+QUnit.test("data", function (assert) {
     var visits = [];
     Utils.get({
         url: getAppRoot() + "api/tools/test/build",
-        success: function(response) {
-            FormData.visitInputs(response.inputs, function(node, name, context) {
+        success: function (response) {
+            FormData.visitInputs(response.inputs, function (node, name, context) {
                 visits.push({ name: name, node: node });
             });
-        }
+        },
     });
     window.fakeserver.respond();
     assert.ok(
@@ -109,11 +106,11 @@ QUnit.test("data", function(assert) {
     );
 });
 
-QUnit.test("input", function(assert) {
+QUnit.test("input", function (assert) {
     var input = new InputElement(
         {},
         {
-            field: new Ui.Input({})
+            field: new Ui.Input({}),
         }
     );
     $("body").prepend(input.$el);
diff --git a/client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js b/client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js
index ab4019539101..941be5d4c41f 100644
--- a/client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js
+++ b/client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js
@@ -3,15 +3,15 @@ import testApp from "qunit/test-app";
 import { getGalaxyInstance, setGalaxyInstance } from "app";
 
 QUnit.module("Galaxy client app tests", {
-    beforeEach: function() {
+    beforeEach: function () {
         testApp.create();
     },
-    afterEach: function() {
+    afterEach: function () {
         testApp.destroy();
-    }
+    },
 });
 
-QUnit.test("App base construction/initializiation defaults", function(assert) {
+QUnit.test("App base construction/initializiation defaults", function (assert) {
     var app = getGalaxyInstance();
     assert.ok(app.hasOwnProperty("options") && typeof app.options === "object");
     assert.ok(app.hasOwnProperty("logger") && typeof app.logger === "object");
@@ -21,46 +21,46 @@ QUnit.test("App base construction/initializiation defaults", function(assert) {
     assert.equal(app.localize, window._l);
 });
 
-QUnit.test("App base default options", function(assert) {
+QUnit.test("App base default options", function (assert) {
     var app = getGalaxyInstance();
     assert.ok(app.hasOwnProperty("options") && typeof app.options === "object");
     assert.equal(app.options.root, "/");
     assert.equal(app.options.patchExisting, true);
 });
 
-QUnit.test("App base extends from Backbone.Events", function(assert) {
+QUnit.test("App base extends from Backbone.Events", function (assert) {
     var app = getGalaxyInstance();
-    ["on", "off", "trigger", "listenTo", "stopListening"].forEach(function(fn) {
+    ["on", "off", "trigger", "listenTo", "stopListening"].forEach(function (fn) {
         assert.ok(app.hasOwnProperty(fn) && typeof app[fn] === "function");
     });
 });
 
-QUnit.test("App base has logging methods from utils/add-logging.js", function(assert) {
+QUnit.test("App base has logging methods from utils/add-logging.js", function (assert) {
     var app = getGalaxyInstance();
-    ["debug", "info", "warn", "error", "metric"].forEach(function(fn) {
+    ["debug", "info", "warn", "error", "metric"].forEach(function (fn) {
         assert.ok(typeof app[fn] === "function");
     });
     assert.ok(app._logNamespace === "GalaxyApp");
 });
 
 // We no longer want this behavior
-QUnit.test("App base will patch in attributes from existing Galaxy objects", function(assert) {
+QUnit.test("App base will patch in attributes from existing Galaxy objects", function (assert) {
     var existingApp = getGalaxyInstance();
     existingApp.foo = 123;
 
-    var newApp = setGalaxyInstance(GalaxyApp => {
+    var newApp = setGalaxyInstance((GalaxyApp) => {
         return new GalaxyApp();
     });
 
     assert.ok(newApp.foo === 123);
 });
 
-QUnit.test("App base logger", function(assert) {
+QUnit.test("App base logger", function (assert) {
     var app = getGalaxyInstance();
     assert.ok(app.hasOwnProperty("logger") && typeof app.config === "object");
 });
 
-QUnit.test("App base config", function(assert) {
+QUnit.test("App base config", function (assert) {
     var app = getGalaxyInstance();
     assert.ok(app.hasOwnProperty("config") && typeof app.config === "object");
     assert.equal(app.config.allow_user_deletion, false);
@@ -69,7 +69,7 @@ QUnit.test("App base config", function(assert) {
     assert.equal(app.config.ftp_upload_site, null);
 });
 
-QUnit.test("App base user", function(assert) {
+QUnit.test("App base user", function (assert) {
     var app = getGalaxyInstance();
     assert.ok(app.hasOwnProperty("user") && typeof app.user === "object");
     assert.ok(app.user.isAdmin() === false);
diff --git a/client/galaxy/scripts/qunit/tests/graph_tests.js b/client/galaxy/scripts/qunit/tests/graph_tests.js
index 0e50f7a5773b..197a85d4644b 100644
--- a/client/galaxy/scripts/qunit/tests/graph_tests.js
+++ b/client/galaxy/scripts/qunit/tests/graph_tests.js
@@ -3,12 +3,12 @@ import testApp from "qunit/test-app";
 import GRAPH from "utils/graph";
 
 QUnit.module("utils/graph.js library tests", {
-    beforeEach: function() {
+    beforeEach: function () {
         testApp.create();
     },
-    afterEach: function() {
+    afterEach: function () {
         testApp.destroy();
-    }
+    },
 });
 
 ///*
@@ -18,7 +18,7 @@ function testEmptyObject(assert, o) {
 }
 
 // ------------------------------------------------------------------------ vertices
-QUnit.test("Empty vertex construction", function(assert) {
+QUnit.test("Empty vertex construction", function (assert) {
     var vert = new GRAPH.Vertex();
     assert.ok(vert instanceof GRAPH.Vertex);
     assert.ok(vert.name === "(unnamed)");
@@ -29,7 +29,7 @@ QUnit.test("Empty vertex construction", function(assert) {
     assert.deepEqual(vert.toJSON(), { name: "(unnamed)", data: null });
 });
 
-QUnit.test("Vertex construction", function(assert) {
+QUnit.test("Vertex construction", function (assert) {
     var vert = new GRAPH.Vertex("blah", { blorp: 1, bleep: 2 });
     assert.ok(vert instanceof GRAPH.Vertex);
     assert.ok(vert.name === "blah");
@@ -41,7 +41,7 @@ QUnit.test("Vertex construction", function(assert) {
 });
 
 // ------------------------------------------------------------------------ edges
-QUnit.test("Empty edge construction", function(assert) {
+QUnit.test("Empty edge construction", function (assert) {
     var edge = new GRAPH.Edge();
     assert.ok(edge instanceof GRAPH.Edge);
     assert.ok(edge.source === null);
@@ -51,7 +51,7 @@ QUnit.test("Empty edge construction", function(assert) {
     assert.deepEqual(edge.toJSON(), { source: null, target: null });
 });
 
-QUnit.test("Edge construction", function(assert) {
+QUnit.test("Edge construction", function (assert) {
     var edge = new GRAPH.Edge("A", "B", { one: 1, two: 2 });
     assert.ok(edge instanceof GRAPH.Edge);
     assert.ok(edge.source === "A");
@@ -68,7 +68,7 @@ function testEmptyGraph(assert, graph) {
     assert.ok(graph.numEdges === 0);
 }
 
-QUnit.test("Empty graph construction", function(assert) {
+QUnit.test("Empty graph construction", function (assert) {
     var graph = new GRAPH.Graph();
 
     assert.ok(graph.directed === false);
@@ -77,7 +77,7 @@ QUnit.test("Empty graph construction", function(assert) {
     testEmptyGraph(assert, graph);
 });
 
-QUnit.test("Bad data graph construction", function(assert) {
+QUnit.test("Bad data graph construction", function (assert) {
     var graph = new GRAPH.Graph(false, {});
     testEmptyGraph(assert, graph);
 
@@ -85,7 +85,7 @@ QUnit.test("Bad data graph construction", function(assert) {
     testEmptyGraph(assert, graph);
 });
 
-QUnit.test("Test directed and options", function(assert) {
+QUnit.test("Test directed and options", function (assert) {
     var graph = new GRAPH.Graph(true, {}, { allowReflexiveEdges: true });
 
     assert.ok(graph.directed);
@@ -147,21 +147,21 @@ var nodeLinkData = {
     nodes: [
         { name: "A", data: 100 },
         { name: "B", data: 200 },
-        { name: "C", data: 300 }
+        { name: "C", data: 300 },
     ],
     links: [
         { source: 0, target: 1 },
         { source: 0, target: 2 },
-        { source: 1, target: 2 }
-    ]
+        { source: 1, target: 2 },
+    ],
 };
 
-QUnit.test("Test nodes and links data input on *non-directed* graph", function(assert) {
+QUnit.test("Test nodes and links data input on *non-directed* graph", function (assert) {
     var graph = new GRAPH.Graph(false, nodeLinkData);
     testSampleDirectedGraph(assert, graph);
 });
 
-QUnit.test("Test nodes and links data input on *directed* graph", function(assert) {
+QUnit.test("Test nodes and links data input on *directed* graph", function (assert) {
     var graph = new GRAPH.Graph(true, nodeLinkData);
     testSampleNonDirectedGraph(assert, graph);
 });
@@ -170,30 +170,30 @@ var vertexEdgeData = {
     vertices: [
         { name: "A", data: 100 },
         { name: "B", data: 200 },
-        { name: "C", data: 300 }
+        { name: "C", data: 300 },
     ],
     edges: [
         { source: "A", target: "B" },
         { source: "A", target: "C" },
-        { source: "B", target: "C" }
-    ]
+        { source: "B", target: "C" },
+    ],
 };
 
-QUnit.test("Test vertex and edge data input on *non-directed* graph", function(assert) {
+QUnit.test("Test vertex and edge data input on *non-directed* graph", function (assert) {
     var graph = new GRAPH.Graph(false, vertexEdgeData);
     testSampleDirectedGraph(assert, graph);
 });
 
-QUnit.test("Test vertex and edge data input on *directed* graph", function(assert) {
+QUnit.test("Test vertex and edge data input on *directed* graph", function (assert) {
     var graph = new GRAPH.Graph(true, vertexEdgeData);
     testSampleNonDirectedGraph(assert, graph);
 });
 
-QUnit.test("Test vertex eachEdge", function(assert) {
+QUnit.test("Test vertex eachEdge", function (assert) {
     var graph = new GRAPH.Graph(false, nodeLinkData);
     assert.ok(typeof graph.vertices.A.eachEdge === "function");
     assert.deepEqual(
-        graph.vertices.A.eachEdge(function(e) {
+        graph.vertices.A.eachEdge(function (e) {
             return e.target;
         }),
         ["B", "C"]
@@ -201,23 +201,23 @@ QUnit.test("Test vertex eachEdge", function(assert) {
     assert.ok(graph.vertices.A.eachEdge({ target: "B" }).length === 1);
 });
 
-QUnit.test("Test graph eachVertex", function(assert) {
+QUnit.test("Test graph eachVertex", function (assert) {
     var graph = new GRAPH.Graph(true, nodeLinkData);
     assert.ok(typeof graph.eachVertex === "function");
     assert.deepEqual(
-        graph.eachVertex(function(v) {
+        graph.eachVertex(function (v) {
             return { n: v.name, d: v.degree };
         }),
         [
             { n: "A", d: 2 },
             { n: "B", d: 1 },
-            { n: "C", d: 0 }
+            { n: "C", d: 0 },
         ]
     );
     assert.ok(graph.eachVertex({ degree: 2 })[0] === graph.vertices.A);
 });
 
-QUnit.test("Test createVertex", function(assert) {
+QUnit.test("Test createVertex", function (assert) {
     var graph = new GRAPH.Graph();
     var vert1 = graph.createVertex("A", { blah: 1 });
     assert.ok(vert1 instanceof GRAPH.Vertex);
@@ -225,7 +225,7 @@ QUnit.test("Test createVertex", function(assert) {
     assert.ok(graph.createVertex("A", { blah: 1 }) === vert1);
 });
 
-QUnit.test("Test createEdge", function(assert) {
+QUnit.test("Test createEdge", function (assert) {
     var graph, A, B, edge;
 
     graph = new GRAPH.Graph();
@@ -274,11 +274,11 @@ QUnit.test("Test createEdge", function(assert) {
     assert.ok(A.edges.A);
 });
 
-QUnit.test("Test graph.edges", function(assert) {
+QUnit.test("Test graph.edges", function (assert) {
     var graph = new GRAPH.Graph(false, nodeLinkData);
     assert.ok(graph.edges().length === 6);
     assert.deepEqual(
-        graph.edges(function(e) {
+        graph.edges(function (e) {
             return e.source;
         }),
         ["A", "A", "B", "B", "C", "C"]
@@ -288,7 +288,7 @@ QUnit.test("Test graph.edges", function(assert) {
     graph = new GRAPH.Graph(true, nodeLinkData);
     assert.ok(graph.edges().length === 3);
     assert.deepEqual(
-        graph.edges(function(e) {
+        graph.edges(function (e) {
             return e.source;
         }),
         ["A", "A", "B"]
@@ -296,17 +296,17 @@ QUnit.test("Test graph.edges", function(assert) {
     assert.deepEqual(graph.edges({ source: "A" }), [graph.vertices.A.edges.B, graph.vertices.A.edges.C]);
 });
 
-QUnit.test("Test graph.adjacent", function(assert) {
+QUnit.test("Test graph.adjacent", function (assert) {
     var graph = new GRAPH.Graph(true, nodeLinkData);
     assert.deepEqual(graph.adjacent(graph.vertices.A), [graph.vertices.B, graph.vertices.C]);
     assert.deepEqual(graph.adjacent(graph.vertices.B), [graph.vertices.C]);
     assert.deepEqual(graph.adjacent(graph.vertices.C), []);
 });
 
-QUnit.test("Test graph.eachAdjacent", function(assert) {
+QUnit.test("Test graph.eachAdjacent", function (assert) {
     var graph = new GRAPH.Graph(true, nodeLinkData);
     assert.deepEqual(
-        graph.eachAdjacent(graph.vertices.A, function(v, e) {
+        graph.eachAdjacent(graph.vertices.A, function (v, e) {
             return v;
         }),
         [graph.vertices.B, graph.vertices.C]
@@ -314,7 +314,7 @@ QUnit.test("Test graph.eachAdjacent", function(assert) {
 });
 
 // ------------------------------------------------------------------------ breadth first search
-QUnit.test("Empty BreadthFirstSearch", function(assert) {
+QUnit.test("Empty BreadthFirstSearch", function (assert) {
     var search = new GRAPH.BreadthFirstSearch();
     assert.ok(search instanceof GRAPH.BreadthFirstSearch);
     assert.ok(search.graph === undefined);
@@ -325,7 +325,7 @@ QUnit.test("Empty BreadthFirstSearch", function(assert) {
     assert.ok(typeof search._cache === "object");
 });
 
-QUnit.test("BreadthFirstSearch on undirected graph", function(assert) {
+QUnit.test("BreadthFirstSearch on undirected graph", function (assert) {
     var graph = new GRAPH.Graph(false, nodeLinkData),
         bfs = new GRAPH.BreadthFirstSearch(graph);
     assert.ok(bfs instanceof GRAPH.BreadthFirstSearch);
@@ -337,13 +337,13 @@ QUnit.test("BreadthFirstSearch on undirected graph", function(assert) {
         discovered: { A: true, B: true, C: true },
         edges: [
             { source: "A", target: "B" },
-            { source: "A", target: "C" }
-        ]
+            { source: "A", target: "C" },
+        ],
     });
     assert.ok(tree instanceof GRAPH.Graph);
     assert.deepEqual(tree.vertices.A.toJSON(), graph.vertices.A.toJSON());
     assert.deepEqual(
-        tree.eachVertex(function(v) {
+        tree.eachVertex(function (v) {
             return v.degree;
         }),
         [2, 0, 0]
@@ -351,17 +351,17 @@ QUnit.test("BreadthFirstSearch on undirected graph", function(assert) {
 
     assert.deepEqual(bfs.search("B").edges, [
         { source: "B", target: "A" },
-        { source: "B", target: "C" }
+        { source: "B", target: "C" },
     ]);
     assert.deepEqual(bfs.search("C").edges, [
         { source: "C", target: "A" },
-        { source: "C", target: "B" }
+        { source: "C", target: "B" },
     ]);
     assert.ok(typeof bfs._cache.A === "object");
     assert.deepEqual(Object.keys(bfs._cache), ["A", "B", "C"]);
 });
 
-QUnit.test("BreadthFirstSearch on directed graph", function(assert) {
+QUnit.test("BreadthFirstSearch on directed graph", function (assert) {
     var graph = new GRAPH.Graph(true, nodeLinkData),
         bfs = new GRAPH.BreadthFirstSearch(graph);
     assert.ok(bfs instanceof GRAPH.BreadthFirstSearch);
@@ -373,13 +373,13 @@ QUnit.test("BreadthFirstSearch on directed graph", function(assert) {
         discovered: { A: true, B: true, C: true },
         edges: [
             { source: "A", target: "B" },
-            { source: "A", target: "C" }
-        ]
+            { source: "A", target: "C" },
+        ],
     });
     assert.ok(tree instanceof GRAPH.Graph);
     assert.deepEqual(tree.vertices.A.toJSON(), graph.vertices.A.toJSON());
     assert.deepEqual(
-        tree.eachVertex(function(v) {
+        tree.eachVertex(function (v) {
             return v.degree;
         }),
         [2, 0, 0]
@@ -403,11 +403,11 @@ var DFSData = {
         { source: "A", target: "E" },
         { source: "E", target: "F" },
         // confound it
-        { source: "F", target: "A" }
-    ]
+        { source: "F", target: "A" },
+    ],
 };
 
-QUnit.test("Empty DepthFirstSearch", function(assert) {
+QUnit.test("Empty DepthFirstSearch", function (assert) {
     var search = new GRAPH.DepthFirstSearch();
     assert.ok(search instanceof GRAPH.DepthFirstSearch);
     assert.ok(search.graph === undefined);
@@ -418,7 +418,7 @@ QUnit.test("Empty DepthFirstSearch", function(assert) {
     assert.ok(typeof search._cache === "object");
 });
 
-QUnit.test("DepthFirstSearch on undirected graph", function(assert) {
+QUnit.test("DepthFirstSearch on undirected graph", function (assert) {
     var graph = new GRAPH.Graph(false, DFSData),
         dfs = new GRAPH.DepthFirstSearch(graph);
     assert.ok(dfs instanceof GRAPH.DepthFirstSearch);
@@ -433,15 +433,15 @@ QUnit.test("DepthFirstSearch on undirected graph", function(assert) {
             { source: "B", target: "C" },
             { source: "C", target: "D" },
             { source: "A", target: "E" },
-            { source: "E", target: "F" }
+            { source: "E", target: "F" },
         ],
         entryTimes: { A: 0, B: 1, C: 2, D: 3, E: 7, F: 8 },
-        exitTimes: { A: 11, B: 6, C: 5, D: 4, E: 10, F: 9 }
+        exitTimes: { A: 11, B: 6, C: 5, D: 4, E: 10, F: 9 },
     });
     assert.ok(tree instanceof GRAPH.Graph);
     assert.deepEqual(tree.vertices.A.toJSON(), graph.vertices.A.toJSON());
     assert.deepEqual(
-        tree.eachVertex(function(v) {
+        tree.eachVertex(function (v) {
             return v.degree;
         }),
         [2, 1, 1, 0, 1, 0]
@@ -452,14 +452,14 @@ QUnit.test("DepthFirstSearch on undirected graph", function(assert) {
         { source: "A", target: "C" },
         { source: "C", target: "D" },
         { source: "A", target: "E" },
-        { source: "E", target: "F" }
+        { source: "E", target: "F" },
     ]);
 
     assert.ok(typeof dfs._cache.A === "object");
     assert.deepEqual(Object.keys(dfs._cache), ["A", "B"]);
 });
 
-QUnit.test("DepthFirstSearch on directed graph", function(assert) {
+QUnit.test("DepthFirstSearch on directed graph", function (assert) {
     var graph = new GRAPH.Graph(true, DFSData),
         dfs = new GRAPH.DepthFirstSearch(graph);
     assert.ok(dfs instanceof GRAPH.DepthFirstSearch);
@@ -474,15 +474,15 @@ QUnit.test("DepthFirstSearch on directed graph", function(assert) {
             { source: "B", target: "C" },
             { source: "C", target: "D" },
             { source: "A", target: "E" },
-            { source: "E", target: "F" }
+            { source: "E", target: "F" },
         ],
         entryTimes: { A: 0, B: 1, C: 2, D: 3, E: 7, F: 8 },
-        exitTimes: { A: 11, B: 6, C: 5, D: 4, E: 10, F: 9 }
+        exitTimes: { A: 11, B: 6, C: 5, D: 4, E: 10, F: 9 },
     });
     assert.ok(tree instanceof GRAPH.Graph);
     assert.deepEqual(tree.vertices.A.toJSON(), graph.vertices.A.toJSON());
     assert.deepEqual(
-        tree.eachVertex(function(v) {
+        tree.eachVertex(function (v) {
             return v.degree;
         }),
         [2, 1, 1, 0, 1, 0]
@@ -490,7 +490,7 @@ QUnit.test("DepthFirstSearch on directed graph", function(assert) {
 
     assert.deepEqual(dfs.search("B").edges, [
         { source: "B", target: "C" },
-        { source: "C", target: "D" }
+        { source: "C", target: "D" },
     ]);
 
     assert.ok(typeof dfs._cache.A === "object");
@@ -499,27 +499,27 @@ QUnit.test("DepthFirstSearch on directed graph", function(assert) {
 
 // ------------------------------------------------------------------------ components
 //*/
-QUnit.test("weakComponents on undirected graph", function(assert) {
+QUnit.test("weakComponents on undirected graph", function (assert) {
     var graph = new GRAPH.Graph(false, {
         vertices: [{ name: "A" }, { name: "B" }, { name: "C" }, { name: "D" }, { name: "E" }],
         edges: [
             { source: "A", target: "B" },
-            { source: "C", target: "D" }
-        ]
+            { source: "C", target: "D" },
+        ],
     });
     assert.equal(graph.numEdges, 4);
     var components = graph.weakComponents();
     assert.equal(components.length, 3);
 });
 
-QUnit.test("weakComponents on directed graph", function(assert) {
+QUnit.test("weakComponents on directed graph", function (assert) {
     var graph, components;
     graph = new GRAPH.Graph(true, {
         vertices: [{ name: "A" }, { name: "B" }, { name: "C" }, { name: "D" }, { name: "E" }],
         edges: [
             { source: "A", target: "B" },
-            { source: "D", target: "C" }
-        ]
+            { source: "D", target: "C" },
+        ],
     });
     assert.equal(graph.numEdges, 2);
 
@@ -534,14 +534,14 @@ QUnit.test("weakComponents on directed graph", function(assert) {
             { name: "D", data: 40 },
             { name: "E", data: 500 },
             { name: "F", data: 600 },
-            { name: "G", data: 7 }
+            { name: "G", data: 7 },
         ],
         edges: [
             { source: "A", target: "B" },
             { source: "D", target: "C" },
             { source: "E", target: "A" },
-            { source: "F", target: "E" }
-        ]
+            { source: "F", target: "E" },
+        ],
     });
     components = graph.weakComponents();
     assert.equal(components.length, 3);
@@ -552,7 +552,7 @@ QUnit.test("weakComponents on directed graph", function(assert) {
     assert.deepEqual(components[0].edges, [
         { source: "A", target: "B" },
         { source: "E", target: "A" },
-        { source: "F", target: "E" }
+        { source: "F", target: "E" },
     ]);
 
     assert.equal(components[1].vertices.length, 2);
diff --git a/client/galaxy/scripts/qunit/tests/hda_base_tests.js b/client/galaxy/scripts/qunit/tests/hda_base_tests.js
index 6c3b0cc4f2ed..d9400b83a953 100644
--- a/client/galaxy/scripts/qunit/tests/hda_base_tests.js
+++ b/client/galaxy/scripts/qunit/tests/hda_base_tests.js
@@ -7,17 +7,17 @@ import HDA_MODEL from "mvc/history/hda-model";
 import HDA_BASE from "mvc/history/hda-li";
 
 QUnit.module("HDA base backbone view tests", {
-    beforeEach: function() {
+    beforeEach: function () {
         testApp.create();
     },
-    afterEach: function() {
+    afterEach: function () {
         testApp.destroy();
-    }
+    },
 });
 
-QUnit.test("Base HDA view default construction, initialize", function(assert) {
+QUnit.test("Base HDA view default construction, initialize", function (assert) {
     var hda = new HDA_MODEL.HistoryDatasetAssociation({
-            id: "123"
+            id: "123",
         }),
         view = new HDA_BASE.HDAListItemView({ model: hda });
 
diff --git a/client/galaxy/scripts/qunit/tests/history_contents_model_tests.js b/client/galaxy/scripts/qunit/tests/history_contents_model_tests.js
index 288ee8a17fa4..d7a1b4ba6132 100644
--- a/client/galaxy/scripts/qunit/tests/history_contents_model_tests.js
+++ b/client/galaxy/scripts/qunit/tests/history_contents_model_tests.js
@@ -5,36 +5,36 @@ import testApp from "qunit/test-app";
 import HDA_MODEL from "mvc/history/hda-model";
 
 QUnit.module("History Contents Model QUnit.Tests", {
-    beforeEach: function() {
+    beforeEach: function () {
         testApp.create();
     },
-    afterEach: function() {
+    afterEach: function () {
         testApp.destroy();
-    }
+    },
 });
 
-QUnit.test("HDA Constructions with Default Attributes", function(assert) {
+QUnit.test("HDA Constructions with Default Attributes", function (assert) {
     var hda = new HDA_MODEL.HistoryDatasetAssociation({});
     assert.equal(hda.get("name"), "(unnamed dataset)");
     assert.equal(hda.get("state"), "new");
 });
 
-QUnit.test("HDA Construction with Supplied Attributes", function(assert) {
+QUnit.test("HDA Construction with Supplied Attributes", function (assert) {
     var hda = new HDA_MODEL.HistoryDatasetAssociation({
         history_content_type: "dataset",
         name: "my dataset",
-        state: "ok"
+        state: "ok",
     });
     assert.equal(hda.get("name"), "my dataset");
     assert.equal(hda.get("state"), "ok");
 });
 
-QUnit.test("HDA Deletion", function(assert) {
+QUnit.test("HDA Deletion", function (assert) {
     var hda = new HDA_MODEL.HistoryDatasetAssociation({
         history_content_type: "dataset",
         id: "hda1",
         history_id: "h1",
-        deleted: false
+        deleted: false,
     });
     assert.equal(hda.get("deleted"), false);
 
diff --git a/client/galaxy/scripts/qunit/tests/job_dag_tests.js b/client/galaxy/scripts/qunit/tests/job_dag_tests.js
index d7d95a150c4e..cd76e31455cd 100644
--- a/client/galaxy/scripts/qunit/tests/job_dag_tests.js
+++ b/client/galaxy/scripts/qunit/tests/job_dag_tests.js
@@ -5,23 +5,23 @@ import JobDAG from "mvc/history/job-dag";
 import testData from "qunit/test-data/job-dag-1";
 
 QUnit.module("mvc/history/job-dag.js tests", {
-    beforeEach: function() {
+    beforeEach: function () {
         testApp.create();
     },
-    afterEach: function() {
+    afterEach: function () {
         testApp.destroy();
-    }
+    },
 });
 
 // ------------------------------------------------------------------------
-QUnit.test("Empty JobDAG construction", function(assert) {
+QUnit.test("Empty JobDAG construction", function (assert) {
     var dag = new JobDAG();
     assert.ok(dag instanceof JobDAG);
 
     // default options
     assert.deepEqual(dag.filters, []);
     assert.deepEqual(dag.options, {
-        excludeSetMetadata: false
+        excludeSetMetadata: false,
     });
 
     // test (empty) instance vars
@@ -38,15 +38,15 @@ QUnit.test("Empty JobDAG construction", function(assert) {
     assert.equal(typeof dag.error, "function");
 });
 
-QUnit.test("Empty JobDAG construction - changing options", function(assert) {
+QUnit.test("Empty JobDAG construction - changing options", function (assert) {
     var dag;
     dag = new JobDAG({
-        excludeSetMetadata: true
+        excludeSetMetadata: true,
     });
 
     // excludeSetMetadata
     assert.deepEqual(dag.options, {
-        excludeSetMetadata: true
+        excludeSetMetadata: true,
     });
     assert.equal(dag.filters.length, 1);
     assert.equal(typeof dag.filters[0], "function");
@@ -56,12 +56,12 @@ QUnit.test("Empty JobDAG construction - changing options", function(assert) {
         return true;
     }
     dag = new JobDAG({
-        filters: [testFilter]
+        filters: [testFilter],
     });
     assert.equal(dag.filters[0], testFilter);
 });
 
-QUnit.test("JobDAG construction with history and jobs", function(assert) {
+QUnit.test("JobDAG construction with history and jobs", function (assert) {
     assert.equal(testData.jobs1.length, 3);
     assert.equal(testData.historyContents1.length, 3);
 
@@ -71,13 +71,13 @@ QUnit.test("JobDAG construction with history and jobs", function(assert) {
     dag = new JobDAG({
         historyContents: history,
         tools: testData.tools,
-        jobs: jobs
+        jobs: jobs,
     });
 
     assert.deepEqual(dag._outputIdToJobMap, {
         "8c959c9304a2bc4b": "8a81cf6f989c4467",
         "132016f833b57406": "6505e875ddb66fd2",
-        "846fb0a2a64137c0": "77f74776fd03cbc5"
+        "846fb0a2a64137c0": "77f74776fd03cbc5",
     });
     assert.deepEqual(dag._jobsData, [
         {
@@ -88,10 +88,10 @@ QUnit.test("JobDAG construction with history and jobs", function(assert) {
                     src: "hda",
                     id: "8c959c9304a2bc4b",
                     name: "output0",
-                    content: _.findWhere(history, { id: "8c959c9304a2bc4b" })
-                }
+                    content: _.findWhere(history, { id: "8c959c9304a2bc4b" }),
+                },
             },
-            tool: {}
+            tool: {},
         },
         {
             job: _.findWhere(jobs, { id: "6505e875ddb66fd2" }),
@@ -100,18 +100,18 @@ QUnit.test("JobDAG construction with history and jobs", function(assert) {
                     src: "hda",
                     id: "8c959c9304a2bc4b",
                     name: "input",
-                    content: _.findWhere(history, { id: "8c959c9304a2bc4b" })
-                }
+                    content: _.findWhere(history, { id: "8c959c9304a2bc4b" }),
+                },
             },
             outputs: {
                 "132016f833b57406": {
                     src: "hda",
                     id: "132016f833b57406",
                     name: "out_file1",
-                    content: _.findWhere(history, { id: "132016f833b57406" })
-                }
+                    content: _.findWhere(history, { id: "132016f833b57406" }),
+                },
             },
-            tool: {}
+            tool: {},
         },
         {
             job: _.findWhere(jobs, { id: "77f74776fd03cbc5" }),
@@ -120,19 +120,19 @@ QUnit.test("JobDAG construction with history and jobs", function(assert) {
                     src: "hda",
                     id: "132016f833b57406",
                     name: "input",
-                    content: _.findWhere(history, { id: "132016f833b57406" })
-                }
+                    content: _.findWhere(history, { id: "132016f833b57406" }),
+                },
             },
             outputs: {
                 "846fb0a2a64137c0": {
                     src: "hda",
                     id: "846fb0a2a64137c0",
                     name: "out_file1",
-                    content: _.findWhere(history, { id: "846fb0a2a64137c0" })
-                }
+                    content: _.findWhere(history, { id: "846fb0a2a64137c0" }),
+                },
             },
-            tool: {}
-        }
+            tool: {},
+        },
     ]);
 
     var jobsDataMap = dag._jobsDataMap();
@@ -140,38 +140,38 @@ QUnit.test("JobDAG construction with history and jobs", function(assert) {
         nodes: [
             { name: "8a81cf6f989c4467", data: jobsDataMap["8a81cf6f989c4467"] },
             { name: "6505e875ddb66fd2", data: jobsDataMap["6505e875ddb66fd2"] },
-            { name: "77f74776fd03cbc5", data: jobsDataMap["77f74776fd03cbc5"] }
+            { name: "77f74776fd03cbc5", data: jobsDataMap["77f74776fd03cbc5"] },
         ],
         links: [
             { source: 0, target: 1, data: { dataset: "8c959c9304a2bc4b" } },
-            { source: 1, target: 2, data: { dataset: "132016f833b57406" } }
-        ]
+            { source: 1, target: 2, data: { dataset: "132016f833b57406" } },
+        ],
     });
 
     assert.deepEqual(dag.toVerticesAndEdges(), {
         vertices: [
             { name: "8a81cf6f989c4467", data: jobsDataMap["8a81cf6f989c4467"] },
             { name: "6505e875ddb66fd2", data: jobsDataMap["6505e875ddb66fd2"] },
-            { name: "77f74776fd03cbc5", data: jobsDataMap["77f74776fd03cbc5"] }
+            { name: "77f74776fd03cbc5", data: jobsDataMap["77f74776fd03cbc5"] },
         ],
         edges: [
             {
                 source: "8a81cf6f989c4467",
                 target: "6505e875ddb66fd2",
-                data: { dataset: "8c959c9304a2bc4b" }
+                data: { dataset: "8c959c9304a2bc4b" },
             },
             {
                 source: "6505e875ddb66fd2",
                 target: "77f74776fd03cbc5",
-                data: { dataset: "132016f833b57406" }
-            }
-        ]
+                data: { dataset: "132016f833b57406" },
+            },
+        ],
     });
 
     // test cloning
 });
 
-QUnit.test("JobDAG removal of __SET_METADATA__ jobs", function(assert) {
+QUnit.test("JobDAG removal of __SET_METADATA__ jobs", function (assert) {
     assert.equal(testData.jobs2.length, 3);
     assert.equal(testData.historyContents2.length, 2);
 
@@ -182,21 +182,21 @@ QUnit.test("JobDAG removal of __SET_METADATA__ jobs", function(assert) {
         historyContents: history,
         tools: testData.tools,
         jobs: jobs,
-        excludeSetMetadata: true
+        excludeSetMetadata: true,
     });
 
     var jobsDataMap = dag._jobsDataMap();
     assert.deepEqual(dag.toNodesAndLinks(), {
         nodes: [
             { name: "bf60fd5f5f7f44bf", data: jobsDataMap["bf60fd5f5f7f44bf"] },
-            { name: "90240358ebde1489", data: jobsDataMap["90240358ebde1489"] }
+            { name: "90240358ebde1489", data: jobsDataMap["90240358ebde1489"] },
         ],
-        links: [{ source: 0, target: 1, data: { dataset: "eca0af6fb47bf90c" } }]
+        links: [{ source: 0, target: 1, data: { dataset: "eca0af6fb47bf90c" } }],
     });
 });
 
 //TODO: test filtering out errored jobs
-QUnit.test("JobDAG construction with history and jobs", function(assert) {
+QUnit.test("JobDAG construction with history and jobs", function (assert) {
     assert.equal(testData.jobs3.length, 5);
     assert.equal(testData.historyContents3.length, 5);
 
@@ -206,7 +206,7 @@ QUnit.test("JobDAG construction with history and jobs", function(assert) {
     dag = new JobDAG({
         historyContents: history,
         tools: testData.tools,
-        jobs: jobs
+        jobs: jobs,
     });
 
     var jobsDataMap = dag._jobsDataMap();
@@ -216,25 +216,25 @@ QUnit.test("JobDAG construction with history and jobs", function(assert) {
             { name: "132016f833b57406", data: jobsDataMap["132016f833b57406"] },
             { name: "846fb0a2a64137c0", data: jobsDataMap["846fb0a2a64137c0"] },
             { name: "eca0af6fb47bf90c", data: jobsDataMap["eca0af6fb47bf90c"] },
-            { name: "6fc9fbb81c497f69", data: jobsDataMap["6fc9fbb81c497f69"] }
+            { name: "6fc9fbb81c497f69", data: jobsDataMap["6fc9fbb81c497f69"] },
         ],
         edges: [
             {
                 source: "8c959c9304a2bc4b",
                 target: "846fb0a2a64137c0",
-                data: { dataset: "6fb17d0cc6e8fae5" }
+                data: { dataset: "6fb17d0cc6e8fae5" },
             },
             {
                 source: "132016f833b57406",
                 target: "eca0af6fb47bf90c",
-                data: { dataset: "5114a2a207b7caff" }
+                data: { dataset: "5114a2a207b7caff" },
             },
             {
                 source: "eca0af6fb47bf90c",
                 target: "6fc9fbb81c497f69",
-                data: { dataset: "b8a0d6158b9961df" }
-            }
-        ]
+                data: { dataset: "b8a0d6158b9961df" },
+            },
+        ],
     });
 
     var components = dag.weakComponents();
@@ -242,26 +242,26 @@ QUnit.test("JobDAG construction with history and jobs", function(assert) {
         {
             vertices: [
                 { name: "8c959c9304a2bc4b", data: jobsDataMap["8c959c9304a2bc4b"] },
-                { name: "846fb0a2a64137c0", data: jobsDataMap["846fb0a2a64137c0"] }
+                { name: "846fb0a2a64137c0", data: jobsDataMap["846fb0a2a64137c0"] },
             ],
-            edges: [{ source: "8c959c9304a2bc4b", target: "846fb0a2a64137c0" }]
+            edges: [{ source: "8c959c9304a2bc4b", target: "846fb0a2a64137c0" }],
         },
         {
             vertices: [
                 { name: "132016f833b57406", data: jobsDataMap["132016f833b57406"] },
                 { name: "eca0af6fb47bf90c", data: jobsDataMap["eca0af6fb47bf90c"] },
-                { name: "6fc9fbb81c497f69", data: jobsDataMap["6fc9fbb81c497f69"] }
+                { name: "6fc9fbb81c497f69", data: jobsDataMap["6fc9fbb81c497f69"] },
             ],
             edges: [
                 { source: "132016f833b57406", target: "eca0af6fb47bf90c" },
-                { source: "eca0af6fb47bf90c", target: "6fc9fbb81c497f69" }
-            ]
-        }
+                { source: "eca0af6fb47bf90c", target: "6fc9fbb81c497f69" },
+            ],
+        },
     ]);
 });
 
 //TODO: test filtering out errored jobs
-QUnit.test("JobDAG construction with copied history contents", function(assert) {
+QUnit.test("JobDAG construction with copied history contents", function (assert) {
     assert.equal(testData.jobs4.length, 1);
     assert.equal(testData.historyContents4.length, 3);
 
@@ -271,7 +271,7 @@ QUnit.test("JobDAG construction with copied history contents", function(assert)
     dag = new JobDAG({
         historyContents: history,
         tools: testData.tools,
-        jobs: jobs
+        jobs: jobs,
     });
 
     var jobsDataMap = dag._jobsDataMap();
@@ -279,19 +279,19 @@ QUnit.test("JobDAG construction with copied history contents", function(assert)
         vertices: [
             { name: "92b83968e0b52980", data: jobsDataMap["92b83968e0b52980"] },
             { name: "copy-422eef6b1b545329", data: _.findWhere(history, { id: "422eef6b1b545329" }) },
-            { name: "copy-c86c1b73aa7102dd", data: _.findWhere(history, { id: "c86c1b73aa7102dd" }) }
+            { name: "copy-c86c1b73aa7102dd", data: _.findWhere(history, { id: "c86c1b73aa7102dd" }) },
         ],
         edges: [
             {
                 source: "copy-422eef6b1b545329",
                 target: "92b83968e0b52980",
-                data: { dataset: "422eef6b1b545329" }
+                data: { dataset: "422eef6b1b545329" },
             },
             {
                 source: "copy-c86c1b73aa7102dd",
                 target: "92b83968e0b52980",
-                data: { dataset: "c86c1b73aa7102dd" }
-            }
-        ]
+                data: { dataset: "c86c1b73aa7102dd" },
+            },
+        ],
     });
 });
diff --git a/client/galaxy/scripts/qunit/tests/jquery_plugin_tests.js b/client/galaxy/scripts/qunit/tests/jquery_plugin_tests.js
index 051f1cb0e190..de5b9cd56427 100644
--- a/client/galaxy/scripts/qunit/tests/jquery_plugin_tests.js
+++ b/client/galaxy/scripts/qunit/tests/jquery_plugin_tests.js
@@ -3,15 +3,15 @@ import $ from "jquery";
 import testApp from "qunit/test-app";
 
 QUnit.module("Galaxy jquery plugin test", {
-    beforeEach: function() {
+    beforeEach: function () {
         testApp.create();
     },
-    afterEach: function() {
+    afterEach: function () {
         testApp.destroy();
-    }
+    },
 });
 
-QUnit.test("Check jquery for tooltip and select2", function(assert) {
+QUnit.test("Check jquery for tooltip and select2", function (assert) {
     assert.ok($.fn.tooltip);
     assert.ok($.fn.select2);
 });
diff --git a/client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js b/client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js
index 59463ed670b5..1d2b5d4bc53a 100644
--- a/client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js
+++ b/client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js
@@ -9,14 +9,14 @@ import DATA from "qunit/test-data/paired-collection-creator.data";
 var PCC = PAIRED_COLLECTION_CREATOR.PairedCollectionCreator;
 
 QUnit.module("Galaxy client app tests", {
-    beforeEach: function() {
+    beforeEach: function () {
         testApp.create();
         $.fx.off = true;
     },
-    afterEach: function() {
+    afterEach: function () {
         testApp.destroy();
         $.fx.off = false;
-    }
+    },
 });
 
 // Following test no longer passes - something is wrong setting up Galaxy.root - but we have multiple Selenium tests that cover verifying
@@ -47,7 +47,7 @@ QUnit.module("Galaxy client app tests", {
 //     server.restore();
 // });
 
-QUnit.test("Creator base/empty construction/initializiation defaults", function(assert) {
+QUnit.test("Creator base/empty construction/initializiation defaults", function (assert) {
     var pcc = new PCC([]);
     assert.ok(pcc instanceof PCC);
     assert.deepEqual(pcc.filters, pcc.commonFilters[pcc.DEFAULT_FILTERS]);
@@ -56,9 +56,9 @@ QUnit.test("Creator base/empty construction/initializiation defaults", function(
     assert.equal(pcc.strategy, "autopairLCS");
 });
 
-QUnit.test("Creator construction/initializiation with datasets", function(assert) {
+QUnit.test("Creator construction/initializiation with datasets", function (assert) {
     var pcc = new PCC({
-        datasets: DATA._1
+        datasets: DATA._1,
     });
     //pcc.initialList.forEach( function( dataset, i ){
     //    console.log( i + ':\n' + JSON.stringify( dataset ) );
@@ -67,7 +67,7 @@ QUnit.test("Creator construction/initializiation with datasets", function(assert
     assert.deepEqual(pcc.initialList, DATA._1);
     // datasets 1 has no ids, so the pcc will create them
     assert.ok(
-        _.every(pcc.initialList, function(dataset) {
+        _.every(pcc.initialList, function (dataset) {
             return dataset.id;
         })
     );
@@ -76,31 +76,31 @@ QUnit.test("Creator construction/initializiation with datasets", function(assert
     assert.equal(pcc.paired.length, pcc.initialList.length / 2);
 });
 
-QUnit.test("Try easy autopairing with simple exact matching", function(assert) {
+QUnit.test("Try easy autopairing with simple exact matching", function (assert) {
     var pcc = new PCC({
         datasets: DATA._1,
         strategy: "simple",
-        twoPassAutopairing: false
+        twoPassAutopairing: false,
     });
     assert.equal(pcc.unpaired.length, 0);
     assert.equal(pcc.paired.length, pcc.initialList.length / 2);
 });
 
-QUnit.test("Try easy autopairing with LCS", function(assert) {
+QUnit.test("Try easy autopairing with LCS", function (assert) {
     var pcc = new PCC({
         datasets: DATA._1,
         strategy: "lcs",
-        twoPassAutopairing: false
+        twoPassAutopairing: false,
     });
     assert.equal(pcc.unpaired.length, 0);
     assert.equal(pcc.paired.length, pcc.initialList.length / 2);
 });
 
-QUnit.test("Try easy autopairing with Levenshtein", function(assert) {
+QUnit.test("Try easy autopairing with Levenshtein", function (assert) {
     var pcc = new PCC({
         datasets: DATA._1,
         strategy: "levenshtein",
-        twoPassAutopairing: false
+        twoPassAutopairing: false,
     });
     assert.equal(pcc.unpaired.length, 0);
     assert.equal(pcc.paired.length, pcc.initialList.length / 2);
diff --git a/client/galaxy/scripts/qunit/tests/masthead_tests.js b/client/galaxy/scripts/qunit/tests/masthead_tests.js
index 6ee8a4de5ab6..88021ed15adb 100644
--- a/client/galaxy/scripts/qunit/tests/masthead_tests.js
+++ b/client/galaxy/scripts/qunit/tests/masthead_tests.js
@@ -6,7 +6,7 @@ import { getAppRoot } from "onload";
 import { getGalaxyInstance } from "app";
 
 QUnit.module("Masthead test", {
-    beforeEach: function() {
+    beforeEach: function () {
         testApp.create();
         this.masthead = new Masthead.View({
             brand: "brand",
@@ -28,18 +28,18 @@ QUnit.module("Masthead test", {
             datatypes_disable_auto: true,
             allow_user_creation: true,
             enable_cloud_launch: true,
-            user_requests: true
+            user_requests: true,
         });
         this.container = this.masthead.render().$el;
         $("body").append(this.container);
     },
-    afterEach: function() {
+    afterEach: function () {
         testApp.destroy();
         this.container.remove();
-    }
+    },
 });
 
-QUnit.test("tabs", function(assert) {
+QUnit.test("tabs", function (assert) {
     var tab = this.masthead.collection.findWhere({ id: "analysis" });
     var $tab = $("#analysis");
     var $toggle = $tab.find(".nav-link");
@@ -104,7 +104,7 @@ QUnit.test("tabs", function(assert) {
     assert.ok($item.length === 0, "All menu items removed");
     tab.set("menu", [
         { title: "_menu_title_0", url: "_menu_url_0", target: "_menu_target_0" },
-        { title: "_menu_title_1", url: "_menu_url_1", target: "_menu_target_1" }
+        { title: "_menu_title_1", url: "_menu_url_1", target: "_menu_target_1" },
     ]);
     $item = $menu.find("a");
     assert.ok($item.length == 2, "Two menu items added");
diff --git a/client/galaxy/scripts/qunit/tests/metrics_logger_tests.js b/client/galaxy/scripts/qunit/tests/metrics_logger_tests.js
index 765067544347..8f6e18bf53db 100644
--- a/client/galaxy/scripts/qunit/tests/metrics_logger_tests.js
+++ b/client/galaxy/scripts/qunit/tests/metrics_logger_tests.js
@@ -7,11 +7,11 @@ import sinon from "sinon";
 import metrics from "utils/metrics-logger";
 import testApp from "qunit/test-app";
 
-var MockConsole = function() {
+var MockConsole = function () {
     var self = this;
     self.lastMessage = null;
-    ["log", "debug", "info", "warn", "error"].forEach(function(fnName) {
-        self[fnName] = function() {
+    ["log", "debug", "info", "warn", "error"].forEach(function (fnName) {
+        self[fnName] = function () {
             var args = Array.prototype.slice.call(arguments, 0);
             self.lastMessage = { level: fnName, args: args };
         };
@@ -20,20 +20,20 @@ var MockConsole = function() {
 };
 
 (window.bootstrapped = {}).user = {
-    id: "test"
+    id: "test",
 };
 
 QUnit.module("Metrics logger tests", {
-    beforeEach: function() {
+    beforeEach: function () {
         testApp.create();
     },
-    afterEach: function() {
+    afterEach: function () {
         testApp.destroy();
-    }
+    },
 });
 
 // ======================================================================== MetricsLogger
-QUnit.test("logger construction/initializiation defaults", function(assert) {
+QUnit.test("logger construction/initializiation defaults", function (assert) {
     var logger = new metrics.MetricsLogger({});
     assert.equal(logger.consoleLogger, null);
     assert.equal(logger.options.logLevel, metrics.MetricsLogger.NONE);
@@ -51,7 +51,7 @@ QUnit.test("logger construction/initializiation defaults", function(assert) {
     assert.equal(logger.cache.constructor, metrics.LoggingCache);
 });
 
-QUnit.test("_parseLevel", function(assert) {
+QUnit.test("_parseLevel", function (assert) {
     var logger = new metrics.MetricsLogger({});
     assert.equal(logger._parseLevel("all"), metrics.MetricsLogger.ALL);
     assert.equal(logger._parseLevel("debug"), metrics.MetricsLogger.DEBUG);
@@ -63,14 +63,14 @@ QUnit.test("_parseLevel", function(assert) {
     assert.equal(logger._parseLevel(15), 15);
 
     assert.throws(
-        function() {
+        function () {
             logger._parseLevel(undefined);
         },
         /Unknown log level/,
         "Unknown log level throws error"
     );
     assert.throws(
-        function() {
+        function () {
             logger._parseLevel("nope");
         },
         /Unknown log level/,
@@ -79,9 +79,9 @@ QUnit.test("_parseLevel", function(assert) {
 });
 
 // ------------------------------------------------------------------------ Emit to cache
-QUnit.test("emit to cache at level", function(assert) {
+QUnit.test("emit to cache at level", function (assert) {
     var logger = new metrics.MetricsLogger({
-        logLevel: "metric"
+        logLevel: "metric",
     });
     logger.cache.empty();
 
@@ -99,9 +99,9 @@ QUnit.test("emit to cache at level", function(assert) {
     assert.ok(cached.time === new Date(cached.time).toISOString());
 });
 
-QUnit.test("emit to cache below does not cache", function(assert) {
+QUnit.test("emit to cache below does not cache", function (assert) {
     var logger = new metrics.MetricsLogger({
-        logLevel: "metric"
+        logLevel: "metric",
     });
     logger.cache.empty();
 
@@ -109,9 +109,9 @@ QUnit.test("emit to cache below does not cache", function(assert) {
     assert.equal(logger.cache.length(), 0);
 });
 
-QUnit.test("emit to cache (silently) drops non-parsable", function(assert) {
+QUnit.test("emit to cache (silently) drops non-parsable", function (assert) {
     var logger = new metrics.MetricsLogger({
-        logLevel: "metric"
+        logLevel: "metric",
     });
     logger.cache.empty();
 
@@ -124,19 +124,19 @@ function metricsFromRequestBody(request) {
     return JSON.parse(decodeURIComponent(request.requestBody.replace("metrics=", "")));
 }
 
-QUnit.test("_postCache success", function(assert) {
+QUnit.test("_postCache success", function (assert) {
     var callback = sinon.spy(),
         logger = new metrics.MetricsLogger({
             logLevel: "metric",
-            onServerResponse: function(response) {
+            onServerResponse: function (response) {
                 callback();
-            }
+            },
         });
     logger.cache.empty();
 
     var server = sinon.fakeServer.create(),
         metricsOnServer;
-    server.respondWith("POST", "/api/metrics", function(request) {
+    server.respondWith("POST", "/api/metrics", function (request) {
         metricsOnServer = metricsFromRequestBody(request);
         //console.debug( 'requestBody:', request.requestBody );
         //console.debug( 'metricsOnServer:', JSON.stringify( metricsOnServer, null, '  ' ) );
@@ -144,7 +144,7 @@ QUnit.test("_postCache success", function(assert) {
             200,
             { "Content-Type": "application/json" },
             JSON.stringify({
-                fakeResponse: "yes"
+                fakeResponse: "yes",
             })
         );
     });
@@ -170,23 +170,23 @@ QUnit.test("_postCache success", function(assert) {
     server.restore();
 });
 
-QUnit.test("_postCache failure", function(assert) {
+QUnit.test("_postCache failure", function (assert) {
     var callback = sinon.spy(),
         logger = new metrics.MetricsLogger({
             logLevel: "metric",
-            onServerResponse: function(response) {
+            onServerResponse: function (response) {
                 callback();
-            }
+            },
         });
     logger.cache.empty();
 
     var server = sinon.fakeServer.create();
-    server.respondWith("POST", "/api/metrics", function(request) {
+    server.respondWith("POST", "/api/metrics", function (request) {
         request.respond(
             500,
             { "Content-Type": "application/json" },
             JSON.stringify({
-                err_msg: "NoooOPE!"
+                err_msg: "NoooOPE!",
             })
         );
     });
@@ -203,11 +203,11 @@ QUnit.test("_postCache failure", function(assert) {
 });
 
 // ------------------------------------------------------------------------ Emit to console
-QUnit.test("emit to console at level", function(assert) {
+QUnit.test("emit to console at level", function (assert) {
     var mockConsole = new MockConsole(),
         logger = new metrics.MetricsLogger({
             consoleLevel: "debug",
-            consoleLogger: mockConsole
+            consoleLogger: mockConsole,
         });
     assert.equal(logger.options.consoleLevel, metrics.MetricsLogger.DEBUG);
     assert.equal(logger.consoleLogger.constructor, MockConsole);
@@ -221,20 +221,20 @@ QUnit.test("emit to console at level", function(assert) {
     assert.equal(mockConsole.lastMessage.args[3].three, 3);
 });
 
-QUnit.test("emit to console below does not output", function(assert) {
+QUnit.test("emit to console below does not output", function (assert) {
     var mockConsole = new MockConsole(),
         logger = new metrics.MetricsLogger({
             consoleLevel: "error",
-            consoleLogger: mockConsole
+            consoleLogger: mockConsole,
         });
     logger.emit("debug", "test", [1, 2, { three: 3 }]);
     assert.equal(mockConsole.lastMessage, null);
 });
 
 // ------------------------------------------------------------------------ Shortcuts
-QUnit.test("logger shortcuts emit to default namespace properly", function(assert) {
+QUnit.test("logger shortcuts emit to default namespace properly", function (assert) {
     var logger = new metrics.MetricsLogger({
-        logLevel: "all"
+        logLevel: "all",
     });
     logger.cache.empty();
 
@@ -250,7 +250,7 @@ QUnit.test("logger shortcuts emit to default namespace properly", function(asser
     var cached = logger.cache.remove(6),
         entry;
 
-    cached.forEach(function(entry) {
+    cached.forEach(function (entry) {
         assert.ok(entry.namespace === logger.options.clientPrefix + logger.options.defaultNamespace);
         assert.ok(jQuery.type(entry.args) === "array");
         assert.ok(typeof entry.time === "string");
@@ -261,7 +261,7 @@ QUnit.test("logger shortcuts emit to default namespace properly", function(asser
     assert.ok(entry.level === 1);
     assert.ok(entry.args[0] === 0);
 
-    ["debug", "info", "warn", "error", "metric"].forEach(function(level, i) {
+    ["debug", "info", "warn", "error", "metric"].forEach(function (level, i) {
         entry = cached[i + 1];
         assert.ok(entry.level === logger._parseLevel(level));
         assert.ok(entry.args[0] === i + 1);
@@ -269,23 +269,23 @@ QUnit.test("logger shortcuts emit to default namespace properly", function(asser
 });
 
 // ======================================================================== LoggingCache
-QUnit.test("cache construction/initializiation defaults", function(assert) {
+QUnit.test("cache construction/initializiation defaults", function (assert) {
     // use empty to prevent tests stepping on one another due to persistence
     var cache = new metrics.LoggingCache({ key: "logs-test" }).empty();
     assert.equal(cache.maxSize, 5000);
     assert.equal(window.localStorage.getItem("logs-test"), "[]");
 });
 
-QUnit.test("cache construction/initializiation failure", function(assert) {
+QUnit.test("cache construction/initializiation failure", function (assert) {
     ////TODO: doesn't work - readonly
     //window.localStorage = null;
     //console.debug( 'localStorage:', window.localStorage );
     var oldFn = metrics.LoggingCache.prototype._hasStorage;
-    metrics.LoggingCache.prototype._hasStorage = function() {
+    metrics.LoggingCache.prototype._hasStorage = function () {
         return false;
     };
     assert.throws(
-        function() {
+        function () {
             return new metrics.LoggingCache({ key: "logs-test" });
         },
         /LoggingCache needs localStorage/,
@@ -294,7 +294,7 @@ QUnit.test("cache construction/initializiation failure", function(assert) {
     metrics.LoggingCache.prototype._hasStorage = oldFn;
 
     assert.throws(
-        function() {
+        function () {
             return new metrics.LoggingCache();
         },
         /LoggingCache needs key for localStorage/,
@@ -302,15 +302,15 @@ QUnit.test("cache construction/initializiation failure", function(assert) {
     );
 });
 
-QUnit.test("cache construction/initializiation setting max cache size", function(assert) {
+QUnit.test("cache construction/initializiation setting max cache size", function (assert) {
     var cache = new metrics.LoggingCache({
         key: "logs-test",
-        maxSize: 5
+        maxSize: 5,
     }).empty();
     assert.equal(cache.maxSize, 5);
 });
 
-QUnit.test("cache plays well with no data", function(assert) {
+QUnit.test("cache plays well with no data", function (assert) {
     var cache = new metrics.LoggingCache({ key: "logs-test" }).empty();
 
     assert.equal(cache.length(), 0);
@@ -321,10 +321,10 @@ QUnit.test("cache plays well with no data", function(assert) {
     assert.equal(cache.length(), 0);
 });
 
-QUnit.test("cache add properly adds and removes data", function(assert) {
+QUnit.test("cache add properly adds and removes data", function (assert) {
     var cache = new metrics.LoggingCache({
         key: "logs-test",
-        maxSize: 5
+        maxSize: 5,
     }).empty();
 
     var entry1 = [{ one: 1 }, "two"];
@@ -346,10 +346,10 @@ QUnit.test("cache add properly adds and removes data", function(assert) {
     assert.ok(jQuery.type(returned0) === "array" && JSON.stringify(returned0) === JSON.stringify(entry1));
 });
 
-QUnit.test("cache past max loses oldest", function(assert) {
+QUnit.test("cache past max loses oldest", function (assert) {
     var cache = new metrics.LoggingCache({
         key: "logs-test",
-        maxSize: 5
+        maxSize: 5,
     }).empty();
 
     for (var i = 0; i < 10; i += 1) {
@@ -364,7 +364,7 @@ QUnit.test("cache past max loses oldest", function(assert) {
     assert.ok(get[4].index === 9);
 });
 
-QUnit.test("cache is properly persistent", function(assert) {
+QUnit.test("cache is properly persistent", function (assert) {
     var cache1 = new metrics.LoggingCache({ key: "logs-test" }).empty(),
         entry = [{ one: 1 }, "two"];
     cache1.add(entry);
diff --git a/client/galaxy/scripts/qunit/tests/modal_tests.js b/client/galaxy/scripts/qunit/tests/modal_tests.js
index 560ec64caa05..d706b091db5b 100644
--- a/client/galaxy/scripts/qunit/tests/modal_tests.js
+++ b/client/galaxy/scripts/qunit/tests/modal_tests.js
@@ -4,7 +4,7 @@ import testApp from "qunit/test-app";
 import GalaxyModal from "mvc/ui/ui-modal";
 
 QUnit.module("Modal dialog test", {
-    beforeEach: function() {
+    beforeEach: function () {
         $.fx.off = true;
         testApp.create();
         var self = this;
@@ -12,26 +12,26 @@ QUnit.module("Modal dialog test", {
             title: "Test title",
             body: "Test body",
             buttons: {
-                Ok: function() {},
-                Cancel: function() {
+                Ok: function () {},
+                Cancel: function () {
                     self.app.hide();
-                }
-            }
+                },
+            },
         });
     },
-    afterEach: function() {
+    afterEach: function () {
         $.fx.off = false;
         testApp.destroy();
         this.app.$el.remove();
-    }
+    },
 });
 
-QUnit.test("test dialog attributes", function(assert) {
+QUnit.test("test dialog attributes", function (assert) {
     assert.ok(this.app.$header.find(".title").html() == "Test title", "Modal header has correct title.");
     assert.ok(this.app.$body.html() == "Test body", "Modal header has correct body.");
 });
 
-QUnit.test("test dialog visibility", function(assert) {
+QUnit.test("test dialog visibility", function (assert) {
     this.app.hide();
     assert.ok(this.app.$el.css("display") == "none", "Modal hidden manually");
     this.app.show();
@@ -50,7 +50,7 @@ QUnit.test("test dialog visibility", function(assert) {
     assert.ok(!this.app.$backdrop.hasClass("in"), "Backdrop tagged as hidden.");
 });
 
-QUnit.test("test dialog closing events", function(assert) {
+QUnit.test("test dialog closing events", function (assert) {
     this.app.show();
     this.app.$backdrop.trigger("click");
     assert.ok(this.app.$el.css("display") == "block", "Modal shown after backdrop click");
@@ -61,7 +61,7 @@ QUnit.test("test dialog closing events", function(assert) {
     assert.ok(this.app.$el.css("display") == "none", "Modal hidden after backdrop click");
 });
 
-QUnit.test("test dialog rendering", function(assert) {
+QUnit.test("test dialog rendering", function (assert) {
     var before = this.app.$el.html();
     this.app.render();
     assert.ok(before == this.app.$el.html(), "Re-rendering successful");
@@ -70,7 +70,7 @@ QUnit.test("test dialog rendering", function(assert) {
     assert.ok(this.app.$header.find(".title").html() == "New Title", "Modal header has correct new title.");
 });
 
-QUnit.test("test button states", function(assert) {
+QUnit.test("test button states", function (assert) {
     assert.ok(this.app.getButton("Ok").html() === "Ok", "Ok has correct label");
     assert.ok(!this.app.getButton("Ok").prop("disabled"), "Ok is active");
     assert.ok(!this.app.getButton("Cancel").prop("disabled"), "Cancel is active");
diff --git a/client/galaxy/scripts/qunit/tests/ui_tests.js b/client/galaxy/scripts/qunit/tests/ui_tests.js
index aa5acd018523..a6e8f0c19f2b 100644
--- a/client/galaxy/scripts/qunit/tests/ui_tests.js
+++ b/client/galaxy/scripts/qunit/tests/ui_tests.js
@@ -9,25 +9,25 @@ import Slider from "mvc/ui/ui-slider";
 import Tabs from "mvc/ui/ui-tabs";
 
 QUnit.module("Ui test", {
-    beforeEach: function() {
+    beforeEach: function () {
         testApp.create();
         this.clock = sinon.useFakeTimers();
     },
-    afterEach: function() {
+    afterEach: function () {
         testApp.destroy();
         this.clock.restore();
-    }
+    },
 });
 
-QUnit.test("tabs", function(assert) {
+QUnit.test("tabs", function (assert) {
     assert.ok($.fn);
     var self = this;
     var tabs = new Tabs.View({});
     var collection = tabs.collection;
     collection.add({ id: "id_a", title: "title_a", icon: "icon_a", $el: "el_a" });
-    var _test = function() {
+    var _test = function () {
         self.clock.tick(window.WAIT_FADE);
-        collection.each(function(model, index) {
+        collection.each(function (model, index) {
             var $tab_element = tabs.$("#tab-" + model.id + " .nav-link");
             var $tab_content = tabs.$("#" + model.id);
             var is_current = model.id == tabs.model.get("current");
@@ -60,7 +60,7 @@ QUnit.test("tabs", function(assert) {
     _test();
 });
 
-QUnit.test("button-default", function(assert) {
+QUnit.test("button-default", function (assert) {
     var button = new Ui.Button({ title: "title" });
     var model = button.model;
     $("body").prepend(button.$el);
@@ -80,7 +80,7 @@ QUnit.test("button-default", function(assert) {
     assert.ok(button.$title.html() == model.get("title"), "Shows correct regular title");
 });
 
-QUnit.test("button-default", function(assert) {
+QUnit.test("button-default", function (assert) {
     var button = new Ui.Button({ title: "title" });
     var model = button.model;
     $("body").prepend(button.$el);
@@ -100,7 +100,7 @@ QUnit.test("button-default", function(assert) {
     assert.ok(button.$title.html() == model.get("title"), "Shows correct regular title");
 });
 
-QUnit.test("button-check", function(assert) {
+QUnit.test("button-check", function (assert) {
     var button = new Ui.ButtonCheck({ title: "title" });
     var model = button.model;
     $("body").prepend(button.$el);
@@ -144,7 +144,7 @@ QUnit.test("button-check", function(assert) {
     );
 });
 
-QUnit.test("options", function(assert) {
+QUnit.test("options", function (assert) {
     function _test(obj, options) {
         assert.ok(JSON.stringify(obj.value()) == JSON.stringify(options.value), "Selected value is " + options.value);
         assert.ok(
@@ -192,7 +192,7 @@ QUnit.test("options", function(assert) {
         message_cls: "alert-danger",
         options_visible: false,
         value: null,
-        length: 0
+        length: 0,
     });
     radio.model.set("wait", true);
     _test(radio, {
@@ -202,7 +202,7 @@ QUnit.test("options", function(assert) {
         message_cls: "alert-info",
         options_visible: false,
         value: null,
-        length: 0
+        length: 0,
     });
     radio.model.set("wait", false);
     _test(radio, {
@@ -212,11 +212,11 @@ QUnit.test("options", function(assert) {
         message_cls: "alert-danger",
         options_visible: false,
         value: null,
-        length: 0
+        length: 0,
     });
     radio.model.set("data", [
         { value: "valuea", label: "labela" },
-        { value: "valueb", label: "labelb" }
+        { value: "valueb", label: "labelb" },
     ]);
     _test(radio, {
         menu_visible: true,
@@ -224,7 +224,7 @@ QUnit.test("options", function(assert) {
         options_visible: true,
         value: "valuea",
         first: "valuea",
-        length: 2
+        length: 2,
     });
     radio.model.set("value", "valueb");
     _test(radio, {
@@ -233,7 +233,7 @@ QUnit.test("options", function(assert) {
         options_visible: true,
         value: "valueb",
         first: "valuea",
-        length: 2
+        length: 2,
     });
     radio.model.set("data", null);
     _test(radio, {
@@ -244,12 +244,12 @@ QUnit.test("options", function(assert) {
         options_visible: false,
         value: null,
         first: null,
-        length: 0
+        length: 0,
     });
     radio.model.set("data", [
         { value: "valuea", label: "labela" },
         { value: "valueb", label: "labelb" },
-        { value: "valuec", label: "labelc" }
+        { value: "valuec", label: "labelc" },
     ]);
     _test(radio, {
         menu_visible: true,
@@ -257,19 +257,16 @@ QUnit.test("options", function(assert) {
         options_visible: true,
         value: "valueb",
         first: "valuea",
-        length: 3
+        length: 3,
     });
-    radio
-        .$("input")
-        .last()
-        .click();
+    radio.$("input").last().click();
     _test(radio, {
         menu_visible: true,
         message_visible: false,
         options_visible: true,
         value: "valuec",
         first: "valuea",
-        length: 3
+        length: 3,
     });
 
     var check = new Ui.Checkbox.View({});
@@ -282,12 +279,12 @@ QUnit.test("options", function(assert) {
         options_visible: false,
         value: null,
         length: 0,
-        all_icon: "fa-square-o"
+        all_icon: "fa-square-o",
     });
     check.model.set("data", [
         { value: "valuea", label: "labela" },
         { value: "valueb", label: "labelb" },
-        { value: "valuec", label: "labelc" }
+        { value: "valuec", label: "labelc" },
     ]);
     _test(check, {
         menu_visible: true,
@@ -295,7 +292,7 @@ QUnit.test("options", function(assert) {
         options_visible: true,
         value: null,
         length: 3,
-        all_icon: "fa-square-o"
+        all_icon: "fa-square-o",
     });
     check.model.set("value", ["valuea", "valuec"]);
     _test(check, {
@@ -304,7 +301,7 @@ QUnit.test("options", function(assert) {
         options_visible: true,
         value: ["valuea", "valuec"],
         length: 3,
-        all_icon: "fa-minus-square-o"
+        all_icon: "fa-minus-square-o",
     });
     check.model.set("value", ["valuea", "valueb", "valuec"]);
     _test(check, {
@@ -313,7 +310,7 @@ QUnit.test("options", function(assert) {
         options_visible: true,
         value: ["valuea", "valueb", "valuec"],
         length: 3,
-        all_icon: "fa-check-square-o"
+        all_icon: "fa-check-square-o",
     });
     check.model.set("data", []);
     _test(check, {
@@ -322,11 +319,11 @@ QUnit.test("options", function(assert) {
         options_visible: false,
         value: null,
         length: 0,
-        all_icon: "fa-square-o"
+        all_icon: "fa-square-o",
     });
     check.model.set("data", [
         { value: "valuea", label: "labela" },
-        { value: "valueb", label: "labelb" }
+        { value: "valueb", label: "labelb" },
     ]);
     _test(check, {
         menu_visible: true,
@@ -335,7 +332,7 @@ QUnit.test("options", function(assert) {
         value: ["valuea", "valueb"],
         first: "valuea",
         length: 2,
-        all_icon: "fa-check-square-o"
+        all_icon: "fa-check-square-o",
     });
     check.all_button.$el.click();
     _test(check, {
@@ -345,7 +342,7 @@ QUnit.test("options", function(assert) {
         value: null,
         first: "valuea",
         length: 2,
-        all_icon: "fa-square-o"
+        all_icon: "fa-square-o",
     });
     check.all_button.$el.click();
     _test(check, {
@@ -355,12 +352,9 @@ QUnit.test("options", function(assert) {
         value: ["valuea", "valueb"],
         first: "valuea",
         length: 2,
-        all_icon: "fa-check-square-o"
+        all_icon: "fa-check-square-o",
     });
-    check
-        .$("input")
-        .last()
-        .click();
+    check.$("input").last().click();
     _test(check, {
         menu_visible: true,
         message_visible: false,
@@ -368,12 +362,9 @@ QUnit.test("options", function(assert) {
         value: ["valuea"],
         first: "valuea",
         length: 2,
-        all_icon: "fa-minus-square-o"
+        all_icon: "fa-minus-square-o",
     });
-    check
-        .$("input")
-        .last()
-        .click();
+    check.$("input").last().click();
     _test(check, {
         menu_visible: true,
         message_visible: false,
@@ -381,14 +372,14 @@ QUnit.test("options", function(assert) {
         value: ["valuea", "valueb"],
         first: "valuea",
         length: 2,
-        all_icon: "fa-check-square-o"
+        all_icon: "fa-check-square-o",
     });
 
     var radiobutton = new Ui.RadioButton.View({});
     $("body").prepend(radiobutton.$el);
     radiobutton.model.set("data", [
         { value: "valuea", label: "labela" },
-        { value: "valueb", label: "labelb" }
+        { value: "valueb", label: "labelb" },
     ]);
     _test(radiobutton, {
         menu_visible: true,
@@ -396,19 +387,16 @@ QUnit.test("options", function(assert) {
         options_visible: true,
         value: "valuea",
         first: "valuea",
-        length: 2
+        length: 2,
     });
-    radiobutton
-        .$("input")
-        .last()
-        .click();
+    radiobutton.$("input").last().click();
     _test(radiobutton, {
         menu_visible: true,
         message_visible: false,
         options_visible: true,
         value: "valueb",
         first: "valuea",
-        length: 2
+        length: 2,
     });
 
     var drilldown = new Drilldown.View({});
@@ -425,10 +413,10 @@ QUnit.test("options", function(assert) {
                     name: "labeld",
                     options: [
                         { value: "valuee", name: "labele" },
-                        { value: "valuef", name: "labelf" }
-                    ]
-                }
-            ]
+                        { value: "valuef", name: "labelf" },
+                    ],
+                },
+            ],
         },
         {
             value: "valueg",
@@ -442,12 +430,12 @@ QUnit.test("options", function(assert) {
                     options: [
                         { value: "valuek", name: "labelk" },
                         { value: "valuel", name: "labell" },
-                        { value: "valuem", name: "labelm" }
-                    ]
-                }
-            ]
+                        { value: "valuem", name: "labelm" },
+                    ],
+                },
+            ],
         },
-        { value: "valuen", name: "labeln" }
+        { value: "valuen", name: "labeln" },
     ]);
     _test(drilldown, {
         menu_visible: true,
@@ -456,7 +444,7 @@ QUnit.test("options", function(assert) {
         value: null,
         first: "valuea",
         length: 14,
-        all_icon: "fa-square-o"
+        all_icon: "fa-square-o",
     });
     drilldown.model.set("value", ["valuek", "valuen"]);
     _test(drilldown, {
@@ -466,7 +454,7 @@ QUnit.test("options", function(assert) {
         value: ["valuek", "valuen"],
         first: "valuea",
         length: 14,
-        all_icon: "fa-minus-square-o"
+        all_icon: "fa-minus-square-o",
     });
     var drillradio = new Drilldown.View({ display: "radio" });
     $("body").prepend(drillradio.$el);
@@ -475,7 +463,7 @@ QUnit.test("options", function(assert) {
         message_visible: true,
         options_visible: false,
         value: null,
-        length: 0
+        length: 0,
     });
     drillradio.model.set("data", drilldown.model.get("data"));
     _test(drillradio, {
@@ -484,11 +472,11 @@ QUnit.test("options", function(assert) {
         options_visible: true,
         value: "valuea",
         first: "valuea",
-        length: 14
+        length: 14,
     });
 });
 
-QUnit.test("select-default", function(assert) {
+QUnit.test("select-default", function (assert) {
     function _test(options) {
         assert.ok(
             JSON.stringify(select.value()) == JSON.stringify(options.value),
@@ -518,54 +506,54 @@ QUnit.test("select-default", function(assert) {
         value: "value",
         label: "label",
         visible: true,
-        count: 1
+        count: 1,
     });
     select.model.set("data", [
         { value: "valuea", label: "labela" },
-        { value: "valueb", label: "labelb" }
+        { value: "valueb", label: "labelb" },
     ]);
     _test({
         value: "valuea",
         label: "labela",
         visible: true,
         count: 2,
-        exists: "valueb"
+        exists: "valueb",
     });
     select.value("valueb");
     _test({
         value: "valueb",
         label: "labelb",
         visible: true,
-        count: 2
+        count: 2,
     });
     select.model.set("data", [{ value: "value", label: "label" }]);
     _test({
         value: "value",
         label: "label",
         visible: true,
-        count: 1
+        count: 1,
     });
     select.model.set({ visible: false, value: "unavailable" });
     _test({
         value: "value",
         label: "label",
         visible: false,
-        count: 1
+        count: 1,
     });
     select.model.set({
         visible: true,
         value: "valueb",
         data: [
             { value: "valuea", label: "labela" },
-            { value: "valueb", label: "labelb" }
-        ]
+            { value: "valueb", label: "labelb" },
+        ],
     });
     _test({
         value: "valueb",
         label: "labelb",
         visible: true,
         count: 2,
-        exists: "valuea"
+        exists: "valuea",
     });
     select.model.set({ multiple: true });
     _test({
@@ -575,7 +563,7 @@ QUnit.test("select-default", function(assert) {
         count: 2,
         exists: "valuea",
         multiple: true,
-        all_icon: "fa-minus-square-o"
+        all_icon: "fa-minus-square-o",
     });
     select.model.set("value", ["valueb", "valuea"]);
     _test({
@@ -585,7 +573,7 @@ QUnit.test("select-default", function(assert) {
         count: 2,
         exists: "valueb",
         multiple: true,
-        all_icon: "fa-check-square-o"
+        all_icon: "fa-check-square-o",
     });
     select.model.set("value", []);
     _test({
@@ -595,7 +583,7 @@ QUnit.test("select-default", function(assert) {
         count: 2,
         exists: "valuea",
         multiple: true,
-        all_icon: "fa-square-o"
+        all_icon: "fa-square-o",
     });
     select.model.set({ multiple: false });
     _test({
@@ -603,7 +591,7 @@ QUnit.test("select-default", function(assert) {
         label: "labela",
         visible: true,
         count: 2,
-        exists: "valuea"
+        exists: "valuea",
     });
     select.model.set({ visible: false });
     _test({
@@ -611,7 +599,7 @@ QUnit.test("select-default", function(assert) {
         label: "labela",
         visible: false,
         count: 2,
-        exists: "valuea"
+        exists: "valuea",
     });
     select.model.set({
         multiple: true,
@@ -620,8 +608,8 @@ QUnit.test("select-default", function(assert) {
         data: [
             { value: "valuea", label: "labela" },
             { value: "valueb", label: "labelb" },
-            { value: "valuec", label: "labelc" }
-        ]
+            { value: "valuec", label: "labelc" },
+        ],
     });
     _test({
         value: ["valueb", "valuec"],
@@ -630,11 +618,11 @@ QUnit.test("select-default", function(assert) {
         count: 3,
         exists: "valuea",
         multiple: true,
-        all_icon: "fa-minus-square-o"
+        all_icon: "fa-minus-square-o",
     });
 });
 
-QUnit.test("slider", function(assert) {
+QUnit.test("slider", function (assert) {
     var input = new Slider.View({ min: 1, max: 100, value: 10 });
     $("body").prepend(input.$el);
     assert.ok(input.$slider.slider("value") == 10, "Correct value.");
@@ -650,7 +638,7 @@ QUnit.test("slider", function(assert) {
     assert.ok(input2.$slider.slider("value") == 10.1, "Correct float slider value.");
 });
 
-QUnit.test("input", function(assert) {
+QUnit.test("input", function (assert) {
     var input = new Ui.Input();
     $("body").prepend(input.$el);
     assert.ok(input.tagName === "input", "Created input.");
@@ -673,7 +661,7 @@ QUnit.test("input", function(assert) {
     assert.ok(input.$el.css("display") === "inline-block", "Shown");
 });
 
-QUnit.test("textarea", function(assert) {
+QUnit.test("textarea", function (assert) {
     var input = new Ui.Input({ area: true });
     $("body").prepend(input.$el);
     assert.ok(input.tagName === "textarea", "Created textarea.");
@@ -685,11 +673,11 @@ QUnit.test("textarea", function(assert) {
     assert.ok(input.$el.hasClass("_cls"), "Has custom class.");
 });
 
-QUnit.test("message", function(assert) {
+QUnit.test("message", function (assert) {
     var message = new Ui.Message({
         persistent: true,
         message: "_message",
-        status: "danger"
+        status: "danger",
     });
     $("body").prepend(message.$el);
     assert.ok(message.$el.hasClass("alert-danger"), "Alert danger.");
@@ -701,7 +689,7 @@ QUnit.test("message", function(assert) {
     assert.ok(message.$el.html() === "_new_message", "Correct new message.");
 });
 
-QUnit.test("hidden", function(assert) {
+QUnit.test("hidden", function (assert) {
     var hidden = new Ui.Hidden();
     $("body").prepend(hidden.$el);
     hidden.model.set("info", "_info");
@@ -713,10 +701,10 @@ QUnit.test("hidden", function(assert) {
     assert.ok(hidden.$hidden.val() === "_value", "Correct value");
 });
 
-QUnit.test("select-content", function(assert) {
+QUnit.test("select-content", function (assert) {
     var select = new SelectContent.View({});
     $("body").prepend(select.$el);
-    var _testSelect = function(tag, options) {
+    var _testSelect = function (tag, options) {
         var field = select.fields[tag == "first" ? 0 : select.fields.length - 1];
         var $select = select.$(".ui-select:" + tag);
         var $button = select.$(".ui-radiobutton").find("label:" + tag);
@@ -729,7 +717,7 @@ QUnit.test("select-content", function(assert) {
         $button.trigger("mouseleave");
         assert.ok(tooltip.indexOf("dataset") != -1 || tooltip.indexOf("collection") != -1, "Basic tooltip check");
     };
-    var _test = function(options) {
+    var _test = function (options) {
         assert.ok(select.button_type.$(".ui-option:first").hasClass("active"), "First one is toggled");
         assert.ok(
             select.$(".ui-select").length == options.selectfields,
@@ -764,13 +752,13 @@ QUnit.test("select-content", function(assert) {
     select.model.set("data", {
         hda: [
             { id: "id0", name: "name0", hid: "hid0" },
-            { id: "id1", name: "name1", hid: "hid1" }
+            { id: "id1", name: "name1", hid: "hid1" },
         ],
         hdca: [
             { id: "id2", name: "name2", hid: "hid2" },
             { id: "id3", name: "name3", hid: "hid3" },
-            { id: "id4", name: "name4", hid: "hid4" }
-        ]
+            { id: "id4", name: "name4", hid: "hid4" },
+        ],
     });
 
     var initial = {
@@ -784,7 +772,7 @@ QUnit.test("select-content", function(assert) {
         lastlabel: "hid2: name2",
         lastlength: 3,
         lastmultiple: false,
-        showdialog: true
+        showdialog: true,
     };
     _test(initial);
 
@@ -801,7 +789,7 @@ QUnit.test("select-content", function(assert) {
         lastlabel: "hid2: name2",
         lastlength: 3,
         lastmultiple: true,
-        showdialog: true
+        showdialog: true,
     });
 
     select.model.set("multiple", false);
@@ -817,7 +805,7 @@ QUnit.test("select-content", function(assert) {
         lastlabel: "hid2: name2",
         lastlength: 3,
         lastmultiple: false,
-        showdialog: false
+        showdialog: false,
     });
 
     select.model.set("type", "module_data_collection");
@@ -832,7 +820,7 @@ QUnit.test("select-content", function(assert) {
         lastlabel: "hid2: name2",
         lastlength: 3,
         lastmultiple: true,
-        showdialog: false
+        showdialog: false,
     });
 
     select.model.set("type", "module_data");
@@ -847,7 +835,7 @@ QUnit.test("select-content", function(assert) {
         lastlabel: "hid0: name0",
         lastlength: 2,
         lastmultiple: true,
-        showdialog: true
+        showdialog: true,
     });
 
     select.model.set("type", "data");
@@ -873,8 +861,8 @@ QUnit.test("select-content", function(assert) {
     select.model.set("value", {
         values: [
             { id: "id0", src: "hda" },
-            { id: "id1", src: "hda" }
-        ]
+            { id: "id1", src: "hda" },
+        ],
     });
     assert.ok(select.config[select.model.get("current")].multiple, "Matched multiple field");
     assert.ok(
@@ -891,7 +879,7 @@ QUnit.test("select-content", function(assert) {
 
     select = new SelectContent.View({});
     $("body").prepend(select.$el);
-    var _testEmptySelect = function(tag, txt_extension, txt_label) {
+    var _testEmptySelect = function (tag, txt_extension, txt_label) {
         var field = select.fields[tag == "first" ? 0 : select.fields.length - 1];
         select.$(".ui-select:" + tag);
         assert.ok(field.data[0].value == "__null__", tag + " option has correct empty value.");
diff --git a/client/galaxy/scripts/qunit/tests/utils_tests.js b/client/galaxy/scripts/qunit/tests/utils_tests.js
index 339ea25b2910..c7d70634eda7 100644
--- a/client/galaxy/scripts/qunit/tests/utils_tests.js
+++ b/client/galaxy/scripts/qunit/tests/utils_tests.js
@@ -3,15 +3,15 @@ import testApp from "qunit/test-app";
 import Utils from "utils/utils";
 
 QUnit.module("Utils test", {
-    beforeEach: function() {
+    beforeEach: function () {
         testApp.create();
     },
-    afterEach: function() {
+    afterEach: function () {
         testApp.destroy();
-    }
+    },
 });
 
-QUnit.test("isEmpty", function(assert) {
+QUnit.test("isEmpty", function (assert) {
     assert.ok(Utils.isEmpty([]), "Empty array");
     assert.ok(Utils.isEmpty(["data", undefined]), "Array contains `undefined`");
     assert.ok(Utils.isEmpty(["data", null]), "Array contains `null`");
diff --git a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
index 6e49e2bbfad0..cead63ec95dd 100644
--- a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
+++ b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
@@ -11,7 +11,7 @@ import TerminalsView from "mvc/workflow/workflow-view-terminals";
 import Connector from "mvc/workflow/workflow-connector";
 
 // create body and app
-var create_app = function() {
+var create_app = function () {
     // build body
     $("body").append(
         '<div id="canvas-viewport">' +
@@ -27,52 +27,52 @@ var create_app = function() {
     return new WorkflowManager(
         {
             datatypes: [],
-            datatypes_mapping: DatatypesMapping
+            datatypes_mapping: DatatypesMapping,
         },
         $("#canvas-container")
     );
 };
 
 QUnit.module("Input terminal model test", {
-    beforeEach: function() {
+    beforeEach: function () {
         this.app = create_app();
         this.node = new Node(this.app, {});
         this.input = { extensions: ["txt"], multiple: false, optional: false };
         this.input_terminal = new Terminals.InputTerminal({ app: this.app, input: this.input });
         this.input_terminal.node = this.node;
     },
-    afterEach: function() {
+    afterEach: function () {
         delete this.node;
     },
-    multiple: function() {
+    multiple: function () {
         this.input.multiple = true;
         this.input_terminal.update(this.input);
     },
-    test_connector: function() {
+    test_connector: function () {
         var outputTerminal = new Terminals.OutputTerminal({ datatypes: ["input"] });
         var inputTerminal = this.input_terminal;
         return new Connector({}, outputTerminal, inputTerminal);
     },
-    with_test_connector: function(f) {
+    with_test_connector: function (f) {
         this.test_connector();
         f();
         this.reset_connectors();
     },
-    reset_connectors: function() {
+    reset_connectors: function () {
         this.input_terminal.connectors = [];
     },
-    test_accept: function(other) {
+    test_accept: function (other) {
         other = other || { node: {}, datatypes: ["txt"], optional: false };
         if (!other.mapOver) {
-            other.mapOver = function() {
+            other.mapOver = function () {
                 return Terminals.NULL_COLLECTION_TYPE_DESCRIPTION;
             };
         }
         return this.input_terminal.canAccept(other).canAccept;
-    }
+    },
 });
 
-QUnit.test("test update", function(assert) {
+QUnit.test("test update", function (assert) {
     assert.deepEqual(this.input_terminal.datatypes, ["txt"]);
     assert.equal(this.input_terminal.multiple, false);
     this.input_terminal.update({ extensions: ["bam"], multiple: true });
@@ -80,7 +80,7 @@ QUnit.test("test update", function(assert) {
     assert.equal(this.input_terminal.multiple, true);
 });
 
-QUnit.test("test connect", function(assert) {
+QUnit.test("test connect", function (assert) {
     this.node.markChanged = sinon.spy();
     var connector = {};
     this.input_terminal.connect(connector);
@@ -90,7 +90,7 @@ QUnit.test("test connect", function(assert) {
     assert.ok(this.input_terminal.connectors[0] === connector);
 });
 
-QUnit.test("test disconnect", function(assert) {
+QUnit.test("test disconnect", function (assert) {
     this.node.markChanged = sinon.spy();
     var connector = this.test_connector();
     this.input_terminal.disconnect(connector);
@@ -100,7 +100,7 @@ QUnit.test("test disconnect", function(assert) {
     assert.equal(this.input_terminal.connectors.length, 0);
 });
 
-QUnit.test("test redraw", function(assert) {
+QUnit.test("test redraw", function (assert) {
     var connector = this.test_connector();
     connector.redraw = sinon.spy();
     this.input_terminal.redraw();
@@ -108,7 +108,7 @@ QUnit.test("test redraw", function(assert) {
     assert.ok(connector.redraw.called);
 });
 
-QUnit.test("test destroy", function(assert) {
+QUnit.test("test destroy", function (assert) {
     var connector = this.test_connector();
     connector.destroy = sinon.spy();
     this.input_terminal.destroy();
@@ -116,44 +116,44 @@ QUnit.test("test destroy", function(assert) {
     assert.ok(connector.destroy.called);
 });
 
-QUnit.test("can accept exact datatype", function(assert) {
+QUnit.test("can accept exact datatype", function (assert) {
     var other = { node: {}, datatypes: ["txt"], force_datatype: null }; // input also txt
     assert.ok(this.test_accept(other));
 });
 
-QUnit.test("can accept subclass datatype", function(assert) {
+QUnit.test("can accept subclass datatype", function (assert) {
     var other = { node: {}, datatypes: ["tabular"] }; // tabular subclass of input txt
     assert.ok(this.test_accept(other));
 });
 
-QUnit.test("cannot accept incorrect datatype", function(assert) {
+QUnit.test("cannot accept incorrect datatype", function (assert) {
     var other = { node: {}, datatypes: ["binary"] }; // binary is not txt
     assert.ok(!this.test_accept(other));
 });
 
-QUnit.test("can accept incorrect datatype if converted with PJA", function(assert) {
+QUnit.test("can accept incorrect datatype if converted with PJA", function (assert) {
     var other = { node: {}, datatypes: ["binary"], force_datatype: "txt", name: "out1" }; // Was binary but converted to txt
     assert.ok(this.test_accept(other));
 });
 
-QUnit.test("cannot accept incorrect datatype if converted with PJA to incompatible type", function(assert) {
+QUnit.test("cannot accept incorrect datatype if converted with PJA to incompatible type", function (assert) {
     var other = { node: {}, datatypes: ["binary"], force_datatype: "bam", name: "out1" };
     assert.ok(!this.test_accept(other));
 });
 
-QUnit.test("can accept inputs", function(assert) {
+QUnit.test("can accept inputs", function (assert) {
     // Other is data input module - always accept (currently - could be
     // more intelligent by looking at what else input is connected to.
     var other = { node: {}, datatypes: ["input"] };
     assert.ok(this.test_accept(other));
 });
 
-QUnit.test("can't connect non-optional", function(assert) {
+QUnit.test("can't connect non-optional", function (assert) {
     var other = { node: {}, datatypes: ["input"], optional: true };
     assert.ok(!this.test_accept(other));
 });
 
-QUnit.test("multiple inputs can accept optional outputs regardless", function(assert) {
+QUnit.test("multiple inputs can accept optional outputs regardless", function (assert) {
     // Galaxy multiple inputs have an optional field but it is hard to resolve that
     // completely until runtime.
     var other = { node: {}, datatypes: ["input"], optional: true };
@@ -161,28 +161,28 @@ QUnit.test("multiple inputs can accept optional outputs regardless", function(as
     assert.ok(this.test_accept(other));
 });
 
-QUnit.test("input type can accept any datatype", function(assert) {
+QUnit.test("input type can accept any datatype", function (assert) {
     this.input.extensions = ["input"];
     this.input_terminal.update(this.input);
     var other = { node: {}, datatypes: ["binary"] };
     assert.ok(this.test_accept(other));
 });
 
-QUnit.test("cannot accept when already connected", function(assert) {
+QUnit.test("cannot accept when already connected", function (assert) {
     // If other is subtype but already connected, cannot accept
     this.with_test_connector(() => {
         assert.ok(!this.test_accept());
     });
 });
 
-QUnit.test("can accept already connected inputs if input is multiple", function(assert) {
+QUnit.test("can accept already connected inputs if input is multiple", function (assert) {
     this.multiple();
     this.with_test_connector(() => {
         assert.ok(this.test_accept());
     });
 });
 
-QUnit.test("cannot accept already connected inputs if input is multiple but datatypes don't match", function(assert) {
+QUnit.test("cannot accept already connected inputs if input is multiple but datatypes don't match", function (assert) {
     var other = { node: {}, datatypes: ["binary"] }; // binary is not txt
     this.multiple();
     this.with_test_connector(() => {
@@ -190,26 +190,26 @@ QUnit.test("cannot accept already connected inputs if input is multiple but data
     });
 });
 
-QUnit.test("can accept list collection for multiple input parameters if datatypes match", function(assert) {
+QUnit.test("can accept list collection for multiple input parameters if datatypes match", function (assert) {
     this.multiple();
     assert.ok(this.test_accept());
 });
 
-QUnit.test("can accept list collection for empty multiple inputs", function(assert) {
+QUnit.test("can accept list collection for empty multiple inputs", function (assert) {
     var other = {
         node: {},
         datatypes: ["tabular"],
-        mapOver: new Terminals.CollectionTypeDescription("list")
+        mapOver: new Terminals.CollectionTypeDescription("list"),
     };
     this.multiple();
     assert.ok(this.test_accept(other));
 });
 
-QUnit.test("cannot accept list collection for multiple input if collection already connected", function(assert) {
+QUnit.test("cannot accept list collection for multiple input if collection already connected", function (assert) {
     var other = {
         node: {},
         datatypes: ["tabular"],
-        mapOver: new Terminals.CollectionTypeDescription("list")
+        mapOver: new Terminals.CollectionTypeDescription("list"),
     };
     this.multiple();
     this.with_test_connector(() => {
@@ -219,7 +219,7 @@ QUnit.test("cannot accept list collection for multiple input if collection alrea
 
 QUnit.module("Connector test", {});
 
-QUnit.test("connects only if both valid handles", function(assert) {
+QUnit.test("connects only if both valid handles", function (assert) {
     const input = { connect: sinon.spy() };
     const output = { connect: sinon.spy() };
     new Connector({}, input, null);
@@ -232,7 +232,7 @@ QUnit.test("connects only if both valid handles", function(assert) {
     assert.ok(output.connect.called);
 });
 
-QUnit.test("default attributes", function(assert) {
+QUnit.test("default attributes", function (assert) {
     const input = { connect: sinon.spy() };
     const output = { connect: sinon.spy() };
     const connector = new Connector({}, input, output);
@@ -240,7 +240,7 @@ QUnit.test("default attributes", function(assert) {
     assert.equal(connector.svg.attr("class"), "ribbon");
 });
 
-QUnit.test("destroy", function(assert) {
+QUnit.test("destroy", function (assert) {
     const input = { connect: sinon.spy(), disconnect: sinon.spy() };
     const output = { connect: sinon.spy(), disconnect: sinon.spy() };
     const connector = new Connector({}, input, output);
@@ -249,20 +249,20 @@ QUnit.test("destroy", function(assert) {
     assert.ok(output.disconnect.called);
 });
 
-QUnit.test("initial redraw", function(assert) {
+QUnit.test("initial redraw", function (assert) {
     const input = {
         connect: sinon.spy(),
         element: $("<div>"),
-        isMappedOver: function() {
+        isMappedOver: function () {
             return false;
-        }
+        },
     };
     const output = {
         connect: sinon.spy(),
         element: $("<div>"),
-        isMappedOver: function() {
+        isMappedOver: function () {
             return false;
-        }
+        },
     };
     const n = $("#canvas-container").find("svg").length;
     const connector = new Connector({}, input, output);
@@ -273,20 +273,20 @@ QUnit.test("initial redraw", function(assert) {
 });
 
 QUnit.module("Input collection terminal model test", {
-    beforeEach: function() {
+    beforeEach: function () {
         this.app = create_app();
         this.node = new Node(this.app, {});
         this.input = { extensions: ["txt"], collection_types: ["list"] };
         this.input_terminal = new Terminals.InputCollectionTerminal({ app: this.app, input: this.input });
         this.input_terminal.node = this.node;
-    }
+    },
 });
 
-QUnit.test("Collection output can connect to same collection input type", function(assert) {
+QUnit.test("Collection output can connect to same collection input type", function (assert) {
     const inputTerminal = this.input_terminal;
     const outputTerminal = new Terminals.OutputCollectionTerminal({
         datatypes: "txt",
-        collection_type: "list"
+        collection_type: "list",
     });
     outputTerminal.node = {};
     assert.ok(
@@ -295,29 +295,29 @@ QUnit.test("Collection output can connect to same collection input type", functi
     );
 });
 
-QUnit.test("Optional collection output can not connect to required collection input", function(assert) {
+QUnit.test("Optional collection output can not connect to required collection input", function (assert) {
     const inputTerminal = this.input_terminal;
     const outputTerminal = new Terminals.OutputCollectionTerminal({
         datatypes: "txt",
         collection_type: "list",
-        optional: true
+        optional: true,
     });
     outputTerminal.node = {};
     assert.ok(!inputTerminal.canAccept(outputTerminal).canAccept);
 });
 
-QUnit.test("Collection output cannot connect to different collection input type", function(assert) {
+QUnit.test("Collection output cannot connect to different collection input type", function (assert) {
     var inputTerminal = this.input_terminal;
     var outputTerminal = new Terminals.OutputCollectionTerminal({
         datatypes: "txt",
-        collection_type: "paired"
+        collection_type: "paired",
     });
     outputTerminal.node = {};
     assert.ok(!inputTerminal.canAccept(outputTerminal).canAccept);
 });
 
 QUnit.module("Node unit test", {
-    beforeEach: function() {
+    beforeEach: function () {
         this.input_terminal = { destroy: sinon.spy(), redraw: sinon.spy() };
         this.output_terminal = { destroy: sinon.spy(), redraw: sinon.spy() };
         this.app = create_app();
@@ -326,44 +326,44 @@ QUnit.module("Node unit test", {
         this.node.input_terminals.i1 = this.input_terminal;
         this.node.output_terminals.o1 = this.output_terminal;
     },
-    $: function(selector) {
+    $: function (selector) {
         return $(this.node.element.find(selector));
     },
-    expect_workflow_node_changed: function(assert, f) {
+    expect_workflow_node_changed: function (assert, f) {
         const node = this.node;
         const node_changed_spy = sinon.spy(this.app, "node_changed");
         f();
         assert.ok(node_changed_spy.calledWith(node));
     },
-    init_field_data_simple: function(option_overrides) {
+    init_field_data_simple: function (option_overrides) {
         const data = Utils.merge(option_overrides, {
             inputs: [{ name: "input1", extensions: ["data"] }],
             outputs: [{ name: "output1", extensions: ["data"] }],
-            label: null
+            label: null,
         });
         this.node.init_field_data(data);
     },
-    update_field_data_with_new_input: function(option_overrides) {
+    update_field_data_with_new_input: function (option_overrides) {
         const new_data = Utils.merge(option_overrides, {
             inputs: [
                 { name: "input1", extensions: ["data"] },
-                { name: "extra_0|input1", extensions: ["data"] }
+                { name: "extra_0|input1", extensions: ["data"] },
             ],
             outputs: [{ name: "output1", extensions: ["data"] }],
             post_job_actions: "{}",
-            label: "New Label"
+            label: "New Label",
         });
         this.node.update_field_data(new_data);
-    }
+    },
 });
 
-QUnit.test("make active", function(assert) {
+QUnit.test("make active", function (assert) {
     assert.ok(!this.element.hasClass("node-active"));
     this.node.make_active();
     assert.ok(this.element.hasClass("node-active"));
 });
 
-QUnit.test("destroy", function(assert) {
+QUnit.test("destroy", function (assert) {
     var remove_node_spy = sinon.spy(this.app, "remove_node");
     this.node.destroy();
     assert.ok(this.input_terminal.destroy.called);
@@ -371,18 +371,18 @@ QUnit.test("destroy", function(assert) {
     assert.ok(remove_node_spy.calledWith(this.node));
 });
 
-QUnit.test("error", function(assert) {
+QUnit.test("error", function (assert) {
     // Test body of div updated and workflow notified of change.
     var test = this;
-    this.expect_workflow_node_changed(assert, function() {
+    this.expect_workflow_node_changed(assert, function () {
         test.node.init_field_data({ errors: "NODE ERROR", inputs: [], outputs: [] });
         assert.equal(test.$(".node-body").html(), "NODE ERROR");
     });
 });
 
-QUnit.test("init_field_data properties", function(assert) {
+QUnit.test("init_field_data properties", function (assert) {
     var node = this.node;
-    this.expect_workflow_node_changed(assert, function() {
+    this.expect_workflow_node_changed(assert, function () {
         var data = {
             inputs: [],
             outputs: [],
@@ -394,7 +394,7 @@ QUnit.test("init_field_data properties", function(assert) {
             tooltip: "tool tooltip",
             annotation: "tool annotation",
             workflow_outputs: [{ output_name: "out1" }],
-            label: "Cat that data."
+            label: "Cat that data.",
         };
         node.init_field_data(data);
         assert.equal(node.type, "tool");
@@ -409,7 +409,7 @@ QUnit.test("init_field_data properties", function(assert) {
     });
 });
 
-QUnit.test("init_field_data data", function(assert) {
+QUnit.test("init_field_data data", function (assert) {
     this.expect_workflow_node_changed(assert, () => {
         // pre-init not tool form body...
         assert.equal(this.$(".output-terminal").length, 0);
@@ -422,15 +422,11 @@ QUnit.test("init_field_data data", function(assert) {
         assert.equal(this.$(".rule").length, 1);
         assert.equal(this.$(".node-body").children().length, 3);
         assert.equal(this.$(".node-title").text(), "newnode");
-        assert.ok(
-            this.$(".node-header")
-                .find("i")
-                .hasClass("fa-wrench")
-        );
+        assert.ok(this.$(".node-header").find("i").hasClass("fa-wrench"));
     });
 });
 
-QUnit.test("node title behavior", function(assert) {
+QUnit.test("node title behavior", function (assert) {
     this.expect_workflow_node_changed(assert, () => {
         // Node created with name newnode
         assert.equal(this.$(".node-title").text(), "newnode");
@@ -444,7 +440,7 @@ QUnit.test("node title behavior", function(assert) {
     });
 });
 
-QUnit.test("update_field_data updated data inputs and outputs", function(assert) {
+QUnit.test("update_field_data updated data inputs and outputs", function (assert) {
     this.expect_workflow_node_changed(assert, () => {
         // Call init with one input and output.
         this.init_field_data_simple();
@@ -458,7 +454,7 @@ QUnit.test("update_field_data updated data inputs and outputs", function(assert)
     });
 });
 
-QUnit.test("update_field_data preserves connectors", function(assert) {
+QUnit.test("update_field_data preserves connectors", function (assert) {
     var node = this.node;
     this.expect_workflow_node_changed(assert, () => {
         // Call init with one input and output.
@@ -480,15 +476,15 @@ QUnit.test("update_field_data preserves connectors", function(assert) {
     });
 });
 
-QUnit.test("update_field_data destroys old terminals", function(assert) {
+QUnit.test("update_field_data destroys old terminals", function (assert) {
     var node = this.node;
     this.expect_workflow_node_changed(assert, () => {
         var data = {
             inputs: [
                 { name: "input1", extensions: ["data"] },
-                { name: "willDisappear", extensions: ["data"] }
+                { name: "willDisappear", extensions: ["data"] },
             ],
-            outputs: [{ name: "output1", extensions: ["data"] }]
+            outputs: [{ name: "output1", extensions: ["data"] }],
         };
         node.init_field_data(data);
         var old_input_terminal = node.input_terminals.willDisappear;
@@ -500,12 +496,12 @@ QUnit.test("update_field_data destroys old terminals", function(assert) {
 });
 
 QUnit.module("create_node", {
-    beforeEach: function() {
+    beforeEach: function () {
         this.app = create_app();
-    }
+    },
 });
 
-QUnit.test("node added to workflow", function(assert) {
+QUnit.test("node added to workflow", function (assert) {
     var add_node_spy = sinon.spy(this.app, "add_node");
     var node = this.app.create_node("tool", "Cat Files", "cat1");
     assert.ok(add_node_spy.calledWith(node));
@@ -513,89 +509,89 @@ QUnit.test("node added to workflow", function(assert) {
 
 // global NodeView
 QUnit.module("Node view ", {
-    beforeEach: function() {
+    beforeEach: function () {
         this.app = create_app();
         this.set_for_node({
             input_terminals: {},
             output_terminals: {},
-            markChanged: function() {},
-            hasConnectedOutputTerminals: function() {},
-            connectedMappedInputTerminals: function() {}
+            markChanged: function () {},
+            hasConnectedOutputTerminals: function () {},
+            connectedMappedInputTerminals: function () {},
         });
     },
-    afterEach: function() {
+    afterEach: function () {
         this.view.$el.remove();
     },
-    set_for_node: function(node) {
+    set_for_node: function (node) {
         var element = $("<div><div class='toolFormBody'></div></div>");
         this.view = new NodeView(this.app, { node: node, $el: element });
     },
-    connectAttachedTerminal: function(inputType, outputType) {
+    connectAttachedTerminal: function (inputType, outputType) {
         this.view.addDataInput({ name: "TestName", extensions: [inputType] });
         var terminal = this.view.node.input_terminals["TestName"];
 
         var outputTerminal = new Terminals.OutputTerminal({
             name: "TestOuptut",
             datatypes: [outputType],
-            mapOver: Terminals.NULL_COLLECTION_TYPE_DESCRIPTION
+            mapOver: Terminals.NULL_COLLECTION_TYPE_DESCRIPTION,
         });
         outputTerminal.node = {
-            markChanged: function() {},
+            markChanged: function () {},
             post_job_actions: [],
-            hasMappedOverInputTerminals: function() {
+            hasMappedOverInputTerminals: function () {
                 return false;
             },
-            hasConnectedOutputTerminals: function() {
+            hasConnectedOutputTerminals: function () {
                 return true;
-            }
+            },
         };
         return new Connector({}, outputTerminal, terminal);
     },
-    connectAttachedMultiInputTerminal: function(inputType, outputType) {
+    connectAttachedMultiInputTerminal: function (inputType, outputType) {
         this.view.addDataInput({ name: "TestName", extensions: [inputType], multiple: true });
         var terminal = this.view.node.input_terminals["TestName"];
 
         var outputTerminal = new Terminals.OutputTerminal({
             name: "TestOuptut",
             datatypes: ["txt"],
-            mapOver: new Terminals.CollectionTypeDescription("list")
+            mapOver: new Terminals.CollectionTypeDescription("list"),
         });
         outputTerminal.node = {
-            markChanged: function() {},
+            markChanged: function () {},
             post_job_actions: [],
-            hasMappedOverInputTerminals: function() {
+            hasMappedOverInputTerminals: function () {
                 return false;
             },
-            hasConnectedOutputTerminals: function() {
+            hasConnectedOutputTerminals: function () {
                 return true;
-            }
+            },
         };
         return new Connector({}, outputTerminal, terminal);
     },
-    connectAttachedMappedOutput: function() {
+    connectAttachedMappedOutput: function () {
         this.view.addDataInput({ name: "TestName", extensions: ["txt"], input_type: "dataset_collection" });
         var terminal = this.view.node.input_terminals["TestName"];
 
         var outputTerminal = new Terminals.OutputTerminal({
             name: "TestOuptut",
             datatypes: ["txt"],
-            mapOver: new Terminals.CollectionTypeDescription("list")
+            mapOver: new Terminals.CollectionTypeDescription("list"),
         });
         outputTerminal.node = {
-            markChanged: function() {},
+            markChanged: function () {},
             post_job_actions: [],
-            hasMappedOverInputTerminals: function() {
+            hasMappedOverInputTerminals: function () {
                 return false;
             },
-            hasConnectedOutputTerminals: function() {
+            hasConnectedOutputTerminals: function () {
                 return true;
-            }
+            },
         };
         return new Connector({}, outputTerminal, terminal);
-    }
+    },
 });
 
-QUnit.test("tool error styling", function(assert) {
+QUnit.test("tool error styling", function (assert) {
     this.set_for_node({ errors: false });
     this.view.render();
     assert.ok(!this.view.$el.hasClass("node-error"));
@@ -604,7 +600,7 @@ QUnit.test("tool error styling", function(assert) {
     assert.ok(this.view.$el.hasClass("node-error"));
 });
 
-QUnit.test("rendering correct width", function(assert) {
+QUnit.test("rendering correct width", function (assert) {
     // Default width is 150
     this.view.render();
     assert.equal(this.view.$el.width(), 150);
@@ -620,7 +616,7 @@ QUnit.test("rendering correct width", function(assert) {
     assert.equal(this.view.$el.width(), 250);
 });
 
-QUnit.test("replacing terminal on data input update preserves connections", function(assert) {
+QUnit.test("replacing terminal on data input update preserves connections", function (assert) {
     var connector = this.connectAttachedTerminal("txt", "txt");
     var newElement = $("<div class='inputs'></div>");
     this.view.addDataInput({ name: "TestName", extensions: ["txt"] }, newElement);
@@ -628,7 +624,7 @@ QUnit.test("replacing terminal on data input update preserves connections", func
     assert.ok(connector.handle2 === terminal);
 });
 
-QUnit.test("replacing terminal on data multiple input update preserves collection connections", function(assert) {
+QUnit.test("replacing terminal on data multiple input update preserves collection connections", function (assert) {
     var connector = this.connectAttachedMultiInputTerminal("txt", "txt");
     var connector_destroy_spy = sinon.spy(connector, "destroy");
     var newElement = $("<div class='inputs'></div>");
@@ -636,7 +632,7 @@ QUnit.test("replacing terminal on data multiple input update preserves collectio
     assert.ok(!connector_destroy_spy.called);
 });
 
-QUnit.test("replacing mapped terminal on data collection input update preserves connections", function(assert) {
+QUnit.test("replacing mapped terminal on data collection input update preserves connections", function (assert) {
     var connector = this.connectAttachedMappedOutput();
     var newElement = $("<div class='inputs'></div>");
     this.view.addDataInput({ name: "TestName", extensions: ["txt"], input_type: "dataset_collection" }, newElement);
@@ -644,7 +640,7 @@ QUnit.test("replacing mapped terminal on data collection input update preserves
     assert.ok(connector.handle2 === terminal);
 });
 
-QUnit.test("replacing terminal on data input destroys invalid connections", function(assert) {
+QUnit.test("replacing terminal on data input destroys invalid connections", function (assert) {
     var connector = this.connectAttachedTerminal("txt", "txt");
     var newElement = $("<div class='inputs'></div>");
     var connector_destroy_spy = sinon.spy(connector, "destroy");
@@ -654,7 +650,7 @@ QUnit.test("replacing terminal on data input destroys invalid connections", func
     assert.ok(connector_destroy_spy.called);
 });
 
-QUnit.test("replacing terminal on data input with collection changes mapping view type", function(assert) {
+QUnit.test("replacing terminal on data input with collection changes mapping view type", function (assert) {
     var connector = this.connectAttachedTerminal("txt", "txt");
     var newElement = $("<div class='inputs'></div>");
     var connector_destroy_spy = sinon.spy(connector, "destroy");
@@ -665,7 +661,9 @@ QUnit.test("replacing terminal on data input with collection changes mapping vie
     assert.ok(connector_destroy_spy.called);
 });
 
-QUnit.test("replacing terminal on data collection input with simple input changes mapping view type", function(assert) {
+QUnit.test("replacing terminal on data collection input with simple input changes mapping view type", function (
+    assert
+) {
     var connector = this.connectAttachedMappedOutput();
     var newElement = $("<div class='inputs'></div>");
     var connector_destroy_spy = sinon.spy(connector, "destroy");
@@ -676,71 +674,71 @@ QUnit.test("replacing terminal on data collection input with simple input change
 
 // global InputTerminalView
 QUnit.module("Input terminal view", {
-    beforeEach: function() {
+    beforeEach: function () {
         this.app = create_app();
         this.node = { input_terminals: [] };
         this.input = { name: "i1", extensions: "txt", multiple: false };
         this.view = new TerminalsView.InputTerminalView(this.app, {
             node: this.node,
-            input: this.input
+            input: this.input,
         });
-    }
+    },
 });
 
-QUnit.test("terminal added to node", function(assert) {
+QUnit.test("terminal added to node", function (assert) {
     assert.ok(this.node.input_terminals.i1);
     assert.equal(this.node.input_terminals.i1.datatypes, ["txt"]);
     assert.equal(this.node.input_terminals.i1.multiple, false);
 });
 
-QUnit.test("terminal element", function(assert) {
+QUnit.test("terminal element", function (assert) {
     var el = this.view.el;
     assert.equal(el.tagName, "DIV");
     assert.equal(el.className, "terminal input-terminal");
 });
 
 QUnit.module("Output terminal view", {
-    beforeEach: function() {
+    beforeEach: function () {
         this.app = create_app();
         this.node = { output_terminals: [] };
         this.output = { name: "o1", extensions: "txt" };
         this.view = new TerminalsView.OutputTerminalView(this.app, {
             node: this.node,
-            output: this.output
+            output: this.output,
         });
-    }
+    },
 });
 
-QUnit.test("terminal added to node", function(assert) {
+QUnit.test("terminal added to node", function (assert) {
     assert.ok(this.node.output_terminals.o1);
     assert.equal(this.node.output_terminals.o1.datatypes, ["txt"]);
 });
 
-QUnit.test("terminal element", function(assert) {
+QUnit.test("terminal element", function (assert) {
     var el = this.view.el;
     assert.equal(el.tagName, "DIV");
     assert.equal(el.className, "terminal output-terminal");
 });
 
 QUnit.module("CollectionTypeDescription", {
-    listType: function() {
+    listType: function () {
         return new Terminals.CollectionTypeDescription("list");
     },
-    pairedType: function() {
+    pairedType: function () {
         return new Terminals.CollectionTypeDescription("paired");
     },
-    pairedListType: function() {
+    pairedListType: function () {
         return new Terminals.CollectionTypeDescription("list:paired");
-    }
+    },
 });
 
-QUnit.test("canMatch", function(assert) {
+QUnit.test("canMatch", function (assert) {
     assert.ok(this.listType().canMatch(this.listType()));
     assert.ok(!this.listType().canMatch(this.pairedType()));
     assert.ok(!this.listType().canMatch(this.pairedListType()));
 });
 
-QUnit.test("canMatch special types", function(assert) {
+QUnit.test("canMatch special types", function (assert) {
     assert.ok(this.listType().canMatch(Terminals.ANY_COLLECTION_TYPE_DESCRIPTION));
     assert.ok(Terminals.ANY_COLLECTION_TYPE_DESCRIPTION.canMatch(this.pairedListType()));
 
@@ -748,14 +746,14 @@ QUnit.test("canMatch special types", function(assert) {
     assert.ok(!Terminals.NULL_COLLECTION_TYPE_DESCRIPTION.canMatch(this.pairedListType()));
 });
 
-QUnit.test("canMapOver", function(assert) {
+QUnit.test("canMapOver", function (assert) {
     assert.ok(!this.listType().canMapOver(this.listType()));
     assert.ok(!this.listType().canMapOver(this.pairedType()));
     assert.ok(this.pairedListType().canMapOver(this.pairedType()));
     assert.ok(!this.listType().canMapOver(this.pairedListType()));
 });
 
-QUnit.test("canMapOver special types", function(assert) {
+QUnit.test("canMapOver special types", function (assert) {
     assert.ok(!this.listType().canMapOver(Terminals.NULL_COLLECTION_TYPE_DESCRIPTION));
     assert.ok(!Terminals.NULL_COLLECTION_TYPE_DESCRIPTION.canMapOver(this.pairedListType()));
 
@@ -766,18 +764,18 @@ QUnit.test("canMapOver special types", function(assert) {
     assert.ok(!Terminals.ANY_COLLECTION_TYPE_DESCRIPTION.canMapOver(this.pairedListType()));
 });
 
-QUnit.test("append", function(assert) {
+QUnit.test("append", function (assert) {
     var appendedType = this.listType().append(this.pairedType());
     assert.equal(appendedType.collectionType, "list:paired");
 });
 
-QUnit.test("isCollection", function(assert) {
+QUnit.test("isCollection", function (assert) {
     assert.ok(this.listType().isCollection);
     assert.ok(Terminals.ANY_COLLECTION_TYPE_DESCRIPTION.isCollection);
     assert.ok(!Terminals.NULL_COLLECTION_TYPE_DESCRIPTION.isCollection);
 });
 
-QUnit.test("equal", function(assert) {
+QUnit.test("equal", function (assert) {
     assert.ok(!this.listType().equal(this.pairedType()));
     assert.ok(this.listType().equal(this.listType()));
 
@@ -792,25 +790,25 @@ QUnit.test("equal", function(assert) {
     assert.ok(!this.listType().equal(Terminals.NULL_COLLECTION_TYPE_DESCRIPTION));
 });
 
-QUnit.test("default constructor", function(assert) {
+QUnit.test("default constructor", function (assert) {
     var terminal = new Terminals.InputTerminal({});
     assert.ok(terminal.mapOver === Terminals.NULL_COLLECTION_TYPE_DESCRIPTION);
 });
 
-QUnit.test("constructing with mapOver", function(assert) {
+QUnit.test("constructing with mapOver", function (assert) {
     var terminal = new Terminals.InputTerminal({
-        mapOver: new Terminals.CollectionTypeDescription("list")
+        mapOver: new Terminals.CollectionTypeDescription("list"),
     });
     assert.ok(terminal.mapOver.collectionType == "list");
 });
 
-QUnit.test("resetMapping", function(assert) {
+QUnit.test("resetMapping", function (assert) {
     var terminal = new Terminals.InputTerminal({
         terminal: terminal,
-        mapOver: new Terminals.CollectionTypeDescription("list")
+        mapOver: new Terminals.CollectionTypeDescription("list"),
     });
     terminal.node = {
-        hasMappedOverInputTerminals: () => true
+        hasMappedOverInputTerminals: () => true,
     };
     var changeSpy = sinon.spy();
     terminal.on("change", changeSpy);
@@ -820,7 +818,7 @@ QUnit.test("resetMapping", function(assert) {
 });
 
 QUnit.module("terminal mapping logic", {
-    newInputTerminal: function(mapOver, input, node) {
+    newInputTerminal: function (mapOver, input, node) {
         input = input || {};
         node = node || this.newNode();
         if (!("extensions" in input)) {
@@ -835,7 +833,7 @@ QUnit.module("terminal mapping logic", {
         }
         return inputTerminal;
     },
-    newInputCollectionTerminal: function(input, node) {
+    newInputCollectionTerminal: function (input, node) {
         input = input || {};
         node = node || this.newNode();
         if (!("extensions" in input)) {
@@ -846,12 +844,12 @@ QUnit.module("terminal mapping logic", {
         const inputTerminal = new Terminals.InputCollectionTerminal({
             app: app,
             element: inputEl,
-            input: input
+            input: input,
         });
         inputTerminal.node = node;
         return inputTerminal;
     },
-    newOutputTerminal: function(mapOver, output, node) {
+    newOutputTerminal: function (mapOver, output, node) {
         output = output || {};
         node = node || this.newNode();
         if (!("extensions" in output)) {
@@ -865,7 +863,7 @@ QUnit.module("terminal mapping logic", {
         }
         return outputTerminal;
     },
-    newOutputCollectionTerminal: function(collectionType, output, node, mapOver) {
+    newOutputCollectionTerminal: function (collectionType, output, node, mapOver) {
         collectionType = collectionType || "list";
         output = output || {};
         node = node || this.newNode();
@@ -876,7 +874,7 @@ QUnit.module("terminal mapping logic", {
         var outputTerminal = new Terminals.OutputCollectionTerminal({
             element: outputEl,
             datatypes: output.extensions,
-            collection_type: collectionType
+            collection_type: collectionType,
         });
         outputTerminal.node = node;
         if (mapOver) {
@@ -884,12 +882,12 @@ QUnit.module("terminal mapping logic", {
         }
         return outputTerminal;
     },
-    newNode: function() {
+    newNode: function () {
         var nodeEl = $("<div>")[0];
         var app = create_app();
         return new Node(app, { element: nodeEl });
     },
-    _addExistingOutput: function(terminal, output, connected) {
+    _addExistingOutput: function (terminal, output, connected) {
         var self = this;
         var node = terminal.node;
         if (connected) {
@@ -899,22 +897,22 @@ QUnit.module("terminal mapping logic", {
         this._addTerminalTo(output, node.output_terminals);
         return output;
     },
-    addOutput: function(terminal, connected) {
+    addOutput: function (terminal, connected) {
         var connectedOutput = this.newOutputTerminal();
         return this._addExistingOutput(terminal, connectedOutput, connected);
     },
-    addCollectionOutput: function(terminal, connected) {
+    addCollectionOutput: function (terminal, connected) {
         var collectionOutput = this.newOutputCollectionTerminal();
         return this._addExistingOutput(terminal, collectionOutput, connected);
     },
-    addConnectedOutput: function(terminal) {
+    addConnectedOutput: function (terminal) {
         return this.addOutput(terminal, true);
     },
-    addConnectedCollectionOutput: function(terminal) {
+    addConnectedCollectionOutput: function (terminal) {
         var connectedOutput = this.newOutputCollectionTerminal();
         return this._addExistingOutput(terminal, connectedOutput, true);
     },
-    addConnectedInput: function(terminal) {
+    addConnectedInput: function (terminal) {
         var self = this;
         var connectedInput = this.newInputTerminal();
         var node = terminal.node;
@@ -923,14 +921,14 @@ QUnit.module("terminal mapping logic", {
         this._addTerminalTo(connectedInput, node.input_terminals);
         return connectedInput;
     },
-    _addTerminalTo: function(terminal, terminals) {
+    _addTerminalTo: function (terminal, terminals) {
         var name = "other";
         while (name in terminals) {
             name += "_";
         }
         terminals[name] = terminal;
     },
-    verifyNotAttachable: function(assert, inputTerminal, output) {
+    verifyNotAttachable: function (assert, inputTerminal, output) {
         var outputTerminal;
         if (typeof output == "string") {
             // Just given a collection type... create terminal out of it.
@@ -941,7 +939,7 @@ QUnit.module("terminal mapping logic", {
 
         assert.ok(!inputTerminal.attachable(outputTerminal).canAccept);
     },
-    verifyAttachable: function(assert, inputTerminal, output) {
+    verifyAttachable: function (assert, inputTerminal, output) {
         var outputTerminal;
         if (typeof output == "string") {
             // Just given a collection type... create terminal out of it.
@@ -960,20 +958,20 @@ QUnit.module("terminal mapping logic", {
         outputTerminal.datatypes = ["txt"];
         assert.ok(!inputTerminal.attachable(outputTerminal).canAccept);
     },
-    verifyMappedOver: function(assert, terminal) {
+    verifyMappedOver: function (assert, terminal) {
         assert.ok(terminal.mapOver.isCollection);
     },
-    verifyNotMappedOver: function(assert, terminal) {
+    verifyNotMappedOver: function (assert, terminal) {
         assert.ok(!terminal.mapOver.isCollection);
-    }
+    },
 });
 
-QUnit.test("unconstrained input can be mapped over", function(assert) {
+QUnit.test("unconstrained input can be mapped over", function (assert) {
     this.inputTerminal1 = this.newInputTerminal();
     this.verifyAttachable(assert, this.inputTerminal1, "list");
 });
 
-QUnit.test("unmapped input can be mapped over if matching connected input terminals map type", function(assert) {
+QUnit.test("unmapped input can be mapped over if matching connected input terminals map type", function (assert) {
     this.inputTerminal1 = this.newInputTerminal();
     this.addConnectedInput(this.inputTerminal1);
     var connectedInput2 = this.addConnectedInput(this.inputTerminal1);
@@ -981,7 +979,9 @@ QUnit.test("unmapped input can be mapped over if matching connected input termin
     this.verifyAttachable(assert, this.inputTerminal1, "list");
 });
 
-QUnit.test("unmapped input cannot be mapped over if not matching connected input terminals map type", function(assert) {
+QUnit.test("unmapped input cannot be mapped over if not matching connected input terminals map type", function (
+    assert
+) {
     this.inputTerminal1 = this.newInputTerminal();
     var connectedInput = this.addConnectedInput(this.inputTerminal1);
     connectedInput.setMapOver(new Terminals.CollectionTypeDescription("paired"));
@@ -990,7 +990,7 @@ QUnit.test("unmapped input cannot be mapped over if not matching connected input
 
 QUnit.test(
     "unmapped input can be attached to by output collection if matching connected input terminals map type",
-    function(assert) {
+    function (assert) {
         this.inputTerminal1 = this.newInputTerminal();
         this.addConnectedInput(this.inputTerminal1);
         var connectedInput2 = this.addConnectedInput(this.inputTerminal1);
@@ -1002,7 +1002,7 @@ QUnit.test(
 
 QUnit.test(
     "unmapped input cannot be attached to by output collection if matching connected input terminals don't match map type",
-    function(assert) {
+    function (assert) {
         this.inputTerminal1 = this.newInputTerminal();
         this.addConnectedInput(this.inputTerminal1);
         var connectedInput2 = this.addConnectedInput(this.inputTerminal1);
@@ -1014,7 +1014,7 @@ QUnit.test(
 
 QUnit.test(
     "unmapped input can be attached to by output collection if effective output type (output+mapover) is same as mapped over input",
-    function(assert) {
+    function (assert) {
         this.inputTerminal1 = this.newInputTerminal();
         this.addConnectedInput(this.inputTerminal1);
         var connectedInput2 = this.addConnectedInput(this.inputTerminal1);
@@ -1027,7 +1027,7 @@ QUnit.test(
 
 QUnit.test(
     "unmapped input cannot be attached to by output collection if effective output type (output+mapover) is not same as mapped over input (1)",
-    function(assert) {
+    function (assert) {
         this.inputTerminal1 = this.newInputTerminal();
         this.addConnectedInput(this.inputTerminal1);
         var connectedInput2 = this.addConnectedInput(this.inputTerminal1);
@@ -1040,7 +1040,7 @@ QUnit.test(
 
 QUnit.test(
     "unmapped input cannot be attached to by output collection if effective output type (output+mapover) is not same as mapped over input (2)",
-    function(assert) {
+    function (assert) {
         this.inputTerminal1 = this.newInputTerminal();
         this.addConnectedInput(this.inputTerminal1);
         var connectedInput2 = this.addConnectedInput(this.inputTerminal1);
@@ -1051,7 +1051,7 @@ QUnit.test(
     }
 );
 
-QUnit.test("unmapped input with unmapped, connected outputs cannot be mapped over", function(assert) {
+QUnit.test("unmapped input with unmapped, connected outputs cannot be mapped over", function (assert) {
     // It would invalidate the connections - someday maybe we could try to
     // recursively map over everything down the DAG - it would be expensive
     // to check that though.
@@ -1060,7 +1060,7 @@ QUnit.test("unmapped input with unmapped, connected outputs cannot be mapped ove
     this.verifyNotAttachable(assert, this.inputTerminal1, "list");
 });
 
-QUnit.test("unmapped input with connected mapped outputs can be mapped over if matching", function(assert) {
+QUnit.test("unmapped input with connected mapped outputs can be mapped over if matching", function (assert) {
     // It would invalidate the connections - someday maybe we could try to
     // recursively map over everything down the DAG - it would be expensive
     // to check that though.
@@ -1070,7 +1070,7 @@ QUnit.test("unmapped input with connected mapped outputs can be mapped over if m
     this.verifyAttachable(assert, this.inputTerminal1, "list");
 });
 
-QUnit.test("unmapped input with connected mapped outputs cannot be mapped over if mapover not matching", function(
+QUnit.test("unmapped input with connected mapped outputs cannot be mapped over if mapover not matching", function (
     assert
 ) {
     // It would invalidate the connections - someday maybe we could try to
@@ -1082,79 +1082,79 @@ QUnit.test("unmapped input with connected mapped outputs cannot be mapped over i
     this.verifyNotAttachable(assert, this.inputTerminal1, "list");
 });
 
-QUnit.test("explicitly constrained input can not be mapped over by incompatible collection type", function(assert) {
+QUnit.test("explicitly constrained input can not be mapped over by incompatible collection type", function (assert) {
     this.inputTerminal1 = this.newInputTerminal();
     this.inputTerminal1.setMapOver(new Terminals.CollectionTypeDescription("paired"));
     this.verifyNotAttachable(assert, this.inputTerminal1, "list");
 });
 
-QUnit.test("explicitly constrained input can be mapped over by compatible collection type", function(assert) {
+QUnit.test("explicitly constrained input can be mapped over by compatible collection type", function (assert) {
     this.inputTerminal1 = this.newInputTerminal();
     this.inputTerminal1.setMapOver(new Terminals.CollectionTypeDescription("list"));
     this.verifyAttachable(assert, this.inputTerminal1, "list");
 });
 
-QUnit.test("unconstrained collection input can be mapped over", function(assert) {
+QUnit.test("unconstrained collection input can be mapped over", function (assert) {
     this.inputTerminal1 = this.newInputCollectionTerminal({ collection_types: ["paired"] });
     this.verifyAttachable(assert, this.inputTerminal1, "list:paired");
 });
 
-QUnit.test("unconstrained collection input cannot be mapped over by incompatible type", function(assert) {
+QUnit.test("unconstrained collection input cannot be mapped over by incompatible type", function (assert) {
     this.inputTerminal1 = this.newInputCollectionTerminal({ collection_types: ["list"] }); // Would need to be paired...
     this.verifyNotAttachable(assert, this.inputTerminal1, "list:paired");
 });
 
-QUnit.test("explicitly mapped over collection input can be attached by explicit mapping", function(assert) {
+QUnit.test("explicitly mapped over collection input can be attached by explicit mapping", function (assert) {
     this.inputTerminal1 = this.newInputCollectionTerminal({ collection_types: ["paired"] });
     this.inputTerminal1.setMapOver(new Terminals.CollectionTypeDescription("list"));
     this.verifyAttachable(assert, this.inputTerminal1, "list:paired");
 });
 
-QUnit.test("explicitly mapped over collection input can be attached by explicit mapping", function(assert) {
+QUnit.test("explicitly mapped over collection input can be attached by explicit mapping", function (assert) {
     this.inputTerminal1 = this.newInputCollectionTerminal({ collection_types: ["list:paired"] });
     this.inputTerminal1.setMapOver(new Terminals.CollectionTypeDescription("list"));
     // effectively input is list:list:paired so shouldn't be able to attach
     this.verifyNotAttachable(assert, this.inputTerminal1, "list:paired");
 });
 
-QUnit.test("unconnected multiple inputs can be connected to rank 1 collections", function(assert) {
+QUnit.test("unconnected multiple inputs can be connected to rank 1 collections", function (assert) {
     this.inputTerminal1 = this.newInputTerminal(null, { multiple: true });
     this.verifyAttachable(assert, this.inputTerminal1, "list");
 });
 
-QUnit.test("multiple input attachable by collections", function(assert) {
+QUnit.test("multiple input attachable by collections", function (assert) {
     this.inputTerminal1 = this.newInputTerminal(null, { multiple: true });
     var connectedInput1 = this.addConnectedInput(this.inputTerminal1);
     this.addConnectedOutput(connectedInput1);
     this.verifyAttachable(assert, this.inputTerminal1, "list");
 });
 
-QUnit.test("multiple input attachable by nested collections", function(assert) {
+QUnit.test("multiple input attachable by nested collections", function (assert) {
     this.inputTerminal1 = this.newInputTerminal(null, { multiple: true });
     var connectedInput1 = this.addConnectedInput(this.inputTerminal1);
     this.addConnectedOutput(connectedInput1);
     this.verifyAttachable(assert, this.inputTerminal1, "list:list");
 });
 
-QUnit.test("Multiple inputs cannot be connected to pairs", function(assert) {
+QUnit.test("Multiple inputs cannot be connected to pairs", function (assert) {
     this.inputTerminal1 = this.newInputTerminal(null, { multiple: true });
     this.verifyNotAttachable(assert, this.inputTerminal1, "list:paired");
 });
 
-QUnit.test("resetMappingIfNeeded does nothing if not mapped", function(assert) {
+QUnit.test("resetMappingIfNeeded does nothing if not mapped", function (assert) {
     this.inputTerminal1 = this.newInputTerminal();
     this.inputTerminal1.resetMappingIfNeeded();
     this.verifyNotMappedOver(assert, this.inputTerminal1);
 });
 
-QUnit.test("resetMappingIfNeeded resets unconstrained input", function(assert) {
+QUnit.test("resetMappingIfNeeded resets unconstrained input", function (assert) {
     this.inputTerminal1 = this.newInputTerminal("list");
     this.verifyMappedOver(assert, this.inputTerminal1);
     this.inputTerminal1.resetMappingIfNeeded();
     this.verifyNotMappedOver(assert, this.inputTerminal1);
 });
 
-QUnit.test("resetMappingIfNeeded does not reset if connected output depends on being mapped", function(assert) {
+QUnit.test("resetMappingIfNeeded does not reset if connected output depends on being mapped", function (assert) {
     this.inputTerminal1 = this.newInputTerminal("list");
     var connectedOutput = this.addConnectedOutput(this.inputTerminal1);
     connectedOutput.setMapOver(new Terminals.CollectionTypeDescription("list"));
@@ -1162,7 +1162,7 @@ QUnit.test("resetMappingIfNeeded does not reset if connected output depends on b
     this.verifyMappedOver(assert, this.inputTerminal1);
 });
 
-QUnit.test("resetMappingIfNeeded resets if node outputs are not connected to anything", function(assert) {
+QUnit.test("resetMappingIfNeeded resets if node outputs are not connected to anything", function (assert) {
     this.inputTerminal1 = this.newInputTerminal("list");
     var output = this.addOutput(this.inputTerminal1);
     output.setMapOver(new Terminals.CollectionTypeDescription("list"));
@@ -1170,7 +1170,7 @@ QUnit.test("resetMappingIfNeeded resets if node outputs are not connected to any
     this.verifyNotMappedOver(assert, this.inputTerminal1);
 });
 
-QUnit.test("resetMappingIfNeeded an input resets node outputs if they not connected to anything", function(assert) {
+QUnit.test("resetMappingIfNeeded an input resets node outputs if they not connected to anything", function (assert) {
     this.inputTerminal1 = this.newInputTerminal("list");
     var output = this.addOutput(this.inputTerminal1);
     output.setMapOver(new Terminals.CollectionTypeDescription("list"));
@@ -1178,7 +1178,7 @@ QUnit.test("resetMappingIfNeeded an input resets node outputs if they not connec
     this.verifyNotMappedOver(assert, output);
 });
 
-QUnit.test("resetMappingIfNeeded an input resets node collection outputs if they not connected to anything", function(
+QUnit.test("resetMappingIfNeeded an input resets node collection outputs if they not connected to anything", function (
     assert
 ) {
     this.inputTerminal1 = this.newInputTerminal("list");
@@ -1188,7 +1188,7 @@ QUnit.test("resetMappingIfNeeded an input resets node collection outputs if they
     this.verifyNotMappedOver(assert, output);
 });
 
-QUnit.test("resetMappingIfNeeded resets if not last mapped over input", function(assert) {
+QUnit.test("resetMappingIfNeeded resets if not last mapped over input", function (assert) {
     // Idea here is that other nodes are forcing output to still be mapped
     // over so don't need to disconnect output nodes.
     this.inputTerminal1 = this.newInputTerminal("list");
@@ -1206,7 +1206,7 @@ QUnit.test("resetMappingIfNeeded resets if not last mapped over input", function
     this.verifyMappedOver(assert, connectedOutput);
 });
 
-QUnit.test("simple mapping over collection outputs works correctly", function(assert) {
+QUnit.test("simple mapping over collection outputs works correctly", function (assert) {
     this.inputTerminal1 = this.newInputTerminal();
     var connectedOutput = this.addConnectedCollectionOutput(this.inputTerminal1);
     this.inputTerminal1.setMapOver(new Terminals.CollectionTypeDescription("list"));
diff --git a/client/galaxy/scripts/reports/run_stats.js b/client/galaxy/scripts/reports/run_stats.js
index 1a2ea951e13f..a0036b9c229a 100644
--- a/client/galaxy/scripts/reports/run_stats.js
+++ b/client/galaxy/scripts/reports/run_stats.js
@@ -115,7 +115,7 @@ export function create_chart(inp_data, name, time, title) {
             curr_margin += +(i * barWidth);
             return `translate(${curr_margin},${margin.top})`;
         })
-        .on("mouseenter", d => {
+        .on("mouseenter", (d) => {
             // Show tool tip
             var i = 1;
             var size = d;
@@ -143,7 +143,7 @@ export function create_chart(inp_data, name, time, title) {
                 .attr("height", "15px")
                 .attr("fill", "#ebd9b2");
         })
-        .on("mouseleave", d => {
+        .on("mouseleave", (d) => {
             // Remove tool tip
             d3.select(currentEvent.target.parentElement)
                 .select(".tool_tip")
@@ -189,7 +189,7 @@ export function create_chart(inp_data, name, time, title) {
         .axis()
         .scale(y)
         .orient("left")
-        .tickFormat(d => d3.round(d * d3.max(data), 0));
+        .tickFormat((d) => d3.round(d * d3.max(data), 0));
 
     // Put the y axis on the chart
     chart
@@ -216,8 +216,8 @@ export function create_chart(inp_data, name, time, title) {
 
     // Add color to the chart's bars
     bar.append("rect")
-        .attr("y", d => height - d * zoom)
-        .attr("height", d => d * zoom)
+        .attr("y", (d) => height - d * zoom)
+        .attr("height", (d) => d * zoom)
         .attr("width", barWidth - 1);
 
     var first = false;
@@ -299,12 +299,9 @@ export function create_chart(inp_data, name, time, title) {
 
                 return time;
             })
-            .attr("transform", function(d, i) {
+            .attr("transform", function (d, i) {
                 var text_height = height;
-                var this_width = d3
-                    .select(this)
-                    .node()
-                    .getBBox().width;
+                var this_width = d3.select(this).node().getBBox().width;
 
                 if (hours_array[i].getDate() != curr_day) {
                     if (!first) {
@@ -395,12 +392,9 @@ export function create_chart(inp_data, name, time, title) {
 
                 return time;
             })
-            .attr("transform", function(d, i) {
+            .attr("transform", function (d, i) {
                 var text_height = height;
-                var this_width = d3
-                    .select(this)
-                    .node()
-                    .getBBox().width;
+                var this_width = d3.select(this).node().getBBox().width;
 
                 if (days_array[i].getMonth() != curr_month) {
                     if (!first) {
@@ -418,10 +412,7 @@ export function create_chart(inp_data, name, time, title) {
     }
 
     // Put an invisible tool tip on the chart
-    chart
-        .append("g")
-        .attr("class", "tool_tip")
-        .append("rect");
+    chart.append("g").attr("class", "tool_tip").append("rect");
     chart.select(".tool_tip").append("text");
 
     // Initialize initial zoomed charts
@@ -477,7 +468,7 @@ export function create_histogram(inp_data, name, title) {
     // Used for y axis and bar initialization
     var y = d3.scale
         .linear()
-        .domain([0, d3.max(data, d => d.y)])
+        .domain([0, d3.max(data, (d) => d.y)])
         .range([height, 0]);
 
     // Function for zooming in and out of charts
@@ -501,7 +492,7 @@ export function create_histogram(inp_data, name, title) {
     }
 
     // Formatter for x axis times (converting minutes to HH:MM).
-    var formatMinutes = d => {
+    var formatMinutes = (d) => {
         var hours = Math.floor(d / 60);
         var minutes = Math.floor(d - hours * 60);
 
@@ -539,8 +530,8 @@ export function create_histogram(inp_data, name, title) {
         .enter()
         .append("g")
         .attr("class", "bar")
-        .attr("transform", d => `translate(${+x(d.x) + margin.left},${+y(d.y) + margin.top})`)
-        .on("mouseenter", d => {
+        .attr("transform", (d) => `translate(${+x(d.x) + margin.left},${+y(d.y) + margin.top})`)
+        .on("mouseenter", (d) => {
             // Show tool tip
             var i = 0;
 
@@ -595,14 +586,10 @@ export function create_histogram(inp_data, name, title) {
     bar.append("rect")
         .attr("x", 1)
         .attr("width", bar_x - 1)
-        .attr("height", d => height - y(d.y));
+        .attr("height", (d) => height - y(d.y));
 
     // Create x axis
-    var xAxis = d3.svg
-        .axis()
-        .scale(x)
-        .orient("bottom")
-        .tickFormat(formatMinutes);
+    var xAxis = d3.svg.axis().scale(x).orient("bottom").tickFormat(formatMinutes);
 
     // Add x axis to chart
     chart
@@ -626,10 +613,7 @@ export function create_histogram(inp_data, name, title) {
         .text("ETA - hrs:mins");
 
     // Create y axis
-    var yAxis = d3.svg
-        .axis()
-        .scale(y)
-        .orient("left");
+    var yAxis = d3.svg.axis().scale(y).orient("left");
 
     // Add y axis to chart
     chart
@@ -653,9 +637,6 @@ export function create_histogram(inp_data, name, title) {
         .text("Number of Jobs");
 
     // Put an invisible tool tip on the chart
-    chart
-        .append("g")
-        .attr("class", "tool_tip")
-        .append("rect");
+    chart.append("g").attr("class", "tool_tip").append("rect");
     chart.select(".tool_tip").append("text");
 }
diff --git a/client/galaxy/scripts/store/configStore/index.js b/client/galaxy/scripts/store/configStore/index.js
index 4dad21f45bf9..7dd354b706a5 100644
--- a/client/galaxy/scripts/store/configStore/index.js
+++ b/client/galaxy/scripts/store/configStore/index.js
@@ -3,13 +3,13 @@ import { getConfig } from "./queries";
 const defaultConfigs = {};
 
 const state = {
-    config: Object.assign({}, defaultConfigs)
+    config: Object.assign({}, defaultConfigs),
 };
 
 const mutations = {
     setConfigs(state, newConfigs = {}) {
         state.config = Object.assign({}, defaultConfigs, state.config, newConfigs);
-    }
+    },
 };
 
 const actions = {
@@ -19,14 +19,14 @@ const actions = {
     },
     async $init({ dispatch }) {
         await dispatch("loadConfigs");
-    }
+    },
 };
 
 export const configStore = {
     namespaced: true,
     state,
     mutations,
-    actions
+    actions,
 };
 
 export default configStore;
diff --git a/client/galaxy/scripts/store/gridSearchStore.js b/client/galaxy/scripts/store/gridSearchStore.js
index c5fc2bb2c5b2..2cf240f68a67 100644
--- a/client/galaxy/scripts/store/gridSearchStore.js
+++ b/client/galaxy/scripts/store/gridSearchStore.js
@@ -6,14 +6,14 @@
 
 export const gridSearchStore = {
     state: {
-        searchTags: new Set()
+        searchTags: new Set(),
     },
     mutations: {
         // TODO: we could write an equivalence comparator here for searchTag
         // Sets and not register a change if the new set is equivalent
         setSearchTags(state, tags) {
             state.searchTags = new Set(tags);
-        }
+        },
     },
     actions: {
         toggleSearchTag({ state, commit }, { text }) {
@@ -28,6 +28,6 @@ export const gridSearchStore = {
         },
         clearSearchTags({ state, commit }) {
             commit("setSearchTags", new Set());
-        }
-    }
+        },
+    },
 };
diff --git a/client/galaxy/scripts/store/historyStore.js b/client/galaxy/scripts/store/historyStore.js
index c1a4973ca7a3..9780d6281fa3 100644
--- a/client/galaxy/scripts/store/historyStore.js
+++ b/client/galaxy/scripts/store/historyStore.js
@@ -4,21 +4,21 @@ import axios from "axios";
 
 const state = {
     historyDetailsById: {},
-    historyById: {}
+    historyById: {},
 };
 
 const getters = {
-    getHistoryById: state => historyId => {
+    getHistoryById: (state) => (historyId) => {
         return state.historyById[historyId];
     },
-    getHistoryNameById: state => historyId => {
+    getHistoryNameById: (state) => (historyId) => {
         const details = state.historyDetailsById[historyId];
         if (details && details.name) {
             return details.name;
         } else {
             return "Unavailable";
         }
-    }
+    },
 };
 
 const actions = {
@@ -30,25 +30,25 @@ const actions = {
         const params = {};
         const { data } = await axios.get(`${getAppRoot()}api/histories/${historyId}`, { params });
         commit("saveHistoryForId", { historyId, historyData: data });
-    }
+    },
 };
 
 const mutations = {
     saveHistories: (state, { histories }) => {
         const historyDetailsById = {};
-        histories.forEach(x => {
+        histories.forEach((x) => {
             historyDetailsById[x.id] = x;
         });
         state.historyDetailsById = historyDetailsById;
     },
     saveHistoryForId: (state, { historyId, historyData }) => {
         Vue.set(state.historyById, historyId, historyData);
-    }
+    },
 };
 
 export const historyStore = {
     state,
     getters,
     actions,
-    mutations
+    mutations,
 };
diff --git a/client/galaxy/scripts/store/index.js b/client/galaxy/scripts/store/index.js
index f87acec7c7df..ecdde654cbab 100644
--- a/client/galaxy/scripts/store/index.js
+++ b/client/galaxy/scripts/store/index.js
@@ -21,10 +21,10 @@ export function createStore() {
     return new Vuex.Store({
         plugins: [
             createCache(),
-            store => {
+            (store) => {
                 store.dispatch("user/$init", { store });
                 store.dispatch("config/$init", { store });
-            }
+            },
         ],
         modules: {
             gridSearch: gridSearchStore,
@@ -34,8 +34,8 @@ export function createStore() {
             invocations: invocationStore,
             user: userStore,
             config: configStore,
-            workflows: workflowStore
-        }
+            workflows: workflowStore,
+        },
     });
 }
 
diff --git a/client/galaxy/scripts/store/invocationStore.js b/client/galaxy/scripts/store/invocationStore.js
index 2c2e767705f3..f23dc5427fea 100644
--- a/client/galaxy/scripts/store/invocationStore.js
+++ b/client/galaxy/scripts/store/invocationStore.js
@@ -1,6 +1,6 @@
 export const state = {
     invocationDetailsById: {},
-    invocationJobsSummaryById: {}
+    invocationJobsSummaryById: {},
 };
 
 import Vue from "vue";
@@ -8,12 +8,12 @@ import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 
 const getters = {
-    getInvocationById: state => invocationId => {
+    getInvocationById: (state) => (invocationId) => {
         return state.invocationDetailsById[invocationId];
     },
-    getInvocationJobsSummaryById: state => invocationId => {
+    getInvocationJobsSummaryById: (state) => (invocationId) => {
         return state.invocationJobsSummaryById[invocationId];
-    }
+    },
 };
 
 const actions = {
@@ -24,7 +24,7 @@ const actions = {
     fetchInvocationJobsSummaryForId: async ({ commit }, invocationId) => {
         const { data } = await axios.get(`${getAppRoot()}api/invocations/${invocationId}/jobs_summary`);
         commit("saveInvocationJobsSummaryForId", { invocationId, jobsSummary: data });
-    }
+    },
 };
 
 const mutations = {
@@ -33,12 +33,12 @@ const mutations = {
     },
     saveInvocationJobsSummaryForId: (state, { invocationId, jobsSummary }) => {
         Vue.set(state.invocationJobsSummaryById, invocationId, jobsSummary);
-    }
+    },
 };
 
 export const invocationStore = {
     state,
     getters,
     actions,
-    mutations
+    mutations,
 };
diff --git a/client/galaxy/scripts/store/jobMetricsStore.js b/client/galaxy/scripts/store/jobMetricsStore.js
index cc3be4d399d2..e11014b6f131 100644
--- a/client/galaxy/scripts/store/jobMetricsStore.js
+++ b/client/galaxy/scripts/store/jobMetricsStore.js
@@ -1,7 +1,7 @@
 export const state = {
     jobMetricsByHdaId: {},
     jobMetricsByLddaId: {},
-    jobMetricsByJobId: {}
+    jobMetricsByJobId: {},
 };
 
 import Vue from "vue";
@@ -9,13 +9,13 @@ import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 
 const getters = {
-    getJobMetricsByDatasetId: state => (datasetId, datasetType = "hda") => {
+    getJobMetricsByDatasetId: (state) => (datasetId, datasetType = "hda") => {
         const jobMetricsObject = datasetType == "hda" ? state.jobMetricsByHdaId : state.jobMetricsByLddaId;
         return jobMetricsObject[datasetId] || [];
     },
-    getJobMetricsByJobId: state => jobId => {
+    getJobMetricsByJobId: (state) => (jobId) => {
         return state.jobMetricsByJobId[jobId] || [];
-    }
+    },
 };
 
 const actions = {
@@ -26,7 +26,7 @@ const actions = {
     fetchJobMetricsForJobId: async ({ commit }, jobId) => {
         const { data } = await axios.get(`${getAppRoot()}api/jobs/${jobId}/metrics`);
         commit("saveJobMetricsForJobId", { jobId, jobMetrics: data });
-    }
+    },
 };
 
 const mutations = {
@@ -36,12 +36,12 @@ const mutations = {
     },
     saveJobMetricsForJobId: (state, { jobId, jobMetrics }) => {
         Vue.set(state.jobMetricsByJobId, jobId, jobMetrics);
-    }
+    },
 };
 
 export const jobMetricsStore = {
     state,
     getters,
     actions,
-    mutations
+    mutations,
 };
diff --git a/client/galaxy/scripts/store/jobMetricsStore.test.js b/client/galaxy/scripts/store/jobMetricsStore.test.js
index 1edd00a9ffa4..a35573cb3346 100644
--- a/client/galaxy/scripts/store/jobMetricsStore.test.js
+++ b/client/galaxy/scripts/store/jobMetricsStore.test.js
@@ -3,7 +3,7 @@ import { jobMetricsStore } from "./jobMetricsStore";
 describe("store/jobMetricsStore.js", () => {
     it("getter should return empty list for unfetched job IDs", () => {
         const state = {
-            jobMetricsByJobId: {}
+            jobMetricsByJobId: {},
         };
         let metrics = jobMetricsStore.getters.getJobMetricsByJobId(state)("123");
         assert(metrics.length == 0);
@@ -11,7 +11,7 @@ describe("store/jobMetricsStore.js", () => {
 
     it("should simply return fetched metrics list for job ID", () => {
         const state = {
-            jobMetricsByJobId: { "123": [{ plugin: "core", value: 123 }] }
+            jobMetricsByJobId: { "123": [{ plugin: "core", value: 123 }] },
         };
         let metrics = jobMetricsStore.getters.getJobMetricsByJobId(state)("123");
         assert(metrics.length == 1);
diff --git a/client/galaxy/scripts/store/tagStore.js b/client/galaxy/scripts/store/tagStore.js
index b04ec8fdff5b..e8c72f959d00 100644
--- a/client/galaxy/scripts/store/tagStore.js
+++ b/client/galaxy/scripts/store/tagStore.js
@@ -1,16 +1,16 @@
 export const state = {
     userTagList: [], // List of recent user tags
-    modelTagCache: new Map() // Maps model id to list of tags
+    modelTagCache: new Map(), // Maps model id to list of tags
 };
 
 export const getters = {
-    getTagsById: state => key => {
+    getTagsById: (state) => (key) => {
         if (state.modelTagCache.has(key)) {
             const tagSet = state.modelTagCache.get(key); //.sort();
             return Array.from(tagSet);
         }
         return [];
-    }
+    },
 };
 
 export const actions = {
@@ -21,7 +21,7 @@ export const actions = {
         if (!state.modelTagCache.has(key)) {
             dispatch("updateTags", { key, tags });
         }
-    }
+    },
 };
 
 export const mutations = {
@@ -32,12 +32,12 @@ export const mutations = {
     reset(state) {
         state.userTagList = [];
         state.modelTagCache = new Map();
-    }
+    },
 };
 
 export const tagStore = {
     state,
     getters,
     actions,
-    mutations
+    mutations,
 };
diff --git a/client/galaxy/scripts/store/tagStore.test.js b/client/galaxy/scripts/store/tagStore.test.js
index 26cb42fe1ca9..f82cb192a96b 100644
--- a/client/galaxy/scripts/store/tagStore.test.js
+++ b/client/galaxy/scripts/store/tagStore.test.js
@@ -22,13 +22,13 @@ describe("store/tagStore.js", () => {
 
         it("should update the state Map and store a Set", () => {
             assert(stateTags instanceof Set, "Stored list should be a Set");
-            testTags.forEach(t => {
+            testTags.forEach((t) => {
                 assert(stateTags.has(t), `Missing tag: ${t}`);
             });
         });
 
         it("that set should contain all the passed tags", () => {
-            testTags.forEach(t => {
+            testTags.forEach((t) => {
                 assert(stateTags.has(t), `Missing tag: ${t}`);
             });
         });
diff --git a/client/galaxy/scripts/store/userStore/userStore.js b/client/galaxy/scripts/store/userStore/userStore.js
index 749557595db4..c3dc79a130f1 100644
--- a/client/galaxy/scripts/store/userStore/userStore.js
+++ b/client/galaxy/scripts/store/userStore/userStore.js
@@ -2,7 +2,7 @@ import { getCurrentUser } from "./queries";
 import User from "./User";
 
 const state = {
-    currentUser: null
+    currentUser: null,
 };
 
 const getters = {
@@ -20,13 +20,13 @@ const getters = {
             }
         }
         return new User(userProps);
-    }
+    },
 };
 
 const mutations = {
     setCurrentUser(state, user) {
         state.currentUser = user;
-    }
+    },
 };
 
 const actions = {
@@ -36,7 +36,7 @@ const actions = {
     },
     async $init({ dispatch }) {
         await dispatch("loadUser");
-    }
+    },
 };
 
 export const userStore = {
@@ -44,5 +44,5 @@ export const userStore = {
     state,
     getters,
     mutations,
-    actions
+    actions,
 };
diff --git a/client/galaxy/scripts/store/workflowStore.js b/client/galaxy/scripts/store/workflowStore.js
index 78945827da97..2c337343099b 100644
--- a/client/galaxy/scripts/store/workflowStore.js
+++ b/client/galaxy/scripts/store/workflowStore.js
@@ -1,5 +1,5 @@
 export const state = {
-    workflowsByInstanceId: {}
+    workflowsByInstanceId: {},
 };
 
 import Vue from "vue";
@@ -7,9 +7,9 @@ import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 
 const getters = {
-    getWorkflowByInstanceId: state => workflowId => {
+    getWorkflowByInstanceId: (state) => (workflowId) => {
         return state.workflowsByInstanceId[workflowId];
-    }
+    },
 };
 
 const actions = {
@@ -17,18 +17,18 @@ const actions = {
         const params = { instance: "true" };
         const { data } = await axios.get(`${getAppRoot()}api/workflows/${workflowId}`, { params });
         commit("saveWorkflowForInstanceId", { workflowId, workflowData: data });
-    }
+    },
 };
 
 const mutations = {
     saveWorkflowForInstanceId: (state, { workflowId, workflowData }) => {
         Vue.set(state.workflowsByInstanceId, workflowId, workflowData);
-    }
+    },
 };
 
 export const workflowStore = {
     state,
     getters,
     actions,
-    mutations
+    mutations,
 };
diff --git a/client/galaxy/scripts/toolshed/groups/group-detail-view.js b/client/galaxy/scripts/toolshed/groups/group-detail-view.js
index 6c3ed575b16b..f42efaca14c5 100644
--- a/client/galaxy/scripts/toolshed/groups/group-detail-view.js
+++ b/client/galaxy/scripts/toolshed/groups/group-detail-view.js
@@ -10,7 +10,7 @@ const GroupDetailView = Backbone.View.extend({
     options: {},
     app: null,
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = _.extend(this.options, options);
         this.app = window.globalTS.groups;
 
@@ -22,34 +22,34 @@ const GroupDetailView = Backbone.View.extend({
         }
     },
 
-    fetchGroup: function(options) {
+    fetchGroup: function (options) {
         const that = this;
         this.options = _.extend(this.options, options);
         this.model = new mod_group_model.Group({ id: this.options.group_id });
         this.model.fetch({
-            success: function(model) {
+            success: function (model) {
                 console.log("received data: ");
                 console.log(model);
                 that.render();
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(response.responseJSON.err_msg);
                 } else {
                     Toast.error("An error occurred.");
                 }
-            }
+            },
         });
     },
 
-    render: function() {
+    render: function () {
         const template = this.templateRow();
         this.$el.html(template({ group: this.model }));
         $('#center [data-toggle="tooltip"]').tooltip({ trigger: "hover" });
         $("#center").css("overflow", "auto");
     },
 
-    templateRow: function() {
+    templateRow: function () {
         return _.template(
             [
                 "<div>",
@@ -131,11 +131,11 @@ const GroupDetailView = Backbone.View.extend({
                 "<% }); %>",
                 "</tbody>",
                 "</table>",
-                "</div>"
+                "</div>",
             ].join("")
         );
-    }
+    },
 });
 export default {
-    GroupDetailView: GroupDetailView
+    GroupDetailView: GroupDetailView,
 };
diff --git a/client/galaxy/scripts/toolshed/groups/group-list-view.js b/client/galaxy/scripts/toolshed/groups/group-list-view.js
index 9556048d14ff..e6c9c097fc9e 100644
--- a/client/galaxy/scripts/toolshed/groups/group-list-view.js
+++ b/client/galaxy/scripts/toolshed/groups/group-list-view.js
@@ -13,30 +13,30 @@ const GroupListView = Backbone.View.extend({
      * Async render afterwards.
      * @param  {object} options an object with options
      */
-    initialize: function(options) {
+    initialize: function (options) {
         this.options = _.defaults(this.options || {}, this.defaults, options);
         const that = this;
         window.globalTS.groups.collection = new mod_group_model.Groups();
         window.globalTS.groups.collection.fetch({
-            success: function(model) {
+            success: function (model) {
                 that.render();
             },
-            error: function(model, response) {
+            error: function (model, response) {
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(response.responseJSON.err_msg);
                 } else {
                     Toast.error("An error occurred.");
                 }
-            }
+            },
         });
     },
 
-    fetch: function() {},
+    fetch: function () {},
 
     /**
      * Render the groups table from the object's own collection.
      */
-    render: function(options) {
+    render: function (options) {
         this.options = _.extend(this.options, options);
         $(".tooltip").hide();
         const template = this.templateGroupsList();
@@ -50,7 +50,7 @@ const GroupListView = Backbone.View.extend({
      * Render all given models as rows in the groups list
      * @param  {array} groups_to_render array of group models to render
      */
-    renderRows: function(groups_to_render) {
+    renderRows: function (groups_to_render) {
         for (let i = 0; i < groups_to_render.length; i++) {
             const group = groups_to_render[i];
             this.renderOne({ group: group });
@@ -61,7 +61,7 @@ const GroupListView = Backbone.View.extend({
      * Create a view for the given model and add it to the groups view.
      * @param {Group} model of the view that will be rendered
      */
-    renderOne: function(options) {
+    renderOne: function (options) {
         const rowView = new mod_group_row.GroupListRowView(options);
         this.$el.find("#group_list_body").append(rowView.el);
     },
@@ -97,7 +97,7 @@ const GroupListView = Backbone.View.extend({
     // === TEMPLATES ====
     // MMMMMMMMMMMMMMMMMM
 
-    templateGroupsList: function() {
+    templateGroupsList: function () {
         const tmpl_array = [];
 
         tmpl_array.push('<div id="groups">');
@@ -121,9 +121,9 @@ const GroupListView = Backbone.View.extend({
         tmpl_array.push("</div>");
 
         return _.template(tmpl_array.join(""));
-    }
+    },
 });
 
 export default {
-    GroupListView: GroupListView
+    GroupListView: GroupListView,
 };
diff --git a/client/galaxy/scripts/toolshed/groups/group-listrow-view.js b/client/galaxy/scripts/toolshed/groups/group-listrow-view.js
index 343fd83ee68a..002a91a1acb2 100644
--- a/client/galaxy/scripts/toolshed/groups/group-listrow-view.js
+++ b/client/galaxy/scripts/toolshed/groups/group-listrow-view.js
@@ -5,18 +5,18 @@ import Backbone from "backbone";
 const GroupListRowView = Backbone.View.extend({
     events: {},
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.render(options.group);
     },
 
-    render: function(group) {
+    render: function (group) {
         const tmpl = this.templateRow();
         this.setElement(tmpl({ group: group }));
         this.$el.show();
         return this;
     },
 
-    templateRow: function() {
+    templateRow: function () {
         return _.template(
             [
                 '<tr class="" data-id="<%- group.get("id") %>">',
@@ -24,12 +24,12 @@ const GroupListRowView = Backbone.View.extend({
                 // '<td>description</td>',
                 '<td><%= group.get("total_members") %></td>',
                 '<td><%= group.get("total_repos") %></td>',
-                "</tr>"
+                "</tr>",
             ].join("")
         );
-    }
+    },
 });
 
 export default {
-    GroupListRowView: GroupListRowView
+    GroupListRowView: GroupListRowView,
 };
diff --git a/client/galaxy/scripts/toolshed/groups/group-model.js b/client/galaxy/scripts/toolshed/groups/group-model.js
index 0d97dc88d72c..e001830830d6 100644
--- a/client/galaxy/scripts/toolshed/groups/group-model.js
+++ b/client/galaxy/scripts/toolshed/groups/group-model.js
@@ -5,16 +5,16 @@ import { getAppRoot } from "onload/loadConfig";
 // TS GROUP RELATED MODELS
 
 const Group = Backbone.Model.extend({
-    urlRoot: `${getAppRoot()}api/groups`
+    urlRoot: `${getAppRoot()}api/groups`,
 });
 
 const Groups = Backbone.Collection.extend({
     url: `${getAppRoot()}api/groups`,
 
-    model: Group
+    model: Group,
 });
 
 export default {
     Group: Group,
-    Groups: Groups
+    Groups: Groups,
 };
diff --git a/client/galaxy/scripts/toolshed/toolshed.groups.js b/client/galaxy/scripts/toolshed/toolshed.groups.js
index 485abac78fa9..5fd5a603173e 100644
--- a/client/galaxy/scripts/toolshed/toolshed.groups.js
+++ b/client/galaxy/scripts/toolshed/toolshed.groups.js
@@ -11,8 +11,8 @@ import mod_group_detail from "toolshed/groups/group-detail-view";
 const ToolshedRouter = Backbone.Router.extend({
     routes: {
         "": "groups",
-        ":group_id": "group_page"
-    }
+        ":group_id": "group_page",
+    },
 });
 
 const ToolshedGroups = Backbone.View.extend({
@@ -20,7 +20,7 @@ const ToolshedGroups = Backbone.View.extend({
     groupDetailView: null,
     collection: null,
 
-    initialize: function() {
+    initialize: function () {
         window.globalTS.groups = this;
 
         this.ts_router = new ToolshedRouter();
@@ -28,16 +28,16 @@ const ToolshedGroups = Backbone.View.extend({
             window.globalTS.groups.groupListView = new mod_group_list.GroupListView();
         });
 
-        this.ts_router.on("route:group_page", group_id => {
+        this.ts_router.on("route:group_page", (group_id) => {
             window.globalTS.groups.groupDetailView = new mod_group_detail.GroupDetailView({
-                group_id: group_id
+                group_id: group_id,
             });
         });
 
         Backbone.history.start({ pushState: false });
-    }
+    },
 });
 
 export default {
-    ToolshedGroups: ToolshedGroups
+    ToolshedGroups: ToolshedGroups,
 };
diff --git a/client/galaxy/scripts/ui/editable-text.js b/client/galaxy/scripts/ui/editable-text.js
index df51782de9f3..b5a35d36b1c1 100644
--- a/client/galaxy/scripts/ui/editable-text.js
+++ b/client/galaxy/scripts/ui/editable-text.js
@@ -9,7 +9,7 @@ var $ = jQuery;
  * is provided for editing; (b) when enter key pressed, element's text is set and on_finish
  * is called.
  */
-$.fn.make_text_editable = function(config_dict) {
+$.fn.make_text_editable = function (config_dict) {
     // Get config options.
     var num_cols = "num_cols" in config_dict ? config_dict.num_cols : 30;
 
@@ -22,7 +22,7 @@ $.fn.make_text_editable = function(config_dict) {
 
     // Add element behavior.
     var container = $(this);
-    container.addClass("editable-text").click(function(e) {
+    container.addClass("editable-text").click(function (e) {
         // If there's already an input element, editing is active, so do nothing.
         if ($(this).children(":input").length > 0) {
             return;
@@ -31,7 +31,7 @@ $.fn.make_text_editable = function(config_dict) {
         container.removeClass("editable-text");
 
         // Handler for setting element text.
-        var set_text = new_text => {
+        var set_text = (new_text) => {
             container.find(":input").remove();
 
             if (new_text !== "") {
@@ -57,7 +57,7 @@ $.fn.make_text_editable = function(config_dict) {
             input_elt = $("<textarea/>")
                 .attr({ rows: num_rows, cols: num_cols })
                 .text($.trim(cur_text))
-                .keyup(e => {
+                .keyup((e) => {
                     if (e.keyCode === 27) {
                         // Escape key.
                         set_text(cur_text);
@@ -77,7 +77,7 @@ $.fn.make_text_editable = function(config_dict) {
                 .blur(() => {
                     set_text(cur_text);
                 })
-                .keyup(function(e) {
+                .keyup(function (e) {
                     if (e.keyCode === 27) {
                         // Escape key.
                         $(this).trigger("blur");
diff --git a/client/galaxy/scripts/ui/fa-icon-button.js b/client/galaxy/scripts/ui/fa-icon-button.js
index 492c427c601f..aa21d8d87c02 100644
--- a/client/galaxy/scripts/ui/fa-icon-button.js
+++ b/client/galaxy/scripts/ui/fa-icon-button.js
@@ -14,10 +14,10 @@ var $ = jQuery;
  *          faIcon          : which font awesome icon to use
  *          onclick         : function to call when the button is clicked
  */
-var faIconButton = options => {
+var faIconButton = (options) => {
     options = options || {};
     options.tooltipConfig = options.tooltipConfig || {
-        placement: "bottom"
+        placement: "bottom",
     };
 
     options.classes = ["icon-btn"].concat(options.classes || []);
@@ -38,16 +38,13 @@ var faIconButton = options => {
         '<span class="fa ',
         options.faIcon,
         '"></span>',
-        "</a>"
+        "</a>",
     ].join("");
     var $button = $(html).tooltip(options.tooltipConfig);
     if (_.isFunction(options.onclick)) {
-        $button.click(function(ev) {
+        $button.click(function (ev) {
             $button.tooltip("hide");
-            $button
-                .parent()
-                .attr("tabindex", -1)
-                .focus();
+            $button.parent().attr("tabindex", -1).focus();
             options.onclick.apply(this, arguments);
         });
     }
diff --git a/client/galaxy/scripts/ui/hoverhighlight.js b/client/galaxy/scripts/ui/hoverhighlight.js
index 6169b8b2b46a..6c04c54f1fd1 100644
--- a/client/galaxy/scripts/ui/hoverhighlight.js
+++ b/client/galaxy/scripts/ui/hoverhighlight.js
@@ -11,24 +11,24 @@ jQuery.fn.extend({
             return this;
         }
 
-        $(this).each(function() {
+        $(this).each(function () {
             var $this = $(this);
             var targetSelector = $this.data("target");
 
             if (targetSelector) {
                 $this
-                    .mouseover(ev => {
+                    .mouseover((ev) => {
                         $(targetSelector, scope).css({
-                            background: color
+                            background: color,
                         });
                     })
-                    .mouseout(ev => {
+                    .mouseout((ev) => {
                         $(targetSelector).css({
-                            background: ""
+                            background: "",
                         });
                     });
             }
         });
         return this;
-    }
+    },
 });
diff --git a/client/galaxy/scripts/ui/loading-indicator.js b/client/galaxy/scripts/ui/loading-indicator.js
index 5cc7dc0f529d..378d847af01a 100644
--- a/client/galaxy/scripts/ui/loading-indicator.js
+++ b/client/galaxy/scripts/ui/loading-indicator.js
@@ -8,7 +8,7 @@ function LoadingIndicator($where, options) {
     // defaults
     options = jQuery.extend(
         {
-            cover: false
+            cover: false,
         },
         options || {}
     );
@@ -20,14 +20,14 @@ function LoadingIndicator($where, options) {
             '<span class="fa fa-spinner fa-spin fa-lg"></span>',
             '<span class="loading-indicator-message">loading...</span>',
             "</div>",
-            "</div>"
+            "</div>",
         ].join("\n");
 
         var $indicator = $(html)
             .hide()
             .css(
                 options.css || {
-                    position: "fixed"
+                    position: "fixed",
                 }
             );
 
@@ -42,20 +42,20 @@ function LoadingIndicator($where, options) {
                 right: $where.css("right"),
                 opacity: 0.5,
                 "background-color": "white",
-                "text-align": "center"
+                "text-align": "center",
             });
             $text = $indicator.children(".loading-indicator-text").css({
-                "margin-top": "20px"
+                "margin-top": "20px",
             });
         } else {
             $text = $indicator.children(".loading-indicator-text").css({
                 margin: "12px 0px 0px 10px",
                 opacity: "0.85",
-                color: "grey"
+                color: "grey",
             });
             $text.children(".loading-indicator-message").css({
                 margin: "0px 8px 0px 0px",
-                "font-style": "italic"
+                "font-style": "italic",
             });
         }
         return $indicator;
@@ -65,10 +65,7 @@ function LoadingIndicator($where, options) {
         msg = msg || "loading...";
         speed = speed || "fast";
         // remove previous
-        $where
-            .parent()
-            .find(".loading-indicator")
-            .remove();
+        $where.parent().find(".loading-indicator").remove();
         // since position is fixed - we insert as sibling
         self.$indicator = render().insertBefore($where);
         self.message(msg);
@@ -76,7 +73,7 @@ function LoadingIndicator($where, options) {
         return self;
     };
 
-    self.message = msg => {
+    self.message = (msg) => {
         self.$indicator.find("i").text(msg);
     };
 
@@ -99,7 +96,7 @@ function LoadingIndicator($where, options) {
     return self;
 }
 
-const markViewAsLoading = function(view) {
+const markViewAsLoading = function (view) {
     view.setElement($('<div><div class="loading"></div></div>'));
     new LoadingIndicator(view.$(".loading")).show();
 };
@@ -107,5 +104,5 @@ const markViewAsLoading = function(view) {
 //============================================================================
 export default {
     LoadingIndicator: LoadingIndicator,
-    markViewAsLoading: markViewAsLoading
+    markViewAsLoading: markViewAsLoading,
 };
diff --git a/client/galaxy/scripts/ui/mode-button.js b/client/galaxy/scripts/ui/mode-button.js
index dded91e1b199..6929a852f847 100644
--- a/client/galaxy/scripts/ui/mode-button.js
+++ b/client/galaxy/scripts/ui/mode-button.js
@@ -52,7 +52,7 @@ function ModeButton(element, options) {
 ModeButton.prototype.DATA_KEY = "mode-button";
 /** default options */
 ModeButton.prototype.defaults = {
-    switchModesOnClick: true
+    switchModesOnClick: true,
 };
 
 // ---- private interface
@@ -165,7 +165,7 @@ $.fn.modeButton = function $modeButton(options) {
 
     //TODO: does map still work with jq multi selection (i.e. $( '.class-for-many-btns' ).modeButton)?
     if ($.type(options) === "object") {
-        return this.map(function() {
+        return this.map(function () {
             var $this = $(this);
             $this.data("mode-button", new ModeButton($this, options));
             return this;
diff --git a/client/galaxy/scripts/ui/pagination.js b/client/galaxy/scripts/ui/pagination.js
index f416a3d11280..50b2a6775d98 100644
--- a/client/galaxy/scripts/ui/pagination.js
+++ b/client/galaxy/scripts/ui/pagination.js
@@ -26,7 +26,7 @@ Pagination.prototype.defaults = {
     /** the total number of data (null == unknown) */
     totalDataSize: null,
     /** size of current data on current page */
-    currDataSize: null
+    currDataSize: null,
 };
 
 /** init the control, calc numPages if possible, and render
@@ -126,7 +126,7 @@ Pagination.prototype._renderPages = function __renderPages() {
 
     var $paginationContainer = $("<ul/>").addClass("pagination pagination-page-list");
 
-    var page$LiClick = function(ev) {
+    var page$LiClick = function (ev) {
         pagination.goToPage($(this).data("page"));
     };
 
@@ -208,7 +208,7 @@ $.fn.extend({
 
         // if passed an object - use that as an options map to create pagination for each selected
         if ($.type(options) === "object") {
-            return this.map(function() {
+            return this.map(function () {
                 Pagination.create($(this), options);
                 return this;
             });
@@ -234,5 +234,5 @@ $.fn.extend({
         }
         // if there is no control already set, return undefined
         return undefined;
-    }
+    },
 });
diff --git a/client/galaxy/scripts/ui/peek-column-selector.js b/client/galaxy/scripts/ui/peek-column-selector.js
index ff65acd58b0b..c4d59cdc2c30 100644
--- a/client/galaxy/scripts/ui/peek-column-selector.js
+++ b/client/galaxy/scripts/ui/peek-column-selector.js
@@ -57,7 +57,7 @@ var defaults = {
     /** should a column of row control prompts be used */
     includePrompts: true,
     /** what is the content of the top left cell (often a title) */
-    topLeftContent: "Columns:"
+    topLeftContent: "Columns:",
 };
 
 /** class added to the pre.peek element (to allow css on just the control) */
@@ -116,16 +116,12 @@ function validateControl(control) {
 
 /** build the inner control surface (i.e. button-like) */
 function buildButton(control, columnIndex) {
-    return $("<div/>")
-        .addClass(BUTTON_CLASS)
-        .text(control.label);
+    return $("<div/>").addClass(BUTTON_CLASS).text(control.label);
 }
 
 /** build the basic (shared) cell structure */
 function buildControlCell(control, columnIndex) {
-    var $td = $("<td/>")
-        .html(buildButton(control, columnIndex))
-        .attr(`data-${COLUMN_INDEX_DATA_KEY}`, columnIndex);
+    var $td = $("<td/>").html(buildButton(control, columnIndex)).attr(`data-${COLUMN_INDEX_DATA_KEY}`, columnIndex);
 
     // disable if index in disabled array
     if (control.disabled && control.disabled.indexOf(columnIndex) !== -1) {
@@ -160,11 +156,8 @@ function buildSingleSelectCell(control, columnIndex) {
             // don't re-select or fire event if already selected
             if (!$cell.hasClass(SELECTED_CLASS)) {
                 // only one can be selected - remove selected on all others, add it here
-                var $otherSelected = $cell
-                    .parent()
-                    .children(`.${SELECTED_CLASS}`)
-                    .removeClass(SELECTED_CLASS);
-                $otherSelected.each(function() {
+                var $otherSelected = $cell.parent().children(`.${SELECTED_CLASS}`).removeClass(SELECTED_CLASS);
+                $otherSelected.each(function () {
                     setSelectedText($(this), control, columnIndex);
                 });
 
@@ -231,13 +224,9 @@ function buildControlCells(count, control) {
 
 /** build a row of controls for the peek */
 function buildControlRow(cellCount, control, includePrompts) {
-    var $controlRow = $("<tr/>")
-        .attr("id", control.id)
-        .addClass(ROW_CLASS);
+    var $controlRow = $("<tr/>").attr("id", control.id).addClass(ROW_CLASS);
     if (includePrompts) {
-        var $promptCell = $("<td/>")
-            .addClass(PROMPT_CLASS)
-            .text(`${control.label}:`);
+        var $promptCell = $("<td/>").addClass(PROMPT_CLASS).text(`${control.label}:`);
         $controlRow.append($promptCell);
     }
     $controlRow.append(buildControlCells(cellCount, control));
@@ -258,13 +247,10 @@ function peekColumnSelector(options) {
     var rowCount = $peektable.find("tr").length;
 
     var // get the rows containing text starting with the comment char (also make them grey)
-        $commentRows = $peektable.find("td[colspan]").map(function(e, i) {
+        $commentRows = $peektable.find("td[colspan]").map(function (e, i) {
             var $this = $(this);
             if ($this.text() && $this.text().match(new RegExp(`^${options.commentChar}`))) {
-                return $(this)
-                    .css("color", "grey")
-                    .parent()
-                    .get(0);
+                return $(this).css("color", "grey").parent().get(0);
             }
             return null;
         });
@@ -278,18 +264,12 @@ function peekColumnSelector(options) {
 
     // should a first column of control prompts be added?
     if (options.includePrompts) {
-        var $topLeft = $("<th/>")
-            .addClass("top-left")
-            .text(options.topLeftContent)
-            .attr("rowspan", rowCount);
-        $peektable
-            .find("tr")
-            .first()
-            .prepend($topLeft);
+        var $topLeft = $("<th/>").addClass("top-left").text(options.topLeftContent).attr("rowspan", rowCount);
+        $peektable.find("tr").first().prepend($topLeft);
     }
 
     // save either the options column name or the parsed text of each column header in html5 data attr and text
-    var $headers = $peektable.find("th:not(.top-left)").each(function(i, e) {
+    var $headers = $peektable.find("th:not(.top-left)").each(function (i, e) {
         var $this = $(this);
 
         var // can be '1.name' or '1'
@@ -319,7 +299,7 @@ function peekColumnSelector(options) {
                     $this
                         .parent()
                         .children("th:not(.top-left)")
-                        .map(function() {
+                        .map(function () {
                             return $(this).data(COLUMN_NAME_DATA_KEY);
                         })
                 );
@@ -341,8 +321,8 @@ function peekColumnSelector(options) {
 // as jq plugin
 $.fn.extend({
     peekColumnSelector: function $peekColumnSelector(options) {
-        return this.map(function() {
+        return this.map(function () {
             return peekColumnSelector.call(this, options);
         });
-    }
+    },
 });
diff --git a/client/galaxy/scripts/ui/popupmenu.js b/client/galaxy/scripts/ui/popupmenu.js
index a79d0180d960..2c517e5af3c5 100644
--- a/client/galaxy/scripts/ui/popupmenu.js
+++ b/client/galaxy/scripts/ui/popupmenu.js
@@ -22,7 +22,7 @@ export function make_popupmenu(button_element, initial_options) {
         return;
     }
 
-    button_element.bind("click.show_popup", e => {
+    button_element.bind("click.show_popup", (e) => {
         // Close existing visible menus
         $(".popmenu-wrapper").remove();
 
@@ -39,11 +39,7 @@ export function make_popupmenu(button_element, initial_options) {
                     // Action can be either an anonymous function and a mapped dict.
                     const action = v.action || v;
                     const url = v.url || "javascript:void(0);";
-                    const $a = $("<a>")
-                        .addClass("dropdown-item")
-                        .attr("href", url)
-                        .html(k)
-                        .click(action);
+                    const $a = $("<a>").addClass("dropdown-item").attr("href", url).html(k).click(action);
                     if (v.class) {
                         $a.addClass(v.class);
                     }
@@ -66,14 +62,14 @@ export function make_popupmenu(button_element, initial_options) {
 
             wrapper.css({
                 top: e.pageY,
-                left: x
+                left: x,
             });
         }, 10);
 
         setTimeout(() => {
             // Bind click event to current window and all frames to remove any visible menus
             // Bind to document object instead of window object for IE compat
-            var close_popup = el => {
+            var close_popup = (el) => {
                 $(el).bind("click.close_popup", () => {
                     $(".popmenu-wrapper").remove();
                     el.unbind("click.close_popup");
@@ -103,12 +99,12 @@ export function make_popupmenu(button_element, initial_options) {
  *  NOTE: make_popup_menus, and make_popupmenu are horrible names
  */
 export function make_popup_menus() {
-    $("div[popupmenu]").each(function() {
+    $("div[popupmenu]").each(function () {
         var options = {};
         var menu = $(this);
 
         // find each anchor in the menu, convert them into an options map: { a.text : click_function }
-        menu.find("a").each(function() {
+        menu.find("a").each(function () {
             var link = $(this);
             var link_dom = link.get(0);
             var confirmtext = link_dom.getAttribute("confirm");
@@ -121,7 +117,7 @@ export function make_popup_menus() {
             } else {
                 options[link.text()] = {
                     url: href,
-                    action: function(event) {
+                    action: function (event) {
                         // if theres confirm text, send the dialog
                         if (!confirmtext || confirm(confirmtext)) {
                             // link.click() doesn't use target for some reason,
@@ -136,7 +132,7 @@ export function make_popup_menus() {
                         } else {
                             event.preventDefault();
                         }
-                    }
+                    },
                 };
             }
         });
@@ -145,7 +141,7 @@ export function make_popup_menus() {
 
         // For menus with clickable link text, make clicking on the link go through instead
         // of activating the popup menu
-        box.find("a").bind("click", e => {
+        box.find("a").bind("click", (e) => {
             e.stopPropagation(); // Stop bubbling so clicking on the link goes through
             return true;
         });
diff --git a/client/galaxy/scripts/ui/scroll-panel.js b/client/galaxy/scripts/ui/scroll-panel.js
index be11d18d5e80..d1192aabace2 100644
--- a/client/galaxy/scripts/ui/scroll-panel.js
+++ b/client/galaxy/scripts/ui/scroll-panel.js
@@ -5,7 +5,7 @@ import $ from "jquery";
 // ("viewport") so that the draggable is always visible.
 
 $.ui.plugin.add("draggable", "scrollPanel", {
-    drag: function(e, ui) {
+    drag: function (e, ui) {
         var instance = $(this).data("draggable");
         clearTimeout(instance.timeout);
         var o = ui.options;
@@ -91,8 +91,8 @@ $.ui.plugin.add("draggable", "scrollPanel", {
             }, 50);
         }
     },
-    stop: function(e, ui) {
+    stop: function (e, ui) {
         var instance = $(this).data("draggable");
         clearTimeout(instance.timeout);
-    }
+    },
 });
diff --git a/client/galaxy/scripts/ui/search-input.js b/client/galaxy/scripts/ui/search-input.js
index e8479d50667c..07b076b8eeac 100644
--- a/client/galaxy/scripts/ui/search-input.js
+++ b/client/galaxy/scripts/ui/search-input.js
@@ -2,7 +2,7 @@ import jQuery from "jquery";
 ("use_strict");
 
 var $ = jQuery;
-var _l = window._l || (s => s);
+var _l = window._l || ((s) => s);
 
 //TODO: consolidate with tool menu functionality, use there
 
@@ -25,24 +25,19 @@ function searchInput(parentNode, options) {
         name: "search",
         placeholder: "search",
         classes: "",
-        onclear: function() {},
+        onclear: function () {},
         onfirstsearch: null,
-        onsearch: function(inputVal) {},
+        onsearch: function (inputVal) {},
         minSearchLen: 0,
         escWillClear: true,
-        oninit: function() {}
+        oninit: function () {},
     };
 
     // .................................................................... input rendering and events
     // visually clear the search, trigger an event, and call the callback
     function clearSearchInput(event) {
-        var $input = $(this)
-            .parent()
-            .children("input");
-        $input
-            .val("")
-            .trigger("searchInput.clear")
-            .blur();
+        var $input = $(this).parent().children("input");
+        $input.val("").trigger("searchInput.clear").blur();
         options.onclear();
     }
 
@@ -72,7 +67,7 @@ function searchInput(parentNode, options) {
             'class="search-query ',
             options.classes,
             '" ',
-            "/>"
+            "/>",
         ].join("");
     }
 
@@ -81,11 +76,11 @@ function searchInput(parentNode, options) {
         return (
             $(inputTemplate())
                 // select all text on a focus
-                .focus(function(event) {
+                .focus(function (event) {
                     $(this).select();
                 })
                 // attach behaviors to esc, return if desired, search on some min len string
-                .keyup(function(event) {
+                .keyup(function (event) {
                     event.preventDefault();
                     event.stopPropagation();
 
@@ -116,7 +111,7 @@ function searchInput(parentNode, options) {
             )
         )
             .tooltip({ placement: "bottom" })
-            .click(function(event) {
+            .click(function (event) {
                 clearSearchInput.call(this, event);
             });
     }
@@ -158,8 +153,8 @@ function searchInput(parentNode, options) {
 // as jq plugin
 jQuery.fn.extend({
     searchInput: function $searchInput(options) {
-        return this.each(function() {
+        return this.each(function () {
             return searchInput(this, options);
         });
-    }
+    },
 });
diff --git a/client/galaxy/scripts/utils/add-logging.js b/client/galaxy/scripts/utils/add-logging.js
index 106e0c95bafc..9b9f040930d3 100644
--- a/client/galaxy/scripts/utils/add-logging.js
+++ b/client/galaxy/scripts/utils/add-logging.js
@@ -11,8 +11,8 @@ function addLogging(obj, namespace) {
     }
 
     // give the object each
-    LOGGING_FNS.forEach(logFn => {
-        addTo[logFn] = function() {
+    LOGGING_FNS.forEach((logFn) => {
+        addTo[logFn] = function () {
             if (!this.logger) {
                 return undefined;
             }
diff --git a/client/galaxy/scripts/utils/ajax-queue.js b/client/galaxy/scripts/utils/ajax-queue.js
index a2e3836973d1..9534b61b438c 100644
--- a/client/galaxy/scripts/utils/ajax-queue.js
+++ b/client/galaxy/scripts/utils/ajax-queue.js
@@ -28,7 +28,7 @@ class AjaxQueue {
 
     /** add all fns in initialFunctions (if any) to the queue */
     init(initialFunctions) {
-        initialFunctions.forEach(fn => {
+        initialFunctions.forEach((fn) => {
             this.add(fn);
         });
     }
@@ -41,16 +41,16 @@ class AjaxQueue {
             var fnIndex = index;
             var xhr = fn();
             // if successful, notify using the deferred to allow tracking progress
-            xhr.done(response => {
+            xhr.done((response) => {
                 this.deferred.notify({
                     curr: fnIndex,
                     total: this.numToProcess,
-                    response: response
+                    response: response,
                 });
             });
             // (regardless of previous error or success) if not last ajax call, shift and call the next
             //  if last fn, resolve deferred
-            xhr.always(response => {
+            xhr.always((response) => {
                 this.responses.push(response);
                 if (this.queue.length) {
                     this.queue.shift()();
@@ -164,5 +164,5 @@ class NamedAjaxQueue extends AjaxQueue {
 //=============================================================================
 export default {
     AjaxQueue: AjaxQueue,
-    NamedAjaxQueue: NamedAjaxQueue
+    NamedAjaxQueue: NamedAjaxQueue,
 };
diff --git a/client/galaxy/scripts/utils/ariaAlert.js b/client/galaxy/scripts/utils/ariaAlert.js
index 8d831abd5957..434d4d05e0ed 100644
--- a/client/galaxy/scripts/utils/ariaAlert.js
+++ b/client/galaxy/scripts/utils/ariaAlert.js
@@ -6,7 +6,7 @@ function ariaAlert(message) {
     alert.textContent = message;
     alert.setAttribute("role", "alert");
     document.body.appendChild(alert);
-    setTimeout(function() {
+    setTimeout(function () {
         document.body.removeChild(alert);
     }, 2000);
 }
diff --git a/client/galaxy/scripts/utils/async-save-text.js b/client/galaxy/scripts/utils/async-save-text.js
index 628ebe0fd4ac..05b1b1b71296 100644
--- a/client/galaxy/scripts/utils/async-save-text.js
+++ b/client/galaxy/scripts/utils/async-save-text.js
@@ -38,24 +38,22 @@ function async_save_text(
             var t;
 
             if (use_textarea) {
-                t = $("<textarea></textarea>")
-                    .attr({ rows: num_rows, cols: num_cols })
-                    .text($.trim(old_text));
+                t = $("<textarea></textarea>").attr({ rows: num_rows, cols: num_cols }).text($.trim(old_text));
             } else {
                 t = $("<input type='text'></input>").attr({
                     value: $.trim(old_text),
-                    size: num_cols
+                    size: num_cols,
                 });
             }
             t.attr("id", "renaming-active");
-            t.blur(function() {
+            t.blur(function () {
                 $(this).remove();
                 text_elt.show();
                 if (on_finish) {
                     on_finish(t);
                 }
             });
-            t.keyup(function(e) {
+            t.keyup(function (e) {
                 if (e.keyCode === 27) {
                     // Escape key
                     $(this).trigger("blur");
@@ -67,11 +65,11 @@ function async_save_text(
                     $.ajax({
                         url: save_url,
                         data: ajax_data,
-                        error: function() {
+                        error: function () {
                             alert(`Text editing for elt ${text_elt_id} failed`);
                             // TODO: call finish or no? For now, let's not because error occurred.
                         },
-                        success: function(processed_text) {
+                        success: function (processed_text) {
                             // Set new text and call finish method.
                             if (processed_text !== "") {
                                 text_elt.text(processed_text);
@@ -81,7 +79,7 @@ function async_save_text(
                             if (on_finish) {
                                 on_finish(t);
                             }
-                        }
+                        },
                     });
                 }
             });
diff --git a/client/galaxy/scripts/utils/config.js b/client/galaxy/scripts/utils/config.js
index 2aba2263936f..4d0323fb0c21 100644
--- a/client/galaxy/scripts/utils/config.js
+++ b/client/galaxy/scripts/utils/config.js
@@ -8,7 +8,7 @@ import { getGalaxyInstance } from "app";
  * A configuration setting. Currently key is used as id.
  */
 var ConfigSetting = Backbone.Model.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         // Use key as id for now.
         var key = this.get("key");
         this.set("id", key);
@@ -20,88 +20,88 @@ var ConfigSetting = Backbone.Model.extend({
                     key: "name",
                     label: "Name",
                     type: "text",
-                    default_value: ""
+                    default_value: "",
                 },
                 {
                     key: "color",
                     label: "Color",
                     type: "color",
-                    default_value: null
+                    default_value: null,
                 },
                 {
                     key: "min_value",
                     label: "Min Value",
                     type: "float",
-                    default_value: null
+                    default_value: null,
                 },
                 {
                     key: "max_value",
                     label: "Max Value",
                     type: "float",
-                    default_value: null
+                    default_value: null,
                 },
                 {
                     key: "mode",
                     type: "string",
                     default_value: this.mode,
-                    hidden: true
+                    hidden: true,
                 },
                 {
                     key: "height",
                     type: "int",
                     default_value: 32,
-                    hidden: true
+                    hidden: true,
                 },
                 {
                     key: "pos_color",
                     label: "Positive Color",
                     type: "color",
-                    default_value: "#FF8C00"
+                    default_value: "#FF8C00",
                 },
                 {
                     key: "neg_color",
                     label: "Negative Color",
                     type: "color",
-                    default_value: "#4169E1"
+                    default_value: "#4169E1",
                 },
                 {
                     key: "block_color",
                     label: "Block color",
                     type: "color",
-                    default_value: null
+                    default_value: null,
                 },
                 {
                     key: "label_color",
                     label: "Label color",
                     type: "color",
-                    default_value: "black"
+                    default_value: "black",
                 },
                 {
                     key: "show_insertions",
                     label: "Show insertions",
                     type: "bool",
-                    default_value: false
+                    default_value: false,
                 },
                 {
                     key: "show_counts",
                     label: "Show summary counts",
                     type: "bool",
-                    default_value: true
+                    default_value: true,
                 },
                 {
                     key: "reverse_strand_color",
                     label: "Antisense strand color",
                     type: "color",
-                    default_value: null
+                    default_value: null,
                 },
                 {
                     key: "show_differences",
                     label: "Show differences only",
                     type: "bool",
-                    default_value: true
-                }
+                    default_value: true,
+                },
             ],
-            s => s.key === key
+            (s) => s.key === key
         );
         if (defaults) {
             this.set(_.extend({}, defaults, options));
@@ -123,7 +123,7 @@ var ConfigSetting = Backbone.Model.extend({
      * Cast and set value. This should be instead of
      *  setting.set('value', new_value)
      */
-    set_value: function(value, options) {
+    set_value: function (value, options) {
         var type = this.get("type");
 
         if (type === "float") {
@@ -134,7 +134,7 @@ var ConfigSetting = Backbone.Model.extend({
         // TODO: handle casting from string to bool?
 
         this.set({ value: value }, options);
-    }
+    },
 });
 
 /**
@@ -148,9 +148,9 @@ var ConfigSettingCollection = Backbone.Collection.extend(
          * Save settings as a dictionary of key-value pairs.
          * This function is needed for backwards compatibility.
          */
-        to_key_value_dict: function() {
+        to_key_value_dict: function () {
             var rval = {};
-            this.each(setting => {
+            this.each((setting) => {
                 rval[setting.get("key")] = setting.get("value");
             });
 
@@ -160,7 +160,7 @@ var ConfigSettingCollection = Backbone.Collection.extend(
         /**
          * Returns value for a given key. Returns undefined if there is no setting with the specified key.
          */
-        get_value: function(key) {
+        get_value: function (key) {
             var s = this.get(key);
             if (s) {
                 return s.get("value");
@@ -172,7 +172,7 @@ var ConfigSettingCollection = Backbone.Collection.extend(
         /**
          * Set value for a setting.
          */
-        set_value: function(key, value, options) {
+        set_value: function (key, value, options) {
             var s = this.get(key);
             if (s) {
                 return s.set_value(value, options);
@@ -184,28 +184,28 @@ var ConfigSettingCollection = Backbone.Collection.extend(
         /**
          * Set default value for a setting.
          */
-        set_default_value: function(key, default_value) {
+        set_default_value: function (key, default_value) {
             var s = this.get(key);
             if (s) {
                 return s.set("default_value", default_value);
             }
 
             return undefined;
-        }
+        },
     },
     {
         /**
          * Utility function that creates a ConfigSettingsCollection from a set of models
          * and a saved_values dictionary.
          */
-        from_models_and_saved_values: function(models, saved_values) {
+        from_models_and_saved_values: function (models, saved_values) {
             // If there are saved values, copy models and update with saved values.
             if (saved_values) {
-                models = _.map(models, m => _.extend({}, m, { value: saved_values[m.key] }));
+                models = _.map(models, (m) => _.extend({}, m, { value: saved_values[m.key] }));
             }
 
             return new ConfigSettingCollection(models);
-        }
+        },
     }
 );
 
@@ -218,7 +218,7 @@ var ConfigSettingCollectionView = Backbone.View.extend({
     /**
      * Renders form for editing configuration settings.
      */
-    render: function() {
+    render: function () {
         var container = this.$el;
 
         this.collection.each((param, index) => {
@@ -240,30 +240,22 @@ var ConfigSettingCollectionView = Backbone.View.extend({
             );
             // Draw parameter as checkbox
             if (type === "bool") {
-                row.append(
-                    $('<input type="checkbox" />')
-                        .attr("id", id)
-                        .attr("name", id)
-                        .attr("checked", value)
-                );
+                row.append($('<input type="checkbox" />').attr("id", id).attr("name", id).attr("checked", value));
             } else if (type === "text") {
                 // Draw parameter as textbox
                 row.append(
                     $('<input type="text"/>')
                         .attr("id", id)
                         .val(value)
-                        .click(function() {
+                        .click(function () {
                             $(this).select();
                         })
                 );
             } else if (type === "select") {
                 // Draw parameter as select area
                 var select = $("<select />").attr("id", id);
-                _.each(param.get("options"), option => {
-                    $("<option/>")
-                        .text(option.label)
-                        .attr("value", option.value)
-                        .appendTo(select);
+                _.each(param.get("options"), (option) => {
+                    $("<option/>").text(option.label).attr("value", option.value).appendTo(select);
                 });
                 select.val(value);
                 row.append(select);
@@ -277,25 +269,23 @@ var ConfigSettingCollectionView = Backbone.View.extend({
                     .val(value)
                     .css("float", "left")
                     .appendTo(container_div)
-                    .click(function(e) {
+                    .click(function (e) {
                         // Hide other pickers.
                         $(".tooltip").removeClass("in");
 
                         // Show input's color picker.
-                        var tip = $(this)
-                            .siblings(".tooltip")
-                            .addClass("in");
+                        var tip = $(this).siblings(".tooltip").addClass("in");
                         tip.css({
                             // left: $(this).position().left + ( $(input).width() / 2 ) - 60,
                             // top: $(this).position().top + $(this.height)
                             left: $(this).position().left + $(this).width() + 5,
-                            top: $(this).position().top - $(tip).height() / 2 + $(this).height() / 2
+                            top: $(this).position().top - $(tip).height() / 2 + $(this).height() / 2,
                         }).show();
 
                         // Click management:
 
                         // Keep showing tip if clicking in tip.
-                        tip.click(e => {
+                        tip.click((e) => {
                             e.stopPropagation();
                         });
 
@@ -316,9 +306,7 @@ var ConfigSettingCollectionView = Backbone.View.extend({
                     .tooltip();
 
                 // Color picker in tool tip style.
-                var tip = $("<div class='tooltip right' style='position: absolute;' />")
-                    .appendTo(container_div)
-                    .hide();
+                var tip = $("<div class='tooltip right' style='position: absolute;' />").appendTo(container_div).hide();
 
                 // Inner div for padding purposes
                 var tip_inner = $("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(tip);
@@ -329,25 +317,20 @@ var ConfigSettingCollectionView = Backbone.View.extend({
                     width: 100,
                     height: 100,
                     callback: input,
-                    color: value
+                    color: value,
                 });
 
                 // Clear floating.
                 container_div.append($("<div/>").css("clear", "both"));
 
                 // Use function to fix farb_obj value.
-                (fixed_farb_obj => {
+                ((fixed_farb_obj) => {
                     new_color_icon.click(() => {
                         fixed_farb_obj.setColor(util_mod.get_random_color());
                     });
                 })(farb_obj);
             } else {
-                row.append(
-                    $("<input />")
-                        .attr("id", id)
-                        .attr("name", id)
-                        .val(value)
-                );
+                row.append($("<input />").attr("id", id).attr("name", id).val(value));
             }
             // Help text
             if (param.help) {
@@ -361,7 +344,7 @@ var ConfigSettingCollectionView = Backbone.View.extend({
     /**
      * Render view in modal.
      */
-    render_in_modal: function(title) {
+    render_in_modal: function (title) {
         // Set up handlers for cancel, ok button and for handling esc key.
         var self = this;
         const Galaxy = getGalaxyInstance();
@@ -377,7 +360,7 @@ var ConfigSettingCollectionView = Backbone.View.extend({
             self.update_from_form();
         };
 
-        var check_enter_esc = e => {
+        var check_enter_esc = (e) => {
             if ((e.keyCode || e.which) === 27) {
                 // Escape key
                 cancel_fn();
@@ -399,15 +382,15 @@ var ConfigSettingCollectionView = Backbone.View.extend({
             body: this.$el,
             buttons: {
                 Cancel: cancel_fn,
-                OK: ok_fn
-            }
+                OK: ok_fn,
+            },
         });
     },
 
     /**
      * Update settings with new values entered via form.
      */
-    update_from_form: function() {
+    update_from_form: function () {
         var self = this;
         this.collection.each((setting, index) => {
             if (!setting.get("hidden")) {
@@ -420,11 +403,11 @@ var ConfigSettingCollectionView = Backbone.View.extend({
                 setting.set_value(value);
             }
         });
-    }
+    },
 });
 
 export default {
     ConfigSetting: ConfigSetting,
     ConfigSettingCollection: ConfigSettingCollection,
-    ConfigSettingCollectionView: ConfigSettingCollectionView
+    ConfigSettingCollectionView: ConfigSettingCollectionView,
 };
diff --git a/client/galaxy/scripts/utils/data.js b/client/galaxy/scripts/utils/data.js
index 6800bd12f9b1..ea9ceab19ee9 100644
--- a/client/galaxy/scripts/utils/data.js
+++ b/client/galaxy/scripts/utils/data.js
@@ -19,10 +19,10 @@ async function getCurrentGalaxyHistory() {
         // Otherwise manually fetch the current history json and use that id.
         return axios
             .get(`${getAppRoot()}history/current_history_json`)
-            .then(response => {
+            .then((response) => {
                 return response.data.id;
             })
-            .catch(err => {
+            .catch((err) => {
                 console.error("Error fetching current user history:", err);
                 return null;
             });
@@ -36,12 +36,12 @@ async function getCurrentGalaxyHistory() {
 export function dialog(callback, options = {}) {
     const galaxy = getGalaxyInstance();
     const host = `${window.location.protocol}//${window.location.hostname}:${window.location.port}`;
-    getCurrentGalaxyHistory().then(history_id => {
+    getCurrentGalaxyHistory().then((history_id) => {
         Object.assign(options, {
             callback: callback,
             history: history_id,
             root: galaxy.root,
-            host: host
+            host: host,
         });
         _mountSelectionDialog(DataDialog, options);
     });
@@ -53,7 +53,7 @@ export function dialog(callback, options = {}) {
  */
 export function workflowDialog(callback, options = {}) {
     Object.assign(options, {
-        callback: callback
+        callback: callback,
     });
     _mountSelectionDialog(WorkflowDialog, options);
 }
@@ -63,10 +63,10 @@ export function workflowDialog(callback, options = {}) {
  * @param {function} callback - Result function called with selection
  */
 export function datasetCollectionDialog(callback, options = {}) {
-    getCurrentGalaxyHistory().then(history_id => {
+    getCurrentGalaxyHistory().then((history_id) => {
         Object.assign(options, {
             callback: callback,
-            history: history_id
+            history: history_id,
         });
         _mountSelectionDialog(DatasetCollectionDialog, options);
     });
@@ -77,7 +77,7 @@ function _mountSelectionDialog(clazz, options) {
     const vm = document.createElement("div");
     $("body").append(vm);
     new instance({
-        propsData: options
+        propsData: options,
     }).$mount(vm);
 }
 
@@ -94,10 +94,10 @@ export function create(options) {
         }
         return options.history_id;
     }
-    getHistory().then(history_id => {
+    getHistory().then((history_id) => {
         $.uploadpost({
             url: `${getAppRoot()}api/tools`,
-            success: response => {
+            success: (response) => {
                 if (history_panel) {
                     history_panel.refreshContents();
                 }
@@ -117,10 +117,10 @@ export function create(options) {
                         "files_0|to_posix_lines": options.to_posix_lines ? "Yes" : null,
                         "files_0|dbkey": options.genome || "?",
                         "files_0|file_type": options.extension || "auto",
-                        "files_0|url_paste": options.url_paste
-                    })
-                }
-            }
+                        "files_0|url_paste": options.url_paste,
+                    }),
+                },
+            },
         });
     });
 }
diff --git a/client/galaxy/scripts/utils/deferred.js b/client/galaxy/scripts/utils/deferred.js
index 7b6e26569074..7dfe38996a14 100644
--- a/client/galaxy/scripts/utils/deferred.js
+++ b/client/galaxy/scripts/utils/deferred.js
@@ -7,7 +7,7 @@ import Utils from "utils/utils";
 import { getGalaxyInstance } from "app";
 
 export default Backbone.Model.extend({
-    initialize: function() {
+    initialize: function () {
         this.active = {};
         this.last = null;
     },
@@ -15,7 +15,7 @@ export default Backbone.Model.extend({
     /** Adds a callback to the queue. Upon execution a deferred object is parsed to the callback i.e. callback( deferred ).
      *  If the callback does not take any arguments, the deferred is resolved instantly.
      */
-    execute: function(callback) {
+    execute: function (callback) {
         var self = this;
         var id = Utils.uid();
         var has_deferred = callback.length > 0;
@@ -26,14 +26,12 @@ export default Backbone.Model.extend({
 
         // deferred process
         var process = $.Deferred();
-        process.promise().always(function() {
+        process.promise().always(function () {
             delete self.active[id];
             has_deferred &&
                 Galaxy.emit.debug(
                     "deferred::execute()",
-                    `${this.state()
-                        .charAt(0)
-                        .toUpperCase() + this.state().slice(1)} ${id}`
+                    `${this.state().charAt(0).toUpperCase() + this.state().slice(1)} ${id}`
                 );
         });
 
@@ -52,7 +50,7 @@ export default Backbone.Model.extend({
 
     /** Resets the promise queue. All currently queued but unexecuted callbacks/promises will be rejected.
      */
-    reset: function() {
+    reset: function () {
         const Galaxy = getGalaxyInstance();
         Galaxy.emit.debug("deferred::execute()", "Reset");
         for (var i in this.active) {
@@ -62,7 +60,7 @@ export default Backbone.Model.extend({
 
     /** Returns true if all processes are done.
      */
-    ready: function() {
+    ready: function () {
         return $.isEmptyObject(this.active);
-    }
+    },
 });
diff --git a/client/galaxy/scripts/utils/genericConfig.js b/client/galaxy/scripts/utils/genericConfig.js
index 057fdd136884..339ba0dbaf39 100644
--- a/client/galaxy/scripts/utils/genericConfig.js
+++ b/client/galaxy/scripts/utils/genericConfig.js
@@ -12,6 +12,6 @@ export function buildConfig(defaultConfigs = {}) {
             } else {
                 console.warn("Requested missing config prop", propName);
             }
-        }
+        },
     });
 }
diff --git a/client/galaxy/scripts/utils/graph.js b/client/galaxy/scripts/utils/graph.js
index ae75ae1b8e07..0f5a56752682 100644
--- a/client/galaxy/scripts/utils/graph.js
+++ b/client/galaxy/scripts/utils/graph.js
@@ -52,17 +52,17 @@ function Edge(source, target, data) {
     return self;
 }
 /** String representation */
-Edge.prototype.toString = function() {
+Edge.prototype.toString = function () {
     return `${this.source}->${this.target}`;
 };
 
 /** Return a plain object representing this edge */
-Edge.prototype.toJSON = function() {
+Edge.prototype.toJSON = function () {
     //TODO: this is safe in most browsers (fns will be stripped) - alter tests to incorporate this in order to pass data
     //return this;
     var json = {
         source: this.source,
-        target: this.target
+        target: this.target,
     };
     if (this.data) {
         json.data = this.data;
@@ -84,22 +84,22 @@ function Vertex(name, data) {
 }
 
 /** String representation */
-Vertex.prototype.toString = function() {
+Vertex.prototype.toString = function () {
     return `Vertex(${this.name})`;
 };
 
 //TODO: better name w no collision for either this.eachEdge or this.edges
 /** Iterate over each edge from this vertex */
-Vertex.prototype.eachEdge = function(propsOrFn) {
+Vertex.prototype.eachEdge = function (propsOrFn) {
     return iterate(this.edges, propsOrFn);
 };
 
 /** Return a plain object representing this vertex */
-Vertex.prototype.toJSON = function() {
+Vertex.prototype.toJSON = function () {
     //return this;
     return {
         name: this.name,
-        data: this.data
+        data: this.data,
     };
 };
 
@@ -108,20 +108,20 @@ Vertex.prototype.toJSON = function() {
  *      Pass in the graph to search
  *      and an optional dictionary containing the 3 vertex/edge processing fns listed below.
  */
-var GraphSearch = function(graph, processFns) {
+var GraphSearch = function (graph, processFns) {
     var self = this;
     self.graph = graph;
 
     self.processFns = processFns || {
-        vertexEarly: function(vertex, search) {
+        vertexEarly: function (vertex, search) {
             //console.debug( 'processing vertex:', vertex.name, vertex );
         },
-        edge: function(from, edge, search) {
+        edge: function (from, edge, search) {
             //console.debug( this, 'edge:', from, edge, search );
         },
-        vertexLate: function(vertex, search) {
+        vertexLate: function (vertex, search) {
             //console.debug( this, 'vertexLate:', vertex, search );
-        }
+        },
     };
 
     self._cache = {};
@@ -147,7 +147,7 @@ GraphSearch.prototype._search = function __search(start, search) {
     search = search || {
         discovered: {},
         //parents : {},
-        edges: []
+        edges: [],
     };
     return search;
 };
@@ -162,14 +162,14 @@ GraphSearch.prototype._searchTree = function __searchTree(search) {
     var self = this;
     return new Graph(true, {
         edges: search.edges,
-        vertices: Object.keys(search.discovered).map(key => self.graph.vertices[key].toJSON())
+        vertices: Object.keys(search.discovered).map((key) => self.graph.vertices[key].toJSON()),
     });
 };
 
 // ============================================================================
 /** Breadth first search algo.
  */
-var BreadthFirstSearch = function(graph, processFns) {
+var BreadthFirstSearch = function (graph, processFns) {
     var self = this;
     GraphSearch.call(this, graph, processFns);
     return self;
@@ -182,7 +182,7 @@ BreadthFirstSearch.prototype._search = function __search(start, search) {
     search = search || {
         discovered: {},
         //parents : {},
-        edges: []
+        edges: [],
     };
 
     var self = this;
@@ -224,7 +224,7 @@ BreadthFirstSearch.prototype._search = function __search(start, search) {
 // ============================================================================
 /** Depth first search algorithm.
  */
-var DepthFirstSearch = function(graph, processFns) {
+var DepthFirstSearch = function (graph, processFns) {
     var self = this;
     GraphSearch.call(this, graph, processFns);
     return self;
@@ -233,14 +233,14 @@ DepthFirstSearch.prototype = new GraphSearch();
 DepthFirstSearch.prototype.constructor = DepthFirstSearch;
 
 /** (Private) implementation of DFS */
-DepthFirstSearch.prototype._search = function(start, search) {
+DepthFirstSearch.prototype._search = function (start, search) {
     //console.debug( 'depthFirstSearch:', start );
     search = search || {
         discovered: {},
         //parents    : {},
         edges: [],
         entryTimes: {},
-        exitTimes: {}
+        exitTimes: {},
     };
     var self = this;
     var time = 0;
@@ -257,7 +257,7 @@ DepthFirstSearch.prototype._search = function(start, search) {
             //search.parents[ adjacent.name ] = sourceVertex;
             search.edges.push({
                 source: sourceVertex.name,
-                target: adjacent.name
+                target: adjacent.name,
             });
             recurse(adjacent);
         }
@@ -296,7 +296,7 @@ function Graph(directed, data, options) {
 window.Graph = Graph;
 
 /** Set up options and instance variables */
-Graph.prototype.init = function(options) {
+Graph.prototype.init = function (options) {
     options = options || {};
     var self = this;
 
@@ -308,7 +308,7 @@ Graph.prototype.init = function(options) {
 };
 
 /** Read data from the plain object data - both in d3 form (nodes and links) or vertices and edges */
-Graph.prototype.read = function(data) {
+Graph.prototype.read = function (data) {
     if (!data) {
         return this;
     }
@@ -324,14 +324,14 @@ Graph.prototype.read = function(data) {
 
 //TODO: the next two could be combined
 /** Create the graph using a list of nodes and a list of edges (where source and target are indeces into nodes) */
-Graph.prototype.readNodesAndLinks = function(data) {
+Graph.prototype.readNodesAndLinks = function (data) {
     if (!(data && Object.prototype.hasOwnProperty.call(data, "nodes"))) {
         return this;
     }
     //console.debug( 'readNodesAndLinks:', data );
     //console.debug( 'data:\n' + JSON.stringify( data, null, '  ' ) );
     var self = this;
-    data.nodes.forEach(node => {
+    data.nodes.forEach((node) => {
         self.createVertex(node.name, node.data);
     });
     //console.debug( JSON.stringify( self.vertices, null, '  ' ) );
@@ -347,14 +347,14 @@ Graph.prototype.readNodesAndLinks = function(data) {
 };
 
 /** Create the graph using a list of nodes and a list of edges (where source and target are names of nodes) */
-Graph.prototype.readVerticesAndEdges = function(data) {
+Graph.prototype.readVerticesAndEdges = function (data) {
     if (!(data && Object.prototype.hasOwnProperty.call(data, "vertices"))) {
         return this;
     }
     //console.debug( 'readVerticesAndEdges:', data );
     //console.debug( 'data:\n' + JSON.stringify( data, null, '  ' ) );
     var self = this;
-    data.vertices.forEach(node => {
+    data.vertices.forEach((node) => {
         self.createVertex(node.name, node.data);
     });
     //console.debug( JSON.stringify( self.vertices, null, '  ' ) );
@@ -368,7 +368,7 @@ Graph.prototype.readVerticesAndEdges = function(data) {
 };
 
 /** Return the vertex with name, creating it if necessary */
-Graph.prototype.createVertex = function(name, data) {
+Graph.prototype.createVertex = function (name, data) {
     //console.debug( 'createVertex:', name, data );
     if (this.vertices[name]) {
         return this.vertices[name];
@@ -379,7 +379,7 @@ Graph.prototype.createVertex = function(name, data) {
 /** Create an edge in vertex named sourceName to targetName (optionally adding data to it)
  *      If directed is false, create a second edge from targetName to sourceName.
  */
-Graph.prototype.createEdge = function(sourceName, targetName, directed, data) {
+Graph.prototype.createEdge = function (sourceName, targetName, directed, data) {
     //note: allows multiple 'equivalent' edges (to/from same source/target)
     //console.debug( 'createEdge:', source, target, directed );
     var isReflexive = sourceName === targetName;
@@ -414,40 +414,40 @@ Graph.prototype.createEdge = function(sourceName, targetName, directed, data) {
 };
 
 /** Walk over all the edges of the graph using the vertex.eachEdge iterator */
-Graph.prototype.edges = function(propsOrFn) {
+Graph.prototype.edges = function (propsOrFn) {
     return Array.prototype.concat.apply(
         [],
-        this.eachVertex(vertex => vertex.eachEdge(propsOrFn))
+        this.eachVertex((vertex) => vertex.eachEdge(propsOrFn))
     );
 };
 
 /** Iterate over all the vertices in the graph */
-Graph.prototype.eachVertex = function(propsOrFn) {
+Graph.prototype.eachVertex = function (propsOrFn) {
     return iterate(this.vertices, propsOrFn);
 };
 
 /** Return a list of the vertices adjacent to vertex */
-Graph.prototype.adjacent = function(vertex) {
+Graph.prototype.adjacent = function (vertex) {
     var self = this;
-    return iterate(vertex.edges, edge => self.vertices[edge.target]);
+    return iterate(vertex.edges, (edge) => self.vertices[edge.target]);
 };
 
 /** Call fn on each vertex adjacent to vertex */
-Graph.prototype.eachAdjacent = function(vertex, fn) {
+Graph.prototype.eachAdjacent = function (vertex, fn) {
     var self = this;
-    return iterate(vertex.edges, edge => {
+    return iterate(vertex.edges, (edge) => {
         var adj = self.vertices[edge.target];
         return fn.call(vertex, adj, edge);
     });
 };
 
 /** Print the graph to the console (debugging) */
-Graph.prototype.print = function() {
+Graph.prototype.print = function () {
     var self = this;
     console.log(`Graph has ${Object.keys(self.vertices).length} vertices`);
-    self.eachVertex(vertex => {
+    self.eachVertex((vertex) => {
         console.log(vertex.toString());
-        vertex.eachEdge(edge => {
+        vertex.eachEdge((edge) => {
             console.log(`\t ${edge}`);
         });
     });
@@ -455,11 +455,11 @@ Graph.prototype.print = function() {
 };
 
 /** Return a DOT format string of this graph */
-Graph.prototype.toDOT = function() {
+Graph.prototype.toDOT = function () {
     var self = this;
     var strings = [];
     strings.push("graph bler {");
-    self.edges(edge => {
+    self.edges((edge) => {
         strings.push(`\t${edge.from} -- ${edge.to};`);
     });
     strings.push("}");
@@ -467,7 +467,7 @@ Graph.prototype.toDOT = function() {
 };
 
 /** Return vertices and edges of this graph in d3 node/link format */
-Graph.prototype.toNodesAndLinks = function() {
+Graph.prototype.toNodesAndLinks = function () {
     var self = this;
     var indeces = {};
     return {
@@ -475,41 +475,41 @@ Graph.prototype.toNodesAndLinks = function() {
             indeces[vertex.name] = i;
             return vertex.toJSON();
         }),
-        links: self.edges(edge => {
+        links: self.edges((edge) => {
             var json = edge.toJSON();
             json.source = indeces[edge.source];
             json.target = indeces[edge.target];
             return json;
-        })
+        }),
     };
 };
 
 /** Return vertices and edges of this graph where edges use the name/id as source and target */
-Graph.prototype.toVerticesAndEdges = function() {
+Graph.prototype.toVerticesAndEdges = function () {
     var self = this;
     return {
         vertices: self.eachVertex((vertex, key) => vertex.toJSON()),
-        edges: self.edges(edge => edge.toJSON())
+        edges: self.edges((edge) => edge.toJSON()),
     };
 };
 
 /** Search this graph using BFS */
-Graph.prototype.breadthFirstSearch = function(start, processFns) {
+Graph.prototype.breadthFirstSearch = function (start, processFns) {
     return new BreadthFirstSearch(this).search(start);
 };
 
 /** Return a searchtree of this graph using BFS */
-Graph.prototype.breadthFirstSearchTree = function(start, processFns) {
+Graph.prototype.breadthFirstSearchTree = function (start, processFns) {
     return new BreadthFirstSearch(this).searchTree(start);
 };
 
 /** Search this graph using DFS */
-Graph.prototype.depthFirstSearch = function(start, processFns) {
+Graph.prototype.depthFirstSearch = function (start, processFns) {
     return new DepthFirstSearch(this).search(start);
 };
 
 /** Return a searchtree of this graph using DFS */
-Graph.prototype.depthFirstSearchTree = function(start, processFns) {
+Graph.prototype.depthFirstSearchTree = function (start, processFns) {
     return new DepthFirstSearch(this).searchTree(start);
 };
 
@@ -526,7 +526,7 @@ Graph.prototype.depthFirstSearchTree = function(start, processFns) {
 //};
 
 /** Return an array of weakly connected (no edges between) sub-graphs in this graph */
-Graph.prototype.weakComponents = function() {
+Graph.prototype.weakComponents = function () {
     //TODO: alternately, instead of returning graph-like objects:
     //  - could simply decorate the vertices (vertex.component = componentIndex), or clone the graph and do that
     var self = this;
@@ -540,11 +540,11 @@ Graph.prototype.weakComponents = function() {
         var search = new DepthFirstSearch(searchGraph)._search(undiscoveredVertex);
 
         // remove curr discovered from undiscovered
-        undiscovered = undiscovered.filter(name => !(name in search.discovered));
+        undiscovered = undiscovered.filter((name) => !(name in search.discovered));
 
         return {
-            vertices: Object.keys(search.discovered).map(vertexName => self.vertices[vertexName].toJSON()),
-            edges: search.edges.map(edge => {
+            vertices: Object.keys(search.discovered).map((vertexName) => self.vertices[vertexName].toJSON()),
+            edges: search.edges.map((edge) => {
                 // restore any reversed edges
                 var hasBeenReversed = self.vertices[edge.target].edges[edge.source] !== undefined;
                 if (self.directed && hasBeenReversed) {
@@ -553,7 +553,7 @@ Graph.prototype.weakComponents = function() {
                     edge.target = swap;
                 }
                 return edge;
-            })
+            }),
         };
     }
 
@@ -574,20 +574,20 @@ Graph.prototype.weakComponents = function() {
 };
 
 /** Return a single graph containing the weakly connected components in this graph */
-Graph.prototype.weakComponentGraph = function() {
+Graph.prototype.weakComponentGraph = function () {
     //note: although this can often look like the original graph - edges can be lost
     var components = this.weakComponents();
     return new Graph(this.directed, {
         vertices: components.reduce((reduction, curr) => reduction.concat(curr.vertices), []),
-        edges: components.reduce((reduction, curr) => reduction.concat(curr.edges), [])
+        edges: components.reduce((reduction, curr) => reduction.concat(curr.edges), []),
     });
 };
 
 /** Return an array of graphs of the weakly connected components in this graph */
-Graph.prototype.weakComponentGraphArray = function() {
+Graph.prototype.weakComponentGraphArray = function () {
     //note: although this can often look like the original graph - edges can be lost
     var graph = this;
-    return this.weakComponents().map(component => new Graph(graph.directed, component));
+    return this.weakComponents().map((component) => new Graph(graph.directed, component));
 };
 
 // ============================================================================
@@ -605,7 +605,7 @@ function randGraph(directed, numVerts, numEdges) {
     for (i = 0; i < numEdges; i++) {
         data.links.push({
             source: randRange(numVerts),
-            target: randRange(numVerts)
+            target: randRange(numVerts),
         });
     }
     //console.debug( JSON.stringify( data, null, '  ' ) );
@@ -619,5 +619,5 @@ export default {
     BreadthFirstSearch: BreadthFirstSearch,
     DepthFirstSearch: DepthFirstSearch,
     Graph: Graph,
-    randGraph: randGraph
+    randGraph: randGraph,
 };
diff --git a/client/galaxy/scripts/utils/installMonitor.js b/client/galaxy/scripts/utils/installMonitor.js
index 68479548ba9d..e7e8cc5f716b 100644
--- a/client/galaxy/scripts/utils/installMonitor.js
+++ b/client/galaxy/scripts/utils/installMonitor.js
@@ -68,7 +68,7 @@ export function installObjectWatcher(globalProp, getter = null, setter = null) {
                 logger.warn(err);
             }
             logger.groupEnd();
-        }
+        },
     });
 }
 
diff --git a/client/galaxy/scripts/utils/localization.js b/client/galaxy/scripts/utils/localization.js
index e4d6a84e4ada..13aec2df0b8f 100644
--- a/client/galaxy/scripts/utils/localization.js
+++ b/client/galaxy/scripts/utils/localization.js
@@ -1,5 +1,5 @@
 // eslint-disable-next-line no-undef
-define(["i18n!nls/locale"], function(localeStrings) {
+define(["i18n!nls/locale"], function (localeStrings) {
     // =============================================================================
     /** Simple string replacement localization. Language data from galaxy/scripts/nls */
 
@@ -24,7 +24,7 @@ define(["i18n!nls/locale"], function(localeStrings) {
      * @param {String} strToLocalize the string to localize
      * @returns either the localized string if found or strToLocalize if not found
      */
-    var localize = function(strToLocalize) {
+    var localize = function (strToLocalize) {
         // console.debug( 'amdi18n.localize:', strToLocalize, '->', localeStrings[ strToLocalize ] || strToLocalize );
 
         // //TODO: conditional compile on DEBUG flag
diff --git a/client/galaxy/scripts/utils/metrics-logger.js b/client/galaxy/scripts/utils/metrics-logger.js
index e8dfb3bac33d..64fdc5456f14 100644
--- a/client/galaxy/scripts/utils/metrics-logger.js
+++ b/client/galaxy/scripts/utils/metrics-logger.js
@@ -91,7 +91,7 @@ MetricsLogger.defaultOptions = {
     /** an (optional) function that should return an object; used to send additional data with the metrics */
     getPingData: undefined,
     /** an (optional) function that will handle the servers response after successfully posting messages */
-    onServerResponse: undefined
+    onServerResponse: undefined,
 };
 
 //----------------------------------------------------------------------------- set up
@@ -127,7 +127,7 @@ MetricsLogger.prototype._initCache = function _initCache() {
     try {
         this.cache = new LoggingCache({
             maxSize: this.options.maxCacheSize,
-            key: this.options.cacheKeyPrefix + this.userId
+            key: this.options.cacheKeyPrefix + this.userId,
         });
     } catch (err) {
         this._emitToConsole("warn", "MetricsLogger", ["Could not intitialize logging cache:", err]);
@@ -180,7 +180,7 @@ MetricsLogger.prototype._addToCache = function _addToCache(level, namespace, log
         "_addToCache:",
         arguments,
         this.options.addTime,
-        this.cache.length()
+        this.cache.length(),
     ]);
     //this._emitToConsole( 'debug', 'MetricsLogger', [ '\t logArguments:', logArguments ]);
     var self = this;
@@ -195,7 +195,7 @@ MetricsLogger.prototype._addToCache = function _addToCache(level, namespace, log
         self._emitToConsole("warn", "MetricsLogger", [
             "Metrics logger could not stringify logArguments:",
             namespace,
-            logArguments
+            logArguments,
         ]);
         self._emitToConsole("error", "MetricsLogger", [err]);
     }
@@ -208,7 +208,7 @@ MetricsLogger.prototype._buildEntry = function _buildEntry(level, namespace, log
     var entry = {
         level: level,
         namespace: this.options.clientPrefix + namespace,
-        args: logArguments
+        args: logArguments,
     };
     if (this.options.addTime) {
         entry.time = new Date().toISOString();
@@ -261,12 +261,12 @@ MetricsLogger.prototype._postCache = function _postCache(options) {
                 "_postCache error:",
                 xhr.readyState,
                 xhr.status,
-                xhr.responseJSON || xhr.responseText
+                xhr.responseJSON || xhr.responseText,
             ]);
             //TODO: still doesn't solve the problem that when cache == max, post will be tried on every emit
             //TODO: see _delayPost
         })
-        .done(response => {
+        .done((response) => {
             if (typeof self.options.onServerResponse === "function") {
                 self.options.onServerResponse(response);
             }
@@ -385,7 +385,7 @@ function LoggingCache(options) {
 /** default options */
 LoggingCache.defaultOptions = {
     /** maximum number of entries to keep before discarding oldest */
-    maxSize: 5000
+    maxSize: 5000,
 };
 
 /** initialize with options */
@@ -493,5 +493,5 @@ LoggingCache.prototype.print = function print() {
 //=============================================================================
 export default {
     MetricsLogger: MetricsLogger,
-    LoggingCache: LoggingCache
+    LoggingCache: LoggingCache,
 };
diff --git a/client/galaxy/scripts/utils/mock.js b/client/galaxy/scripts/utils/mock.js
index 6761196706c7..1083f42a5a38 100644
--- a/client/galaxy/scripts/utils/mock.js
+++ b/client/galaxy/scripts/utils/mock.js
@@ -2,9 +2,9 @@
 
 const doNothing = () => null;
 
-export const mock = source =>
+export const mock = (source) =>
     Object.keys(source)
-        .filter(prop => typeof source[prop] == "function")
+        .filter((prop) => typeof source[prop] == "function")
         .reduce((result, prop) => {
             result[prop] = doNothing;
             return result;
diff --git a/client/galaxy/scripts/utils/mountVueComponent.js b/client/galaxy/scripts/utils/mountVueComponent.js
index e46180ac5411..4ba99d9d5fd4 100644
--- a/client/galaxy/scripts/utils/mountVueComponent.js
+++ b/client/galaxy/scripts/utils/mountVueComponent.js
@@ -6,9 +6,9 @@ import store from "../store";
 import _l from "utils/localization";
 
 // make localization filter available to all components
-Vue.filter("localize", value => _l(value));
+Vue.filter("localize", (value) => _l(value));
 
-export const mountVueComponent = ComponentDefinition => (propsData, el) => {
+export const mountVueComponent = (ComponentDefinition) => (propsData, el) => {
     const component = Vue.extend(ComponentDefinition);
     return new component({ store, propsData, el });
 };
diff --git a/client/galaxy/scripts/utils/query-string-parsing.js b/client/galaxy/scripts/utils/query-string-parsing.js
index 533aca2e35f0..9d15ce641b52 100644
--- a/client/galaxy/scripts/utils/query-string-parsing.js
+++ b/client/galaxy/scripts/utils/query-string-parsing.js
@@ -7,7 +7,7 @@ function get(key, queryString) {
     if (!matches || !matches.length) {
         return undefined;
     }
-    matches = _.map(matches, match => decodeURIComponent(match.substr(key.length + 1).replace(/\+/g, " ")));
+    matches = _.map(matches, (match) => decodeURIComponent(match.substr(key.length + 1).replace(/\+/g, " ")));
     if (matches.length === 1) {
         return matches[0];
     }
@@ -20,7 +20,7 @@ function parse(queryString) {
     }
     var parsed = {};
     var split = queryString.split("&");
-    split.forEach(pairString => {
+    split.forEach((pairString) => {
         var pair = pairString.split("=");
         parsed[pair[0]] = decodeURI(pair[1]);
     });
@@ -30,5 +30,5 @@ function parse(queryString) {
 // ============================================================================
 export default {
     get: get,
-    parse: parse
+    parse: parse,
 };
diff --git a/client/galaxy/scripts/utils/safeAssign.js b/client/galaxy/scripts/utils/safeAssign.js
index fda9c7724fec..52d4cff9d0bb 100644
--- a/client/galaxy/scripts/utils/safeAssign.js
+++ b/client/galaxy/scripts/utils/safeAssign.js
@@ -6,6 +6,6 @@ export function safeAssign(target, source = {}) {
         source = {};
     }
     Object.keys(source)
-        .filter(prop => Object.prototype.hasOwnProperty.call(target, prop))
-        .forEach(prop => (target[prop] = source[prop]));
+        .filter((prop) => Object.prototype.hasOwnProperty.call(target, prop))
+        .forEach((prop) => (target[prop] = source[prop]));
 }
diff --git a/client/galaxy/scripts/utils/uploadbox.js b/client/galaxy/scripts/utils/uploadbox.js
index 1e69b6b713ed..ce377b595c6e 100644
--- a/client/galaxy/scripts/utils/uploadbox.js
+++ b/client/galaxy/scripts/utils/uploadbox.js
@@ -6,20 +6,20 @@ import _ from "underscore";
 import jQuery from "jquery";
 import { getAppRoot } from "onload/loadConfig";
 
-($ => {
+(($) => {
     // add event properties
     jQuery.event.props.push("dataTransfer");
 
     /**
         xhr request helper
     */
-    var _uploadrequest = config => {
+    var _uploadrequest = (config) => {
         var cnf = $.extend(
             {
                 error_default: "Please make sure the file is available.",
                 error_server: "Upload request failed.",
                 error_login: "Uploads require you to log in.",
-                error_retry: "Waiting for server to resume..."
+                error_retry: "Waiting for server to resume...",
             },
             config
         );
@@ -63,7 +63,7 @@ import { getAppRoot } from "onload/loadConfig";
     /**
         Posts chunked files to the API.
     */
-    $.uploadchunk = function(config) {
+    $.uploadchunk = function (config) {
         // parse options
         var cnf = $.extend(
             {},
@@ -78,7 +78,7 @@ import { getAppRoot } from "onload/loadConfig";
                 url: null,
                 error_file: "File not provided.",
                 error_attempt: "Maximum number of attempts reached.",
-                error_tool: "Tool submission failed."
+                error_tool: "Tool submission failed.",
             },
             config
         );
@@ -118,7 +118,7 @@ import { getAppRoot } from "onload/loadConfig";
             _uploadrequest({
                 url: `${getAppRoot()}api/uploads`,
                 data: form,
-                success: upload_response => {
+                success: (upload_response) => {
                     var new_start = start + chunk_size;
                     if (new_start < size) {
                         attempts = cnf.attempts;
@@ -128,25 +128,25 @@ import { getAppRoot } from "onload/loadConfig";
                         data.payload.inputs = JSON.parse(data.payload.inputs);
                         data.payload.inputs["files_0|file_data"] = {
                             session_id: session_id,
-                            name: file.name
+                            name: file.name,
                         };
                         data.payload.inputs = JSON.stringify(data.payload.inputs);
                         $.ajax({
                             url: `${getAppRoot()}api/tools`,
                             method: "POST",
                             data: data.payload,
-                            success: tool_response => {
+                            success: (tool_response) => {
                                 cnf.success(tool_response);
                             },
-                            error: tool_response => {
+                            error: (tool_response) => {
                                 var err_msg =
                                     tool_response && tool_response.responseJSON && tool_response.responseJSON.err_msg;
                                 cnf.error(err_msg || cnf.error_tool);
-                            }
+                            },
                         });
                     }
                 },
-                warning: upload_response => {
+                warning: (upload_response) => {
                     if (--attempts > 0) {
                         console.debug("Retrying last chunk...");
                         cnf.warning(upload_response);
@@ -156,15 +156,15 @@ import { getAppRoot } from "onload/loadConfig";
                         cnf.error(cnf.error_attempt);
                     }
                 },
-                error: upload_response => {
+                error: (upload_response) => {
                     console.debug(upload_response);
                     cnf.error(upload_response);
                 },
-                progress: e => {
+                progress: (e) => {
                     if (e.lengthComputable) {
                         cnf.progress(Math.min(Math.round(((start + e.loaded) * 100) / file.size), 100));
                     }
-                }
+                },
             });
         }
 
@@ -175,7 +175,7 @@ import { getAppRoot } from "onload/loadConfig";
     /**
         Posts multiple files without chunking to the API.
     */
-    $.uploadpost = function(config) {
+    $.uploadpost = function (config) {
         var cnf = $.extend(
             {},
             {
@@ -185,7 +185,7 @@ import { getAppRoot } from "onload/loadConfig";
                 progress: () => {},
                 url: null,
                 maxfilesize: 1048576 * 2048,
-                error_filesize: "File exceeds 2GB. Please use a FTP client."
+                error_filesize: "File exceeds 2GB. Please use a FTP client.",
             },
             config
         );
@@ -221,18 +221,18 @@ import { getAppRoot } from "onload/loadConfig";
             data: form,
             success: cnf.success,
             error: cnf.error,
-            progress: e => {
+            progress: (e) => {
                 if (e.lengthComputable) {
                     cnf.progress(Math.round((e.loaded * 100) / e.total));
                 }
-            }
+            },
         });
     };
 
     /**
         Handles the upload events drag/drop etc.
     */
-    $.fn.uploadinput = function(options) {
+    $.fn.uploadinput = function (options) {
         // initialize
         var el = this;
         var opts = $.extend(
@@ -241,7 +241,7 @@ import { getAppRoot } from "onload/loadConfig";
                 ondragover: () => {},
                 ondragleave: () => {},
                 onchange: () => {},
-                multiple: false
+                multiple: false,
             },
             options
         );
@@ -249,7 +249,7 @@ import { getAppRoot } from "onload/loadConfig";
         // append hidden upload field
         var $input = $(`<input type="file" style="display: none" ${(opts.multiple && "multiple") || ""}/>`);
         el.append(
-            $input.change(e => {
+            $input.change((e) => {
                 opts.onchange(e.target.files);
                 e.target.value = null;
             })
@@ -257,18 +257,18 @@ import { getAppRoot } from "onload/loadConfig";
 
         // drag/drop events
         const element = el.get(0);
-        element.addEventListener("drop", e => {
+        element.addEventListener("drop", (e) => {
             opts.ondragleave(e);
             if (e.dataTransfer) {
                 opts.onchange(e.dataTransfer.files);
                 e.preventDefault();
             }
         });
-        element.addEventListener("dragover", e => {
+        element.addEventListener("dragover", (e) => {
             e.preventDefault();
             opts.ondragover(e);
         });
-        element.addEventListener("dragleave", e => {
+        element.addEventListener("dragleave", (e) => {
             e.stopPropagation();
             opts.ondragleave(e);
         });
@@ -277,29 +277,29 @@ import { getAppRoot } from "onload/loadConfig";
         return {
             dialog: () => {
                 $input.trigger("click");
-            }
+            },
         };
     };
 
     /**
         Handles the upload queue and events such as drag/drop etc.
     */
-    $.fn.uploadbox = function(options) {
+    $.fn.uploadbox = function (options) {
         // parse options
         var opts = $.extend(
             {},
             {
                 dragover: () => {},
                 dragleave: () => {},
-                announce: d => {},
-                initialize: d => {},
+                announce: (d) => {},
+                initialize: (d) => {},
                 progress: (d, m) => {},
                 success: (d, m) => {},
                 warning: (d, m) => {},
                 error: (d, m) => {
                     alert(m);
                 },
-                complete: () => {}
+                complete: () => {},
             },
             options
         );
@@ -321,14 +321,14 @@ import { getAppRoot } from "onload/loadConfig";
         // element
         var uploadinput = $(this).uploadinput({
             multiple: true,
-            onchange: files => {
-                _.each(files, file => {
+            onchange: (files) => {
+                _.each(files, (file) => {
                     file.chunk_mode = true;
                 });
                 add(files);
             },
             ondragover: options.ondragover,
-            ondragleave: options.ondragleave
+            ondragleave: options.ondragleave,
         });
 
         // add new files to upload queue
@@ -338,12 +338,12 @@ import { getAppRoot } from "onload/loadConfig";
                 _.each(files, (file, key) => {
                     if (
                         file.mode !== "new" &&
-                        _.filter(queue, f => f.name === file.name && f.size === file.size).length
+                        _.filter(queue, (f) => f.name === file.name && f.size === file.size).length
                     ) {
                         file.duplicate = true;
                     }
                 });
-                _.each(files, file => {
+                _.each(files, (file) => {
                     if (!file.duplicate) {
                         index = String(queue_index++);
                         queue[index] = file;
@@ -403,20 +403,20 @@ import { getAppRoot } from "onload/loadConfig";
                 url: opts.url,
                 data: opts.initialize(index),
                 session: session,
-                success: message => {
+                success: (message) => {
                     opts.success(index, message);
                     process();
                 },
-                warning: message => {
+                warning: (message) => {
                     opts.warning(index, message);
                 },
-                error: message => {
+                error: (message) => {
                     opts.error(index, message);
                     process();
                 },
-                progress: percentage => {
+                progress: (percentage) => {
                     opts.progress(index, percentage);
-                }
+                },
             });
         }
 
@@ -470,7 +470,7 @@ import { getAppRoot } from "onload/loadConfig";
             stop: stop,
             reset: reset,
             configure: configure,
-            compatible: compatible
+            compatible: compatible,
         };
     };
 })(jQuery);
diff --git a/client/galaxy/scripts/utils/utils.js b/client/galaxy/scripts/utils/utils.js
index 9c7b3fed1413..6eb1c5790df8 100644
--- a/client/galaxy/scripts/utils/utils.js
+++ b/client/galaxy/scripts/utils/utils.js
@@ -73,9 +73,7 @@ export function isJSON(text) {
  * @param{String}   content - Content to be sanitized
  */
 export function sanitize(content) {
-    return $("<div/>")
-        .text(content)
-        .html();
+    return $("<div/>").text(content).html();
 }
 
 /**
@@ -133,17 +131,17 @@ export function get(options) {
         request({
             url: options.url,
             data: options.data,
-            success: function(response) {
+            success: function (response) {
                 top.__utils__get__[cache_key] = response;
                 if (options.success) {
                     options.success(response);
                 }
             },
-            error: function(response, status) {
+            error: function (response, status) {
                 if (options.error) {
                     options.error(response, status);
                 }
-            }
+            },
         });
     }
 }
@@ -162,7 +160,7 @@ export function request(options) {
         contentType: "application/json",
         type: options.type || "GET",
         data: options.data || {},
-        url: options.url
+        url: options.url,
     };
     // encode data into url
     if (ajaxConfig.type == "GET" || ajaxConfig.type == "DELETE") {
@@ -178,7 +176,7 @@ export function request(options) {
 
     // make request
     $.ajax(ajaxConfig)
-        .done(response => {
+        .done((response) => {
             if (typeof response === "string") {
                 try {
                     response = response.replace("Infinity,", '"Infinity",');
@@ -191,7 +189,7 @@ export function request(options) {
                 options.success(response);
             }
         })
-        .fail(response => {
+        .fail((response) => {
             var response_text = null;
             try {
                 response_text = $.parseJSON(response.responseText);
@@ -317,15 +315,11 @@ export function time() {
 export function appendScriptStyle(data) {
     // create a script tag inside head tag
     if (data.script && data.script !== "") {
-        $("<script/>", { type: "text/javascript" })
-            .text(data.script)
-            .appendTo("head");
+        $("<script/>", { type: "text/javascript" }).text(data.script).appendTo("head");
     }
     // create a style tag inside head tag
     if (data.styles && data.styles !== "") {
-        $("<style/>", { type: "text/css" })
-            .text(data.styles)
-            .appendTo("head");
+        $("<style/>", { type: "text/css" }).text(data.styles).appendTo("head");
     }
 }
 
@@ -387,5 +381,5 @@ export default {
     linkify: linkify,
     appendScriptStyle: appendScriptStyle,
     getQueryString: getQueryString,
-    setWindowTitle: setWindowTitle
+    setWindowTitle: setWindowTitle,
 };
diff --git a/client/galaxy/scripts/viz/bbi-data-manager.js b/client/galaxy/scripts/viz/bbi-data-manager.js
index f347b7eadfc8..05bd4d57619f 100644
--- a/client/galaxy/scripts/viz/bbi-data-manager.js
+++ b/client/galaxy/scripts/viz/bbi-data-manager.js
@@ -12,7 +12,7 @@ var BBIDataManager = visualization.GenomeDataManager.extend({
      * for region; when data becomes available, replaces Deferred with data.
      * Returns the Deferred that resolves when data is available.
      */
-    load_data: function(region, mode, resolution, extra_params) {
+    load_data: function (region, mode, resolution, extra_params) {
         var deferred = $.Deferred();
         this.set_data(region, deferred);
 
@@ -20,13 +20,13 @@ var BBIDataManager = visualization.GenomeDataManager.extend({
 
         var self = this;
         $.when(bigwig.makeBwg(url)).then((bb, err) => {
-            $.when(bb.readWigData(region.get("chrom"), region.get("start"), region.get("end"))).then(data => {
+            $.when(bb.readWigData(region.get("chrom"), region.get("start"), region.get("end"))).then((data) => {
                 // Transform data into "bigwig" format for LinePainter. "bigwig" format is an array of 2-element arrays
                 // where each element is [position, score]; unlike real bigwig format, no gaps are allowed.
                 var result = [];
 
                 var prev = { max: Number.MIN_VALUE };
-                data.forEach(d => {
+                data.forEach((d) => {
                     // If there is a gap between prev and d, fill it with an interval with score 0.
                     // This is necessary for LinePainter to draw correctly.
                     if (prev.max !== d.min - 1) {
@@ -50,7 +50,7 @@ var BBIDataManager = visualization.GenomeDataManager.extend({
                 var entry = {
                     data: result,
                     region: region,
-                    dataset_type: "bigwig"
+                    dataset_type: "bigwig",
                 };
 
                 self.set_data(region, entry);
@@ -59,9 +59,9 @@ var BBIDataManager = visualization.GenomeDataManager.extend({
         });
 
         return deferred;
-    }
+    },
 });
 
 export default {
-    BBIDataManager: BBIDataManager
+    BBIDataManager: BBIDataManager,
 };
diff --git a/client/galaxy/scripts/viz/circster.js b/client/galaxy/scripts/viz/circster.js
index 432c37daca0e..158644ff3a70 100644
--- a/client/galaxy/scripts/viz/circster.js
+++ b/client/galaxy/scripts/viz/circster.js
@@ -20,7 +20,7 @@ var SVGUtils = Backbone.Model.extend({
     /**
      * Returns true if element is visible.
      */
-    is_visible: function(svg_elt, svg) {
+    is_visible: function (svg_elt, svg) {
         var eltBRect = svg_elt.getBoundingClientRect();
         var svgBRect = $("svg")[0].getBoundingClientRect();
 
@@ -37,14 +37,14 @@ var SVGUtils = Backbone.Model.extend({
             return false;
         }
         return true;
-    }
+    },
 });
 
 /**
  * Mixin for using ticks.
  */
 var UsesTicks = {
-    drawTicks: function(parent_elt, data, dataHandler, textTransform, horizontal) {
+    drawTicks: function (parent_elt, data, dataHandler, textTransform, horizontal) {
         // Set up group elements for chroms and for each tick.
         var ticks = parent_elt
             .append("g")
@@ -57,14 +57,14 @@ var UsesTicks = {
             .enter()
             .append("g")
             .attr("class", "tick")
-            .attr("transform", d => `rotate(${(d.angle * 180) / Math.PI - 90})translate(${d.radius},0)`);
+            .attr("transform", (d) => `rotate(${(d.angle * 180) / Math.PI - 90})translate(${d.radius},0)`);
 
         // Add line + text for ticks.
         var tick_coords = [];
 
         var text_coords = [];
 
-        var text_anchor = d => (d.angle > Math.PI ? "end" : null);
+        var text_anchor = (d) => (d.angle > Math.PI ? "end" : null);
 
         if (horizontal) {
             tick_coords = [0, 0, 0, -4];
@@ -91,13 +91,13 @@ var UsesTicks = {
             .attr("dy", text_coords[3])
             .attr("text-anchor", text_anchor)
             .attr("transform", textTransform)
-            .text(d => d.label);
+            .text((d) => d.label);
     },
 
     /**
      * Format number for display at a tick.
      */
-    formatNum: function(num, sigDigits) {
+    formatNum: function (num, sigDigits) {
         // Use default of 2 sig. digits.
         if (sigDigits === undefined) sigDigits = 2;
 
@@ -126,7 +126,7 @@ var UsesTicks = {
         }
 
         return rval;
-    }
+    },
 };
 
 /**
@@ -140,7 +140,7 @@ var CircsterLabelTrack = Backbone.Model.extend({});
 var CircsterView = Backbone.View.extend({
     className: "circster",
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.genome = options.genome;
         this.label_arc_height = 50;
         this.scale = 1;
@@ -162,21 +162,21 @@ var CircsterView = Backbone.View.extend({
     /**
      * Returns tracks to be rendered using circular view.
      */
-    get_circular_tracks: function() {
-        return this.model.get("drawables").filter(track => track.get("track_type") !== "DiagonalHeatmapTrack");
+    get_circular_tracks: function () {
+        return this.model.get("drawables").filter((track) => track.get("track_type") !== "DiagonalHeatmapTrack");
     },
 
     /**
      * Returns tracks to be rendered using chords view.
      */
-    get_chord_tracks: function() {
-        return this.model.get("drawables").filter(track => track.get("track_type") === "DiagonalHeatmapTrack");
+    get_chord_tracks: function () {
+        return this.model.get("drawables").filter((track) => track.get("track_type") === "DiagonalHeatmapTrack");
     },
 
     /**
      * Returns a list of circular tracks' radius bounds.
      */
-    get_tracks_bounds: function() {
+    get_tracks_bounds: function () {
         var circular_tracks = this.get_circular_tracks();
 
         var dataset_arc_height = this.model.get("config").get_value("arc_dataset_height");
@@ -199,13 +199,13 @@ var CircsterView = Backbone.View.extend({
             tracks_start_radii = d3.range(radius_start, min_dimension / 2, dataset_arc_height + track_gap);
 
         // Map from track start to bounds.
-        return _.map(tracks_start_radii, radius => [radius, radius + dataset_arc_height]);
+        return _.map(tracks_start_radii, (radius) => [radius, radius + dataset_arc_height]);
     },
 
     /**
      * Renders circular tracks, chord tracks, and label tracks.
      */
-    render: function() {
+    render: function () {
         var self = this;
         var width = self.$el.width();
         var height = self.$el.height();
@@ -262,7 +262,7 @@ var CircsterView = Backbone.View.extend({
                 track: track,
                 radius_bounds: tracks_bounds[index],
                 genome: self.genome,
-                total_gap: total_gap
+                total_gap: total_gap,
             });
 
             view.render();
@@ -272,13 +272,13 @@ var CircsterView = Backbone.View.extend({
 
         // -- Render chords tracks. --
 
-        this.chords_views = chords_tracks.map(track => {
+        this.chords_views = chords_tracks.map((track) => {
             var view = new CircsterChromInteractionsTrackView({
                 el: svg.append("g")[0],
                 track: track,
                 radius_bounds: tracks_bounds[0],
                 genome: self.genome,
-                total_gap: total_gap
+                total_gap: total_gap,
             });
 
             view.render();
@@ -300,7 +300,7 @@ var CircsterView = Backbone.View.extend({
             track: new CircsterLabelTrack(),
             radius_bounds: track_bounds,
             genome: self.genome,
-            total_gap: total_gap
+            total_gap: total_gap,
         });
 
         this.label_track_view.render();
@@ -309,7 +309,7 @@ var CircsterView = Backbone.View.extend({
     /**
      * Render a single track on the outside of the current visualization.
      */
-    add_track: function(new_track) {
+    add_track: function (new_track) {
         var total_gap = this.model.get("config").get_value("total_gap");
 
         if (new_track.get("track_type") === "DiagonalHeatmapTrack") {
@@ -321,7 +321,7 @@ var CircsterView = Backbone.View.extend({
                 track: new_track,
                 radius_bounds: innermost_radius_bounds,
                 genome: this.genome,
-                total_gap: total_gap
+                total_gap: total_gap,
             });
 
             new_view.render();
@@ -336,7 +336,7 @@ var CircsterView = Backbone.View.extend({
             });
 
             // Update chords tracks.
-            _.each(this.chords_views, track_view => {
+            _.each(this.chords_views, (track_view) => {
                 track_view.update_radius_bounds(new_track_bounds[0]);
             });
 
@@ -348,7 +348,7 @@ var CircsterView = Backbone.View.extend({
                 track: new_track,
                 radius_bounds: new_track_bounds[track_index],
                 genome: this.genome,
-                total_gap: total_gap
+                total_gap: total_gap,
             });
 
             track_view.render();
@@ -368,7 +368,7 @@ var CircsterView = Backbone.View.extend({
     /**
      * Remove a track from the view.
      */
-    remove_track: function(track, tracks, options) {
+    remove_track: function (track, tracks, options) {
         // -- Remove track from view. --
         var track_view = this.circular_views[options.index];
         this.circular_views.splice(options.index, 1);
@@ -381,7 +381,7 @@ var CircsterView = Backbone.View.extend({
         });
     },
 
-    update_track_bounds: function() {
+    update_track_bounds: function () {
         // Recompute and update track bounds.
         var new_track_bounds = this.get_tracks_bounds();
         _.each(this.circular_views, (track_view, i) => {
@@ -389,10 +389,10 @@ var CircsterView = Backbone.View.extend({
         });
 
         // Update chords tracks.
-        _.each(this.chords_views, track_view => {
+        _.each(this.chords_views, (track_view) => {
             track_view.update_radius_bounds(new_track_bounds[0]);
         });
-    }
+    },
 });
 
 /**
@@ -403,7 +403,7 @@ var CircsterTrackView = Backbone.View.extend({
 
     /* ----------------------- Public Methods ------------------------- */
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.bg_stroke = "#ddd";
         // Fill color when loading data.
         this.loading_bg_fill = "#ffc";
@@ -422,7 +422,7 @@ var CircsterTrackView = Backbone.View.extend({
     /**
      * Get fill color from config.
      */
-    get_fill_color: function() {
+    get_fill_color: function () {
         var color = this.track.get("config").get_value("block_color");
         if (!color) {
             color = this.track.get("config").get_value("color");
@@ -433,24 +433,17 @@ var CircsterTrackView = Backbone.View.extend({
     /**
      * Render track's data by adding SVG elements to parent.
      */
-    render: function() {
+    render: function () {
         // -- Create track group element. --
         var track_parent_elt = this.parent_elt;
 
         // -- Render background arcs. --
         var genome_arcs = this.chroms_layout;
 
-        var arc_gen = d3.svg
-            .arc()
-            .innerRadius(this.radius_bounds[0])
-            .outerRadius(this.radius_bounds[1]);
+        var arc_gen = d3.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);
 
         var // Attach data to group element.
-            chroms_elts = track_parent_elt
-                .selectAll("g")
-                .data(genome_arcs)
-                .enter()
-                .append("svg:g");
+            chroms_elts = track_parent_elt.selectAll("g").data(genome_arcs).enter().append("svg:g");
 
         var // Draw chrom arcs/paths.
             chroms_paths = chroms_elts
@@ -461,7 +454,7 @@ var CircsterTrackView = Backbone.View.extend({
                 .style("fill", this.loading_bg_fill);
 
         // Append titles to paths.
-        chroms_paths.append("title").text(d => d.data.chrom);
+        chroms_paths.append("title").text((d) => d.data.chrom);
 
         // -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. --
 
@@ -486,26 +479,19 @@ var CircsterTrackView = Backbone.View.extend({
     /**
      * Render track labels.
      */
-    render_labels: function() {},
+    render_labels: function () {},
 
     /**
      * Update radius bounds.
      */
-    update_radius_bounds: function(radius_bounds) {
+    update_radius_bounds: function (radius_bounds) {
         // Update bounds.
         this.radius_bounds = radius_bounds;
 
         // -- Update background arcs. --
-        var new_d = d3.svg
-            .arc()
-            .innerRadius(this.radius_bounds[0])
-            .outerRadius(this.radius_bounds[1]);
+        var new_d = d3.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);
 
-        this.parent_elt
-            .selectAll("g>path.chrom-background")
-            .transition()
-            .duration(1000)
-            .attr("d", new_d);
+        this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d", new_d);
 
         this._transition_chrom_data();
 
@@ -515,7 +501,7 @@ var CircsterTrackView = Backbone.View.extend({
     /**
      * Update view scale. This fetches more data if scale is increased.
      */
-    update_scale: function(new_scale) {
+    update_scale: function (new_scale) {
         // -- Update scale and return if new scale is less than old scale. --
 
         var old_scale = this.scale;
@@ -533,10 +519,10 @@ var CircsterTrackView = Backbone.View.extend({
         // Select all chrom data and filter to operate on those that are visible.
         this.parent_elt
             .selectAll("path.chrom-data")
-            .filter(function(d, i) {
+            .filter(function (d, i) {
                 return utils.is_visible(this);
             })
-            .each(function(d, i) {
+            .each(function (d, i) {
                 // -- Now operating on a single path element representing chromosome data. --
 
                 var path_elt = d3.select(this);
@@ -557,7 +543,7 @@ var CircsterTrackView = Backbone.View.extend({
                     .get_more_detailed_data(chrom_region, "Coverage", 0, new_scale);
 
                 // When more data is available, use new data to redraw path.
-                $.when(data_deferred).then(data => {
+                $.when(data_deferred).then((data) => {
                     // Remove current data path.
                     path_elt.remove();
 
@@ -565,7 +551,7 @@ var CircsterTrackView = Backbone.View.extend({
                     self._update_data_bounds();
 
                     // Find chromosome arc to draw data on.
-                    var chrom_arc = _.find(self.chroms_layout, layout => layout.data.chrom === chrom);
+                    var chrom_arc = _.find(self.chroms_layout, (layout) => layout.data.chrom === chrom);
 
                     // Add new data path and apply preferences.
                     var color = self.get_fill_color();
@@ -583,7 +569,7 @@ var CircsterTrackView = Backbone.View.extend({
     /**
      * Transitions chrom data to new values (e.g new radius or data bounds).
      */
-    _transition_chrom_data: function() {
+    _transition_chrom_data: function () {
         var track = this.track;
         var chrom_arcs = this.chroms_layout;
         var chrom_data_paths = this.parent_elt.selectAll("g>path.chrom-data");
@@ -591,7 +577,7 @@ var CircsterTrackView = Backbone.View.extend({
 
         if (num_paths > 0) {
             var self = this;
-            $.when(track.get("data_manager").get_genome_wide_data(this.genome)).then(genome_wide_data => {
+            $.when(track.get("data_manager").get_genome_wide_data(this.genome)).then((genome_wide_data) => {
                 // Map chrom data to path data, filtering out null values.
                 var path_data = _.reject(
                     _.map(genome_wide_data, (chrom_data, i) => {
@@ -604,12 +590,12 @@ var CircsterTrackView = Backbone.View.extend({
                         }
                         return rval;
                     }),
-                    p_data => p_data === null
+                    (p_data) => p_data === null
                 );
 
                 // Transition each path for data and color.
                 var color = track.get("config").get_value("color");
-                chrom_data_paths.each(function(path, index) {
+                chrom_data_paths.each(function (path, index) {
                     d3.select(this)
                         .transition()
                         .duration(1000)
@@ -624,13 +610,13 @@ var CircsterTrackView = Backbone.View.extend({
     /**
      * Transition labels to new values (e.g new radius or data bounds).
      */
-    _transition_labels: function() {},
+    _transition_labels: function () {},
 
     /**
      * Update data bounds. If there are new_bounds, use them; otherwise use
      * default data bounds.
      */
-    _update_data_bounds: function(new_bounds) {
+    _update_data_bounds: function (new_bounds) {
         this.data_bounds =
             new_bounds || this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));
         this._transition_chrom_data();
@@ -639,14 +625,14 @@ var CircsterTrackView = Backbone.View.extend({
     /**
      * Render data as elements attached to svg.
      */
-    _render_data: function(svg) {
+    _render_data: function (svg) {
         var self = this;
         var chrom_arcs = this.chroms_layout;
         var track = this.track;
         var rendered_deferred = $.Deferred();
 
         // When genome-wide data is available, render data.
-        $.when(track.get("data_manager").get_genome_wide_data(this.genome)).then(genome_wide_data => {
+        $.when(track.get("data_manager").get_genome_wide_data(this.genome)).then((genome_wide_data) => {
             // Set bounds.
             self.data_bounds = self.get_data_bounds(genome_wide_data);
 
@@ -655,17 +641,17 @@ var CircsterTrackView = Backbone.View.extend({
             // accordingly (set up in initialize). Because we are setting up, we don't want
             // the watch to trigger events here.
             track.get("config").set_value("min_value", self.data_bounds[0], {
-                silent: true
+                silent: true,
             });
             track.get("config").set_value("max_value", self.data_bounds[1], {
-                silent: true
+                silent: true,
             });
 
             // Merge chroms layout with data.
             var layout_and_data = _.zip(chrom_arcs, genome_wide_data);
 
             // Render each chromosome's data.
-            _.each(layout_and_data, chrom_info => {
+            _.each(layout_and_data, (chrom_info) => {
                 var chrom_arc = chrom_info[0];
                 var data = chrom_info[1];
                 return self._render_chrom_data(svg, chrom_arc, data);
@@ -673,10 +659,7 @@ var CircsterTrackView = Backbone.View.extend({
 
             // Apply prefs to all track data.
             var color = self.get_fill_color();
-            self.parent_elt
-                .selectAll("path.chrom-data")
-                .style("stroke", color)
-                .style("fill", color);
+            self.parent_elt.selectAll("path.chrom-data").style("stroke", color).style("fill", color);
 
             rendered_deferred.resolve(svg);
         });
@@ -687,24 +670,24 @@ var CircsterTrackView = Backbone.View.extend({
     /**
      * Render a chromosome data and attach elements to svg.
      */
-    _render_chrom_data: function(svg, chrom_arc, data) {},
+    _render_chrom_data: function (svg, chrom_arc, data) {},
 
     /**
      * Returns data for creating a path for the given data using chrom_arc and data bounds.
      */
-    _get_path_function: function(chrom_arc, chrom_data) {},
+    _get_path_function: function (chrom_arc, chrom_data) {},
 
     /**
      * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle
      * separated by gaps.
      */
-    _chroms_layout: function() {
+    _chroms_layout: function () {
         // Setup chroms layout using pie.
         var chroms_info = this.genome.get_chroms_info();
 
         var pie_layout = d3.layout
             .pie()
-            .value(d => d.len)
+            .value((d) => d.len)
             .sort(null);
 
         var init_arcs = pie_layout(chroms_info);
@@ -718,14 +701,14 @@ var CircsterTrackView = Backbone.View.extend({
         });
 
         return chrom_arcs;
-    }
+    },
 });
 
 /**
  * Render chromosome labels.
  */
 var CircsterChromLabelTrackView = CircsterTrackView.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         CircsterTrackView.prototype.initialize.call(this, options);
         // Use a single arc for rendering data.
         this.innerRadius = this.radius_bounds[0];
@@ -740,35 +723,35 @@ var CircsterChromLabelTrackView = CircsterTrackView.extend({
     /**
      * Render labels.
      */
-    _render_data: function(svg) {
+    _render_data: function (svg) {
         // -- Add chromosome label where it will fit; an alternative labeling mechanism
         // would be nice for small chromosomes. --
         var self = this;
 
         var chrom_arcs = svg.selectAll("g");
 
-        chrom_arcs.selectAll("path").attr("id", d => `label-${d.data.chrom}`);
+        chrom_arcs.selectAll("path").attr("id", (d) => `label-${d.data.chrom}`);
 
         chrom_arcs
             .append("svg:text")
-            .filter(d => d.endAngle - d.startAngle > self.min_arc_len)
+            .filter((d) => d.endAngle - d.startAngle > self.min_arc_len)
             .attr("text-anchor", "middle")
             .append("svg:textPath")
             .attr("class", "chrom-label")
-            .attr("xlink:href", d => `#label-${d.data.chrom}`)
+            .attr("xlink:href", (d) => `#label-${d.data.chrom}`)
             .attr("startOffset", "25%")
-            .text(d => d.data.chrom);
+            .text((d) => d.data.chrom);
 
         // -- Add ticks to denote chromosome length. --
 
         /** Returns an array of tick angles and labels, given a chrom arc. */
-        var chromArcTicks = d => {
+        var chromArcTicks = (d) => {
             var k = (d.endAngle - d.startAngle) / d.value;
 
             var ticks = d3.range(0, d.value, 25000000).map((v, i) => ({
                 radius: self.innerRadius,
                 angle: v * k + d.startAngle,
-                label: i === 0 ? 0 : i % 3 ? null : self.formatNum(v)
+                label: i === 0 ? 0 : i % 3 ? null : self.formatNum(v),
             }));
 
             // If there are fewer that 4 ticks, label last tick so that at least one non-zero tick is labeled.
@@ -782,13 +765,13 @@ var CircsterChromLabelTrackView = CircsterTrackView.extend({
         };
 
         /** Rotate and move text as needed. */
-        var textTransform = d => (d.angle > Math.PI ? "rotate(180)translate(-16)" : null);
+        var textTransform = (d) => (d.angle > Math.PI ? "rotate(180)translate(-16)" : null);
 
         // Filter chroms for only those large enough for display.
-        var visibleChroms = _.filter(this.chroms_layout, c => c.endAngle - c.startAngle > self.min_arc_len);
+        var visibleChroms = _.filter(this.chroms_layout, (c) => c.endAngle - c.startAngle > self.min_arc_len);
 
         this.drawTicks(this.parent_elt, visibleChroms, chromArcTicks, textTransform);
-    }
+    },
 });
 _.extend(CircsterChromLabelTrackView.prototype, UsesTicks);
 
@@ -796,7 +779,7 @@ _.extend(CircsterChromLabelTrackView.prototype, UsesTicks);
  * View for quantitative track in Circster.
  */
 var CircsterQuantitativeTrackView = CircsterTrackView.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         CircsterTrackView.prototype.initialize.call(this, options);
 
         // When config settings change, update view.
@@ -809,7 +792,7 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
     /**
      * Update track when min and/or max are changed.
      */
-    _update_min_max: function() {
+    _update_min_max: function () {
         var track_config = this.track.get("config");
 
         var new_bounds = [track_config.get_value("min_value"), track_config.get_value("max_value")];
@@ -824,7 +807,7 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
     /**
      * Returns quantile for an array of numbers.
      */
-    _quantile: function(numbers, quantile) {
+    _quantile: function (numbers, quantile) {
         numbers.sort(d3.ascending);
         return d3.quantile(numbers, quantile);
     },
@@ -833,7 +816,7 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
      * Renders quantitative data with the form [x, value] and assumes data is equally spaced across
      * chromosome. Attachs a dict with track and chrom name information to DOM element.
      */
-    _render_chrom_data: function(svg, chrom_arc, chrom_data) {
+    _render_chrom_data: function (svg, chrom_arc, chrom_data) {
         var path_data = this._get_path_function(chrom_arc, chrom_data);
 
         if (!path_data) {
@@ -855,18 +838,14 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
     /**
      * Returns function for creating a path across the chrom arc.
      */
-    _get_path_function: function(chrom_arc, chrom_data) {
+    _get_path_function: function (chrom_arc, chrom_data) {
         // If no chrom data, return null.
         if (typeof chrom_data === "string" || !chrom_data.data || chrom_data.data.length === 0) {
             return null;
         }
 
         // Radius scaler.
-        var radius = d3.scale
-            .linear()
-            .domain(this.data_bounds)
-            .range(this.radius_bounds)
-            .clamp(true);
+        var radius = d3.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);
 
         // Scaler for placing data points across arc.
         var angle = d3.scale
@@ -878,7 +857,7 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
         var line = d3.svg.line
             .radial()
             .interpolate("linear")
-            .radius(d => radius(d[1]))
+            .radius((d) => radius(d[1]))
             .angle((d, i) => angle(i));
 
         return d3.svg.area
@@ -892,7 +871,7 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
     /**
      * Render track min, max using ticks.
      */
-    render_labels: function() {
+    render_labels: function () {
         var self = this;
 
         var // Keep counter of visible chroms.
@@ -912,10 +891,10 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
         ).classed("min_max", true);
 
         // Show config when ticks are clicked on.
-        _.each(ticks, tick => {
+        _.each(ticks, (tick) => {
             $(tick).click(() => {
                 var view = new config.ConfigSettingCollectionView({
-                    collection: self.track.get("config")
+                    collection: self.track.get("config"),
                 });
                 view.render_in_modal("Configure Track");
             });
@@ -933,7 +912,7 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
     /**
      * Transition labels to new values (e.g new radius or data bounds).
      */
-    _transition_labels: function() {
+    _transition_labels: function () {
         // FIXME: (a) pull out function for getting labeled chroms? and (b) function used in transition below
         // is copied from UseTicks mixin, so pull out and make generally available.
 
@@ -945,23 +924,23 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
         // Transition labels to new radius bounds.
         var self = this;
 
-        var visibleChroms = _.filter(this.chroms_layout, c => c.endAngle - c.startAngle > 0.08);
+        var visibleChroms = _.filter(this.chroms_layout, (c) => c.endAngle - c.startAngle > 0.08);
 
         var labeledChroms = _.filter(visibleChroms, (c, i) => i % 3 === 0);
 
-        var new_data = _.flatten(_.map(labeledChroms, c => self._data_bounds_ticks_fn()(c)));
+        var new_data = _.flatten(_.map(labeledChroms, (c) => self._data_bounds_ticks_fn()(c)));
 
         this.parent_elt
             .selectAll("g.tick")
             .data(new_data)
             .transition()
-            .attr("transform", d => `rotate(${(d.angle * 180) / Math.PI - 90})translate(${d.radius},0)`);
+            .attr("transform", (d) => `rotate(${(d.angle * 180) / Math.PI - 90})translate(${d.radius},0)`);
     },
 
     /**
      * Get function for locating data bounds ticks.
      */
-    _data_bounds_ticks_fn: function() {
+    _data_bounds_ticks_fn: function () {
         // Closure vars.
         var self = this;
 
@@ -972,13 +951,13 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
             {
                 radius: self.radius_bounds[0],
                 angle: d.startAngle,
-                label: self.formatNum(self.data_bounds[0])
+                label: self.formatNum(self.data_bounds[0]),
             },
             {
                 radius: self.radius_bounds[1],
                 angle: d.startAngle,
-                label: self.formatNum(self.data_bounds[1])
-            }
+                label: self.formatNum(self.data_bounds[1]),
+            },
         ];
     },
 
@@ -986,7 +965,7 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
      * Returns an array with two values denoting the minimum and maximum
      * values for the track.
      */
-    get_data_bounds: function(data) {}
+    get_data_bounds: function (data) {},
 });
 _.extend(CircsterQuantitativeTrackView.prototype, UsesTicks);
 
@@ -994,11 +973,11 @@ _.extend(CircsterQuantitativeTrackView.prototype, UsesTicks);
  * Bigwig track view in Circster.
  */
 var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({
-    get_data_bounds: function(data) {
+    get_data_bounds: function (data) {
         // Set max across dataset by extracting all values, flattening them into a
         // single array, and getting third quartile.
         var values = _.flatten(
-            _.map(data, d => {
+            _.map(data, (d) => {
                 if (d) {
                     // Each data point has the form [position, value], so return all values.
                     return _.map(
@@ -1016,27 +995,27 @@ var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({
         // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0
         // for sparsely populated data, so use max in that case.
         return [_.min(values), this._quantile(values, 0.98) || _.max(values)];
-    }
+    },
 });
 
 /**
  * Chromosome interactions track view in Circster.
  */
 var CircsterChromInteractionsTrackView = CircsterTrackView.extend({
-    render: function() {
+    render: function () {
         var self = this;
 
         // When data is ready, render track.
         $.when(self.track.get("data_manager").data_is_ready()).then(() => {
             // When data has been fetched, render track.
-            $.when(self.track.get("data_manager").get_genome_wide_data(self.genome)).then(genome_wide_data => {
+            $.when(self.track.get("data_manager").get_genome_wide_data(self.genome)).then((genome_wide_data) => {
                 var chord_data = [];
                 var chroms_info = self.genome.get_chroms_info();
                 // Convert chromosome data into chord data.
                 _.each(genome_wide_data, (chrom_data, index) => {
                     // Map each interaction into chord data.
                     var cur_chrom = chroms_info[index].chrom;
-                    var chrom_chord_data = _.map(chrom_data.data, datum => {
+                    var chrom_chord_data = _.map(chrom_data.data, (datum) => {
                         // Each datum is an interaction/chord.
                         var source_angle = self._get_region_angle(cur_chrom, datum[1]);
 
@@ -1045,12 +1024,12 @@ var CircsterChromInteractionsTrackView = CircsterTrackView.extend({
                         return {
                             source: {
                                 startAngle: source_angle,
-                                endAngle: source_angle + 0.01
+                                endAngle: source_angle + 0.01,
                             },
                             target: {
                                 startAngle: target_angle,
-                                endAngle: target_angle + 0.01
-                            }
+                                endAngle: target_angle + 0.01,
+                            },
                         };
                     });
 
@@ -1071,20 +1050,17 @@ var CircsterChromInteractionsTrackView = CircsterTrackView.extend({
         });
     },
 
-    update_radius_bounds: function(radius_bounds) {
+    update_radius_bounds: function (radius_bounds) {
         this.radius_bounds = radius_bounds;
-        this.parent_elt
-            .selectAll("path")
-            .transition()
-            .attr("d", d3.svg.chord().radius(this.radius_bounds[0]));
+        this.parent_elt.selectAll("path").transition().attr("d", d3.svg.chord().radius(this.radius_bounds[0]));
     },
 
     /**
      * Returns radians for a genomic position.
      */
-    _get_region_angle: function(chrom, position) {
+    _get_region_angle: function (chrom, position) {
         // Find chrom angle data
-        var chrom_angle_data = _.find(this.chroms_layout, chrom_layout => chrom_layout.data.chrom === chrom);
+        var chrom_angle_data = _.find(this.chroms_layout, (chrom_layout) => chrom_layout.data.chrom === chrom);
 
         // Return angle at position.
         return (
@@ -1092,12 +1068,12 @@ var CircsterChromInteractionsTrackView = CircsterTrackView.extend({
             ((chrom_angle_data.endAngle - chrom_angle_data.startAngle) * (chrom_angle_data.data.len - position)) /
                 chrom_angle_data.data.len
         );
-    }
+    },
 });
 
 // circster app loader
 var Circster = Backbone.View.extend({
-    initialize: function() {
+    initialize: function () {
         // load css
         mod_utils.cssLoadFile("static/style/circster.css");
         // -- Configure visualization --
@@ -1112,14 +1088,14 @@ var Circster = Backbone.View.extend({
                 label: "Arc Dataset Height",
                 type: "int",
                 value: 25,
-                view: "circster"
+                view: "circster",
             },
             {
                 key: "track_gap",
                 label: "Gap Between Tracks",
                 type: "int",
                 value: 5,
-                view: "circster"
+                view: "circster",
             },
             {
                 key: "total_gap",
@@ -1127,15 +1103,15 @@ var Circster = Backbone.View.extend({
                 type: "float",
                 value: 0.4,
                 view: "circster",
-                hidden: true
-            }
+                hidden: true,
+            },
         ]);
 
         var viz_view = new CircsterView({
             // view pane
             el: $("#center .unified-panel-body"),
             genome: genome,
-            model: vis
+            model: vis,
         });
 
         // Render vizualization
@@ -1152,32 +1128,32 @@ var Circster = Backbone.View.extend({
                 {
                     icon_class: "plus-button",
                     title: _l("Add tracks"),
-                    on_click: function() {
-                        visualization.select_datasets({ dbkey: vis.get("dbkey") }, tracks => {
+                    on_click: function () {
+                        visualization.select_datasets({ dbkey: vis.get("dbkey") }, (tracks) => {
                             vis.add_tracks(tracks);
                         });
-                    }
+                    },
                 },
                 {
                     icon_class: "gear",
                     title: _l("Settings"),
-                    on_click: function() {
+                    on_click: function () {
                         var view = new config.ConfigSettingCollectionView({
-                            collection: vis.get("config")
+                            collection: vis.get("config"),
                         });
                         view.render_in_modal("Configure Visualization");
-                    }
+                    },
                 },
                 {
                     icon_class: "disk--arrow",
                     title: _l("Save"),
-                    on_click: function() {
+                    on_click: function () {
                         const Galaxy = getGalaxyInstance();
 
                         // show saving dialog box
                         Galaxy.modal.show({
                             title: _l("Saving..."),
-                            body: "progress"
+                            body: "progress",
                         });
 
                         // send to server
@@ -1190,10 +1166,10 @@ var Circster = Backbone.View.extend({
                                 title: vis.get("title"),
                                 dbkey: vis.get("dbkey"),
                                 type: "trackster",
-                                vis_json: JSON.stringify(vis)
-                            }
+                                vis_json: JSON.stringify(vis),
+                            },
                         })
-                            .success(vis_info => {
+                            .success((vis_info) => {
                                 Galaxy.modal.hide();
                                 vis.set("vis_id", vis_info.vis_id);
                             })
@@ -1203,21 +1179,21 @@ var Circster = Backbone.View.extend({
                                     title: _l("Could Not Save"),
                                     body: "Could not save visualization. Please try again later.",
                                     buttons: {
-                                        Cancel: function() {
+                                        Cancel: function () {
                                             Galaxy.modal.hide();
-                                        }
-                                    }
+                                        },
+                                    },
                                 });
                             });
-                    }
+                    },
                 },
                 {
                     icon_class: "cross-circle",
                     title: _l("Close"),
-                    on_click: function() {
+                    on_click: function () {
                         window.top.location = `${getAppRoot()}visualizations/list`;
-                    }
-                }
+                    },
+                },
             ],
             { tooltip_config: { placement: "bottom" } }
         );
@@ -1228,10 +1204,10 @@ var Circster = Backbone.View.extend({
 
         // manual tooltip config because default gravity is S and cannot be changed
         $(".menu-button").tooltip({ placement: "bottom" });
-    }
+    },
 });
 
 // Module exports.
 export default {
-    GalaxyApp: Circster
+    GalaxyApp: Circster,
 };
diff --git a/client/galaxy/scripts/viz/phyloviz.js b/client/galaxy/scripts/viz/phyloviz.js
index 762f74734cb1..b71098e33898 100644
--- a/client/galaxy/scripts/viz/phyloviz.js
+++ b/client/galaxy/scripts/viz/phyloviz.js
@@ -16,7 +16,7 @@ var UserMenuBase = Backbone.View.extend({
     /**
      * Check if an input value is a number and falls within max min.
      */
-    isAcceptableValue: function($inputKey, min, max) {
+    isAcceptableValue: function ($inputKey, min, max) {
         //TODO: use better feedback than alert
         var value = $inputKey.val();
 
@@ -44,7 +44,7 @@ var UserMenuBase = Backbone.View.extend({
     /**
      * Check if any user string inputs has illegal characters that json cannot accept
      */
-    hasIllegalJsonCharacters: function($inputKey) {
+    hasIllegalJsonCharacters: function ($inputKey) {
         if ($inputKey.val().search(/"|'|\\/) !== -1) {
             alert(
                 "Named fields cannot contain these illegal characters: " +
@@ -53,7 +53,7 @@ var UserMenuBase = Backbone.View.extend({
             return true;
         }
         return false;
-    }
+    },
 });
 
 /**
@@ -64,10 +64,7 @@ var UserMenuBase = Backbone.View.extend({
 function PhyloTreeLayout() {
     var self = this; // maximum length of the text labels
 
-    var hierarchy = d3.layout
-        .hierarchy()
-        .sort(null)
-        .value(null);
+    var hierarchy = d3.layout.hierarchy().sort(null).value(null);
 
     var // ! represents both the layout angle and the height of the layout, in px
         height = 360;
@@ -88,7 +85,7 @@ function PhyloTreeLayout() {
 
     var maxTextWidth = 50;
 
-    self.leafHeight = inputLeafHeight => {
+    self.leafHeight = (inputLeafHeight) => {
         if (typeof inputLeafHeight === "undefined") {
             return leafHeight;
         } else {
@@ -97,7 +94,7 @@ function PhyloTreeLayout() {
         }
     };
 
-    self.layoutMode = mode => {
+    self.layoutMode = (mode) => {
         if (typeof mode === "undefined") {
             return layoutMode;
         } else {
@@ -107,7 +104,7 @@ function PhyloTreeLayout() {
     };
 
     // changes the layout angle of the display, which is really changing the height
-    self.layoutAngle = angle => {
+    self.layoutAngle = (angle) => {
         if (typeof angle === "undefined") {
             return height;
         }
@@ -120,7 +117,7 @@ function PhyloTreeLayout() {
         }
     };
 
-    self.separation = dist => {
+    self.separation = (dist) => {
         // changes the dist between the nodes of different depth
         if (typeof dist === "undefined") {
             return depthSeparation;
@@ -154,13 +151,13 @@ function PhyloTreeLayout() {
 
         //TODO: remove dbl-touch loop
         // changing from hierarchy's custom format for data to usable format
-        _nodes.forEach(node => {
+        _nodes.forEach((node) => {
             maxDepth = node.depth > maxDepth ? node.depth : maxDepth; //finding max depth of tree
             nodes.push(node);
         });
         // counting the number of leaf nodes and assigning max depth
         //  to nodes that do not have children to flush all the leave nodes
-        nodes.forEach(node => {
+        nodes.forEach((node) => {
             if (!node.children) {
                 //&& !node._children
                 numLeaves += 1;
@@ -205,7 +202,7 @@ function PhyloTreeLayout() {
             leafIndex += 1;
         } else {
             // if it has children, we will visit all its children and calculate its position from its children
-            children.forEach(child => {
+            children.forEach((child) => {
                 child.parent = node;
                 sumChildVertSeparation += layout(child, maxDepth, vertSeparation, node);
             });
@@ -234,14 +231,14 @@ var PhyloTree = visualization_mod.Visualization.extend({
         translate: [0, 0],
         fontSize: 12, //fontSize of node label
         selectedNode: null,
-        nodeAttrChangedTime: 0
+        nodeAttrChangedTime: 0,
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.set(
             "dataset",
             new Dataset({
-                id: options.dataset_id
+                id: options.dataset_id,
             })
         );
     },
@@ -253,7 +250,7 @@ var PhyloTree = visualization_mod.Visualization.extend({
      * contracted nodes the list is stored in _children. Nodes with their children data stored in _children will not
      * have their children rendered.
      */
-    toggle: function(d) {
+    toggle: function (d) {
         if (typeof d === "undefined") {
             return;
         }
@@ -270,7 +267,7 @@ var PhyloTree = visualization_mod.Visualization.extend({
      *  Contracts the phylotree to a single node by repeatedly calling itself to place all the list
      *  of children under _children.
      */
-    toggleAll: function(d) {
+    toggleAll: function (d) {
         if (d.children && d.children.length !== 0) {
             d.children.forEach(this.toggleAll);
             this.toggle(d);
@@ -280,7 +277,7 @@ var PhyloTree = visualization_mod.Visualization.extend({
     /**
      *  Return the data of the tree. Used for preserving state.
      */
-    getData: function() {
+    getData: function () {
         return this.root;
     },
 
@@ -288,7 +285,7 @@ var PhyloTree = visualization_mod.Visualization.extend({
      * Overriding the default save mechanism to do some clean of circular reference of the
      * phyloTree and to include phyloTree in the saved json
      */
-    save: function() {
+    save: function () {
         var root = this.root;
         cleanTree(root);
         //this.set("root", root);
@@ -321,13 +318,13 @@ var PhyloTree = visualization_mod.Visualization.extend({
             dataType: "json",
             data: {
                 config: JSON.stringify(config),
-                type: "phyloviz"
+                type: "phyloviz",
             },
-            success: function(res) {
+            success: function (res) {
                 hide_modal();
-            }
+            },
         });
-    }
+    },
 });
 
 // -- Views --
@@ -336,13 +333,13 @@ var PhyloTree = visualization_mod.Visualization.extend({
  */
 var PhylovizLayoutBase = Backbone.View.extend({
     defaults: {
-        nodeRadius: 4.5 // radius of each node in the diagram
+        nodeRadius: 4.5, // radius of each node in the diagram
     },
 
     /**
      *  Common initialization in layouts
      */
-    stdInit: function(options) {
+    stdInit: function (options) {
         var self = this;
         self.model.on(
             "change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime",
@@ -362,7 +359,7 @@ var PhylovizLayoutBase = Backbone.View.extend({
      *  Updates the visualization whenever there are changes in the expansion and contraction of nodes
      *  AND possibly when the tree is edited.
      */
-    updateAndRender: function(source) {
+    updateAndRender: function (source) {
         var self = this;
         source = source || self.model.root;
 
@@ -374,11 +371,11 @@ var PhylovizLayoutBase = Backbone.View.extend({
     /**
      * Renders the links for the visualization.
      */
-    renderLinks: function(source) {
+    renderLinks: function (source) {
         var self = this;
-        var link = self.vis.selectAll("g.completeLink").data(self.tree.links(self.nodes), d => d.target.id);
+        var link = self.vis.selectAll("g.completeLink").data(self.tree.links(self.nodes), (d) => d.target.id);
 
-        var calcalateLinePos = d => {
+        var calcalateLinePos = (d) => {
             // position of the source node <=> starting location of the line drawn
             d.pos0 = `${d.source.y0} ${d.source.x0}`;
             // position where the line makes a right angle bend
@@ -387,22 +384,19 @@ var PhylovizLayoutBase = Backbone.View.extend({
             d.pos2 = `${d.target.y0} ${d.target.x0}`;
         };
 
-        var linkEnter = link
-            .enter()
-            .insert("svg:g", "g.node")
-            .attr("class", "completeLink");
+        var linkEnter = link.enter().insert("svg:g", "g.node").attr("class", "completeLink");
 
         linkEnter
             .append("svg:path")
             .attr("class", "link")
-            .attr("d", d => {
+            .attr("d", (d) => {
                 calcalateLinePos(d);
                 return `M ${d.pos0} L ${d.pos1}`;
             });
 
         var linkUpdate = link.transition().duration(500);
 
-        linkUpdate.select("path.link").attr("d", d => {
+        linkUpdate.select("path.link").attr("d", (d) => {
             calcalateLinePos(d);
             return `M ${d.pos0} L ${d.pos1} L ${d.pos2}`;
         });
@@ -415,9 +409,9 @@ var PhylovizLayoutBase = Backbone.View.extend({
     /**
      *  Displays the information for editing
      */
-    selectNode: function(node) {
+    selectNode: function (node) {
         var self = this;
-        d3.selectAll("g.node").classed("selectedHighlight", d => {
+        d3.selectAll("g.node").classed("selectedHighlight", (d) => {
             if (node.id === d.id) {
                 if (node._selected) {
                     // for de=selecting node.
@@ -441,10 +435,10 @@ var PhylovizLayoutBase = Backbone.View.extend({
      *  Creates bootstrap tooltip for the visualization. Has to be called repeatedly due to newly generated
      *  enterNodes
      */
-    addTooltips: function() {
+    addTooltips: function () {
         $(".tooltip").remove(); //clean up tooltip, just in case its listeners are removed by d3
         $(".node")
-            .attr("data-original-title", function() {
+            .attr("data-original-title", function () {
                 var d = this.__data__;
                 var annotation = d.annotation || "None";
                 return d
@@ -454,7 +448,7 @@ var PhylovizLayoutBase = Backbone.View.extend({
                     : "";
             })
             .tooltip({ placement: "top", trigger: "hover" });
-    }
+    },
 });
 
 /**
@@ -462,7 +456,7 @@ var PhylovizLayoutBase = Backbone.View.extend({
  * calls PhyloTreeLayout to determine the positions of the nodes
  */
 var PhylovizLinearView = PhylovizLayoutBase.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         // Default values of linear layout
         var self = this;
         self.margins = options.margins;
@@ -478,16 +472,16 @@ var PhylovizLinearView = PhylovizLayoutBase.extend({
      * Creates the basic layout of a linear tree by precalculating fixed values.
      * One of calculations are also made here
      */
-    layout: function() {
+    layout: function () {
         var self = this;
         self.tree = new PhyloTreeLayout().layoutMode("Linear");
-        self.diagonal = d3.svg.diagonal().projection(d => [d.y, d.x]);
+        self.diagonal = d3.svg.diagonal().projection((d) => [d.y, d.x]);
     },
 
     /**
      * Renders the nodes base on Linear layout.
      */
-    renderNodes: function(source) {
+    renderNodes: function (source) {
         var self = this;
         var fontSize = `${self.model.get("fontSize")}px`;
 
@@ -498,7 +492,7 @@ var PhylovizLinearView = PhylovizLayoutBase.extend({
 
         var nodes = self.tree.separation(self.model.get("separation")).nodes(self.model.root);
 
-        var node = self.vis.selectAll("g.node").data(nodes, d => d.name + d.id || (d.id = ++self.i));
+        var node = self.vis.selectAll("g.node").data(nodes, (d) => d.name + d.id || (d.id = ++self.i));
 
         // These variables has to be passed into update links which are in the base methods
         self.nodes = nodes;
@@ -513,7 +507,7 @@ var PhylovizLinearView = PhylovizLayoutBase.extend({
             .on("dblclick", () => {
                 d3.event.stopPropagation();
             })
-            .on("click", d => {
+            .on("click", (d) => {
                 if (d3.event.altKey) {
                     self.selectNode(d); // display info if alt is pressed
                 } else {
@@ -529,62 +523,58 @@ var PhylovizLinearView = PhylovizLayoutBase.extend({
             // if d is an array, replate with the first object (newick, phyloxml)
             source = source[0];
         }
-        nodeEnter.attr("transform", d => `translate(${source.y0},${source.x0})`);
+        nodeEnter.attr("transform", (d) => `translate(${source.y0},${source.x0})`);
 
         nodeEnter
             .append("svg:circle")
             .attr("r", 1e-6)
-            .style("fill", d => (d._children ? "lightsteelblue" : "#fff"));
+            .style("fill", (d) => (d._children ? "lightsteelblue" : "#fff"));
 
         nodeEnter
             .append("svg:text")
             .attr("class", "nodeLabel")
-            .attr("x", d => (d.children || d._children ? -10 : 10))
+            .attr("x", (d) => (d.children || d._children ? -10 : 10))
             .attr("dy", ".35em")
-            .attr("text-anchor", d => (d.children || d._children ? "end" : "start"))
+            .attr("text-anchor", (d) => (d.children || d._children ? "end" : "start"))
             .style("fill-opacity", 1e-6);
 
         // ------- D3 TRANSITION --------
         // Transition nodes to their new position.
         var nodeUpdate = node.transition().duration(duration);
 
-        nodeUpdate.attr("transform", d => `translate(${d.y},${d.x})`);
+        nodeUpdate.attr("transform", (d) => `translate(${d.y},${d.x})`);
 
         nodeUpdate
             .select("circle")
             .attr("r", self.defaults.nodeRadius)
-            .style("fill", d => (d._children ? "lightsteelblue" : "#fff"));
+            .style("fill", (d) => (d._children ? "lightsteelblue" : "#fff"));
 
         nodeUpdate
             .select("text")
             .style("fill-opacity", 1)
             .style("font-size", fontSize)
-            .text(d => (d.name && d.name !== "" ? d.name : d.bootstrap ? Math.round(100 * d.bootstrap) : ""));
+            .text((d) => (d.name && d.name !== "" ? d.name : d.bootstrap ? Math.round(100 * d.bootstrap) : ""));
 
         // ------- D3 EXIT --------
         // Transition exiting nodes to the parent's new position.
-        var nodeExit = node
-            .exit()
-            .transition()
-            .duration(duration)
-            .remove();
+        var nodeExit = node.exit().transition().duration(duration).remove();
 
         nodeExit.select("circle").attr("r", 1e-6);
 
         nodeExit.select("text").style("fill-opacity", 1e-6);
 
         // Stash the old positions for transition.
-        nodes.forEach(d => {
+        nodes.forEach((d) => {
             d.x0 = d.x; // we need the x0, y0 for parents with children
             d.y0 = d.y;
         });
-    }
+    },
 });
 
 export var PhylovizView = Backbone.View.extend({
     className: "phyloviz",
 
-    initialize: function(options) {
+    initialize: function (options) {
         var self = this;
         // -- Default values of the vis
         self.MIN_SCALE = 0.05; //for zooming
@@ -616,10 +606,10 @@ export var PhylovizView = Backbone.View.extend({
         // -- set up header buttons, search and settings menu
         self.navMenu = new HeaderButtons(self);
         self.settingsMenu = new SettingsMenu({
-            phyloTree: self.phyloTree
+            phyloTree: self.phyloTree,
         });
         self.nodeSelectionView = new NodeSelectionView({
-            phyloTree: self.phyloTree
+            phyloTree: self.phyloTree,
         });
         self.search = new PhyloVizSearch();
 
@@ -629,7 +619,7 @@ export var PhylovizView = Backbone.View.extend({
         }, 1000);
     },
 
-    render: function() {
+    render: function () {
         // -- Creating helper function for vis. --
         var self = this;
         $("#PhyloViz").empty();
@@ -662,7 +652,7 @@ export var PhylovizView = Backbone.View.extend({
             width: self.width,
             height: self.height,
             vis: self.vis,
-            margins: self.margins
+            margins: self.margins,
         };
 
         // -- Creating Title
@@ -676,7 +666,7 @@ export var PhylovizView = Backbone.View.extend({
      * Function to zoom and pan the svg element which the entire tree is contained within
      * Uses d3.zoom events, and extend them to allow manual updates and keeping states in model
      */
-    zoomAndPan: function(event) {
+    zoomAndPan: function (event) {
         var zoomParams;
         var translateParams;
         if (typeof event !== "undefined") {
@@ -739,26 +729,26 @@ export var PhylovizView = Backbone.View.extend({
     /**
      * Primes the Ajax URL to load another Nexus tree
      */
-    reloadViz: function() {
+    reloadViz: function () {
         var self = this;
         var treeIndex = $("#phylovizNexSelector :selected").val();
         $.getJSON(
             self.phyloTree.get("dataset").url(),
             {
                 tree_index: treeIndex,
-                data_type: "raw_data"
+                data_type: "raw_data",
             },
-            packedJson => {
+            (packedJson) => {
                 self.data = packedJson.data;
                 self.config = packedJson;
                 self.render();
             }
         );
-    }
+    },
 });
 
 var HeaderButtons = Backbone.View.extend({
-    initialize: function(phylovizView) {
+    initialize: function (phylovizView) {
         var self = this;
         self.phylovizView = phylovizView;
 
@@ -778,7 +768,7 @@ var HeaderButtons = Backbone.View.extend({
             });
     },
 
-    initRightHeaderBtns: function() {
+    initRightHeaderBtns: function () {
         var self = this;
 
         var rightMenu = mod_icon_btn.create_icon_buttons_menu(
@@ -786,46 +776,46 @@ var HeaderButtons = Backbone.View.extend({
                 {
                     icon_class: "gear",
                     title: _l("PhyloViz Settings"),
-                    on_click: function() {
+                    on_click: function () {
                         $("#SettingsMenu").show();
                         self.settingsMenu.updateUI();
-                    }
+                    },
                 },
                 {
                     icon_class: "disk",
                     title: _l("Save visualization"),
-                    on_click: function() {
+                    on_click: function () {
                         var nexSelected = $("#phylovizNexSelector option:selected").text();
                         if (nexSelected) {
                             self.phylovizView.phyloTree.set("title", nexSelected);
                         }
                         self.phylovizView.phyloTree.save();
-                    }
+                    },
                 },
                 {
                     icon_class: "chevron-expand",
                     title: "Search / Edit Nodes",
-                    on_click: function() {
+                    on_click: function () {
                         $("#nodeSelectionView").show();
-                    }
+                    },
                 },
                 {
                     icon_class: "information",
                     title: _l("Phyloviz Help"),
-                    on_click: function() {
+                    on_click: function () {
                         window.open("https://galaxyproject.org/learn/visualization/phylogenetic-tree/");
                         // https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs3EyMe1B1X_KFPouzIgrCz3zk/edit
-                    }
-                }
+                    },
+                },
             ],
             {
-                tooltip_config: { placement: "bottom" }
+                tooltip_config: { placement: "bottom" },
             }
         );
         $("#panelHeaderRightBtns").append(rightMenu.$el);
     },
 
-    initNavBtns: function() {
+    initNavBtns: function () {
         var self = this;
 
         var navMenu = mod_icon_btn.create_icon_buttons_menu(
@@ -833,40 +823,40 @@ var HeaderButtons = Backbone.View.extend({
                 {
                     icon_class: "zoom-in",
                     title: _l("Zoom in"),
-                    on_click: function() {
+                    on_click: function () {
                         self.phylovizView.zoomAndPan({ zoom: "+" });
-                    }
+                    },
                 },
                 {
                     icon_class: "zoom-out",
                     title: _l("Zoom out"),
-                    on_click: function() {
+                    on_click: function () {
                         self.phylovizView.zoomAndPan({ zoom: "-" });
-                    }
+                    },
                 },
                 {
                     icon_class: "arrow-circle",
                     title: "Reset Zoom/Pan",
-                    on_click: function() {
+                    on_click: function () {
                         self.phylovizView.zoomAndPan({
-                            zoom: "reset"
+                            zoom: "reset",
                         });
-                    }
-                }
+                    },
+                },
             ],
             {
-                tooltip_config: { placement: "bottom" }
+                tooltip_config: { placement: "bottom" },
             }
         );
 
         $("#phyloVizNavBtns").append(navMenu.$el);
-    }
+    },
 });
 
 var SettingsMenu = UserMenuBase.extend({
     className: "Settings",
 
-    initialize: function(options) {
+    initialize: function (options) {
         // settings needs to directly interact with the phyloviz model so it will get access to it.
         var self = this;
         self.phyloTree = options.phyloTree;
@@ -874,7 +864,7 @@ var SettingsMenu = UserMenuBase.extend({
         self.inputs = {
             separation: $("#phyloVizTreeSeparation"),
             leafHeight: $("#phyloVizTreeLeafHeight"),
-            fontSize: $("#phyloVizTreeFontSize")
+            fontSize: $("#phyloVizTreeFontSize"),
         };
 
         //init all buttons of settings
@@ -898,7 +888,7 @@ var SettingsMenu = UserMenuBase.extend({
     /**
      * Applying user values to phylotree model.
      */
-    apply: function() {
+    apply: function () {
         var self = this;
         if (
             !self.isAcceptableValue(self.inputs.separation, 50, 2500) ||
@@ -914,7 +904,7 @@ var SettingsMenu = UserMenuBase.extend({
     /**
      * Called to update the values input to that stored in the model
      */
-    updateUI: function() {
+    updateUI: function () {
         var self = this;
         $.each(self.inputs, (key, $input) => {
             $input.val(self.phyloTree.get(key));
@@ -923,7 +913,7 @@ var SettingsMenu = UserMenuBase.extend({
     /**
      * Resets the value of the phyloTree model to its default
      */
-    resetToDefaults: function() {
+    resetToDefaults: function () {
         $(".tooltip").remove(); // just in case the tool tip was not removed
         var self = this;
         $.each(self.phyloTree.defaults, (key, value) => {
@@ -932,7 +922,7 @@ var SettingsMenu = UserMenuBase.extend({
         self.updateUI();
     },
 
-    render: function() {}
+    render: function () {},
 });
 
 /**
@@ -941,7 +931,7 @@ var SettingsMenu = UserMenuBase.extend({
 var NodeSelectionView = UserMenuBase.extend({
     className: "Settings",
 
-    initialize: function(options) {
+    initialize: function (options) {
         var self = this;
         self.el = $("#nodeSelectionView");
         self.phyloTree = options.phyloTree;
@@ -952,14 +942,14 @@ var NodeSelectionView = UserMenuBase.extend({
             cancelChanges: $("#phylovizNodeCancelChanges"),
             name: $("#phyloVizSelectedNodeName"),
             dist: $("#phyloVizSelectedNodeDist"),
-            annotation: $("#phyloVizSelectedNodeAnnotation")
+            annotation: $("#phyloVizSelectedNodeAnnotation"),
         };
 
         // temporarily stores the values in case user change their mind
         self.valuesOfConcern = {
             name: null,
             dist: null,
-            annotation: null
+            annotation: null,
         };
 
         //init UI buttons
@@ -975,10 +965,10 @@ var NodeSelectionView = UserMenuBase.extend({
             self.cancelChanges();
         });
 
-        ($ => {
+        (($) => {
             // extending jquery fxn for enabling and disabling nodes.
-            $.fn.enable = function(isEnabled) {
-                return $(this).each(function() {
+            $.fn.enable = function (isEnabled) {
+                return $(this).each(function () {
                     if (isEnabled) {
                         $(this).removeAttr("disabled");
                     } else {
@@ -996,7 +986,7 @@ var NodeSelectionView = UserMenuBase.extend({
     /**
      * For turning on and off the child elements
      */
-    toggleUI: function() {
+    toggleUI: function () {
         var self = this;
         var checked = self.UI.enableEdit.is(":checked");
 
@@ -1019,7 +1009,7 @@ var NodeSelectionView = UserMenuBase.extend({
     /**
      * Reverting to previous values in case user change their minds
      */
-    cancelChanges: function() {
+    cancelChanges: function () {
         var self = this;
         var node = self.phyloTree.get("selectedNode");
         if (node) {
@@ -1032,7 +1022,7 @@ var NodeSelectionView = UserMenuBase.extend({
     /**
      * Changing the data in the underlying tree with user-specified values
      */
-    updateNodes: function() {
+    updateNodes: function () {
         var self = this;
         var node = self.phyloTree.get("selectedNode");
         if (node) {
@@ -1050,7 +1040,7 @@ var NodeSelectionView = UserMenuBase.extend({
         } else {
             alert("No node selected");
         }
-    }
+    },
 });
 
 /**
@@ -1058,15 +1048,13 @@ var NodeSelectionView = UserMenuBase.extend({
  * It allows user to search the entire free based on some qualifer, like dist <= val.
  */
 var PhyloVizSearch = UserMenuBase.extend({
-    initialize: function() {
+    initialize: function () {
         var self = this;
 
         $("#phyloVizSearchBtn").on("click", () => {
             var searchTerm = $("#phyloVizSearchTerm");
 
-            var searchConditionVal = $("#phyloVizSearchCondition")
-                .val()
-                .split("-");
+            var searchConditionVal = $("#phyloVizSearchCondition").val().split("-");
 
             var attr = searchConditionVal[0];
             var condition = searchConditionVal[1];
@@ -1082,8 +1070,8 @@ var PhyloVizSearch = UserMenuBase.extend({
     /**
      * Searches the entire tree and will highlight the nodes that match the condition in green
      */
-    searchTree: function(attr, condition, val) {
-        d3.selectAll("g.node").classed("searchHighlight", d => {
+    searchTree: function (attr, condition, val) {
+        d3.selectAll("g.node").classed("searchHighlight", (d) => {
             var attrVal = d[attr];
             if (typeof attrVal !== "undefined" && attrVal !== null) {
                 if (attr === "dist") {
@@ -1100,5 +1088,5 @@ var PhyloVizSearch = UserMenuBase.extend({
                 }
             }
         });
-    }
+    },
 });
diff --git a/client/galaxy/scripts/viz/sweepster.js b/client/galaxy/scripts/viz/sweepster.js
index 3e941e69ae61..8578d4812473 100644
--- a/client/galaxy/scripts/viz/sweepster.js
+++ b/client/galaxy/scripts/viz/sweepster.js
@@ -25,8 +25,8 @@ import { show_modal, hide_modal } from "layout/modal";
 var ToolInputsSettings = Backbone.Model.extend({
     defaults: {
         inputs: null,
-        values: null
-    }
+        values: null,
+    },
 });
 
 /**
@@ -35,19 +35,19 @@ var ToolInputsSettings = Backbone.Model.extend({
 var ToolParameterTree = Backbone.Model.extend({
     defaults: {
         tool: null,
-        tree_data: null
+        tree_data: null,
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         // Set up tool parameters to work with tree.
         var self = this;
         this.get("tool")
             .get("inputs")
-            .each(input => {
+            .each((input) => {
                 // Listen for changes to input's attributes.
                 input.on(
                     "change:min change:max change:num_samples",
-                    input => {
+                    (input) => {
                         if (input.get("in_ptree")) {
                             self.set_tree_data();
                         }
@@ -56,7 +56,7 @@ var ToolParameterTree = Backbone.Model.extend({
                 );
                 input.on(
                     "change:in_ptree",
-                    input => {
+                    (input) => {
                         if (input.get("in_ptree")) {
                             self.add_param(input);
                         } else {
@@ -70,18 +70,18 @@ var ToolParameterTree = Backbone.Model.extend({
 
         // If there is a config, use it.
         if (options.config) {
-            _.each(options.config, input_config => {
+            _.each(options.config, (input_config) => {
                 var input = self
                     .get("tool")
                     .get("inputs")
-                    .find(input => input.get("name") === input_config.name);
+                    .find((input) => input.get("name") === input_config.name);
                 self.add_param(input);
                 input.set(input_config);
             });
         }
     },
 
-    add_param: function(param) {
+    add_param: function (param) {
         // If parameter already present, do not add it.
         if (param.get("ptree_index")) {
             return;
@@ -91,7 +91,7 @@ var ToolParameterTree = Backbone.Model.extend({
         param.set("ptree_index", this.get_tree_params().length);
     },
 
-    remove_param: function(param) {
+    remove_param: function (param) {
         // Remove param from tree.
         param.set("in_ptree", false);
         param.set("ptree_index", null);
@@ -106,11 +106,11 @@ var ToolParameterTree = Backbone.Model.extend({
     /**
      * Sets tree data using tool's inputs.
      */
-    set_tree_data: function() {
+    set_tree_data: function () {
         // Get samples for each parameter.
-        var params_samples = _.map(this.get_tree_params(), param => ({
+        var params_samples = _.map(this.get_tree_params(), (param) => ({
             param: param,
-            samples: param.get_samples()
+            samples: param.get_samples(),
         }));
         var node_id = 0;
 
@@ -122,51 +122,47 @@ var ToolParameterTree = Backbone.Model.extend({
 
                 // Create leaves when last parameter setting is reached.
                 if (params_samples.length - 1 === index) {
-                    return _.map(settings, setting => ({
+                    return _.map(settings, (setting) => ({
                         id: node_id++,
                         name: setting,
                         param: param,
-                        value: setting
+                        value: setting,
                     }));
                 }
 
                 // Recurse to handle other parameters.
-                return _.map(settings, setting => ({
+                return _.map(settings, (setting) => ({
                     id: node_id++,
                     name: setting,
                     param: param,
                     value: setting,
-                    children: create_tree_data(params_samples, index + 1)
+                    children: create_tree_data(params_samples, index + 1),
                 }));
             };
 
         this.set("tree_data", {
             name: "Root",
             id: node_id++,
-            children: params_samples.length !== 0 ? create_tree_data(params_samples, 0) : null
+            children: params_samples.length !== 0 ? create_tree_data(params_samples, 0) : null,
         });
     },
 
-    get_tree_params: function() {
+    get_tree_params: function () {
         // Filter and sort parameters to get list in tree.
-        return _(
-            this.get("tool")
-                .get("inputs")
-                .where({ in_ptree: true })
-        ).sortBy(input => input.get("ptree_index"));
+        return _(this.get("tool").get("inputs").where({ in_ptree: true })).sortBy((input) => input.get("ptree_index"));
     },
 
     /**
      * Returns number of leaves in tree.
      */
-    get_num_leaves: function() {
+    get_num_leaves: function () {
         return this.get_tree_params().reduce((memo, param) => memo * param.get_samples().length, 1);
     },
 
     /**
      * Returns array of ToolInputsSettings objects based on a node and its subtree.
      */
-    get_node_settings: function(target_node) {
+    get_node_settings: function (target_node) {
         // -- Get fixed settings from tool and parent nodes.
 
         // Start with tool's settings.
@@ -195,11 +191,11 @@ var ToolParameterTree = Backbone.Model.extend({
                 // At leaf node, so return settings.
                 return new ToolInputsSettings({
                     inputs: self.get("tool").get("inputs"),
-                    values: settings
+                    values: settings,
                 });
             } else {
                 // At interior node: return list of subtree settings.
-                return _.flatten(_.map(node.children, c => get_settings(c, _.clone(settings))));
+                return _.flatten(_.map(node.children, (c) => get_settings(c, _.clone(settings))));
             }
         };
 
@@ -216,13 +212,13 @@ var ToolParameterTree = Backbone.Model.extend({
     /**
      * Returns all nodes connected a particular node; this includes parents and children of the node.
      */
-    get_connected_nodes: function(node) {
-        var get_subtree_nodes = a_node => {
+    get_connected_nodes: function (node) {
+        var get_subtree_nodes = (a_node) => {
             if (!a_node.children) {
                 return a_node;
             } else {
                 // At interior node: return subtree nodes.
-                return _.flatten([a_node, _.map(a_node.children, c => get_subtree_nodes(c))]);
+                return _.flatten([a_node, _.map(a_node.children, (c) => get_subtree_nodes(c))]);
             }
         };
 
@@ -241,10 +237,10 @@ var ToolParameterTree = Backbone.Model.extend({
     /**
      * Returns the leaf that corresponds to a settings collection.
      */
-    get_leaf: function(settings) {
+    get_leaf: function (settings) {
         var cur_node = this.get("tree_data");
 
-        var find_child = children => _.find(children, child => settings[child.param.get("name")] === child.value);
+        var find_child = (children) => _.find(children, (child) => settings[child.param.get("name")] === child.value);
 
         while (cur_node.children) {
             cur_node = find_child(cur_node.children);
@@ -255,16 +251,16 @@ var ToolParameterTree = Backbone.Model.extend({
     /**
      * Returns a list of parameters used in tree.
      */
-    toJSON: function() {
+    toJSON: function () {
         // FIXME: returning and jsonifying complete param causes trouble on the server side,
         // so just use essential attributes for now.
-        return this.get_tree_params().map(param => ({
+        return this.get_tree_params().map((param) => ({
             name: param.get("name"),
             min: param.get("min"),
             max: param.get("max"),
-            num_samples: param.get("num_samples")
+            num_samples: param.get("num_samples"),
         }));
-    }
+    },
 });
 
 var SweepsterTrack = Backbone.Model.extend({
@@ -272,17 +268,17 @@ var SweepsterTrack = Backbone.Model.extend({
         track: null,
         mode: "Pack",
         settings: null,
-        regions: null
+        regions: null,
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.set("regions", options.regions);
         if (options.track) {
             // FIXME: find a better way to deal with needed URLs:
             var track_config = _.extend(
                 {
                     data_url: `${getAppRoot()}dummy1`,
-                    converted_datasets_state_url: `${getAppRoot()}dummy2`
+                    converted_datasets_state_url: `${getAppRoot()}dummy2`,
                 },
                 options.track
             );
@@ -290,7 +286,7 @@ var SweepsterTrack = Backbone.Model.extend({
         }
     },
 
-    same_settings: function(a_track) {
+    same_settings: function (a_track) {
         var this_settings = this.get("settings");
         var other_settings = a_track.get("settings");
         for (var prop in this_settings) {
@@ -301,17 +297,17 @@ var SweepsterTrack = Backbone.Model.extend({
         return true;
     },
 
-    toJSON: function() {
+    toJSON: function () {
         return {
             track: this.get("track").to_dict(),
             settings: this.get("settings"),
-            regions: this.get("regions")
+            regions: this.get("regions"),
         };
-    }
+    },
 });
 
 var TrackCollection = Backbone.Collection.extend({
-    model: SweepsterTrack
+    model: SweepsterTrack,
 });
 
 /**
@@ -324,10 +320,10 @@ export var SweepsterVisualization = visualization.Visualization.extend({
         parameter_tree: null,
         regions: null,
         tracks: null,
-        default_mode: "Pack"
+        default_mode: "Pack",
     }),
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.set("dataset", new Dataset(options.dataset));
         this.set("tool", new tools.Tool(options.tool));
         this.set("regions", new visualization.GenomeRegionCollection(options.regions));
@@ -342,16 +338,16 @@ export var SweepsterVisualization = visualization.Visualization.extend({
             "parameter_tree",
             new ToolParameterTree({
                 tool: tool_with_samplable_inputs,
-                config: options.tree_config
+                config: options.tree_config,
             })
         );
     },
 
-    add_track: function(track) {
+    add_track: function (track) {
         this.get("tracks").add(track);
     },
 
-    toJSON: function() {
+    toJSON: function () {
         return {
             id: this.get("id"),
             title: `Parameter exploration for dataset '${this.get("dataset").get("name")}'`,
@@ -360,9 +356,9 @@ export var SweepsterVisualization = visualization.Visualization.extend({
             tool_id: this.get("tool").id,
             regions: this.get("regions").toJSON(),
             tree_config: this.get("parameter_tree").toJSON(),
-            tracks: this.get("tracks").toJSON()
+            tracks: this.get("tracks").toJSON(),
         };
-    }
+    },
 });
 
 /**
@@ -377,34 +373,25 @@ var SweepsterTrackView = Backbone.View.extend({
 
     TILE_LEN: 250,
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.canvas_manager = options.canvas_manager;
         this.render();
         this.model.on("change:track change:mode", this.draw_tiles, this);
     },
 
-    render: function() {
+    render: function () {
         // Render settings icon and popup.
         // TODO: use template.
         var settings = this.model.get("settings");
 
         var values = settings.get("values");
 
-        var settings_td = $("<td/>")
-            .addClass("settings")
-            .appendTo(this.$el);
+        var settings_td = $("<td/>").addClass("settings").appendTo(this.$el);
 
-        var settings_div = $("<div/>")
-            .addClass("track-info")
-            .hide()
-            .appendTo(settings_td);
+        var settings_div = $("<div/>").addClass("track-info").hide().appendTo(settings_td);
 
-        settings_div.append(
-            $("<div/>")
-                .css("font-weight", "bold")
-                .text("Track Settings")
-        );
-        settings.get("inputs").each(input => {
+        settings_div.append($("<div/>").css("font-weight", "bold").text("Track Settings"));
+        settings.get("inputs").each((input) => {
             settings_div.append(`${input.get("label")}: ${values[input.get("name")]}<br/>`);
         });
         var self = this;
@@ -421,19 +408,19 @@ var SweepsterTrackView = Backbone.View.extend({
             {
                 title: _l("Settings"),
                 icon_class: "gear track-settings",
-                on_click: function() {
+                on_click: function () {
                     settings_div.toggle();
-                }
+                },
             },
             {
                 title: _l("Remove"),
                 icon_class: "cross-circle",
-                on_click: function() {
+                on_click: function () {
                     self.$el.remove();
                     $(".tooltip").remove();
                     // TODO: remove track from viz collection.
-                }
-            }
+                },
+            },
         ]);
         settings_td.prepend(icon_menu.$el);
 
@@ -454,7 +441,7 @@ var SweepsterTrackView = Backbone.View.extend({
     /**
      * Draw tiles for regions.
      */
-    draw_tiles: function() {
+    draw_tiles: function () {
         var self = this;
         var track = this.model.get("track");
         var regions = this.model.get("regions");
@@ -466,24 +453,22 @@ var SweepsterTrackView = Backbone.View.extend({
         }
 
         // When data is ready, draw tiles.
-        $.when(track.data_manager.data_is_ready()).then(data_ok => {
+        $.when(track.data_manager.data_is_ready()).then((data_ok) => {
             // Draw tile for each region.
             regions.each((region, index) => {
                 var resolution = region.length() / self.TILE_LEN;
                 var w_scale = 1 / resolution;
                 var mode = self.model.get("mode");
-                $.when(track.data_manager.get_data(region, mode, resolution, {})).then(tile_data => {
+                $.when(track.data_manager.get_data(region, mode, resolution, {})).then((tile_data) => {
                     var canvas = self.canvas_manager.new_canvas();
                     canvas.width = self.TILE_LEN;
                     canvas.height = track.get_canvas_height(tile_data, mode, w_scale, canvas.width);
                     track.draw_tile(tile_data, canvas.getContext("2d"), mode, region, w_scale);
-                    $(tile_containers[index])
-                        .empty()
-                        .append(canvas);
+                    $(tile_containers[index]).empty().append(canvas);
                 });
             });
         });
-    }
+    },
 });
 
 /**
@@ -501,18 +486,18 @@ var ToolInputValOrSweepView = Backbone.View.extend({
 
     select_input_template: '<div class="form-row-input sweep"><%= options %></div>',
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.$el = options.tool_row;
         this.render();
     },
 
-    render: function() {
+    render: function () {
         var input = this.model;
         var single_input_row = this.$el.find(".form-row-input");
         var sweep_inputs_row = null;
 
         // Update tool inputs as single input changes.
-        single_input_row.find(":input").change(function() {
+        single_input_row.find(":input").change(function () {
             input.set("value", $(this).val());
         });
 
@@ -520,12 +505,12 @@ var ToolInputValOrSweepView = Backbone.View.extend({
         if (input instanceof tools.IntegerToolParameter) {
             sweep_inputs_row = $(_.template(this.number_input_template)(this.model.toJSON()));
         } else if (input instanceof tools.SelectToolParameter) {
-            var options = _.map(this.$el.find("select option"), option => $(option).val());
+            var options = _.map(this.$el.find("select option"), (option) => $(option).val());
 
             var options_text = options.join(", ");
             sweep_inputs_row = $(
                 _.template(this.select_input_template)({
-                    options: options_text
+                    options: options_text,
                 })
             );
         }
@@ -539,26 +524,26 @@ var ToolInputValOrSweepView = Backbone.View.extend({
                 {
                     title: _l("Add parameter to tree"),
                     icon_class: "plus-button",
-                    on_click: function() {
+                    on_click: function () {
                         input.set("in_ptree", true);
                         single_input_row.hide();
                         sweep_inputs_row.show();
                         $(this).hide();
                         self.$el.find(".icon-button.toggle").show();
-                    }
+                    },
                 },
                 {
                     title: _l("Remove parameter from tree"),
                     icon_class: "toggle",
-                    on_click: function() {
+                    on_click: function () {
                         // Remove parameter from tree params where name matches clicked paramter.
                         input.set("in_ptree", false);
                         sweep_inputs_row.hide();
                         single_input_row.show();
                         $(this).hide();
                         self.$el.find(".icon-button.plus-button").show();
-                    }
-                }
+                    },
+                },
             ],
             {}
         );
@@ -575,25 +560,25 @@ var ToolInputValOrSweepView = Backbone.View.extend({
         }
 
         // Update input's min, max, number of samples as values change.
-        _.each(["min", "max", "num_samples"], attr => {
-            sweep_inputs_row.find(`.${attr}`).change(function() {
+        _.each(["min", "max", "num_samples"], (attr) => {
+            sweep_inputs_row.find(`.${attr}`).change(function () {
                 input.set(attr, parseFloat($(this).val()));
             });
         });
-    }
+    },
 });
 
 var ToolParameterTreeDesignView = Backbone.View.extend({
     className: "tree-design",
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.render();
     },
 
-    render: function() {
+    render: function () {
         // Start with tool form view.
         var tool_form_view = new tools.ToolFormView({
-            model: this.model.get("tool")
+            model: this.model.get("tool"),
         });
         tool_form_view.render();
         this.$el.append(tool_form_view.$el);
@@ -605,13 +590,13 @@ var ToolParameterTreeDesignView = Backbone.View.extend({
         this.$el
             .find(".form-row")
             .not(".form-actions")
-            .each(function(i) {
+            .each(function (i) {
                 new ToolInputValOrSweepView({
                     model: inputs.at(i),
-                    tool_row: $(this)
+                    tool_row: $(this),
                 });
             });
-    }
+    },
 });
 
 /**
@@ -620,12 +605,12 @@ var ToolParameterTreeDesignView = Backbone.View.extend({
 var ToolParameterTreeView = Backbone.View.extend({
     className: "tool-parameter-tree",
 
-    initialize: function(options) {
+    initialize: function (options) {
         // When tree data changes, re-render.
         this.model.on("change:tree_data", this.render, this);
     },
 
-    render: function() {
+    render: function () {
         // Start fresh.
         this.$el.children().remove();
 
@@ -643,7 +628,7 @@ var ToolParameterTreeView = Backbone.View.extend({
         // Layout tree.
         var cluster = d3.layout.cluster().size([this.height, this.width - 160]);
 
-        var diagonal = d3.svg.diagonal().projection(d => [d.y, d.x]);
+        var diagonal = d3.svg.diagonal().projection((d) => [d.y, d.x]);
 
         // Layout nodes.
         var nodes = cluster.nodes(this.model.get("tree_data"));
@@ -685,11 +670,11 @@ var ToolParameterTreeView = Backbone.View.extend({
             .enter()
             .append("g")
             .attr("class", "node")
-            .attr("transform", d => `translate(${d.y},${d.x})`)
-            .on("mouseover", a_node => {
+            .attr("transform", (d) => `translate(${d.y},${d.x})`)
+            .on("mouseover", (a_node) => {
                 var connected_node_ids = _.pluck(self.model.get_connected_nodes(a_node), "id");
                 // TODO: probably can use enter() to do this more easily.
-                node.filter(d => _.find(connected_node_ids, id => id === d.id) !== undefined).style("fill", "#f00");
+                node.filter((d) => _.find(connected_node_ids, (id) => id === d.id) !== undefined).style("fill", "#f00");
             })
             .on("mouseout", () => {
                 node.style("fill", "#000");
@@ -698,11 +683,11 @@ var ToolParameterTreeView = Backbone.View.extend({
         node.append("circle").attr("r", 9);
 
         node.append("text")
-            .attr("dx", d => (d.children ? -12 : 12))
+            .attr("dx", (d) => (d.children ? -12 : 12))
             .attr("dy", 3)
-            .attr("text-anchor", d => (d.children ? "end" : "start"))
-            .text(d => d.name);
-    }
+            .attr("text-anchor", (d) => (d.children ? "end" : "start"))
+            .text((d) => d.name);
+    },
 });
 
 /**
@@ -718,10 +703,10 @@ export var SweepsterVisualizationView = Backbone.View.extend({
         "<li>Run the tool with different settings by clicking on tree nodes" +
         "</ol></div>",
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.canvas_manager = new visualization.CanvasManager(this.$el.parents("body"));
         this.tool_param_tree_view = new ToolParameterTreeView({
-            model: this.model.get("parameter_tree")
+            model: this.model.get("parameter_tree"),
         });
         this.track_collection_container = $("<table/>").addClass("tracks");
 
@@ -730,7 +715,7 @@ export var SweepsterVisualizationView = Backbone.View.extend({
 
         // Each track must have a view so it has a canvas manager.
         var self = this;
-        this.model.get("tracks").each(track => {
+        this.model.get("tracks").each((track) => {
             track.get("track").view = self;
         });
 
@@ -741,57 +726,57 @@ export var SweepsterVisualizationView = Backbone.View.extend({
                     key: "name",
                     label: "Name",
                     type: "text",
-                    default_value: ""
+                    default_value: "",
                 },
                 {
                     key: "a_color",
                     label: "A Color",
                     type: "color",
-                    default_value: "#FF0000"
+                    default_value: "#FF0000",
                 },
                 {
                     key: "c_color",
                     label: "C Color",
                     type: "color",
-                    default_value: "#00FF00"
+                    default_value: "#00FF00",
                 },
                 {
                     key: "g_color",
                     label: "G Color",
                     type: "color",
-                    default_value: "#0000FF"
+                    default_value: "#0000FF",
                 },
                 {
                     key: "t_color",
                     label: "T Color",
                     type: "color",
-                    default_value: "#FF00FF"
+                    default_value: "#FF00FF",
                 },
                 {
                     key: "n_color",
                     label: "N Color",
                     type: "color",
-                    default_value: "#AAAAAA"
+                    default_value: "#AAAAAA",
                 },
                 {
                     key: "block_color",
                     label: "Block color",
-                    type: "color"
+                    type: "color",
                 },
                 {
                     key: "reverse_strand_color",
                     label: "Antisense strand color",
-                    type: "color"
-                }
+                    type: "color",
+                },
             ],
             {}
         );
     },
 
-    render: function() {
+    render: function () {
         // Render tree design view in left panel.
         var tree_design_view = new ToolParameterTreeDesignView({
-            model: this.model.get("parameter_tree")
+            model: this.model.get("parameter_tree"),
         });
 
         $("#left").append(tree_design_view.$el);
@@ -802,17 +787,15 @@ export var SweepsterVisualizationView = Backbone.View.extend({
         var regions = self.model.get("regions");
         var tr = $("<tr/>").appendTo(this.track_collection_container);
 
-        regions.each(region => {
+        regions.each((region) => {
             tr.append($("<th>").text(region.toString()));
         });
-        tr.children()
-            .first()
-            .attr("colspan", 2);
+        tr.children().first().attr("colspan", 2);
 
         var tracks_div = $("<div>").addClass("tiles");
         $("#right").append(tracks_div.append(this.track_collection_container));
 
-        self.model.get("tracks").each(track => {
+        self.model.get("tracks").each((track) => {
             self.add_track(track);
         });
 
@@ -825,11 +808,11 @@ export var SweepsterVisualizationView = Backbone.View.extend({
             {
                 title: _l("Close"),
                 icon_class: "cross-circle",
-                on_click: function() {
+                on_click: function () {
                     $(".tooltip").remove();
                     help_div.remove();
-                }
-            }
+                },
+            },
         ]);
 
         help_div.prepend(close_button.$el.css("float", "right"));
@@ -867,19 +850,19 @@ export var SweepsterVisualizationView = Backbone.View.extend({
                 // Change track modes.
                 {
                     icon_class: "chevron-expand",
-                    title: "Set display mode"
+                    title: "Set display mode",
                 },
                 // Close viz.
                 {
                     icon_class: "cross-circle",
                     title: _l("Close"),
-                    on_click: function() {
+                    on_click: function () {
                         window.top.location = `${getAppRoot()}visualizations/list`;
-                    }
-                }
+                    },
+                },
             ],
             {
-                tooltip_config: { placement: "bottom" }
+                tooltip_config: { placement: "bottom" },
             }
         );
 
@@ -887,10 +870,10 @@ export var SweepsterVisualizationView = Backbone.View.extend({
         var modes = ["Squish", "Pack"];
 
         var mode_mapping = {};
-        _.each(modes, mode => {
+        _.each(modes, (mode) => {
             mode_mapping[mode] = () => {
                 self.model.set("default_mode", mode);
-                self.model.get("tracks").each(track => {
+                self.model.get("tracks").each((track) => {
                     track.set("mode", mode);
                 });
             };
@@ -902,16 +885,16 @@ export var SweepsterVisualizationView = Backbone.View.extend({
         $("#right .unified-panel-header-inner").append(menu.$el);
     },
 
-    get_base_color: function(base) {
+    get_base_color: function (base) {
         return this.config.get_value(`${base.toLowerCase()}_color`) || this.config.get_value("n_color");
     },
 
-    run_tool_on_dataset: function(settings) {
+    run_tool_on_dataset: function (settings) {
         var tool = this.model.get("tool");
         var tool_name = tool.get("name");
         var dataset = this.model.get("dataset");
         tool.set_input_values(settings.get("values"));
-        $.when(tool.rerun(dataset)).then(outputs => {
+        $.when(tool.rerun(dataset)).then((outputs) => {
             // TODO.
         });
 
@@ -919,9 +902,9 @@ export var SweepsterVisualizationView = Backbone.View.extend({
             `Running ${tool_name} on complete dataset`,
             `${tool_name} is running on dataset '${dataset.get("name")}'. Outputs are in the dataset's history.`,
             {
-                Ok: function() {
+                Ok: function () {
                     hide_modal();
-                }
+                },
             }
         );
     },
@@ -929,7 +912,7 @@ export var SweepsterVisualizationView = Backbone.View.extend({
     /**
      * Add track to model and view.
      */
-    add_track: function(pm_track) {
+    add_track: function (pm_track) {
         var self = this;
         var param_tree = this.model.get("parameter_tree");
 
@@ -938,7 +921,7 @@ export var SweepsterVisualizationView = Backbone.View.extend({
 
         var track_view = new SweepsterTrackView({
             model: pm_track,
-            canvas_manager: self.canvas_manager
+            canvas_manager: self.canvas_manager,
         });
         track_view.on("run_on_dataset", self.run_tool_on_dataset, self);
         self.track_collection_container.append(track_view.$el);
@@ -950,13 +933,11 @@ export var SweepsterVisualizationView = Backbone.View.extend({
                 // TODO: can do faster with enter?
                 d3.select(self.tool_param_tree_view.$el[0])
                     .selectAll("g.node")
-                    .filter(d => _.find(connected_node_ids, id => id === d.id) !== undefined)
+                    .filter((d) => _.find(connected_node_ids, (id) => id === d.id) !== undefined)
                     .style("fill", "#f00");
             },
             () => {
-                d3.select(self.tool_param_tree_view.$el[0])
-                    .selectAll("g.node")
-                    .style("fill", "#000");
+                d3.select(self.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill", "#000");
             }
         );
         return pm_track;
@@ -966,7 +947,7 @@ export var SweepsterVisualizationView = Backbone.View.extend({
      * Sets up handling when tree nodes are clicked. When a node is clicked, the tool is run for each of
      * the settings defined by the node's subtree and tracks are added for each run.
      */
-    handle_node_clicks: function() {
+    handle_node_clicks: function () {
         // When node clicked in tree, run tool and add tracks to model.
         var self = this;
 
@@ -991,10 +972,10 @@ export var SweepsterVisualizationView = Backbone.View.extend({
                         all_settings.length
                     } different combinations of settings. You can only run 10 jobs at a time.`,
                     {
-                        Ok: function() {
+                        Ok: function () {
                             hide_modal();
                             run_jobs_deferred.resolve(false);
-                        }
+                        },
                     }
                 );
             } else {
@@ -1002,17 +983,17 @@ export var SweepsterVisualizationView = Backbone.View.extend({
             }
 
             // Take action when deferred resolves.
-            $.when(run_jobs_deferred).then(run_jobs => {
+            $.when(run_jobs_deferred).then((run_jobs) => {
                 if (!run_jobs) {
                     return;
                 }
 
                 // Create and add tracks for each settings group.
-                var new_tracks = _.map(all_settings, settings => {
+                var new_tracks = _.map(all_settings, (settings) => {
                     var pm_track = new SweepsterTrack({
                         settings: settings,
                         regions: regions,
-                        mode: self.model.get("default_mode")
+                        mode: self.model.get("default_mode"),
                     });
                     self.add_track(pm_track);
                     return pm_track;
@@ -1023,7 +1004,7 @@ export var SweepsterVisualizationView = Backbone.View.extend({
                     setTimeout(() => {
                         // Set inputs and run tool.
                         tool.set_input_values(pm_track.get("settings").get("values"));
-                        $.when(tool.rerun(dataset, regions)).then(output => {
+                        $.when(tool.rerun(dataset, regions)).then((output) => {
                             // HACKish: output is an HDA with track config attribute. To create a track
                             // that works correctly with Backbone relational, it is necessary to
                             // use a modified version of the track config.
@@ -1048,5 +1029,5 @@ export var SweepsterVisualizationView = Backbone.View.extend({
                 });
             });
         });
-    }
+    },
 });
diff --git a/client/galaxy/scripts/viz/tools.js b/client/galaxy/scripts/viz/tools.js
index 106ab01bdaac..53799f0f5971 100644
--- a/client/galaxy/scripts/viz/tools.js
+++ b/client/galaxy/scripts/viz/tools.js
@@ -15,21 +15,21 @@ import { DatasetCollection } from "mvc/dataset/data";
 var VisibilityMixin = {
     hidden: false,
 
-    show: function() {
+    show: function () {
         this.set("hidden", false);
     },
 
-    hide: function() {
+    hide: function () {
         this.set("hidden", true);
     },
 
-    toggle: function() {
+    toggle: function () {
         this.set("hidden", !this.get("hidden"));
     },
 
-    is_visible: function() {
+    is_visible: function () {
         return !this.attributes.hidden;
-    }
+    },
 };
 
 /**
@@ -42,24 +42,24 @@ var ToolParameter = Backbone.Model.extend({
         type: null,
         value: null,
         html: null,
-        num_samples: 5
+        num_samples: 5,
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.attributes.html = unescape(this.attributes.html);
     },
 
-    copy: function() {
+    copy: function () {
         return new ToolParameter(this.toJSON());
     },
 
-    set_value: function(value) {
+    set_value: function (value) {
         this.set("value", value || "");
-    }
+    },
 });
 
 var ToolParameterCollection = Backbone.Collection.extend({
-    model: ToolParameter
+    model: ToolParameter,
 });
 
 /**
@@ -71,25 +71,25 @@ var DataToolParameter = ToolParameter.extend({});
  * An integer tool parameter.
  */
 var IntegerToolParameter = ToolParameter.extend({
-    set_value: function(value) {
+    set_value: function (value) {
         this.set("value", parseInt(value, 10));
     },
 
     /**
      * Returns samples from a tool input.
      */
-    get_samples: function() {
+    get_samples: function () {
         return d3.scale
             .linear()
             .domain([this.get("min"), this.get("max")])
             .ticks(this.get("num_samples"));
-    }
+    },
 });
 
 var FloatToolParameter = IntegerToolParameter.extend({
-    set_value: function(value) {
+    set_value: function (value) {
         this.set("value", parseFloat(value));
-    }
+    },
 });
 
 /**
@@ -99,9 +99,9 @@ var SelectToolParameter = ToolParameter.extend({
     /**
      * Returns tool options.
      */
-    get_samples: function() {
-        return _.map(this.get("options"), option => option[0]);
-    }
+    get_samples: function () {
+        return _.map(this.get("options"), (option) => option[0]);
+    },
 });
 
 // Set up dictionary of parameter types.
@@ -109,7 +109,7 @@ ToolParameter.subModelTypes = {
     integer: IntegerToolParameter,
     float: FloatToolParameter,
     data: DataToolParameter,
-    select: SelectToolParameter
+    select: SelectToolParameter,
 };
 
 /**
@@ -123,17 +123,17 @@ var Tool = Backbone.Model.extend({
         description: null,
         target: null,
         inputs: [],
-        outputs: []
+        outputs: [],
     },
 
     urlRoot: `${getAppRoot()}api/tools`,
 
-    initialize: function(options) {
+    initialize: function (options) {
         // Set parameters.
         this.set(
             "inputs",
             new ToolParameterCollection(
-                _.map(options.inputs, p => {
+                _.map(options.inputs, (p) => {
                     var p_class = ToolParameter.subModelTypes[p.type] || ToolParameter;
                     return new p_class(p);
                 })
@@ -144,11 +144,11 @@ var Tool = Backbone.Model.extend({
     /**
      *
      */
-    toJSON: function() {
+    toJSON: function () {
         var rval = Backbone.Model.prototype.toJSON.call(this);
 
         // Convert inputs to JSON manually.
-        rval.inputs = this.get("inputs").map(i => i.toJSON());
+        rval.inputs = this.get("inputs").map((i) => i.toJSON());
         return rval;
     },
 
@@ -156,10 +156,10 @@ var Tool = Backbone.Model.extend({
      * Removes inputs of a particular type; this is useful because not all inputs can be handled by
      * client and server yet.
      */
-    remove_inputs: function(types) {
+    remove_inputs: function (types) {
         var tool = this;
 
-        var incompatible_inputs = tool.get("inputs").filter(input => types.indexOf(input.get("type")) !== -1);
+        var incompatible_inputs = tool.get("inputs").filter((input) => types.indexOf(input.get("type")) !== -1);
 
         tool.get("inputs").remove(incompatible_inputs);
     },
@@ -167,13 +167,13 @@ var Tool = Backbone.Model.extend({
     /**
      * Returns object copy, optionally including only inputs that can be sampled.
      */
-    copy: function(only_samplable_inputs) {
+    copy: function (only_samplable_inputs) {
         var copy = new Tool(this.toJSON());
 
         // Return only samplable inputs if flag is set.
         if (only_samplable_inputs) {
             var valid_inputs = new Backbone.Collection();
-            copy.get("inputs").each(input => {
+            copy.get("inputs").each((input) => {
                 if (input.get_samples()) {
                     valid_inputs.push(input);
                 }
@@ -184,7 +184,7 @@ var Tool = Backbone.Model.extend({
         return copy;
     },
 
-    apply_search_results: function(results) {
+    apply_search_results: function (results) {
         _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide();
         return this.is_visible();
     },
@@ -192,18 +192,18 @@ var Tool = Backbone.Model.extend({
     /**
      * Set a tool input's value.
      */
-    set_input_value: function(name, value) {
+    set_input_value: function (name, value) {
         this.get("inputs")
-            .find(input => input.get("name") === name)
+            .find((input) => input.get("name") === name)
             .set("value", value);
     },
 
     /**
      * Set many input values at once.
      */
-    set_input_values: function(inputs_dict) {
+    set_input_values: function (inputs_dict) {
         var self = this;
-        _.each(_.keys(inputs_dict), input_name => {
+        _.each(_.keys(inputs_dict), (input_name) => {
             self.set_input_value(input_name, inputs_dict[input_name]);
         });
     },
@@ -211,27 +211,27 @@ var Tool = Backbone.Model.extend({
     /**
      * Run tool; returns a Deferred that resolves to the tool's output(s).
      */
-    run: function() {
+    run: function () {
         return this._run();
     },
 
     /**
      * Rerun tool using regions and a target dataset.
      */
-    rerun: function(target_dataset, regions) {
+    rerun: function (target_dataset, regions) {
         return this._run({
             action: "rerun",
             target_dataset_id: target_dataset.id,
-            regions: regions
+            regions: regions,
         });
     },
 
     /**
      * Returns input dict for tool's inputs.
      */
-    get_inputs_dict: function() {
+    get_inputs_dict: function () {
         var input_dict = {};
-        this.get("inputs").each(input => {
+        this.get("inputs").each((input) => {
             input_dict[input.get("name")] = input.get("value");
         });
         return input_dict;
@@ -241,12 +241,12 @@ var Tool = Backbone.Model.extend({
      * Run tool; returns a Deferred that resolves to the tool's output(s).
      * NOTE: this method is a helper method and should not be called directly.
      */
-    _run: function(additional_params) {
+    _run: function (additional_params) {
         // Create payload.
         var payload = _.extend(
             {
                 tool_id: this.id,
-                inputs: this.get_inputs_dict()
+                inputs: this.get_inputs_dict(),
             },
             additional_params
         );
@@ -262,20 +262,20 @@ var Tool = Backbone.Model.extend({
                 data: JSON.stringify(payload),
                 dataType: "json",
                 contentType: "application/json",
-                type: "POST"
+                type: "POST",
             },
             interval: 2000,
-            success_fn: function(response) {
+            success_fn: function (response) {
                 return response !== "pending";
-            }
+            },
         });
 
         // Run job and resolve run_deferred to tool outputs.
-        $.when(ss_deferred.go()).then(result => {
+        $.when(ss_deferred.go()).then((result) => {
             run_deferred.resolve(new DatasetCollection(result));
         });
         return run_deferred;
-    }
+    },
 });
 _.extend(Tool.prototype, VisibilityMixin);
 
@@ -285,10 +285,10 @@ _.extend(Tool.prototype, VisibilityMixin);
 var ToolFormView = Backbone.View.extend({
     className: "toolForm",
 
-    render: function() {
+    render: function () {
         this.$el.children().remove();
         this.$el.append(templates.tool_form(this.model.toJSON()));
-    }
+    },
 });
 
 // TODO: move into relevant views
@@ -317,12 +317,12 @@ var templates = {
             "</div>",
             '<div class="toolHelp">',
             '<div class="toolHelpBody"><% tool.help %></div>',
-            "</div>"
+            "</div>",
             // TODO: we need scoping here because 'help' is the dom for the help menu in the masthead
             // which implies a leaky variable that I can't find
         ].join(""),
         { variable: "tool" }
-    )
+    ),
 };
 
 // Exports
@@ -331,5 +331,5 @@ export default {
     IntegerToolParameter: IntegerToolParameter,
     SelectToolParameter: SelectToolParameter,
     Tool: Tool,
-    ToolFormView: ToolFormView
+    ToolFormView: ToolFormView,
 };
diff --git a/client/galaxy/scripts/viz/trackster.js b/client/galaxy/scripts/viz/trackster.js
index a1ee47b9ef7b..98c82c1418b3 100644
--- a/client/galaxy/scripts/viz/trackster.js
+++ b/client/galaxy/scripts/viz/trackster.js
@@ -54,12 +54,8 @@ export class TracksterUI extends Backbone.Model {
         var bookmarks = [];
         $(".bookmark").each(() => {
             bookmarks.push({
-                position: $(this)
-                    .children(".position")
-                    .text(),
-                annotation: $(this)
-                    .children(".annotation")
-                    .text()
+                position: $(this).children(".position").text(),
+                annotation: $(this).children(".annotation").text(),
             });
         });
 
@@ -74,9 +70,9 @@ export class TracksterUI extends Backbone.Model {
                 chrom: this.view.chrom,
                 start: this.view.low,
                 end: this.view.high,
-                overview: overview_track_name
+                overview: overview_track_name,
             },
-            bookmarks: bookmarks
+            bookmarks: bookmarks,
         };
 
         // Make call to save visualization.
@@ -89,10 +85,10 @@ export class TracksterUI extends Backbone.Model {
                 title: this.view.config.get_value("name"),
                 dbkey: this.view.dbkey,
                 type: "trackster",
-                vis_json: JSON.stringify(viz_config)
-            }
+                vis_json: JSON.stringify(viz_config),
+            },
         })
-            .success(vis_info => {
+            .success((vis_info) => {
                 Galaxy.modal.hide();
                 this.view.vis_id = vis_info.vis_id;
                 this.view.has_changes = false;
@@ -108,8 +104,8 @@ export class TracksterUI extends Backbone.Model {
                     buttons: {
                         Cancel: () => {
                             Galaxy.modal.hide();
-                        }
-                    }
+                        },
+                    },
                 });
             });
     }
@@ -124,12 +120,12 @@ export class TracksterUI extends Backbone.Model {
                     icon_class: "plus-button",
                     title: _l("Add tracks"),
                     on_click: () => {
-                        visualization.select_datasets({ dbkey: this.view.dbkey }, new_tracks => {
-                            _.each(new_tracks, track => {
+                        visualization.select_datasets({ dbkey: this.view.dbkey }, (new_tracks) => {
+                            _.each(new_tracks, (track) => {
                                 this.view.add_drawable(tracks.object_from_template(track, this.view, this.view));
                             });
                         });
-                    }
+                    },
                 },
                 {
                     icon_class: "block--plus",
@@ -137,10 +133,10 @@ export class TracksterUI extends Backbone.Model {
                     on_click: () => {
                         this.view.add_drawable(
                             new tracks.DrawableGroup(this.view, this.view, {
-                                name: "New Group"
+                                name: "New Group",
                             })
                         );
-                    }
+                    },
                 },
                 {
                     icon_class: "bookmarks",
@@ -148,7 +144,7 @@ export class TracksterUI extends Backbone.Model {
                     on_click: () => {
                         // HACK -- use style to determine if panel is hidden and hide/show accordingly.
                         window.force_right_panel($("div#right").css("right") == "0px" ? "hide" : "show");
-                    }
+                    },
                 },
                 {
                     icon_class: "globe",
@@ -160,25 +156,25 @@ export class TracksterUI extends Backbone.Model {
                             circster_q = `dataset_id=${this.view.drawables[0].dataset.id}&hda_ldda=${this.view.drawables[0].dataset.attributes.hda_ldda}`;
                         }
                         window.top.location = `${this.baseURL}visualization/circster?${circster_q}`;
-                    }
+                    },
                 },
                 {
                     icon_class: "disk--arrow",
                     title: _l("Save"),
                     on_click: () => {
                         this.save_viz();
-                    }
+                    },
                 },
                 {
                     icon_class: "cross-circle",
                     title: _l("Close"),
                     on_click: () => {
                         this.handle_unsaved_changes(this.view);
-                    }
-                }
+                    },
+                },
             ],
             {
-                tooltip_config: { placement: "bottom" }
+                tooltip_config: { placement: "bottom" },
             }
         );
 
@@ -193,13 +189,9 @@ export class TracksterUI extends Backbone.Model {
         // Create HTML.
         var bookmarks_container = $("#right .unified-panel-body");
 
-        var new_bookmark = $("<div/>")
-            .addClass("bookmark")
-            .appendTo(bookmarks_container);
+        var new_bookmark = $("<div/>").addClass("bookmark").appendTo(bookmarks_container);
 
-        var position_div = $("<div/>")
-            .addClass("position")
-            .appendTo(new_bookmark);
+        var position_div = $("<div/>").addClass("position").appendTo(new_bookmark);
 
         //position_link
         $("<a href='javascript:void(0)'/>")
@@ -210,9 +202,7 @@ export class TracksterUI extends Backbone.Model {
                 return false;
             });
 
-        var annotation_div = $("<div/>")
-            .text(annotation)
-            .appendTo(new_bookmark);
+        var annotation_div = $("<div/>").text(annotation).appendTo(new_bookmark);
 
         // If editable, enable bookmark deletion and annotation editing.
         if (editable) {
@@ -228,15 +218,13 @@ export class TracksterUI extends Backbone.Model {
                 });
 
             // delete_icon
-            $("<a href='javascript:void(0)'/>")
-                .addClass("icon-button delete")
-                .appendTo(delete_icon_container);
+            $("<a href='javascript:void(0)'/>").addClass("icon-button delete").appendTo(delete_icon_container);
 
             annotation_div
                 .make_text_editable({
                     num_rows: 3,
                     use_textarea: true,
-                    help_text: "Edit bookmark note"
+                    help_text: "Edit bookmark note",
                 })
                 .addClass("annotation");
         }
@@ -253,7 +241,7 @@ export class TracksterUI extends Backbone.Model {
         this.view = new tracks.TracksterView(_.extend(view_config, { header: false }));
         this.view.editor = true;
 
-        $.when(this.view.load_chroms_deferred).then(chrom_info => {
+        $.when(this.view.load_chroms_deferred).then((chrom_info) => {
             var overview_drawable_name = null;
             // Viewport config.
             if (viewport_config) {
@@ -322,7 +310,7 @@ export class TracksterUI extends Backbone.Model {
      */
     init_keyboard_nav(view) {
         // Keyboard navigation. Scroll ~7% of height when scrolling up/down.
-        $(document).keyup(e => {
+        $(document).keyup((e) => {
             // Do not navigate if arrow keys used in input element.
             if ($(e.srcElement).is(":input")) {
                 return;
@@ -369,8 +357,8 @@ export class TracksterUI extends Backbone.Model {
                         $.when(this.save_viz()).then(() => {
                             window.top.location = `${getAppRoot()}visualizations/list`;
                         });
-                    }
-                }
+                    },
+                },
             });
         } else {
             window.top.location = `${getAppRoot()}visualizations/list`;
@@ -429,7 +417,7 @@ export class TracksterUIView extends Backbone.View {
             dbkey: dbkey,
             dataset_id: query_string.get("dataset_id"),
             hda_ldda: query_string.get("hda_ldda"),
-            gene_region: query_string.get("gene_region")
+            gene_region: query_string.get("gene_region"),
         };
 
         if (dbkey) {
@@ -439,8 +427,9 @@ export class TracksterUIView extends Backbone.View {
         Galaxy.modal.show({
             title: "View Data in a New or Saved Visualization?",
             // either have text in here or have to remove body and the header/footer margins
-            body: `<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>${dbkey ||
-                "Not available."}</b></li><li>or create a new session with this dataset as the only track</li></ul></p>`,
+            body: `<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>${
+                dbkey || "Not available."
+            }</b></li><li>or create a new session with this dataset as the only track</li></ul></p>`,
             buttons: {
                 Cancel: () => {
                     window.top.location = `${getAppRoot()}visualizations/list`;
@@ -450,8 +439,8 @@ export class TracksterUIView extends Backbone.View {
                 },
                 "View in new visualization": () => {
                     this.view_new();
-                }
-            }
+                },
+            },
         });
     }
 
@@ -460,7 +449,7 @@ export class TracksterUIView extends Backbone.View {
         const Galaxy = getGalaxyInstance();
         var tracks_grid = new GridView({
             url_base: `${getAppRoot()}visualization/list_tracks`,
-            embedded: true
+            embedded: true,
         });
         Galaxy.modal.show({
             title: _l("Add Data to Saved Visualization"),
@@ -476,8 +465,8 @@ export class TracksterUIView extends Backbone.View {
                             dataset_params.id = $(this).val();
                             window.top.location = `${getAppRoot()}visualization/trackster?${$.param(dataset_params)}`;
                         });
-                }
-            }
+                },
+            },
         });
     }
 
@@ -492,7 +481,7 @@ export class TracksterUIView extends Backbone.View {
                 container: $("#center .unified-panel-body"),
                 name: viz_config.title,
                 vis_id: viz_config.vis_id,
-                dbkey: viz_config.dbkey
+                dbkey: viz_config.dbkey,
             },
             viz_config.viewport,
             viz_config.tracks,
@@ -514,7 +503,7 @@ export class TracksterUIView extends Backbone.View {
             error: () => {
                 alert("Couldn't create new browser.");
             },
-            success: response => {
+            success: (response) => {
                 // show dialog
                 Galaxy.modal.show({
                     title: _l("New Visualization"),
@@ -526,12 +515,12 @@ export class TracksterUIView extends Backbone.View {
                         Create: () => {
                             this.create_browser($("#new-title").val(), $("#new-dbkey").val());
                             Galaxy.modal.hide();
-                        }
-                    }
+                        },
+                    },
                 });
 
                 // select default
-                var dbkeys_in_genomes = response.map(r => r[1]);
+                var dbkeys_in_genomes = response.map((r) => r[1]);
                 if (
                     window.galaxy_config.app.default_dbkey &&
                     _.contains(dbkeys_in_genomes, window.galaxy_config.app.default_dbkey)
@@ -545,7 +534,7 @@ export class TracksterUIView extends Backbone.View {
 
                 // to support the large number of options for dbkey, enable scrolling in overlay.
                 $("#overlay").css("overflow", "auto");
-            }
+            },
         });
     }
 
@@ -589,9 +578,9 @@ export class TracksterUIView extends Backbone.View {
                 url: `${getAppRoot()}api/datasets/${window.galaxy_config.app.add_dataset}`,
                 data: { hda_ldda: "hda", data_type: "track_config" },
                 dataType: "json",
-                success: track_data => {
+                success: (track_data) => {
                     this.ui.view.add_drawable(tracks.object_from_template(track_data, this.ui.view, this.ui.view));
-                }
+                },
             });
 
         // initialize icons
@@ -621,7 +610,7 @@ export class TracksterUIView extends Backbone.View {
             {
                 container: $("#center .unified-panel-body"),
                 name: name,
-                dbkey: dbkey
+                dbkey: dbkey,
             },
             window.galaxy_config.app.gene_region
         );
diff --git a/client/galaxy/scripts/viz/trackster/filters.js b/client/galaxy/scripts/viz/trackster/filters.js
index aae4ee876b25..53eb7fdd116e 100644
--- a/client/galaxy/scripts/viz/trackster/filters.js
+++ b/client/galaxy/scripts/viz/trackster/filters.js
@@ -6,7 +6,7 @@ import { getGalaxyInstance } from "app";
 /**
  * Filters that enable users to show/hide data points dynamically.
  */
-var Filter = function(obj_dict) {
+var Filter = function (obj_dict) {
     this.manager = null;
     this.name = obj_dict.name;
     // Index into payload to filter.
@@ -20,14 +20,14 @@ _.extend(Filter.prototype, {
     /**
      * Convert filter to dictionary.
      */
-    to_dict: function() {
+    to_dict: function () {
         return {
             name: this.name,
             index: this.index,
             tool_id: this.tool_id,
-            tool_exp_name: this.tool_exp_name
+            tool_exp_name: this.tool_exp_name,
         };
-    }
+    },
 });
 
 /**
@@ -45,7 +45,7 @@ var create_action_icon = (title, css_class, on_click_fn) =>
 /**
  * Number filters have a min, max as well as a low, high; low and high are used
  */
-var NumberFilter = function(obj_dict) {
+var NumberFilter = function (obj_dict) {
     //
     // Attribute init.
     //
@@ -68,7 +68,7 @@ var NumberFilter = function(obj_dict) {
     // Function that supports inline text editing of slider values.
     // Enable users to edit parameter's value via a text box.
     var edit_slider_values = (container, span, slider) => {
-        container.click(function() {
+        container.click(function () {
             var cur_value = span.text();
             var max = parseFloat(slider.slider("option", "max"));
 
@@ -94,16 +94,16 @@ var NumberFilter = function(obj_dict) {
                 .appendTo(span)
                 .focus()
                 .select()
-                .click(e => {
+                .click((e) => {
                     // Don't want click to propogate up to values_span and restart everything.
                     e.stopPropagation();
                 })
-                .blur(function() {
+                .blur(function () {
                     $(this).remove();
                     span.text(cur_value);
                     slider_row.removeClass("input");
                 })
-                .keyup(function(e) {
+                .keyup(function (e) {
                     if (e.keyCode === 27) {
                         // Escape key.
                         $(this).trigger("blur");
@@ -116,7 +116,7 @@ var NumberFilter = function(obj_dict) {
 
                         var slider_max = slider.slider("option", "max");
 
-                        var invalid = a_val => isNaN(a_val) || a_val > slider_max || a_val < slider_min;
+                        var invalid = (a_val) => isNaN(a_val) || a_val > slider_max || a_val < slider_min;
 
                         var new_value = $(this).val();
                         if (!multi_value) {
@@ -148,14 +148,9 @@ var NumberFilter = function(obj_dict) {
     filter.parent_div = $("<div/>").addClass("filter-row slider-row");
 
     // Set up filter label (name, values).
-    var filter_label = $("<div/>")
-        .addClass("elt-label")
-        .appendTo(filter.parent_div);
+    var filter_label = $("<div/>").addClass("elt-label").appendTo(filter.parent_div);
 
-    $("<span/>")
-        .addClass("slider-name")
-        .text(`${filter.name}  `)
-        .appendTo(filter_label);
+    $("<span/>").addClass("slider-name").text(`${filter.name}  `).appendTo(filter_label);
 
     var values_span = $("<span/>").text(`${this.low}-${this.high}`);
 
@@ -169,24 +164,20 @@ var NumberFilter = function(obj_dict) {
     filter.values_span = values_span;
 
     // Set up slider for filter.
-    var slider_div = $("<div/>")
-        .addClass("slider")
-        .appendTo(filter.parent_div);
-    filter.control_element = $("<div/>")
-        .attr("id", `${filter.name}-filter-control`)
-        .appendTo(slider_div);
+    var slider_div = $("<div/>").addClass("slider").appendTo(filter.parent_div);
+    filter.control_element = $("<div/>").attr("id", `${filter.name}-filter-control`).appendTo(slider_div);
     filter.control_element.slider({
         range: true,
         min: this.min,
         max: this.max,
         step: this.get_slider_step(this.min, this.max),
         values: [this.low, this.high],
-        slide: function(event, ui) {
+        slide: function (event, ui) {
             filter.slide(event, ui);
         },
-        change: function(event, ui) {
+        change: function (event, ui) {
             filter.control_element.slider("option", "slide").call(filter.control_element, event, ui);
-        }
+        },
     });
     filter.slider = filter.control_element;
     filter.slider_label = values_span;
@@ -195,18 +186,13 @@ var NumberFilter = function(obj_dict) {
     edit_slider_values(values_span_container, values_span, filter.control_element);
 
     // Set up filter display controls.
-    var display_controls_div = $("<div/>")
-        .addClass("display-controls")
-        .appendTo(filter.parent_div);
+    var display_controls_div = $("<div/>").addClass("display-controls").appendTo(filter.parent_div);
     this.transparency_icon = create_action_icon("Use filter for data transparency", "layer-transparent", () => {
         if (filter.manager.alpha_filter !== filter) {
             // Setting this filter as the alpha filter.
             filter.manager.alpha_filter = filter;
             // Update UI for new filter.
-            filter.manager.parent_div
-                .find(".layer-transparent")
-                .removeClass("active")
-                .hide();
+            filter.manager.parent_div.find(".layer-transparent").removeClass("active").hide();
             filter.transparency_icon.addClass("active").show();
         } else {
             // Clearing filter as alpha filter.
@@ -215,7 +201,7 @@ var NumberFilter = function(obj_dict) {
         }
         filter.manager.track.request_draw({
             force: true,
-            clear_after: true
+            clear_after: true,
         });
     })
         .appendTo(display_controls_div)
@@ -225,10 +211,7 @@ var NumberFilter = function(obj_dict) {
             // Setting this filter as the height filter.
             filter.manager.height_filter = filter;
             // Update UI for new filter.
-            filter.manager.parent_div
-                .find(".arrow-resize-090")
-                .removeClass("active")
-                .hide();
+            filter.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();
             filter.height_icon.addClass("active").show();
         } else {
             // Clearing filter as alpha filter.
@@ -237,7 +220,7 @@ var NumberFilter = function(obj_dict) {
         }
         filter.manager.track.request_draw({
             force: true,
-            clear_after: true
+            clear_after: true,
         });
     })
         .appendTo(display_controls_div)
@@ -265,39 +248,39 @@ _.extend(NumberFilter.prototype, {
     /**
      * Convert filter to dictionary.
      */
-    to_dict: function() {
+    to_dict: function () {
         var obj_dict = Filter.prototype.to_dict.call(this);
         return _.extend(obj_dict, {
             type: "number",
             min: this.min,
             max: this.max,
             low: this.low,
-            high: this.high
+            high: this.high,
         });
     },
     /**
      * Return a copy of filter.
      */
-    copy: function() {
+    copy: function () {
         return new NumberFilter({
             name: this.name,
             index: this.index,
             tool_id: this.tool_id,
-            tool_exp_name: this.tool_exp_name
+            tool_exp_name: this.tool_exp_name,
         });
     },
     /**
      * Get step for slider.
      */
     // FIXME: make this a "static" function.
-    get_slider_step: function(min, max) {
+    get_slider_step: function (min, max) {
         var range = max - min;
         return range <= 2 ? 0.01 : 1;
     },
     /**
      * Handle slide events.
      */
-    slide: function(event, ui) {
+    slide: function (event, ui) {
         var values = ui.values;
 
         // Set new values in UI.
@@ -313,7 +296,7 @@ _.extend(NumberFilter.prototype, {
             if (values[0] === self.low && values[1] === self.high) {
                 self.manager.track.request_draw({
                     force: true,
-                    clear_after: true
+                    clear_after: true,
                 });
             }
         }, 25);
@@ -321,20 +304,20 @@ _.extend(NumberFilter.prototype, {
     /**
      * Returns true if filter can be applied to element.
      */
-    applies_to: function(element) {
+    applies_to: function (element) {
         return element.length > this.index;
     },
     /**
      * Helper function: returns true if value in in filter's [low, high] range.
      */
-    _keep_val: function(val) {
+    _keep_val: function (val) {
         return isNaN(val) || (val >= this.low && val <= this.high);
     },
     /**
      * Returns true if (a) element's value(s) is in [low, high] (range is inclusive)
      * or (b) if value is non-numeric and hence unfilterable.
      */
-    keep: function(element) {
+    keep: function (element) {
         if (!this.applies_to(element)) {
             // No element to filter on.
             return true;
@@ -359,7 +342,7 @@ _.extend(NumberFilter.prototype, {
     /**
      * Update filter's min and max values based on element's values.
      */
-    update_attrs: function(element) {
+    update_attrs: function (element) {
         var updated = false;
         if (!this.applies_to(element)) {
             return updated;
@@ -392,7 +375,7 @@ _.extend(NumberFilter.prototype, {
     /**
      * Update filter's slider.
      */
-    update_ui_elt: function() {
+    update_ui_elt: function () {
         // Only show filter if min < max because filter is not useful otherwise. This
         // covers all corner cases, such as when min, max have not been defined and
         // when min == max.
@@ -417,13 +400,13 @@ _.extend(NumberFilter.prototype, {
             //var values = this.slider.slider( "option", "values" );
             //this.slider.slider( "option", "values", values );
         }
-    }
+    },
 });
 
 /**
  * Manages a set of filters.
  */
-var FiltersManager = function(track, obj_dict) {
+var FiltersManager = function (track, obj_dict) {
     this.track = track;
     this.alpha_filter = null;
     this.height_filter = null;
@@ -436,21 +419,19 @@ var FiltersManager = function(track, obj_dict) {
     //
     // Create parent div.
     //
-    this.parent_div = $("<div/>")
-        .addClass("filters")
-        .hide();
+    this.parent_div = $("<div/>").addClass("filters").hide();
     // Disable dragging, double clicking, keys on div so that actions on slider do not impact viz.
     this.parent_div
-        .bind("drag", e => {
+        .bind("drag", (e) => {
             e.stopPropagation();
         })
-        .click(e => {
+        .click((e) => {
             e.stopPropagation();
         })
-        .bind("dblclick", e => {
+        .bind("dblclick", (e) => {
             e.stopPropagation();
         })
-        .bind("keydown", e => {
+        .bind("keydown", (e) => {
             e.stopPropagation();
         });
 
@@ -489,9 +470,7 @@ var FiltersManager = function(track, obj_dict) {
 
     // Add button to filter complete dataset.
     if (this.filters.length !== 0) {
-        var run_buttons_row = $("<div/>")
-            .addClass("param-row")
-            .appendTo(this.parent_div);
+        var run_buttons_row = $("<div/>").addClass("param-row").appendTo(this.parent_div);
         var run_on_dataset_button = $("<input type='submit'/>")
             .attr("value", "Run on complete dataset")
             .appendTo(run_buttons_row);
@@ -504,22 +483,22 @@ var FiltersManager = function(track, obj_dict) {
 
 _.extend(FiltersManager.prototype, {
     // HTML manipulation and inspection.
-    show: function() {
+    show: function () {
         this.parent_div.show();
     },
-    hide: function() {
+    hide: function () {
         this.parent_div.hide();
     },
-    toggle: function() {
+    toggle: function () {
         this.parent_div.toggle();
     },
-    visible: function() {
+    visible: function () {
         return this.parent_div.is(":visible");
     },
     /**
      * Returns dictionary for manager.
      */
-    to_dict: function() {
+    to_dict: function () {
         var obj_dict = {};
         var filter_dicts = [];
         var filter;
@@ -543,7 +522,7 @@ _.extend(FiltersManager.prototype, {
     /**
      * Return a copy of the manager.
      */
-    copy: function(new_track) {
+    copy: function (new_track) {
         var copy = new FiltersManager(new_track);
         for (var i = 0; i < this.filters.length; i++) {
             copy.add_filter(this.filters[i].copy());
@@ -553,7 +532,7 @@ _.extend(FiltersManager.prototype, {
     /**
      * Add a filter to the manager.
      */
-    add_filter: function(filter) {
+    add_filter: function (filter) {
         filter.manager = this;
         this.parent_div.append(filter.parent_div);
         this.filters.push(filter);
@@ -561,7 +540,7 @@ _.extend(FiltersManager.prototype, {
     /**
      * Remove all filters from manager.
      */
-    remove_all: function() {
+    remove_all: function () {
         this.filters = [];
         this.parent_div.children().remove();
     },
@@ -569,7 +548,7 @@ _.extend(FiltersManager.prototype, {
      * Initialize filters.
      */
 
-    init_filters: function() {
+    init_filters: function () {
         for (var i = 0; i < this.filters.length; i++) {
             var filter = this.filters[i];
             filter.update_ui_elt();
@@ -578,7 +557,7 @@ _.extend(FiltersManager.prototype, {
     /**
      * Clear filters so that they do not impact track display.
      */
-    clear_filters: function() {
+    clear_filters: function () {
         for (var i = 0; i < this.filters.length; i++) {
             var filter = this.filters[i];
             filter.slider.slider("option", "values", [filter.min, filter.max]);
@@ -589,7 +568,7 @@ _.extend(FiltersManager.prototype, {
         // Hide icons for setting filters.
         this.parent_div.find(".icon-button").hide();
     },
-    run_on_dataset: function() {
+    run_on_dataset: function () {
         // Get or create dictionary item.
         var get_or_create_dict_item = (dict, key, new_item) => {
             // Add new item to dict if
@@ -646,7 +625,7 @@ _.extend(FiltersManager.prototype, {
                 cond: tool_filter_str,
                 input: input_dataset_id,
                 target_dataset_id: input_dataset_id,
-                tool_id: tool_id
+                tool_id: tool_id,
             };
 
             // Remove current filter.
@@ -655,21 +634,21 @@ _.extend(FiltersManager.prototype, {
             // DBTODO: This will never work, run_tool_url doesn't exist?
             // https://github.com/galaxyproject/galaxy/issues/7224
             // eslint-disable-next-line no-undef
-            $.getJSON(run_tool_url, url_params, response => {
+            $.getJSON(run_tool_url, url_params, (response) => {
                 const Galaxy = getGalaxyInstance();
                 if (response.error) {
                     // General error.
                     Galaxy.modal.show({
                         title: _l("Filter Dataset"),
                         body: `Error running tool ${tool_id}`,
-                        buttons: { Close: Galaxy.modal.hide() }
+                        buttons: { Close: Galaxy.modal.hide() },
                     });
                 } else if (filters.length === 0) {
                     // No more filters to run.
                     Galaxy.modal.show({
                         title: _l("Filtering Dataset"),
                         body: "Filter(s) are running on the complete dataset. Outputs are in dataset's history.",
-                        buttons: { Close: Galaxy.modal.hide() }
+                        buttons: { Close: Galaxy.modal.hide() },
                     });
                 } else {
                     // More filters to run.
@@ -677,10 +656,10 @@ _.extend(FiltersManager.prototype, {
                 }
             });
         })(this.track.dataset_id, active_filters_list);
-    }
+    },
 });
 
 export default {
     FiltersManager: FiltersManager,
-    NumberFilter: NumberFilter
+    NumberFilter: NumberFilter,
 };
diff --git a/client/galaxy/scripts/viz/trackster/painters.js b/client/galaxy/scripts/viz/trackster/painters.js
index da31494b4be6..b9a81044d124 100644
--- a/client/galaxy/scripts/viz/trackster/painters.js
+++ b/client/galaxy/scripts/viz/trackster/painters.js
@@ -202,7 +202,7 @@ class LinePainter extends Painter {
             max_value: undefined,
             mode: "Histogram",
             color: "#000",
-            overflow_color: "#F66"
+            overflow_color: "#F66",
         };
     }
 
@@ -369,7 +369,7 @@ class FeaturePositionMapper {
         this.feature_positions[slot].push({
             data: feature_data,
             x_start: x_start,
-            x_end: x_end
+            x_end: x_end,
         });
     }
 
@@ -414,7 +414,7 @@ class FeaturePainter extends Painter {
     static get default_prefs() {
         return {
             block_color: "#FFF",
-            connector_color: "#FFF"
+            connector_color: "#FFF",
         };
     }
     get_required_height(rows_required, width) {
@@ -491,7 +491,7 @@ class FeaturePainter extends Painter {
         feature_mapper.y_translation = this.get_top_padding(width);
         return new DrawResults({
             incomplete_features: incomplete_features,
-            feature_mapper: feature_mapper
+            feature_mapper: feature_mapper,
         });
     }
 
@@ -816,7 +816,7 @@ class ReadPainter extends FeaturePainter {
         var base_pos = 0;
 
         var // Parse cigar operations out and update/create blocks as needed.
-            parsed_cigar = _.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g), op => {
+            parsed_cigar = _.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g), (op) => {
                 // Get operation length, character.
                 var op_len = parseInt(op.slice(0, -1), 10);
                 var op_char = op.slice(-1);
@@ -841,7 +841,7 @@ class ReadPainter extends FeaturePainter {
 
         return {
             blocks: blocks,
-            cigar: parsed_cigar
+            cigar: parsed_cigar,
         };
     }
 
@@ -1038,7 +1038,7 @@ class ReadPainter extends FeaturePainter {
                                 ctx.fillRect(x_center - gap, y_start - 9, s_end - s_start, 9);
                                 draw_last[draw_last.length] = {
                                     type: "triangle",
-                                    data: [insert_x_coord, y_start + 4, 5]
+                                    data: [insert_x_coord, y_start + 4, 5],
                                 };
                                 ctx.fillStyle = CONNECTOR_COLOR;
                                 // Based on overlap b/t sequence and tile, get sequence to be drawn.
@@ -1081,7 +1081,7 @@ class ReadPainter extends FeaturePainter {
                                 // Show insertions with a single number at the insertion point.
                                 draw_last.push({
                                     type: "text",
-                                    data: [seq.length, insert_x_coord, y_start + 9]
+                                    data: [seq.length, insert_x_coord, y_start + 9],
                                 });
                             } else {
                                 // TODO: probably can merge this case with code above.
@@ -1275,14 +1275,14 @@ class Color {
         if (Array.isArray(rgb)) {
             this.rgb = rgb;
         } else if (rgb.length == 6) {
-            this.rgb = rgb.match(/.{2}/g).map(c => parseInt(c, 16));
+            this.rgb = rgb.match(/.{2}/g).map((c) => parseInt(c, 16));
         } else if (rgb.length == 7) {
             this.rgb = rgb
                 .substring(1, 7)
                 .match(/.{2}/g)
-                .map(c => parseInt(c, 16));
+                .map((c) => parseInt(c, 16));
         } else {
-            this.rgb = rgb.split("").map(c => parseInt(c + c, 16));
+            this.rgb = rgb.split("").map((c) => parseInt(c + c, 16));
         }
         this.alpha = typeof a === "number" ? a : 1;
     }
@@ -1300,12 +1300,12 @@ class Color {
     toCSS() {
         if (this.alpha < 1.0) {
             return `rgba(${this.rgb
-                .map(c => Math.round(c))
+                .map((c) => Math.round(c))
                 .concat(this.alpha)
                 .join(", ")})`;
         } else {
             return `#${this.rgb
-                .map(i => {
+                .map((i) => {
                     i = Math.round(i);
                     i = (i > 255 ? 255 : i < 0 ? 0 : i).toString(16);
                     return i.length === 1 ? `0${i}` : i;
@@ -1350,7 +1350,7 @@ class Color {
     toARGB() {
         var argb = [Math.round(this.alpha * 255)].concat(this.rgb);
         return `#${argb
-            .map(i => {
+            .map((i) => {
                 i = Math.round(i);
                 i = (i > 255 ? 255 : i < 0 ? 0 : i).toString(16);
                 return i.length === 1 ? `0${i}` : i;
@@ -1371,7 +1371,7 @@ class Color {
         var rgb = [
             color1.rgb[0] * w1 + color2.rgb[0] * w2,
             color1.rgb[1] * w1 + color2.rgb[1] * w2,
-            color1.rgb[2] * w1 + color2.rgb[2] * w2
+            color1.rgb[2] * w1 + color2.rgb[2] * w2,
         ];
 
         var alpha = color1.alpha * p + color2.alpha * (1 - p);
@@ -1454,7 +1454,7 @@ class DiagonalHeatmapPainter extends Painter {
             max_value: undefined,
             mode: "Heatmap",
             pos_color: "#FF8C00",
-            neg_color: "#4169E1"
+            neg_color: "#4169E1",
         };
     }
 
@@ -1473,7 +1473,7 @@ class DiagonalHeatmapPainter extends Painter {
         var e2;
         var value;
 
-        var scale = p => (p - view_start) * w_scale;
+        var scale = (p) => (p - view_start) * w_scale;
 
         ctx.save();
 
@@ -1661,11 +1661,11 @@ class VariantPainter extends Painter {
             allele_counts = locus_data.slice(8);
 
             // Process alterate values to derive information about each alt.
-            alt = _.map(_.flatten(alt), a => {
+            alt = _.map(_.flatten(alt), (a) => {
                 var alt_info = {
                     type: "snp",
                     value: a,
-                    start: 0
+                    start: 0,
                 };
 
                 var indel_info = get_indel_info(ref, a);
@@ -1757,5 +1757,5 @@ export default {
     ReadPainter: ReadPainter,
     ArcLinkedFeaturePainter: ArcLinkedFeaturePainter,
     DiagonalHeatmapPainter: DiagonalHeatmapPainter,
-    VariantPainter: VariantPainter
+    VariantPainter: VariantPainter,
 };
diff --git a/client/galaxy/scripts/viz/trackster/slotting.js b/client/galaxy/scripts/viz/trackster/slotting.js
index cff791d64d04..7d6ab021da39 100644
--- a/client/galaxy/scripts/viz/trackster/slotting.js
+++ b/client/galaxy/scripts/viz/trackster/slotting.js
@@ -9,7 +9,7 @@ var PACK_SPACING = 5;
 /**
  * Hold slotting information for a feature.
  */
-var SlottedInfo = function(slot, feature) {
+var SlottedInfo = function (slot, feature) {
     this.slot = slot;
     this.feature = feature;
 };
@@ -21,7 +21,7 @@ var SlottedInfo = function(slot, feature) {
  * This implementation is incremental, any feature assigned a slot will be
  * retained for slotting future features.
  */
-var FeatureSlotter = function(w_scale, mode, max_rows, measureText) {
+var FeatureSlotter = function (w_scale, mode, max_rows, measureText) {
     this.slots = {};
     this.start_end_dct = {};
     this.w_scale = w_scale;
@@ -39,7 +39,7 @@ extend(FeatureSlotter.prototype, {
     /**
      * Get drawing coordinate for a feature.
      */
-    _get_draw_coords: function(feature) {
+    _get_draw_coords: function (feature) {
         // Get initial draw coordinates using w_scale.
         var draw_start = Math.floor(feature[1] * this.w_scale);
 
@@ -91,7 +91,7 @@ extend(FeatureSlotter.prototype, {
      * Find the first slot such that current feature doesn't overlap any other features in that slot.
      * Returns -1 if no slot was found.
      */
-    _find_slot: function(draw_coords) {
+    _find_slot: function (draw_coords) {
         // TODO: Use a data structure for faster searching of available slots.
         var draw_start = draw_coords[0];
 
@@ -120,7 +120,7 @@ extend(FeatureSlotter.prototype, {
     /**
      * Slot features.
      */
-    slot_features: function(features) {
+    slot_features: function (features) {
         var start_end_dct = this.start_end_dct;
         var undone = [];
         var highest_slot = 0;
@@ -196,9 +196,9 @@ extend(FeatureSlotter.prototype, {
         }
         */
         return highest_slot + 1;
-    }
+    },
 });
 
 export default {
-    FeatureSlotter: FeatureSlotter
+    FeatureSlotter: FeatureSlotter,
 };
diff --git a/client/galaxy/scripts/viz/trackster/tracks.js b/client/galaxy/scripts/viz/trackster/tracks.js
index db2c2f1bc9ad..5f063a7e58fe 100644
--- a/client/galaxy/scripts/viz/trackster/tracks.js
+++ b/client/galaxy/scripts/viz/trackster/tracks.js
@@ -51,7 +51,7 @@ function moveable(element, handle_class, container_selector, element_js_obj) {
 
     // Need to provide selector for handle, not class.
     element
-        .bind("drag", { handle: `.${handle_class}`, relative: true }, function(e, d) {
+        .bind("drag", { handle: `.${handle_class}`, relative: true }, function (e, d) {
             var element = $(this);
             var parent = element.parent();
             // Only sorting amongst tracks and groups.
@@ -141,10 +141,10 @@ function moveable(element, handle_class, container_selector, element_js_obj) {
                 html_elt_js_obj_dict[parent.attr("id")].move_drawable(this_obj, d.deltaY > 0 ? i - 1 : i);
             }
         })
-        .bind("dragstart", function() {
+        .bind("dragstart", function () {
             $(this).addClass("dragging");
         })
-        .bind("dragend", function() {
+        .bind("dragend", function () {
             $(this).removeClass("dragging");
         });
 }
@@ -210,12 +210,12 @@ function supportsByteRanges(url) {
     $.ajax({
         type: "HEAD",
         url: url,
-        beforeSend: function(xhr) {
+        beforeSend: function (xhr) {
             xhr.setRequestHeader("Range", "bytes=0-10");
         },
-        success: function(result, status, xhr) {
+        success: function (result, status, xhr) {
             promise.resolve(xhr.status === 206);
-        }
+        },
     });
 
     return promise;
@@ -240,7 +240,7 @@ function supportsByteRanges(url) {
  *
  * They optionally have a drag handle class.
  */
-var Drawable = function(view, container, obj_dict) {
+var Drawable = function (view, container, obj_dict) {
     if (!Drawable.id_counter) {
         Drawable.id_counter = 0;
     }
@@ -274,7 +274,7 @@ var Drawable = function(view, container, obj_dict) {
     if (obj_dict.header !== false) {
         var header_view = new viz_views.TrackHeaderView({
             model: this,
-            id: this.id
+            id: this.id,
         });
 
         this.header_div = header_view.$el;
@@ -301,7 +301,7 @@ Drawable.prototype.action_icons_def = [
         name: "toggle_icon",
         title: "Hide/show content",
         css_class: "toggle",
-        on_click_fn: function(drawable) {
+        on_click_fn: function (drawable) {
             if (drawable.config.get_value("content_visible")) {
                 drawable.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");
                 drawable.hide_contents();
@@ -311,31 +311,31 @@ Drawable.prototype.action_icons_def = [
                 drawable.config.set_value("content_visible", true);
                 drawable.show_contents();
             }
-        }
+        },
     },
     // Edit settings.
     {
         name: "settings_icon",
         title: _l("Edit settings"),
         css_class: "gear",
-        on_click_fn: function(drawable) {
+        on_click_fn: function (drawable) {
             var view = new config_mod.ConfigSettingCollectionView({
-                collection: drawable.config
+                collection: drawable.config,
             });
             view.render_in_modal("Configure Track");
-        }
+        },
     },
     // Remove.
     {
         name: "remove_icon",
         title: _l("Remove"),
         css_class: "remove-icon",
-        on_click_fn: function(drawable) {
+        on_click_fn: function (drawable) {
             // Tooltip for remove icon must be deleted when drawable is deleted.
             $(".tooltip").remove();
             drawable.remove();
-        }
-    }
+        },
+    },
 ];
 
 extend(Drawable.prototype, {
@@ -345,23 +345,23 @@ extend(Drawable.prototype, {
             key: "content_visible",
             type: "bool",
             default_value: true,
-            hidden: true
-        }
+            hidden: true,
+        },
     ],
 
-    build_config_params: function() {
+    build_config_params: function () {
         return this.config_params;
     },
 
-    config_onchange: function() {},
+    config_onchange: function () {},
 
-    init: function() {},
+    init: function () {},
 
-    changed: function() {
+    changed: function () {
         this.view.changed();
     },
 
-    can_draw: function() {
+    can_draw: function () {
         if (this.enabled && this.config.get_value("content_visible")) {
             return true;
         }
@@ -369,20 +369,20 @@ extend(Drawable.prototype, {
         return false;
     },
 
-    request_draw: function() {},
+    request_draw: function () {},
 
-    _draw: function(options) {},
+    _draw: function (options) {},
 
     /**
      * Returns representation of object in a dictionary for easy saving.
      * Use from_dict to recreate object.
      */
-    to_dict: function() {},
+    to_dict: function () {},
 
     /**
      * Set drawable name.
      */
-    set_name: function(new_name) {
+    set_name: function (new_name) {
         this.old_name = this.config.get_value("name");
         this.config.set_value("name", new_name);
     },
@@ -390,7 +390,7 @@ extend(Drawable.prototype, {
     /**
      * Revert track name; currently name can be reverted only once.
      */
-    revert_name: function() {
+    revert_name: function () {
         if (this.old_name) {
             this.config.set_value("name", this.old_name);
         }
@@ -399,12 +399,12 @@ extend(Drawable.prototype, {
     /**
      * Remove drawable (a) from its container and (b) from the HTML.
      */
-    remove: function() {
+    remove: function () {
         this.changed();
 
         this.container.remove_drawable(this);
         var view = this.view;
-        this.container_div.hide(0, function() {
+        this.container_div.hide(0, function () {
             $(this).remove();
             // HACK: is there a better way to update the view?
             view.update_intro_div();
@@ -414,33 +414,33 @@ extend(Drawable.prototype, {
     /**
      * Build drawable's container div; this is the parent div for all drawable's elements.
      */
-    build_container_div: function() {},
+    build_container_div: function () {},
 
     /**
      * Update icons.
      */
-    update_icons: function() {},
+    update_icons: function () {},
 
     /**
      * Hide drawable's contents.
      */
-    hide_contents: function() {},
+    hide_contents: function () {},
 
     /**
      * Show drawable's contents.
      */
-    show_contents: function() {},
+    show_contents: function () {},
 
     /**
      * Returns a shallow copy of all drawables in this drawable.
      */
-    get_drawables: function() {}
+    get_drawables: function () {},
 });
 
 /**
  * A collection of drawable objects.
  */
-var DrawableCollection = function(view, container, obj_dict) {
+var DrawableCollection = function (view, container, obj_dict) {
     Drawable.call(this, view, container, obj_dict);
 
     // Attribute init.
@@ -452,7 +452,7 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
     /**
      * Unpack and add drawables to the collection.
      */
-    unpack_drawables: function(drawables_array) {
+    unpack_drawables: function (drawables_array) {
         // Add drawables to collection.
         this.drawables = [];
         var drawable;
@@ -465,7 +465,7 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
     /**
      * Init each drawable in the collection.
      */
-    init: function() {
+    init: function () {
         for (var i = 0; i < this.drawables.length; i++) {
             this.drawables[i].init();
         }
@@ -474,7 +474,7 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
     /**
      * Draw each drawable in the collection.
      */
-    _draw: function(options) {
+    _draw: function (options) {
         for (var i = 0; i < this.drawables.length; i++) {
             this.drawables[i]._draw(options);
         }
@@ -484,7 +484,7 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
      * Returns representation of object in a dictionary for easy saving.
      * Use from_dict to recreate object.
      */
-    to_dict: function() {
+    to_dict: function () {
         var dictified_drawables = [];
         for (var i = 0; i < this.drawables.length; i++) {
             dictified_drawables.push(this.drawables[i].to_dict());
@@ -492,14 +492,14 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
         return {
             prefs: this.config.to_key_value_dict(),
             obj_type: this.obj_type,
-            drawables: dictified_drawables
+            drawables: dictified_drawables,
         };
     },
 
     /**
      * Add a drawable to the end of the collection.
      */
-    add_drawable: function(drawable) {
+    add_drawable: function (drawable) {
         this.drawables.push(drawable);
         drawable.container = this;
         this.changed();
@@ -508,7 +508,7 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
     /**
      * Add a drawable before another drawable.
      */
-    add_drawable_before: function(drawable, other) {
+    add_drawable_before: function (drawable, other) {
         this.changed();
         var index = this.drawables.indexOf(other);
         if (index !== -1) {
@@ -521,7 +521,7 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
     /**
      * Replace one drawable with another.
      */
-    replace_drawable: function(old_drawable, new_drawable, update_html) {
+    replace_drawable: function (old_drawable, new_drawable, update_html) {
         var index = this.drawables.indexOf(old_drawable);
         if (index !== -1) {
             this.drawables[index] = new_drawable;
@@ -536,7 +536,7 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
     /**
      * Remove drawable from this collection.
      */
-    remove_drawable: function(drawable) {
+    remove_drawable: function (drawable) {
         var index = this.drawables.indexOf(drawable);
         if (index !== -1) {
             // Found drawable to remove.
@@ -551,7 +551,7 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
     /**
      * Move drawable to another location in collection.
      */
-    move_drawable: function(drawable, new_position) {
+    move_drawable: function (drawable, new_position) {
         var index = this.drawables.indexOf(drawable);
         if (index !== -1) {
             // Remove from current position:
@@ -567,14 +567,14 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
     /**
      * Returns all drawables in this drawable.
      */
-    get_drawables: function() {
+    get_drawables: function () {
         return this.drawables;
     },
 
     /**
      * Returns all <track_type> tracks in collection.
      */
-    get_tracks: function(track_type) {
+    get_tracks: function (track_type) {
         // Initialize queue with copy of drawables array.
         var queue = this.drawables.slice(0);
 
@@ -589,16 +589,16 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
             }
         }
         return tracks;
-    }
+    },
 });
 
 /**
  * A group of drawables that are moveable, visible.
  */
-var DrawableGroup = function(view, container, obj_dict) {
+var DrawableGroup = function (view, container, obj_dict) {
     extend(obj_dict, {
         obj_type: "DrawableGroup",
-        drag_handle_class: "group-handle"
+        drag_handle_class: "group-handle",
     });
     DrawableCollection.call(this, view, container, obj_dict);
 
@@ -650,17 +650,17 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
             name: "composite_icon",
             title: _l("Show composite track"),
             css_class: "layers-stack",
-            on_click_fn: function(group) {
+            on_click_fn: function (group) {
                 $(".tooltip").remove();
                 group.show_composite_track();
-            }
+            },
         },
         // Toggle track filters.
         {
             name: "filters_icon",
             title: _l("Filters"),
             css_class: "ui-slider-050",
-            on_click_fn: function(group) {
+            on_click_fn: function (group) {
                 // TODO: update Tooltip text.
                 if (group.filters_manager.visible()) {
                     // Hiding filters.
@@ -675,33 +675,31 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
                     group.request_draw({ clear_tile_cache: true });
                 }
                 group.filters_manager.toggle();
-            }
+            },
         },
-        Drawable.prototype.action_icons_def[2]
+        Drawable.prototype.action_icons_def[2],
     ],
 
-    build_container_div: function() {
-        var container_div = $("<div/>")
-            .addClass("group")
-            .attr("id", `group_${this.id}`);
+    build_container_div: function () {
+        var container_div = $("<div/>").addClass("group").attr("id", `group_${this.id}`);
         if (this.container) {
             this.container.content_div.append(container_div);
         }
         return container_div;
     },
 
-    hide_contents: function() {
+    hide_contents: function () {
         this.tiles_div.hide();
     },
 
-    show_contents: function() {
+    show_contents: function () {
         // Show the contents div and labels (if present)
         this.tiles_div.show();
         // Request a redraw of the content
         this.request_draw();
     },
 
-    update_icons: function() {
+    update_icons: function () {
         //
         // Handle update when there are no tracks.
         //
@@ -789,7 +787,7 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
                         // FIXME: can filter.copy() be used?
                         const new_filter = new filters_mod.NumberFilter({
                             name: filters[0].name,
-                            index: filters[0].index
+                            index: filters[0].index,
                         });
                         this.filters_manager.add_filter(new_filter);
                     }
@@ -806,7 +804,7 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
     /**
      * Restore individual track filter managers.
      */
-    _restore_filter_managers: function() {
+    _restore_filter_managers: function () {
         for (var i = 0; i < this.drawables.length; i++) {
             this.drawables[i].filters_manager = this.saved_filters_managers[i];
         }
@@ -816,7 +814,7 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
     /**
      *
      */
-    setup_multitrack_filtering: function() {
+    setup_multitrack_filtering: function () {
         // Save tracks' managers and set up shared manager.
         if (this.filters_manager.filters.length > 0) {
             // For all tracks, save current filter manager and set manager to shared (this object's) manager.
@@ -835,33 +833,33 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
     /**
      * Replace group with a single composite track that includes all group's tracks.
      */
-    show_composite_track: function() {
+    show_composite_track: function () {
         var composite_track = new CompositeTrack(this.view, this.view, {
             name: this.config.get_value("name"),
-            drawables: this.drawables
+            drawables: this.drawables,
         });
         this.container.replace_drawable(this, composite_track, true);
         composite_track.request_draw();
     },
 
-    add_drawable: function(drawable) {
+    add_drawable: function (drawable) {
         DrawableCollection.prototype.add_drawable.call(this, drawable);
         this.update_icons();
     },
 
-    remove_drawable: function(drawable) {
+    remove_drawable: function (drawable) {
         DrawableCollection.prototype.remove_drawable.call(this, drawable);
         this.update_icons();
     },
 
-    to_dict: function() {
+    to_dict: function () {
         // If filters are visible, need to restore original filter managers before converting to dict.
         if (this.filters_manager.visible()) {
             this._restore_filter_managers();
         }
 
         var obj_dict = extend(DrawableCollection.prototype.to_dict.call(this), {
-            filters: this.filters_manager.to_dict()
+            filters: this.filters_manager.to_dict(),
         });
 
         // Setup multi-track filtering again.
@@ -872,11 +870,11 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
         return obj_dict;
     },
 
-    request_draw: function(options) {
-        _.each(this.drawables, d => {
+    request_draw: function (options) {
+        _.each(this.drawables, (d) => {
             d.request_draw(options);
         });
-    }
+    },
 });
 
 /**
@@ -885,9 +883,9 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
  *      navigate: when browser view changes to a new locations
  */
 var TracksterView = Backbone.View.extend({
-    initialize: function(obj_dict) {
+    initialize: function (obj_dict) {
         extend(obj_dict, {
-            obj_type: "View"
+            obj_type: "View",
         });
         DrawableCollection.call(this, "View", obj_dict.container, obj_dict);
         this.chrom = null;
@@ -914,44 +912,44 @@ var TracksterView = Backbone.View.extend({
                     key: "name",
                     label: "Name",
                     type: "text",
-                    default_value: ""
+                    default_value: "",
                 },
                 {
                     key: "a_color",
                     label: "A Color",
                     type: "color",
-                    default_value: "#FF0000"
+                    default_value: "#FF0000",
                 },
                 {
                     key: "c_color",
                     label: "C Color",
                     type: "color",
-                    default_value: "#00FF00"
+                    default_value: "#00FF00",
                 },
                 {
                     key: "g_color",
                     label: "G Color",
                     type: "color",
-                    default_value: "#0000FF"
+                    default_value: "#0000FF",
                 },
                 {
                     key: "t_color",
                     label: "T Color",
                     type: "color",
-                    default_value: "#FF00FF"
+                    default_value: "#FF00FF",
                 },
                 {
                     key: "n_color",
                     label: "N Color",
                     type: "color",
-                    default_value: "#AAAAAA"
-                }
+                    default_value: "#AAAAAA",
+                },
             ],
             { name: obj_dict.name }
         );
     },
 
-    render: function() {
+    render: function () {
         // Attribute init.
         this.requested_redraw = false;
 
@@ -960,21 +958,13 @@ var TracksterView = Backbone.View.extend({
 
         var view = this;
         // Top container for things that are fixed at the top
-        this.top_container = $("<div/>")
-            .addClass("top-container")
-            .appendTo(parent_element);
+        this.top_container = $("<div/>").addClass("top-container").appendTo(parent_element);
         // Browser content, primary tracks are contained in here
-        this.browser_content_div = $("<div/>")
-            .addClass("content")
-            .appendTo(parent_element);
+        this.browser_content_div = $("<div/>").addClass("content").appendTo(parent_element);
         // Bottom container for things that are fixed at the bottom
-        this.bottom_container = $("<div/>")
-            .addClass("bottom-container")
-            .appendTo(parent_element);
+        this.bottom_container = $("<div/>").addClass("bottom-container").appendTo(parent_element);
         // Label track fixed at top
-        this.top_labeltrack = $("<div/>")
-            .addClass("top-labeltrack")
-            .appendTo(this.top_container);
+        this.top_labeltrack = $("<div/>").addClass("top-labeltrack").appendTo(this.top_container);
         // Viewport for dragging tracks in center
         this.viewport_container = $("<div/>")
             .addClass("viewport-container")
@@ -984,17 +974,15 @@ var TracksterView = Backbone.View.extend({
         this.content_div = this.viewport_container;
         is_container(this.viewport_container, view);
         // Introduction div shown when there are no tracks.
-        this.intro_div = $("<div/>")
-            .addClass("intro")
-            .appendTo(this.viewport_container);
+        this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container);
         // Add tracks button
         $("<div/>")
             .text("Add Datasets to Visualization")
             .addClass("action-button")
             .appendTo(this.intro_div)
             .click(() => {
-                visualization.select_datasets({ dbkey: view.dbkey }, tracks => {
-                    _.each(tracks, track => {
+                visualization.select_datasets({ dbkey: view.dbkey }, (tracks) => {
+                    _.each(tracks, (track) => {
                         view.add_drawable(object_from_template(track, view, view));
                     });
                 });
@@ -1004,12 +992,8 @@ var TracksterView = Backbone.View.extend({
         // things?) so we need to override any overflow settings here.
         parent_element.attr("style", "overflow: visible !important");
         // Navigation at top
-        this.nav_container = $("<div/>")
-            .addClass("trackster-nav-container")
-            .prependTo(this.top_container);
-        this.nav = $("<div/>")
-            .addClass("trackster-nav")
-            .appendTo(this.nav_container);
+        this.nav_container = $("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);
+        this.nav = $("<div/>").addClass("trackster-nav").appendTo(this.nav_container);
 
         if (this.stand_alone) {
             this.nav_container.addClass("stand-alone");
@@ -1017,38 +1001,25 @@ var TracksterView = Backbone.View.extend({
         }
 
         // Overview (scrollbar and overview plot) at bottom
-        this.overview = $("<div/>")
-            .addClass("overview")
-            .appendTo(this.bottom_container);
-        this.overview_viewport = $("<div/>")
-            .addClass("overview-viewport")
-            .appendTo(this.overview);
+        this.overview = $("<div/>").addClass("overview").appendTo(this.bottom_container);
+        this.overview_viewport = $("<div/>").addClass("overview-viewport").appendTo(this.overview);
         this.overview_close = $("<a/>")
             .attr("title", "Close overview")
             .addClass("icon-button overview-close tooltip")
             .hide()
             .appendTo(this.overview_viewport);
-        this.overview_highlight = $("<div/>")
-            .addClass("overview-highlight")
-            .hide()
-            .appendTo(this.overview_viewport);
-        this.overview_box_background = $("<div/>")
-            .addClass("overview-boxback")
-            .appendTo(this.overview_viewport);
-        this.overview_box = $("<div/>")
-            .addClass("overview-box")
-            .appendTo(this.overview_viewport);
+        this.overview_highlight = $("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);
+        this.overview_box_background = $("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);
+        this.overview_box = $("<div/>").addClass("overview-box").appendTo(this.overview_viewport);
         this.default_overview_height = this.overview_box.height();
 
-        this.nav_controls = $("<div/>")
-            .addClass("nav-controls")
-            .appendTo(this.nav);
+        this.nav_controls = $("<div/>").addClass("nav-controls").appendTo(this.nav);
         this.chrom_select = $("<select/>")
             .attr({ name: "chrom" })
             .addClass("chrom-nav")
             .append("<option value=''>Loading</option>")
             .appendTo(this.nav_controls);
-        var submit_nav = function(e) {
+        var submit_nav = function (e) {
             if (e.type === "focusout" || (e.keyCode || e.which) === 13 || (e.keyCode || e.which) === 27) {
                 if ((e.keyCode || e.which) !== 27) {
                     // Not escape key
@@ -1082,12 +1053,12 @@ var TracksterView = Backbone.View.extend({
             view.nav_input.focus();
             // Set up autocomplete for tracks' features.
             view.nav_input.autocomplete({
-                source: function(request, response) {
+                source: function (request, response) {
                     // Using current text, query each track and create list of all matching features.
                     var all_features = [];
 
-                    var feature_search_deferreds = $.map(view.get_tracks(FeatureTrack), t =>
-                        t.data_manager.search_features(request.term).success(dataset_features => {
+                    var feature_search_deferreds = $.map(view.get_tracks(FeatureTrack), (t) =>
+                        t.data_manager.search_features(request.term).success((dataset_features) => {
                             all_features = all_features.concat(dataset_features);
                         })
                     );
@@ -1095,21 +1066,18 @@ var TracksterView = Backbone.View.extend({
                     // When all searching is done, fill autocomplete.
                     $.when.apply($, feature_search_deferreds).done(() => {
                         response(
-                            $.map(all_features, feature => ({
+                            $.map(all_features, (feature) => ({
                                 label: feature[0],
-                                value: feature[1]
+                                value: feature[1],
                             }))
                         );
                     });
                 },
-                minLength: 2
+                minLength: 2,
             });
         });
         if (this.vis_id !== undefined) {
-            this.hidden_input = $("<input/>")
-                .attr("type", "hidden")
-                .val(this.vis_id)
-                .appendTo(this.nav_controls);
+            this.hidden_input = $("<input/>").attr("type", "hidden").val(this.vis_id).appendTo(this.nav_controls);
         }
 
         this.zo_link = $("<a/>")
@@ -1150,23 +1118,21 @@ var TracksterView = Backbone.View.extend({
         */
 
         // Blur tool/filter inputs when user clicks on content div.
-        this.browser_content_div.click(function(e) {
-            $(this)
-                .find("input")
-                .trigger("blur");
+        this.browser_content_div.click(function (e) {
+            $(this).find("input").trigger("blur");
         });
 
         // Double clicking zooms in
-        this.browser_content_div.bind("dblclick", function(e) {
+        this.browser_content_div.bind("dblclick", function (e) {
             view.zoom_in(e.pageX, this.viewport_container);
         });
 
         // Dragging the overview box (~ horizontal scroll bar)
         this.overview_box
-            .bind("dragstart", function(e, d) {
+            .bind("dragstart", function (e, d) {
                 this.current_x = d.offsetX;
             })
-            .bind("drag", function(e, d) {
+            .bind("drag", function (e, d) {
                 var delta = d.offsetX - this.current_x;
                 this.current_x = d.offsetX;
                 var delta_chrom = Math.round(
@@ -1192,7 +1158,7 @@ var TracksterView = Backbone.View.extend({
                 d.current_height = e.clientY;
                 d.current_x = d.offsetX;
             })
-            .bind("drag", function(e, d) {
+            .bind("drag", function (e, d) {
                 var container = $(this);
                 var delta = d.offsetX - d.current_x;
                 var new_scroll = container.scrollTop() - (e.clientY - d.current_height);
@@ -1219,7 +1185,7 @@ var TracksterView = Backbone.View.extend({
 
         // Dragging in the top label track allows selecting a region to zoom in on selected region.
         this.top_labeltrack
-            .bind("dragstart", function(e, d) {
+            .bind("dragstart", function (e, d) {
                 return $("<div/>")
                     .addClass("zoom-area")
                     .css("height", view.browser_content_div.height() + view.top_labeltrack.height() + 1)
@@ -1228,7 +1194,7 @@ var TracksterView = Backbone.View.extend({
             .bind("drag", (e, d) => {
                 $(d.proxy).css({
                     left: Math.min(e.pageX, d.startX) - view.container.offset().left,
-                    width: Math.abs(e.pageX - d.startX)
+                    width: Math.abs(e.pageX - d.startX),
                 });
 
                 var min = Math.min(e.pageX, d.startX) - view.container.offset().left;
@@ -1279,7 +1245,7 @@ var TracksterView = Backbone.View.extend({
 
         this.add_label_track(new LabelTrack(this, { content_div: this.top_labeltrack }));
 
-        $(window).bind("resize", function() {
+        $(window).bind("resize", function () {
             // Stop previous timer.
             if (this.resize_timer) {
                 window.clearTimeout(this.resize_timer);
@@ -1298,19 +1264,19 @@ var TracksterView = Backbone.View.extend({
         $(window).trigger("resize");
     },
 
-    get_base_color: function(base) {
+    get_base_color: function (base) {
         return this.config.get_value(`${base.toLowerCase()}_color`) || this.config.get_value("n_color");
-    }
+    },
 });
 
 // FIXME: need to use this approach to enable inheritance of DrawableCollection functions.
 extend(TracksterView.prototype, DrawableCollection.prototype, {
-    changed: function() {
+    changed: function () {
         this.has_changes = true;
     },
 
     /** Add or remove intro div depending on view state. */
-    update_intro_div: function() {
+    update_intro_div: function () {
         this.intro_div.toggle(this.drawables.length === 0);
     },
 
@@ -1318,7 +1284,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
      * Triggers navigate events as needed. If there is a delay,
      * then event is triggered only after navigation has stopped.
      */
-    trigger_navigate: function(new_chrom, new_low, new_high, delay) {
+    trigger_navigate: function (new_chrom, new_low, new_high, delay) {
         // Stop previous timer.
         if (this.timer) {
             window.clearTimeout(this.timer);
@@ -1335,7 +1301,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
         }
     },
 
-    update_location: function(low, high) {
+    update_location: function (low, high) {
         this.location_span.text(`${util.commatize(low)} - ${util.commatize(high)}`);
         this.nav_input.val(`${this.chrom}:${util.commatize(low)}-${util.commatize(high)}`);
 
@@ -1351,7 +1317,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
      * Load chrom data for the view. Returns a jQuery Deferred.
      */
     // FIXME: instead of loading chrom data, should load and store genome object.
-    load_chroms: function(url_parms) {
+    load_chroms: function (url_parms) {
         url_parms.num = MAX_CHROMS_SELECTABLE;
 
         var chrom_data = $.Deferred();
@@ -1359,7 +1325,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
             url: `${getAppRoot()}api/genomes/${this.dbkey}`,
             data: url_parms,
             dataType: "json",
-            success: result => {
+            success: (result) => {
                 // Do nothing if could not load chroms.
                 if (result.chrom_info.length === 0) {
                     return;
@@ -1393,14 +1359,14 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
 
                 chrom_data.resolve(result.chrom_info);
             },
-            error: function() {
+            error: function () {
                 alert(`Could not load chroms for this dbkey: ${this.dbkey}`);
-            }
+            },
         });
         return chrom_data;
     },
 
-    change_chrom: function(chrom, low, high) {
+    change_chrom: function (chrom, low, high) {
         var view = this;
         // If chrom data is still loading, wait for it.
         if (!view.chrom_data) {
@@ -1420,13 +1386,13 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
         //
         if (chrom === "previous") {
             view.load_chroms({
-                low: this.chrom_start_index - MAX_CHROMS_SELECTABLE
+                low: this.chrom_start_index - MAX_CHROMS_SELECTABLE,
             });
             return;
         }
         if (chrom === "next") {
             view.load_chroms({
-                low: this.chrom_start_index + MAX_CHROMS_SELECTABLE
+                low: this.chrom_start_index + MAX_CHROMS_SELECTABLE,
             });
             return;
         }
@@ -1496,7 +1462,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
      * chr7 89999
      * chr8 90000 990000
      */
-    go_to: function(str) {
+    go_to: function (str) {
         // Remove commas.
         str = str.replace(/,/g, "");
 
@@ -1513,13 +1479,13 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
         this.change_chrom(chrom, new_low, new_high);
     },
 
-    move_fraction: function(fraction) {
+    move_fraction: function (fraction) {
         var view = this;
         var span = view.high - view.low;
         this.move_delta(fraction * span);
     },
 
-    move_delta: function(delta_chrom) {
+    move_delta: function (delta_chrom) {
         //
         // Update low, high.
         //
@@ -1562,7 +1528,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
     /**
      * Add a drawable to the view.
      */
-    add_drawable: function(drawable) {
+    add_drawable: function (drawable) {
         DrawableCollection.prototype.add_drawable.call(this, drawable);
         drawable.init();
         this.changed();
@@ -1576,7 +1542,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
         });
     },
 
-    add_label_track: function(label_track) {
+    add_label_track: function (label_track) {
         label_track.view = this;
         label_track.init();
         this.label_tracks.push(label_track);
@@ -1585,18 +1551,18 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
     /**
      * Remove drawable from the view.
      */
-    remove_drawable: function(drawable, hide) {
+    remove_drawable: function (drawable, hide) {
         DrawableCollection.prototype.remove_drawable.call(this, drawable);
         if (hide) {
             var view = this;
-            drawable.container_div.hide(0, function() {
+            drawable.container_div.hide(0, function () {
                 $(this).remove();
                 view.update_intro_div();
             });
         }
     },
 
-    reset: function() {
+    reset: function () {
         this.low = this.max_low;
         this.high = this.max_high;
         this.viewport_container.find(".yaxislabel").remove();
@@ -1606,15 +1572,15 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
      * Request that view redraw one or more of view's drawables. If drawable is not specified,
      * all drawables are redrawn.
      */
-    request_redraw: function(options, drawable) {
+    request_redraw: function (options, drawable) {
         var view = this;
 
         var // Either redrawing a single drawable or all view's drawables.
             track_list = drawable ? [drawable] : view.drawables;
 
         // Add/update tracks in track list to redraw list.
-        _.each(track_list, track => {
-            var track_options = _.find(view.tracks_to_be_redrawn, to => to[0] === track);
+        _.each(track_list, (track) => {
+            var track_options = _.find(view.tracks_to_be_redrawn, (to) => to[0] === track);
 
             if (track_options) {
                 // Track already in list; update options.
@@ -1639,7 +1605,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
      * NOTE: this method should never be called directly; request_redraw() should be used so
      * that requestAnimationFrame can manage redrawing.
      */
-    _redraw: function() {
+    _redraw: function () {
         // TODO: move this code to function that does location setting.
 
         // Clear because requested redraw is being handled now.
@@ -1676,7 +1642,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
         this.overview_box
             .css({
                 left: left_px,
-                width: Math.max(min_width_px, width_px)
+                width: Math.max(min_width_px, width_px),
             })
             .show();
         if (width_px < min_width_px) {
@@ -1685,12 +1651,12 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
         if (this.overview_highlight) {
             this.overview_highlight.css({
                 left: left_px,
-                width: width_px
+                width: width_px,
             });
         }
 
         // Draw data tracks.
-        _.each(this.tracks_to_be_redrawn, track_options => {
+        _.each(this.tracks_to_be_redrawn, (track_options) => {
             var track = track_options[0];
             var options = track_options[1];
             if (track) {
@@ -1700,12 +1666,12 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
         this.tracks_to_be_redrawn = [];
 
         // Draw label tracks.
-        _.each(this.label_tracks, label_track => {
+        _.each(this.label_tracks, (label_track) => {
             label_track._draw();
         });
     },
 
-    zoom_in: function(point, container) {
+    zoom_in: function (point, container) {
         if (this.max_high === 0 || this.high - this.low <= this.min_separation) {
             return;
         }
@@ -1722,7 +1688,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
         this.request_redraw();
     },
 
-    zoom_out: function() {
+    zoom_out: function () {
         if (this.max_high === 0) {
             return;
         }
@@ -1736,20 +1702,20 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
     },
 
     /** Resize viewport. Use this method if header/footer content has changed in size. */
-    resize_viewport: function() {
+    resize_viewport: function () {
         this.viewport_container.height(
             this.container.height() - this.top_container.height() - this.bottom_container.height()
         );
     },
 
     /** Called when window is resized. */
-    resize_window: function() {
+    resize_window: function () {
         this.resize_viewport();
         this.request_redraw();
     },
 
     /** Show a Drawable in the overview. */
-    set_overview: function(drawable) {
+    set_overview: function (drawable) {
         if (this.overview_drawable) {
             // If drawable to be set as overview is already in overview, do nothing.
             // Otherwise, remove overview.
@@ -1761,7 +1727,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
 
         // Set new overview.
         var overview_drawable = drawable.copy({
-            content_div: this.overview_viewport
+            content_div: this.overview_viewport,
         });
 
         var view = this;
@@ -1781,7 +1747,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
     },
 
     /** Close and reset overview. */
-    reset_overview: function() {
+    reset_overview: function () {
         // Update UI.
         $(".tooltip").remove();
         this.overview_viewport.find(".track-tile").remove();
@@ -1791,7 +1757,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
         this.overview_highlight.hide();
         this.resize_window();
         this.overview_drawable = null;
-    }
+    },
 });
 
 /**
@@ -1799,10 +1765,10 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
  */
 var TracksterTool = tools_mod.Tool.extend({
     defaults: {
-        track: null
+        track: null,
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         tools_mod.Tool.prototype.initialize.call(this, options);
 
         // Restore tool visibility from state; default to hidden.
@@ -1818,11 +1784,11 @@ var TracksterTool = tools_mod.Tool.extend({
         this.remove_inputs(["data", "hidden_data", "conditional"]);
     },
 
-    state_dict: function(options) {
+    state_dict: function (options) {
         return _.extend(this.get_inputs_dict(), {
-            hidden: !this.is_visible()
+            hidden: !this.is_visible(),
         });
-    }
+    },
 });
 
 /**
@@ -1830,23 +1796,17 @@ var TracksterTool = tools_mod.Tool.extend({
  */
 var ToolParameterView = Backbone.View.extend({
     events: {
-        "change :input": "update_value"
+        "change :input": "update_value",
     },
 
-    render: function() {
+    render: function () {
         var param_div = this.$el.addClass("param-row");
         var param = this.model;
 
         // Param label.
-        $("<div>")
-            .addClass("param-label")
-            .text(param.get("label"))
-            .appendTo(param_div);
+        $("<div>").addClass("param-label").text(param.get("label")).appendTo(param_div);
         // Param HTML.
-        var html_div = $("<div/>")
-            .addClass("param-input")
-            .html(param.get("html"))
-            .appendTo(param_div);
+        var html_div = $("<div/>").addClass("param-input").html(param.get("html")).appendTo(param_div);
         // Set initial value.
         html_div.find(":input").val(param.get("value"));
 
@@ -1854,47 +1814,45 @@ var ToolParameterView = Backbone.View.extend({
         $("<div style='clear: both;'/>").appendTo(param_div);
     },
 
-    update_value: function(update_event) {
+    update_value: function (update_event) {
         this.model.set_value($(update_event.target).val());
-    }
+    },
 });
 
 /**
  * View for TracksterTool.
  */
 var TracksterToolView = Backbone.View.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.model.on("change:hidden", this.set_visible, this);
     },
 
     /**
      * Render tool UI.
      */
-    render: function() {
+    render: function () {
         var self = this;
         var tool = this.model;
         var parent_div = this.$el.addClass("dynamic-tool").hide();
 
         // Prevent div events from propogating to other elements.
         parent_div
-            .bind("drag", e => {
+            .bind("drag", (e) => {
                 e.stopPropagation();
             })
-            .click(e => {
+            .click((e) => {
                 e.stopPropagation();
             })
-            .bind("dblclick", e => {
+            .bind("dblclick", (e) => {
                 e.stopPropagation();
             })
-            .keydown(e => {
+            .keydown((e) => {
                 e.stopPropagation();
             });
 
         // Add name, inputs.
-        $("<div class='tool-name'>")
-            .appendTo(parent_div)
-            .text(tool.get("name"));
-        tool.get("inputs").each(param => {
+        $("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));
+        tool.get("inputs").each((param) => {
             // Render parameter.
             var param_view = new ToolParameterView({ model: param });
             param_view.render();
@@ -1902,14 +1860,12 @@ var TracksterToolView = Backbone.View.extend({
         });
 
         // Highlight value for inputs for easy replacement.
-        parent_div.find("input").click(function() {
+        parent_div.find("input").click(function () {
             $(this).select();
         });
 
         // Add buttons for running on dataset, region.
-        var run_tool_row = $("<div>")
-            .addClass("param-row")
-            .appendTo(parent_div);
+        var run_tool_row = $("<div>").addClass("param-row").appendTo(parent_div);
         var run_on_dataset_button = $("<input type='submit'>")
             .attr("value", "Run on complete dataset")
             .appendTo(run_tool_row);
@@ -1932,14 +1888,14 @@ var TracksterToolView = Backbone.View.extend({
     /**
      * Show or hide tool depending on tool visibility state.
      */
-    set_visible: function() {
+    set_visible: function () {
         this.$el.toggle(this.model.is_visible());
     },
 
     /**
      * Update tool parameters.
      */
-    update_params: function() {
+    update_params: function () {
         for (var i = 0; i < this.params.length; i++) {
             this.params[i].update_value();
         }
@@ -1948,7 +1904,7 @@ var TracksterToolView = Backbone.View.extend({
     /**
      * Run tool on dataset. Output is placed in dataset's history and no changes to viz are made.
      */
-    run_on_dataset: function() {
+    run_on_dataset: function () {
         var tool = this.model;
         const Galaxy = getGalaxyInstance();
         this.run(
@@ -1956,20 +1912,20 @@ var TracksterToolView = Backbone.View.extend({
             {
                 target_dataset_id: this.model.get("track").dataset.id,
                 action: "rerun",
-                tool_id: tool.id
+                tool_id: tool.id,
             },
             null,
-            track_data => {
+            (track_data) => {
                 Galaxy.modal.show({
                     title: `${tool.get("name")} is Running`,
                     body: `${tool.get(
                         "name"
                     )} is running on the complete dataset. Tool outputs are in dataset's history.`,
                     buttons: {
-                        Close: function() {
+                        Close: function () {
                             Galaxy.modal.hide();
-                        }
-                    }
+                        },
+                    },
                 });
             }
         );
@@ -1979,7 +1935,7 @@ var TracksterToolView = Backbone.View.extend({
      * Run dataset on visible region. This creates a new track and sets the track's contents
      * to the tool's output.
      */
-    run_on_region: function() {
+    run_on_region: function () {
         //
         // Create track for tool's output immediately to provide user feedback.
         //
@@ -1990,14 +1946,14 @@ var TracksterToolView = Backbone.View.extend({
         var region = new visualization.GenomeRegion({
             chrom: track.view.chrom,
             start: track.view.low,
-            end: track.view.high
+            end: track.view.high,
         });
 
         var url_params = {
             target_dataset_id: track.dataset.id,
             action: "rerun",
             tool_id: tool.id,
-            regions: [region.toJSON()]
+            regions: [region.toJSON()],
         };
 
         // Set name of track to include tool name, parameters, and region used.
@@ -2010,7 +1966,7 @@ var TracksterToolView = Backbone.View.extend({
         if (track.container === track.view) {
             // Create new group.
             var group = new DrawableGroup(track.view, track.view, {
-                name: track.config.get_value("name")
+                name: track.config.get_value("name"),
             });
 
             // Replace track with group.
@@ -2031,7 +1987,7 @@ var TracksterToolView = Backbone.View.extend({
         // Create and init new track.
         var new_track = new track.constructor(track.view, container, {
             name: track_name,
-            hda_ldda: "hda"
+            hda_ldda: "hda",
         });
         new_track.init_for_tool_data();
         new_track.change_mode(track.mode);
@@ -2041,7 +1997,7 @@ var TracksterToolView = Backbone.View.extend({
         new_track.tiles_div.text("Starting job.");
 
         // Run tool.
-        this.run(url_params, new_track, track_data => {
+        this.run(url_params, new_track, (track_data) => {
             new_track.set_dataset(new Dataset(track_data));
             new_track.tiles_div.text("Running job.");
             new_track.init();
@@ -2051,7 +2007,7 @@ var TracksterToolView = Backbone.View.extend({
     /**
      * Run tool using a set of URL params and a success callback.
      */
-    run: function(url_params, new_track, success_callback) {
+    run: function (url_params, new_track, success_callback) {
         // Run tool.
         url_params.inputs = this.model.get_inputs_dict();
         var ss_deferred = new util.ServerStateDeferred({
@@ -2060,19 +2016,19 @@ var TracksterToolView = Backbone.View.extend({
                 data: JSON.stringify(url_params),
                 dataType: "json",
                 contentType: "application/json",
-                type: "POST"
+                type: "POST",
             },
             interval: 2000,
-            success_fn: function(response) {
+            success_fn: function (response) {
                 return response !== "pending";
-            }
+            },
         });
 
         // Start with this status message.
         //new_track.container_div.addClass("pending");
         //new_track.content_div.html(DATA_PENDING);
 
-        $.when(ss_deferred.go()).then(response => {
+        $.when(ss_deferred.go()).then((response) => {
             if (response === "no converter") {
                 // No converter available for input datasets, so cannot run tool.
                 new_track.container_div.addClass("error");
@@ -2086,18 +2042,18 @@ var TracksterToolView = Backbone.View.extend({
                 success_callback(response);
             }
         });
-    }
+    },
 });
 
 /**
  * Generates scale values based on filter and feature's value for filter.
  */
-var FilterScaler = function(filter, default_val) {
+var FilterScaler = function (filter, default_val) {
     painters.Scaler.call(this, default_val);
     this.filter = filter;
 };
 
-FilterScaler.prototype.gen_val = function(feature_data) {
+FilterScaler.prototype.gen_val = function (feature_data) {
     // If filter is not initalized yet, return default val.
     if (
         this.filter.high === Number.MAX_VALUE ||
@@ -2114,7 +2070,7 @@ FilterScaler.prototype.gen_val = function(feature_data) {
 /**
  * Tiles drawn by tracks.
  */
-var Tile = function(track, region, w_scale, canvas, data) {
+var Tile = function (track, region, w_scale, canvas, data) {
     this.track = track;
     this.region = region;
     this.low = region.get("start");
@@ -2132,12 +2088,12 @@ var Tile = function(track, region, w_scale, canvas, data) {
  */
 Tile.prototype.predisplay_actions = () => {};
 
-var LineTrackTile = function(track, region, w_scale, canvas, data) {
+var LineTrackTile = function (track, region, w_scale, canvas, data) {
     Tile.call(this, track, region, w_scale, canvas, data);
 };
 LineTrackTile.prototype.predisplay_actions = () => {};
 
-var FeatureTrackTile = function(
+var FeatureTrackTile = function (
     track,
     region,
     w_scale,
@@ -2332,10 +2288,10 @@ FeatureTrackTile.prototype.predisplay_actions = () => {
  * -------> ReadTrack
  * ----> VariantTrack
  */
-var Track = function(view, container, obj_dict) {
+var Track = function (view, container, obj_dict) {
     // For now, track's container is always view.
     extend(obj_dict, {
-        drag_handle_class: "draghandle"
+        drag_handle_class: "draghandle",
     });
     Drawable.call(this, view, container, obj_dict);
 
@@ -2363,11 +2319,11 @@ var Track = function(view, container, obj_dict) {
                   genome: new visualization.Genome({
                       key: view.dbkey,
                       chroms_info: {
-                          chrom_info: view.chrom_data
-                      }
+                          chrom_info: view.chrom_data,
+                      },
                   }),
                   data_mode_compatible: this.data_and_mode_compatible,
-                  can_subset: this.can_subset
+                  can_subset: this.can_subset,
               });
 
     // Height attributes: min height, max height, and visible height.
@@ -2394,7 +2350,7 @@ extend(Track.prototype, Drawable.prototype, {
             name: "mode_icon",
             title: _l("Set display mode"),
             css_class: "chevron-expand",
-            on_click_fn: function() {}
+            on_click_fn: function () {},
         },
         // Hide/show content.
         Drawable.prototype.action_icons_def[0],
@@ -2403,9 +2359,9 @@ extend(Track.prototype, Drawable.prototype, {
             name: "overview_icon",
             title: _l("Set as overview"),
             css_class: "application-dock-270",
-            on_click_fn: function(track) {
+            on_click_fn: function (track) {
                 track.view.set_overview(track);
-            }
+            },
         },
         // Edit config.
         Drawable.prototype.action_icons_def[1],
@@ -2414,7 +2370,7 @@ extend(Track.prototype, Drawable.prototype, {
             name: "filters_icon",
             title: _l("Filters"),
             css_class: "ui-slider-050",
-            on_click_fn: function(drawable) {
+            on_click_fn: function (drawable) {
                 // TODO: update Tooltip text.
                 if (drawable.filters_manager.visible()) {
                     drawable.filters_manager.clear_filters();
@@ -2422,14 +2378,14 @@ extend(Track.prototype, Drawable.prototype, {
                     drawable.filters_manager.init_filters();
                 }
                 drawable.filters_manager.toggle();
-            }
+            },
         },
         // Toggle track tool.
         {
             name: "tools_icon",
             title: _l("Tool"),
             css_class: "hammer",
-            on_click_fn: function(track) {
+            on_click_fn: function (track) {
                 // TODO: update Tooltip text.
 
                 track.tool.toggle();
@@ -2442,14 +2398,14 @@ extend(Track.prototype, Drawable.prototype, {
                 }
                 // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed.
                 $(".tooltip").remove();
-            }
+            },
         },
         // Go to parameter exploration visualization.
         {
             name: "param_space_viz_icon",
             title: _l("Tool parameter space visualization"),
             css_class: "arrow-split",
-            on_click_fn: track => {
+            on_click_fn: (track) => {
                 const Galaxy = getGalaxyInstance();
 
                 var html = `
@@ -2474,15 +2430,13 @@ extend(Track.prototype, Drawable.prototype, {
                     var view_region = new visualization.GenomeRegion({
                         chrom: this.view.chrom,
                         start: this.view.low,
-                        end: this.view.high
+                        end: this.view.high,
                     });
                     var bookmarked_regions = _.map(
                         $(".bookmark"),
-                        elt =>
+                        (elt) =>
                             new visualization.GenomeRegion({
-                                from_str: $(elt)
-                                    .children(".position")
-                                    .text()
+                                from_str: $(elt).children(".position").text(),
                             })
                     );
 
@@ -2504,7 +2458,7 @@ extend(Track.prototype, Drawable.prototype, {
                     window.top.location.href = `${getAppRoot()}visualization/sweepster?${$.param({
                         dataset_id: track.dataset.id,
                         hda_ldda: track.dataset.get("hda_ldda"),
-                        regions: JSON.stringify(new Backbone.Collection(regions).toJSON())
+                        regions: JSON.stringify(new Backbone.Collection(regions).toJSON()),
                     })}`;
                 };
 
@@ -2525,28 +2479,26 @@ extend(Track.prototype, Drawable.prototype, {
                 Galaxy.modal.show({
                     title: "Visualize tool parameter space and output from different parameter settings?",
                     body: html,
-                    buttons: { No: cancel_fn, Yes: ok_fn }
+                    buttons: { No: cancel_fn, Yes: ok_fn },
                 });
-            }
+            },
         },
         // Remove track.
-        Drawable.prototype.action_icons_def[2]
+        Drawable.prototype.action_icons_def[2],
     ],
 
-    can_draw: function() {
+    can_draw: function () {
         return this.dataset && Drawable.prototype.can_draw.call(this);
     },
 
-    build_container_div: function() {
-        return $("<div/>")
-            .addClass("track")
-            .attr("id", `track_${this.id}`);
+    build_container_div: function () {
+        return $("<div/>").addClass("track").attr("id", `track_${this.id}`);
     },
 
     /**
      * Set track's dataset.
      */
-    set_dataset: function(dataset) {
+    set_dataset: function (dataset) {
         this.dataset = dataset;
         this.data_manager.set("dataset", dataset);
     },
@@ -2554,14 +2506,14 @@ extend(Track.prototype, Drawable.prototype, {
     /**
      * Action to take during resize.
      */
-    on_resize: function() {
+    on_resize: function () {
         this.request_draw({ clear_tile_cache: true });
     },
 
     /**
      * Add resizing handle to drawable's container_div.
      */
-    add_resize_handle: function() {
+    add_resize_handle: function () {
         var track = this;
         var in_handle = false;
         var in_drag = false;
@@ -2614,14 +2566,14 @@ extend(Track.prototype, Drawable.prototype, {
      * Hide any elements that are part of the tracks contents area. Should
      * remove as approprite, the track will be redrawn by show_contents.
      */
-    hide_contents: function() {
+    hide_contents: function () {
         // Hide tiles.
         this.tiles_div.hide();
         // Hide any y axis labels (common to several track types)
         this.container_div.find(".yaxislabel, .track-resize").hide();
     },
 
-    show_contents: function() {
+    show_contents: function () {
         // Show the contents div and labels (if present)
         this.tiles_div.show();
         this.container_div.find(".yaxislabel, .track-resize").show();
@@ -2632,7 +2584,7 @@ extend(Track.prototype, Drawable.prototype, {
     /**
      * Returns track type.
      */
-    get_type: function() {
+    get_type: function () {
         // Order is important: start with most-specific classes and go up the track hierarchy.
         if (this instanceof LabelTrack) {
             return "LabelTrack";
@@ -2655,18 +2607,15 @@ extend(Track.prototype, Drawable.prototype, {
     /**
      * Remove visualization content and display message.
      */
-    show_message: function(msg_html) {
+    show_message: function (msg_html) {
         this.tiles_div.remove();
-        return $("<span/>")
-            .addClass("message")
-            .html(msg_html)
-            .appendTo(this.content_div);
+        return $("<span/>").addClass("message").html(msg_html).appendTo(this.content_div);
     },
 
     /**
      * Initialize and draw the track.
      */
-    init: function(retry) {
+    init: function (retry) {
         // FIXME: track should have a 'state' attribute that is checked on load; this state attribute should be
         // used in this function to determine what action(s) to take.
 
@@ -2683,9 +2632,7 @@ extend(Track.prototype, Drawable.prototype, {
         track.content_div.children().remove();
         track.container_div.removeClass("nodata error pending");
 
-        track.tiles_div = $("<div/>")
-            .addClass("tiles")
-            .appendTo(track.content_div);
+        track.tiles_div = $("<div/>").addClass("tiles").appendTo(track.content_div);
 
         //
         // Tracks with no dataset id are handled differently.
@@ -2703,10 +2650,10 @@ extend(Track.prototype, Drawable.prototype, {
             hda_ldda: track.dataset.get("hda_ldda"),
             data_type: this.dataset_check_type,
             chrom: track.view.chrom,
-            retry: retry
+            retry: retry,
         };
 
-        $.getJSON(this.dataset.url(), params, result => {
+        $.getJSON(this.dataset.url(), params, (result) => {
             if (!result || result === "error" || result.kind === "error") {
                 // Dataset is in error state.
                 track.container_div.addClass("error");
@@ -2722,10 +2669,10 @@ extend(Track.prototype, Drawable.prototype, {
                                     title: _l("Trackster Error"),
                                     body: `<pre>${result.message}</pre>`,
                                     buttons: {
-                                        Close: function() {
+                                        Close: function () {
                                             Galaxy.modal.hide();
-                                        }
-                                    }
+                                        },
+                                    },
                                 });
                             })
                     );
@@ -2783,7 +2730,7 @@ extend(Track.prototype, Drawable.prototype, {
     /**
      * Additional initialization required before drawing track for the first time.
      */
-    predraw_init: function() {
+    predraw_init: function () {
         var track = this;
         return $.getJSON(
             track.dataset.url(),
@@ -2793,9 +2740,9 @@ extend(Track.prototype, Drawable.prototype, {
                 chrom: track.view.chrom,
                 low: 0,
                 high: track.view.max_high,
-                hda_ldda: track.dataset.get("hda_ldda")
+                hda_ldda: track.dataset.get("hda_ldda"),
             },
-            result => {
+            (result) => {
                 var data = result.data;
 
                 // Tracks may not have stat data either because there is no data or data is not yet ready.
@@ -2821,12 +2768,12 @@ extend(Track.prototype, Drawable.prototype, {
     /**
      * Returns all drawables in this drawable.
      */
-    get_drawables: function() {
+    get_drawables: function () {
         return this;
-    }
+    },
 });
 
-var TiledTrack = function(view, container, obj_dict) {
+var TiledTrack = function (view, container, obj_dict) {
     Track.call(this, view, container, obj_dict);
 
     var track = this;
@@ -2844,7 +2791,7 @@ var TiledTrack = function(view, container, obj_dict) {
         ? new TracksterTool(
               _.extend(obj_dict.tool, {
                   track: this,
-                  tool_state: obj_dict.tool_state
+                  tool_state: obj_dict.tool_state,
               })
           )
         : null;
@@ -2869,15 +2816,11 @@ var TiledTrack = function(view, container, obj_dict) {
     }
 
     // Add tiles_div, overlay_div to content_div.
-    this.tiles_div = $("<div/>")
-        .addClass("tiles")
-        .appendTo(this.content_div);
+    this.tiles_div = $("<div/>").addClass("tiles").appendTo(this.content_div);
     if (!this.config.get_value("content_visible")) {
         this.tiles_div.hide();
     }
-    this.overlay_div = $("<div/>")
-        .addClass("overlay")
-        .appendTo(this.content_div);
+    this.overlay_div = $("<div/>").addClass("overlay").appendTo(this.content_div);
 
     if (obj_dict.mode) {
         this.change_mode(obj_dict.mode);
@@ -2890,23 +2833,23 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             name: "show_more_rows_icon",
             title: "To minimize track height, not all feature rows are displayed. Click to display more rows.",
             css_class: "exclamation",
-            on_click_fn: function(track) {
+            on_click_fn: function (track) {
                 $(".tooltip").remove();
                 track.slotters[track.view.resolution_px_b].max_rows *= 2;
                 track.request_draw({ clear_tile_cache: true });
             },
-            hide: true
-        }
+            hide: true,
+        },
     ]),
 
     /**
      * Returns a copy of the track. The copy uses the same data manager so that the tracks can share data.
      */
-    copy: function(container) {
+    copy: function (container) {
         // Create copy.
         var obj_dict = this.to_dict();
         extend(obj_dict, {
-            data_manager: this.data_manager
+            data_manager: this.data_manager,
         });
         var new_track = new this.constructor(this.view, container, obj_dict);
         // Misc. init and return.
@@ -2918,7 +2861,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Set filters manager + HTML elements.
      */
-    set_filters_manager: function(filters_manager) {
+    set_filters_manager: function (filters_manager) {
         this.filters_manager = filters_manager;
         this.header_div.after(this.filters_manager.parent_div);
     },
@@ -2927,24 +2870,24 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * Returns representation of object in a dictionary for easy saving.
      * Use from_dict to recreate object.
      */
-    to_dict: function() {
+    to_dict: function () {
         return {
             track_type: this.get_type(),
             dataset: {
                 id: this.dataset.id,
-                hda_ldda: this.dataset.get("hda_ldda")
+                hda_ldda: this.dataset.get("hda_ldda"),
             },
             prefs: this.config.to_key_value_dict(),
             mode: this.mode,
             filters: this.filters_manager.to_dict(),
-            tool_state: this.tool ? this.tool.state_dict() : {}
+            tool_state: this.tool ? this.tool.state_dict() : {},
         };
     },
 
     /**
      * Set track bounds for current chromosome.
      */
-    set_min_max: function() {
+    set_min_max: function () {
         var track = this;
 
         return $.getJSON(
@@ -2955,9 +2898,9 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
                 chrom: track.view.chrom,
                 low: 0,
                 high: track.view.max_high,
-                hda_ldda: track.dataset.get("hda_ldda")
+                hda_ldda: track.dataset.get("hda_ldda"),
             },
-            result => {
+            (result) => {
                 var data = result.data;
                 if (
                     isNaN(parseFloat(track.config.get_value("min_value"))) ||
@@ -2982,7 +2925,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Change track's mode.
      */
-    change_mode: function(new_mode) {
+    change_mode: function (new_mode) {
         var track = this;
         // TODO: is it necessary to store the mode in two places (.mode and track_config)?
         track.mode = new_mode;
@@ -3001,7 +2944,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Update track's buttons.
      */
-    update_icons: function() {
+    update_icons: function () {
         var track = this;
 
         //
@@ -3020,14 +2963,14 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * Generate a key for the tile cache.
      * TODO: create a TileCache object (like DataCache) and generate key internally.
      */
-    _gen_tile_cache_key: function(w_scale, tile_region) {
+    _gen_tile_cache_key: function (w_scale, tile_region) {
         return `${w_scale}_${tile_region}`;
     },
 
     /**
      * Request that track be drawn.
      */
-    request_draw: function(options) {
+    request_draw: function (options) {
         if (options && options.clear_tile_cache) {
             this.tile_cache.clear();
         }
@@ -3037,7 +2980,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Actions to be taken before drawing.
      */
-    before_draw: function() {
+    before_draw: function () {
         // Clear because this is set when drawing.
         this.max_height_px = 0;
     },
@@ -3051,7 +2994,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * NOTE: this function should never be called directly; use request_draw() so that drawing
      * management can be used.
      */
-    _draw: function(options) {
+    _draw: function (options) {
         if (!this.can_draw()) {
             return;
         }
@@ -3103,11 +3046,11 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
                 chrom: this.view.chrom,
                 start: tile_index * tile_width,
                 // Tile high cannot be larger than view.max_high, which the chromosome length.
-                end: Math.min((tile_index + 1) * tile_width, this.view.max_high)
+                end: Math.min((tile_index + 1) * tile_width, this.view.max_high),
             });
             tile_promise = this.draw_helper(tile_region, w_scale, options);
             tile_promises.push(tile_promise);
-            $.when(tile_promise).then(tile => {
+            $.when(tile_promise).then((tile) => {
                 tiles.push(tile);
             });
 
@@ -3117,10 +3060,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
 
         // Step (c) for (re)moving tiles when clear_after is false.
         if (!clear_after) {
-            this.tiles_div
-                .children(".remove")
-                .removeClass("remove")
-                .remove();
+            this.tiles_div.children(".remove").removeClass("remove").remove();
         }
 
         // When all tiles are drawn, call post-draw actions.
@@ -3131,7 +3071,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             // Only do postdraw actions for tiles; instances where tiles may not be drawn include:
             // (a) ReferenceTrack without sufficient resolution;
             // (b) data_fetch = false.
-            tiles = _.filter(tiles, t => t !== null);
+            tiles = _.filter(tiles, (t) => t !== null);
             if (tiles.length !== 0) {
                 this.postdraw_actions(tiles, width, w_scale, clear_after);
             }
@@ -3141,7 +3081,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Add a maximum/minimum label to track.
      */
-    _add_yaxis_label: function(type, on_change) {
+    _add_yaxis_label: function (type, on_change) {
         var css_class = type === "max" ? "top" : "bottom";
         var text = type === "max" ? "max" : "min";
         var pref_name = type === "max" ? "max_value" : "min_value";
@@ -3164,12 +3104,12 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
                 .text(value)
                 .make_text_editable({
                     num_cols: 12,
-                    on_finish: function(new_val) {
+                    on_finish: function (new_val) {
                         $(".tooltip").remove();
                         this.config.set_value(pref_name, round(new_val, 1));
                         on_change();
                     },
-                    help_text: `Set ${text} value`
+                    help_text: `Set ${text} value`,
                 })
                 .addClass(`yaxislabel ${css_class}`)
                 .css("color", this.config.get_value("label_color"));
@@ -3181,8 +3121,8 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * Actions to be taken after draw has been completed. Draw is completed when all tiles have been
      * drawn/fetched and shown.
      */
-    postdraw_actions: function(tiles, width, w_scale, clear_after) {
-        var line_track_tiles = _.filter(tiles, tile => tile instanceof LineTrackTile);
+    postdraw_actions: function (tiles, width, w_scale, clear_after) {
+        var line_track_tiles = _.filter(tiles, (tile) => tile instanceof LineTrackTile);
 
         //
         // Take different actions depending on whether there are LineTrack/Coverage tiles.
@@ -3193,12 +3133,12 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
 
             // Clear because this is set when drawing.
             this.max_height_px = 0;
-            _.each(tiles, tile => {
+            _.each(tiles, (tile) => {
                 if (!(tile instanceof LineTrackTile)) {
                     tile.html_elt.remove();
                     this.draw_helper(tile.region, w_scale, {
                         force: true,
-                        mode: "Coverage"
+                        mode: "Coverage",
                     });
                 }
             });
@@ -3213,10 +3153,10 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             //
             // If some tiles have icons, set padding of tiles without icons so features and rows align.
             //
-            var icons_present = _.find(tiles, tile => tile.has_icons);
+            var icons_present = _.find(tiles, (tile) => tile.has_icons);
 
             if (icons_present) {
-                _.each(tiles, tile => {
+                _.each(tiles, (tile) => {
                     if (!tile.has_icons) {
                         // Need to align with other tile(s) that have icons.
                         tile.html_elt.css("padding-top", ERROR_PADDING);
@@ -3229,21 +3169,21 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Returns appropriate display mode based on data.
      */
-    get_mode: function(data) {
+    get_mode: function (data) {
         return this.mode;
     },
 
     /**
      * Update track interface to show display mode being used.
      */
-    update_auto_mode: function(display_mode) {
+    update_auto_mode: function (display_mode) {
         // FIXME: needs to be implemented.
     },
 
     /**
      * Returns a list of drawables to draw. Defaults to current track.
      */
-    _get_drawables: function() {
+    _get_drawables: function () {
         return [this];
     },
 
@@ -3253,7 +3193,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * -force: force a redraw rather than use cached tiles (default: false)
      * -data_fetch: fetch data if necessary (default: true)
      */
-    draw_helper: function(region, w_scale, options) {
+    draw_helper: function (region, w_scale, options) {
         // Init options if necessary to avoid having to check if options defined.
         if (!options) {
             options = {};
@@ -3266,7 +3206,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         var drawables = this._get_drawables();
         var key = this._gen_tile_cache_key(w_scale, region);
 
-        var is_tile = o => o && "track" in o;
+        var is_tile = (o) => o && "track" in o;
 
         // Check tile cache, if found show existing tile in correct position
         var tile = force ? undefined : this.tile_cache.get_elt(key);
@@ -3285,7 +3225,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         // Function that returns data/Deferreds needed to draw tile.
         var get_tile_data = () => {
             // HACK: if display mode (mode) is in continuous data modes, data mode must be coverage to get coverage data.
-            var data_mode = _.find(CONTINUOUS_DATA_MODES, m => m === mode) ? "Coverage" : mode;
+            var data_mode = _.find(CONTINUOUS_DATA_MODES, (m) => m === mode) ? "Coverage" : mode;
 
             // Map drawable object to data needed for drawing.
             var tile_data = _.map(drawables, (
@@ -3321,9 +3261,9 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             // that cannot be subsetted. This may occur if the superset has a message. If there is a
             // Deferred, try again from the top. NOTE: this condition could (should?) be handled by the
             // GenomeDataManager in visualization module.
-            if (_.find(tile_data, d => util.is_deferred(d))) {
+            if (_.find(tile_data, (d) => util.is_deferred(d))) {
                 this.tile_cache.set_elt(key, undefined);
-                $.when(this.draw_helper(region, w_scale, options)).then(tile => {
+                $.when(this.draw_helper(region, w_scale, options)).then((tile) => {
                     tile_drawn.resolve(tile);
                 });
                 return;
@@ -3387,14 +3327,14 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * Returns canvas height needed to display data; return value is an integer that denotes the
      * number of pixels required.
      */
-    get_canvas_height: function(result, mode, w_scale, canvas_width) {
+    get_canvas_height: function (result, mode, w_scale, canvas_width) {
         return this.visible_height_px;
     },
 
     /**
      * Draw line (bigwig) data onto tile.
      */
-    _draw_line_track_tile: function(result, ctx, mode, region, w_scale) {
+    _draw_line_track_tile: function (result, ctx, mode, region, w_scale) {
         // Set min/max if they are not already set.
         // FIXME: checking for different null/undefined/0 is messy; it would be nice to
         // standardize this.
@@ -3402,7 +3342,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             this.config.set_value("min_value", 0);
         }
         if ([undefined, null, 0].indexOf(this.config.get_value("max_value")) !== -1) {
-            this.config.set_value("max_value", _.max(_.map(result.data, d => d[1])) || 0);
+            this.config.set_value("max_value", _.max(_.map(result.data, (d) => d[1])) || 0);
         }
 
         var canvas = ctx.canvas;
@@ -3429,13 +3369,13 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * @param w_scale pixels per base
      * @param ref_seq reference sequence data
      */
-    draw_tile: function(result, ctx, mode, region, w_scale, ref_seq) {},
+    draw_tile: function (result, ctx, mode, region, w_scale, ref_seq) {},
 
     /**
      * Show track tile and perform associated actions. Showing tile may actually move
      * an existing tile rather than reshowing it.
      */
-    show_tile: function(tile, w_scale) {
+    show_tile: function (tile, w_scale) {
         var tile_element = tile.html_elt;
 
         // -- Show/move tile element. --
@@ -3468,10 +3408,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         this.max_height_px = Math.max(this.max_height_px, tile_element.height() - 2);
 
         // Update height for all tiles based on max height.
-        tile_element
-            .parent()
-            .children()
-            .css("height", `${this.max_height_px}px`);
+        tile_element.parent().children().css("height", `${this.max_height_px}px`);
 
         // Update track height based on max height and visible height.
         var track_height = this.max_height_px;
@@ -3484,7 +3421,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Utility function that creates a label string describing the region and parameters of a track's tool.
      */
-    tool_region_and_parameters_str: function(region) {
+    tool_region_and_parameters_str: function (region) {
         var track = this;
         var region_str = region !== undefined ? region.toString() : "all";
         var param_str = _.values(track.tool.get_inputs_dict()).join(", ");
@@ -3494,7 +3431,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Returns true if data is compatible with a given mode.
      */
-    data_and_mode_compatible: function(data, mode) {
+    data_and_mode_compatible: function (data, mode) {
         // Only handle modes that user can set.
         if (mode === "Auto") {
             return true;
@@ -3512,7 +3449,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Returns true if entry can be subsetted.
      */
-    can_subset: function(entry) {
+    can_subset: function (entry) {
         // Do not subset entries with a message or data with no detail.
         if (entry.message || entry.extra_info === "no_detail") {
             return false;
@@ -3527,7 +3464,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Set up track to receive tool data.
      */
-    init_for_tool_data: function() {
+    init_for_tool_data: function () {
         // Set up track to fetch raw data rather than converted data.
         this.data_manager.set("data_type", "raw_data");
         this.data_query_wait = 1000;
@@ -3570,18 +3507,18 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             self.postdraw_actions = self.normal_postdraw_actions;
         };
         */
-    }
+    },
 });
 
-var LabelTrack = function(view, container) {
+var LabelTrack = function (view, container) {
     Track.call(this, view, container, {
         resize: false,
-        header: false
+        header: false,
     });
     this.container_div.addClass("label-track");
 };
 extend(LabelTrack.prototype, Track.prototype, {
-    init: function() {
+    init: function () {
         // Enable by default because there should always be data when drawing track.
         this.enabled = true;
     },
@@ -3589,9 +3526,9 @@ extend(LabelTrack.prototype, Track.prototype, {
     /**
      * Additional initialization required before drawing track for the first time.
      */
-    predraw_init: function() {},
+    predraw_init: function () {},
 
-    _draw: function(options) {
+    _draw: function (options) {
         var view = this.view;
         var range = view.high - view.low;
 
@@ -3603,18 +3540,15 @@ extend(LabelTrack.prototype, Track.prototype, {
         while (position < view.high) {
             var screenPosition = Math.floor(((position - view.low) / range) * width);
             new_div.append(
-                $("<div/>")
-                    .addClass("pos-label")
-                    .text(util.commatize(position))
-                    .css({
-                        left: screenPosition
-                    })
+                $("<div/>").addClass("pos-label").text(util.commatize(position)).css({
+                    left: screenPosition,
+                })
             );
             position += tickDistance;
         }
         this.content_div.children(":first").remove();
         this.content_div.append(new_div);
-    }
+    },
 });
 
 // FIXME: Composite tracks have code for showing composite tracks with line tracks and
@@ -3625,7 +3559,7 @@ extend(LabelTrack.prototype, Track.prototype, {
  * A tiled track composed of multiple other tracks. Composite tracks only work with
  * bigwig data for now.
  */
-var CompositeTrack = function(view, container, obj_dict) {
+var CompositeTrack = function (view, container, obj_dict) {
     TiledTrack.call(this, view, container, obj_dict);
 
     // Init drawables; each drawable is a copy so that config/preferences
@@ -3646,7 +3580,7 @@ var CompositeTrack = function(view, container, obj_dict) {
     }
 
     // Set all feature tracks to use Coverage mode.
-    _.each(this.drawables, d => {
+    _.each(this.drawables, (d) => {
         if (d instanceof FeatureTrack || d instanceof ReadTrack) {
             d.change_mode("Coverage");
         }
@@ -3662,32 +3596,32 @@ var CompositeTrack = function(view, container, obj_dict) {
 extend(CompositeTrack.prototype, TiledTrack.prototype, {
     display_modes: CONTINUOUS_DATA_MODES,
 
-    build_config_params: function() {
+    build_config_params: function () {
         return _.union(Drawable.prototype.config_params, [
             {
                 key: "min_value",
                 label: "Min Value",
                 type: "float",
-                default_value: undefined
+                default_value: undefined,
             },
             {
                 key: "max_value",
                 label: "Max Value",
                 type: "float",
-                default_value: undefined
+                default_value: undefined,
             },
             {
                 key: "mode",
                 type: "string",
                 default_value: this.mode,
-                hidden: true
+                hidden: true,
             },
             {
                 key: "height",
                 type: "int",
                 default_value: 30,
-                hidden: true
-            }
+                hidden: true,
+            },
         ]);
     },
 
@@ -3697,11 +3631,11 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
             name: "composite_icon",
             title: _l("Show individual tracks"),
             css_class: "layers-stack",
-            on_click_fn: function(track) {
+            on_click_fn: function (track) {
                 $(".tooltip").remove();
                 track.show_group();
-            }
-        }
+            },
+        },
     ].concat(TiledTrack.prototype.action_icons_def),
 
     // HACK: CompositeTrack should inherit from DrawableCollection as well.
@@ -3715,7 +3649,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
 
     unpack_drawables: DrawableCollection.prototype.unpack_drawables,
 
-    config_onchange: function() {
+    config_onchange: function () {
         this.set_name(this.config.get_value("name"));
         this.request_draw({ clear_tile_cache: true });
     },
@@ -3723,10 +3657,10 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
     /**
      * Action to take during resize.
      */
-    on_resize: function() {
+    on_resize: function () {
         // Propogate visible height to other tracks.
         var visible_height = this.visible_height_px;
-        _.each(this.drawables, d => {
+        _.each(this.drawables, (d) => {
             d.visible_height_px = visible_height;
         });
         Track.prototype.on_resize.call(this);
@@ -3735,7 +3669,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
     /**
      * Change mode for all tracks.
      */
-    change_mode: function(new_mode) {
+    change_mode: function (new_mode) {
         TiledTrack.prototype.change_mode.call(this, new_mode);
         for (var i = 0; i < this.drawables.length; i++) {
             this.drawables[i].change_mode(new_mode);
@@ -3745,7 +3679,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
     /**
      * Initialize component tracks and draw composite track when all components are initialized.
      */
-    init: function() {
+    init: function () {
         // Init components.
         var init_deferreds = [];
         for (var i = 0; i < this.drawables.length; i++) {
@@ -3760,7 +3694,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
         });
     },
 
-    update_icons: function() {
+    update_icons: function () {
         // For now, hide filters and tool.
         this.action_icons.filters_icon.hide();
         this.action_icons.tools_icon.hide();
@@ -3769,17 +3703,17 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
 
     can_draw: Drawable.prototype.can_draw,
 
-    _get_drawables: function() {
+    _get_drawables: function () {
         return this.drawables;
     },
 
     /**
      * Replace this track with group that includes individual tracks.
      */
-    show_group: function() {
+    show_group: function () {
         // Create group with individual tracks.
         var group = new DrawableGroup(this.view, this.container, {
-            name: this.config.get_value("name")
+            name: this.config.get_value("name"),
         });
 
         var track;
@@ -3799,7 +3733,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
     /**
      * Actions taken before drawing.
      */
-    before_draw: function() {
+    before_draw: function () {
         // FIXME: this is needed only if there are feature tracks in the composite track.
         // TiledTrack.prototype.before_draw.call(this);
 
@@ -3808,15 +3742,15 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
         //
 
         // Get smallest min, biggest max.
-        var min = _.min(_.map(this.drawables, d => d.config.get_value("min_value")));
+        var min = _.min(_.map(this.drawables, (d) => d.config.get_value("min_value")));
 
-        var max = _.max(_.map(this.drawables, d => d.config.get_value("max_value")));
+        var max = _.max(_.map(this.drawables, (d) => d.config.get_value("max_value")));
 
         this.config.set_value("min_value", min);
         this.config.set_value("max_value", max);
 
         // Set all tracks to smallest min, biggest max.
-        _.each(this.drawables, d => {
+        _.each(this.drawables, (d) => {
             d.config.set_value("min_value", min);
             d.config.set_value("max_value", max);
         });
@@ -3825,10 +3759,10 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
     /**
      * Update minimum, maximum for component tracks.
      */
-    update_all_min_max: function() {
+    update_all_min_max: function () {
         var min_value = this.config.get_value("min_value");
         var max_value = this.config.get_value("max_value");
-        _.each(this.drawables, d => {
+        _.each(this.drawables, (d) => {
             d.config.set_value("min_value", min_value);
             d.config.set_value("max_value", max_value);
         });
@@ -3839,7 +3773,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
      * Actions to be taken after draw has been completed. Draw is completed when all tiles have been
      * drawn/fetched and shown.
      */
-    postdraw_actions: function(tiles, width, w_scale, clear_after) {
+    postdraw_actions: function (tiles, width, w_scale, clear_after) {
         // All tiles must be the same height in order to draw LineTracks, so redraw tiles as needed.
         var max_height = -1;
 
@@ -3856,7 +3790,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
             if (tile.html_elt.find("canvas").height() !== max_height) {
                 this.draw_helper(tile.region, w_scale, {
                     force: true,
-                    height: max_height
+                    height: max_height,
                 });
                 tile.html_elt.remove();
             }
@@ -3872,13 +3806,13 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
         // Add min, max labels.
         this._add_yaxis_label("min", t);
         this._add_yaxis_label("max", t);
-    }
+    },
 });
 
 /**
  * Displays reference genome data.
  */
-var ReferenceTrack = function(view) {
+var ReferenceTrack = function (view) {
     TiledTrack.call(this, view, { content_div: view.top_labeltrack }, { resize: false, header: false });
 
     // Use offset to ensure that bases at tile edges are drawn.
@@ -3888,23 +3822,23 @@ var ReferenceTrack = function(view) {
     this.data_url_extra_params = { reference: true };
     this.data_manager = new visualization.GenomeReferenceDataManager({
         data_url: this.data_url,
-        can_subset: this.can_subset
+        can_subset: this.can_subset,
     });
     this.hide_contents();
 };
 extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
-    build_config_params: function() {
+    build_config_params: function () {
         return _.union(Drawable.prototype.config_params, [
             {
                 key: "height",
                 type: "int",
                 default_value: 13,
-                hidden: true
-            }
+                hidden: true,
+            },
         ]);
     },
 
-    init: function() {
+    init: function () {
         this.data_manager.clear();
         // Enable by default because there should always be data when drawing track.
         this.enabled = true;
@@ -3913,14 +3847,14 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     /**
      * Additional initialization required before drawing track for the first time.
      */
-    predraw_init: function() {},
+    predraw_init: function () {},
 
     can_draw: Drawable.prototype.can_draw,
 
     /**
      * Draws and shows tile if reference data can be displayed; otherwise track is hidden.
      */
-    draw_helper: function(region, w_scale, options) {
+    draw_helper: function (region, w_scale, options) {
         var cur_visible = this.tiles_div.is(":visible");
         var new_visible;
         var tile = null;
@@ -3946,14 +3880,14 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         return tile;
     },
 
-    can_subset: function(entry) {
+    can_subset: function (entry) {
         return true;
     },
 
     /**
      * Draw ReferenceTrack tile.
      */
-    draw_tile: function(data, ctx, mode, region, w_scale) {
+    draw_tile: function (data, ctx, mode, region, w_scale) {
         // Try to subset data.
         var subset = this.data_manager.subset_entry(data, region);
 
@@ -3968,13 +3902,13 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             ctx.fillText(seq_data[c], Math.floor(c * w_scale), 10);
         }
         return new Tile(this, region, w_scale, canvas, subset);
-    }
+    },
 });
 
 /**
  * Track displays continuous/numerical data. Track expects position data in 1-based format, i.e. wiggle format.
  */
-var LineTrack = function(view, container, obj_dict) {
+var LineTrack = function (view, container, obj_dict) {
     this.mode = "Histogram";
     TiledTrack.call(this, view, container, obj_dict);
     // Need left offset for drawing overlap near tile boundaries.
@@ -3983,10 +3917,10 @@ var LineTrack = function(view, container, obj_dict) {
     // If server has byte-range support, use BBI data manager to read directly from the BBI file.
     // FIXME: there should be a flag to wait for this check to complete before loading the track.
     var self = this;
-    $.when(supportsByteRanges(`${getAppRoot()}datasets/${this.dataset.id}/display`)).then(supportsByteRanges => {
+    $.when(supportsByteRanges(`${getAppRoot()}datasets/${this.dataset.id}/display`)).then((supportsByteRanges) => {
         if (supportsByteRanges) {
             self.data_manager = new bbi.BBIDataManager({
-                dataset: self.dataset
+                dataset: self.dataset,
             });
         }
     });
@@ -3995,37 +3929,37 @@ var LineTrack = function(view, container, obj_dict) {
 extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     display_modes: CONTINUOUS_DATA_MODES,
 
-    build_config_params: function() {
+    build_config_params: function () {
         return _.union(Drawable.prototype.config_params, [
             { key: "color", label: "Color", type: "color" },
             {
                 key: "min_value",
                 label: "Min Value",
                 type: "float",
-                default_value: undefined
+                default_value: undefined,
             },
             {
                 key: "max_value",
                 label: "Max Value",
                 type: "float",
-                default_value: undefined
+                default_value: undefined,
             },
             {
                 key: "mode",
                 type: "string",
                 default_value: this.mode,
-                hidden: true
+                hidden: true,
             },
             {
                 key: "height",
                 type: "int",
                 default_value: 30,
-                hidden: true
-            }
+                hidden: true,
+            },
         ]);
     },
 
-    config_onchange: function() {
+    config_onchange: function () {
         this.set_name(this.config.get_value("name"));
         this.request_draw({ clear_tile_cache: true });
     },
@@ -4034,36 +3968,36 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * Actions to be taken before drawing.
      */
     // FIXME: can the default behavior be used; right now it breaks during resize.
-    before_draw: function() {},
+    before_draw: function () {},
 
     /**
      * Draw track tile.
      */
-    draw_tile: function(result, ctx, mode, region, w_scale) {
+    draw_tile: function (result, ctx, mode, region, w_scale) {
         return this._draw_line_track_tile(result, ctx, mode, region, w_scale);
     },
 
     /**
      * Subset data only if data is at single-base pair resolution.
      */
-    can_subset: function(entry) {
+    can_subset: function (entry) {
         return entry.data[1][0] - entry.data[0][0] === 1;
     },
 
     /**
      * Add min, max labels.
      */
-    postdraw_actions: function(tiles, width, w_scale, clear_after) {
+    postdraw_actions: function (tiles, width, w_scale, clear_after) {
         // Add min, max labels.
         this._add_yaxis_label("max");
         this._add_yaxis_label("min");
-    }
+    },
 });
 
 /**
  * Diagonal heatmap for showing interactions data.
  */
-var DiagonalHeatmapTrack = function(view, container, obj_dict) {
+var DiagonalHeatmapTrack = function (view, container, obj_dict) {
     this.mode = "Heatmap";
     TiledTrack.call(this, view, container, obj_dict);
 };
@@ -4071,48 +4005,48 @@ var DiagonalHeatmapTrack = function(view, container, obj_dict) {
 extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     display_modes: ["Heatmap"],
 
-    build_config_params: function() {
+    build_config_params: function () {
         return _.union(Drawable.prototype.config_params, [
             {
                 key: "pos_color",
                 label: "Positive Color",
                 type: "color",
-                default_value: "#FF8C00"
+                default_value: "#FF8C00",
             },
             {
                 key: "neg_color",
                 label: "Negative Color",
                 type: "color",
-                default_value: "#4169E1"
+                default_value: "#4169E1",
             },
             {
                 key: "min_value",
                 label: "Min Value",
                 type: "int",
-                default_value: undefined
+                default_value: undefined,
             },
             {
                 key: "max_value",
                 label: "Max Value",
                 type: "int",
-                default_value: undefined
+                default_value: undefined,
             },
             {
                 key: "mode",
                 type: "string",
                 default_value: this.mode,
-                hidden: true
+                hidden: true,
             },
             {
                 key: "height",
                 type: "int",
                 default_value: 500,
-                hidden: true
-            }
+                hidden: true,
+            },
         ]);
     },
 
-    config_onchange: function() {
+    config_onchange: function () {
         this.set_name(this.config.get_value("name"));
         this.request_draw({ clear_tile_cache: true });
     },
@@ -4120,7 +4054,7 @@ extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype,
     /**
      * Additional initialization required before drawing track for the first time.
      */
-    predraw_init: function() {
+    predraw_init: function () {
         var track = this;
         return $.getJSON(
             track.dataset.url(),
@@ -4130,9 +4064,9 @@ extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype,
                 chrom: track.view.chrom,
                 low: 0,
                 high: track.view.max_high,
-                hda_ldda: track.dataset.get("hda_ldda")
+                hda_ldda: track.dataset.get("hda_ldda"),
             },
-            result => {
+            (result) => {
                 // What does this do?  Is it meant to be attached to some higher scope state object?
                 // var data = result.data;
             }
@@ -4142,7 +4076,7 @@ extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype,
     /**
      * Draw tile.
      */
-    draw_tile: function(result, ctx, mode, region, w_scale) {
+    draw_tile: function (result, ctx, mode, region, w_scale) {
         // Paint onto canvas.
         var canvas = ctx.canvas;
 
@@ -4157,13 +4091,13 @@ extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype,
         painter.draw(ctx, canvas.width, canvas.height, w_scale);
 
         return new Tile(this, region, w_scale, canvas, result.data);
-    }
+    },
 });
 
 /**
  * A track that displays features/regions. Track expects position data in BED format, i.e. 0-based, half-open.
  */
-var FeatureTrack = function(view, container, obj_dict) {
+var FeatureTrack = function (view, container, obj_dict) {
     TiledTrack.call(this, view, container, obj_dict);
     this.container_div.addClass("feature-track");
     this.summary_draw_height = 30;
@@ -4176,44 +4110,44 @@ var FeatureTrack = function(view, container, obj_dict) {
 extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"],
 
-    build_config_params: function() {
+    build_config_params: function () {
         return _.union(Drawable.prototype.config_params, [
             {
                 key: "block_color",
                 label: "Block color",
-                type: "color"
+                type: "color",
             },
             {
                 key: "reverse_strand_color",
                 label: "Antisense strand color",
-                type: "color"
+                type: "color",
             },
             {
                 key: "label_color",
                 label: "Label color",
                 type: "color",
-                default_value: "black"
+                default_value: "black",
             },
             {
                 key: "show_counts",
                 label: "Show summary counts",
                 type: "bool",
                 default_value: true,
-                help: "Show the number of items in each bin when drawing summary histogram"
+                help: "Show the number of items in each bin when drawing summary histogram",
             },
             {
                 key: "min_value",
                 label: "Histogram minimum",
                 type: "float",
                 default_value: undefined,
-                help: "clear value to set automatically"
+                help: "clear value to set automatically",
             },
             {
                 key: "max_value",
                 label: "Histogram maximum",
                 type: "float",
                 default_value: undefined,
-                help: "clear value to set automatically"
+                help: "clear value to set automatically",
             },
             {
                 key: "connector_style",
@@ -4223,33 +4157,33 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                 options: [
                     {
                         label: "Line with arrows",
-                        value: "fishbone"
+                        value: "fishbone",
                     },
-                    { label: "Arcs", value: "arcs" }
-                ]
+                    { label: "Arcs", value: "arcs" },
+                ],
             },
             {
                 key: "mode",
                 type: "string",
                 default_value: this.mode,
-                hidden: true
+                hidden: true,
             },
             {
                 key: "height",
                 type: "int",
                 default_value: 0,
-                hidden: true
-            }
+                hidden: true,
+            },
         ]);
     },
 
-    config_onchange: function() {
+    config_onchange: function () {
         this.set_name(this.config.get_value("name"));
         this.set_painter_from_config();
         this.request_draw({ clear_tile_cache: true });
     },
 
-    set_painter_from_config: function() {
+    set_painter_from_config: function () {
         if (this.config.get_value("connector_style") === "arcs") {
             this.painter = painters.ArcLinkedFeaturePainter;
         } else {
@@ -4261,10 +4195,10 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * Actions to be taken after draw has been completed. Draw is completed when all tiles have been
      * drawn/fetched and shown.
      */
-    postdraw_actions: function(tiles, width, w_scale, clear_after) {
+    postdraw_actions: function (tiles, width, w_scale, clear_after) {
         TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after);
 
-        var line_track_tiles = _.filter(tiles, t => t instanceof LineTrackTile);
+        var line_track_tiles = _.filter(tiles, (t) => t instanceof LineTrackTile);
 
         //
         // Finish drawing of features that span multiple tiles. Features that span multiple tiles
@@ -4273,18 +4207,18 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         if (line_track_tiles.length === 0) {
             // Gather incomplete features together.
             var all_incomplete_features = {};
-            _.each(_.pluck(tiles, "incomplete_features"), inc_features => {
-                _.each(inc_features, feature => {
+            _.each(_.pluck(tiles, "incomplete_features"), (inc_features) => {
+                _.each(inc_features, (feature) => {
                     all_incomplete_features[feature[0]] = feature;
                 });
             });
 
             // Draw incomplete features on each tile.
-            _.each(tiles, tile => {
+            _.each(tiles, (tile) => {
                 // Remove features already drawn on tile originally.
                 var tile_incomplete_features = _.omit(
                     all_incomplete_features,
-                    _.map(tile.incomplete_features, f => f[0])
+                    _.map(tile.incomplete_features, (f) => f[0])
                 );
 
                 // Remove features already drawn on tile in past postdraw actions.
@@ -4295,7 +4229,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                     // To draw incomplete features, create new canvas, copy original canvas/tile onto new
                     // canvas, and then draw incomplete features on the new canvas.
                     var features = {
-                        data: _.values(tile_incomplete_features)
+                        data: _.values(tile_incomplete_features),
                     };
 
                     var new_canvas = this.view.canvas_manager.new_canvas();
@@ -4406,7 +4340,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     /**
      * Update track interface to show display mode being used.
      */
-    update_auto_mode: function(mode) {
+    update_auto_mode: function (mode) {
         if (this.mode === "Auto") {
             if (mode === "no_detail") {
                 mode = "feature spans";
@@ -4420,7 +4354,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * this.slotters[level] is created in this method. this.slotters[level]
      * is a Slotter object. Returns the number of slots used to pack features.
      */
-    incremental_slots: function(level, features, mode) {
+    incremental_slots: function (level, features, mode) {
         // Get/create incremental slots for level. If display mode changed,
         // need to create new slots.
 
@@ -4428,7 +4362,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
 
         var slotter = this.slotters[level];
         if (!slotter || slotter.mode !== mode) {
-            slotter = new slotting.FeatureSlotter(level, mode, MAX_FEATURE_DEPTH, x => dummy_context.measureText(x));
+            slotter = new slotting.FeatureSlotter(level, mode, MAX_FEATURE_DEPTH, (x) => dummy_context.measureText(x));
             this.slotters[level] = slotter;
         }
 
@@ -4438,7 +4372,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     /**
      * Returns appropriate display mode based on data.
      */
-    get_mode: function(data) {
+    get_mode: function (data) {
         var mode;
         // HACK: use no_detail mode track is in overview to prevent overview from being too large.
         if (data.extra_info === "no_detail" || this.is_overview) {
@@ -4469,7 +4403,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * Returns canvas height needed to display data; return value is an integer that denotes the
      * number of pixels required.
      */
-    get_canvas_height: function(result, mode, w_scale, canvas_width) {
+    get_canvas_height: function (result, mode, w_scale, canvas_width) {
         if (mode === "Coverage" || result.dataset_type === "bigwig") {
             return this.summary_draw_height;
         } else {
@@ -4492,7 +4426,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * @param ref_seq reference sequence data
      * @param cur_tile true if drawing is occurring on a currently visible tile.
      */
-    draw_tile: function(result, ctx, mode, region, w_scale, ref_seq, cur_tile) {
+    draw_tile: function (result, ctx, mode, region, w_scale, ref_seq, cur_tile) {
         var track = this;
         var canvas = ctx.canvas;
         var tile_low = region.get("start");
@@ -4555,7 +4489,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             filter_height_scaler,
             // HACK: ref_seq only be defined for ReadTracks, and only the ReadPainter accepts that argument
             ref_seq,
-            b => track.view.get_base_color(b)
+            (b) => track.view.get_base_color(b)
         );
 
         var feature_mapper = null;
@@ -4589,13 +4523,13 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                 ref_seq
             );
         }
-    }
+    },
 });
 
 /**
  * Displays variant data.
  */
-var VariantTrack = function(view, container, obj_dict) {
+var VariantTrack = function (view, container, obj_dict) {
     TiledTrack.call(this, view, container, obj_dict);
     this.painter = painters.VariantPainter;
     this.summary_draw_height = 30;
@@ -4608,47 +4542,47 @@ var VariantTrack = function(view, container, obj_dict) {
 extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"],
 
-    build_config_params: function() {
+    build_config_params: function () {
         return _.union(Drawable.prototype.config_params, [
             {
                 key: "color",
                 label: "Histogram color",
-                type: "color"
+                type: "color",
             },
             {
                 key: "show_sample_data",
                 label: "Show sample data",
                 type: "bool",
-                default_value: true
+                default_value: true,
             },
             {
                 key: "show_labels",
                 label: "Show summary and sample labels",
                 type: "bool",
-                default_value: true
+                default_value: true,
             },
             {
                 key: "summary_height",
                 label: "Locus summary height",
                 type: "float",
-                default_value: 20
+                default_value: 20,
             },
             {
                 key: "mode",
                 type: "string",
                 default_value: this.mode,
-                hidden: true
+                hidden: true,
             },
             {
                 key: "height",
                 type: "int",
                 default_value: 0,
-                hidden: true
-            }
+                hidden: true,
+            },
         ]);
     },
 
-    config_onchange: function() {
+    config_onchange: function () {
         this.set_name(this.config.get_value("name"));
         this.request_draw({ clear_tile_cache: true });
     },
@@ -4656,7 +4590,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     /**
      * Draw tile.
      */
-    draw_tile: function(result, ctx, mode, region, w_scale) {
+    draw_tile: function (result, ctx, mode, region, w_scale) {
         // Data could be coverage data or variant data.
         if (result.dataset_type === "bigwig") {
             return this._draw_line_track_tile(result, ctx, "Histogram", region, w_scale);
@@ -4670,7 +4604,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                 region.get("end"),
                 this.config.to_key_value_dict(),
                 mode,
-                b => view.get_base_color(b)
+                (b) => view.get_base_color(b)
             );
 
             painter.draw(ctx, ctx.canvas.width, ctx.canvas.height, w_scale);
@@ -4682,7 +4616,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * Returns canvas height needed to display data; return value is an integer that denotes the
      * number of pixels required.
      */
-    get_canvas_height: function(result, mode, w_scale, canvas_width) {
+    get_canvas_height: function (result, mode, w_scale, canvas_width) {
         if (result.dataset_type === "bigwig") {
             return this.summary_draw_height;
         } else {
@@ -4711,7 +4645,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     /**
      * Additional initialization required before drawing track for the first time.
      */
-    predraw_init: function() {
+    predraw_init: function () {
         var deferreds = [Track.prototype.predraw_init.call(this)];
         // FIXME: updating dataset metadata is only needed for visual analysis. Can
         // this be moved somewhere else?
@@ -4725,10 +4659,10 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * Actions to be taken after draw has been completed. Draw is completed when all tiles have been
      * drawn/fetched and shown.
      */
-    postdraw_actions: function(tiles, width, w_scale, clear_after) {
+    postdraw_actions: function (tiles, width, w_scale, clear_after) {
         TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after);
 
-        var line_track_tiles = _.filter(tiles, t => t instanceof LineTrackTile);
+        var line_track_tiles = _.filter(tiles, (t) => t instanceof LineTrackTile);
 
         // Add summary/sample labels if needed and not already included.
         var sample_names = this.dataset.get_metadata("sample_names");
@@ -4752,7 +4686,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                         .addClass("yaxislabel variant top")
                         .css({
                             "font-size": `${font_size}px`,
-                            top: `${(this.config.get_value("summary_height") - font_size) / 2}px`
+                            top: `${(this.config.get_value("summary_height") - font_size) / 2}px`,
                         })
                 );
 
@@ -4765,7 +4699,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                             .html(samples_div_html)
                             .addClass("yaxislabel variant top sample")
                             .css({
-                                top: this.config.get_value("summary_height")
+                                top: this.config.get_value("summary_height"),
                             })
                     );
                 }
@@ -4775,109 +4709,105 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
 
             // Match sample font size to mode.
             font_size = `${this.mode === "Squish" ? 5 : 10}px`;
-            $(this.tiles_div)
-                .find(".sample")
-                .css({
-                    "font-size": font_size,
-                    "line-height": font_size
-                });
+            $(this.tiles_div).find(".sample").css({
+                "font-size": font_size,
+                "line-height": font_size,
+            });
             // Color labels to preference color.
-            $(this.tiles_div)
-                .find(".yaxislabel")
-                .css("color", this.config.get_value("label_color"));
+            $(this.tiles_div).find(".yaxislabel").css("color", this.config.get_value("label_color"));
         } else {
             // Remove all labels.
             this.container_div.find(".yaxislabel.variant").remove();
         }
-    }
+    },
 });
 
 /**
  * Track that displays mapped reads. Track expects position data in 1-based, closed format, i.e. SAM/BAM format.
  */
-var ReadTrack = function(view, container, obj_dict) {
+var ReadTrack = function (view, container, obj_dict) {
     FeatureTrack.call(this, view, container, obj_dict);
     this.painter = painters.ReadPainter;
     this.update_icons();
 };
 
 extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, {
-    build_config_params: function() {
+    build_config_params: function () {
         return _.union(Drawable.prototype.config_params, [
             {
                 key: "block_color",
                 label: "Histogram color",
-                type: "color"
+                type: "color",
             },
             {
                 key: "detail_block_color",
                 label: "Sense strand block color",
                 type: "color",
-                default_value: "#AAAAAA"
+                default_value: "#AAAAAA",
             },
             {
                 key: "reverse_strand_color",
                 label: "Antisense strand block color",
                 type: "color",
-                default_value: "#DDDDDD"
+                default_value: "#DDDDDD",
             },
             {
                 key: "label_color",
                 label: "Label color",
                 type: "color",
-                default_value: "black"
+                default_value: "black",
             },
             {
                 key: "show_insertions",
                 label: "Show insertions",
                 type: "bool",
-                default_value: false
+                default_value: false,
             },
             {
                 key: "show_differences",
                 label: "Show differences only",
                 type: "bool",
-                default_value: true
+                default_value: true,
             },
             {
                 key: "show_counts",
                 label: "Show summary counts",
                 type: "bool",
-                default_value: true
+                default_value: true,
             },
             {
                 key: "mode",
                 type: "string",
                 default_value: this.mode,
-                hidden: true
+                hidden: true,
             },
             {
                 key: "min_value",
                 label: "Histogram minimum",
                 type: "float",
                 default_value: undefined,
-                help: "clear value to set automatically"
+                help: "clear value to set automatically",
             },
             {
                 key: "max_value",
                 label: "Histogram maximum",
                 type: "float",
                 default_value: undefined,
-                help: "clear value to set automatically"
+                help: "clear value to set automatically",
             },
             {
                 key: "height",
                 type: "int",
                 default_value: 0,
-                hidden: true
-            }
+                hidden: true,
+            },
         ]);
     },
 
-    config_onchange: function() {
+    config_onchange: function () {
         this.set_name(this.config.get_value("name"));
         this.request_draw({ clear_tile_cache: true });
-    }
+    },
 });
 
 /**
@@ -4892,7 +4822,7 @@ var addable_objects = {
     ReadTrack: ReadTrack,
     VariantTrack: VariantTrack,
     // For backward compatibility, map vcf track to variant.
-    VcfTrack: VariantTrack
+    VcfTrack: VariantTrack,
 };
 
 /**
@@ -4923,5 +4853,5 @@ export default {
     ReadTrack: ReadTrack,
     VariantTrack: VariantTrack,
     CompositeTrack: CompositeTrack,
-    object_from_template: object_from_template
+    object_from_template: object_from_template,
 };
diff --git a/client/galaxy/scripts/viz/trackster/util.js b/client/galaxy/scripts/viz/trackster/util.js
index 14898c89acce..3fdbb6ded742 100644
--- a/client/galaxy/scripts/viz/trackster/util.js
+++ b/client/galaxy/scripts/viz/trackster/util.js
@@ -16,7 +16,7 @@ function commatize(number) {
 /**
  * Helper to determine if object is jQuery deferred.
  */
-var is_deferred = d => "promise" in d;
+var is_deferred = (d) => "promise" in d;
 
 /**
  * Implementation of a server-state based deferred. Server is repeatedly polled, and when
@@ -26,15 +26,15 @@ var ServerStateDeferred = Backbone.Model.extend({
     defaults: {
         ajax_settings: {},
         interval: 1000,
-        success_fn: function(result) {
+        success_fn: function (result) {
             return true;
-        }
+        },
     },
 
     /**
      * Returns a deferred that resolves when success function returns true.
      */
-    go: function() {
+    go: function () {
         var deferred = $.Deferred();
         var self = this;
         var ajax_settings = self.get("ajax_settings");
@@ -42,7 +42,7 @@ var ServerStateDeferred = Backbone.Model.extend({
         var interval = self.get("interval");
 
         var _go = () => {
-            $.ajax(ajax_settings).success(result => {
+            $.ajax(ajax_settings).success((result) => {
                 if (success_fn(result)) {
                     // Result is good, so resolve.
                     deferred.resolve(result);
@@ -55,7 +55,7 @@ var ServerStateDeferred = Backbone.Model.extend({
 
         _go();
         return deferred;
-    }
+    },
 });
 
 /**
@@ -63,7 +63,7 @@ var ServerStateDeferred = Backbone.Model.extend({
  * or set of colors.
  * @param colors a color or list of colors in the format '#RRGGBB'
  */
-var get_random_color = colors => {
+var get_random_color = (colors) => {
     // Default for colors is white.
     if (!colors) {
         colors = "#ffffff";
@@ -141,5 +141,5 @@ export default {
     commatize: commatize,
     is_deferred: is_deferred,
     ServerStateDeferred: ServerStateDeferred,
-    get_random_color: get_random_color
+    get_random_color: get_random_color,
 };
diff --git a/client/galaxy/scripts/viz/visualization.js b/client/galaxy/scripts/viz/visualization.js
index a439e8cae951..e3a35c4cb475 100644
--- a/client/galaxy/scripts/viz/visualization.js
+++ b/client/galaxy/scripts/viz/visualization.js
@@ -18,10 +18,10 @@ var CustomToJSON = {
     /**
      * Returns JSON representation of object using to_json_keys and to_json_mappers.
      */
-    toJSON: function() {
+    toJSON: function () {
         var self = this;
         var json = {};
-        _.each(self.constructor.to_json_keys, k => {
+        _.each(self.constructor.to_json_keys, (k) => {
             var val = self.get(k);
             if (k in self.constructor.to_json_mappers) {
                 val = self.constructor.to_json_mappers[k](val, self);
@@ -29,7 +29,7 @@ var CustomToJSON = {
             json[k] = val;
         });
         return json;
-    }
+    },
 };
 
 /**
@@ -50,13 +50,13 @@ var select_datasets = (filters, success_fn) => {
     var history_grid = new GridView({
         url_base: `${getAppRoot()}visualization/list_history_datasets`,
         filters: filters,
-        embedded: true
+        embedded: true,
     });
 
     // library dataset selection tab
     var library_grid = new GridView({
         url_base: `${getAppRoot()}visualization/list_library_datasets`,
-        embedded: true
+        embedded: true,
     });
 
     // build tabs
@@ -64,12 +64,12 @@ var select_datasets = (filters, success_fn) => {
     tabs.add({
         id: "histories",
         title: _l("Histories"),
-        $el: $("<div/>").append(history_grid.$el)
+        $el: $("<div/>").append(history_grid.$el),
     });
     tabs.add({
         id: "libraries",
         title: _l("Libraries"),
-        $el: $("<div/>").append(library_grid.$el)
+        $el: $("<div/>").append(library_grid.$el),
     });
 
     // modal
@@ -79,34 +79,34 @@ var select_datasets = (filters, success_fn) => {
         body: tabs.$el,
         closing_events: true,
         buttons: {
-            Cancel: function() {
+            Cancel: function () {
                 Galaxy.modal.hide();
             },
-            Add: function() {
+            Add: function () {
                 var requests = [];
-                tabs.$("input.grid-row-select-checkbox[name=id]:checked").each(function() {
+                tabs.$("input.grid-row-select-checkbox[name=id]:checked").each(function () {
                     window.console.log($(this).val());
                     requests[requests.length] = $.ajax({
                         url: `${getAppRoot()}api/datasets/${$(this).val()}`,
                         dataType: "json",
                         data: {
                             data_type: "track_config",
-                            hda_ldda: tabs.current() == "histories" ? "hda" : "ldda"
-                        }
+                            hda_ldda: tabs.current() == "histories" ? "hda" : "ldda",
+                        },
                     });
                 });
                 // To preserve order, wait until there are definitions for all tracks and then add
                 // them sequentially.
-                $.when.apply($, requests).then(function() {
+                $.when.apply($, requests).then(function () {
                     // jQuery always returns an Array for arguments, so need to look at first element
                     // to determine whether multiple requests were made and consequently how to
                     // map arguments to track definitions.
-                    var track_defs = arguments[0] instanceof Array ? $.map(arguments, arg => arg[0]) : [arguments[0]];
+                    var track_defs = arguments[0] instanceof Array ? $.map(arguments, (arg) => arg[0]) : [arguments[0]];
                     success_fn(track_defs);
                 });
                 Galaxy.modal.hide();
-            }
-        }
+            },
+        },
     });
 };
 
@@ -115,7 +115,7 @@ var select_datasets = (filters, success_fn) => {
 /**
  * Canvas manager is used to create canvases for browsers as well as providing a pattern cache
  */
-var CanvasManager = function(default_font) {
+var CanvasManager = function (default_font) {
     this.default_font = default_font !== undefined ? default_font : "9px Monaco, Lucida Console, monospace";
 
     this.dummy_canvas = this.new_canvas();
@@ -134,7 +134,7 @@ var CanvasManager = function(default_font) {
 };
 
 _.extend(CanvasManager.prototype, {
-    load_pattern: function(key, path) {
+    load_pattern: function (key, path) {
         var patterns = this.patterns;
         var dummy_context = this.dummy_context;
         var image = new Image();
@@ -143,15 +143,15 @@ _.extend(CanvasManager.prototype, {
             patterns[key] = dummy_context.createPattern(image, "repeat");
         };
     },
-    get_pattern: function(key) {
+    get_pattern: function (key) {
         return this.patterns[key];
     },
-    new_canvas: function() {
+    new_canvas: function () {
         var canvas = $("<canvas/>")[0];
         // Keep a reference back to the manager
         canvas.manager = this;
         return canvas;
-    }
+    },
 });
 
 /**
@@ -164,22 +164,22 @@ var Cache = Backbone.Model.extend({
         // Objects in cache; indexes into cache are strings of keys.
         obj_cache: null,
         // key_ary contains keys for objects in cache.
-        key_ary: null
+        key_ary: null,
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.clear();
     },
 
     /**
      * Get an element from the cache using its key.
      */
-    get_elt: function(key) {
+    get_elt: function (key) {
         var obj_cache = this.attributes.obj_cache;
         var key_ary = this.attributes.key_ary;
         var key_str = key.toString();
 
-        var index = _.indexOf(key_ary, k => k.toString() === key_str);
+        var index = _.indexOf(key_ary, (k) => k.toString() === key_str);
 
         // Update cache.
         if (index !== -1) {
@@ -200,7 +200,7 @@ var Cache = Backbone.Model.extend({
     /**
      * Put an element into the cache.
      */
-    set_elt: function(key, value) {
+    set_elt: function (key, value) {
         var obj_cache = this.attributes.obj_cache;
         var key_ary = this.attributes.key_ary;
         var key_str = key.toString();
@@ -229,7 +229,7 @@ var Cache = Backbone.Model.extend({
      * Move key to end of cache. Keys are removed from the front, so moving a key to the end
      * delays the key's removal.
      */
-    move_key_to_end: function(key, index) {
+    move_key_to_end: function (key, index) {
         this.attributes.key_ary.splice(index, 1);
         this.attributes.key_ary.push(key);
     },
@@ -237,23 +237,23 @@ var Cache = Backbone.Model.extend({
     /**
      * Clear all elements from the cache.
      */
-    clear: function() {
+    clear: function () {
         this.attributes.obj_cache = {};
         this.attributes.key_ary = [];
     },
 
     /** Returns the number of elements in the cache. */
-    size: function() {
+    size: function () {
         return this.attributes.key_ary.length;
     },
 
     /** Returns key most recently added to cache. */
-    most_recently_added: function() {
+    most_recently_added: function () {
         return this.size() === 0
             ? null
             : // Most recent key is at the end of key array.
               this.attributes.key_ary[this.attributes.key_ary.length - 1];
-    }
+    },
 });
 
 /**
@@ -267,18 +267,18 @@ var GenomeDataManager = Cache.extend({
         min_region_size: 200,
         filters_manager: null,
         data_type: "data",
-        data_mode_compatible: function(entry, mode) {
+        data_mode_compatible: function (entry, mode) {
             return true;
         },
-        can_subset: function(entry) {
+        can_subset: function (entry) {
             return false;
-        }
+        },
     }),
 
     /**
      * Initialization.
      */
-    initialize: function(options) {
+    initialize: function (options) {
         Cache.prototype.initialize.call(this);
 
         // Set initial entries in data manager.
@@ -292,7 +292,7 @@ var GenomeDataManager = Cache.extend({
      * Add data entries to manager; each entry should be a dict with attributes region (key), data, and data_type.
      * If necessary, manager size is increased to hold all data.
      */
-    add_data: function(entries) {
+    add_data: function (entries) {
         // Increase size to accomodate all entries.
         if (this.get("num_elements") < entries.length) {
             this.set("num_elements", entries.length);
@@ -300,7 +300,7 @@ var GenomeDataManager = Cache.extend({
 
         // Put data into manager.
         var self = this;
-        _.each(entries, entry => {
+        _.each(entries, (entry) => {
             self.set_data(entry.region, entry);
         });
     },
@@ -309,7 +309,7 @@ var GenomeDataManager = Cache.extend({
      * Returns deferred that resolves to true when dataset is ready (or false if dataset
      * cannot be used).
      */
-    data_is_ready: function() {
+    data_is_ready: function () {
         var dataset = this.get("dataset");
         var ready_deferred = $.Deferred();
 
@@ -327,17 +327,17 @@ var GenomeDataManager = Cache.extend({
                 url: this.get("dataset").url(),
                 data: {
                     hda_ldda: dataset.get("hda_ldda"),
-                    data_type: query_type
+                    data_type: query_type,
                 },
-                dataType: "json"
+                dataType: "json",
             },
             interval: 5000,
-            success_fn: function(response) {
+            success_fn: function (response) {
                 return response !== "pending";
-            }
+            },
         });
 
-        $.when(ss_deferred.go()).then(response => {
+        $.when(ss_deferred.go()).then((response) => {
             ready_deferred.resolve(response === "ok" || response === "data");
         });
         return ready_deferred;
@@ -346,13 +346,13 @@ var GenomeDataManager = Cache.extend({
     /**
      * Perform a feature search from server; returns Deferred object that resolves when data is available.
      */
-    search_features: function(query) {
+    search_features: function (query) {
         var dataset = this.get("dataset");
 
         var params = {
             query: query,
             hda_ldda: dataset.get("hda_ldda"),
-            data_type: "features"
+            data_type: "features",
         };
 
         return $.getJSON(dataset.url(), params);
@@ -363,7 +363,7 @@ var GenomeDataManager = Cache.extend({
      * for region; when data becomes available, replaces Deferred with data.
      * Returns the Deferred that resolves when data is available.
      */
-    load_data: function(region, mode, resolution, extra_params) {
+    load_data: function (region, mode, resolution, extra_params) {
         // Setup data request params.
         var dataset = this.get("dataset");
 
@@ -374,7 +374,7 @@ var GenomeDataManager = Cache.extend({
             high: region.get("end"),
             mode: mode,
             resolution: resolution,
-            hda_ldda: dataset.get("hda_ldda")
+            hda_ldda: dataset.get("hda_ldda"),
         };
 
         $.extend(params, extra_params);
@@ -393,7 +393,7 @@ var GenomeDataManager = Cache.extend({
         // Do request.
         var manager = this;
 
-        var entry = $.getJSON(dataset.url(), params, result => {
+        var entry = $.getJSON(dataset.url(), params, (result) => {
             // Add region to the result.
             result.region = region;
             manager.set_data(region, result);
@@ -406,7 +406,7 @@ var GenomeDataManager = Cache.extend({
     /**
      * Get data from dataset.
      */
-    get_data: function(region, mode, resolution, extra_params) {
+    get_data: function (region, mode, resolution, extra_params) {
         // Look for entry and return if it's a deferred or if data available is compatible with mode.
         var entry = this.get_elt(region);
         if (entry && (util_mod.is_deferred(entry) || this.get("data_mode_compatible")(entry, mode))) {
@@ -483,7 +483,7 @@ var GenomeDataManager = Cache.extend({
     /**
      * Alias for set_elt for readbility.
      */
-    set_data: function(region, entry) {
+    set_data: function (region, entry) {
         this.set_elt(region, entry);
     },
 
@@ -496,7 +496,7 @@ var GenomeDataManager = Cache.extend({
     /**
      * Gets more data for a region using either a depth-first or a breadth-first approach.
      */
-    get_more_data: function(region, mode, resolution, extra_params, req_type) {
+    get_more_data: function (region, mode, resolution, extra_params, req_type) {
         var cur_data = this._mark_stale(region);
         if (!(cur_data && this.get("data_mode_compatible")(cur_data, mode))) {
             console.log("ERROR: problem with getting more data: current data is not compatible");
@@ -510,7 +510,7 @@ var GenomeDataManager = Cache.extend({
         if (req_type === this.DEEP_DATA_REQ) {
             // Use same interval but set start_val to skip data that's already in cur_data.
             $.extend(extra_params, {
-                start_val: cur_data.data.length + 1
+                start_val: cur_data.data.length + 1,
             });
         } else if (req_type === this.BROAD_DATA_REQ) {
             // To get past an area of extreme feature depth, set query low to be after either
@@ -531,7 +531,7 @@ var GenomeDataManager = Cache.extend({
         // load_data sets cache to new_data_request, but use custom deferred object so that signal and data
         // is all data, not just new data.
         this.set_data(region, new_data_available);
-        $.when(new_data_request).then(result => {
+        $.when(new_data_request).then((result) => {
             // Update data and message.
             if (result.data) {
                 result.data = cur_data.data.concat(result.data);
@@ -552,7 +552,7 @@ var GenomeDataManager = Cache.extend({
     /**
      * Returns true if more detailed data can be obtained for entry.
      */
-    can_get_more_detailed_data: function(region) {
+    can_get_more_detailed_data: function (region) {
         var cur_data = this.get_elt(region);
 
         // Can only get more detailed data for bigwig data that has less than 8000 data points.
@@ -563,7 +563,7 @@ var GenomeDataManager = Cache.extend({
     /**
      * Returns more detailed data for an entry.
      */
-    get_more_detailed_data: function(region, mode, resolution, detail_multiplier, extra_params) {
+    get_more_detailed_data: function (region, mode, resolution, detail_multiplier, extra_params) {
         // Mark current entry as stale.
         var cur_data = this._mark_stale(region);
         if (!cur_data) {
@@ -587,7 +587,7 @@ var GenomeDataManager = Cache.extend({
     /**
      * Marks cache data as stale.
      */
-    _mark_stale: function(region) {
+    _mark_stale: function (region) {
         var entry = this.get_elt(region);
         if (!entry) {
             console.log("ERROR: no data to mark as stale: ", this.get("dataset"), region.toString());
@@ -601,7 +601,7 @@ var GenomeDataManager = Cache.extend({
      * of data or, if data is not available, returns a Deferred that resolves to the
      * data when it becomes available.
      */
-    get_genome_wide_data: function(genome) {
+    get_genome_wide_data: function (genome) {
         // -- Get all data. --
 
         var self = this;
@@ -609,12 +609,12 @@ var GenomeDataManager = Cache.extend({
         var all_data_available = true;
 
         var //  Map chromosome info into genome data.
-            gw_data = _.map(genome.get("chroms_info").chrom_info, chrom_info => {
+            gw_data = _.map(genome.get("chroms_info").chrom_info, (chrom_info) => {
                 var chrom_data = self.get_elt(
                     new GenomeRegion({
                         chrom: chrom_info.chrom,
                         start: 0,
-                        end: chrom_info.len
+                        end: chrom_info.len,
                     })
                 );
 
@@ -634,7 +634,7 @@ var GenomeDataManager = Cache.extend({
         // -- All data is not available, so load from server. --
 
         var deferred = $.Deferred();
-        $.getJSON(this.get("dataset").url(), { data_type: "genome_data" }, genome_wide_data => {
+        $.getJSON(this.get("dataset").url(), { data_type: "genome_data" }, (genome_wide_data) => {
             self.add_data(genome_wide_data.data);
             deferred.resolve(genome_wide_data.data);
         });
@@ -645,19 +645,19 @@ var GenomeDataManager = Cache.extend({
     /**
      * Returns entry with only data in the subregion.
      */
-    subset_entry: function(entry, subregion) {
+    subset_entry: function (entry, subregion) {
         // Dictionary from entry type to function for subsetting data.
         var subset_fns = {
-            bigwig: function(data, subregion) {
+            bigwig: function (data, subregion) {
                 return _.filter(
                     data,
-                    data_point => data_point[0] >= subregion.get("start") && data_point[0] <= subregion.get("end")
+                    (data_point) => data_point[0] >= subregion.get("start") && data_point[0] <= subregion.get("end")
                 );
             },
-            refseq: function(data, subregion) {
+            refseq: function (data, subregion) {
                 var seq_start = subregion.get("start") - entry.region.get("start");
                 return entry.data.slice(seq_start, seq_start + subregion.length());
-            }
+            },
         };
 
         // Subset entry if there is a function for subsetting and regions are not the same.
@@ -670,25 +670,25 @@ var GenomeDataManager = Cache.extend({
         return {
             region: subregion,
             data: subregion_data,
-            dataset_type: entry.dataset_type
+            dataset_type: entry.dataset_type,
         };
-    }
+    },
 });
 
 var GenomeReferenceDataManager = GenomeDataManager.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         // Use generic object in place of dataset and set urlRoot to fetch data.
         var dataset_placeholder = new Backbone.Model();
         dataset_placeholder.urlRoot = options.data_url;
         this.set("dataset", dataset_placeholder);
     },
 
-    load_data: function(region, mode, resolution, extra_params) {
+    load_data: function (region, mode, resolution, extra_params) {
         // Fetch data if region is not too large.
         return region.length() <= 100000
             ? GenomeDataManager.prototype.load_data.call(this, region, mode, resolution, extra_params)
             : { data: null, region: region };
-    }
+    },
 });
 
 /**
@@ -698,37 +698,37 @@ var Genome = Backbone.Model.extend({
     defaults: {
         name: null,
         key: null,
-        chroms_info: null
+        chroms_info: null,
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.id = options.dbkey;
     },
 
     /**
      * Shorthand for getting to chromosome information.
      */
-    get_chroms_info: function() {
+    get_chroms_info: function () {
         return this.attributes.chroms_info.chrom_info;
     },
 
     /**
      * Returns a GenomeRegion object denoting a complete chromosome.
      */
-    get_chrom_region: function(chr_name) {
+    get_chrom_region: function (chr_name) {
         // FIXME: use findWhere in underscore 1.4
-        var chrom_info = _.find(this.get_chroms_info(), chrom_info => chrom_info.chrom === chr_name);
+        var chrom_info = _.find(this.get_chroms_info(), (chrom_info) => chrom_info.chrom === chr_name);
         return new GenomeRegion({
             chrom: chrom_info.chrom,
-            end: chrom_info.len
+            end: chrom_info.len,
         });
     },
 
     /** Returns the length of a chromosome. */
-    get_chrom_len: function(chr_name) {
+    get_chrom_len: function (chr_name) {
         // FIXME: use findWhere in underscore 1.4
-        return _.find(this.get_chroms_info(), chrom_info => chrom_info.chrom === chr_name).len;
-    }
+        return _.find(this.get_chroms_info(), (chrom_info) => chrom_info.chrom === chr_name).len;
+    },
 });
 
 /**
@@ -741,14 +741,14 @@ var GenomeRegion = Backbone.Model.extend(
             start: 0,
             end: 0,
             str_val: null,
-            genome: null
+            genome: null,
         },
 
         /**
          * Returns true if this region is the same as a given region.
          * It does not test the genome right now.
          */
-        same: function(region) {
+        same: function (region) {
             return (
                 this.attributes.chrom === region.get("chrom") &&
                 this.attributes.start === region.get("start") &&
@@ -759,7 +759,7 @@ var GenomeRegion = Backbone.Model.extend(
         /**
          * If from_str specified, use it to initialize attributes.
          */
-        initialize: function(options) {
+        initialize: function (options) {
             if (options.from_str) {
                 var pieces = options.from_str.split(":");
                 var chrom = pieces[0];
@@ -767,7 +767,7 @@ var GenomeRegion = Backbone.Model.extend(
                 this.set({
                     chrom: chrom,
                     start: parseInt(start_end[0], 10),
-                    end: parseInt(start_end[1], 10)
+                    end: parseInt(start_end[1], 10),
                 });
             }
 
@@ -777,35 +777,35 @@ var GenomeRegion = Backbone.Model.extend(
             // Set str_val on attribute change.
             this.on(
                 "change",
-                function() {
+                function () {
                     this.attributes.str_val = `${this.get("chrom")}:${this.get("start")}-${this.get("end")}`;
                 },
                 this
             );
         },
 
-        copy: function() {
+        copy: function () {
             return new GenomeRegion({
                 chrom: this.get("chrom"),
                 start: this.get("start"),
-                end: this.get("end")
+                end: this.get("end"),
             });
         },
 
-        length: function() {
+        length: function () {
             return this.get("end") - this.get("start");
         },
 
         /** Returns region in canonical form chrom:start-end */
-        toString: function() {
+        toString: function () {
             return this.attributes.str_val;
         },
 
-        toJSON: function() {
+        toJSON: function () {
             return {
                 chrom: this.get("chrom"),
                 start: this.get("start"),
-                end: this.get("end")
+                end: this.get("end"),
             };
         },
 
@@ -813,7 +813,7 @@ var GenomeRegion = Backbone.Model.extend(
          * Compute the type of overlap between this region and another region. The overlap is computed relative to the given/second region;
          * hence, OVERLAP_START indicates that the first region overlaps the start (but not the end) of the second region.
          */
-        compute_overlap: function(a_region) {
+        compute_overlap: function (a_region) {
             var first_chrom = this.get("chrom");
             var second_chrom = a_region.get("chrom");
             var first_start = this.get("start");
@@ -859,7 +859,7 @@ var GenomeRegion = Backbone.Model.extend(
         /**
          * Trim a region to match genome's constraints.
          */
-        trim: function(genome) {
+        trim: function (genome) {
             // Assume that all chromosome/contigs start at 0.
             if (this.attributes.start < 0) {
                 this.attributes.start = 0;
@@ -879,25 +879,25 @@ var GenomeRegion = Backbone.Model.extend(
         /**
          * Returns true if this region contains a given region.
          */
-        contains: function(a_region) {
+        contains: function (a_region) {
             return this.compute_overlap(a_region) === GenomeRegion.overlap_results.CONTAINS;
         },
 
         /**
          * Returns true if regions overlap.
          */
-        overlaps: function(a_region) {
+        overlaps: function (a_region) {
             return (
                 _.intersection(
                     [this.compute_overlap(a_region)],
                     [
                         GenomeRegion.overlap_results.DIF_CHROMS,
                         GenomeRegion.overlap_results.BEFORE,
-                        GenomeRegion.overlap_results.AFTER
+                        GenomeRegion.overlap_results.AFTER,
                     ]
                 ).length === 0
             );
-        }
+        },
     },
     {
         overlap_results: {
@@ -907,13 +907,13 @@ var GenomeRegion = Backbone.Model.extend(
             OVERLAP_START: 1003,
             OVERLAP_END: 1004,
             CONTAINED_BY: 1005,
-            AFTER: 1006
-        }
+            AFTER: 1006,
+        },
     }
 );
 
 var GenomeRegionCollection = Backbone.Collection.extend({
-    model: GenomeRegion
+    model: GenomeRegion,
 });
 
 /**
@@ -922,19 +922,19 @@ var GenomeRegionCollection = Backbone.Collection.extend({
 var BrowserBookmark = Backbone.Model.extend({
     defaults: {
         region: null,
-        note: ""
+        note: "",
     },
 
-    initialize: function(options) {
+    initialize: function (options) {
         this.set("region", new GenomeRegion(options.region));
-    }
+    },
 });
 
 /**
  * Bookmarks collection.
  */
 var BrowserBookmarkCollection = Backbone.Collection.extend({
-    model: BrowserBookmark
+    model: BrowserBookmark,
 });
 
 /**
@@ -944,31 +944,31 @@ var BrowserBookmarkCollection = Backbone.Collection.extend({
 var BackboneTrack = Backbone.Model.extend(CustomToJSON).extend(
     {
         defaults: {
-            mode: "Auto"
+            mode: "Auto",
         },
 
-        initialize: function(options) {
+        initialize: function (options) {
             this.set("dataset", new Dataset(options.dataset));
 
             // -- Set up config settings. --
             var models = [
                 {
                     key: "name",
-                    default_value: this.get("dataset").get("name")
+                    default_value: this.get("dataset").get("name"),
                 },
                 { key: "color" },
                 {
                     key: "min_value",
                     label: "Min Value",
                     type: "float",
-                    default_value: 0
+                    default_value: 0,
                 },
                 {
                     key: "max_value",
                     label: "Max Value",
                     type: "float",
-                    default_value: 1
-                }
+                    default_value: 1,
+                },
             ];
 
             this.set("config", config_mod.ConfigSettingCollection.from_models_and_saved_values(models, options.prefs));
@@ -984,42 +984,36 @@ var BackboneTrack = Backbone.Model.extend(CustomToJSON).extend(
                 "data_manager",
                 new GenomeDataManager({
                     dataset: this.get("dataset"),
-                    init_data: preloaded_data
+                    init_data: preloaded_data,
                 })
             );
-        }
+        },
     },
     {
         // This definition matches that produced by to_dict() methods in tracks.js
         to_json_keys: ["track_type", "dataset", "prefs", "mode", "filters", "tool_state"],
         to_json_mappers: {
-            prefs: function(p, self) {
+            prefs: function (p, self) {
                 if (_.size(p) === 0) {
                     p = {
-                        name: self
-                            .get("config")
-                            .get("name")
-                            .get("value"),
-                        color: self
-                            .get("config")
-                            .get("color")
-                            .get("value")
+                        name: self.get("config").get("name").get("value"),
+                        color: self.get("config").get("color").get("value"),
                     };
                 }
                 return p;
             },
-            dataset: function(d) {
+            dataset: function (d) {
                 return {
                     id: d.id,
-                    hda_ldda: d.get("hda_ldda")
+                    hda_ldda: d.get("hda_ldda"),
                 };
-            }
-        }
+            },
+        },
     }
 );
 
 var BackboneTrackCollection = Backbone.Collection.extend({
-    model: BackboneTrack
+    model: BackboneTrack,
 });
 
 /**
@@ -1028,7 +1022,7 @@ var BackboneTrackCollection = Backbone.Collection.extend({
 var Visualization = Backbone.Model.extend({
     defaults: {
         title: "",
-        type: ""
+        type: "",
     },
 
     urlRoot: `${getAppRoot()}api/visualizations`,
@@ -1038,16 +1032,16 @@ var Visualization = Backbone.Model.extend({
      * Note: This is necessary because (a) Galaxy requires keyword args and
      * (b) Galaxy does not handle PUT now.
      */
-    save: function() {
+    save: function () {
         return $.ajax({
             url: this.url(),
             type: "POST",
             dataType: "json",
             data: {
-                vis_json: JSON.stringify(this)
-            }
+                vis_json: JSON.stringify(this),
+            },
         });
-    }
+    },
 });
 
 /**
@@ -1059,10 +1053,10 @@ var GenomeVisualization = Visualization.extend(CustomToJSON).extend(
             dbkey: "",
             drawables: null,
             bookmarks: null,
-            viewport: null
+            viewport: null,
         }),
 
-        initialize: function(options) {
+        initialize: function (options) {
             // Replace drawables with tracks.
             this.set("drawables", new BackboneTrackCollection(options.tracks));
 
@@ -1071,7 +1065,7 @@ var GenomeVisualization = Visualization.extend(CustomToJSON).extend(
 
             // Clear track and data definitions to avoid storing large objects.
             this.unset("tracks");
-            this.get("drawables").each(d => {
+            this.get("drawables").each((d) => {
                 d.unset("preloaded_data");
             });
         },
@@ -1079,26 +1073,26 @@ var GenomeVisualization = Visualization.extend(CustomToJSON).extend(
         /**
          * Add a track or array of tracks to the visualization.
          */
-        add_tracks: function(tracks) {
+        add_tracks: function (tracks) {
             this.get("drawables").add(tracks);
-        }
+        },
     },
     {
         // This definition matches that produced by to_dict() methods in tracks.js
         to_json_keys: ["view", "viewport", "bookmarks"],
 
         to_json_mappers: {
-            view: function(dummy, self) {
+            view: function (dummy, self) {
                 return {
                     obj_type: "View",
                     prefs: {
                         name: self.get("title"),
-                        content_visible: true
+                        content_visible: true,
                     },
-                    drawables: self.get("drawables")
+                    drawables: self.get("drawables"),
                 };
-            }
-        }
+            },
+        },
     }
 );
 
@@ -1110,7 +1104,7 @@ var GenomeVisualization = Visualization.extend(CustomToJSON).extend(
  * Router for track browser.
  */
 var TrackBrowserRouter = Backbone.Router.extend({
-    initialize: function(options) {
+    initialize: function (options) {
         this.view = options.view;
 
         // Can't put regular expression in routes dictionary.
@@ -1119,14 +1113,14 @@ var TrackBrowserRouter = Backbone.Router.extend({
         this.route(/([\w+]+:[\d,]+-[\d,]+)$/, "change_location");
 
         // Handle navigate events from view.
-        this.view.on("navigate", new_loc => {
+        this.view.on("navigate", (new_loc) => {
             this.navigate(new_loc);
         });
     },
 
-    change_location: function(new_loc) {
+    change_location: function (new_loc) {
         this.view.go_to(new_loc);
-    }
+    },
 });
 
 export default {
@@ -1143,5 +1137,5 @@ export default {
     GenomeReferenceDataManager: GenomeReferenceDataManager,
     TrackBrowserRouter: TrackBrowserRouter,
     Visualization: Visualization,
-    select_datasets: select_datasets
+    select_datasets: select_datasets,
 };
diff --git a/client/galaxy/scripts/viz/viz_views.js b/client/galaxy/scripts/viz/viz_views.js
index cfc75bf8bd3b..451455911a2d 100644
--- a/client/galaxy/scripts/viz/viz_views.js
+++ b/client/galaxy/scripts/viz/viz_views.js
@@ -8,26 +8,22 @@ import { make_popupmenu } from "ui/popupmenu";
 var TrackHeaderView = Backbone.View.extend({
     className: "track-header",
 
-    initialize: function() {
+    initialize: function () {
         // Watch and update name changes.
         this.model.config.get("name").on("change:value", this.update_name, this);
         this.render();
     },
 
-    render: function() {
+    render: function () {
         this.$el.append($("<div/>").addClass(this.model.drag_handle_class));
-        this.$el.append(
-            $("<div/>")
-                .addClass("track-name")
-                .text(this.model.config.get_value("name"))
-        );
+        this.$el.append($("<div/>").addClass("track-name").text(this.model.config.get_value("name")));
 
         // Icons container.
         this.action_icons = {};
         this.render_action_icons();
 
         // Suppress double clicks in header so that they do not impact viz under header.
-        this.$el.dblclick(e => {
+        this.$el.dblclick((e) => {
             e.stopPropagation();
         });
 
@@ -35,17 +31,14 @@ var TrackHeaderView = Backbone.View.extend({
         this.$el.append($("<div style='clear: both'/>"));
     },
 
-    update_name: function() {
+    update_name: function () {
         this.$el.find(".track-name").text(this.model.config.get_value("name"));
     },
 
-    render_action_icons: function() {
+    render_action_icons: function () {
         var self = this;
-        this.icons_div = $("<div/>")
-            .addClass("track-icons")
-            .hide()
-            .appendTo(this.$el);
-        _.each(this.model.action_icons_def, icon_dict => {
+        this.icons_div = $("<div/>").addClass("track-icons").hide().appendTo(this.$el);
+        _.each(this.model.action_icons_def, (icon_dict) => {
             self.add_action_icon(
                 icon_dict.name,
                 icon_dict.title,
@@ -63,7 +56,7 @@ var TrackHeaderView = Backbone.View.extend({
     /**
      * Add an action icon to this object. Appends icon unless prepend flag is specified.
      */
-    add_action_icon: function(name, title, css_class, on_click_fn, prepend, hide) {
+    add_action_icon: function (name, title, css_class, on_click_fn, prepend, hide) {
         var self = this;
         this.action_icons[name] = $("<a/>")
             .attr("title", title)
@@ -82,7 +75,7 @@ var TrackHeaderView = Backbone.View.extend({
     /**
      * Set track's modes and update mode icon popup.
      */
-    set_display_modes: function(new_modes, init_mode) {
+    set_display_modes: function (new_modes, init_mode) {
         if (!new_modes) {
             return;
         }
@@ -100,7 +93,7 @@ var TrackHeaderView = Backbone.View.extend({
         var mode_mapping = {};
         for (var i = 0, len = track.display_modes.length; i < len; i++) {
             var mode = track.display_modes[i];
-            mode_mapping[mode] = (mode => () => {
+            mode_mapping[mode] = ((mode) => () => {
                 track.change_mode(mode);
                 // HACK: the popup menu messes with the track's hover event, so manually show/hide
                 // icons div for now.
@@ -110,9 +103,9 @@ var TrackHeaderView = Backbone.View.extend({
         }
 
         make_popupmenu(this.action_icons.mode_icon, mode_mapping);
-    }
+    },
 });
 
 export default {
-    TrackHeaderView: TrackHeaderView
+    TrackHeaderView: TrackHeaderView,
 };
diff --git a/client/galaxy/style/scss/jquery.rating.scss b/client/galaxy/style/scss/jquery.rating.scss
index c635ae429e0d..f94681c67d78 100644
--- a/client/galaxy/style/scss/jquery.rating.scss
+++ b/client/galaxy/style/scss/jquery.rating.scss
@@ -1,44 +1,44 @@
-/* jQuery.Rating Plugin CSS - http://www.fyneworks.com/jquery/star-rating/ */
-div.rating-cancel,
-div.star-rating {
-    float: left;
-    width: 17px;
-    height: 15px;
-    text-indent: -999em;
-    cursor: pointer;
-    display: block;
-    background: transparent;
-    overflow: hidden;
-}
-div.rating-cancel,
-div.rating-cancel a {
-    background: url(../../images/delete.gif) no-repeat 0 -16px;
-}
-div.star-rating,
-div.star-rating a {
-    background: url(../../images/star.gif) no-repeat 0 0px;
-}
-div.rating-cancel a,
-div.star-rating a {
-    display: block;
-    width: 16px;
-    height: 100%;
-    background-position: 0 0px;
-    border: 0;
-}
-div.star-rating-on a {
-    background-position: 0 -16px !important;
-}
-div.star-rating-hover a {
-    background-position: 0 -32px;
-}
-/* Read Only CSS */
-div.star-rating-readonly a {
-    cursor: default !important;
-}
-/* Partial Star CSS */
-div.star-rating {
-    background: transparent !important;
-    overflow: hidden !important;
-}
-/* END jQuery.Rating Plugin CSS */
+/* jQuery.Rating Plugin CSS - http://www.fyneworks.com/jquery/star-rating/ */
+div.rating-cancel,
+div.star-rating {
+    float: left;
+    width: 17px;
+    height: 15px;
+    text-indent: -999em;
+    cursor: pointer;
+    display: block;
+    background: transparent;
+    overflow: hidden;
+}
+div.rating-cancel,
+div.rating-cancel a {
+    background: url(../../images/delete.gif) no-repeat 0 -16px;
+}
+div.star-rating,
+div.star-rating a {
+    background: url(../../images/star.gif) no-repeat 0 0px;
+}
+div.rating-cancel a,
+div.star-rating a {
+    display: block;
+    width: 16px;
+    height: 100%;
+    background-position: 0 0px;
+    border: 0;
+}
+div.star-rating-on a {
+    background-position: 0 -16px !important;
+}
+div.star-rating-hover a {
+    background-position: 0 -32px;
+}
+/* Read Only CSS */
+div.star-rating-readonly a {
+    cursor: default !important;
+}
+/* Partial Star CSS */
+div.star-rating {
+    background: transparent !important;
+    overflow: hidden !important;
+}
+/* END jQuery.Rating Plugin CSS */
diff --git a/client/galaxy/style/scss/theme/blue.scss b/client/galaxy/style/scss/theme/blue.scss
index 49961495ceb6..98a54a20f145 100644
--- a/client/galaxy/style/scss/theme/blue.scss
+++ b/client/galaxy/style/scss/theme/blue.scss
@@ -48,7 +48,7 @@ $theme-colors: map-merge(
         "warning": $brand-warning,
         "info": $brand-info,
         "light": $brand-light,
-        "dark": $brand-dark
+        "dark": $brand-dark,
     ),
     $theme-colors
 );

From 43bfeb3b764466f0b76f191d1d6f5c77946f4a39 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 22 Mar 2020 16:39:21 -0400
Subject: [PATCH 511/853] Upgrade eslint-plugin-vue as well

---
 client/package.json | 2 +-
 client/yarn.lock    | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/package.json b/client/package.json
index 1e3229a7f6dc..50c07294b601 100644
--- a/client/package.json
+++ b/client/package.json
@@ -100,7 +100,7 @@
     "del": "^5.1.0",
     "duplicate-package-checker-webpack-plugin": "^3.0.0",
     "eslint": "^6.8.0",
-    "eslint-plugin-vue": "^6.2.1",
+    "eslint-plugin-vue": "^6.2.2",
     "expose-loader": "^0.7.5",
     "file-loader": "^5.0.2",
     "gulp": "^4.0.2",
diff --git a/client/yarn.lock b/client/yarn.lock
index 0a41e99c61f4..0dc61e10769e 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -5239,10 +5239,10 @@ escodegen@^1.11.1:
   optionalDependencies:
     source-map "~0.6.1"
 
-eslint-plugin-vue@^6.2.1:
-  version "6.2.1"
-  resolved "https://registry.yarnpkg.com/eslint-plugin-vue/-/eslint-plugin-vue-6.2.1.tgz#ca802df5c33146aed1e56bb21d250c1abb6120a3"
-  integrity sha512-MiIDOotoWseIfLIfGeDzF6sDvHkVvGd2JgkvjyHtN3q4RoxdAXrAMuI3SXTOKatljgacKwpNAYShmcKZa4yZzw==
+eslint-plugin-vue@^6.2.2:
+  version "6.2.2"
+  resolved "https://registry.yarnpkg.com/eslint-plugin-vue/-/eslint-plugin-vue-6.2.2.tgz#27fecd9a3a24789b0f111ecdd540a9e56198e0fe"
+  integrity sha512-Nhc+oVAHm0uz/PkJAWscwIT4ijTrK5fqNqz9QB1D35SbbuMG1uB6Yr5AJpvPSWg+WOw7nYNswerYh0kOk64gqQ==
   dependencies:
     natural-compare "^1.4.0"
     semver "^5.6.0"

From e9c743dab8b1bb5c538f68b9d15e4645db252214 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 10:38:08 -0400
Subject: [PATCH 512/853] More changes per code review feedback.

---
 lib/galaxy/objectstore/irods.py               |  82 +-----------------
 .../irods_beginner_training_2016.pdf          | Bin 497249 -> 0 bytes
 test/integration/objectstore/test_irods.py    |  72 ---------------
 .../integration/test_datatype_upload_irods.py |  31 +------
 4 files changed, 8 insertions(+), 177 deletions(-)
 delete mode 100644 test/integration/objectstore/irods_beginner_training_2016.pdf
 delete mode 100644 test/integration/objectstore/test_irods.py

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 14f99b22339b..951fa8926d89 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -29,7 +29,6 @@
     umask_fix_perms,
 )
 from galaxy.util.path import safe_relpath
-from galaxy.util.sleeper import Sleeper
 from ..objectstore import (
     DiskObjectStore,
     local_extra_dirs,
@@ -207,15 +206,6 @@ def _initialize(self):
         self.home =  "/" + self.zone + "/home/" + self.username
 
         self.session = self._configure_connection(host=self.host, port=self.port, user=self.username, password=self.password, zone=self.zone)
-        # Clean cache only if value is set in galaxy config file
-        if self.cache_size != -1:
-            # Convert GBs to bytes for comparison
-            self.cache_size = self.cache_size * bytesize.SUFFIX_TO_BYTES['GI']
-            # Helper for interruptable sleep
-            self.sleeper = Sleeper()
-            self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
-            self.cache_monitor_thread.start()
-            log.info("Cache cleaner manager started")
 
     def _configure_connection(self, host='localhost', port='1247', user='rods', password='rods', zone='tempZone'):
         with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
@@ -236,70 +226,6 @@ def to_dict(self):
         as_dict.update(self._config_to_dict())
         return as_dict
 
-    def __cache_monitor(self):
-        time.sleep(5)  # Wait for things to load before starting the monitor
-        while self.running:
-            total_size = 0
-            # Is this going to be too expensive of an operation to be done frequently?
-            file_list = []
-            for dirpath, _, filenames in os.walk(self.staging_path):
-                for filename in filenames:
-                    filepath = os.path.join(dirpath, filename)
-                    file_size = os.path.getsize(filepath)
-                    total_size += file_size
-                    # Get the time given file was last accessed
-                    last_access_time = time.localtime(os.stat(filepath)[7])
-                    # Compose a tuple of the access time and the file path
-                    file_tuple = last_access_time, filepath, file_size
-                    file_list.append(file_tuple)
-            # Sort the file list (based on access time)
-            file_list.sort()
-            # Initiate cleaning once within 10% of the defined cache size?
-            cache_limit = self.cache_size * 0.9
-            if total_size > cache_limit:
-                log.info("Initiating cache cleaning: current cache size: %s; clean until smaller than: %s",
-                         convert_bytes(total_size), convert_bytes(cache_limit))
-                # How much to delete? If simply deleting up to the cache-10% limit,
-                # is likely to be deleting frequently and may run the risk of hitting
-                # the limit - maybe delete additional #%?
-                # For now, delete enough to leave at least 10% of the total cache free
-                delete_this_much = total_size - cache_limit
-                self.__clean_cache(file_list, delete_this_much)
-            self.sleeper.sleep(30)  # Test cache size every 30 seconds?
-
-    def __clean_cache(self, file_list, delete_this_much):
-        """ Keep deleting files from the file_list until the size of the deleted
-        files is greater than the value in delete_this_much parameter.
-
-        :type file_list: list
-        :param file_list: List of candidate files that can be deleted. This method
-            will start deleting files from the beginning of the list so the list
-            should be sorted accordingly. The list must contains 3-element tuples,
-            positioned as follows: position 0 holds file last accessed timestamp
-            (as time.struct_time), position 1 holds file path, and position 2 has
-            file size (e.g., (<access time>, /mnt/data/dataset_1.dat), 472394)
-
-        :type delete_this_much: int
-        :param delete_this_much: Total size of files, in bytes, that should be deleted.
-        """
-        # Keep deleting datasets from file_list until deleted_amount does not
-        # exceed delete_this_much; start deleting from the front of the file list,
-        # which assumes the oldest files come first on the list.
-        deleted_amount = 0
-        for entry in file_list:
-            if deleted_amount < delete_this_much:
-                deleted_amount += entry[2]
-                os.remove(entry[1])
-                # Debugging code for printing deleted files' stats
-                # folder, file_name = os.path.split(f[1])
-                # file_date = time.strftime("%m/%d/%y %H:%M:%S", f[0])
-                # log.debug("%s. %-25s %s, size %s (deleted %s/%s)" \
-                #     % (i, file_name, convert_bytes(f[2]), file_date, \
-                #     convert_bytes(deleted_amount), convert_bytes(delete_this_much)))
-            else:
-                log.debug("Cache cleaning done. Total space freed: %s", convert_bytes(deleted_amount))
-                return
-
     def _fix_permissions(self, rel_path):
         """ Set permissions on rel_path"""
         for basedir, _, files in os.walk(rel_path):
@@ -445,7 +371,7 @@ def _download(self, rel_path):
             cache_fp.write(content)
         return True
 
-    def _push_to_os(self, rel_path, source_file=None, from_string=None):
+    def _push_to_irods(self, rel_path, source_file=None, from_string=None):
         """
         Push the file pointed to by ``rel_path`` to the iRODS. Extract folder name 
         from rel_path as iRODS collection name, and extract file name from rel_path
@@ -539,7 +465,7 @@ def exists(self, obj, **kwargs):
 
         # TODO: Sync should probably not be done here. Add this to an async upload stack?
         if in_cache and not in_irods:
-            self._push_to_os(rel_path, source_file=self._get_cache_path(rel_path))
+            self._push_to_irods(rel_path, source_file=self._get_cache_path(rel_path))
             return True
         elif in_irods:
             return True
@@ -572,7 +498,7 @@ def create(self, obj, **kwargs):
             if not dir_only:
                 rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
-                self._push_to_os(rel_path, from_string='')
+                self._push_to_irods(rel_path, from_string='')
 
     def empty(self, obj, **kwargs):
         if self.exists(obj, **kwargs):
@@ -725,7 +651,7 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
             else:
                 source_file = self._get_cache_path(rel_path)
             # Update the file on iRODS 
-            self._push_to_os(rel_path, source_file)
+            self._push_to_irods(rel_path, source_file)
         else:
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
diff --git a/test/integration/objectstore/irods_beginner_training_2016.pdf b/test/integration/objectstore/irods_beginner_training_2016.pdf
deleted file mode 100644
index 2344e41888a526cb3697b1c1b6c241a7cd974069..0000000000000000000000000000000000000000
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diff --git a/test/integration/objectstore/test_irods.py b/test/integration/objectstore/test_irods.py
deleted file mode 100644
index f70f036630c6..000000000000
--- a/test/integration/objectstore/test_irods.py
+++ /dev/null
@@ -1,72 +0,0 @@
-import os
-import pytest
-import shutil
-import ssl
-import subprocess
-import time
-
-from irods.exception import CollectionDoesNotExist
-from irods.exception import DataObjectDoesNotExist
-from irods.session import iRODSSession
-
-from galaxy.config import GalaxyAppConfiguration
-from galaxy.objectstore.irods import IRODSObjectStore
-
-SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-
-CONFIG_DICT = {
-    'auth': {
-        'username': 'rods',
-        'password': 'rods'
-    },
-    'resource': {
-        'name': 'demoResc'
-    },
-    'zone': {
-        'name': 'tempZone'
-    },
-    'connection': {
-        'host': 'localhost',
-        'port': '1247'
-    },
-    'cache': {
-        'size': 1000.0, 
-        'path': 'database/object_store_cache'
-    },
-    'extra_dirs': [{'type': 'job_work', 'path': 'database/job_working_directory_irods'}, {'type': 'temp', 'path': 'database/tmp_irods'}]
-}
-
-#class IrodsObjectStoreIntegrationTestCase(object):
-
-#config = None 
-#config_dict = None
-#irods_os = None
-
-@pytest.fixture(scope='module')
-def setup_module():
-    config = GalaxyAppConfiguration()
-
-    config.object_store_cache_path = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/object_store_cache'
-    config.file_path = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/objects'
-    config.object_store_store_by = 'uuid'
-    config.object_store_check_old_style = False
-    config.jobs_directory = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/job_working_directory_k5dk3021'
-    config.new_file_path = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/new_files_path_sej_tqh7'
-
-    config_dict = CONFIG_DICT
-
-    irods_os = IRODSObjectStore(config, CONFIG_DICT)
-    return irods_os
-
-#    @classmethod
-#def teardown_module(module):
-#     del irods_os
-#     del config_dict
-#     del config
-
-def test_instantiate_irods(setup_module):
-    print('**********************')
-    print('setup_module.to_dict()')
-    print(setup_module.to_dict())
-    print('**********************')
-    assert 1 == 1
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index c1de59b14762..06fb628c5a04 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -13,33 +13,15 @@
 from galaxy.util.hash_util import md5_hash_file
 from galaxy_test.driver import integration_util
 from .test_upload_configuration_options import BaseUploadContentConfigurationInstance
+from .test_datatype_upload import TEST_CASES
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-TEST_FILE_DIR = '%s/../../lib/galaxy/datatypes/test' % SCRIPT_DIRECTORY
-TestData = collections.namedtuple('UploadDatatypesData', 'path datatype uploadable')
 GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
 DATATYPES_CONFIG = os.path.join(GALAXY_ROOT, 'lib/galaxy/config/sample/datatypes_conf.xml.sample')
 PARENT_SNIFFER_MAP = {'fastqsolexa': 'fastq'}
 OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "irods_object_store_conf.xml")
-
-
-def find_datatype(registry, filename):
-    # match longest extension first
-    sorted_extensions = sorted(registry.datatypes_by_extension.keys(), key=len, reverse=True)
-    for extension in sorted_extensions:
-        if filename.endswith(extension) or filename.startswith(extension):
-            return registry.datatypes_by_extension[extension]
-    raise Exception("Couldn't guess datatype for file '%s'" % filename)
-
-
-def collect_test_data(registry):
-    test_files = [f for f in os.listdir(TEST_FILE_DIR) if "." in f]
-    files = [os.path.join(TEST_FILE_DIR, f) for f in test_files]
-    datatypes = [find_datatype(registry, f) for f in test_files]
-    uploadable = [datatype.file_ext in registry.upload_file_formats for datatype in datatypes]
-    test_data_description = [TestData(*items) for items in zip(files, datatypes, uploadable)]
-    return {os.path.basename(data.path): data for data in test_data_description}
-
+# Run test for only the first 10 test files
+IRODS_TEST_CASES = dict(list(TEST_CASES.items())[0:10])
 
 class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
     framework_tool_and_types = False
@@ -49,22 +31,17 @@ class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
     def handle_galaxy_config_kwds(cls, config):
         config["object_store_config_file"] = OBJECT_STORE_CONFIG_FILE
 
-
 instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
 
-
 @pytest.fixture
 def temp_file():
     with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
         yield fh
 
-
 registry = Registry()
 registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG)
-TEST_CASES = collect_test_data(registry)
-
 
-@pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))
+@pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
     is_compressed = False
     for is_method in (is_bz2, is_gzip, is_zip):

From cbe69e97e6e5178038b75fa72617b85839451fc7 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 18 Mar 2020 11:50:03 -0400
Subject: [PATCH 513/853] Define default values in workflow components

---
 client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue | 5 ++++-
 client/galaxy/scripts/mvc/workflow/workflow-manager.js      | 3 +--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue b/client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue
index a44c15ee5aec..4636ce6b48a1 100644
--- a/client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue
+++ b/client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue
@@ -77,13 +77,16 @@ export default {
         },
         workflows: {
             type: Array,
+            required: true
         },
         dataManagers: {
             type: Array,
+            required: true
         },
         moduleSections: {
             type: Array,
-        },
+            required: true
+        }
     },
     computed: {
         workflowSection() {
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index 0fdf0b5b2d8b..e3c309ab0a3a 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -316,8 +316,7 @@ class Workflow extends EventEmitter {
         const report = this.report;
         return { steps: nodes, report: report };
     }
-    from_simple(data, initialImport_) {
-        var initialImport = initialImport_ === undefined ? true : initialImport_;
+    from_simple(data, initialImport = true) {
         var wf = this;
         var offset = 0;
         if (initialImport) {

From 14f5f5de2852b96d45cf0673864f6de3f8cdfdac Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 18 Mar 2020 23:21:14 -0400
Subject: [PATCH 514/853] More default parameters for props

---
 client/galaxy/scripts/components/Workflow/Editor/Node.vue | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index d3d91f178869..a258043c1e90 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -46,6 +46,7 @@ export default {
     props: {
         id: {
             type: String,
+            default: "",
         },
         title: {
             type: String,
@@ -57,7 +58,8 @@ export default {
         },
         node: {
             type: Object,
-        },
+            default: null,
+        }
     },
     computed: {
         iconClass() {

From 62dabc969a687be8b28e0ffa31332e2e7a6b9c19 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 20 Mar 2020 21:04:34 -0400
Subject: [PATCH 515/853] Dataset and fixed inputs should not be connectable in
 workflow forms

---
 client/galaxy/scripts/mvc/workflow/workflow-forms.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
index c83d7f0dc645..441311b12bd9 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
@@ -94,12 +94,12 @@ export class ToolForm {
         var options = form.model.attributes;
         Utils.deepeach(options.inputs, (input) => {
             if (input.type) {
-                input.connectable = true;
                 if (["data", "data_collection"].indexOf(input.type) != -1) {
                     input.type = "hidden";
                     input.info = `Data input '${input.name}' (${Utils.textify(input.extensions)})`;
                     input.value = { __class__: "RuntimeValue" };
                 } else if (!input.fixed) {
+                    input.connectable = true;
                     input.collapsible_value = {
                         __class__: "RuntimeValue",
                     };

From 1121af1a5a89034b4cadc7b830c1c7fbba3a9175 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 20 Mar 2020 22:12:12 -0400
Subject: [PATCH 516/853] Avoid form rebuilding in workflow form manager

---
 .../scripts/mvc/workflow/workflow-forms.js    | 42 +++++++------------
 lib/galaxy/managers/workflows.py              |  3 +-
 2 files changed, 16 insertions(+), 29 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
index 441311b12bd9..b94e54312131 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
@@ -11,6 +11,7 @@ export class DefaultForm {
     constructor(options) {
         var self = this;
         var node = options.node;
+        _addLabelAnnotation(this, options);
         this.form = new Form(
             Utils.merge(options, {
                 onchange: function () {
@@ -30,16 +31,14 @@ export class DefaultForm {
                 },
             })
         );
-        _addLabelAnnotation(this.form);
-        this.form.render();
     }
 }
 
 /** Tool form wrapper for the workflow editor. */
 export class ToolForm {
     constructor(options) {
-        var self = this;
         var node = options.node;
+        this._customize(options);
         this.form = new ToolFormBase(
             Utils.merge(options, {
                 text_enable: "Set in Advance",
@@ -47,14 +46,7 @@ export class ToolForm {
                 narrow: true,
                 initial_errors: true,
                 cls: "ui-portlet-section",
-                initialmodel: function (process, form) {
-                    self._customize(form);
-                    process.resolve();
-                },
-                buildmodel: function (process, form) {
-                    form.model.get("postchange")(process, form);
-                },
-                postchange: function (process, form) {
+                postchange: function(process, form) {
                     const Galaxy = getGalaxyInstance();
                     var options = form.model.attributes;
                     var current_state = {
@@ -68,9 +60,7 @@ export class ToolForm {
                         type: "POST",
                         url: `${getAppRoot()}api/workflows/build_module`,
                         data: current_state,
-                        success: function (data) {
-                            form.model.set(data.config_form);
-                            self._customize(form);
+                        success: function(data) {
                             form.update(data.config_form);
                             form.errors(data.config_form);
                             // This hasn't modified the workflow, just returned
@@ -90,9 +80,9 @@ export class ToolForm {
             })
         );
     }
-    _customize(form) {
-        var options = form.model.attributes;
-        Utils.deepeach(options.inputs, (input) => {
+    _customize(options) {
+        options.inputs = options.inputs || [];
+        Utils.deepeach(options.inputs, input => {
             if (input.type) {
                 if (["data", "data_collection"].indexOf(input.type) != -1) {
                     input.type = "hidden";
@@ -114,14 +104,13 @@ export class ToolForm {
                 input.test_param.collapsible_value = undefined;
             }
         });
-        _addSections(form);
-        _addLabelAnnotation(form);
+        _addSections(options);
+        _addLabelAnnotation(this, options);
     }
 }
 
 /** Augments the module form definition by adding label and annotation fields */
-function _addLabelAnnotation(form) {
-    var options = form.model.attributes;
+function _addLabelAnnotation(self, options) {
     var workflow = options.workflow;
     var node = options.node;
     options.inputs.unshift({
@@ -149,14 +138,14 @@ function _addLabelAnnotation(form) {
                     break;
                 }
             }
-            var input_id = form.data.match("__label");
-            var input_element = form.element_list[input_id];
+            var input_id = self.form.data.match("__label");
+            var input_element = self.form.element_list[input_id];
             input_element.model.set(
                 "error_text",
                 duplicate && "Duplicate label. Please fix this before saving the workflow."
             );
-            form.trigger("change");
-        },
+            self.form.trigger("change");
+        }
     });
 }
 
@@ -355,8 +344,7 @@ function _makeSection(output_id, label, options) {
 }
 
 /** Builds all sub sections */
-function _addSections(form) {
-    var options = form.model.attributes;
+function _addSections(options) {
     var inputs = options.inputs;
     var node = options.node;
     var post_job_actions = node.post_job_actions;
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 0dc8075ed462..494aeb1e81f7 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -618,7 +618,6 @@ def _workflow_to_dict_editor(self, trans, stored, workflow, tooltip=True, is_sub
                     data['upgrade_messages'][step.order_index] = {module.tool.name: "\n".join(module.version_changes)}
             # Get user annotation.
             annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ''
-            config_form = module.get_config_form(step=step)
             # Pack attributes into plain dictionary
             step_dict = {
                 'id': step.order_index,
@@ -630,7 +629,7 @@ def _workflow_to_dict_editor(self, trans, stored, workflow, tooltip=True, is_sub
                 'errors': module.get_errors(),
                 'inputs': module.get_all_inputs(connectable_only=True),
                 'outputs': module.get_all_outputs(),
-                'config_form': config_form,
+                'config_form': module.get_config_form(step=step),
                 'annotation': annotation_str,
                 'post_job_actions': {},
                 'uuid': str(step.uuid) if step.uuid else None,

From deb6dbdc917bcbf07358b0235c7befe9c4ffc071 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 20 Mar 2020 22:14:05 -0400
Subject: [PATCH 517/853] Remove unused form model flag from client view

---
 client/galaxy/scripts/mvc/tool/tool-form-base.js | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js
index 084484ee74df..115cd412edb8 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-base.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js
@@ -23,9 +23,6 @@ export default FormBase.extend({
         this.deferred = new Deferred();
         FormBase.prototype.initialize.call(this, options);
 
-        // optional model update
-        this._update(this.model.get("initialmodel"));
-
         // listen to history panel
         if (this.model.get("listen_to_history") && Galaxy.currHistoryPanel) {
             this.listenTo(Galaxy.currHistoryPanel.collection, "change", () => {
@@ -39,9 +36,9 @@ export default FormBase.extend({
     },
 
     /** Allows tool form variation to update tool model */
-    _update: function (callback) {
+    _update: function() {
         var self = this;
-        callback = callback || this.model.get("buildmodel");
+        var callback = this.model.get("buildmodel");
         if (callback) {
             this.deferred.reset();
             this.deferred.execute((process) => {

From 29e0342130ceee04c8995a966719314995e88e8a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 21 Mar 2020 00:27:06 -0400
Subject: [PATCH 518/853] Fix workflow form model creation handling

---
 .../galaxy/scripts/mvc/tool/tool-form-base.js |  3 +
 .../scripts/mvc/workflow/workflow-forms.js    | 61 ++++++++++---------
 2 files changed, 35 insertions(+), 29 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js
index 115cd412edb8..6d1552e93090 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-base.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js
@@ -23,6 +23,9 @@ export default FormBase.extend({
         this.deferred = new Deferred();
         FormBase.prototype.initialize.call(this, options);
 
+        // optional model update
+        this._update();
+
         // listen to history panel
         if (this.model.get("listen_to_history") && Galaxy.currHistoryPanel) {
             this.listenTo(Galaxy.currHistoryPanel.collection, "change", () => {
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
index b94e54312131..72e638e33316 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
@@ -11,10 +11,11 @@ export class DefaultForm {
     constructor(options) {
         var self = this;
         var node = options.node;
-        _addLabelAnnotation(this, options);
+        this.workflow = options.workflow;
+        _addLabelAnnotation(this, node);
         this.form = new Form(
-            Utils.merge(options, {
-                onchange: function () {
+            Object.assign(options, {
+                onchange: function() {
                     Utils.request({
                         type: "POST",
                         url: `${getAppRoot()}api/workflows/build_module`,
@@ -37,10 +38,13 @@ export class DefaultForm {
 /** Tool form wrapper for the workflow editor. */
 export class ToolForm {
     constructor(options) {
+        var self = this;
         var node = options.node;
-        this._customize(options);
+        this.workflow = options.workflow;
+        this.datatypes = options.datatypes;
+        this._customize(node);
         this.form = new ToolFormBase(
-            Utils.merge(options, {
+            Object.assign(node.config_form, {
                 text_enable: "Set in Advance",
                 text_disable: "Set at Runtime",
                 narrow: true,
@@ -61,6 +65,8 @@ export class ToolForm {
                         url: `${getAppRoot()}api/workflows/build_module`,
                         data: current_state,
                         success: function(data) {
+                            self._customize(data);
+                            form.model.set(data.config_form);
                             form.update(data.config_form);
                             form.errors(data.config_form);
                             // This hasn't modified the workflow, just returned
@@ -80,9 +86,9 @@ export class ToolForm {
             })
         );
     }
-    _customize(options) {
-        options.inputs = options.inputs || [];
-        Utils.deepeach(options.inputs, input => {
+    _customize(node) {
+        const inputs = node.config_form.inputs;
+        Utils.deepeach(inputs, input => {
             if (input.type) {
                 if (["data", "data_collection"].indexOf(input.type) != -1) {
                     input.type = "hidden";
@@ -98,22 +104,22 @@ export class ToolForm {
                 }
             }
         });
-        Utils.deepeach(options.inputs, (input) => {
+        Utils.deepeach(inputs, (input) => {
             if (input.type === "conditional") {
                 input.connectable = false;
                 input.test_param.collapsible_value = undefined;
             }
         });
-        _addSections(options);
-        _addLabelAnnotation(this, options);
+        _addSections(this, node);
+        _addLabelAnnotation(this, node);
     }
 }
 
 /** Augments the module form definition by adding label and annotation fields */
-function _addLabelAnnotation(self, options) {
-    var workflow = options.workflow;
-    var node = options.node;
-    options.inputs.unshift({
+function _addLabelAnnotation(self, node) {
+    var workflow = self.workflow;
+    const inputs = node.config_form.inputs;
+    inputs.unshift({
         type: "text",
         name: "__annotation",
         label: "Annotation",
@@ -122,7 +128,7 @@ function _addLabelAnnotation(self, options) {
         area: true,
         help: "Add an annotation or notes to this step. Annotations are available when a workflow is viewed.",
     });
-    options.inputs.unshift({
+    inputs.unshift({
         type: "text",
         name: "__label",
         label: "Label",
@@ -150,8 +156,8 @@ function _addLabelAnnotation(self, options) {
 }
 
 /** Visit input nodes and enrich by name/value pairs from server data */
-function _visit(head, head_list, output_id, options) {
-    var post_job_actions = options.node.post_job_actions;
+function _visit(head, head_list, output_id, node) {
+    var post_job_actions = node.post_job_actions;
     head_list = head_list || [];
     head_list.push(head);
     for (var i in head.inputs) {
@@ -181,7 +187,7 @@ function _visit(head, head_list, output_id, options) {
             }
         }
         if (input.inputs) {
-            _visit(input, head_list.slice(0), output_id, options);
+            _visit(input, head_list.slice(0), output_id, node);
         }
     }
 }
@@ -204,13 +210,11 @@ function _makeRenameHelp(name_labels) {
 }
 
 /** Builds sub section with step actions/annotation */
-function _makeSection(output_id, label, options) {
+function _makeSection(self, output_id, label, node) {
     var extensions = [];
     var name_label_map = [];
-    var datatypes = options.datatypes;
-    var node = options.node;
-    var workflow = options.workflow;
-
+    var datatypes = self.datatypes;
+    var workflow = self.workflow;
     for (const key in datatypes) {
         extensions.push({ 0: datatypes[key], 1: datatypes[key] });
     }
@@ -339,14 +343,13 @@ function _makeSection(output_id, label, options) {
             },
         ],
     };
-    _visit(input_config, [], output_id, options);
+    _visit(input_config, [], output_id, node);
     return input_config;
 }
 
 /** Builds all sub sections */
-function _addSections(options) {
-    var inputs = options.inputs;
-    var node = options.node;
+function _addSections(self, node) {
+    var inputs = node.config_form.inputs;
     var post_job_actions = node.post_job_actions;
     var output_id = node.output_terminals && Object.keys(node.output_terminals)[0];
 
@@ -373,7 +376,7 @@ function _addSections(options) {
         });
         for (const output_id in node.output_terminals) {
             const label = node.output_terminals[output_id].label || output_id;
-            inputs.push(_makeSection(output_id, label, options));
+            inputs.push(_makeSection(self, output_id, label, node));
         }
     }
 }

From e4cd1f2cd17480002806b5afdb62c9c0f491a9d6 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 21 Mar 2020 08:59:39 -0400
Subject: [PATCH 519/853] Strip jquery from workflow forms helper class, use
 axios

---
 .../scripts/mvc/workflow/workflow-forms.js    | 119 +++++++++---------
 1 file changed, 56 insertions(+), 63 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
index 72e638e33316..cbd7c34b614c 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
@@ -1,4 +1,4 @@
-import $ from "jquery";
+import axios from "axios";
 import { getAppRoot } from "onload/loadConfig";
 import { getGalaxyInstance } from "app";
 import _l from "utils/localization";
@@ -13,78 +13,71 @@ export class DefaultForm {
         var node = options.node;
         this.workflow = options.workflow;
         _addLabelAnnotation(this, node);
-        this.form = new Form(
-            Object.assign(options, {
-                onchange: function() {
-                    Utils.request({
-                        type: "POST",
-                        url: `${getAppRoot()}api/workflows/build_module`,
-                        data: {
-                            id: node.id,
-                            type: node.type,
-                            content_id: node.content_id,
-                            inputs: self.form.data.create(),
-                        },
-                        success: function (data) {
-                            node.update_field_data(data);
-                        },
-                    });
-                },
-            })
-        );
+        this.form = new Form({
+            ...options,
+            onchange() {
+                axios.post(`${getAppRoot()}api/workflows/build_module`, {
+                    id: node.id,
+                    type: node.type,
+                    content_id: node.content_id,
+                    inputs: self.form.data.create()
+                })
+                .then(response => {
+                    const data = response.data;
+                    node.update_field_data(data);
+                });
+            }
+        });
     }
 }
 
 /** Tool form wrapper for the workflow editor. */
 export class ToolForm {
     constructor(options) {
-        var self = this;
-        var node = options.node;
+        const self = this;
+        const node = options.node;
         this.workflow = options.workflow;
         this.datatypes = options.datatypes;
         this._customize(node);
-        this.form = new ToolFormBase(
-            Object.assign(node.config_form, {
-                text_enable: "Set in Advance",
-                text_disable: "Set at Runtime",
-                narrow: true,
-                initial_errors: true,
-                cls: "ui-portlet-section",
-                postchange: function(process, form) {
-                    const Galaxy = getGalaxyInstance();
-                    var options = form.model.attributes;
-                    var current_state = {
-                        tool_id: options.id,
-                        tool_version: options.version,
-                        type: "tool",
-                        inputs: $.extend(true, {}, form.data.create()),
-                    };
-                    Galaxy.emit.debug("tool-form-workflow::postchange()", "Sending current state.", current_state);
-                    Utils.request({
-                        type: "POST",
-                        url: `${getAppRoot()}api/workflows/build_module`,
-                        data: current_state,
-                        success: function(data) {
-                            self._customize(data);
-                            form.model.set(data.config_form);
-                            form.update(data.config_form);
-                            form.errors(data.config_form);
-                            // This hasn't modified the workflow, just returned
-                            // module information for the tool to update the workflow
-                            // state stored on the client with. User needs to save
-                            // for this to take effect.
-                            node.update_field_data(data);
-                            Galaxy.emit.debug("tool-form-workflow::postchange()", "Received new model.", data);
-                            process.resolve();
-                        },
-                        error: function (response) {
-                            Galaxy.emit.debug("tool-form-workflow::postchange()", "Refresh request failed.", response);
-                            process.reject();
-                        },
+        this.form = new ToolFormBase({
+            ...node.config_form,
+            text_enable: "Set in Advance",
+            text_disable: "Set at Runtime",
+            narrow: true,
+            initial_errors: true,
+            cls: "ui-portlet-section",
+            postchange(process, form) {
+                const Galaxy = getGalaxyInstance();
+                const options = form.model.attributes;
+                const current_state = {
+                    tool_id: options.id,
+                    tool_version: options.version,
+                    type: "tool",
+                    inputs: Object.assign({}, form.data.create())
+                };
+                Galaxy.emit.debug("tool-form-workflow::postchange()", "Sending current state.", current_state);
+                axios
+                    .post(`${getAppRoot()}api/workflows/build_module`, current_state)
+                    .then(response => {
+                        const data = response.data;
+                        self._customize(data);
+                        self.form.model.set(data.config_form);
+                        self.form.update(data.config_form);
+                        self.form.errors(data.config_form);
+                        // This hasn't modified the workflow, just returned
+                        // module information for the tool to update the workflow
+                        // state stored on the client with. User needs to save
+                        // for this to take effect.
+                        node.update_field_data(data);
+                        Galaxy.emit.debug("tool-form-workflow::postchange()", "Received new model.", data);
+                        process.resolve();
+                    })
+                    .catch(response => {
+                        Galaxy.emit.debug("tool-form-workflow::postchange()", "Refresh request failed.", response);
+                        process.reject();
                     });
-                },
-            })
-        );
+            }
+        });
     }
     _customize(node) {
         const inputs = node.config_form.inputs;

From e50bb6d49e36c502e9a36aa5279437c44c125c3e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 21 Mar 2020 09:05:17 -0400
Subject: [PATCH 520/853] Format client

---
 .../scripts/mvc/workflow/workflow-forms.js    | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
index cbd7c34b614c..98890b4ae05e 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
@@ -16,16 +16,17 @@ export class DefaultForm {
         this.form = new Form({
             ...options,
             onchange() {
-                axios.post(`${getAppRoot()}api/workflows/build_module`, {
-                    id: node.id,
-                    type: node.type,
-                    content_id: node.content_id,
-                    inputs: self.form.data.create()
-                })
-                .then(response => {
-                    const data = response.data;
-                    node.update_field_data(data);
-                });
+                axios
+                    .post(`${getAppRoot()}api/workflows/build_module`, {
+                        id: node.id,
+                        type: node.type,
+                        content_id: node.content_id,
+                        inputs: self.form.data.create()
+                    })
+                    .then(response => {
+                        const data = response.data;
+                        node.update_field_data(data);
+                    });
             }
         });
     }
@@ -345,7 +346,6 @@ function _addSections(self, node) {
     var inputs = node.config_form.inputs;
     var post_job_actions = node.post_job_actions;
     var output_id = node.output_terminals && Object.keys(node.output_terminals)[0];
-
     if (output_id) {
         inputs.push({
             name: `pja__${output_id}__EmailAction`,

From 13990d60654302fdb8557b90f6b6a6476bdbb05e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 22 Mar 2020 14:18:36 -0400
Subject: [PATCH 521/853] Fix workflow editor side panel switch

---
 .../galaxy/scripts/components/Workflow/Editor/EditorPanel.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/EditorPanel.vue b/client/galaxy/scripts/components/Workflow/Editor/EditorPanel.vue
index fff5e0f55e6f..c1a4df0f285e 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/EditorPanel.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/EditorPanel.vue
@@ -6,11 +6,11 @@
             </div>
         </div>
         <div class="unified-panel-body workflow-right">
-            <div v-if="canvas" class="m-1">
+            <div class="m-1" v-show="canvas">
                 <slot name="attributes" />
                 <div id="right-content" class="right-content" />
             </div>
-            <ReportHelp v-else />
+            <ReportHelp v-show="!canvas" />
         </div>
     </div>
 </template>

From 176a8813937458b6784b515fdd51802cf56a2cfe Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 11:18:02 -0400
Subject: [PATCH 522/853] Added helper method to avoid duplicate code

---
 test/integration/test_datatype_upload.py      |  3 ++
 .../integration/test_datatype_upload_irods.py | 43 +------------------
 2 files changed, 5 insertions(+), 41 deletions(-)

diff --git a/test/integration/test_datatype_upload.py b/test/integration/test_datatype_upload.py
index 83ac60f82c24..e139c38c2f8b 100644
--- a/test/integration/test_datatype_upload.py
+++ b/test/integration/test_datatype_upload.py
@@ -61,6 +61,9 @@ def temp_file():
 
 @pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
+    upload_datatype_helper(instance, test_data, temp_file)
+
+def upload_datatype_helper(instance, test_data, temp_file):
     is_compressed = False
     for is_method in (is_bz2, is_gzip, is_zip):
         is_compressed = is_method(test_data.path)
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 06fb628c5a04..de3678f78225 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -14,6 +14,7 @@
 from galaxy_test.driver import integration_util
 from .test_upload_configuration_options import BaseUploadContentConfigurationInstance
 from .test_datatype_upload import TEST_CASES
+from .test_datatype_upload import upload_datatype_helper
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
@@ -43,44 +44,4 @@ def temp_file():
 
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
-    is_compressed = False
-    for is_method in (is_bz2, is_gzip, is_zip):
-        is_compressed = is_method(test_data.path)
-        if is_compressed:
-            break
-    with open(test_data.path, 'rb') as content:
-        if hasattr(test_data.datatype, 'sniff') or 'false' in test_data.path:
-            file_type = 'auto'
-        else:
-            file_type = test_data.datatype.file_ext
-        dataset = instance.dataset_populator.new_dataset(instance.history_id, content=content, wait=False, file_type=file_type)
-    dataset = instance.dataset_populator.get_history_dataset_details(instance.history_id, dataset=dataset, assert_ok=False)
-    expected_file_ext = test_data.datatype.file_ext
-    # State might be error if the datatype can't be uploaded
-    if dataset['state'] == 'error' and not test_data.uploadable:
-        # Some things can't be uploaded, if attempting to upload these datasets we mention why
-        assert 'invalid' in dataset['misc_info'] or 'unsupported' in dataset['misc_info']
-        return
-    elif dataset['state'] == 'error' and 'empty' in dataset['misc_info']:
-        return
-    else:
-        # state should be OK
-        assert dataset['state'] == 'ok'
-    # Check that correct datatype has been detected
-    file_ext = dataset['file_ext']
-    if 'false' in test_data.path:
-        # datasets with false in their name are not of a specific datatype
-        assert file_ext != PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
-    else:
-        assert file_ext == PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
-    datatype = registry.datatypes_by_extension[file_ext]
-    datatype_compressed = getattr(datatype, "compressed", False)
-    if not is_compressed or datatype_compressed:
-        # download file and verify it hasn't been manipulated
-        temp_file.write(instance.dataset_populator.get_history_dataset_content(history_id=instance.history_id,
-                                                                               dataset=dataset,
-                                                                               type='bytes',
-                                                                               assert_ok=False,
-                                                                               raw=True))
-        temp_file.flush()
-        assert md5_hash_file(test_data.path) == md5_hash_file(temp_file.name)
+    upload_datatype_helper(instance, test_data, temp_file)
\ No newline at end of file

From 67e03a6e2451810e5dbf0436e4f71364c7036639 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 11:35:34 -0400
Subject: [PATCH 523/853] Removed un-used imports from iRODS integration test

---
 test/integration/test_datatype_upload_irods.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index de3678f78225..a5d22d45fcc3 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,16 +1,9 @@
-import collections
 import os
 import tempfile
 
 import pytest
 
 from galaxy.datatypes.registry import Registry
-from galaxy.util.checkers import (
-    is_bz2,
-    is_gzip,
-    is_zip
-)
-from galaxy.util.hash_util import md5_hash_file
 from galaxy_test.driver import integration_util
 from .test_upload_configuration_options import BaseUploadContentConfigurationInstance
 from .test_datatype_upload import TEST_CASES

From b74b7ce3a707aaf717389a2960ae515e6d305879 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 11:54:23 -0400
Subject: [PATCH 524/853] Ran flake8 linter

---
 test/integration/test_datatype_upload_irods.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index a5d22d45fcc3..b8b7e13f3e44 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -5,9 +5,10 @@
 
 from galaxy.datatypes.registry import Registry
 from galaxy_test.driver import integration_util
-from .test_upload_configuration_options import BaseUploadContentConfigurationInstance
-from .test_datatype_upload import TEST_CASES
-from .test_datatype_upload import upload_datatype_helper
+
+from .test_datatype_upload import TEST_CASES, upload_datatype_helper
+from .test_upload_configuration_options import \
+    BaseUploadContentConfigurationInstance
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
@@ -17,6 +18,7 @@
 # Run test for only the first 10 test files
 IRODS_TEST_CASES = dict(list(TEST_CASES.items())[0:10])
 
+
 class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
     framework_tool_and_types = False
     datatypes_conf_override = DATATYPES_CONFIG
@@ -25,16 +27,20 @@ class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
     def handle_galaxy_config_kwds(cls, config):
         config["object_store_config_file"] = OBJECT_STORE_CONFIG_FILE
 
+
 instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
 
+
 @pytest.fixture
 def temp_file():
     with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
         yield fh
 
+
 registry = Registry()
 registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG)
 
+
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
-    upload_datatype_helper(instance, test_data, temp_file)
\ No newline at end of file
+    upload_datatype_helper(instance, test_data, temp_file)

From 52172782e8db0e607c4d3b775166acc26187240e Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 23 Mar 2020 12:20:49 -0400
Subject: [PATCH 525/853] Update test/integration/test_datatype_upload_irods.py

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 test/integration/test_datatype_upload_irods.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index b8b7e13f3e44..f197ec45df29 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -3,7 +3,6 @@
 
 import pytest
 
-from galaxy.datatypes.registry import Registry
 from galaxy_test.driver import integration_util
 
 from .test_datatype_upload import TEST_CASES, upload_datatype_helper

From 89900f74146b0a57e37579b1153c45cf4d1b1476 Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 23 Mar 2020 12:21:03 -0400
Subject: [PATCH 526/853] Update test/integration/test_datatype_upload_irods.py

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 test/integration/test_datatype_upload_irods.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index f197ec45df29..ad3a0cb9fb91 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,5 +1,4 @@
 import os
-import tempfile
 
 import pytest
 

From bc12ecac6befdca3360591cb23a7d25a844d4dc4 Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 23 Mar 2020 12:21:34 -0400
Subject: [PATCH 527/853] Update test/integration/test_datatype_upload_irods.py

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 test/integration/test_datatype_upload_irods.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index ad3a0cb9fb91..59f60908bd90 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -5,8 +5,6 @@
 from galaxy_test.driver import integration_util
 
 from .test_datatype_upload import TEST_CASES, upload_datatype_helper
-from .test_upload_configuration_options import \
-    BaseUploadContentConfigurationInstance
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)

From 6233ac469fcd0f6f6e710695f1acfae2838b0534 Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 23 Mar 2020 12:24:44 -0400
Subject: [PATCH 528/853] Apply suggestions from code review

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 .../integration/test_datatype_upload_irods.py | 25 ++++++-------------
 1 file changed, 7 insertions(+), 18 deletions(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 59f60908bd90..a0046b5b2873 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,23 +1,22 @@
-import os
 
 import pytest
 
 from galaxy_test.driver import integration_util
 
-from .test_datatype_upload import TEST_CASES, upload_datatype_helper
+from .test_datatype_upload import (
+    temp_file,
+    TEST_CASES,
+    upload_datatype_helper,
+    UploadTestDatatypeDataTestCase
+)
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
-DATATYPES_CONFIG = os.path.join(GALAXY_ROOT, 'lib/galaxy/config/sample/datatypes_conf.xml.sample')
-PARENT_SNIFFER_MAP = {'fastqsolexa': 'fastq'}
 OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "irods_object_store_conf.xml")
 # Run test for only the first 10 test files
 IRODS_TEST_CASES = dict(list(TEST_CASES.items())[0:10])
 
 
-class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
-    framework_tool_and_types = False
-    datatypes_conf_override = DATATYPES_CONFIG
+class UploadTestDatatypeDataTestCase(UploadTestDatatypeDataTestCase):
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
@@ -27,16 +26,6 @@ def handle_galaxy_config_kwds(cls, config):
 instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
 
 
-@pytest.fixture
-def temp_file():
-    with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
-        yield fh
-
-
-registry = Registry()
-registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG)
-
-
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
     upload_datatype_helper(instance, test_data, temp_file)

From 5bc7fae10db1d84d5a3d84b0b9b67ace2b6e73ea Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 12:56:19 -0400
Subject: [PATCH 529/853] More code cleanup per flake8 linter

---
 lib/galaxy/objectstore/irods.py | 71 ++++++++++++++++-----------------
 1 file changed, 35 insertions(+), 36 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 951fa8926d89..a0fcae9c42f2 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -6,8 +6,6 @@
 import os
 from pathlib import Path
 import shutil
-import threading
-import time
 
 try:
     import irods
@@ -24,29 +22,29 @@
     ObjectNotFound
 )
 from galaxy.util import (
-    bytesize,
     directory_hash_id,
     umask_fix_perms,
 )
 from galaxy.util.path import safe_relpath
 from ..objectstore import (
     DiskObjectStore,
-    local_extra_dirs,
-    convert_bytes
 )
 
 IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this feature, please install it')
 
 log = logging.getLogger(__name__)
 
+
 def _config_xml_error(tag):
     msg = 'No {tag} element in config XML tree'.format(tag=tag)
     raise Exception(msg)
 
+
 def _config_dict_error(key):
     msg = 'No {key} key in config dictionary'.forma(key=key)
     raise Exception(msg)
 
+
 def parse_config_xml(config_xml):
     try:
         a_xml = config_xml.findall('auth')
@@ -109,6 +107,7 @@ def parse_config_xml(config_xml):
         log.exception("Malformed iRODS ObjectStore Configuration XML -- unable to continue.")
         raise
 
+
 class CloudConfigMixin(object):
 
     def _config_to_dict(self):
@@ -133,14 +132,15 @@ def _config_to_dict(self):
             }
         }
 
+
 class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
     """
-    Object store that stores objects as data objects in an iRODS collections. A local cache 
+    Object store that stores objects as data objects in an iRODS collections. A local cache
     exists that is used as an intermediate location for files between Galaxy and iRODS.
     """
-    
+
     store_type = 'irods'
-    
+
     def __init__(self, config, config_dict):
         super(IRODSObjectStore, self).__init__(config, config_dict)
 
@@ -195,7 +195,7 @@ def __init__(self, config, config_dict):
         self.extra_dirs.update(extra_dirs)
 
         self._initialize()
-        
+
     def __del__(self):
         self.session.cleanup()
 
@@ -203,14 +203,14 @@ def _initialize(self):
         if irods is None:
             raise Exception(IRODS_IMPORT_MESSAGE)
 
-        self.home =  "/" + self.zone + "/home/" + self.username
+        self.home = "/" + self.zone + "/home/" + self.username
 
         self.session = self._configure_connection(host=self.host, port=self.port, user=self.username, password=self.password, zone=self.zone)
 
     def _configure_connection(self, host='localhost', port='1247', user='rods', password='rods', zone='tempZone'):
         with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
             # Throws NetworkException if connection fails
-            try:  
+            try:
                 session.pool.get_connection()
             except NetworkException as e:
                 log.error('Could not create iRODS session: ' + str(e))
@@ -276,11 +276,11 @@ def _get_cache_path(self, rel_path):
     # rel_path is file or folder?
     def _get_size_in_irods(self, rel_path):
         p = Path(rel_path)
-        data_object_name =  p.stem + p.suffix
+        data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
         collection_path = self.home + "/" + str(subcollection_name)
-        data_object_path = collection_path + "/" + str(data_object_name) 
+        data_object_path = collection_path + "/" + str(data_object_name)
 
         try:
             data_obj = self.session.data_objects.get(data_object_path)
@@ -292,18 +292,18 @@ def _get_size_in_irods(self, rel_path):
     # rel_path is file or folder?
     def _data_object_exists(self, rel_path):
         p = Path(rel_path)
-        data_object_name =  p.stem + p.suffix
+        data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
         collection_path = self.home + "/" + str(subcollection_name)
-        data_object_path = collection_path + "/" + str(data_object_name) 
+        data_object_path = collection_path + "/" + str(data_object_name)
 
         try:
             self.session.data_objects.get(data_object_path)
-            return True 
+            return True
         except (DataObjectDoesNotExist, CollectionDoesNotExist):
             log.warn("Collection or data object (%s) does not exist", data_object_path)
-            return False 
+            return False
 
     def _in_cache(self, rel_path):
         """ Check if the given dataset is in the local cache and return True if so. """
@@ -346,18 +346,18 @@ def _download(self, rel_path):
         log.debug("Pulling data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
 
         p = Path(rel_path)
-        data_object_name =  p.stem + p.suffix
+        data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
         collection_path = self.home + "/" + str(subcollection_name)
-        data_object_path = collection_path + "/" + str(data_object_name) 
+        data_object_path = collection_path + "/" + str(data_object_name)
         data_obj = None
 
         try:
             data_obj = self.session.data_objects.get(data_object_path)
         except (DataObjectDoesNotExist, CollectionDoesNotExist):
             log.warn("Collection or data object (%s) does not exist", data_object_path)
-            return False 
+            return False
 
         if self.cache_size > 0 and data_obj.__sizeof__() > self.cache_size:
             log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
@@ -365,7 +365,7 @@ def _download(self, rel_path):
             return False
 
         log.debug("Pulled data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
-        
+
         with data_obj.open('r') as data_obj_fp, open(self._get_cache_path(rel_path), "wb") as cache_fp:
             content = data_obj_fp.read()
             cache_fp.write(content)
@@ -373,7 +373,7 @@ def _download(self, rel_path):
 
     def _push_to_irods(self, rel_path, source_file=None, from_string=None):
         """
-        Push the file pointed to by ``rel_path`` to the iRODS. Extract folder name 
+        Push the file pointed to by ``rel_path`` to the iRODS. Extract folder name
         from rel_path as iRODS collection name, and extract file name from rel_path
         as iRODS data object name.
         If ``source_file`` is provided, push that file instead while
@@ -381,7 +381,7 @@ def _push_to_irods(self, rel_path, source_file=None, from_string=None):
         If ``from_string`` is provided, set contents of the file to the value of the string.
         """
         p = Path(rel_path)
-        data_object_name =  p.stem + p.suffix
+        data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
         source_file = source_file if source_file else self._get_cache_path(rel_path)
@@ -390,7 +390,7 @@ def _push_to_irods(self, rel_path, source_file=None, from_string=None):
         if os.path.exists(source_file):
             # Check if the data object exists in iRODS
             collection_path = self.home + "/" + str(subcollection_name)
-            data_object_path = collection_path + "/" + str(data_object_name) 
+            data_object_path = collection_path + "/" + str(data_object_name)
             exists = self.session.data_objects.exists(data_object_path)
             if os.path.getsize(source_file) == 0 and exists:
                 log.debug("Wanted to push file '%s' to iRODS collection '%s' but its size is 0; skipping.", source_file, rel_path)
@@ -403,14 +403,14 @@ def _push_to_irods(self, rel_path, source_file=None, from_string=None):
             else:
                 start_time = datetime.now()
                 log.debug("Pushing cache file '%s' of size %s bytes to collection '%s'", source_file, os.path.getsize(source_file), rel_path)
-                
+
                 # Create sub-collection first
                 self.session.collections.create(collection_path, recurse=True)
 
                 file_content = None
                 with open(source_file, 'rb') as content_file:
                     file_content = content_file.read()
-                
+
                 # Write to file in subcollection created above
                 data_obj = self.session.data_objects.create(data_object_path, self.resource, **options)
                 with data_obj.open('w') as data_obj_fp:
@@ -446,7 +446,7 @@ def exists(self, obj, **kwargs):
         # Check cache
         if self._in_cache(rel_path):
             in_cache = True
-        # Check iRODS 
+        # Check iRODS
         in_irods = self._data_object_exists(rel_path)
 
         # dir_only does not get synced so shortcut the decision
@@ -465,7 +465,6 @@ def exists(self, obj, **kwargs):
 
         # TODO: Sync should probably not be done here. Add this to an async upload stack?
         if in_cache and not in_irods:
-            self._push_to_irods(rel_path, source_file=self._get_cache_path(rel_path))
             return True
         elif in_irods:
             return True
@@ -547,7 +546,7 @@ def delete(self, obj, entire_dir=False, **kwargs):
                     return False
 
                 cols = col.walk()
-                # Traverse the tree only one level deep 
+                # Traverse the tree only one level deep
                 for _ in range(2):
                     # get next result
                     _, _, data_objects = next(cols)
@@ -563,11 +562,11 @@ def delete(self, obj, entire_dir=False, **kwargs):
                 os.unlink(self._get_cache_path(rel_path))
                 # Delete from irods as well
                 p = Path(rel_path)
-                data_object_name =  p.stem + p.suffix
+                data_object_name = p.stem + p.suffix
                 subcollection_name = p.parent
 
                 collection_path = self.home + "/" + str(subcollection_name)
-                data_object_path = collection_path + "/" + str(data_object_name) 
+                data_object_path = collection_path + "/" + str(data_object_name)
 
                 try:
                     data_obj = self.session.data_objects.get(data_object_path)
@@ -576,7 +575,7 @@ def delete(self, obj, entire_dir=False, **kwargs):
                     return True
                 except (DataObjectDoesNotExist, CollectionDoesNotExist):
                     log.info("Collection or data object (%s) does not exist", data_object_path)
-                    return True 
+                    return True
 
         except OSError:
             log.exception('%s delete error', self.get_filename(obj, **kwargs))
@@ -650,7 +649,7 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
                     log.exception("Trouble copying source file '%s' to cache '%s'", source_file, cache_file)
             else:
                 source_file = self._get_cache_path(rel_path)
-            # Update the file on iRODS 
+            # Update the file on iRODS
             self._push_to_irods(rel_path, source_file)
         else:
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
@@ -662,13 +661,13 @@ def get_object_url(self, obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
 
             p = Path(rel_path)
-            data_object_name =  p.stem + p.suffix
+            data_object_name = p.stem + p.suffix
             subcollection_name = p.parent
 
             collection_path = self.home + "/" + str(subcollection_name)
             data_object_path = collection_path + "/" + str(data_object_name)
-            
+
             return data_object_path
 
     def get_store_usage_percent(self):
-        return 0.0
\ No newline at end of file
+        return 0.0

From 699eb9a7ac66a9037d394b3eec859c183293b5af Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 13:23:25 -0400
Subject: [PATCH 530/853] More flake8 linyer changes

---
 test/unit/objectstore/test_irods.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/test/unit/objectstore/test_irods.py b/test/unit/objectstore/test_irods.py
index 43cc604b90f1..d7c6f57fb38f 100644
--- a/test/unit/objectstore/test_irods.py
+++ b/test/unit/objectstore/test_irods.py
@@ -4,7 +4,6 @@
 import pytest
 
 from galaxy.objectstore.irods import parse_config_xml
-from galaxy.objectstore.irods import IRODSObjectStore
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 
@@ -17,6 +16,7 @@
 CONFIG_FILE_NAME_NO_AUTH = 'irods_object_store_conf_no_auth.xml'
 CONFIG_FILE_NO_AUTH = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME_NO_AUTH)
 
+
 def test_parse_valid_config_xml():
     tree = ET.parse(CONFIG_FILE)
     root = tree.getroot()
@@ -35,14 +35,16 @@ def test_parse_valid_config_xml():
     assert config['extra_dirs'][1]['type'] == 'temp'
     assert config['extra_dirs'][1]['path'] == 'database/tmp_irods'
 
+
 def test_parse_config_xml_no_extra_dir():
     tree = ET.parse(CONFIG_FILE_NO_EXTRA_DIR)
     root = tree.getroot()
-    with pytest.raises(Exception, match='No extra_dir element in XML tree'): 
+    with pytest.raises(Exception, match='No extra_dir element in XML tree'):
         parse_config_xml(root)
 
+
 def test_parse_config_xml_no_auth():
     tree = ET.parse(CONFIG_FILE_NO_AUTH)
     root = tree.getroot()
-    with pytest.raises(Exception, match='No auth element in XML tree'): 
-        parse_config_xml(root)
\ No newline at end of file
+    with pytest.raises(Exception, match='No auth element in XML tree'):
+        parse_config_xml(root)

From bfb41750c66de7e5b5ef5988e19986208dad5114 Mon Sep 17 00:00:00 2001
From: Estelle Ancelet <34435064+eancelet@users.noreply.github.com>
Date: Mon, 23 Mar 2020 18:51:05 +0100
Subject: [PATCH 531/853] paramiko: load system host keys

Related to issue #9539
---
 lib/galaxy/jobs/runners/util/cli/shell/rsh.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/jobs/runners/util/cli/shell/rsh.py b/lib/galaxy/jobs/runners/util/cli/shell/rsh.py
index c6c7e1fbd1a4..45a59791c879 100644
--- a/lib/galaxy/jobs/runners/util/cli/shell/rsh.py
+++ b/lib/galaxy/jobs/runners/util/cli/shell/rsh.py
@@ -72,6 +72,7 @@ def connect(self):
         log.info("Attempting establishment of new paramiko SSH channel")
         self.ssh = paramiko.SSHClient()
         self.ssh.set_missing_host_key_policy(paramiko.RejectPolicy() if self.strict_host_key_checking else paramiko.WarningPolicy())
+        self.ssh.load_system_host_keys()
         self.ssh.connect(hostname=self.hostname,
                          port=self.port,
                          username=self.username,

From 3fbc2d985b539ef7619ffe043532b5f52c0e4664 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 22 Mar 2020 17:39:16 -0400
Subject: [PATCH 532/853] Replace jquery for each with es6 methods in workflow
 manager client

---
 .../components/Panels/ToolBoxWorkflow.vue     |  8 +--
 .../components/Workflow/Editor/Index.vue      | 17 +++--
 .../components/Workflow/Editor/Node.vue       |  2 +-
 .../components/Workflow/Editor/utilities.js   |  7 ++-
 .../galaxy/scripts/mvc/tool/tool-form-base.js |  2 +-
 .../scripts/mvc/workflow/workflow-forms.js    | 18 +++---
 .../scripts/mvc/workflow/workflow-manager.js  | 62 +++++++++----------
 client/galaxy/scripts/utils/simple-error.js   |  1 +
 lib/galaxy/managers/workflows.py              |  3 +-
 .../webapps/galaxy/controllers/workflow.py    |  4 +-
 10 files changed, 68 insertions(+), 56 deletions(-)

diff --git a/client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue b/client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue
index 4636ce6b48a1..71ff9f6647f3 100644
--- a/client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue
+++ b/client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue
@@ -77,16 +77,16 @@ export default {
         },
         workflows: {
             type: Array,
-            required: true
+            required: true,
         },
         dataManagers: {
             type: Array,
-            required: true
+            required: true,
         },
         moduleSections: {
             type: Array,
-            required: true
-        }
+            required: true,
+        },
     },
     computed: {
         workflowSection() {
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Index.vue b/client/galaxy/scripts/components/Workflow/Editor/Index.vue
index 4c3e9938739d..96e6e392e724 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Index.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Index.vue
@@ -4,8 +4,8 @@
             <template v-slot:panel>
                 <ToolBoxWorkflow
                     :toolbox="toolbox"
-                    :module-sections="module_sections"
-                    :data-managers="data_managers"
+                    :module-sections="moduleSections"
+                    :data-managers="dataManagers"
                     :workflows="workflows"
                     @onInsertTool="onInsertTool"
                     @onInsertModule="onInsertModule"
@@ -110,30 +110,39 @@ export default {
     props: {
         id: {
             type: String,
+            required: true,
         },
         version: {
             type: Number,
+            required: true,
         },
         name: {
             type: String,
+            required: true,
         },
         tags: {
             type: Array,
+            required: true,
         },
         annotation: {
             type: String,
+            required: true,
         },
-        module_sections: {
+        moduleSections: {
             type: Array,
+            required: true,
         },
-        data_managers: {
+        dataManagers: {
             type: Array,
+            required: true,
         },
         workflows: {
             type: Array,
+            required: true,
         },
         toolbox: {
             type: Array,
+            required: true,
         },
     },
     data() {
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index a258043c1e90..6ab50cf172a8 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -59,7 +59,7 @@ export default {
         node: {
             type: Object,
             default: null,
-        }
+        },
     },
     computed: {
         iconClass() {
diff --git a/client/galaxy/scripts/components/Workflow/Editor/utilities.js b/client/galaxy/scripts/components/Workflow/Editor/utilities.js
index dcd01b05aaf8..e2534b6072c2 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/utilities.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/utilities.js
@@ -144,9 +144,9 @@ export function getWorkflowParameters(nodes) {
             });
         }
         if (node.post_job_actions) {
-            Object.entries(node.post_job_actions).forEach(([k, pja]) => {
+            Object.values(node.post_job_actions).forEach((pja) => {
                 if (pja.action_arguments) {
-                    Object.entries(pja.action_arguments).forEach(([k, action_argument]) => {
+                    Object.values(pja.action_arguments).forEach((action_argument) => {
                         if (typeof action_argument === "string") {
                             const arg_matches = action_argument.match(parameter_re);
                             if (arg_matches) {
@@ -198,7 +198,8 @@ export function saveAs(workflow) {
                     window.location = `${getAppRoot()}workflow/editor?id=${id}`;
                     hide_modal();
                 })
-                .fail(() => {
+                .fail((err) => {
+                    console.debug(err);
                     hide_modal();
                     alert("Saving this workflow failed. Please contact this site's administrator.");
                 });
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js
index 6d1552e93090..2724cdd4db8d 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-base.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js
@@ -39,7 +39,7 @@ export default FormBase.extend({
     },
 
     /** Allows tool form variation to update tool model */
-    _update: function() {
+    _update: function () {
         var self = this;
         var callback = this.model.get("buildmodel");
         if (callback) {
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
index 98890b4ae05e..21ddc881447e 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
@@ -21,13 +21,13 @@ export class DefaultForm {
                         id: node.id,
                         type: node.type,
                         content_id: node.content_id,
-                        inputs: self.form.data.create()
+                        inputs: self.form.data.create(),
                     })
-                    .then(response => {
+                    .then((response) => {
                         const data = response.data;
                         node.update_field_data(data);
                     });
-            }
+            },
         });
     }
 }
@@ -54,12 +54,12 @@ export class ToolForm {
                     tool_id: options.id,
                     tool_version: options.version,
                     type: "tool",
-                    inputs: Object.assign({}, form.data.create())
+                    inputs: Object.assign({}, form.data.create()),
                 };
                 Galaxy.emit.debug("tool-form-workflow::postchange()", "Sending current state.", current_state);
                 axios
                     .post(`${getAppRoot()}api/workflows/build_module`, current_state)
-                    .then(response => {
+                    .then((response) => {
                         const data = response.data;
                         self._customize(data);
                         self.form.model.set(data.config_form);
@@ -73,16 +73,16 @@ export class ToolForm {
                         Galaxy.emit.debug("tool-form-workflow::postchange()", "Received new model.", data);
                         process.resolve();
                     })
-                    .catch(response => {
+                    .catch((response) => {
                         Galaxy.emit.debug("tool-form-workflow::postchange()", "Refresh request failed.", response);
                         process.reject();
                     });
-            }
+            },
         });
     }
     _customize(node) {
         const inputs = node.config_form.inputs;
-        Utils.deepeach(inputs, input => {
+        Utils.deepeach(inputs, (input) => {
             if (input.type) {
                 if (["data", "data_collection"].indexOf(input.type) != -1) {
                     input.type = "hidden";
@@ -145,7 +145,7 @@ function _addLabelAnnotation(self, node) {
                 duplicate && "Duplicate label. Please fix this before saving the workflow."
             );
             self.form.trigger("change");
-        }
+        },
     });
 }
 
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index e3c309ab0a3a..1bbcc0f94aa8 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -49,7 +49,7 @@ class Workflow extends EventEmitter {
     set_node(node, data) {
         node.init_field_data(data);
         node.update_field_data(data);
-        $.each(node.output_terminals, (ot_id, ot) => {
+        Object.values(node.output_terminals).forEach((ot) => {
             node.addWorkflowOutput(ot.name);
             node.markWorkflowOutput(ot.name);
         });
@@ -195,20 +195,20 @@ class Workflow extends EventEmitter {
     }
     remove_all() {
         var wf = this;
-        $.each(this.nodes, (k, v) => {
-            v.destroy();
-            wf.remove_node(v);
+        Object.values(this.nodes).forEach((node) => {
+            node.destroy();
+            wf.remove_node(node);
         });
     }
     rectify_workflow_outputs() {
         // Find out if we're using workflow_outputs or not.
         var using_workflow_outputs = false;
         var has_existing_pjas = false;
-        $.each(this.nodes, (k, node) => {
+        Object.values(this.nodes).forEach((node) => {
             if (node.type === "tool" && node.workflow_outputs && node.workflow_outputs.length > 0) {
                 using_workflow_outputs = true;
             }
-            $.each(node.post_job_actions, (pja_id, pja) => {
+            Object.values(node.post_job_actions).forEach((pja) => {
                 if (pja.action_type === "HideDatasetAction") {
                     has_existing_pjas = true;
                 }
@@ -216,26 +216,26 @@ class Workflow extends EventEmitter {
         });
         if (using_workflow_outputs !== false || has_existing_pjas !== false) {
             // Using workflow outputs, or has existing pjas.  Remove all PJAs and recreate based on outputs.
-            $.each(this.nodes, (k, node) => {
+            Object.values(this.nodes).forEach((node) => {
                 var node_changed = false;
                 if (node.post_job_actions === null) {
                     node.post_job_actions = {};
                     node_changed = true;
                 }
                 var pjas_to_rem = [];
-                $.each(node.post_job_actions, (pja_id, pja) => {
+                Object.entries(node.post_job_actions).forEach(([pja_id, pja]) => {
                     if (pja.action_type == "HideDatasetAction") {
                         pjas_to_rem.push(pja_id);
                     }
                 });
                 if (pjas_to_rem.length > 0) {
-                    $.each(pjas_to_rem, (i, pja_name) => {
+                    pjas_to_rem.forEach((pja_name) => {
                         node_changed = true;
                         delete node.post_job_actions[pja_name];
                     });
                 }
                 if (using_workflow_outputs) {
-                    $.each(node.output_terminals, (ot_id, ot) => {
+                    Object.values(node.output_terminals).forEach((ot) => {
                         var create_pja = !node.isWorkflowOutput(ot.name);
                         if (create_pja === true) {
                             node_changed = true;
@@ -258,14 +258,14 @@ class Workflow extends EventEmitter {
     }
     to_simple() {
         var nodes = {};
-        $.each(this.nodes, (i, node) => {
+        Object.values(this.nodes).forEach((node) => {
             var input_connections = {};
-            $.each(node.input_terminals, (k, t) => {
+            Object.values(node.input_terminals).forEach((t) => {
                 input_connections[t.name] = null;
                 // There should only be 0 or 1 connectors, so this is
                 // really a sneaky if statement
                 var cons = [];
-                $.each(t.connectors, (i, c) => {
+                t.connectors.forEach((c, i) => {
                     if (c.handle1) {
                         var con_dict = {
                             id: c.handle1.node.id,
@@ -282,8 +282,8 @@ class Workflow extends EventEmitter {
             });
             var post_job_actions = {};
             if (node.post_job_actions) {
-                $.each(node.post_job_actions, (i, act) => {
-                    var pja = {
+                Object.values(node.post_job_actions).forEach((act) => {
+                    const pja = {
                         action_type: act.action_type,
                         output_name: act.output_name,
                         action_arguments: act.action_arguments,
@@ -329,13 +329,13 @@ class Workflow extends EventEmitter {
         var using_workflow_outputs = false;
         wf.workflow_version = data.version;
         wf.report = data.report || {};
-        $.each(data.steps, (id, step) => {
+        Object.entries(data.steps).forEach(([id, step]) => {
             var node = wf.prebuildNode(step.type, step.name, step.content_id);
             // If workflow being copied into another, wipe UUID and let
             // Galaxy assign new ones.
             if (!initialImport) {
                 step.uuid = null;
-                $.each(step.workflow_outputs, (name, workflow_output) => {
+                step.workflow_outputs.forEach((workflow_output) => {
                     workflow_output.uuid = null;
                 });
             }
@@ -357,7 +357,7 @@ class Workflow extends EventEmitter {
                 if (node.workflow_outputs.length > 0) {
                     using_workflow_outputs = true;
                 } else {
-                    $.each(node.post_job_actions || [], (pja_id, pja) => {
+                    Object.values(node.post_job_actions).forEach((pja) => {
                         if (pja.action_type === "HideDatasetAction") {
                             using_workflow_outputs = true;
                         }
@@ -367,14 +367,14 @@ class Workflow extends EventEmitter {
         });
         wf.id_counter = max_id + 1;
         // Second pass, connections
-        $.each(data.steps, (id, step) => {
+        Object.entries(data.steps).forEach(([id, step]) => {
             const node = wf.nodes[parseInt(id) + offset];
-            $.each(step.input_connections, (k, v) => {
+            Object.entries(step.input_connections).forEach(([k, v]) => {
                 if (v) {
-                    if (!$.isArray(v)) {
+                    if (!Array.isArray(v)) {
                         v = [v];
                     }
-                    $.each(v, (l, x) => {
+                    v.forEach((x) => {
                         const other_node = wf.nodes[parseInt(x.id) + offset];
                         const c = new Connector(this.canvas_manager);
                         c.connect(other_node.output_terminals[x.output_name], node.input_terminals[k]);
@@ -384,7 +384,7 @@ class Workflow extends EventEmitter {
             });
             if (using_workflow_outputs) {
                 // Ensure that every output terminal has a WorkflowOutput or HideDatasetAction.
-                $.each(node.output_terminals, (ot_id, ot) => {
+                Object.values(node.output_terminals).forEach((ot) => {
                     if (node.post_job_actions[`HideDatasetAction${ot.name}`] === undefined) {
                         node.addWorkflowOutput(ot.name);
                         node.markWorkflowOutput(ot.name);
@@ -450,7 +450,7 @@ class Workflow extends EventEmitter {
         var n_pred = {};
         var successors = {};
         // First pass to initialize arrays even for nodes with no connections
-        $.each(this.nodes, (id, node) => {
+        Object.keys(this.nodes).forEach((id) => {
             if (n_pred[id] === undefined) {
                 n_pred[id] = 0;
             }
@@ -459,9 +459,9 @@ class Workflow extends EventEmitter {
             }
         });
         // Second pass to count predecessors and successors
-        $.each(this.nodes, (id, node) => {
-            $.each(node.input_terminals, (j, t) => {
-                $.each(t.connectors, (k, c) => {
+        Object.values(this.nodes).forEach((node) => {
+            Object.values(node.input_terminals).forEach((t) => {
+                t.connectors.forEach((c) => {
                     // A connection exists from `other` to `node`
                     var other = c.handle1.node;
                     // node gains a predecessor
@@ -504,14 +504,14 @@ class Workflow extends EventEmitter {
         var h_pad = 80;
         var v_pad = 30;
         var left = h_pad;
-        $.each(node_ids_by_level, (i, ids) => {
+        node_ids_by_level.forEach((ids) => {
             // We keep nodes in the same order in a level to give the user
             // some control over ordering
             ids.sort((a, b) => $(all_nodes[a].element).position().top - $(all_nodes[b].element).position().top);
             // Position each node
             var max_width = 0;
             var top = v_pad;
-            $.each(ids, (j, id) => {
+            ids.forEach((id) => {
                 var node = all_nodes[id];
                 var element = $(node.element);
                 $(element).css({ top: top, left: left });
@@ -521,7 +521,7 @@ class Workflow extends EventEmitter {
             left += max_width + h_pad;
         });
         // Need to redraw all connectors
-        $.each(all_nodes, (_, node) => {
+        Object.values(all_nodes).forEach((node) => {
             node.redraw();
         });
     }
@@ -531,7 +531,7 @@ class Workflow extends EventEmitter {
         var ymin = Infinity;
         var ymax = -Infinity;
         var p;
-        $.each(this.nodes, (id, node) => {
+        Object.values(this.nodes).forEach((node) => {
             var e = $(node.element);
             p = e.position();
             xmin = Math.min(xmin, p.left);
diff --git a/client/galaxy/scripts/utils/simple-error.js b/client/galaxy/scripts/utils/simple-error.js
index 1341c1301f4d..9c6f3f4ccdd3 100644
--- a/client/galaxy/scripts/utils/simple-error.js
+++ b/client/galaxy/scripts/utils/simple-error.js
@@ -9,5 +9,6 @@ export function errorMessageAsString(e) {
 }
 
 export function rethrowSimple(e) {
+    console.debug(e);
     throw errorMessageAsString(e);
 }
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 494aeb1e81f7..0d760ba884cb 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -617,6 +617,7 @@ def _workflow_to_dict_editor(self, trans, stored, workflow, tooltip=True, is_sub
                 else:
                     data['upgrade_messages'][step.order_index] = {module.tool.name: "\n".join(module.version_changes)}
             # Get user annotation.
+            config_form = module.get_config_form(step=step)
             annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ''
             # Pack attributes into plain dictionary
             step_dict = {
@@ -629,7 +630,7 @@ def _workflow_to_dict_editor(self, trans, stored, workflow, tooltip=True, is_sub
                 'errors': module.get_errors(),
                 'inputs': module.get_all_inputs(connectable_only=True),
                 'outputs': module.get_all_outputs(),
-                'config_form': module.get_config_form(step=step),
+                'config_form': config_form,
                 'annotation': annotation_str,
                 'post_job_actions': {},
                 'uuid': str(step.uuid) if step.uuid else None,
diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index 3b57e15e9617..60b20b10de2b 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -707,8 +707,8 @@ def editor(self, trans, id=None, version=None):
             'version'                 : version,
             'annotation'              : self.get_item_annotation_str(trans.sa_session, trans.user, stored),
             'toolbox'                 : trans.app.toolbox.to_dict(trans),
-            'module_sections'         : module_sections,
-            'data_managers'           : data_managers,
+            'moduleSections'          : module_sections,
+            'dataManagers'            : data_managers,
             'workflows'               : workflows
         }
 

From 880a3365794c9a28d3c8d5870fb1f9721b2f2f30 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 23 Mar 2020 14:19:46 -0400
Subject: [PATCH 533/853] Add default values to properties in workflow
 attributes component

---
 .../galaxy/scripts/components/Workflow/Editor/Attributes.vue  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Attributes.vue b/client/galaxy/scripts/components/Workflow/Editor/Attributes.vue
index a37bcd95591c..dfdb0ce4799f 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Attributes.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Attributes.vue
@@ -68,15 +68,19 @@ export default {
         },
         annotation: {
             type: String,
+            default: "",
         },
         version: {
             type: Number,
+            default: null,
         },
         versions: {
             type: Array,
+            default: null,
         },
         parameters: {
             type: Array,
+            default: null,
         },
     },
     data() {

From 11005c4983c091ddcd9d09d8c0b586073f898d86 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 15:34:22 -0400
Subject: [PATCH 534/853] Updating contributors.

---
 CONTRIBUTORS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
index 800d4762594d..d6507a7be425 100644
--- a/CONTRIBUTORS.md
+++ b/CONTRIBUTORS.md
@@ -86,6 +86,7 @@ The following individuals have contributed code to Galaxy:
 * Joachim Jacob <joachim.jacob@gmail.com>
 * Xiaoqian Jiang <jxq198409@hotmail.com>
 * Jim Johnson <jj@umn.edu> <jj@msi.umn.edu>
+* Kaivan Kamali <kxk302@gmail.com>
 * Radhesh Kamath <radhesh@bx.psu.edu>
 * Iyad Kandalaft <ik@iyadk.com>
 * Jan Kanis <jan.code@jankanis.nl>

From 0b5356888130fde5fd9edcc4385699fb906827dc Mon Sep 17 00:00:00 2001
From: "jalili.vahid@gmail.com" <LetMeIn%#01>
Date: Mon, 23 Mar 2020 13:39:50 -0700
Subject: [PATCH 535/853] Separate ObjectStore interface and base
 implementation.

# - Interface name follows naming convention (with I prefix);
# - Interface does not implement any methods;
# - Base provides common methods for all the derived types.
---
 lib/galaxy/objectstore/__init__.py | 85 ++++++++++++++++--------------
 1 file changed, 44 insertions(+), 41 deletions(-)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index b1dccf8b2494..380003371815 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -38,9 +38,9 @@
 log = logging.getLogger(__name__)
 
 
-class ObjectStore(object):
+class IObjectStore(object):
 
-    """ObjectStore abstract interface.
+    """ObjectStore interface.
 
     FIELD DESCRIPTIONS (these apply to all the methods in this class):
 
@@ -82,47 +82,10 @@ class ObjectStore(object):
         000/obj.id)
     """
 
-    def __init__(self, config, config_dict=None, **kwargs):
-        """
-        :type config: object
-        :param config: An object, most likely populated from
-            `galaxy/config.ini`, having the following attributes:
-
-            * object_store_check_old_style (only used by the
-              :class:`DiskObjectStore` subclass)
-            * jobs_directory -- Each job is given a unique empty directory
-              as its current working directory. This option defines in what
-              parent directory those directories will be created.
-            * new_file_path -- Used to set the 'temp' extra_dir.
-        """
-        if config_dict is None:
-            config_dict = {}
-        self.running = True
-        self.config = config
-        self.check_old_style = config.object_store_check_old_style
-        extra_dirs = {}
-        extra_dirs['job_work'] = config.jobs_directory
-        extra_dirs['temp'] = config.new_file_path
-        extra_dirs.update(dict(
-            (e['type'], e['path']) for e in config_dict.get('extra_dirs', [])))
-        self.extra_dirs = extra_dirs
-
-    def shutdown(self):
-        """Close any connections for this ObjectStore."""
-        self.running = False
-
     def exists(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         """Return True if the object identified by `obj` exists, False otherwise."""
         raise NotImplementedError()
 
-    def file_ready(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Check if a file corresponding to a dataset is ready to be used.
-
-        Return True if so, False otherwise
-        """
-        return True
-
     def create(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Mark the object (`obj`) as existing in the store, but with no content.
@@ -219,6 +182,46 @@ def get_store_by(self, obj):
         """
         raise NotImplementedError()
 
+
+class BaseObjectStore(IObjectStore):
+
+    def __init__(self, config, config_dict=None, **kwargs):
+        """
+        :type config: object
+        :param config: An object, most likely populated from
+            `galaxy/config.ini`, having the following attributes:
+
+            * object_store_check_old_style (only used by the
+              :class:`DiskObjectStore` subclass)
+            * jobs_directory -- Each job is given a unique empty directory
+              as its current working directory. This option defines in what
+              parent directory those directories will be created.
+            * new_file_path -- Used to set the 'temp' extra_dir.
+        """
+        if config_dict is None:
+            config_dict = {}
+        self.running = True
+        self.config = config
+        self.check_old_style = config.object_store_check_old_style
+        extra_dirs = {}
+        extra_dirs['job_work'] = config.jobs_directory
+        extra_dirs['temp'] = config.new_file_path
+        extra_dirs.update(dict(
+            (e['type'], e['path']) for e in config_dict.get('extra_dirs', [])))
+        self.extra_dirs = extra_dirs
+
+    def shutdown(self):
+        """Close any connections for this ObjectStore."""
+        self.running = False
+
+    def file_ready(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Check if a file corresponding to a dataset is ready to be used.
+
+        Return True if so, False otherwise
+        """
+        return True
+
     @classmethod
     def parse_xml(clazz, config_xml):
         """Parse an XML description of a configuration for this object store.
@@ -252,7 +255,7 @@ def _get_object_id(self, obj):
             return obj.id
 
 
-class ConcreteObjectStore(ObjectStore):
+class ConcreteObjectStore(BaseObjectStore):
     """Subclass of ObjectStore for stores that don't delegate (non-nested).
 
     Currently only adds store_by functionality. Which doesn't make
@@ -548,7 +551,7 @@ def get_store_usage_percent(self):
         return (float(st.f_blocks - st.f_bavail) / st.f_blocks) * 100
 
 
-class NestedObjectStore(ObjectStore):
+class NestedObjectStore(BaseObjectStore):
 
     """
     Base for ObjectStores that use other ObjectStores.

From d4abc786c74fe17d092c6039a097c0ab17b603e6 Mon Sep 17 00:00:00 2001
From: "jalili.vahid@gmail.com" <LetMeIn%#01>
Date: Mon, 23 Mar 2020 18:53:49 -0700
Subject: [PATCH 536/853] Shadow interface methods in the BaseObjectStore.

---
 lib/galaxy/objectstore/__init__.py   | 132 +++++++++++++++++----------
 lib/galaxy/objectstore/azure_blob.py |  38 ++++----
 lib/galaxy/objectstore/cloud.py      |  38 ++++----
 lib/galaxy/objectstore/pithos.py     |  36 ++++----
 lib/galaxy/objectstore/pulsar.py     |  24 ++---
 lib/galaxy/objectstore/rods.py       |  26 +++---
 lib/galaxy/objectstore/s3.py         |  38 ++++----
 7 files changed, 184 insertions(+), 148 deletions(-)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index 380003371815..f826a91c701c 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -254,6 +254,42 @@ def _get_object_id(self, obj):
             # job working directories.
             return obj.id
 
+    def _invoke(self, delegate, obj, **kwargs):
+        return self.__getattribute__("_" + delegate)(obj, **kwargs)
+
+    def exists(self, obj, **kwargs):
+        return self._invoke('exists', obj, **kwargs)
+
+    def create(self, obj, **kwargs):
+        return self._invoke('create', obj, **kwargs)
+
+    def empty(self, obj, **kwargs):
+        return self._invoke('empty', obj, **kwargs)
+
+    def size(self, obj, **kwargs):
+        return self._invoke('size', obj, **kwargs)
+
+    def delete(self, obj, **kwargs):
+        return self._invoke('delete', obj, **kwargs)
+
+    def get_data(self, obj, **kwargs):
+        return self._invoke('get_data', obj, **kwargs)
+
+    def get_filename(self, obj, **kwargs):
+        return self._invoke('get_filename', obj, **kwargs)
+
+    def update_from_file(self, obj, **kwargs):
+        return self._invoke('update_from_file', obj, **kwargs)
+
+    def get_object_url(self, obj, **kwargs):
+        return self._invoke('get_object_url', obj, **kwargs)
+
+    def get_store_usage_percent(self, **kwargs):
+        return self._invoke('get_store_usage_percent', **kwargs)
+
+    def get_store_by(self, obj, **kwargs):
+        return self._invoke('get_store_by', obj, **kwargs)
+
 
 class ConcreteObjectStore(BaseObjectStore):
     """Subclass of ObjectStore for stores that don't delegate (non-nested).
@@ -283,7 +319,7 @@ def to_dict(self):
         rval["store_by"] = self.store_by
         return rval
 
-    def get_store_by(self, obj):
+    def _get_store_by(self, obj):
         return self.store_by
 
 
@@ -346,7 +382,7 @@ def to_dict(self):
         as_dict["files_dir"] = self.file_path
         return as_dict
 
-    def _get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+    def __get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Return the absolute path for the file corresponding to the `obj.id`.
 
@@ -428,7 +464,7 @@ def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, e
             path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % obj_id)
         return os.path.abspath(path)
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         """Override `ObjectStore`'s stub and check on disk."""
         if self.check_old_style:
             path = self._construct_path(obj, old_style=True, **kwargs)
@@ -438,9 +474,9 @@ def exists(self, obj, **kwargs):
                 return True
         return os.path.exists(self._construct_path(obj, **kwargs))
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """Override `ObjectStore`'s stub by creating any files and folders on disk."""
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
             path = self._construct_path(obj, **kwargs)
             dir_only = kwargs.get('dir_only', False)
             # Create directory if it does not exist
@@ -451,18 +487,18 @@ def create(self, obj, **kwargs):
                 open(path, 'w').close()  # Should be rb?
                 umask_fix_perms(path, self.config.umask, 0o666)
 
-    def empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs):
         """Override `ObjectStore`'s stub by checking file size on disk."""
         return self.size(obj, **kwargs) == 0
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         """Override `ObjectStore`'s stub by return file size on disk.
 
         Returns 0 if the object doesn't exist yet or other error.
         """
-        if self.exists(obj, **kwargs):
+        if self._exists(obj, **kwargs):
             try:
-                filepath = self.get_filename(obj, **kwargs)
+                filepath = self._get_filename(obj, **kwargs)
                 for _ in range(0, 2):
                     size = os.path.getsize(filepath)
                     if size != 0:
@@ -475,31 +511,31 @@ def size(self, obj, **kwargs):
         else:
             return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         """Override `ObjectStore`'s stub; delete the file or folder on disk."""
-        path = self.get_filename(obj, **kwargs)
+        path = self._get_filename(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         obj_dir = kwargs.get('obj_dir', False)
         try:
             if entire_dir and (extra_dir or obj_dir):
                 shutil.rmtree(path)
                 return True
-            if self.exists(obj, **kwargs):
+            if self._exists(obj, **kwargs):
                 os.remove(path)
                 return True
         except OSError as ex:
-            log.critical('%s delete error %s' % (self._get_filename(obj, **kwargs), ex))
+            log.critical('%s delete error %s' % (self.__get_filename(obj, **kwargs), ex))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         """Override `ObjectStore`'s stub; retrieve data directly from disk."""
-        data_file = open(self.get_filename(obj, **kwargs), 'r')  # Should be rb?
+        data_file = open(self._get_filename(obj, **kwargs), 'r')  # Should be rb?
         data_file.seek(start)
         content = data_file.read(count)
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         """
         Override `ObjectStore`'s stub.
 
@@ -517,27 +553,27 @@ def get_filename(self, obj, **kwargs):
             raise ObjectNotFound
         return path
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         """`create` parameter is not used in this implementation."""
         preserve_symlinks = kwargs.pop('preserve_symlinks', False)
         # FIXME: symlinks and the object store model may not play well together
         # these should be handled better, e.g. registering the symlink'd file
         # as an object
         if create:
-            self.create(obj, **kwargs)
-        if file_name and self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if file_name and self._exists(obj, **kwargs):
             try:
                 if preserve_symlinks and os.path.islink(file_name):
-                    force_symlink(os.readlink(file_name), self.get_filename(obj, **kwargs))
+                    force_symlink(os.readlink(file_name), self._get_filename(obj, **kwargs))
                 else:
-                    path = self.get_filename(obj, **kwargs)
+                    path = self._get_filename(obj, **kwargs)
                     shutil.copy(file_name, path)
                     umask_fix_perms(path, self.config.umask, 0o666)
             except IOError as ex:
-                log.critical('Error copying %s to %s: %s' % (file_name, self._get_filename(obj, **kwargs), ex))
+                log.critical('Error copying %s to %s: %s' % (file_name, self.__get_filename(obj, **kwargs), ex))
                 raise ex
 
-    def get_object_url(self, obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
         """
         Override `ObjectStore`'s stub.
 
@@ -545,7 +581,7 @@ def get_object_url(self, obj, **kwargs):
         """
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         """Override `ObjectStore`'s stub by return percent storage used."""
         st = os.statvfs(self.file_path)
         return (float(st.f_blocks - st.f_bavail) / st.f_blocks) * 100
@@ -570,51 +606,51 @@ def shutdown(self):
             store.shutdown()
         super(NestedObjectStore, self).shutdown()
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         """Determine if the `obj` exists in any of the backends."""
-        return self._call_method('exists', obj, False, False, **kwargs)
+        return self._call_method('_exists', obj, False, False, **kwargs)
 
     def file_ready(self, obj, **kwargs):
         """Determine if the file for `obj` is ready to be used by any of the backends."""
         return self._call_method('file_ready', obj, False, False, **kwargs)
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """Create a backing file in a random backend."""
         random.choice(list(self.backends.values())).create(obj, **kwargs)
 
-    def empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs):
         """For the first backend that has this `obj`, determine if it is empty."""
-        return self._call_method('empty', obj, True, False, **kwargs)
+        return self._call_method('_empty', obj, True, False, **kwargs)
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         """For the first backend that has this `obj`, return its size."""
-        return self._call_method('size', obj, 0, False, **kwargs)
+        return self._call_method('_size', obj, 0, False, **kwargs)
 
-    def delete(self, obj, **kwargs):
+    def _delete(self, obj, **kwargs):
         """For the first backend that has this `obj`, delete it."""
-        return self._call_method('delete', obj, False, False, **kwargs)
+        return self._call_method('_delete', obj, False, False, **kwargs)
 
-    def get_data(self, obj, **kwargs):
+    def _get_data(self, obj, **kwargs):
         """For the first backend that has this `obj`, get data from it."""
-        return self._call_method('get_data', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('_get_data', obj, ObjectNotFound, True, **kwargs)
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         """For the first backend that has this `obj`, get its filename."""
-        return self._call_method('get_filename', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('_get_filename', obj, ObjectNotFound, True, **kwargs)
 
-    def update_from_file(self, obj, **kwargs):
+    def _update_from_file(self, obj, **kwargs):
         """For the first backend that has this `obj`, update it from the given file."""
         if kwargs.get('create', False):
-            self.create(obj, **kwargs)
+            self._create(obj, **kwargs)
             kwargs['create'] = False
-        return self._call_method('update_from_file', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('_update_from_file', obj, ObjectNotFound, True, **kwargs)
 
-    def get_object_url(self, obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
         """For the first backend that has this `obj`, get its URL."""
-        return self._call_method('get_object_url', obj, None, False, **kwargs)
+        return self._call_method('_get_object_url', obj, None, False, **kwargs)
 
-    def get_store_by(self, obj):
-        return self._call_method('get_store_by', obj, None, False)
+    def _get_store_by(self, obj):
+        return self._call_method('_get_store_by', obj, None, False)
 
     def _repr_object_for_exception(self, obj):
         try:
@@ -794,9 +830,9 @@ def __filesystem_monitor(self):
             self.weighted_backend_ids = new_weighted_backend_ids
             self.sleeper.sleep(120)  # Test free space every 2 minutes
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """The only method in which obj.object_store_id may be None."""
-        if obj.object_store_id is None or not self.exists(obj, **kwargs):
+        if obj.object_store_id is None or not self._exists(obj, **kwargs):
             if obj.object_store_id is None or obj.object_store_id not in self.backends:
                 try:
                     obj.object_store_id = random.choice(self.weighted_backend_ids)
@@ -883,14 +919,14 @@ def to_dict(self):
         as_dict["backends"] = backends
         return as_dict
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         """Check all child object stores."""
         for store in self.backends.values():
             if store.exists(obj, **kwargs):
                 return True
         return False
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """Call the primary object store."""
         self.backends[0].create(obj, **kwargs)
 
diff --git a/lib/galaxy/objectstore/azure_blob.py b/lib/galaxy/objectstore/azure_blob.py
index 93c8c335d8c1..b47c152edb29 100644
--- a/lib/galaxy/objectstore/azure_blob.py
+++ b/lib/galaxy/objectstore/azure_blob.py
@@ -310,7 +310,7 @@ def _push_to_os(self, rel_path, source_file=None, from_string=None):
     # Public Methods #
     ##################
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         in_cache = in_azure = False
         rel_path = self._construct_path(obj, **kwargs)
 
@@ -357,9 +357,9 @@ def file_ready(self, obj, **kwargs):
 
         return False
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
 
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
 
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
@@ -393,25 +393,25 @@ def create(self, obj, **kwargs):
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
                 self._push_to_os(rel_path, from_string='')
 
-    def empty(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
-            return bool(self.size(obj, **kwargs) > 0)
+    def _empty(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
+            return bool(self._size(obj, **kwargs) > 0)
         else:
             raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s' % (str(obj), str(kwargs)))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
                 return os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try Azure. Error: %s", rel_path, ex)
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             return self._get_size_in_azure(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
         return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         base_dir = kwargs.get('base_dir', None)
@@ -445,10 +445,10 @@ def delete(self, obj, entire_dir=False, **kwargs):
         except AzureHttpError:
             log.exception("Could not delete blob '%s' from Azure", rel_path)
         except OSError:
-            log.exception('%s delete error', self.get_filename(obj, **kwargs))
+            log.exception('%s delete error', self._get_filename(obj, **kwargs))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         # Check cache first and get file if not there
         if not self._in_cache(rel_path):
@@ -460,7 +460,7 @@ def get_data(self, obj, start=0, count=-1, **kwargs):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
@@ -483,7 +483,7 @@ def get_filename(self, obj, **kwargs):
         if self._in_cache(rel_path):
             return cache_path
         # Check if the file exists in persistent storage and, if it does, pull it into cache
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if dir_only:  # Directories do not get pulled into cache
                 return cache_path
             else:
@@ -495,10 +495,10 @@ def get_filename(self, obj, **kwargs):
         #     return cache_path
         raise ObjectNotFound('objectstore.get_filename, no cache_path: %s, kwargs: %s' % (str(obj), str(kwargs)))
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         if create is True:
-            self.create(obj, **kwargs)
-        elif self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        elif self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             # Chose whether to use the dataset file itself or an alternate file
             if file_name:
@@ -520,8 +520,8 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
         else:
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s' % (str(obj), str(kwargs)))
 
-    def get_object_url(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             try:
                 url = self.service.make_blob_url(container_name=self.container_name, blob_name=rel_path)
@@ -530,7 +530,7 @@ def get_object_url(self, obj, **kwargs):
                 log.exception("Trouble generating URL for dataset '%s'", rel_path)
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return 0.0
 
     ##################
diff --git a/lib/galaxy/objectstore/cloud.py b/lib/galaxy/objectstore/cloud.py
index 49d1fa778e75..b94c9eba9eaf 100644
--- a/lib/galaxy/objectstore/cloud.py
+++ b/lib/galaxy/objectstore/cloud.py
@@ -510,7 +510,7 @@ def file_ready(self, obj, **kwargs):
                       os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_cloud(rel_path))
         return False
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         in_cache = False
         rel_path = self._construct_path(obj, **kwargs)
 
@@ -543,8 +543,8 @@ def exists(self, obj, **kwargs):
         else:
             return False
 
-    def create(self, obj, **kwargs):
-        if not self.exists(obj, **kwargs):
+    def _create(self, obj, **kwargs):
+        if not self._exists(obj, **kwargs):
 
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
@@ -572,26 +572,26 @@ def create(self, obj, **kwargs):
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
                 self._push_to_os(rel_path, from_string='')
 
-    def empty(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
-            return bool(self.size(obj, **kwargs) > 0)
+    def _empty(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
+            return bool(self._size(obj, **kwargs) > 0)
         else:
             raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
                 return os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try cloud. Error: %s", rel_path, ex)
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             return self._get_size_in_cloud(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
         return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         base_dir = kwargs.get('base_dir', None)
@@ -626,10 +626,10 @@ def delete(self, obj, entire_dir=False, **kwargs):
         except Exception:
             log.exception("Could not delete key '%s' from cloud", rel_path)
         except OSError:
-            log.exception('%s delete error', self.get_filename(obj, **kwargs))
+            log.exception('%s delete error', self._get_filename(obj, **kwargs))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         # Check cache first and get file if not there
         if not self._in_cache(rel_path):
@@ -641,7 +641,7 @@ def get_data(self, obj, start=0, count=-1, **kwargs):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
         obj_dir = kwargs.get('obj_dir', False)
@@ -664,7 +664,7 @@ def get_filename(self, obj, **kwargs):
         if self._in_cache(rel_path):
             return cache_path
         # Check if the file exists in persistent storage and, if it does, pull it into cache
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if dir_only:  # Directories do not get pulled into cache
                 return cache_path
             else:
@@ -678,10 +678,10 @@ def get_filename(self, obj, **kwargs):
                              % (str(obj), str(kwargs)))
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         if create:
-            self.create(obj, **kwargs)
-        if self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             # Chose whether to use the dataset file itself or an alternate file
             if file_name:
@@ -703,8 +703,8 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def get_object_url(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             try:
                 key = self.bucket.objects.get(rel_path)
@@ -713,5 +713,5 @@ def get_object_url(self, obj, **kwargs):
                 log.exception("Trouble generating URL for dataset '%s'", rel_path)
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return 0.0
diff --git a/lib/galaxy/objectstore/pithos.py b/lib/galaxy/objectstore/pithos.py
index 2d658f0133b0..63bc8e23e94a 100644
--- a/lib/galaxy/objectstore/pithos.py
+++ b/lib/galaxy/objectstore/pithos.py
@@ -221,7 +221,7 @@ def _pull_into_cache(self, rel_path):
 
     # No need to overwrite "shutdown"
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         """Check if file exists, fix if file in cache and not on Pithos+
         :returns: weather the file exists remotely or in cache
         """
@@ -253,9 +253,9 @@ def exists(self, obj, **kwargs):
             return True
         return False
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """Touch a file (aka create empty), if it doesn't exist"""
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
             extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
@@ -288,18 +288,18 @@ def create(self, obj, **kwargs):
                 open(new_file, 'w').close()
                 self.pithos.upload_from_string(rel_path, '')
 
-    def empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs):
         """
         :returns: weather the object has content
         :raises ObjectNotFound:
         """
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
             raise ObjectNotFound(
                 'objectstore.empty, object does not exist: {obj}, '
                 'kwargs: {kwargs}'.format(obj=obj, kwargs=kwargs))
-        return bool(self.size(obj, **kwargs))
+        return bool(self._size(obj, **kwargs))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         """
         :returns: The size of the object, or 0 if it doesn't exist (sorry for
             that, not our fault, the ObjectStore interface is like that some
@@ -321,7 +321,7 @@ def size(self, obj, **kwargs):
             return 0
         return int(file['content-length'])
 
-    def delete(self, obj, **kwargs):
+    def _delete(self, obj, **kwargs):
         """Delete the object
         :returns: weather the object was deleted
         """
@@ -347,13 +347,13 @@ def delete(self, obj, **kwargs):
                 self.pithos.del_object(path)
         except OSError:
             log.exception(
-                '{0} delete error'.format(self.get_filename(obj, **kwargs)))
+                '{0} delete error'.format(self._get_filename(obj, **kwargs)))
         except ClientError as ce:
             log.exception('Could not delete {path} from Pithos, {err}'.format(
                 path=path, err=ce))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         """Fetch (e.g., download) data
         :param start: Chunk of data starts here
         :param count: Fetch at most as many data, fetch all if negative
@@ -369,7 +369,7 @@ def get_data(self, obj, start=0, count=-1, **kwargs):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         """Get the expected filename with absolute path"""
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
@@ -386,7 +386,7 @@ def get_filename(self, obj, **kwargs):
             return cache_path
         if self._in_cache(path):
             return cache_path
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if not dir_only:
                 self._pull_into_cache(path)
                 return cache_path
@@ -394,11 +394,11 @@ def get_filename(self, obj, **kwargs):
             'objectstore.get_filename, no cache_path: {obj}, '
             'kwargs: {kwargs}'.format(obj, kwargs))
 
-    def update_from_file(self, obj, **kwargs):
+    def _update_from_file(self, obj, **kwargs):
         """Update the store when a file is updated"""
         if kwargs.get('create'):
-            self.create(obj, **kwargs)
-        if not self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if not self._exists(obj, **kwargs):
             raise ObjectNotFound(
                 'objectstore.update_from_file, object does not exist: {obj}, '
                 'kwargs: {kwargs}'.format(obj, kwargs))
@@ -420,11 +420,11 @@ def update_from_file(self, obj, **kwargs):
             with open(cache_path) as f:
                 self.pithos.upload_object(obj, f)
 
-    def get_object_url(self, obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
         """
         :returns: URL for direct access, None if no object
         """
-        if self.exists(obj, **kwargs):
+        if self._exists(obj, **kwargs):
             path = self._construct_path(obj, **kwargs)
             try:
                 return self.pithos.publish_object(path)
@@ -434,7 +434,7 @@ def get_object_url(self, obj, **kwargs):
                 log.exception('Kamaki: {0}'.format(ce))
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         """
         :returns: percentage indicating how full the store is
         """
diff --git a/lib/galaxy/objectstore/pulsar.py b/lib/galaxy/objectstore/pulsar.py
index d7d1e8b7cffc..c2217311ae4b 100644
--- a/lib/galaxy/objectstore/pulsar.py
+++ b/lib/galaxy/objectstore/pulsar.py
@@ -1,6 +1,6 @@
 from __future__ import absolute_import  # Need to import pulsar_client absolutely.
 
-from ..objectstore import ObjectStore
+from ..objectstore import BaseObjectStore
 
 try:
     from pulsar.client.manager import ObjectStoreClientManager
@@ -8,7 +8,7 @@
     ObjectStoreClientManager = None
 
 
-class PulsarObjectStore(ObjectStore):
+class PulsarObjectStore(BaseObjectStore):
     """
     Object store implementation that delegates to a remote Pulsar server.
 
@@ -26,38 +26,38 @@ class PulsarObjectStore(ObjectStore):
     def __init__(self, config, config_xml):
         self.pulsar_client = self.__build_pulsar_client(config_xml)
 
-    def exists(self, obj, **kwds):
+    def _exists(self, obj, **kwds):
         return self.pulsar_client.exists(**self.__build_kwds(obj, **kwds))
 
     def file_ready(self, obj, **kwds):
         return self.pulsar_client.file_ready(**self.__build_kwds(obj, **kwds))
 
-    def create(self, obj, **kwds):
+    def _create(self, obj, **kwds):
         return self.pulsar_client.create(**self.__build_kwds(obj, **kwds))
 
-    def empty(self, obj, **kwds):
+    def _empty(self, obj, **kwds):
         return self.pulsar_client.empty(**self.__build_kwds(obj, **kwds))
 
-    def size(self, obj, **kwds):
+    def _size(self, obj, **kwds):
         return self.pulsar_client.size(**self.__build_kwds(obj, **kwds))
 
-    def delete(self, obj, **kwds):
+    def _delete(self, obj, **kwds):
         return self.pulsar_client.delete(**self.__build_kwds(obj, **kwds))
 
     # TODO: Optimize get_data.
-    def get_data(self, obj, **kwds):
+    def _get_data(self, obj, **kwds):
         return self.pulsar_client.get_data(**self.__build_kwds(obj, **kwds))
 
-    def get_filename(self, obj, **kwds):
+    def _get_filename(self, obj, **kwds):
         return self.pulsar_client.get_filename(**self.__build_kwds(obj, **kwds))
 
-    def update_from_file(self, obj, **kwds):
+    def _update_from_file(self, obj, **kwds):
         return self.pulsar_client.update_from_file(**self.__build_kwds(obj, **kwds))
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return self.pulsar_client.get_store_usage_percent()
 
-    def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+    def _get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         return None
 
     def __build_kwds(self, obj, **kwds):
diff --git a/lib/galaxy/objectstore/rods.py b/lib/galaxy/objectstore/rods.py
index 65114037c16b..f01c87720c4d 100644
--- a/lib/galaxy/objectstore/rods.py
+++ b/lib/galaxy/objectstore/rods.py
@@ -148,15 +148,15 @@ def __mkcolls(self, rods_path):
             assert status == 0, '__mkcolls(): Failed to create collection: %s' % collname
 
     @local_extra_dirs
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         doi = irods.dataObjInp_t()
         doi.objPath = self.__get_rods_path(obj, **kwargs)
         log.debug('exists(): checking: %s', doi.objPath)
         return irods.rcObjStat(self.rods_conn, doi) is not None
 
     @local_extra_dirs
-    def create(self, obj, **kwargs):
-        if not self.exists(obj, **kwargs):
+    def _create(self, obj, **kwargs):
+        if not self._exists(obj, **kwargs):
             rods_path = self.__get_rods_path(obj, **kwargs)
             log.debug('create(): %s', rods_path)
             dir_only = kwargs.get('dir_only', False)
@@ -177,7 +177,7 @@ def create(self, obj, **kwargs):
                 assert status >= 0, 'create(): rcDataObjCreate() failed: %s: %s: %s' % (rods_path, status, irods.strerror(status))
 
     @local_extra_dirs
-    def empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs):
         assert 'dir_only' not in kwargs, 'empty(): `dir_only` parameter is invalid here'
         h = self.__get_rods_handle(obj, **kwargs)
         try:
@@ -186,7 +186,7 @@ def empty(self, obj, **kwargs):
             # h is None
             raise ObjectNotFound()
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         assert 'dir_only' not in kwargs, 'size(): `dir_only` parameter is invalid here'
         h = self.__get_rods_handle(obj, **kwargs)
         try:
@@ -196,7 +196,7 @@ def size(self, obj, **kwargs):
             return 0
 
     @local_extra_dirs
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         assert 'dir_only' not in kwargs, 'delete(): `dir_only` parameter is invalid here'
         rods_path = self.__get_rods_path(obj, **kwargs)
         # __get_rods_path prepends self.root_collection_path but we are going
@@ -223,7 +223,7 @@ def delete(self, obj, entire_dir=False, **kwargs):
         return False
 
     @local_extra_dirs
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         log.debug('get_data(): %s')
         h = self.__get_rods_handle(obj, **kwargs)
         try:
@@ -238,11 +238,11 @@ def get_data(self, obj, start=0, count=-1, **kwargs):
         # reads data into a var, closes, and returns the var
 
     @local_extra_dirs
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         log.debug("get_filename(): called on %s %s. For better performance, avoid this method and use get_data() instead.", obj.__class__.__name__, obj.id)
         cached_path = self.__get_cache_path(obj, **kwargs)
 
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
             raise ObjectNotFound()
 
         # TODO: implement or define whether dir_only is valid
@@ -286,11 +286,11 @@ def get_filename(self, obj, **kwargs):
         return os.path.abspath(cached_path)
 
     @local_extra_dirs
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         assert 'dir_only' not in kwargs, 'update_from_file(): `dir_only` parameter is invalid here'
 
         # do not create if not requested
-        if create and not self.exists(obj, **kwargs):
+        if create and not self._exists(obj, **kwargs):
             raise ObjectNotFound()
 
         if file_name is None:
@@ -311,10 +311,10 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
         status = irods.rcDataObjPut(self.rods_conn, doi, file_name)
         assert status == 0, 'update_from_file(): iput %s failed (%s): %s' % (doi.objPath, status, irods.strerror(status))
 
-    def get_object_url(self, obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return 0.0
 
 
diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index a17294983915..ca0b35a178ff 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -504,7 +504,7 @@ def file_ready(self, obj, **kwargs):
                       os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_s3(rel_path))
         return False
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         in_cache = in_s3 = False
         rel_path = self._construct_path(obj, **kwargs)
 
@@ -537,8 +537,8 @@ def exists(self, obj, **kwargs):
         else:
             return False
 
-    def create(self, obj, **kwargs):
-        if not self.exists(obj, **kwargs):
+    def _create(self, obj, **kwargs):
+        if not self._exists(obj, **kwargs):
 
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
@@ -572,26 +572,26 @@ def create(self, obj, **kwargs):
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
                 self._push_to_os(rel_path, from_string='')
 
-    def empty(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
-            return bool(self.size(obj, **kwargs) > 0)
+    def _empty(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
+            return bool(self._size(obj, **kwargs) > 0)
         else:
             raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
                 return os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s", rel_path, ex)
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             return self._get_size_in_s3(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
         return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         base_dir = kwargs.get('base_dir', None)
@@ -626,10 +626,10 @@ def delete(self, obj, entire_dir=False, **kwargs):
         except S3ResponseError:
             log.exception("Could not delete key '%s' from S3", rel_path)
         except OSError:
-            log.exception('%s delete error', self.get_filename(obj, **kwargs))
+            log.exception('%s delete error', self._get_filename(obj, **kwargs))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         # Check cache first and get file if not there
         if not self._in_cache(rel_path):
@@ -641,7 +641,7 @@ def get_data(self, obj, start=0, count=-1, **kwargs):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
         obj_dir = kwargs.get('obj_dir', False)
@@ -664,7 +664,7 @@ def get_filename(self, obj, **kwargs):
         if self._in_cache(rel_path):
             return cache_path
         # Check if the file exists in persistent storage and, if it does, pull it into cache
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if dir_only:  # Directories do not get pulled into cache
                 return cache_path
             else:
@@ -678,10 +678,10 @@ def get_filename(self, obj, **kwargs):
                              % (str(obj), str(kwargs)))
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         if create:
-            self.create(obj, **kwargs)
-        if self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             # Chose whether to use the dataset file itself or an alternate file
             if file_name:
@@ -703,8 +703,8 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def get_object_url(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             try:
                 key = Key(self._bucket, rel_path)
@@ -713,7 +713,7 @@ def get_object_url(self, obj, **kwargs):
                 log.exception("Trouble generating URL for dataset '%s'", rel_path)
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return 0.0
 
     def shutdown(self):

From 4aa223e0a30265a8c7a2da78a70048dc9aa4867f Mon Sep 17 00:00:00 2001
From: "jalili.vahid@gmail.com" <LetMeIn%#01>
Date: Mon, 23 Mar 2020 19:14:23 -0700
Subject: [PATCH 537/853] Ensure interface methods implemented by
 BaseObjectStore cannot be overridden.

---
 lib/galaxy/objectstore/__init__.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index f826a91c701c..3f200288d64a 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -183,7 +183,18 @@ def get_store_by(self, obj):
         raise NotImplementedError()
 
 
+class NonOverridable(type):
+    def __new__(mcs, name, bases, dct):
+        # The following is a list of methods implemented in BaseObjectStore type, which shall not be overridden.
+        for method in ["exists", "create", "empty", "size", "delete", "get_data", "get_filename",
+                       "update_from_file", "get_object_url", "get_store_usage_percent", "get_store_by"]:
+            if bases and method in dct:
+                raise SyntaxError("Overriding {0} is not allowed".format(method))
+        return type.__new__(mcs, name, bases, dct)
+
+
 class BaseObjectStore(IObjectStore):
+    __metaclass__ = NonOverridable
 
     def __init__(self, config, config_dict=None, **kwargs):
         """

From 01548f714444ed66ccc843d83c78b635fbb681b8 Mon Sep 17 00:00:00 2001
From: "jalili.vahid@gmail.com" <LetMeIn%#01>
Date: Mon, 23 Mar 2020 19:40:04 -0700
Subject: [PATCH 538/853] Add abstractmethod attribute to IObjectStore methods.

---
 lib/galaxy/objectstore/__init__.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index 3f200288d64a..b1e1ae4545a4 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -5,6 +5,7 @@
 tools
 """
 
+import abc
 import logging
 import os
 import random
@@ -39,6 +40,7 @@
 
 
 class IObjectStore(object):
+    __metaclass__ = abc.ABCMeta
 
     """ObjectStore interface.
 
@@ -82,10 +84,12 @@ class IObjectStore(object):
         000/obj.id)
     """
 
+    @abc.abstractmethod
     def exists(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         """Return True if the object identified by `obj` exists, False otherwise."""
         raise NotImplementedError()
 
+    @abc.abstractmethod
     def create(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Mark the object (`obj`) as existing in the store, but with no content.
@@ -95,6 +99,7 @@ def create(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_a
         """
         raise NotImplementedError()
 
+    @abc.abstractmethod
     def empty(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Test if the object identified by `obj` has content.
@@ -103,6 +108,7 @@ def empty(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt
         """
         raise NotImplementedError()
 
+    @abc.abstractmethod
     def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Return size of the object identified by `obj`.
@@ -111,6 +117,7 @@ def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_
         """
         raise NotImplementedError()
 
+    @abc.abstractmethod
     def delete(self, obj, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Delete the object identified by `obj`.
@@ -123,6 +130,7 @@ def delete(self, obj, entire_dir=False, base_dir=None, extra_dir=None, extra_dir
         """
         raise NotImplementedError()
 
+    @abc.abstractmethod
     def get_data(self, obj, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Fetch `count` bytes of data offset by `start` bytes using `obj.id`.
@@ -137,6 +145,7 @@ def get_data(self, obj, start=0, count=-1, base_dir=None, extra_dir=None, extra_
         """
         raise NotImplementedError()
 
+    @abc.abstractmethod
     def get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Get the expected filename with absolute path for object with id `obj.id`.
@@ -145,6 +154,7 @@ def get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra
         """
         raise NotImplementedError()
 
+    @abc.abstractmethod
     def update_from_file(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, file_name=None, create=False):
         """
         Inform the store that the file associated with `obj.id` has been updated.
@@ -163,6 +173,7 @@ def update_from_file(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root
         """
         raise NotImplementedError()
 
+    @abc.abstractmethod
     def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Return the URL for direct acces if supported, otherwise return None.
@@ -171,10 +182,12 @@ def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=
         """
         raise NotImplementedError()
 
+    @abc.abstractmethod
     def get_store_usage_percent(self):
         """Return the percentage indicating how full the store is."""
         raise NotImplementedError()
 
+    @abc.abstractmethod
     def get_store_by(self, obj):
         """Return how object is stored (by 'uuid', 'id', or None if not yet saved).
 

From 9dc85a604d6c7809df271332fbe1726df6027483 Mon Sep 17 00:00:00 2001
From: "jalili.vahid@gmail.com" <LetMeIn%#01>
Date: Mon, 23 Mar 2020 22:00:39 -0700
Subject: [PATCH 539/853] Make obj optional.

---
 lib/galaxy/objectstore/__init__.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index b1e1ae4545a4..52267e9397d6 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -278,8 +278,8 @@ def _get_object_id(self, obj):
             # job working directories.
             return obj.id
 
-    def _invoke(self, delegate, obj, **kwargs):
-        return self.__getattribute__("_" + delegate)(obj, **kwargs)
+    def _invoke(self, delegate, obj=None, **kwargs):
+        return self.__getattribute__("_" + delegate)(obj=obj, **kwargs)
 
     def exists(self, obj, **kwargs):
         return self._invoke('exists', obj, **kwargs)
@@ -308,8 +308,8 @@ def update_from_file(self, obj, **kwargs):
     def get_object_url(self, obj, **kwargs):
         return self._invoke('get_object_url', obj, **kwargs)
 
-    def get_store_usage_percent(self, **kwargs):
-        return self._invoke('get_store_usage_percent', **kwargs)
+    def get_store_usage_percent(self):
+        return self._invoke('get_store_usage_percent')
 
     def get_store_by(self, obj, **kwargs):
         return self._invoke('get_store_by', obj, **kwargs)
@@ -605,7 +605,7 @@ def _get_object_url(self, obj, **kwargs):
         """
         return None
 
-    def _get_store_usage_percent(self):
+    def _get_store_usage_percent(self, **kwargs):
         """Override `ObjectStore`'s stub by return percent storage used."""
         st = os.statvfs(self.file_path)
         return (float(st.f_blocks - st.f_bavail) / st.f_blocks) * 100

From 384f14862f3bb83396277c350fb20f50a0b1c4d8 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 24 Mar 2020 09:18:05 -0400
Subject: [PATCH 540/853] Removed stale commnt

---
 lib/galaxy/objectstore/irods.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index a0fcae9c42f2..26af846bddbe 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -463,7 +463,6 @@ def exists(self, obj, **kwargs):
             else:
                 return False
 
-        # TODO: Sync should probably not be done here. Add this to an async upload stack?
         if in_cache and not in_irods:
             return True
         elif in_irods:

From 6bfcecf375dd5cc7915bd68679fa06b5a031c8aa Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 6 Feb 2020 12:48:49 -0500
Subject: [PATCH 541/853] Added integration test that spins up a Dockerized
 iRODS server, and runs a few tests agianst it.

---
 .../default/pinned-dev-requirements.txt       |   1 +
 lib/galaxy_test/driver/integration_util.py    |   2 +-
 .../irods_beginner_training_2016.pdf          | Bin 0 -> 497249 bytes
 test/integration/objectstore/test_irods.py    | 177 ++++++++++++++++++
 4 files changed, 179 insertions(+), 1 deletion(-)
 create mode 100644 test/integration/objectstore/irods_beginner_training_2016.pdf
 create mode 100644 test/integration/objectstore/test_irods.py

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index 8dffa3ebf0e9..13e8e7864c78 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -44,6 +44,7 @@ pytest-metadata==1.8.0
 pytest-postgresql==1.4.1
 pytest-pythonpath==0.7.3
 pytest==4.6.9
+python-irodsclient==0.8.2
 pytz==2019.3
 recommonmark==0.6.0
 requests==2.23.0
diff --git a/lib/galaxy_test/driver/integration_util.py b/lib/galaxy_test/driver/integration_util.py
index 59e3ef17b860..2e402984cc0b 100644
--- a/lib/galaxy_test/driver/integration_util.py
+++ b/lib/galaxy_test/driver/integration_util.py
@@ -2,7 +2,7 @@
 
 Tests that start an actual Galaxy server with a particular configuration in
 order to test something that cannot be tested with the default functional/api
-tessting configuration.
+testing configuration.
 """
 import os
 from unittest import skip, SkipTest, TestCase
diff --git a/test/integration/objectstore/irods_beginner_training_2016.pdf b/test/integration/objectstore/irods_beginner_training_2016.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..2344e41888a526cb3697b1c1b6c241a7cd974069
GIT binary patch
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diff --git a/test/integration/objectstore/test_irods.py b/test/integration/objectstore/test_irods.py
new file mode 100644
index 000000000000..636b73ee7ed6
--- /dev/null
+++ b/test/integration/objectstore/test_irods.py
@@ -0,0 +1,177 @@
+import os
+import pytest
+import shutil
+import ssl
+import subprocess
+import time
+
+from irods.exception import CollectionDoesNotExist
+from irods.exception import DataObjectDoesNotExist
+from irods.session import iRODSSession
+
+from galaxy_test.driver import integration_util
+
+SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
+
+class IrodsObjectStoreIntegrationTestCase(integration_util.IntegrationTestCase):
+
+    container_name = "irods_server"
+
+    @classmethod
+    def setUpClass(cls):
+        print('Starting setUpClass')
+        super(IrodsObjectStoreIntegrationTestCase, cls).setUpClass()
+        IrodsObjectStoreIntegrationTestCase.start_irods_server(container_name=IrodsObjectStoreIntegrationTestCase.container_name)
+
+        # Let the server start before running the test
+        time.sleep(10)
+        print('Finishing setUpClass')
+
+    @classmethod
+    def tearDownClass(cls): 
+        print('Starting tearDownClass')
+        super(IrodsObjectStoreIntegrationTestCase, cls).tearDownClass()
+        IrodsObjectStoreIntegrationTestCase.stop_irods_server(container_name=IrodsObjectStoreIntegrationTestCase.container_name)       
+        print('Finishing tearDownClass')
+
+    @classmethod
+    def start_irods_server(cls, container_name, postgres_port=5432, irods_port=1247, docker_image='kxk302/irods-server:0.1'):
+        start_server = ['docker', 'run', '-h', 'localhost', '-p', '{port}:5432'.format(port=postgres_port), '-p', '{port}:1247'.format(port=irods_port), '-d', '--name', container_name, docker_image]
+        subprocess.check_call(start_server) 
+        
+    @classmethod
+    def stop_irods_server(cls, container_name):
+        subprocess.check_call(['docker', 'rm', '-f', container_name])
+
+    def test_get_existing_collection(self):
+        with iRODSSession(host='localhost', 
+            port='1247', 
+            user='rods',  
+            password='rods', 
+            zone='tempZone') as session:
+
+            zone='tempZone'
+            user='rods'
+        
+            aCollection = "/" + zone + "/home/" + user
+
+            coll = session.collections.get(aCollection)
+            assert coll.path == aCollection, "Error! Got wrong collection path"
+            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
+            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!"
+
+    def test_create_delete_new_collection(self):
+        with iRODSSession(host='localhost', 
+            port='1247', 
+            user='rods',  
+            password='rods', 
+            zone='tempZone') as session:
+
+            zone='tempZone'
+            user='rods'
+
+            newCollection = "/" + zone + "/home/" + user + "/testdir"
+    
+            coll = session.collections.create(newCollection)
+            assert coll.path == newCollection, "Error! Got wrong collection path"
+            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
+            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!" 
+
+            coll.remove(recurse=True, force=True)
+
+            with pytest.raises(CollectionDoesNotExist):
+                coll = session.collections.get(newCollection)
+
+    def test_create_delete_new_data_object(self):
+        with iRODSSession(host='localhost', 
+            port='1247', 
+            user='rods',  
+            password='rods', 
+            zone='tempZone') as session:
+
+            zone='tempZone'
+            user='rods'
+     
+            newCollection = "/" + zone + "/home/" + user + "/testdir"
+            newDataObject = newCollection + "/testDataObject"
+
+            # Create new collection
+            coll = session.collections.create(newCollection)
+            assert coll.path == newCollection, "Error! Got wrong collection path"
+            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
+            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!"
+
+            # Create data object
+            obj = session.data_objects.create(newDataObject)
+            assert obj.name == "testDataObject", "Error! Got wrong data object"
+
+            # Delete data object
+            obj.unlink(force=True)
+
+            # Get data object
+            with pytest.raises(DataObjectDoesNotExist):
+                obj = session.data_objects.get(newDataObject)
+
+            # Delete collection
+            coll.remove(recurse=True, force=True)
+
+            with pytest.raises(CollectionDoesNotExist):
+                coll = session.collections.get(newCollection)
+
+    def test_populate_fetch_new_data_object(self):
+        with iRODSSession(host='localhost', 
+            port='1247', 
+            user='rods',  
+            password='rods', 
+            zone='tempZone') as session:
+
+            zone='tempZone'
+            user='rods'
+
+            newCollection = "/" + zone + "/home/" + user + "/testdir"
+            fileName = "irods_beginner_training_2016.pdf"
+            fileNamePath = os.path.join(SCRIPT_DIRECTORY, fileName)
+            backupFileName = "irods_beginner_training_2016_backup.pdf"
+            backupFileNamePath = os.path.join(SCRIPT_DIRECTORY, backupFileName)
+ 
+            # Copy file from backup
+            shutil.copyfile(fileNamePath, backupFileNamePath)
+
+            # Create new collection 
+            coll = session.collections.create(newCollection)
+            assert coll.path == newCollection, "Error! Got wrong collection path"
+            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
+            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!" 
+
+            # Create new data object
+            session.data_objects.put(backupFileNamePath, newCollection + "/" + backupFileName)
+    
+            # Delete local file
+            os.remove(backupFileNamePath)         
+    
+            # Get the data object back
+            obj = session.data_objects.get(newCollection + "/" + backupFileName)
+    
+            # Write the data object to the file system
+            with obj.open("r") as f_in, open(backupFileNamePath, "wb") as f_out:
+                f_out.write(f_in.read())
+    
+            # Assert the size of file fetched from iRODS matches the local backup copy
+            assert os.path.getsize(fileNamePath) == os.path.getsize(backupFileNamePath), "Error! Size of file fetched from iRODS does not match the size of the original file" 
+    
+            # Delete local file
+            os.remove(backupFileNamePath)         
+    
+            # Delete data object
+            obj.unlink(force=True)
+    
+            # Get data object
+            with pytest.raises(DataObjectDoesNotExist):
+                obj = session.data_objects.get(newCollection + "/" + backupFileName)
+    
+            # Delete collection
+            coll.remove(recurse=True, force=True)
+    
+            # Get collection
+            with pytest.raises(CollectionDoesNotExist):
+                coll = session.collections.get(newCollection)

From 8725cee995b491767fa5d39f9e973ddddca8a9af Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Wed, 19 Feb 2020 13:53:17 -0500
Subject: [PATCH 542/853] Revised parts of rods.py to use the new iRods Python
 client code. test_datatype_upload.py passes now with iRods as the object
 store.

---
 lib/galaxy/objectstore/rods.py | 985 ++++++++++++++++++++++++---------
 1 file changed, 711 insertions(+), 274 deletions(-)

diff --git a/lib/galaxy/objectstore/rods.py b/lib/galaxy/objectstore/rods.py
index 65114037c16b..872354330f85 100644
--- a/lib/galaxy/objectstore/rods.py
+++ b/lib/galaxy/objectstore/rods.py
@@ -1,20 +1,27 @@
 """
 Object Store plugin for the Integrated Rule-Oriented Data Store (iRODS)
-
-The module is named rods to avoid conflicting with the PyRods module, irods
 """
-
 import logging
+import multiprocessing
 import os
+from pathlib import Path
+import shutil
+import subprocess
+import threading
 import time
+from datetime import datetime
+
 from posixpath import (
     basename as path_basename,
     dirname as path_dirname,
     join as path_join
 )
-
 try:
     import irods
+    import irods.keywords as kw
+    from irods.exception import CollectionDoesNotExist
+    from irods.exception import DataObjectDoesNotExist
+    from irods.session import iRODSSession
 except ImportError:
     irods = None
 
@@ -22,59 +29,275 @@
     ObjectInvalid,
     ObjectNotFound
 )
+from galaxy.util import (
+    directory_hash_id,
+    string_as_bool,
+    umask_fix_perms,
+    which,
+)
 from galaxy.util.path import safe_relpath
+from galaxy.util.sleeper import Sleeper
+from .s3_multipart_upload import multipart_upload
 from ..objectstore import (
     DiskObjectStore,
-    local_extra_dirs
+    local_extra_dirs,
+    convert_bytes
 )
 
-IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this '
-                        'feature, please install it')
+IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this feature, please install it')
 
 log = logging.getLogger(__name__)
 
+def parse_config_xml(config_xml):
+    print('IRODS2: inside parse_config_xml')
+    try:
+        a_xml = config_xml.findall('auth')[0]
+        username = a_xml.get('username')
+        password = a_xml.get('password')
 
-class IRODSObjectStore(DiskObjectStore):
-    """
-    Galaxy object store based on iRODS
-    """
+        b_xml = config_xml.findall('resource')[0]
+        resource_name = b_xml.get('name')
 
-    def __init__(self, config, file_path=None, extra_dirs=None):
-        super(IRODSObjectStore, self).__init__(config, file_path=file_path, extra_dirs=extra_dirs)
-        assert irods is not None, IRODS_IMPORT_MESSAGE
-        self.cache_path = config.object_store_cache_path
-        self.default_resource = config.irods_default_resource or None
+        b_xml = config_xml.findall('zone')[0]
+        zone_name = b_xml.get('name')
 
-        # Connect to iRODS (AssertionErrors will be raised if anything goes wrong)
-        self.rods_env, self.rods_conn = rods_connect()
-
-        # if the root collection path in the config is unset or relative, try to use a sensible default
-        if config.irods_root_collection_path is None or (config.irods_root_collection_path is not None and not config.irods_root_collection_path.startswith('/')):
-            rods_home = self.rods_env.rodsHome
-            assert rods_home != '', "Unable to initialize iRODS Object Store: rodsHome cannot be determined and irods_root_collection_path in Galaxy config is unset or not absolute."
-            if config.irods_root_collection_path is None:
-                self.root_collection_path = path_join(rods_home, 'galaxy_data')
-            else:
-                self.root_collection_path = path_join(rods_home, config.irods_root_collection_path)
+        cn_xml = config_xml.findall('connection')
+        if not cn_xml:
+            cn_xml = {}
         else:
-            self.root_collection_path = config.irods_root_collection_path
-
-        # will return a collection object regardless of whether it exists
-        self.root_collection = irods.irodsCollection(self.rods_conn, self.root_collection_path)
-
-        if self.root_collection.getId() == -1:
-            log.warning("iRODS root collection does not exist, will attempt to create: %s", self.root_collection_path)
-            self.root_collection.upCollection()
-            assert self.root_collection.createCollection(os.path.basename(self.root_collection_path)) == 0, "iRODS root collection creation failed: %s" % self.root_collection_path
-            self.root_collection = irods.irodsCollection(self.rods_conn, self.root_collection_path)
-            assert self.root_collection.getId() != -1, "iRODS root collection creation claimed success but still does not exist"
-
-        if self.default_resource is None:
-            self.default_resource = self.rods_env.rodsDefResource
-
-        log.info("iRODS data for this instance will be stored in collection: %s, resource: %s", self.root_collection_path, self.default_resource)
-
-    def __get_rods_path(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, strip_dat=True, **kwargs):
+            cn_xml = cn_xml[0]
+
+        host = cn_xml.get('host', None)
+        port = int(cn_xml.get('port', 0))
+
+        c_xml = config_xml.findall('cache')[0]
+        cache_size = float(c_xml.get('size', -1))
+        staging_path = c_xml.get('path', None)
+
+        tag, attrs = 'extra_dir', ('type', 'path')
+        extra_dirs = config_xml.findall(tag)
+        if not extra_dirs:
+            msg = 'No {tag} element in XML tree'.format(tag=tag)
+            log.error(msg)
+            raise Exception(msg)
+        extra_dirs = [dict(((k, e.get(k)) for k in attrs)) for e in extra_dirs]
+
+        return {
+            'auth': {
+                'username': username,
+                'password': password,
+            },
+            'resource': {
+                'name': resource_name,
+            },
+            'zone': {
+                'name': zone_name,
+            },
+            'connection': {
+                'host': host,
+                'port': port,
+            },
+            'cache': {
+                'size': cache_size,
+                'path': staging_path,
+            },
+            'extra_dirs': extra_dirs,
+        }
+    except Exception:
+        # Toss it back up after logging, we can't continue loading at this point.
+        log.exception("Malformed iRODS ObjectStore Configuration XML -- unable to continue")
+        raise
+
+class CloudConfigMixin(object):
+
+    def _config_to_dict(self):
+        print('IRODS2: inside _config_to_dict')
+        return {
+            'auth': {
+                'username': self.username,
+                'password': self.password,
+            },
+            'resource': {
+                'name': self.resource,
+            },
+            'zone': {
+                'name': self.zone,
+            },
+            'connection': {
+                'host': self.host,
+                'port': self.port,
+            },
+            'cache': {
+                'size': self.cache_size,
+                'path': self.staging_path,
+            }
+        }
+
+class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
+    """
+    Object store that stores objects as data objects in an iRODS collection. A local cache 
+    exists that is used as an intermediate location for files between Galaxy and iRODS.
+    """
+    
+    store_type = 'irods'
+    
+    #def _get_bucket(self, bucket_name):
+    #def _get_size_in_s3(self, rel_path):
+    #def _key_exists(self, rel_path):
+
+    def __init__(self, config, config_dict):
+        super(IRODSObjectStore, self).__init__(config, config_dict)
+        print('IRODS2: inside __init__')
+
+        auth_dict = config_dict['auth']
+        self.username = auth_dict.get('username')
+        self.password = auth_dict.get('password')
+
+        resource_dict = config_dict['resource']
+        self.resource = resource_dict.get('name')
+
+        zone_dict = config_dict['zone']
+        self.zone = zone_dict.get('name')
+
+        connection_dict = config_dict['connection']
+        self.host = connection_dict.get('host')
+        self.port = connection_dict.get('port')
+
+        cache_dict = config_dict['cache']
+        self.cache_size = cache_dict.get('size', -1)
+        self.staging_path = cache_dict.get('path') or self.config.object_store_cache_path
+
+        extra_dirs = dict((e['type'], e['path']) for e in config_dict.get('extra_dirs', []))
+        self.extra_dirs.update(extra_dirs)
+
+        log.debug("Object cache dir: %s", self.staging_path)
+        log.debug("Job work dir: %s", self.extra_dirs['job_work'])
+
+        self._initialize()
+        
+    def __del__(self):
+        print('IRODS2: inside __del__')
+        self.session.cleanup()
+
+    def _initialize(self):
+        if irods is None:
+            raise Exception(IRODS_IMPORT_MESSAGE)
+
+        self.home =  "/" + self.zone + "/home/" + self.username
+
+        self.session = self._configure_connection()
+        #self.bucket = self._get_bucket(self.bucket)
+        # Clean cache only if value is set in galaxy.ini
+        if self.cache_size != -1:
+            # Convert GBs to bytes for comparison
+            self.cache_size = self.cache_size * 1073741824
+            # Helper for interruptable sleep
+            self.sleeper = Sleeper()
+            self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
+            self.cache_monitor_thread.start()
+            log.info("Cache cleaner manager started")
+        # Test if 'axel' is available for parallel download and pull the key into cache
+        if which('axel'):
+            self.use_axel = True
+        else:
+            self.use_axel = False
+
+    def _configure_connection(self, host='localhost', port='1247', user='rods', password='rods', zone='tempZone'):
+         with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
+            ###assert session.pool.get_connection() == 1, 'Failed to establish iRODS session'
+            print('IRODS2: inside iRODSSession')
+            return session
+
+    @classmethod
+    def parse_xml(cls, config_xml):
+        print('IRODS2: inside parse_xml')
+        return parse_config_xml(config_xml)
+
+    def to_dict(self):
+        print('IRODS: inside to_dict') 
+        as_dict = super(IRODSObjectStore, self).to_dict()
+        as_dict.update(self._config_to_dict())
+        return as_dict
+
+    def __cache_monitor(self):
+        time.sleep(2)  # Wait for things to load before starting the monitor
+        while self.running:
+            total_size = 0
+            # Is this going to be too expensive of an operation to be done frequently?
+            file_list = []
+            for dirpath, _, filenames in os.walk(self.staging_path):
+                for filename in filenames:
+                    filepath = os.path.join(dirpath, filename)
+                    file_size = os.path.getsize(filepath)
+                    total_size += file_size
+                    # Get the time given file was last accessed
+                    last_access_time = time.localtime(os.stat(filepath)[7])
+                    # Compose a tuple of the access time and the file path
+                    file_tuple = last_access_time, filepath, file_size
+                    file_list.append(file_tuple)
+            # Sort the file list (based on access time)
+            file_list.sort()
+            # Initiate cleaning once within 10% of the defined cache size?
+            cache_limit = self.cache_size * 0.9
+            if total_size > cache_limit:
+                log.info("Initiating cache cleaning: current cache size: %s; clean until smaller than: %s",
+                         convert_bytes(total_size), convert_bytes(cache_limit))
+                # How much to delete? If simply deleting up to the cache-10% limit,
+                # is likely to be deleting frequently and may run the risk of hitting
+                # the limit - maybe delete additional #%?
+                # For now, delete enough to leave at least 10% of the total cache free
+                delete_this_much = total_size - cache_limit
+                self.__clean_cache(file_list, delete_this_much)
+            self.sleeper.sleep(30)  # Test cache size every 30 seconds?
+
+    def __clean_cache(self, file_list, delete_this_much):
+        """ Keep deleting files from the file_list until the size of the deleted
+        files is greater than the value in delete_this_much parameter.
+
+        :type file_list: list
+        :param file_list: List of candidate files that can be deleted. This method
+            will start deleting files from the beginning of the list so the list
+            should be sorted accordingly. The list must contains 3-element tuples,
+            positioned as follows: position 0 holds file last accessed timestamp
+            (as time.struct_time), position 1 holds file path, and position 2 has
+            file size (e.g., (<access time>, /mnt/data/dataset_1.dat), 472394)
+
+        :type delete_this_much: int
+        :param delete_this_much: Total size of files, in bytes, that should be deleted.
+        """
+        # Keep deleting datasets from file_list until deleted_amount does not
+        # exceed delete_this_much; start deleting from the front of the file list,
+        # which assumes the oldest files come first on the list.
+        deleted_amount = 0
+        for entry in file_list:
+            if deleted_amount < delete_this_much:
+                deleted_amount += entry[2]
+                os.remove(entry[1])
+                # Debugging code for printing deleted files' stats
+                # folder, file_name = os.path.split(f[1])
+                # file_date = time.strftime("%m/%d/%y %H:%M:%S", f[0])
+                # log.debug("%s. %-25s %s, size %s (deleted %s/%s)" \
+                #     % (i, file_name, convert_bytes(f[2]), file_date, \
+                #     convert_bytes(deleted_amount), convert_bytes(delete_this_much)))
+            else:
+                log.debug("Cache cleaning done. Total space freed: %s", convert_bytes(deleted_amount))
+                return
+
+   # def _get_bucket(self, bucket_name):
+
+    def _fix_permissions(self, rel_path):
+        """ Set permissions on rel_path"""
+        for basedir, _, files in os.walk(rel_path):
+            umask_fix_perms(basedir, self.config.umask, 0o777, self.config.gid)
+            for filename in files:
+                path = os.path.join(basedir, filename)
+                # Ignore symlinks
+                if os.path.islink(path):
+                    continue
+                umask_fix_perms(path, self.config.umask, 0o666, self.config.gid)
+
+    def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs):
+        print('************* Entering _construct_path **************')
         # extra_dir should never be constructed from provided data but just
         # make sure there are no shenannigans afoot
         if extra_dir and extra_dir != os.path.normpath(extra_dir):
@@ -86,270 +309,484 @@ def __get_rods_path(self, obj, base_dir=None, dir_only=False, extra_dir=None, ex
             if not safe_relpath(alt_name):
                 log.warning('alt_name would locate path outside dir: %s', alt_name)
                 raise ObjectInvalid("The requested object is invalid")
-            # alt_name can contain parent directory references, but iRODS will
-            # not follow them, so if they are valid we normalize them out
+            # alt_name can contain parent directory references, but S3 will not
+            # follow them, so if they are valid we normalize them out
             alt_name = os.path.normpath(alt_name)
-        path = ""
+        rel_path = os.path.join(*directory_hash_id(obj.id))
+        print('obj.id: ', obj.id)
+        print('rel_path: ', rel_path)
         if extra_dir is not None:
-            path = extra_dir
+            if extra_dir_at_root:
+                rel_path = os.path.join(extra_dir, rel_path)
+                print('rel_path: ', rel_path)
+            else:
+                rel_path = os.path.join(rel_path, extra_dir)
+                print('rel_path: ', rel_path)
 
-        # extra_dir_at_root is ignored - since the iRODS plugin does not use
-        # the directory hash, there is only one level of subdirectory.
+        # for JOB_WORK directory
+        if obj_dir:
+            rel_path = os.path.join(rel_path, str(obj.id))
+        if base_dir:
+            base = self.extra_dirs.get(base_dir)
+            print('************* Exiting 1 _construct_path **************')
+            return os.path.join(base, rel_path)
+
+        # S3 folders are marked by having trailing '/' so add it now
+        ###rel_path = '%s/' % rel_path
 
         if not dir_only:
-            # the .dat extension is stripped when stored in iRODS
-            # TODO: is the strip_dat kwarg the best way to implement this?
-            if strip_dat and alt_name and alt_name.endswith('.dat'):
-                alt_name = os.path.splitext(alt_name)[0]
-            default_name = 'dataset_%s' % obj.id
-            if not strip_dat:
-                default_name += '.dat'
-            path = path_join(path, alt_name if alt_name else default_name)
-
-        path = path_join(self.root_collection_path, path)
-        return path
-
-    def __get_cache_path(self, obj, **kwargs):
-        # FIXME: does not handle collections
-        # FIXME: collisions could occur here
-        return os.path.join(self.cache_path, path_basename(self.__get_rods_path(obj, strip_dat=False, **kwargs)))
-
-    def __clean_cache_entry(self, obj, **kwargs):
-        # FIXME: does not handle collections
+            rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
+        print('************* Exiting 2 _construct_path **************')
+        return rel_path
+
+    def _get_cache_path(self, rel_path):
+        return os.path.abspath(os.path.join(self.staging_path, rel_path))
+
+    #def _get_transfer_progress(self):
+    #    return self.transfer_progress
+
+    #def _get_size_in_s3(self, rel_path):
+
+    def _get_size_in_irods(self, rel_path):
+        '''
         try:
-            os.unlink(self.__get_cache_path(obj, **kwargs))
-        except OSError:
-            # it is expected that we'll call this method a lot regardless of
-            # whether we think the cached file exists
-            pass
+            key = self.bucket.get_key(rel_path)
+            if key:
+                return key.size
+        except S3ResponseError:
+            log.exception("Could not get size of key '%s' from S3", rel_path)
+            return -1
+        '''
+
+    def _data_object_exists(self, rel_path):
+        exists = False
+        try:
+            # A hackish way of testing if the rel_path is a folder vs a file
+            is_dir = rel_path[-1] == '/'
+            if is_dir:
+                keyresult = self.bucket.get_all_keys(prefix=rel_path)
+                if len(keyresult) > 0:
+                    exists = True
+                else:
+                    exists = False
+            else:
+                key = Key(self.bucket, rel_path)
+                exists = key.exists()
+        except S3ResponseError:
+            log.exception("Trouble checking existence of S3 key '%s'", rel_path)
+            return False
+        if rel_path[0] == '/':
+            raise
+        return exists
+
+    def _in_cache(self, rel_path):
+        """ Check if the given dataset is in the local cache and return True if so. """
+        # log.debug("------ Checking cache for rel_path %s" % rel_path)
+        print('*************** Entering _in_cache() *****************')
+        cache_path = self._get_cache_path(rel_path)
+        print('cache_path: ', cache_path)
+        print('os.path.exists: ', os.path.exists(cache_path))
+        print('*************** Exiting _in_cache() *****************')
+        return os.path.exists(cache_path)
+        # TODO: Part of checking if a file is in cache should be to ensure the
+        # size of the cached file matches that on S3. Once the upload tool explicitly
+        # creates, this check sould be implemented- in the mean time, it's not
+        # looking likely to be implementable reliably.
+        # if os.path.exists(cache_path):
+        #     # print("***1 %s exists" % cache_path)
+        #     if self._key_exists(rel_path):
+        #         # print("***2 %s exists in S3" % rel_path)
+        #         # Make sure the size in cache is available in its entirety
+        #         # print("File '%s' cache size: %s, S3 size: %s" % (cache_path, os.path.getsize(cache_path), self._get_size_in_s3(rel_path)))
+        #         if os.path.getsize(cache_path) == self._get_size_in_s3(rel_path):
+        #             # print("***2.1 %s exists in S3 and the size is the same as in cache (in_cache=True)" % rel_path)
+        #             exists = True
+        #         else:
+        #             # print("***2.2 %s exists but differs in size from cache (in_cache=False)" % cache_path)
+        #             exists = False
+        #     else:
+        #         # Although not perfect decision making, this most likely means
+        #         # that the file is currently being uploaded
+        #         # print("***3 %s found in cache but not in S3 (in_cache=True)" % cache_path)
+        #         exists = True
+        # else:
+
+    def _pull_into_cache(self, rel_path):
+        # Ensure the cache directory structure exists (e.g., dataset_#_files/)
+        rel_path_dir = os.path.dirname(rel_path)
+        if not os.path.exists(self._get_cache_path(rel_path_dir)):
+            os.makedirs(self._get_cache_path(rel_path_dir))
+        # Now pull in the file
+        file_ok = self._download(rel_path)
+        self._fix_permissions(self._get_cache_path(rel_path_dir))
+        return file_ok
+
+    #def _transfer_cb(self, complete, total):
+    #    self.transfer_progress += 10
+
+    def _download(self, rel_path):
+        try:
+            log.debug("Pulling key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
+            key = self.bucket.get_key(rel_path)
+            # Test if cache is large enough to hold the new file
+            if self.cache_size > 0 and key.size > self.cache_size:
+                log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
+                             rel_path, key.size, self.cache_size)
+                return False
+            if self.use_axel:
+                log.debug("Parallel pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
+                ncores = multiprocessing.cpu_count()
+                url = key.generate_url(7200)
+                ret_code = subprocess.call(['axel', '-a', '-n', ncores, url])
+                if ret_code == 0:
+                    return True
+            else:
+                log.debug("Pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
+                self.transfer_progress = 0  # Reset transfer progress counter
+                key.get_contents_to_filename(self._get_cache_path(rel_path), cb=self._transfer_cb, num_cb=10)
+                return True
+        except S3ResponseError:
+            log.exception("Problem downloading key '%s' from S3 bucket '%s'", rel_path, self.bucket.name)
+        return False
 
-    def __get_rods_handle(self, obj, mode='r', **kwargs):
-        if kwargs.get('dir_only', False):
-            return irods.irodsCollection(self.rods_conn, self.__get_rods_path(obj, **kwargs))
+    def _push_to_os(self, rel_path, source_file=None, from_string=None):
+        """
+        Push the file pointed to by ``rel_path`` to the iRODS. Extract folder name 
+        from rel_path as iRODS collection name, and extract file name from rel_path
+        as iRODS data object name.
+        If ``source_file`` is provided, push that file instead while
+        still using ``rel_path`` for collection and object tore names.
+        If ``from_string`` is provided, set contents of the file to the value of
+        the string.
+        """
+        print('**** Entering _push_to_os ****')
+        print('IRODS: rel_path: ', rel_path)
+        p = Path(rel_path)
+        print('p: ', p)
+        print('p.parent: ', p.parent)
+        print('p.stem: ', p.stem)
+        print('p.suffix: ', p.suffix)
+
+        data_object =  p.stem + p.suffix
+        subcollection = p.parent
+        print('data_object: ', data_object)
+        print('subcollection: ', subcollection)
+
+        source_file = source_file if source_file else self._get_cache_path(rel_path)
+        print('IRODS: source_file: ', source_file)
+
+        options = {kw.FORCE_FLAG_KW: ''}
+
+        if os.path.exists(source_file):
+            # Check if the data object exists in iRODS
+            subcollection_path = self.home + "/" + str(subcollection)
+            full_irods_path = subcollection_path + "/" + str(data_object) 
+            print('full_irods_path: ', full_irods_path)
+            exists = self.session.data_objects.exists(full_irods_path)
+            if os.path.getsize(source_file) == 0 and exists:
+                log.debug("Wanted to push file '%s' to iRODS collection '%s' but its size is 0; skipping.", source_file, rel_path)
+                print('**** Exiting 1 _push_to_os ****')
+                return True
+            if from_string:
+                data_obj = self.session.data_objects.create(full_irods_path, recurse=True, **options)
+                with data_obj.open('w') as data_obj_fp:
+                    data_obj_fp.write(from_string)
+                log.debug("Pushed data from string '%s' to collection '%s'", from_string, full_irods_path)
+            else:
+                start_time = datetime.now()
+                log.debug("Pushing cache file '%s' of size %s bytes to collection '%s'", source_file, os.path.getsize(source_file), rel_path)
+                
+                # Create sub-collection first
+                self.session.collections.create(subcollection_path)
+
+                file_content = None
+                with open(source_file, 'rb') as content_file:
+                    file_content = content_file.read()
+                
+                # Write to file in subcollection created above
+                data_obj = self.session.data_objects.create(full_irods_path, recurse=True, **options)
+                with data_obj.open('w') as data_obj_fp:
+                    data_obj_fp.write(file_content)
+
+                end_time = datetime.now()
+                log.debug("Pushed cache file '%s' to collection '%s' (%s bytes transfered in %s sec)",
+                          source_file, rel_path, os.path.getsize(source_file), end_time - start_time)
+            print('**** Exiting 2 _push_to_os ****')
+            return True
         else:
-            return irods.irodsOpen(self.rods_conn, self.__get_rods_path(obj, **kwargs), mode)
+            log.error("Tried updating key '%s' from source file '%s', but source file does not exist.",
+                      rel_path, source_file)
+
+        print('**** Exiting 3 _push_to_os ****')
+        return False
 
-    def __mkcolls(self, rods_path):
+    def file_ready(self, obj, **kwargs):
         """
-        An os.makedirs() for iRODS collections.  `rods_path` is the desired collection to create.
+        A helper method that checks if a file corresponding to a dataset is
+        ready and available to be used. Return ``True`` if so, ``False`` otherwise.
         """
-        assert rods_path.startswith(self.root_collection_path + '/'), '__mkcolls(): Creating collections outside the root collection is not allowed (requested path was: %s)' % rods_path
-        mkcolls = []
-        c = irods.irodsCollection(self.rods_conn, rods_path)
-        while c.getId() == -1:
-            assert c.getCollName().startswith(self.root_collection_path + '/'), '__mkcolls(): Attempted to move above the root collection: %s' % c.getCollName()
-            mkcolls.append(c.getCollName())
-            c.upCollection()
-        for collname in reversed(mkcolls):
-            log.debug('Creating collection %s' % collname)
-            ci = irods.collInp_t()
-            ci.collName = collname
-            status = irods.rcCollCreate(self.rods_conn, ci)
-            assert status == 0, '__mkcolls(): Failed to create collection: %s' % collname
-
-    @local_extra_dirs
+        rel_path = self._construct_path(obj, **kwargs)
+        # Make sure the size in cache is available in its entirety
+        if self._in_cache(rel_path):
+            if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_s3(rel_path):
+                return True
+            log.debug("Waiting for dataset %s to transfer from OS: %s/%s", rel_path,
+                      os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_s3(rel_path))
+        return False
+
     def exists(self, obj, **kwargs):
-        doi = irods.dataObjInp_t()
-        doi.objPath = self.__get_rods_path(obj, **kwargs)
-        log.debug('exists(): checking: %s', doi.objPath)
-        return irods.rcObjStat(self.rods_conn, doi) is not None
+        print('*************Entering exists()*************')
+        in_cache = in_irods = False
+        for key, value in kwargs.items():
+            print("The value of {} is {}".format(key, value))
+        rel_path = self._construct_path(obj, **kwargs)
+        print('rel_path: ', rel_path)
+
+        # Check cache
+        if self._in_cache(rel_path):
+            in_cache = True
+        # Check iRODS 
+        ###in_irods = self._data_object_exists(rel_path)
+
+        # dir_only does not get synced so shortcut the decision
+        dir_only = kwargs.get('dir_only', False)
+        base_dir = kwargs.get('base_dir', None)
+        if dir_only:
+            if in_cache or in_irods:
+                print('*************Exiting  1 exists()*************')
+                return True
+            # for JOB_WORK directory
+            elif base_dir:
+                if not os.path.exists(rel_path):
+                    os.makedirs(rel_path)
+                print('*************Exiting  2 exists()*************')
+                return True
+            else:
+                print('*************Exiting  3 exists()*************')
+                return False
+
+        # TODO: Sync should probably not be done here. Add this to an async upload stack?
+        if in_cache and not in_irods:
+            self._push_to_os(rel_path, source_file=self._get_cache_path(rel_path))
+            print('*************Exiting  4 exists()*************')
+            return True
+        elif in_irods:
+            print('*************Exiting  5 exists()*************')
+            return True
+        else:
+            print('*************Exiting  6 exists()*************')
+            return False
 
-    @local_extra_dirs
     def create(self, obj, **kwargs):
         if not self.exists(obj, **kwargs):
-            rods_path = self.__get_rods_path(obj, **kwargs)
-            log.debug('create(): %s', rods_path)
+
+            # Pull out locally used fields
+            extra_dir = kwargs.get('extra_dir', None)
+            extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
             dir_only = kwargs.get('dir_only', False)
-            # short circuit collection creation since most of the time it will
-            # be the root collection which already exists
-            collection_path = rods_path if dir_only else path_dirname(rods_path)
-            if collection_path != self.root_collection_path:
-                self.__mkcolls(collection_path)
+            alt_name = kwargs.get('alt_name', None)
+
+            # Construct hashed path
+            rel_path = os.path.join(*directory_hash_id(obj.id))
+
+            # Optionally append extra_dir
+            if extra_dir is not None:
+                if extra_dir_at_root:
+                    rel_path = os.path.join(extra_dir, rel_path)
+                else:
+                    rel_path = os.path.join(rel_path, extra_dir)
+
+            # Create given directory in cache
+            cache_dir = os.path.join(self.staging_path, rel_path)
+            if not os.path.exists(cache_dir):
+                os.makedirs(cache_dir)
+
+            # Although not really necessary to create S3 folders (because S3 has
+            # flat namespace), do so for consistency with the regular file system
+            # S3 folders are marked by having trailing '/' so add it now
+            # s3_dir = '%s/' % rel_path
+            # self._push_to_os(s3_dir, from_string='')
+            # If instructed, create the dataset in cache & in S3
             if not dir_only:
-                # rcDataObjCreate is used instead of the irodsOpen wrapper so
-                # that we can prevent overwriting
-                doi = irods.dataObjInp_t()
-                doi.objPath = rods_path
-                doi.createMode = 0o640
-                doi.dataSize = 0  # 0 actually means "unknown", although literally 0 would be preferable
-                irods.addKeyVal(doi.condInput, irods.DEST_RESC_NAME_KW, self.default_resource)
-                status = irods.rcDataObjCreate(self.rods_conn, doi)
-                assert status >= 0, 'create(): rcDataObjCreate() failed: %s: %s: %s' % (rods_path, status, irods.strerror(status))
-
-    @local_extra_dirs
+                rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
+                open(os.path.join(self.staging_path, rel_path), 'w').close()
+                self._push_to_os(rel_path, from_string='')
+
     def empty(self, obj, **kwargs):
-        assert 'dir_only' not in kwargs, 'empty(): `dir_only` parameter is invalid here'
-        h = self.__get_rods_handle(obj, **kwargs)
-        try:
-            return h.getSize() == 0
-        except AttributeError:
-            # h is None
-            raise ObjectNotFound()
+        if self.exists(obj, **kwargs):
+            return bool(self.size(obj, **kwargs) > 0)
+        else:
+            raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
+                                 % (str(obj), str(kwargs)))
 
     def size(self, obj, **kwargs):
-        assert 'dir_only' not in kwargs, 'size(): `dir_only` parameter is invalid here'
-        h = self.__get_rods_handle(obj, **kwargs)
-        try:
-            return h.getSize()
-        except AttributeError:
-            # h is None
-            return 0
+        print('*************** Entering size ****************')
+        rel_path = self._construct_path(obj, **kwargs)
+        if self._in_cache(rel_path):
+            try:
+                print('*************** Exiting 1 size ****************')
+                return os.path.getsize(self._get_cache_path(rel_path))
+            except OSError as ex:
+                log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s", rel_path, ex)
+        elif self.exists(obj, **kwargs):
+            print('*************** Exiting 2 size ****************')
+            ## 
+            ## TODO
+            ## 
+            return self._get_size_in_s3(rel_path)
+        log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
+        print('*************** Exiting 3 size ****************')
+        return 0
 
-    @local_extra_dirs
     def delete(self, obj, entire_dir=False, **kwargs):
-        assert 'dir_only' not in kwargs, 'delete(): `dir_only` parameter is invalid here'
-        rods_path = self.__get_rods_path(obj, **kwargs)
-        # __get_rods_path prepends self.root_collection_path but we are going
-        # to ensure that it's valid anyway for safety's sake
-        assert rods_path.startswith(self.root_collection_path + '/'), 'ERROR: attempt to delete object outside root collection (path was: %s)' % rods_path
-        if entire_dir:
-            # TODO
-            raise NotImplementedError()
-        h = self.__get_rods_handle(obj, **kwargs)
+        rel_path = self._construct_path(obj, **kwargs)
+        extra_dir = kwargs.get('extra_dir', None)
+        base_dir = kwargs.get('base_dir', None)
+        dir_only = kwargs.get('dir_only', False)
+        obj_dir = kwargs.get('obj_dir', False)
         try:
-            # note: PyRods' irodsFile.delete() does not set force
-            status = h.delete()
-            assert status == 0, '%d: %s' % (status, irods.strerror(status))
-            return True
-        except AttributeError:
-            log.warning('delete(): operation failed: object does not exist: %s', rods_path)
-        except AssertionError as e:
-            # delete() does not raise on deletion failure
-            log.error('delete(): operation failed: %s', e)
-        finally:
-            # remove the cached entry (finally is executed even when the try
-            # contains a return)
-            self.__clean_cache_entry(self, obj, **kwargs)
+            # Remove temparory data in JOB_WORK directory
+            if base_dir and dir_only and obj_dir:
+                shutil.rmtree(os.path.abspath(rel_path))
+                return True
+
+            # For the case of extra_files, because we don't have a reference to
+            # individual files/keys we need to remove the entire directory structure
+            # with all the files in it. This is easy for the local file system,
+            # but requires iterating through each individual key in S3 and deleing it.
+            if entire_dir and extra_dir:
+                shutil.rmtree(self._get_cache_path(rel_path))
+                results = self.bucket.get_all_keys(prefix=rel_path)
+                for key in results:
+                    log.debug("Deleting key %s", key.name)
+                    key.delete()
+                return True
+            else:
+                # Delete from cache first
+                os.unlink(self._get_cache_path(rel_path))
+                # Delete from S3 as well
+                if self._key_exists(rel_path):
+                    key = Key(self.bucket, rel_path)
+                    log.debug("Deleting key %s", key.name)
+                    key.delete()
+                    return True
+        except S3ResponseError:
+            log.exception("Could not delete key '%s' from S3", rel_path)
+        except OSError:
+            log.exception('%s delete error', self.get_filename(obj, **kwargs))
         return False
 
-    @local_extra_dirs
     def get_data(self, obj, start=0, count=-1, **kwargs):
-        log.debug('get_data(): %s')
-        h = self.__get_rods_handle(obj, **kwargs)
-        try:
-            h.seek(start)
-        except AttributeError:
-            raise ObjectNotFound()
-        if count == -1:
-            return h.read()
-        else:
-            return h.read(count)
-        # TODO: make sure implicit close is okay, DiskObjectStore actually
-        # reads data into a var, closes, and returns the var
+        rel_path = self._construct_path(obj, **kwargs)
+        # Check cache first and get file if not there
+        if not self._in_cache(rel_path):
+            self._pull_into_cache(rel_path)
+        # Read the file content from cache
+        data_file = open(self._get_cache_path(rel_path), 'r')
+        data_file.seek(start)
+        content = data_file.read(count)
+        data_file.close()
+        return content
 
-    @local_extra_dirs
     def get_filename(self, obj, **kwargs):
-        log.debug("get_filename(): called on %s %s. For better performance, avoid this method and use get_data() instead.", obj.__class__.__name__, obj.id)
-        cached_path = self.__get_cache_path(obj, **kwargs)
+        base_dir = kwargs.get('base_dir', None)
+        dir_only = kwargs.get('dir_only', False)
+        obj_dir = kwargs.get('obj_dir', False)
+        rel_path = self._construct_path(obj, **kwargs)
+
+        # for JOB_WORK directory
+        if base_dir and dir_only and obj_dir:
+            return os.path.abspath(rel_path)
+
+        cache_path = self._get_cache_path(rel_path)
+        # S3 does not recognize directories as files so cannot check if those exist.
+        # So, if checking dir only, ensure given dir exists in cache and return
+        # the expected cache path.
+        # dir_only = kwargs.get('dir_only', False)
+        # if dir_only:
+        #     if not os.path.exists(cache_path):
+        #         os.makedirs(cache_path)
+        #     return cache_path
+        # Check if the file exists in the cache first
+        if self._in_cache(rel_path):
+            return cache_path
+        # Check if the file exists in persistent storage and, if it does, pull it into cache
+        elif self.exists(obj, **kwargs):
+            if dir_only:  # Directories do not get pulled into cache
+                return cache_path
+            else:
+                if self._pull_into_cache(rel_path):
+                    return cache_path
+        # For the case of retrieving a directory only, return the expected path
+        # even if it does not exist.
+        # if dir_only:
+        #     return cache_path
+        raise ObjectNotFound('objectstore.get_filename, no cache_path: %s, kwargs: %s'
+                             % (str(obj), str(kwargs)))
+        # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
-        if not self.exists(obj, **kwargs):
-            raise ObjectNotFound()
-
-        # TODO: implement or define whether dir_only is valid
-        if 'dir_only' in kwargs:
-            raise NotImplementedError()
-
-        # cache hit
-        if os.path.exists(cached_path):
-            return os.path.abspath(cached_path)
-
-        # cache miss
-        # TODO: thread this
-        incoming_path = os.path.join(os.path.dirname(cached_path), "__incoming_%s" % os.path.basename(cached_path))
-        doi = irods.dataObjInp_t()
-        doi.objPath = self.__get_rods_path(obj, **kwargs)
-        doi.dataSize = 0  # TODO: does this affect performance? should we get size?
-        doi.numThreads = 0
-        # TODO: might want to VERIFY_CHKSUM_KW
-        log.debug('get_filename(): caching %s to %s', doi.objPath, incoming_path)
-
-        # do the iget
-        status = irods.rcDataObjGet(self.rods_conn, doi, incoming_path)
-
-        # if incoming already exists, we'll wait for another process or thread
-        # to finish caching
-        if status != irods.OVERWRITE_WITHOUT_FORCE_FLAG:
-            assert status == 0, 'get_filename(): iget %s failed (%s): %s' % (doi.objPath, status, irods.strerror(status))
-            # POSIX rename is atomic
-            # TODO: rename without clobbering
-            os.rename(incoming_path, cached_path)
-            log.debug('get_filename(): cached %s to %s', doi.objPath, cached_path)
-
-        # another process or thread is caching, wait for it
-        while not os.path.exists(cached_path):
-            # TODO: force restart after mod time > some configurable, or
-            # otherwise deal with this potential deadlock and interrupted
-            # transfers
-            time.sleep(5)
-            log.debug("get_filename(): waiting on incoming '%s' for %s %s", incoming_path, obj.__class__.__name__, obj.id)
-
-        return os.path.abspath(cached_path)
-
-    @local_extra_dirs
     def update_from_file(self, obj, file_name=None, create=False, **kwargs):
-        assert 'dir_only' not in kwargs, 'update_from_file(): `dir_only` parameter is invalid here'
-
-        # do not create if not requested
-        if create and not self.exists(obj, **kwargs):
-            raise ObjectNotFound()
-
-        if file_name is None:
-            file_name = self.__get_cache_path(obj, **kwargs)
-
-        # put will create if necessary
-        doi = irods.dataObjInp_t()
-        doi.objPath = self.__get_rods_path(obj, **kwargs)
-        doi.createMode = 0o640
-        doi.dataSize = os.stat(file_name).st_size
-        doi.numThreads = 0
-        irods.addKeyVal(doi.condInput, irods.DEST_RESC_NAME_KW, self.default_resource)
-        irods.addKeyVal(doi.condInput, irods.FORCE_FLAG_KW, '')
-        # TODO: might want to VERIFY_CHKSUM_KW
-        log.debug('update_from_file(): updating %s to %s', file_name, doi.objPath)
-
-        # do the iput
-        status = irods.rcDataObjPut(self.rods_conn, doi, file_name)
-        assert status == 0, 'update_from_file(): iput %s failed (%s): %s' % (doi.objPath, status, irods.strerror(status))
+        if create:
+            self.create(obj, **kwargs)
+        if self.exists(obj, **kwargs):
+            rel_path = self._construct_path(obj, **kwargs)
+            # Chose whether to use the dataset file itself or an alternate file
+            if file_name:
+                source_file = os.path.abspath(file_name)
+                # Copy into cache
+                cache_file = self._get_cache_path(rel_path)
+                try:
+                    if source_file != cache_file:
+                        # FIXME? Should this be a `move`?
+                        shutil.copy2(source_file, cache_file)
+                    self._fix_permissions(cache_file)
+                except OSError:
+                    log.exception("Trouble copying source file '%s' to cache '%s'", source_file, cache_file)
+            else:
+                source_file = self._get_cache_path(rel_path)
+            # Update the file on S3
+            self._push_to_os(rel_path, source_file)
+        else:
+            raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
+                                 % (str(obj), str(kwargs)))
 
     def get_object_url(self, obj, **kwargs):
+        if self.exists(obj, **kwargs):
+            rel_path = self._construct_path(obj, **kwargs)
+            try:
+                key = Key(self.bucket, rel_path)
+                return key.generate_url(expires_in=86400)  # 24hrs
+            except S3ResponseError:
+                log.exception("Trouble generating URL for dataset '%s'", rel_path)
         return None
 
     def get_store_usage_percent(self):
         return 0.0
 
+'''
+        ###########################################################        
+        ## These should be read from env variables or a config file
+        ###########################################################        
+        # host='localhost' 
+        host='127.0.0.1' 
+        port='1247' 
+        user='rods'  
+        password='rods' 
+        zone='tempZone'
+        ###defaultResource = 'demoResc'
 
-# monkeypatch an strerror method into the irods module
-def _rods_strerror(errno):
-    """
-    The missing `strerror` for iRODS error codes
-    """
-    if not hasattr(irods, '__rods_strerror_map'):
-        irods.__rods_strerror_map = {}
-        for name in dir(irods):
-            v = getattr(irods, name)
-            if type(v) == int and v < 0:
-                irods.__rods_strerror_map[v] = name
-    return irods.__rods_strerror_map.get(errno, 'GALAXY_NO_ERRNO_MAPPING_FOUND')
-
-
-if irods is not None:
-    irods.strerror = _rods_strerror
-
-
-def rods_connect():
-    """
-    A basic iRODS connection mechanism that connects using the current iRODS
-    environment
-    """
-    status, env = irods.getRodsEnv()
-    assert status == 0, 'connect(): getRodsEnv() failed (%s): %s' % (status, irods.strerror(status))
-    conn, err = irods.rcConnect(env.rodsHost,
-                                env.rodsPort,
-                                env.rodsUserName,
-                                env.rodsZone)
-    assert err.status == 0, 'connect(): rcConnect() failed (%s): %s' % (err.status, err.msg)
-    status, pw = irods.obfGetPw()
-    assert status == 0, 'connect(): getting password with obfGetPw() failed (%s): %s' % (status, irods.strerror(status))
-    status = irods.clientLoginWithObfPassword(conn, pw)
-    assert status == 0, 'connect(): logging in with clientLoginWithObfPassword() failed (%s): %s' % (status, irods.strerror(status))
-    return env, conn
+        # Connect to iRODS (AssertionErrors will be raised if anything goes wrong)
+        self.session = irods_connect(host, port, user, password, zone)
+
+        # Set iRODS home path
+        ###self.home_path = "/" + zone + "/home/" + user + '/galaxy_data'
+        self.home_path = "/" + zone + "/home/" + user
+        assert self.home_path != '', "Unable to initialize iRODS Object Store: irods_home cannot be determined."
+
+        # Will return a collection object regardless of whether it exists
+        self.root_collection = self.session.collections.get(self.home_path)
+        if self.root_collection.path != self.home_path:
+            log.warning("iRODS root collection does not exist, will attempt to create: %s", self.home_path)
+            self.root_collection = self.session.collections.create(self.home_path)
+            assert self.root_collection.path == self.home_path, "iRODS root collection creation failed: %s" % self.home_path
+'''
\ No newline at end of file

From 638030093e6cb830d25f031216498334e359f15d Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 20 Feb 2020 16:33:39 -0500
Subject: [PATCH 543/853] More revision to rods.py

---
 lib/galaxy/objectstore/rods.py | 305 ++++++++++++---------------------
 1 file changed, 105 insertions(+), 200 deletions(-)

diff --git a/lib/galaxy/objectstore/rods.py b/lib/galaxy/objectstore/rods.py
index 872354330f85..2ec313d86c36 100644
--- a/lib/galaxy/objectstore/rods.py
+++ b/lib/galaxy/objectstore/rods.py
@@ -1,26 +1,20 @@
 """
 Object Store plugin for the Integrated Rule-Oriented Data Store (iRODS)
 """
+from datetime import datetime
 import logging
-import multiprocessing
 import os
 from pathlib import Path
 import shutil
-import subprocess
 import threading
 import time
-from datetime import datetime
 
-from posixpath import (
-    basename as path_basename,
-    dirname as path_dirname,
-    join as path_join
-)
 try:
     import irods
     import irods.keywords as kw
     from irods.exception import CollectionDoesNotExist
     from irods.exception import DataObjectDoesNotExist
+    from irods.exception import NetworkException
     from irods.session import iRODSSession
 except ImportError:
     irods = None
@@ -31,13 +25,10 @@
 )
 from galaxy.util import (
     directory_hash_id,
-    string_as_bool,
     umask_fix_perms,
-    which,
 )
 from galaxy.util.path import safe_relpath
 from galaxy.util.sleeper import Sleeper
-from .s3_multipart_upload import multipart_upload
 from ..objectstore import (
     DiskObjectStore,
     local_extra_dirs,
@@ -49,7 +40,6 @@
 log = logging.getLogger(__name__)
 
 def parse_config_xml(config_xml):
-    print('IRODS2: inside parse_config_xml')
     try:
         a_xml = config_xml.findall('auth')[0]
         username = a_xml.get('username')
@@ -111,7 +101,6 @@ def parse_config_xml(config_xml):
 class CloudConfigMixin(object):
 
     def _config_to_dict(self):
-        print('IRODS2: inside _config_to_dict')
         return {
             'auth': {
                 'username': self.username,
@@ -135,19 +124,17 @@ def _config_to_dict(self):
 
 class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
     """
-    Object store that stores objects as data objects in an iRODS collection. A local cache 
+    Object store that stores objects as data objects in an iRODS collections. A local cache 
     exists that is used as an intermediate location for files between Galaxy and iRODS.
     """
     
     store_type = 'irods'
     
     #def _get_bucket(self, bucket_name):
-    #def _get_size_in_s3(self, rel_path):
     #def _key_exists(self, rel_path):
 
     def __init__(self, config, config_dict):
         super(IRODSObjectStore, self).__init__(config, config_dict)
-        print('IRODS2: inside __init__')
 
         auth_dict = config_dict['auth']
         self.username = auth_dict.get('username')
@@ -176,7 +163,6 @@ def __init__(self, config, config_dict):
         self._initialize()
         
     def __del__(self):
-        print('IRODS2: inside __del__')
         self.session.cleanup()
 
     def _initialize(self):
@@ -185,8 +171,7 @@ def _initialize(self):
 
         self.home =  "/" + self.zone + "/home/" + self.username
 
-        self.session = self._configure_connection()
-        #self.bucket = self._get_bucket(self.bucket)
+        self.session = self._configure_connection(host=self.host, port=self.port, user=self.username, password=self.password, zone=self.zone)
         # Clean cache only if value is set in galaxy.ini
         if self.cache_size != -1:
             # Convert GBs to bytes for comparison
@@ -196,25 +181,18 @@ def _initialize(self):
             self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
             self.cache_monitor_thread.start()
             log.info("Cache cleaner manager started")
-        # Test if 'axel' is available for parallel download and pull the key into cache
-        if which('axel'):
-            self.use_axel = True
-        else:
-            self.use_axel = False
 
     def _configure_connection(self, host='localhost', port='1247', user='rods', password='rods', zone='tempZone'):
-         with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
-            ###assert session.pool.get_connection() == 1, 'Failed to establish iRODS session'
-            print('IRODS2: inside iRODSSession')
+        with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
+            # Throws NetworkException if connection fails  
+            session.pool.get_connection()
             return session
 
     @classmethod
     def parse_xml(cls, config_xml):
-        print('IRODS2: inside parse_xml')
         return parse_config_xml(config_xml)
 
     def to_dict(self):
-        print('IRODS: inside to_dict') 
         as_dict = super(IRODSObjectStore, self).to_dict()
         as_dict.update(self._config_to_dict())
         return as_dict
@@ -283,8 +261,6 @@ def __clean_cache(self, file_list, delete_this_much):
                 log.debug("Cache cleaning done. Total space freed: %s", convert_bytes(deleted_amount))
                 return
 
-   # def _get_bucket(self, bucket_name):
-
     def _fix_permissions(self, rel_path):
         """ Set permissions on rel_path"""
         for basedir, _, files in os.walk(rel_path):
@@ -297,7 +273,6 @@ def _fix_permissions(self, rel_path):
                 umask_fix_perms(path, self.config.umask, 0o666, self.config.gid)
 
     def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs):
-        print('************* Entering _construct_path **************')
         # extra_dir should never be constructed from provided data but just
         # make sure there are no shenannigans afoot
         if extra_dir and extra_dir != os.path.normpath(extra_dir):
@@ -313,80 +288,61 @@ def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, ext
             # follow them, so if they are valid we normalize them out
             alt_name = os.path.normpath(alt_name)
         rel_path = os.path.join(*directory_hash_id(obj.id))
-        print('obj.id: ', obj.id)
-        print('rel_path: ', rel_path)
         if extra_dir is not None:
             if extra_dir_at_root:
                 rel_path = os.path.join(extra_dir, rel_path)
-                print('rel_path: ', rel_path)
             else:
                 rel_path = os.path.join(rel_path, extra_dir)
-                print('rel_path: ', rel_path)
 
         # for JOB_WORK directory
         if obj_dir:
             rel_path = os.path.join(rel_path, str(obj.id))
         if base_dir:
             base = self.extra_dirs.get(base_dir)
-            print('************* Exiting 1 _construct_path **************')
             return os.path.join(base, rel_path)
 
-        # S3 folders are marked by having trailing '/' so add it now
-        ###rel_path = '%s/' % rel_path
-
         if not dir_only:
             rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
-        print('************* Exiting 2 _construct_path **************')
         return rel_path
 
     def _get_cache_path(self, rel_path):
         return os.path.abspath(os.path.join(self.staging_path, rel_path))
 
-    #def _get_transfer_progress(self):
-    #    return self.transfer_progress
+    # rel_path is file or folder?
+    def _get_size_in_irods(self, rel_path):
+        p = Path(rel_path)
+        data_object_name =  p.stem + p.suffix
+        subcollection_name = p.parent
 
-    #def _get_size_in_s3(self, rel_path):
+        collection_path = self.home + "/" + str(subcollection_name)
+        data_object_path = collection_path + "/" + str(data_object_name) 
 
-    def _get_size_in_irods(self, rel_path):
-        '''
         try:
-            key = self.bucket.get_key(rel_path)
-            if key:
-                return key.size
-        except S3ResponseError:
-            log.exception("Could not get size of key '%s' from S3", rel_path)
+            data_obj = self.session.data_objects.get(data_object_path)
+            return data_obj.__sizeof__()
+        except (DataObjectDoesNotExist, CollectionDoesNotExist):
+            log.warn("Collection or data object (%s) does not exist", data_object_path)
             return -1
-        '''
 
+    # rel_path is file or folder?
     def _data_object_exists(self, rel_path):
-        exists = False
+        p = Path(rel_path)
+        data_object_name =  p.stem + p.suffix
+        subcollection_name = p.parent
+
+        collection_path = self.home + "/" + str(subcollection_name)
+        data_object_path = collection_path + "/" + str(data_object_name) 
+
         try:
-            # A hackish way of testing if the rel_path is a folder vs a file
-            is_dir = rel_path[-1] == '/'
-            if is_dir:
-                keyresult = self.bucket.get_all_keys(prefix=rel_path)
-                if len(keyresult) > 0:
-                    exists = True
-                else:
-                    exists = False
-            else:
-                key = Key(self.bucket, rel_path)
-                exists = key.exists()
-        except S3ResponseError:
-            log.exception("Trouble checking existence of S3 key '%s'", rel_path)
-            return False
-        if rel_path[0] == '/':
-            raise
-        return exists
+            self.session.data_objects.get(data_object_path)
+            return True 
+        except (DataObjectDoesNotExist, CollectionDoesNotExist):
+            log.warn("Collection or data object (%s) does not exist", data_object_path)
+            return False 
 
     def _in_cache(self, rel_path):
         """ Check if the given dataset is in the local cache and return True if so. """
-        # log.debug("------ Checking cache for rel_path %s" % rel_path)
-        print('*************** Entering _in_cache() *****************')
         cache_path = self._get_cache_path(rel_path)
-        print('cache_path: ', cache_path)
-        print('os.path.exists: ', os.path.exists(cache_path))
-        print('*************** Exiting _in_cache() *****************')
         return os.path.exists(cache_path)
         # TODO: Part of checking if a file is in cache should be to ensure the
         # size of the cached file matches that on S3. Once the upload tool explicitly
@@ -421,33 +377,34 @@ def _pull_into_cache(self, rel_path):
         self._fix_permissions(self._get_cache_path(rel_path_dir))
         return file_ok
 
-    #def _transfer_cb(self, complete, total):
-    #    self.transfer_progress += 10
-
     def _download(self, rel_path):
+        log.debug("Pulling data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
+
+        p = Path(rel_path)
+        data_object_name =  p.stem + p.suffix
+        subcollection_name = p.parent
+
+        collection_path = self.home + "/" + str(subcollection_name)
+        data_object_path = collection_path + "/" + str(data_object_name) 
+        data_obj = None
+
         try:
-            log.debug("Pulling key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
-            key = self.bucket.get_key(rel_path)
-            # Test if cache is large enough to hold the new file
-            if self.cache_size > 0 and key.size > self.cache_size:
-                log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
-                             rel_path, key.size, self.cache_size)
-                return False
-            if self.use_axel:
-                log.debug("Parallel pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
-                ncores = multiprocessing.cpu_count()
-                url = key.generate_url(7200)
-                ret_code = subprocess.call(['axel', '-a', '-n', ncores, url])
-                if ret_code == 0:
-                    return True
-            else:
-                log.debug("Pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
-                self.transfer_progress = 0  # Reset transfer progress counter
-                key.get_contents_to_filename(self._get_cache_path(rel_path), cb=self._transfer_cb, num_cb=10)
-                return True
-        except S3ResponseError:
-            log.exception("Problem downloading key '%s' from S3 bucket '%s'", rel_path, self.bucket.name)
-        return False
+            data_obj = self.session.data_objects.get(data_object_path)
+        except (DataObjectDoesNotExist, CollectionDoesNotExist):
+            log.warn("Collection or data object (%s) does not exist", data_object_path)
+            return False 
+
+        if self.cache_size > 0 and data_obj.__sizeof__() > self.cache_size:
+            log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
+                         rel_path, data_obj.__sizeof__(), self.cache_size)
+            return False
+
+        log.debug("Pulled data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
+        
+        with data_obj.open('rb') as data_obj_fp, open(self._get_cache_path(rel_path), "wb") as cache_fp:
+            content = data_obj_fp.read()
+            cache_fp.write(content)
+        return True
 
     def _push_to_os(self, rel_path, source_file=None, from_string=None):
         """
@@ -455,69 +412,52 @@ def _push_to_os(self, rel_path, source_file=None, from_string=None):
         from rel_path as iRODS collection name, and extract file name from rel_path
         as iRODS data object name.
         If ``source_file`` is provided, push that file instead while
-        still using ``rel_path`` for collection and object tore names.
-        If ``from_string`` is provided, set contents of the file to the value of
-        the string.
+        still using ``rel_path`` for collection and object store names.
+        If ``from_string`` is provided, set contents of the file to the value of the string.
         """
-        print('**** Entering _push_to_os ****')
-        print('IRODS: rel_path: ', rel_path)
         p = Path(rel_path)
-        print('p: ', p)
-        print('p.parent: ', p.parent)
-        print('p.stem: ', p.stem)
-        print('p.suffix: ', p.suffix)
-
-        data_object =  p.stem + p.suffix
-        subcollection = p.parent
-        print('data_object: ', data_object)
-        print('subcollection: ', subcollection)
+        data_object_name =  p.stem + p.suffix
+        subcollection_name = p.parent
 
         source_file = source_file if source_file else self._get_cache_path(rel_path)
-        print('IRODS: source_file: ', source_file)
-
         options = {kw.FORCE_FLAG_KW: ''}
 
         if os.path.exists(source_file):
             # Check if the data object exists in iRODS
-            subcollection_path = self.home + "/" + str(subcollection)
-            full_irods_path = subcollection_path + "/" + str(data_object) 
-            print('full_irods_path: ', full_irods_path)
-            exists = self.session.data_objects.exists(full_irods_path)
+            collection_path = self.home + "/" + str(subcollection_name)
+            data_object_path = collection_path + "/" + str(data_object_name) 
+            exists = self.session.data_objects.exists(data_object_path)
             if os.path.getsize(source_file) == 0 and exists:
                 log.debug("Wanted to push file '%s' to iRODS collection '%s' but its size is 0; skipping.", source_file, rel_path)
-                print('**** Exiting 1 _push_to_os ****')
                 return True
             if from_string:
-                data_obj = self.session.data_objects.create(full_irods_path, recurse=True, **options)
+                data_obj = self.session.data_objects.create(data_object_path, recurse=True, **options)
                 with data_obj.open('w') as data_obj_fp:
                     data_obj_fp.write(from_string)
-                log.debug("Pushed data from string '%s' to collection '%s'", from_string, full_irods_path)
+                log.debug("Pushed data from string '%s' to collection '%s'", from_string, data_object_path)
             else:
                 start_time = datetime.now()
                 log.debug("Pushing cache file '%s' of size %s bytes to collection '%s'", source_file, os.path.getsize(source_file), rel_path)
                 
                 # Create sub-collection first
-                self.session.collections.create(subcollection_path)
+                self.session.collections.create(collection_path, recurse=True)
 
                 file_content = None
                 with open(source_file, 'rb') as content_file:
                     file_content = content_file.read()
                 
                 # Write to file in subcollection created above
-                data_obj = self.session.data_objects.create(full_irods_path, recurse=True, **options)
+                data_obj = self.session.data_objects.create(data_object_path, recurse=True, **options)
                 with data_obj.open('w') as data_obj_fp:
                     data_obj_fp.write(file_content)
 
                 end_time = datetime.now()
                 log.debug("Pushed cache file '%s' to collection '%s' (%s bytes transfered in %s sec)",
                           source_file, rel_path, os.path.getsize(source_file), end_time - start_time)
-            print('**** Exiting 2 _push_to_os ****')
             return True
         else:
             log.error("Tried updating key '%s' from source file '%s', but source file does not exist.",
                       rel_path, source_file)
-
-        print('**** Exiting 3 _push_to_os ****')
         return False
 
     def file_ready(self, obj, **kwargs):
@@ -528,53 +468,43 @@ def file_ready(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         # Make sure the size in cache is available in its entirety
         if self._in_cache(rel_path):
-            if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_s3(rel_path):
+            if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_irods(rel_path):
                 return True
             log.debug("Waiting for dataset %s to transfer from OS: %s/%s", rel_path,
-                      os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_s3(rel_path))
+                      os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_irods(rel_path))
         return False
 
     def exists(self, obj, **kwargs):
-        print('*************Entering exists()*************')
         in_cache = in_irods = False
-        for key, value in kwargs.items():
-            print("The value of {} is {}".format(key, value))
         rel_path = self._construct_path(obj, **kwargs)
-        print('rel_path: ', rel_path)
 
         # Check cache
         if self._in_cache(rel_path):
             in_cache = True
         # Check iRODS 
-        ###in_irods = self._data_object_exists(rel_path)
+        in_irods = self._data_object_exists(rel_path)
 
         # dir_only does not get synced so shortcut the decision
         dir_only = kwargs.get('dir_only', False)
         base_dir = kwargs.get('base_dir', None)
         if dir_only:
             if in_cache or in_irods:
-                print('*************Exiting  1 exists()*************')
                 return True
             # for JOB_WORK directory
             elif base_dir:
                 if not os.path.exists(rel_path):
                     os.makedirs(rel_path)
-                print('*************Exiting  2 exists()*************')
                 return True
             else:
-                print('*************Exiting  3 exists()*************')
                 return False
 
         # TODO: Sync should probably not be done here. Add this to an async upload stack?
         if in_cache and not in_irods:
             self._push_to_os(rel_path, source_file=self._get_cache_path(rel_path))
-            print('*************Exiting  4 exists()*************')
             return True
         elif in_irods:
-            print('*************Exiting  5 exists()*************')
             return True
         else:
-            print('*************Exiting  6 exists()*************')
             return False
 
     def create(self, obj, **kwargs):
@@ -601,12 +531,6 @@ def create(self, obj, **kwargs):
             if not os.path.exists(cache_dir):
                 os.makedirs(cache_dir)
 
-            # Although not really necessary to create S3 folders (because S3 has
-            # flat namespace), do so for consistency with the regular file system
-            # S3 folders are marked by having trailing '/' so add it now
-            # s3_dir = '%s/' % rel_path
-            # self._push_to_os(s3_dir, from_string='')
-            # If instructed, create the dataset in cache & in S3
             if not dir_only:
                 rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
@@ -620,22 +544,15 @@ def empty(self, obj, **kwargs):
                                  % (str(obj), str(kwargs)))
 
     def size(self, obj, **kwargs):
-        print('*************** Entering size ****************')
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
-                print('*************** Exiting 1 size ****************')
                 return os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s", rel_path, ex)
         elif self.exists(obj, **kwargs):
-            print('*************** Exiting 2 size ****************')
-            ## 
-            ## TODO
-            ## 
-            return self._get_size_in_s3(rel_path)
+            return self._get_size_in_irods(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
-        print('*************** Exiting 3 size ****************')
         return 0
 
     def delete(self, obj, entire_dir=False, **kwargs):
@@ -651,9 +568,12 @@ def delete(self, obj, entire_dir=False, **kwargs):
                 return True
 
             # For the case of extra_files, because we don't have a reference to
-            # individual files/keys we need to remove the entire directory structure
+            # individual files we need to remove the entire directory structure
             # with all the files in it. This is easy for the local file system,
-            # but requires iterating through each individual key in S3 and deleing it.
+            # but requires iterating through each individual key in irods and deleing it.
+            #
+            # TODO!!!
+            #
             if entire_dir and extra_dir:
                 shutil.rmtree(self._get_cache_path(rel_path))
                 results = self.bucket.get_all_keys(prefix=rel_path)
@@ -664,14 +584,23 @@ def delete(self, obj, entire_dir=False, **kwargs):
             else:
                 # Delete from cache first
                 os.unlink(self._get_cache_path(rel_path))
-                # Delete from S3 as well
-                if self._key_exists(rel_path):
-                    key = Key(self.bucket, rel_path)
-                    log.debug("Deleting key %s", key.name)
-                    key.delete()
+                # Delete from irods as well
+                p = Path(rel_path)
+                data_object_name =  p.stem + p.suffix
+                subcollection_name = p.parent
+
+                collection_path = self.home + "/" + str(subcollection_name)
+                data_object_path = collection_path + "/" + str(data_object_name) 
+
+                try:
+                    data_obj = self.session.data_objects.get(data_object_path)
+                    # remove object
+                    data_obj.unlink(force=True)
                     return True
-        except S3ResponseError:
-            log.exception("Could not delete key '%s' from S3", rel_path)
+                except (DataObjectDoesNotExist, CollectionDoesNotExist):
+                    log.info("Collection or data object (%s) does not exist", data_object_path)
+                    return True 
+
         except OSError:
             log.exception('%s delete error', self.get_filename(obj, **kwargs))
         return False
@@ -699,7 +628,7 @@ def get_filename(self, obj, **kwargs):
             return os.path.abspath(rel_path)
 
         cache_path = self._get_cache_path(rel_path)
-        # S3 does not recognize directories as files so cannot check if those exist.
+        # iRODS does not recognize directories as files so cannot check if those exist.
         # So, if checking dir only, ensure given dir exists in cache and return
         # the expected cache path.
         # dir_only = kwargs.get('dir_only', False)
@@ -750,43 +679,19 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
+    # Unlike S3, url is not really applicable to iRODS
     def get_object_url(self, obj, **kwargs):
         if self.exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
-            try:
-                key = Key(self.bucket, rel_path)
-                return key.generate_url(expires_in=86400)  # 24hrs
-            except S3ResponseError:
-                log.exception("Trouble generating URL for dataset '%s'", rel_path)
-        return None
+
+            p = Path(rel_path)
+            data_object_name =  p.stem + p.suffix
+            subcollection_name = p.parent
+
+            collection_path = self.home + "/" + str(subcollection_name)
+            data_object_path = collection_path + "/" + str(data_object_name)
+            
+            return data_object_path
 
     def get_store_usage_percent(self):
-        return 0.0
-
-'''
-        ###########################################################        
-        ## These should be read from env variables or a config file
-        ###########################################################        
-        # host='localhost' 
-        host='127.0.0.1' 
-        port='1247' 
-        user='rods'  
-        password='rods' 
-        zone='tempZone'
-        ###defaultResource = 'demoResc'
-
-        # Connect to iRODS (AssertionErrors will be raised if anything goes wrong)
-        self.session = irods_connect(host, port, user, password, zone)
-
-        # Set iRODS home path
-        ###self.home_path = "/" + zone + "/home/" + user + '/galaxy_data'
-        self.home_path = "/" + zone + "/home/" + user
-        assert self.home_path != '', "Unable to initialize iRODS Object Store: irods_home cannot be determined."
-
-        # Will return a collection object regardless of whether it exists
-        self.root_collection = self.session.collections.get(self.home_path)
-        if self.root_collection.path != self.home_path:
-            log.warning("iRODS root collection does not exist, will attempt to create: %s", self.home_path)
-            self.root_collection = self.session.collections.create(self.home_path)
-            assert self.root_collection.path == self.home_path, "iRODS root collection creation failed: %s" % self.home_path
-'''
\ No newline at end of file
+        return 0.0
\ No newline at end of file

From b6a45b38abc89988a52b92addbe51c3b99b5dcd8 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 20 Feb 2020 16:40:29 -0500
Subject: [PATCH 544/853] Renamed file to irods

---
 lib/galaxy/objectstore/__init__.py           | 2 +-
 lib/galaxy/objectstore/{rods.py => irods.py} | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename lib/galaxy/objectstore/{rods.py => irods.py} (100%)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index b1dccf8b2494..6bbbeda7d127 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -913,7 +913,7 @@ def type_to_object_store_class(store, fsmon=False):
         objectstore_class = HierarchicalObjectStore
         objectstore_constructor_kwds["fsmon"] = fsmon
     elif store == 'irods':
-        from .rods import IRODSObjectStore
+        from .irods import IRODSObjectStore
         objectstore_class = IRODSObjectStore
     elif store == 'azure_blob':
         from .azure_blob import AzureBlobObjectStore
diff --git a/lib/galaxy/objectstore/rods.py b/lib/galaxy/objectstore/irods.py
similarity index 100%
rename from lib/galaxy/objectstore/rods.py
rename to lib/galaxy/objectstore/irods.py

From 5bf36de43ec5a6702df49a5b0df9f3c2dfce343f Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 21 Feb 2020 16:12:30 -0500
Subject: [PATCH 545/853] Added code to delete all data objects in a
 collection.

---
 lib/galaxy/objectstore/irods.py | 27 ++++++++++++++++++++-------
 1 file changed, 20 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 2ec313d86c36..c77a2ea003a8 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -571,16 +571,29 @@ def delete(self, obj, entire_dir=False, **kwargs):
             # individual files we need to remove the entire directory structure
             # with all the files in it. This is easy for the local file system,
             # but requires iterating through each individual key in irods and deleing it.
-            #
-            # TODO!!!
-            #
             if entire_dir and extra_dir:
                 shutil.rmtree(self._get_cache_path(rel_path))
-                results = self.bucket.get_all_keys(prefix=rel_path)
-                for key in results:
-                    log.debug("Deleting key %s", key.name)
-                    key.delete()
+
+                col_path = self.home + "/" + str(rel_path)
+                col = None
+                try:
+                    col = self.session.collections.get(col_path)
+                except CollectionDoesNotExist:
+                    log.warn("Collection (%s) does not exist!", col_path)
+                    return False
+
+                cols = col.walk()
+                # Traverse the tree only one level deep 
+                for _ in range(2):
+                    # get next result
+                    _, _, data_objects = next(cols)
+
+                    # Delete data objects
+                    for data_object in data_objects:
+                        data_object.unlink(force=True)
+
                 return True
+
             else:
                 # Delete from cache first
                 os.unlink(self._get_cache_path(rel_path))

From a826ebf191eb7b9dd101e1d4c45db819738a3df5 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 25 Feb 2020 15:14:42 -0500
Subject: [PATCH 546/853] Added datatype upload test to iRODS.

---
 .gitignore                                    |   1 -
 test/integration/object_store_conf.xml        |  11 ++
 .../integration/test_datatype_upload_irods.py | 109 ++++++++++++++++++
 3 files changed, 120 insertions(+), 1 deletion(-)
 create mode 100644 test/integration/object_store_conf.xml
 create mode 100644 test/integration/test_datatype_upload_irods.py

diff --git a/.gitignore b/.gitignore
index e4d13b558e78..1ca8e3da4fa4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -79,7 +79,6 @@ shed_tool_data_table_conf.xml
 job_conf.xml
 data_manager_conf.xml
 shed_data_manager_conf.xml
-object_store_conf.xml
 job_metrics_conf.xml
 workflow_schedulers_conf.xml
 config/*
diff --git a/test/integration/object_store_conf.xml b/test/integration/object_store_conf.xml
new file mode 100644
index 000000000000..e87548784cc0
--- /dev/null
+++ b/test/integration/object_store_conf.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<object_store type="irods"> 
+    <files_dir path="database/files3"/>
+    <auth username="rods" password="rods" />
+    <resource name="demoResc" />
+    <zone name="tempZone" />
+    <connection host="localhost" port="1247"/>
+    <cache path="database/object_store_cache" size="1000" />
+    <extra_dir type="job_work" path="database/job_working_directory_irods"/>
+    <extra_dir type="temp" path="database/tmp_irods"/>
+</object_store>
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
new file mode 100644
index 000000000000..575628a8aa01
--- /dev/null
+++ b/test/integration/test_datatype_upload_irods.py
@@ -0,0 +1,109 @@
+import collections
+import os
+import tempfile
+
+import pytest
+
+from galaxy.datatypes.registry import Registry
+from galaxy.util.checkers import (
+    is_bz2,
+    is_gzip,
+    is_zip
+)
+from galaxy.util.hash_util import md5_hash_file
+from galaxy_test.driver import integration_util
+from .test_upload_configuration_options import BaseUploadContentConfigurationInstance
+
+SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
+TEST_FILE_DIR = '%s/../../lib/galaxy/datatypes/test' % SCRIPT_DIRECTORY
+TestData = collections.namedtuple('UploadDatatypesData', 'path datatype uploadable')
+GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
+DATATYPES_CONFIG = os.path.join(GALAXY_ROOT, 'lib/galaxy/config/sample/datatypes_conf.xml.sample')
+PARENT_SNIFFER_MAP = {'fastqsolexa': 'fastq'}
+OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "object_store_conf.xml")
+
+
+def find_datatype(registry, filename):
+    # match longest extension first
+    sorted_extensions = sorted(registry.datatypes_by_extension.keys(), key=len, reverse=True)
+    for extension in sorted_extensions:
+        if filename.endswith(extension) or filename.startswith(extension):
+            return registry.datatypes_by_extension[extension]
+    raise Exception("Couldn't guess datatype for file '%s'" % filename)
+
+
+def collect_test_data(registry):
+    test_files = [f for f in os.listdir(TEST_FILE_DIR) if "." in f]
+    files = [os.path.join(TEST_FILE_DIR, f) for f in test_files]
+    datatypes = [find_datatype(registry, f) for f in test_files]
+    uploadable = [datatype.file_ext in registry.upload_file_formats for datatype in datatypes]
+    test_data_description = [TestData(*items) for items in zip(files, datatypes, uploadable)]
+    return {os.path.basename(data.path): data for data in test_data_description}
+
+
+class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
+    framework_tool_and_types = False
+    datatypes_conf_override = DATATYPES_CONFIG
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["object_store_config_file"] = OBJECT_STORE_CONFIG_FILE
+
+
+instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
+
+
+@pytest.fixture
+def temp_file():
+    with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
+        yield fh
+
+
+registry = Registry()
+registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG)
+TEST_CASES = collect_test_data(registry)
+
+
+@pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))
+def test_upload_datatype_auto(instance, test_data, temp_file):
+    is_compressed = False
+    for is_method in (is_bz2, is_gzip, is_zip):
+        is_compressed = is_method(test_data.path)
+        if is_compressed:
+            break
+    with open(test_data.path, 'rb') as content:
+        if hasattr(test_data.datatype, 'sniff') or 'false' in test_data.path:
+            file_type = 'auto'
+        else:
+            file_type = test_data.datatype.file_ext
+        dataset = instance.dataset_populator.new_dataset(instance.history_id, content=content, wait=False, file_type=file_type)
+    dataset = instance.dataset_populator.get_history_dataset_details(instance.history_id, dataset=dataset, assert_ok=False)
+    expected_file_ext = test_data.datatype.file_ext
+    # State might be error if the datatype can't be uploaded
+    if dataset['state'] == 'error' and not test_data.uploadable:
+        # Some things can't be uploaded, if attempting to upload these datasets we mention why
+        assert 'invalid' in dataset['misc_info'] or 'unsupported' in dataset['misc_info']
+        return
+    elif dataset['state'] == 'error' and 'empty' in dataset['misc_info']:
+        return
+    else:
+        # state should be OK
+        assert dataset['state'] == 'ok'
+    # Check that correct datatype has been detected
+    file_ext = dataset['file_ext']
+    if 'false' in test_data.path:
+        # datasets with false in their name are not of a specific datatype
+        assert file_ext != PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
+    else:
+        assert file_ext == PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
+    datatype = registry.datatypes_by_extension[file_ext]
+    datatype_compressed = getattr(datatype, "compressed", False)
+    if not is_compressed or datatype_compressed:
+        # download file and verify it hasn't been manipulated
+        temp_file.write(instance.dataset_populator.get_history_dataset_content(history_id=instance.history_id,
+                                                                               dataset=dataset,
+                                                                               type='bytes',
+                                                                               assert_ok=False,
+                                                                               raw=True))
+        temp_file.flush()
+        assert md5_hash_file(test_data.path) == md5_hash_file(temp_file.name)

From 57293e57055f9b50a8443e32ef13ca28ba915f3a Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Wed, 26 Feb 2020 11:59:41 -0500
Subject: [PATCH 547/853] Revised code based on code review feedback

---
 .../dependencies/conditional-requirements.txt      |  2 +-
 lib/galaxy/objectstore/irods.py                    |  7 ++++---
 test/integration/object_store_conf.xml             |  1 -
 test/integration/objectstore/test_irods.py         | 14 +++++++-------
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index b1f96df95255..5f2eb54fc9f7 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -8,7 +8,7 @@ drmaa
 statsd
 docker
 azure-storage==0.32.0
-# PyRods not in PyPI
+python-irodsclient==0.8.2
 python-ldap==3.2.0
 python-pam
 galaxycloudrunner
diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index c77a2ea003a8..a0d8085ffe22 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -24,6 +24,7 @@
     ObjectNotFound
 )
 from galaxy.util import (
+    bytesize,
     directory_hash_id,
     umask_fix_perms,
 )
@@ -172,10 +173,10 @@ def _initialize(self):
         self.home =  "/" + self.zone + "/home/" + self.username
 
         self.session = self._configure_connection(host=self.host, port=self.port, user=self.username, password=self.password, zone=self.zone)
-        # Clean cache only if value is set in galaxy.ini
+        # Clean cache only if value is set in galaxy config file
         if self.cache_size != -1:
             # Convert GBs to bytes for comparison
-            self.cache_size = self.cache_size * 1073741824
+            self.cache_size = self.cache_size * bytesize.SUFFIX_TO_BYTES['GI']
             # Helper for interruptable sleep
             self.sleeper = Sleeper()
             self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
@@ -686,7 +687,7 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
                     log.exception("Trouble copying source file '%s' to cache '%s'", source_file, cache_file)
             else:
                 source_file = self._get_cache_path(rel_path)
-            # Update the file on S3
+            # Update the file on iRODS 
             self._push_to_os(rel_path, source_file)
         else:
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
diff --git a/test/integration/object_store_conf.xml b/test/integration/object_store_conf.xml
index e87548784cc0..778b42f4083e 100644
--- a/test/integration/object_store_conf.xml
+++ b/test/integration/object_store_conf.xml
@@ -1,6 +1,5 @@
 <?xml version="1.0"?>
 <object_store type="irods"> 
-    <files_dir path="database/files3"/>
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
diff --git a/test/integration/objectstore/test_irods.py b/test/integration/objectstore/test_irods.py
index 636b73ee7ed6..19bf3a388e24 100644
--- a/test/integration/objectstore/test_irods.py
+++ b/test/integration/objectstore/test_irods.py
@@ -17,26 +17,26 @@ class IrodsObjectStoreIntegrationTestCase(integration_util.IntegrationTestCase):
 
     container_name = "irods_server"
 
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["object_store_config_file"] = "object_store_conf.xml" 
+
     @classmethod
     def setUpClass(cls):
-        print('Starting setUpClass')
         super(IrodsObjectStoreIntegrationTestCase, cls).setUpClass()
         IrodsObjectStoreIntegrationTestCase.start_irods_server(container_name=IrodsObjectStoreIntegrationTestCase.container_name)
 
         # Let the server start before running the test
         time.sleep(10)
-        print('Finishing setUpClass')
 
     @classmethod
     def tearDownClass(cls): 
-        print('Starting tearDownClass')
         super(IrodsObjectStoreIntegrationTestCase, cls).tearDownClass()
         IrodsObjectStoreIntegrationTestCase.stop_irods_server(container_name=IrodsObjectStoreIntegrationTestCase.container_name)       
-        print('Finishing tearDownClass')
 
     @classmethod
-    def start_irods_server(cls, container_name, postgres_port=5432, irods_port=1247, docker_image='kxk302/irods-server:0.1'):
-        start_server = ['docker', 'run', '-h', 'localhost', '-p', '{port}:5432'.format(port=postgres_port), '-p', '{port}:1247'.format(port=irods_port), '-d', '--name', container_name, docker_image]
+    def start_irods_server(cls, container_name, irods_port=1247, docker_image='kxk302/irods-server:0.1'):
+        start_server = ['docker', 'run', '-h', 'localhost', '-p', '{port}:1247'.format(port=irods_port), '-d', '--name', container_name, docker_image]
         subprocess.check_call(start_server) 
         
     @classmethod
@@ -117,7 +117,7 @@ def test_create_delete_new_data_object(self):
 
             with pytest.raises(CollectionDoesNotExist):
                 coll = session.collections.get(newCollection)
-
+ 
     def test_populate_fetch_new_data_object(self):
         with iRODSSession(host='localhost', 
             port='1247', 

From 4c4d8cecb29054b12d714024b8aa0bc090fdd9d7 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Wed, 26 Feb 2020 13:29:49 -0500
Subject: [PATCH 548/853] More code review changes

---
 .gitignore                                                      | 1 +
 .../{object_store_conf.xml => irods_object_store_conf.xml}      | 0
 test/integration/test_datatype_upload_irods.py                  | 2 +-
 test/unit/objectstore/test_irods.py                             | 0
 4 files changed, 2 insertions(+), 1 deletion(-)
 rename test/integration/{object_store_conf.xml => irods_object_store_conf.xml} (100%)
 create mode 100644 test/unit/objectstore/test_irods.py

diff --git a/.gitignore b/.gitignore
index 1ca8e3da4fa4..e4d13b558e78 100644
--- a/.gitignore
+++ b/.gitignore
@@ -79,6 +79,7 @@ shed_tool_data_table_conf.xml
 job_conf.xml
 data_manager_conf.xml
 shed_data_manager_conf.xml
+object_store_conf.xml
 job_metrics_conf.xml
 workflow_schedulers_conf.xml
 config/*
diff --git a/test/integration/object_store_conf.xml b/test/integration/irods_object_store_conf.xml
similarity index 100%
rename from test/integration/object_store_conf.xml
rename to test/integration/irods_object_store_conf.xml
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 575628a8aa01..c1de59b14762 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -20,7 +20,7 @@
 GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
 DATATYPES_CONFIG = os.path.join(GALAXY_ROOT, 'lib/galaxy/config/sample/datatypes_conf.xml.sample')
 PARENT_SNIFFER_MAP = {'fastqsolexa': 'fastq'}
-OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "object_store_conf.xml")
+OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "irods_object_store_conf.xml")
 
 
 def find_datatype(registry, filename):
diff --git a/test/unit/objectstore/test_irods.py b/test/unit/objectstore/test_irods.py
new file mode 100644
index 000000000000..e69de29bb2d1

From fe399ec0b82082ff06dba811fa90430a9d3bdf2b Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 27 Feb 2020 15:08:31 -0500
Subject: [PATCH 549/853] Added the first unit test for iRODS. Some code
 cleanup from previous code review comments.

---
 .../dependencies/pipfiles/default/Pipfile     |  1 +
 lib/galaxy/objectstore/irods.py               | 70 +++++++++++--------
 .../objectstore/irods_object_store_conf.xml   | 10 +++
 .../irods_object_store_conf_no_auth.xml       | 10 +++
 .../irods_object_store_conf_no_extra_dir.xml  | 10 +++
 test/unit/objectstore/test_irods.py           | 48 +++++++++++++
 6 files changed, 118 insertions(+), 31 deletions(-)
 create mode 100644 test/unit/objectstore/irods_object_store_conf.xml
 create mode 100644 test/unit/objectstore/irods_object_store_conf_no_auth.xml
 create mode 100644 test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml

diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/lib/galaxy/dependencies/pipfiles/default/Pipfile
index 5cf77f61560c..bf8281d506c7 100644
--- a/lib/galaxy/dependencies/pipfiles/default/Pipfile
+++ b/lib/galaxy/dependencies/pipfiles/default/Pipfile
@@ -27,6 +27,7 @@ sphinx_rtd_theme = "*"
 testfixtures = "*"
 twill = {version = "==0.9.1", markers = "python_version < '3'"}
 watchdog = "*"
+python-irodsclient = "*"
 
 [packages]
 numpy = "*"
diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index a0d8085ffe22..ba4156d26cc1 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -40,38 +40,46 @@
 
 log = logging.getLogger(__name__)
 
+def _parse_error(tag):
+    msg = 'No {tag} element in XML tree'.format(tag=tag)
+    log.error(msg)
+    raise Exception(msg)
+
 def parse_config_xml(config_xml):
     try:
-        a_xml = config_xml.findall('auth')[0]
-        username = a_xml.get('username')
-        password = a_xml.get('password')
-
-        b_xml = config_xml.findall('resource')[0]
-        resource_name = b_xml.get('name')
-
-        b_xml = config_xml.findall('zone')[0]
-        zone_name = b_xml.get('name')
-
-        cn_xml = config_xml.findall('connection')
-        if not cn_xml:
-            cn_xml = {}
-        else:
-            cn_xml = cn_xml[0]
-
-        host = cn_xml.get('host', None)
-        port = int(cn_xml.get('port', 0))
-
-        c_xml = config_xml.findall('cache')[0]
-        cache_size = float(c_xml.get('size', -1))
-        staging_path = c_xml.get('path', None)
-
-        tag, attrs = 'extra_dir', ('type', 'path')
-        extra_dirs = config_xml.findall(tag)
-        if not extra_dirs:
-            msg = 'No {tag} element in XML tree'.format(tag=tag)
-            log.error(msg)
-            raise Exception(msg)
-        extra_dirs = [dict(((k, e.get(k)) for k in attrs)) for e in extra_dirs]
+        a_xml = config_xml.findall('auth')
+        if not a_xml:
+            _parse_error('auth')
+        username = a_xml[0].get('username')
+        password = a_xml[0].get('password')
+
+        r_xml = config_xml.findall('resource')
+        if not r_xml:
+            _parse_error('resource')
+        resource_name = r_xml[0].get('name')
+
+        z_xml = config_xml.findall('zone')
+        if not z_xml:
+            _parse_error('zone')
+        zone_name = z_xml[0].get('name')
+
+        c_xml = config_xml.findall('connection')
+        if not c_xml:
+            _parse_error('connection')
+        host = c_xml[0].get('host', None)
+        port = int(c_xml[0].get('port', 0))
+
+        c_xml = config_xml.findall('cache')
+        if not c_xml:
+            _parse_error('cache')
+        cache_size = float(c_xml[0].get('size', -1))
+        staging_path = c_xml[0].get('path', None)
+
+        attrs = ('type', 'path')
+        e_xml = config_xml.findall('extra_dir')
+        if not e_xml:
+            _parse_error('extra_dir')
+        extra_dirs = [dict(((k, e.get(k)) for k in attrs)) for e in e_xml]
 
         return {
             'auth': {
@@ -96,7 +104,7 @@ def parse_config_xml(config_xml):
         }
     except Exception:
         # Toss it back up after logging, we can't continue loading at this point.
-        log.exception("Malformed iRODS ObjectStore Configuration XML -- unable to continue")
+        log.exception("Malformed iRODS ObjectStore Configuration XML -- unable to continue.")
         raise
 
 class CloudConfigMixin(object):
diff --git a/test/unit/objectstore/irods_object_store_conf.xml b/test/unit/objectstore/irods_object_store_conf.xml
new file mode 100644
index 000000000000..778b42f4083e
--- /dev/null
+++ b/test/unit/objectstore/irods_object_store_conf.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<object_store type="irods"> 
+    <auth username="rods" password="rods" />
+    <resource name="demoResc" />
+    <zone name="tempZone" />
+    <connection host="localhost" port="1247"/>
+    <cache path="database/object_store_cache" size="1000" />
+    <extra_dir type="job_work" path="database/job_working_directory_irods"/>
+    <extra_dir type="temp" path="database/tmp_irods"/>
+</object_store>
diff --git a/test/unit/objectstore/irods_object_store_conf_no_auth.xml b/test/unit/objectstore/irods_object_store_conf_no_auth.xml
new file mode 100644
index 000000000000..7388b11fe358
--- /dev/null
+++ b/test/unit/objectstore/irods_object_store_conf_no_auth.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<object_store type="irods"> 
+    <!--<auth username="rods" password="rods" />-->
+    <resource name="demoResc" />
+    <zone name="tempZone" />
+    <connection host="localhost" port="1247"/>
+    <cache path="database/object_store_cache" size="1000" />
+    <extra_dir type="job_work" path="database/job_working_directory_irods"/>
+    <extra_dir type="temp" path="database/tmp_irods"/>
+</object_store>
diff --git a/test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml b/test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml
new file mode 100644
index 000000000000..d2c07a428ac0
--- /dev/null
+++ b/test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<object_store type="irods"> 
+    <auth username="rods" password="rods" />
+    <resource name="demoResc" />
+    <zone name="tempZone" />
+    <connection host="localhost" port="1247"/>
+    <cache path="database/object_store_cache" size="1000" />
+    <!--<extra_dir type="job_work" path="database/job_working_directory_irods"/>-->
+    <!--<extra_dir type="temp" path="database/tmp_irods"/>-->
+</object_store>
diff --git a/test/unit/objectstore/test_irods.py b/test/unit/objectstore/test_irods.py
index e69de29bb2d1..43cc604b90f1 100644
--- a/test/unit/objectstore/test_irods.py
+++ b/test/unit/objectstore/test_irods.py
@@ -0,0 +1,48 @@
+import os
+import xml.etree.ElementTree as ET
+
+import pytest
+
+from galaxy.objectstore.irods import parse_config_xml
+from galaxy.objectstore.irods import IRODSObjectStore
+
+SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
+
+CONFIG_FILE_NAME = 'irods_object_store_conf.xml'
+CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME)
+
+CONFIG_FILE_NAME_NO_EXTRA_DIR = 'irods_object_store_conf_no_extra_dir.xml'
+CONFIG_FILE_NO_EXTRA_DIR = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME_NO_EXTRA_DIR)
+
+CONFIG_FILE_NAME_NO_AUTH = 'irods_object_store_conf_no_auth.xml'
+CONFIG_FILE_NO_AUTH = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME_NO_AUTH)
+
+def test_parse_valid_config_xml():
+    tree = ET.parse(CONFIG_FILE)
+    root = tree.getroot()
+    config = parse_config_xml(root)
+
+    assert config['auth']['username'] == 'rods'
+    assert config['auth']['password'] == 'rods'
+    assert config['resource']['name'] == 'demoResc'
+    assert config['zone']['name'] == 'tempZone'
+    assert config['connection']['host'] == 'localhost'
+    assert config['connection']['port'] == 1247
+    assert config['cache']['path'] == 'database/object_store_cache'
+    assert config['cache']['size'] == 1000
+    assert config['extra_dirs'][0]['type'] == 'job_work'
+    assert config['extra_dirs'][0]['path'] == 'database/job_working_directory_irods'
+    assert config['extra_dirs'][1]['type'] == 'temp'
+    assert config['extra_dirs'][1]['path'] == 'database/tmp_irods'
+
+def test_parse_config_xml_no_extra_dir():
+    tree = ET.parse(CONFIG_FILE_NO_EXTRA_DIR)
+    root = tree.getroot()
+    with pytest.raises(Exception, match='No extra_dir element in XML tree'): 
+        parse_config_xml(root)
+
+def test_parse_config_xml_no_auth():
+    tree = ET.parse(CONFIG_FILE_NO_AUTH)
+    root = tree.getroot()
+    with pytest.raises(Exception, match='No auth element in XML tree'): 
+        parse_config_xml(root)
\ No newline at end of file

From 0b2fa6825ac4cb923db8afb2189cbb9e3c5a75d6 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 28 Feb 2020 15:44:59 -0500
Subject: [PATCH 550/853] Added some input validation. Added first integration
 test.

---
 lib/galaxy/objectstore/irods.py            |  68 +++++--
 test/integration/objectstore/test_irods.py | 221 ++++++---------------
 2 files changed, 107 insertions(+), 182 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index ba4156d26cc1..a9ec524cfb11 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -40,45 +40,48 @@
 
 log = logging.getLogger(__name__)
 
-def _parse_error(tag):
-    msg = 'No {tag} element in XML tree'.format(tag=tag)
-    log.error(msg)
+def _config_xml_error(tag):
+    msg = 'No {tag} element in config XML tree'.format(tag=tag)
+    raise Exception(msg)
+
+def _config_dict_error(key):
+    msg = 'No {key} key in config dictionary'.forma(key=key)
     raise Exception(msg)
 
 def parse_config_xml(config_xml):
     try:
         a_xml = config_xml.findall('auth')
         if not a_xml:
-            _parse_error('auth')
+            _config_xml_error('auth')
         username = a_xml[0].get('username')
         password = a_xml[0].get('password')
 
         r_xml = config_xml.findall('resource')
         if not r_xml:
-            _parse_error('resource')
+            _config_xml_error('resource')
         resource_name = r_xml[0].get('name')
 
         z_xml = config_xml.findall('zone')
         if not z_xml:
-            _parse_error('zone')
+            _config_xml_error('zone')
         zone_name = z_xml[0].get('name')
 
         c_xml = config_xml.findall('connection')
         if not c_xml:
-            _parse_error('connection')
+            _config_xml_error('connection')
         host = c_xml[0].get('host', None)
         port = int(c_xml[0].get('port', 0))
 
         c_xml = config_xml.findall('cache')
         if not c_xml:
-            _parse_error('cache')
+            _config_xml_error('cache')
         cache_size = float(c_xml[0].get('size', -1))
         staging_path = c_xml[0].get('path', None)
 
         attrs = ('type', 'path')
         e_xml = config_xml.findall('extra_dir')
         if not e_xml:
-            _parse_error('extra_dir')
+            _config_xml_error('extra_dir')
         extra_dirs = [dict(((k, e.get(k)) for k in attrs)) for e in e_xml]
 
         return {
@@ -139,36 +142,59 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
     
     store_type = 'irods'
     
-    #def _get_bucket(self, bucket_name):
-    #def _key_exists(self, rel_path):
-
     def __init__(self, config, config_dict):
         super(IRODSObjectStore, self).__init__(config, config_dict)
 
-        auth_dict = config_dict['auth']
+        auth_dict = config_dict.get('auth')
+        if auth_dict is None:
+            _config_dict_error('auth')
+
         self.username = auth_dict.get('username')
+        if self.username is None:
+            _config_dict_error('auth->username')
         self.password = auth_dict.get('password')
+        if self.password is None:
+            _config_dict_error('auth->password')
 
         resource_dict = config_dict['resource']
+        if resource_dict is None:
+            _config_dict_error('resource')
         self.resource = resource_dict.get('name')
+        if self.resource is None:
+            _config_dict_error('resource->name')
 
         zone_dict = config_dict['zone']
+        if zone_dict is None:
+            _config_dict_error('zone')
         self.zone = zone_dict.get('name')
+        if self.zone is None:
+            _config_dict_error('zone->name')
 
         connection_dict = config_dict['connection']
+        if connection_dict is None:
+            _config_dict_error('connection')
         self.host = connection_dict.get('host')
+        if self.host is None:
+            _config_dict_error('connection->host')
         self.port = connection_dict.get('port')
+        if self.port is None:
+            _config_dict_error('connection->port')
 
         cache_dict = config_dict['cache']
+        if cache_dict is None:
+            _config_dict_error('cache')
         self.cache_size = cache_dict.get('size', -1)
+        if self.cache_size is None:
+            _config_dict_error('cache->size')
         self.staging_path = cache_dict.get('path') or self.config.object_store_cache_path
+        if self.staging_path is None:
+            _config_dict_error('cache->path')
 
         extra_dirs = dict((e['type'], e['path']) for e in config_dict.get('extra_dirs', []))
+        if not extra_dirs:
+            _config_dict_error('extra_dirs')
         self.extra_dirs.update(extra_dirs)
 
-        log.debug("Object cache dir: %s", self.staging_path)
-        log.debug("Job work dir: %s", self.extra_dirs['job_work'])
-
         self._initialize()
         
     def __del__(self):
@@ -193,8 +219,12 @@ def _initialize(self):
 
     def _configure_connection(self, host='localhost', port='1247', user='rods', password='rods', zone='tempZone'):
         with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
-            # Throws NetworkException if connection fails  
-            session.pool.get_connection()
+            # Throws NetworkException if connection fails
+            try:  
+                session.pool.get_connection()
+            except NetworkException as e:
+                log.error('Could not create iRODS session: ' + str(e))
+                raise
             return session
 
     @classmethod
@@ -207,7 +237,7 @@ def to_dict(self):
         return as_dict
 
     def __cache_monitor(self):
-        time.sleep(2)  # Wait for things to load before starting the monitor
+        time.sleep(5)  # Wait for things to load before starting the monitor
         while self.running:
             total_size = 0
             # Is this going to be too expensive of an operation to be done frequently?
diff --git a/test/integration/objectstore/test_irods.py b/test/integration/objectstore/test_irods.py
index 19bf3a388e24..f70f036630c6 100644
--- a/test/integration/objectstore/test_irods.py
+++ b/test/integration/objectstore/test_irods.py
@@ -9,169 +9,64 @@
 from irods.exception import DataObjectDoesNotExist
 from irods.session import iRODSSession
 
-from galaxy_test.driver import integration_util
+from galaxy.config import GalaxyAppConfiguration
+from galaxy.objectstore.irods import IRODSObjectStore
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 
-class IrodsObjectStoreIntegrationTestCase(integration_util.IntegrationTestCase):
-
-    container_name = "irods_server"
-
-    @classmethod
-    def handle_galaxy_config_kwds(cls, config):
-        config["object_store_config_file"] = "object_store_conf.xml" 
-
-    @classmethod
-    def setUpClass(cls):
-        super(IrodsObjectStoreIntegrationTestCase, cls).setUpClass()
-        IrodsObjectStoreIntegrationTestCase.start_irods_server(container_name=IrodsObjectStoreIntegrationTestCase.container_name)
-
-        # Let the server start before running the test
-        time.sleep(10)
-
-    @classmethod
-    def tearDownClass(cls): 
-        super(IrodsObjectStoreIntegrationTestCase, cls).tearDownClass()
-        IrodsObjectStoreIntegrationTestCase.stop_irods_server(container_name=IrodsObjectStoreIntegrationTestCase.container_name)       
-
-    @classmethod
-    def start_irods_server(cls, container_name, irods_port=1247, docker_image='kxk302/irods-server:0.1'):
-        start_server = ['docker', 'run', '-h', 'localhost', '-p', '{port}:1247'.format(port=irods_port), '-d', '--name', container_name, docker_image]
-        subprocess.check_call(start_server) 
-        
-    @classmethod
-    def stop_irods_server(cls, container_name):
-        subprocess.check_call(['docker', 'rm', '-f', container_name])
-
-    def test_get_existing_collection(self):
-        with iRODSSession(host='localhost', 
-            port='1247', 
-            user='rods',  
-            password='rods', 
-            zone='tempZone') as session:
-
-            zone='tempZone'
-            user='rods'
-        
-            aCollection = "/" + zone + "/home/" + user
-
-            coll = session.collections.get(aCollection)
-            assert coll.path == aCollection, "Error! Got wrong collection path"
-            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
-            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!"
-
-    def test_create_delete_new_collection(self):
-        with iRODSSession(host='localhost', 
-            port='1247', 
-            user='rods',  
-            password='rods', 
-            zone='tempZone') as session:
-
-            zone='tempZone'
-            user='rods'
-
-            newCollection = "/" + zone + "/home/" + user + "/testdir"
-    
-            coll = session.collections.create(newCollection)
-            assert coll.path == newCollection, "Error! Got wrong collection path"
-            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
-            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!" 
-
-            coll.remove(recurse=True, force=True)
-
-            with pytest.raises(CollectionDoesNotExist):
-                coll = session.collections.get(newCollection)
-
-    def test_create_delete_new_data_object(self):
-        with iRODSSession(host='localhost', 
-            port='1247', 
-            user='rods',  
-            password='rods', 
-            zone='tempZone') as session:
-
-            zone='tempZone'
-            user='rods'
-     
-            newCollection = "/" + zone + "/home/" + user + "/testdir"
-            newDataObject = newCollection + "/testDataObject"
-
-            # Create new collection
-            coll = session.collections.create(newCollection)
-            assert coll.path == newCollection, "Error! Got wrong collection path"
-            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
-            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!"
-
-            # Create data object
-            obj = session.data_objects.create(newDataObject)
-            assert obj.name == "testDataObject", "Error! Got wrong data object"
-
-            # Delete data object
-            obj.unlink(force=True)
-
-            # Get data object
-            with pytest.raises(DataObjectDoesNotExist):
-                obj = session.data_objects.get(newDataObject)
-
-            # Delete collection
-            coll.remove(recurse=True, force=True)
-
-            with pytest.raises(CollectionDoesNotExist):
-                coll = session.collections.get(newCollection)
- 
-    def test_populate_fetch_new_data_object(self):
-        with iRODSSession(host='localhost', 
-            port='1247', 
-            user='rods',  
-            password='rods', 
-            zone='tempZone') as session:
-
-            zone='tempZone'
-            user='rods'
-
-            newCollection = "/" + zone + "/home/" + user + "/testdir"
-            fileName = "irods_beginner_training_2016.pdf"
-            fileNamePath = os.path.join(SCRIPT_DIRECTORY, fileName)
-            backupFileName = "irods_beginner_training_2016_backup.pdf"
-            backupFileNamePath = os.path.join(SCRIPT_DIRECTORY, backupFileName)
- 
-            # Copy file from backup
-            shutil.copyfile(fileNamePath, backupFileNamePath)
-
-            # Create new collection 
-            coll = session.collections.create(newCollection)
-            assert coll.path == newCollection, "Error! Got wrong collection path"
-            assert len(coll.subcollections) == 0, "Error! Collection should not have any subcollections!"
-            assert len(coll.data_objects) == 0, "Error! Collection should not have any data objects!" 
-
-            # Create new data object
-            session.data_objects.put(backupFileNamePath, newCollection + "/" + backupFileName)
-    
-            # Delete local file
-            os.remove(backupFileNamePath)         
-    
-            # Get the data object back
-            obj = session.data_objects.get(newCollection + "/" + backupFileName)
-    
-            # Write the data object to the file system
-            with obj.open("r") as f_in, open(backupFileNamePath, "wb") as f_out:
-                f_out.write(f_in.read())
-    
-            # Assert the size of file fetched from iRODS matches the local backup copy
-            assert os.path.getsize(fileNamePath) == os.path.getsize(backupFileNamePath), "Error! Size of file fetched from iRODS does not match the size of the original file" 
-    
-            # Delete local file
-            os.remove(backupFileNamePath)         
-    
-            # Delete data object
-            obj.unlink(force=True)
-    
-            # Get data object
-            with pytest.raises(DataObjectDoesNotExist):
-                obj = session.data_objects.get(newCollection + "/" + backupFileName)
-    
-            # Delete collection
-            coll.remove(recurse=True, force=True)
-    
-            # Get collection
-            with pytest.raises(CollectionDoesNotExist):
-                coll = session.collections.get(newCollection)
+CONFIG_DICT = {
+    'auth': {
+        'username': 'rods',
+        'password': 'rods'
+    },
+    'resource': {
+        'name': 'demoResc'
+    },
+    'zone': {
+        'name': 'tempZone'
+    },
+    'connection': {
+        'host': 'localhost',
+        'port': '1247'
+    },
+    'cache': {
+        'size': 1000.0, 
+        'path': 'database/object_store_cache'
+    },
+    'extra_dirs': [{'type': 'job_work', 'path': 'database/job_working_directory_irods'}, {'type': 'temp', 'path': 'database/tmp_irods'}]
+}
+
+#class IrodsObjectStoreIntegrationTestCase(object):
+
+#config = None 
+#config_dict = None
+#irods_os = None
+
+@pytest.fixture(scope='module')
+def setup_module():
+    config = GalaxyAppConfiguration()
+
+    config.object_store_cache_path = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/object_store_cache'
+    config.file_path = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/objects'
+    config.object_store_store_by = 'uuid'
+    config.object_store_check_old_style = False
+    config.jobs_directory = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/job_working_directory_k5dk3021'
+    config.new_file_path = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/new_files_path_sej_tqh7'
+
+    config_dict = CONFIG_DICT
+
+    irods_os = IRODSObjectStore(config, CONFIG_DICT)
+    return irods_os
+
+#    @classmethod
+#def teardown_module(module):
+#     del irods_os
+#     del config_dict
+#     del config
+
+def test_instantiate_irods(setup_module):
+    print('**********************')
+    print('setup_module.to_dict()')
+    print(setup_module.to_dict())
+    print('**********************')
+    assert 1 == 1

From 0c8acb3d68e5985427b28dce198604a3c79f9174 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 19 Mar 2020 16:36:59 -0400
Subject: [PATCH 551/853] Passing the resource name in to create method, since
 now we can have multiple resources (S3, unix file system, etc.)

---
 lib/galaxy/objectstore/irods.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index a9ec524cfb11..14f99b22339b 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -440,7 +440,7 @@ def _download(self, rel_path):
 
         log.debug("Pulled data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
         
-        with data_obj.open('rb') as data_obj_fp, open(self._get_cache_path(rel_path), "wb") as cache_fp:
+        with data_obj.open('r') as data_obj_fp, open(self._get_cache_path(rel_path), "wb") as cache_fp:
             content = data_obj_fp.read()
             cache_fp.write(content)
         return True
@@ -470,7 +470,7 @@ def _push_to_os(self, rel_path, source_file=None, from_string=None):
                 log.debug("Wanted to push file '%s' to iRODS collection '%s' but its size is 0; skipping.", source_file, rel_path)
                 return True
             if from_string:
-                data_obj = self.session.data_objects.create(data_object_path, recurse=True, **options)
+                data_obj = self.session.data_objects.create(data_object_path, self.resource, **options)
                 with data_obj.open('w') as data_obj_fp:
                     data_obj_fp.write(from_string)
                 log.debug("Pushed data from string '%s' to collection '%s'", from_string, data_object_path)
@@ -486,7 +486,7 @@ def _push_to_os(self, rel_path, source_file=None, from_string=None):
                     file_content = content_file.read()
                 
                 # Write to file in subcollection created above
-                data_obj = self.session.data_objects.create(data_object_path, recurse=True, **options)
+                data_obj = self.session.data_objects.create(data_object_path, self.resource, **options)
                 with data_obj.open('w') as data_obj_fp:
                     data_obj_fp.write(file_content)
 
@@ -548,7 +548,6 @@ def exists(self, obj, **kwargs):
 
     def create(self, obj, **kwargs):
         if not self.exists(obj, **kwargs):
-
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
             extra_dir_at_root = kwargs.get('extra_dir_at_root', False)

From 2764716ce32a3c05c4824910f48c14f2ea4a0849 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 10:38:08 -0400
Subject: [PATCH 552/853] More changes per code review feedback.

---
 lib/galaxy/objectstore/irods.py               |  82 +-----------------
 .../irods_beginner_training_2016.pdf          | Bin 497249 -> 0 bytes
 test/integration/objectstore/test_irods.py    |  72 ---------------
 .../integration/test_datatype_upload_irods.py |  31 +------
 4 files changed, 8 insertions(+), 177 deletions(-)
 delete mode 100644 test/integration/objectstore/irods_beginner_training_2016.pdf
 delete mode 100644 test/integration/objectstore/test_irods.py

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 14f99b22339b..951fa8926d89 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -29,7 +29,6 @@
     umask_fix_perms,
 )
 from galaxy.util.path import safe_relpath
-from galaxy.util.sleeper import Sleeper
 from ..objectstore import (
     DiskObjectStore,
     local_extra_dirs,
@@ -207,15 +206,6 @@ def _initialize(self):
         self.home =  "/" + self.zone + "/home/" + self.username
 
         self.session = self._configure_connection(host=self.host, port=self.port, user=self.username, password=self.password, zone=self.zone)
-        # Clean cache only if value is set in galaxy config file
-        if self.cache_size != -1:
-            # Convert GBs to bytes for comparison
-            self.cache_size = self.cache_size * bytesize.SUFFIX_TO_BYTES['GI']
-            # Helper for interruptable sleep
-            self.sleeper = Sleeper()
-            self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
-            self.cache_monitor_thread.start()
-            log.info("Cache cleaner manager started")
 
     def _configure_connection(self, host='localhost', port='1247', user='rods', password='rods', zone='tempZone'):
         with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
@@ -236,70 +226,6 @@ def to_dict(self):
         as_dict.update(self._config_to_dict())
         return as_dict
 
-    def __cache_monitor(self):
-        time.sleep(5)  # Wait for things to load before starting the monitor
-        while self.running:
-            total_size = 0
-            # Is this going to be too expensive of an operation to be done frequently?
-            file_list = []
-            for dirpath, _, filenames in os.walk(self.staging_path):
-                for filename in filenames:
-                    filepath = os.path.join(dirpath, filename)
-                    file_size = os.path.getsize(filepath)
-                    total_size += file_size
-                    # Get the time given file was last accessed
-                    last_access_time = time.localtime(os.stat(filepath)[7])
-                    # Compose a tuple of the access time and the file path
-                    file_tuple = last_access_time, filepath, file_size
-                    file_list.append(file_tuple)
-            # Sort the file list (based on access time)
-            file_list.sort()
-            # Initiate cleaning once within 10% of the defined cache size?
-            cache_limit = self.cache_size * 0.9
-            if total_size > cache_limit:
-                log.info("Initiating cache cleaning: current cache size: %s; clean until smaller than: %s",
-                         convert_bytes(total_size), convert_bytes(cache_limit))
-                # How much to delete? If simply deleting up to the cache-10% limit,
-                # is likely to be deleting frequently and may run the risk of hitting
-                # the limit - maybe delete additional #%?
-                # For now, delete enough to leave at least 10% of the total cache free
-                delete_this_much = total_size - cache_limit
-                self.__clean_cache(file_list, delete_this_much)
-            self.sleeper.sleep(30)  # Test cache size every 30 seconds?
-
-    def __clean_cache(self, file_list, delete_this_much):
-        """ Keep deleting files from the file_list until the size of the deleted
-        files is greater than the value in delete_this_much parameter.
-
-        :type file_list: list
-        :param file_list: List of candidate files that can be deleted. This method
-            will start deleting files from the beginning of the list so the list
-            should be sorted accordingly. The list must contains 3-element tuples,
-            positioned as follows: position 0 holds file last accessed timestamp
-            (as time.struct_time), position 1 holds file path, and position 2 has
-            file size (e.g., (<access time>, /mnt/data/dataset_1.dat), 472394)
-
-        :type delete_this_much: int
-        :param delete_this_much: Total size of files, in bytes, that should be deleted.
-        """
-        # Keep deleting datasets from file_list until deleted_amount does not
-        # exceed delete_this_much; start deleting from the front of the file list,
-        # which assumes the oldest files come first on the list.
-        deleted_amount = 0
-        for entry in file_list:
-            if deleted_amount < delete_this_much:
-                deleted_amount += entry[2]
-                os.remove(entry[1])
-                # Debugging code for printing deleted files' stats
-                # folder, file_name = os.path.split(f[1])
-                # file_date = time.strftime("%m/%d/%y %H:%M:%S", f[0])
-                # log.debug("%s. %-25s %s, size %s (deleted %s/%s)" \
-                #     % (i, file_name, convert_bytes(f[2]), file_date, \
-                #     convert_bytes(deleted_amount), convert_bytes(delete_this_much)))
-            else:
-                log.debug("Cache cleaning done. Total space freed: %s", convert_bytes(deleted_amount))
-                return
-
     def _fix_permissions(self, rel_path):
         """ Set permissions on rel_path"""
         for basedir, _, files in os.walk(rel_path):
@@ -445,7 +371,7 @@ def _download(self, rel_path):
             cache_fp.write(content)
         return True
 
-    def _push_to_os(self, rel_path, source_file=None, from_string=None):
+    def _push_to_irods(self, rel_path, source_file=None, from_string=None):
         """
         Push the file pointed to by ``rel_path`` to the iRODS. Extract folder name 
         from rel_path as iRODS collection name, and extract file name from rel_path
@@ -539,7 +465,7 @@ def exists(self, obj, **kwargs):
 
         # TODO: Sync should probably not be done here. Add this to an async upload stack?
         if in_cache and not in_irods:
-            self._push_to_os(rel_path, source_file=self._get_cache_path(rel_path))
+            self._push_to_irods(rel_path, source_file=self._get_cache_path(rel_path))
             return True
         elif in_irods:
             return True
@@ -572,7 +498,7 @@ def create(self, obj, **kwargs):
             if not dir_only:
                 rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
-                self._push_to_os(rel_path, from_string='')
+                self._push_to_irods(rel_path, from_string='')
 
     def empty(self, obj, **kwargs):
         if self.exists(obj, **kwargs):
@@ -725,7 +651,7 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
             else:
                 source_file = self._get_cache_path(rel_path)
             # Update the file on iRODS 
-            self._push_to_os(rel_path, source_file)
+            self._push_to_irods(rel_path, source_file)
         else:
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
diff --git a/test/integration/objectstore/irods_beginner_training_2016.pdf b/test/integration/objectstore/irods_beginner_training_2016.pdf
deleted file mode 100644
index 2344e41888a526cb3697b1c1b6c241a7cd974069..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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diff --git a/test/integration/objectstore/test_irods.py b/test/integration/objectstore/test_irods.py
deleted file mode 100644
index f70f036630c6..000000000000
--- a/test/integration/objectstore/test_irods.py
+++ /dev/null
@@ -1,72 +0,0 @@
-import os
-import pytest
-import shutil
-import ssl
-import subprocess
-import time
-
-from irods.exception import CollectionDoesNotExist
-from irods.exception import DataObjectDoesNotExist
-from irods.session import iRODSSession
-
-from galaxy.config import GalaxyAppConfiguration
-from galaxy.objectstore.irods import IRODSObjectStore
-
-SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-
-CONFIG_DICT = {
-    'auth': {
-        'username': 'rods',
-        'password': 'rods'
-    },
-    'resource': {
-        'name': 'demoResc'
-    },
-    'zone': {
-        'name': 'tempZone'
-    },
-    'connection': {
-        'host': 'localhost',
-        'port': '1247'
-    },
-    'cache': {
-        'size': 1000.0, 
-        'path': 'database/object_store_cache'
-    },
-    'extra_dirs': [{'type': 'job_work', 'path': 'database/job_working_directory_irods'}, {'type': 'temp', 'path': 'database/tmp_irods'}]
-}
-
-#class IrodsObjectStoreIntegrationTestCase(object):
-
-#config = None 
-#config_dict = None
-#irods_os = None
-
-@pytest.fixture(scope='module')
-def setup_module():
-    config = GalaxyAppConfiguration()
-
-    config.object_store_cache_path = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/object_store_cache'
-    config.file_path = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/objects'
-    config.object_store_store_by = 'uuid'
-    config.object_store_check_old_style = False
-    config.jobs_directory = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/job_working_directory_k5dk3021'
-    config.new_file_path = '/private/var/folders/pk/jwrvp5115zg81729h2x46f080000gn/T/tmpkffyrtx1/tmpb5xoh_67/tmp_ry_69z8/database/new_files_path_sej_tqh7'
-
-    config_dict = CONFIG_DICT
-
-    irods_os = IRODSObjectStore(config, CONFIG_DICT)
-    return irods_os
-
-#    @classmethod
-#def teardown_module(module):
-#     del irods_os
-#     del config_dict
-#     del config
-
-def test_instantiate_irods(setup_module):
-    print('**********************')
-    print('setup_module.to_dict()')
-    print(setup_module.to_dict())
-    print('**********************')
-    assert 1 == 1
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index c1de59b14762..06fb628c5a04 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -13,33 +13,15 @@
 from galaxy.util.hash_util import md5_hash_file
 from galaxy_test.driver import integration_util
 from .test_upload_configuration_options import BaseUploadContentConfigurationInstance
+from .test_datatype_upload import TEST_CASES
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-TEST_FILE_DIR = '%s/../../lib/galaxy/datatypes/test' % SCRIPT_DIRECTORY
-TestData = collections.namedtuple('UploadDatatypesData', 'path datatype uploadable')
 GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
 DATATYPES_CONFIG = os.path.join(GALAXY_ROOT, 'lib/galaxy/config/sample/datatypes_conf.xml.sample')
 PARENT_SNIFFER_MAP = {'fastqsolexa': 'fastq'}
 OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "irods_object_store_conf.xml")
-
-
-def find_datatype(registry, filename):
-    # match longest extension first
-    sorted_extensions = sorted(registry.datatypes_by_extension.keys(), key=len, reverse=True)
-    for extension in sorted_extensions:
-        if filename.endswith(extension) or filename.startswith(extension):
-            return registry.datatypes_by_extension[extension]
-    raise Exception("Couldn't guess datatype for file '%s'" % filename)
-
-
-def collect_test_data(registry):
-    test_files = [f for f in os.listdir(TEST_FILE_DIR) if "." in f]
-    files = [os.path.join(TEST_FILE_DIR, f) for f in test_files]
-    datatypes = [find_datatype(registry, f) for f in test_files]
-    uploadable = [datatype.file_ext in registry.upload_file_formats for datatype in datatypes]
-    test_data_description = [TestData(*items) for items in zip(files, datatypes, uploadable)]
-    return {os.path.basename(data.path): data for data in test_data_description}
-
+# Run test for only the first 10 test files
+IRODS_TEST_CASES = dict(list(TEST_CASES.items())[0:10])
 
 class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
     framework_tool_and_types = False
@@ -49,22 +31,17 @@ class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
     def handle_galaxy_config_kwds(cls, config):
         config["object_store_config_file"] = OBJECT_STORE_CONFIG_FILE
 
-
 instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
 
-
 @pytest.fixture
 def temp_file():
     with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
         yield fh
 
-
 registry = Registry()
 registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG)
-TEST_CASES = collect_test_data(registry)
-
 
-@pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))
+@pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
     is_compressed = False
     for is_method in (is_bz2, is_gzip, is_zip):

From 2b8a510fabae3ee142abc921b38cf37bc017da60 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 11:18:02 -0400
Subject: [PATCH 553/853] Added helper method to avoid duplicate code

---
 test/integration/test_datatype_upload.py      |  3 ++
 .../integration/test_datatype_upload_irods.py | 43 +------------------
 2 files changed, 5 insertions(+), 41 deletions(-)

diff --git a/test/integration/test_datatype_upload.py b/test/integration/test_datatype_upload.py
index 83ac60f82c24..e139c38c2f8b 100644
--- a/test/integration/test_datatype_upload.py
+++ b/test/integration/test_datatype_upload.py
@@ -61,6 +61,9 @@ def temp_file():
 
 @pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
+    upload_datatype_helper(instance, test_data, temp_file)
+
+def upload_datatype_helper(instance, test_data, temp_file):
     is_compressed = False
     for is_method in (is_bz2, is_gzip, is_zip):
         is_compressed = is_method(test_data.path)
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 06fb628c5a04..de3678f78225 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -14,6 +14,7 @@
 from galaxy_test.driver import integration_util
 from .test_upload_configuration_options import BaseUploadContentConfigurationInstance
 from .test_datatype_upload import TEST_CASES
+from .test_datatype_upload import upload_datatype_helper
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
@@ -43,44 +44,4 @@ def temp_file():
 
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
-    is_compressed = False
-    for is_method in (is_bz2, is_gzip, is_zip):
-        is_compressed = is_method(test_data.path)
-        if is_compressed:
-            break
-    with open(test_data.path, 'rb') as content:
-        if hasattr(test_data.datatype, 'sniff') or 'false' in test_data.path:
-            file_type = 'auto'
-        else:
-            file_type = test_data.datatype.file_ext
-        dataset = instance.dataset_populator.new_dataset(instance.history_id, content=content, wait=False, file_type=file_type)
-    dataset = instance.dataset_populator.get_history_dataset_details(instance.history_id, dataset=dataset, assert_ok=False)
-    expected_file_ext = test_data.datatype.file_ext
-    # State might be error if the datatype can't be uploaded
-    if dataset['state'] == 'error' and not test_data.uploadable:
-        # Some things can't be uploaded, if attempting to upload these datasets we mention why
-        assert 'invalid' in dataset['misc_info'] or 'unsupported' in dataset['misc_info']
-        return
-    elif dataset['state'] == 'error' and 'empty' in dataset['misc_info']:
-        return
-    else:
-        # state should be OK
-        assert dataset['state'] == 'ok'
-    # Check that correct datatype has been detected
-    file_ext = dataset['file_ext']
-    if 'false' in test_data.path:
-        # datasets with false in their name are not of a specific datatype
-        assert file_ext != PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
-    else:
-        assert file_ext == PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
-    datatype = registry.datatypes_by_extension[file_ext]
-    datatype_compressed = getattr(datatype, "compressed", False)
-    if not is_compressed or datatype_compressed:
-        # download file and verify it hasn't been manipulated
-        temp_file.write(instance.dataset_populator.get_history_dataset_content(history_id=instance.history_id,
-                                                                               dataset=dataset,
-                                                                               type='bytes',
-                                                                               assert_ok=False,
-                                                                               raw=True))
-        temp_file.flush()
-        assert md5_hash_file(test_data.path) == md5_hash_file(temp_file.name)
+    upload_datatype_helper(instance, test_data, temp_file)
\ No newline at end of file

From a04acabb1188baae7fcbbf14caffc14549385779 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 11:35:34 -0400
Subject: [PATCH 554/853] Removed un-used imports from iRODS integration test

---
 test/integration/test_datatype_upload_irods.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index de3678f78225..a5d22d45fcc3 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,16 +1,9 @@
-import collections
 import os
 import tempfile
 
 import pytest
 
 from galaxy.datatypes.registry import Registry
-from galaxy.util.checkers import (
-    is_bz2,
-    is_gzip,
-    is_zip
-)
-from galaxy.util.hash_util import md5_hash_file
 from galaxy_test.driver import integration_util
 from .test_upload_configuration_options import BaseUploadContentConfigurationInstance
 from .test_datatype_upload import TEST_CASES

From 406662135859d565010b3e75fb154f994196f29b Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 11:54:23 -0400
Subject: [PATCH 555/853] Ran flake8 linter

---
 test/integration/test_datatype_upload_irods.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index a5d22d45fcc3..b8b7e13f3e44 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -5,9 +5,10 @@
 
 from galaxy.datatypes.registry import Registry
 from galaxy_test.driver import integration_util
-from .test_upload_configuration_options import BaseUploadContentConfigurationInstance
-from .test_datatype_upload import TEST_CASES
-from .test_datatype_upload import upload_datatype_helper
+
+from .test_datatype_upload import TEST_CASES, upload_datatype_helper
+from .test_upload_configuration_options import \
+    BaseUploadContentConfigurationInstance
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
@@ -17,6 +18,7 @@
 # Run test for only the first 10 test files
 IRODS_TEST_CASES = dict(list(TEST_CASES.items())[0:10])
 
+
 class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
     framework_tool_and_types = False
     datatypes_conf_override = DATATYPES_CONFIG
@@ -25,16 +27,20 @@ class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
     def handle_galaxy_config_kwds(cls, config):
         config["object_store_config_file"] = OBJECT_STORE_CONFIG_FILE
 
+
 instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
 
+
 @pytest.fixture
 def temp_file():
     with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
         yield fh
 
+
 registry = Registry()
 registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG)
 
+
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
-    upload_datatype_helper(instance, test_data, temp_file)
\ No newline at end of file
+    upload_datatype_helper(instance, test_data, temp_file)

From ee514350359f7b700fb8064d8b16f801ea6669d2 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 12:56:19 -0400
Subject: [PATCH 556/853] More code cleanup per flake8 linter

---
 lib/galaxy/objectstore/irods.py | 71 ++++++++++++++++-----------------
 1 file changed, 35 insertions(+), 36 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 951fa8926d89..a0fcae9c42f2 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -6,8 +6,6 @@
 import os
 from pathlib import Path
 import shutil
-import threading
-import time
 
 try:
     import irods
@@ -24,29 +22,29 @@
     ObjectNotFound
 )
 from galaxy.util import (
-    bytesize,
     directory_hash_id,
     umask_fix_perms,
 )
 from galaxy.util.path import safe_relpath
 from ..objectstore import (
     DiskObjectStore,
-    local_extra_dirs,
-    convert_bytes
 )
 
 IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this feature, please install it')
 
 log = logging.getLogger(__name__)
 
+
 def _config_xml_error(tag):
     msg = 'No {tag} element in config XML tree'.format(tag=tag)
     raise Exception(msg)
 
+
 def _config_dict_error(key):
     msg = 'No {key} key in config dictionary'.forma(key=key)
     raise Exception(msg)
 
+
 def parse_config_xml(config_xml):
     try:
         a_xml = config_xml.findall('auth')
@@ -109,6 +107,7 @@ def parse_config_xml(config_xml):
         log.exception("Malformed iRODS ObjectStore Configuration XML -- unable to continue.")
         raise
 
+
 class CloudConfigMixin(object):
 
     def _config_to_dict(self):
@@ -133,14 +132,15 @@ def _config_to_dict(self):
             }
         }
 
+
 class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
     """
-    Object store that stores objects as data objects in an iRODS collections. A local cache 
+    Object store that stores objects as data objects in an iRODS collections. A local cache
     exists that is used as an intermediate location for files between Galaxy and iRODS.
     """
-    
+
     store_type = 'irods'
-    
+
     def __init__(self, config, config_dict):
         super(IRODSObjectStore, self).__init__(config, config_dict)
 
@@ -195,7 +195,7 @@ def __init__(self, config, config_dict):
         self.extra_dirs.update(extra_dirs)
 
         self._initialize()
-        
+
     def __del__(self):
         self.session.cleanup()
 
@@ -203,14 +203,14 @@ def _initialize(self):
         if irods is None:
             raise Exception(IRODS_IMPORT_MESSAGE)
 
-        self.home =  "/" + self.zone + "/home/" + self.username
+        self.home = "/" + self.zone + "/home/" + self.username
 
         self.session = self._configure_connection(host=self.host, port=self.port, user=self.username, password=self.password, zone=self.zone)
 
     def _configure_connection(self, host='localhost', port='1247', user='rods', password='rods', zone='tempZone'):
         with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
             # Throws NetworkException if connection fails
-            try:  
+            try:
                 session.pool.get_connection()
             except NetworkException as e:
                 log.error('Could not create iRODS session: ' + str(e))
@@ -276,11 +276,11 @@ def _get_cache_path(self, rel_path):
     # rel_path is file or folder?
     def _get_size_in_irods(self, rel_path):
         p = Path(rel_path)
-        data_object_name =  p.stem + p.suffix
+        data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
         collection_path = self.home + "/" + str(subcollection_name)
-        data_object_path = collection_path + "/" + str(data_object_name) 
+        data_object_path = collection_path + "/" + str(data_object_name)
 
         try:
             data_obj = self.session.data_objects.get(data_object_path)
@@ -292,18 +292,18 @@ def _get_size_in_irods(self, rel_path):
     # rel_path is file or folder?
     def _data_object_exists(self, rel_path):
         p = Path(rel_path)
-        data_object_name =  p.stem + p.suffix
+        data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
         collection_path = self.home + "/" + str(subcollection_name)
-        data_object_path = collection_path + "/" + str(data_object_name) 
+        data_object_path = collection_path + "/" + str(data_object_name)
 
         try:
             self.session.data_objects.get(data_object_path)
-            return True 
+            return True
         except (DataObjectDoesNotExist, CollectionDoesNotExist):
             log.warn("Collection or data object (%s) does not exist", data_object_path)
-            return False 
+            return False
 
     def _in_cache(self, rel_path):
         """ Check if the given dataset is in the local cache and return True if so. """
@@ -346,18 +346,18 @@ def _download(self, rel_path):
         log.debug("Pulling data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
 
         p = Path(rel_path)
-        data_object_name =  p.stem + p.suffix
+        data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
         collection_path = self.home + "/" + str(subcollection_name)
-        data_object_path = collection_path + "/" + str(data_object_name) 
+        data_object_path = collection_path + "/" + str(data_object_name)
         data_obj = None
 
         try:
             data_obj = self.session.data_objects.get(data_object_path)
         except (DataObjectDoesNotExist, CollectionDoesNotExist):
             log.warn("Collection or data object (%s) does not exist", data_object_path)
-            return False 
+            return False
 
         if self.cache_size > 0 and data_obj.__sizeof__() > self.cache_size:
             log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
@@ -365,7 +365,7 @@ def _download(self, rel_path):
             return False
 
         log.debug("Pulled data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
-        
+
         with data_obj.open('r') as data_obj_fp, open(self._get_cache_path(rel_path), "wb") as cache_fp:
             content = data_obj_fp.read()
             cache_fp.write(content)
@@ -373,7 +373,7 @@ def _download(self, rel_path):
 
     def _push_to_irods(self, rel_path, source_file=None, from_string=None):
         """
-        Push the file pointed to by ``rel_path`` to the iRODS. Extract folder name 
+        Push the file pointed to by ``rel_path`` to the iRODS. Extract folder name
         from rel_path as iRODS collection name, and extract file name from rel_path
         as iRODS data object name.
         If ``source_file`` is provided, push that file instead while
@@ -381,7 +381,7 @@ def _push_to_irods(self, rel_path, source_file=None, from_string=None):
         If ``from_string`` is provided, set contents of the file to the value of the string.
         """
         p = Path(rel_path)
-        data_object_name =  p.stem + p.suffix
+        data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
         source_file = source_file if source_file else self._get_cache_path(rel_path)
@@ -390,7 +390,7 @@ def _push_to_irods(self, rel_path, source_file=None, from_string=None):
         if os.path.exists(source_file):
             # Check if the data object exists in iRODS
             collection_path = self.home + "/" + str(subcollection_name)
-            data_object_path = collection_path + "/" + str(data_object_name) 
+            data_object_path = collection_path + "/" + str(data_object_name)
             exists = self.session.data_objects.exists(data_object_path)
             if os.path.getsize(source_file) == 0 and exists:
                 log.debug("Wanted to push file '%s' to iRODS collection '%s' but its size is 0; skipping.", source_file, rel_path)
@@ -403,14 +403,14 @@ def _push_to_irods(self, rel_path, source_file=None, from_string=None):
             else:
                 start_time = datetime.now()
                 log.debug("Pushing cache file '%s' of size %s bytes to collection '%s'", source_file, os.path.getsize(source_file), rel_path)
-                
+
                 # Create sub-collection first
                 self.session.collections.create(collection_path, recurse=True)
 
                 file_content = None
                 with open(source_file, 'rb') as content_file:
                     file_content = content_file.read()
-                
+
                 # Write to file in subcollection created above
                 data_obj = self.session.data_objects.create(data_object_path, self.resource, **options)
                 with data_obj.open('w') as data_obj_fp:
@@ -446,7 +446,7 @@ def exists(self, obj, **kwargs):
         # Check cache
         if self._in_cache(rel_path):
             in_cache = True
-        # Check iRODS 
+        # Check iRODS
         in_irods = self._data_object_exists(rel_path)
 
         # dir_only does not get synced so shortcut the decision
@@ -465,7 +465,6 @@ def exists(self, obj, **kwargs):
 
         # TODO: Sync should probably not be done here. Add this to an async upload stack?
         if in_cache and not in_irods:
-            self._push_to_irods(rel_path, source_file=self._get_cache_path(rel_path))
             return True
         elif in_irods:
             return True
@@ -547,7 +546,7 @@ def delete(self, obj, entire_dir=False, **kwargs):
                     return False
 
                 cols = col.walk()
-                # Traverse the tree only one level deep 
+                # Traverse the tree only one level deep
                 for _ in range(2):
                     # get next result
                     _, _, data_objects = next(cols)
@@ -563,11 +562,11 @@ def delete(self, obj, entire_dir=False, **kwargs):
                 os.unlink(self._get_cache_path(rel_path))
                 # Delete from irods as well
                 p = Path(rel_path)
-                data_object_name =  p.stem + p.suffix
+                data_object_name = p.stem + p.suffix
                 subcollection_name = p.parent
 
                 collection_path = self.home + "/" + str(subcollection_name)
-                data_object_path = collection_path + "/" + str(data_object_name) 
+                data_object_path = collection_path + "/" + str(data_object_name)
 
                 try:
                     data_obj = self.session.data_objects.get(data_object_path)
@@ -576,7 +575,7 @@ def delete(self, obj, entire_dir=False, **kwargs):
                     return True
                 except (DataObjectDoesNotExist, CollectionDoesNotExist):
                     log.info("Collection or data object (%s) does not exist", data_object_path)
-                    return True 
+                    return True
 
         except OSError:
             log.exception('%s delete error', self.get_filename(obj, **kwargs))
@@ -650,7 +649,7 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
                     log.exception("Trouble copying source file '%s' to cache '%s'", source_file, cache_file)
             else:
                 source_file = self._get_cache_path(rel_path)
-            # Update the file on iRODS 
+            # Update the file on iRODS
             self._push_to_irods(rel_path, source_file)
         else:
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
@@ -662,13 +661,13 @@ def get_object_url(self, obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
 
             p = Path(rel_path)
-            data_object_name =  p.stem + p.suffix
+            data_object_name = p.stem + p.suffix
             subcollection_name = p.parent
 
             collection_path = self.home + "/" + str(subcollection_name)
             data_object_path = collection_path + "/" + str(data_object_name)
-            
+
             return data_object_path
 
     def get_store_usage_percent(self):
-        return 0.0
\ No newline at end of file
+        return 0.0

From 1d3d3d58f868daed9c63142bbcba2e4c8036c288 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 13:23:25 -0400
Subject: [PATCH 557/853] More flake8 linyer changes

---
 test/unit/objectstore/test_irods.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/test/unit/objectstore/test_irods.py b/test/unit/objectstore/test_irods.py
index 43cc604b90f1..d7c6f57fb38f 100644
--- a/test/unit/objectstore/test_irods.py
+++ b/test/unit/objectstore/test_irods.py
@@ -4,7 +4,6 @@
 import pytest
 
 from galaxy.objectstore.irods import parse_config_xml
-from galaxy.objectstore.irods import IRODSObjectStore
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 
@@ -17,6 +16,7 @@
 CONFIG_FILE_NAME_NO_AUTH = 'irods_object_store_conf_no_auth.xml'
 CONFIG_FILE_NO_AUTH = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME_NO_AUTH)
 
+
 def test_parse_valid_config_xml():
     tree = ET.parse(CONFIG_FILE)
     root = tree.getroot()
@@ -35,14 +35,16 @@ def test_parse_valid_config_xml():
     assert config['extra_dirs'][1]['type'] == 'temp'
     assert config['extra_dirs'][1]['path'] == 'database/tmp_irods'
 
+
 def test_parse_config_xml_no_extra_dir():
     tree = ET.parse(CONFIG_FILE_NO_EXTRA_DIR)
     root = tree.getroot()
-    with pytest.raises(Exception, match='No extra_dir element in XML tree'): 
+    with pytest.raises(Exception, match='No extra_dir element in XML tree'):
         parse_config_xml(root)
 
+
 def test_parse_config_xml_no_auth():
     tree = ET.parse(CONFIG_FILE_NO_AUTH)
     root = tree.getroot()
-    with pytest.raises(Exception, match='No auth element in XML tree'): 
-        parse_config_xml(root)
\ No newline at end of file
+    with pytest.raises(Exception, match='No auth element in XML tree'):
+        parse_config_xml(root)

From 3125b9668ae7aea050160de0ea1590a0d80487e2 Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 23 Mar 2020 12:20:49 -0400
Subject: [PATCH 558/853] Update test/integration/test_datatype_upload_irods.py

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 test/integration/test_datatype_upload_irods.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index b8b7e13f3e44..f197ec45df29 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -3,7 +3,6 @@
 
 import pytest
 
-from galaxy.datatypes.registry import Registry
 from galaxy_test.driver import integration_util
 
 from .test_datatype_upload import TEST_CASES, upload_datatype_helper

From bc40f4df70e6286469b83a5ac214c19f08b5a5df Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 23 Mar 2020 12:21:03 -0400
Subject: [PATCH 559/853] Update test/integration/test_datatype_upload_irods.py

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 test/integration/test_datatype_upload_irods.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index f197ec45df29..ad3a0cb9fb91 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,5 +1,4 @@
 import os
-import tempfile
 
 import pytest
 

From 6f6f4518b7a6c2d4f421d2f071da67072f4e9b2b Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 23 Mar 2020 12:21:34 -0400
Subject: [PATCH 560/853] Update test/integration/test_datatype_upload_irods.py

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 test/integration/test_datatype_upload_irods.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index ad3a0cb9fb91..59f60908bd90 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -5,8 +5,6 @@
 from galaxy_test.driver import integration_util
 
 from .test_datatype_upload import TEST_CASES, upload_datatype_helper
-from .test_upload_configuration_options import \
-    BaseUploadContentConfigurationInstance
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)

From e09631ee97820c909fc8fa981b777ff83d82e8eb Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 23 Mar 2020 12:24:44 -0400
Subject: [PATCH 561/853] Apply suggestions from code review

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 .../integration/test_datatype_upload_irods.py | 25 ++++++-------------
 1 file changed, 7 insertions(+), 18 deletions(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 59f60908bd90..a0046b5b2873 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,23 +1,22 @@
-import os
 
 import pytest
 
 from galaxy_test.driver import integration_util
 
-from .test_datatype_upload import TEST_CASES, upload_datatype_helper
+from .test_datatype_upload import (
+    temp_file,
+    TEST_CASES,
+    upload_datatype_helper,
+    UploadTestDatatypeDataTestCase
+)
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
-DATATYPES_CONFIG = os.path.join(GALAXY_ROOT, 'lib/galaxy/config/sample/datatypes_conf.xml.sample')
-PARENT_SNIFFER_MAP = {'fastqsolexa': 'fastq'}
 OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "irods_object_store_conf.xml")
 # Run test for only the first 10 test files
 IRODS_TEST_CASES = dict(list(TEST_CASES.items())[0:10])
 
 
-class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
-    framework_tool_and_types = False
-    datatypes_conf_override = DATATYPES_CONFIG
+class UploadTestDatatypeDataTestCase(UploadTestDatatypeDataTestCase):
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
@@ -27,16 +26,6 @@ def handle_galaxy_config_kwds(cls, config):
 instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
 
 
-@pytest.fixture
-def temp_file():
-    with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
-        yield fh
-
-
-registry = Registry()
-registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG)
-
-
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
     upload_datatype_helper(instance, test_data, temp_file)

From 0e26ea2a8dfd48682a5171faa67cee18b31bdf40 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 23 Mar 2020 15:34:22 -0400
Subject: [PATCH 562/853] Updating contributors.

---
 CONTRIBUTORS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
index 800d4762594d..d6507a7be425 100644
--- a/CONTRIBUTORS.md
+++ b/CONTRIBUTORS.md
@@ -86,6 +86,7 @@ The following individuals have contributed code to Galaxy:
 * Joachim Jacob <joachim.jacob@gmail.com>
 * Xiaoqian Jiang <jxq198409@hotmail.com>
 * Jim Johnson <jj@umn.edu> <jj@msi.umn.edu>
+* Kaivan Kamali <kxk302@gmail.com>
 * Radhesh Kamath <radhesh@bx.psu.edu>
 * Iyad Kandalaft <ik@iyadk.com>
 * Jan Kanis <jan.code@jankanis.nl>

From 8382f5d438a898ed7eb6bd8b41fb0dd47f6cf5cf Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 24 Mar 2020 09:18:05 -0400
Subject: [PATCH 563/853] Removed stale commnt

---
 lib/galaxy/objectstore/irods.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index a0fcae9c42f2..26af846bddbe 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -463,7 +463,6 @@ def exists(self, obj, **kwargs):
             else:
                 return False
 
-        # TODO: Sync should probably not be done here. Add this to an async upload stack?
         if in_cache and not in_irods:
             return True
         elif in_irods:

From 52c00cacbb43b761069935f3560c389038239887 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 6 Mar 2020 17:16:21 -0500
Subject: [PATCH 564/853] Integration test for GxITs against remote proxies.

Instructions for setting up external goodies documented in docstring.

Small tweaks included:
 - Allow serving proxies on ports different than Galaxy (so it can target external proxies without nginx/uwsgi).
 - Fix up config options a bit.
---
 lib/galaxy/config/__init__.py                 |  3 ++-
 lib/galaxy/managers/interactivetool.py        | 11 +++++++---
 lib/galaxy/webapps/galaxy/config_schema.yml   | 13 +++++++++++
 lib/galaxy_test/driver/driver_util.py         | 15 ++++++++++---
 test/integration/test_interactivetools_api.py | 22 +++++++++++++++++++
 5 files changed, 57 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 47fe8b74cdfd..6f529186bff4 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -634,8 +634,9 @@ def _process_config(self, kwargs):
         self.manage_dynamic_proxy = self.dynamic_proxy_manage  # Set to false if being launched externally
 
         # InteractiveTools propagator mapping file
-        self.interactivetool_map = self.resolve_path(kwargs.get("interactivetools_map", os.path.join(self.data_dir, "interactivetools_map.sqlite")))
+        self.interactivetools_map = self.resolve_path(kwargs.get("interactivetools_map", os.path.join(self.data_dir, "interactivetools_map.sqlite")))
         self.interactivetool_prefix = kwargs.get("interactivetools_prefix", "interactivetool")
+        self.interactivetool_proxy_host = kwargs.get("interactivetool_proxy_host", None)
 
         self.containers_conf = parse_containers_config(self.containers_config_file)
 
diff --git a/lib/galaxy/managers/interactivetool.py b/lib/galaxy/managers/interactivetool.py
index a6504c5c5871..3c7c2d1aa5af 100644
--- a/lib/galaxy/managers/interactivetool.py
+++ b/lib/galaxy/managers/interactivetool.py
@@ -139,7 +139,7 @@ def __init__(self, app):
         self.security = app.security
         self.sa_session = app.model.context
         self.job_manager = app.job_manager
-        self.propagator = InteractiveToolSqlite(app.config.interactivetool_map, app.security.encode_id)
+        self.propagator = InteractiveToolSqlite(app.config.interactivetools_map, app.security.encode_id)
 
     def create_entry_points(self, job, tool, entry_points=None, flush=True):
         entry_points = entry_points or tool.ports
@@ -260,8 +260,13 @@ def remove_entry_point(self, entry_point, flush=True):
     def target_if_active(self, trans, entry_point):
         if entry_point.active and not entry_point.deleted:
             request_host = trans.request.host
-            rval = '%s//%s-%s.%s.%s.%s/' % (trans.request.host_url.split('//', 1)[0], trans.security.encode_id(entry_point.id),
-                    entry_point.token, entry_point.__class__.__name__.lower(), self.app.config.interactivetool_prefix, request_host)
+            protocol = trans.request.host_url.split('//', 1)[0]
+            entry_point_encoded_id = trans.security.encode_id(entry_point.id)
+            entry_point_class = entry_point.__class__.__name__.lower()
+            entry_point_prefix = self.app.config.interactivetool_prefix
+            interactivetool_proxy_host = self.app.config.interactivetool_proxy_host or request_host
+            rval = '%s//%s-%s.%s.%s.%s/' % (protocol, entry_point_encoded_id,
+                    entry_point.token, entry_point_class, entry_point_prefix, interactivetool_proxy_host)
             if entry_point.entry_url:
                 rval = '%s/%s' % (rval.rstrip('/'), entry_point.entry_url.lstrip('/'))
             return rval
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index d8101b9a342a..2a3de5fd8748 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -1004,6 +1004,19 @@ mapping:
         desc: |
           Enable InteractiveTools.
 
+      interactivetools_proxy_host:
+        type: str
+        desc: |
+          Proxy host - assumed to just be hosted on the same hostname and port as
+          Galaxy by default.
+
+      interactivetools_map:
+        type: str
+        default: interactivetools_map.sqlite
+        path_resolves_to: data_dir
+        desc: |
+          Map for interactivetool proxy.
+
       visualizations_visible:
         type: bool
         default: true
diff --git a/lib/galaxy_test/driver/driver_util.py b/lib/galaxy_test/driver/driver_util.py
index 1475c8669e1b..cfb5b10b0a3c 100644
--- a/lib/galaxy_test/driver/driver_util.py
+++ b/lib/galaxy_test/driver/driver_util.py
@@ -66,12 +66,16 @@
   http-raw-body: true
   interactivetools_map: $tempdir/interactivetools_map.sqlite
   python-raw: scripts/interactivetools/key_type_token_mapping.py
+  # if interactive tool path, jump to interactive tool, else skip to
+  # endendend (default uwsgi params).
   route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)-([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(interactivetool\.$test_host:$test_port)$ goto:interactivetool
   route-run: goto:endendend
+
   route-label: interactivetool
   route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)-([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(interactivetool\.$test_host:$test_port)$ rpcvar:TARGET_HOST rtt_key_type_token_mapper_cached $1 $3 $2 $4 $0 5
   route-if-not: empty:${TARGET_HOST} httpdumb:${TARGET_HOST}
   route: .* break:404 Not Found
+
   route-label: endendend
 """)
 
@@ -732,9 +736,14 @@ def launch_uwsgi(kwargs, tempdir, prefix=DEFAULT_CONFIG_PREFIX, config_object=No
 
     enable_realtime_mapping = getattr(config_object, "enable_realtime_mapping", False)
     if enable_realtime_mapping:
-        config["galaxy"]["interactivetools_prefix"] = "interactivetool"
-        config["galaxy"]["interactivetools_map"] = os.path.join(tempdir, "interactivetools_map.sqlite")
-        config['galaxy']['interactivetools_enable'] = True
+        interactive_tool_defaults = {
+            "interactivetools_prefix": "interactivetool",
+            "interactivetools_map": os.path.join(tempdir, "interactivetools_map.sqlite"),
+            "interactivetools_enable": True
+        }
+        for key, value in interactive_tool_defaults.items():
+            if key not in config["galaxy"]:
+                config["galaxy"][key] = value
 
     yaml_config_path = os.path.join(tempdir, "galaxy.yml")
     with open(yaml_config_path, "w") as f:
diff --git a/test/integration/test_interactivetools_api.py b/test/integration/test_interactivetools_api.py
index bdccee5391d9..762ecd458a05 100644
--- a/test/integration/test_interactivetools_api.py
+++ b/test/integration/test_interactivetools_api.py
@@ -2,6 +2,7 @@
 
 import os
 
+import pytest
 import requests
 
 from galaxy_test.base import api_asserts
@@ -12,6 +13,7 @@
 from .test_containerized_jobs import (
     ContainerizedIntegrationTestCase,
     disable_dependency_resolution,
+    DOCKERIZED_JOB_CONFIG_FILE,
 )
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
@@ -120,3 +122,23 @@ def handle_galaxy_config_kwds(cls, config):
         config["job_config_file"] = EMBEDDED_PULSAR_JOB_CONFIG_FILE_DOCKER
         config["galaxy_infrastructure_url"] = 'http://localhost:$UWSGI_PORT'
         disable_dependency_resolution(config)
+
+
+class InteractiveToolsRemoteProxyIntegrationTestCase(BaseInteractiveToolsIntegrationTestCase, RunsInterativeToolTests):
+    """
+    $ cd gx-it-proxy
+    $ ./lib/createdb.js --sessions $HOME/gxitexproxy.sqlite
+    $ ./lib/main.js --port 9001 --ip 0.0.0.0 --verbose --sessions $HOME/gxitexproxy.sqlite
+    $ # Need to create new DB for each test I think, duplicate IDs are the problem I think because each test starts at 1
+    $ GALAXY_TEST_EXTERNAL_PROXY_HOST="localhost:9001" GALAXY_TEST_EXTERNAL_PROXY_MAP="$HOME/gxitexproxy.sqlite" pytest -s test/integration/test_interactivetools_api.py::InteractiveToolsRemoteProxyIntegrationTestCase
+    """
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        interactivetools_map = os.environ.get("GALAXY_TEST_EXTERNAL_PROXY_MAP")
+        interactivetools_proxy_host = os.environ.get("GALAXY_TEST_EXTERNAL_PROXY_HOST")
+        if not interactivetools_map or not interactivetools_proxy_host:
+            pytest.skip("External proxy not configured for test [map=%s,host=%s]" % (interactivetools_map, interactivetools_proxy_host))
+        config["job_config_file"] = DOCKERIZED_JOB_CONFIG_FILE
+        config["interactivetools_proxy_host"] = interactivetools_proxy_host
+        config["interactivetools_map"] = interactivetools_map
+        disable_dependency_resolution(config)

From 6fffe50261082c617f4c2df59ff0ff93b0050d45 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 12 Mar 2020 16:08:20 -0400
Subject: [PATCH 565/853] Setup rabbitmq in Integration tests.

---
 .github/workflows/integration.yaml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 3d11cf634cad..4af6a9cd7272 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -2,8 +2,8 @@ name: Integration
 on: [push, pull_request]
 env:
   GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_AMQP_URL: 'amqp://rabbitmq:5672//'
 jobs:
-
   test:
     name: Test
     runs-on: ubuntu-18.04
@@ -20,6 +20,10 @@ jobs:
           POSTGRES_DB: postgres
         ports:
           - 5432:5432
+      rabbitmq:
+        image: rabbitmq
+        ports:
+          - 5672:5672
     steps:
     - name: Prune unused docker image, volumes and containers
       run: docker system prune -a -f

From 08f1a705b17fb788b9bce53f891a4ea6427fcb27 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 12 Mar 2020 13:43:07 -0400
Subject: [PATCH 566/853] Allow embedded Pulsar to use a MQ.

---
 lib/galaxy/jobs/runners/pulsar.py | 64 +++++++++++++++++--------------
 1 file changed, 35 insertions(+), 29 deletions(-)

diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index a13935f403bc..ebd72250e582 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -54,6 +54,7 @@
     'PulsarRESTJobRunner',
     'PulsarMQJobRunner',
     'PulsarEmbeddedJobRunner',
+    'PulsarEmbeddedMQJobRunner',
 )
 
 MINIMUM_PULSAR_VERSIONS = {
@@ -187,6 +188,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
 
     runner_name = "PulsarJobRunner"
     default_build_pulsar_app = False
+    use_mq = False
 
     def __init__(self, app, nworkers, **kwds):
         """Start the job runner."""
@@ -202,8 +204,15 @@ def __init__(self, app, nworkers, **kwds):
         self._monitor()
 
     def _monitor(self):
-        # Extension point allow MQ variant to setup callback instead
-        self._init_monitor_thread()
+        if self.use_mq:
+            # This is a message queue driven runner, don't monitor
+            # just setup required callback.
+            self._init_noop_monitor()
+
+            self.client_manager.ensure_has_status_update_callback(self.__async_update)
+            self.client_manager.ensure_has_ack_consumers()
+        else:
+            self._init_monitor_thread()
 
     def __init_client_manager(self):
         pulsar_conf = self.runner_params.get('pulsar_app_config', None)
@@ -813,6 +822,24 @@ def __build_metadata_configuration(self, client, job_wrapper, remote_metadata, r
                 metadata_kwds['datatypes_config'] = datatypes_config
         return metadata_kwds
 
+    def __async_update(self, full_status):
+        galaxy_job_id = None
+        try:
+            remote_job_id = full_status["job_id"]
+            if len(remote_job_id) == 32:
+                # It is a UUID - assign_ids = uuid in destination params...
+                sa_session = self.app.model.context.current
+                galaxy_job_id = sa_session.query(model.Job).filter(model.Job.job_runner_external_id == remote_job_id).one().id
+            else:
+                galaxy_job_id = remote_job_id
+            job, job_wrapper = self.app.job_manager.job_handler.job_queue.job_pair_for_id(galaxy_job_id)
+            job_state = self._job_state(job, job_wrapper)
+            self._update_job_state_for_status(job_state, full_status["status"], full_status=full_status)
+        except Exception:
+            log.exception("Failed to update Pulsar job status for job_id %s", galaxy_job_id)
+            raise
+            # Nothing else to do? - Attempt to fail the job?
+
 
 class PulsarLegacyJobRunner(PulsarJobRunner):
     """Flavor of Pulsar job runner mimicking behavior of old LWR runner."""
@@ -825,6 +852,7 @@ class PulsarLegacyJobRunner(PulsarJobRunner):
 
 class PulsarMQJobRunner(PulsarJobRunner):
     """Flavor of Pulsar job runner with sensible defaults for message queue communication."""
+    use_mq = True
 
     destination_defaults = dict(
         default_file_action="remote_transfer",
@@ -835,32 +863,6 @@ class PulsarMQJobRunner(PulsarJobRunner):
         private_token=PARAMETER_SPECIFICATION_IGNORED
     )
 
-    def _monitor(self):
-        # This is a message queue driven runner, don't monitor
-        # just setup required callback.
-        self._init_noop_monitor()
-
-        self.client_manager.ensure_has_status_update_callback(self.__async_update)
-        self.client_manager.ensure_has_ack_consumers()
-
-    def __async_update(self, full_status):
-        galaxy_job_id = None
-        try:
-            remote_job_id = full_status["job_id"]
-            if len(remote_job_id) == 32:
-                # It is a UUID - assign_ids = uuid in destination params...
-                sa_session = self.app.model.context.current
-                galaxy_job_id = sa_session.query(model.Job).filter(model.Job.job_runner_external_id == remote_job_id).one().id
-            else:
-                galaxy_job_id = remote_job_id
-            job, job_wrapper = self.app.job_manager.job_handler.job_queue.job_pair_for_id(galaxy_job_id)
-            job_state = self._job_state(job, job_wrapper)
-            self._update_job_state_for_status(job_state, full_status["status"], full_status=full_status)
-        except Exception:
-            log.exception("Failed to update Pulsar job status for job_id %s", galaxy_job_id)
-            raise
-            # Nothing else to do? - Attempt to fail the job?
-
 
 KUBERNETES_DESTINATION_DEFAULTS = {
     "default_file_action": "remote_transfer",
@@ -901,7 +903,7 @@ class PulsarRESTJobRunner(PulsarJobRunner):
 
 
 class PulsarEmbeddedJobRunner(PulsarJobRunner):
-    """Flavor of Puslar job runnner that runs Pulsar's server code directly within Galaxy.
+    """Flavor of Puslar job runner that runs Pulsar's server code directly within Galaxy.
 
     This is an appropriate job runner for when the desire is to use Pulsar staging
     but their is not need to run a remote service.
@@ -915,6 +917,10 @@ class PulsarEmbeddedJobRunner(PulsarJobRunner):
     default_build_pulsar_app = True
 
 
+class PulsarEmbeddedMQJobRunner(PulsarMQJobRunner):
+    default_build_pulsar_app = True
+
+
 class PulsarComputeEnvironment(ComputeEnvironment):
 
     def __init__(self, pulsar_client, job_wrapper, remote_job_config):

From 80138afedc991c5c466c2390cf0823861701a627 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 12 Mar 2020 13:52:11 -0400
Subject: [PATCH 567/853] Integration test for embedded Pulsar in MQ mode.

---
 .github/workflows/integration.yaml          |  2 +-
 test/integration/test_pulsar_embedded_mq.py | 80 +++++++++++++++++++++
 2 files changed, 81 insertions(+), 1 deletion(-)
 create mode 100644 test/integration/test_pulsar_embedded_mq.py

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 4af6a9cd7272..25edfff1b8c1 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -2,7 +2,7 @@ name: Integration
 on: [push, pull_request]
 env:
   GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
-  GALAXY_TEST_AMQP_URL: 'amqp://rabbitmq:5672//'
+  GALAXY_TEST_AMQP_URL: 'amqp://localhost:5672//'
 jobs:
   test:
     name: Test
diff --git a/test/integration/test_pulsar_embedded_mq.py b/test/integration/test_pulsar_embedded_mq.py
new file mode 100644
index 000000000000..f6f043bd0b76
--- /dev/null
+++ b/test/integration/test_pulsar_embedded_mq.py
@@ -0,0 +1,80 @@
+"""Integration tests for the Pulsar embedded runner with outputs to working directory."""
+
+import os
+import string
+import tempfile
+
+import pytest
+
+from galaxy.util import safe_makedirs
+from galaxy_test.driver import integration_util
+
+SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
+EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_mq_job_conf.yml")
+AMQP_URL = os.environ.get("GALAXY_TEST_AMQP_URL", "amqp://guest:guest@localhost:5672//")
+
+JOB_CONF_TEMPLATE = """
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 1
+  pulsar:
+    load: galaxy.jobs.runners.pulsar:PulsarEmbeddedMQJobRunner
+    pulsar_app_config:
+      tool_dependency_dir: none
+      conda_auto_init: false
+      conda_auto_install: false
+      message_queue_url: ${amqp_url}
+      staging_directory: ${jobs_directory}
+    amqp_url: ${amqp_url}
+execution:
+  default: pulsar_mq_environment
+  environments:
+    pulsar_mq_environment:
+      runner: pulsar
+      rewrite_parameters: true
+      dependency_resolution: none
+      default_file_action: remote_transfer
+      jobs_directory: ${jobs_directory}
+    local_environment:
+      runner: local
+tools:
+  - id: upload1
+    environment: local_environment
+"""
+
+
+class EmbeddedMessageQueuePulsarIntegrationInstance(integration_util.IntegrationInstance):
+    """Describe a Galaxy test instance with embedded pulsar configured.
+
+    $ Setup RabbitMQ (e.g. https://www.rabbitmq.com/install-homebrew.html)
+    $ GALAXY_TEST_AMQP_URL='amqp://guest:guest@localhost:5672//' pytest -s test/integration/test_pulsar_embedded_mq.py
+    """
+
+    framework_tool_and_types = True
+    # Test leverages $UWSGI_PORT in job code, need to set this up.
+    require_uwsgi = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        amqp_url = os.environ.get("GALAXY_TEST_AMQP_URL", None)
+        if amqp_url is None:
+            pytest.skip("External AMQP URL not configured for test")
+
+        jobs_directory = os.path.join(cls._test_driver.mkdtemp(), "pulsar_staging")
+        safe_makedirs(jobs_directory)
+        job_conf_template = string.Template(JOB_CONF_TEMPLATE)
+        job_conf_str = job_conf_template.substitute(
+            amqp_url=AMQP_URL,
+            jobs_directory=jobs_directory,
+        )
+        with tempfile.NamedTemporaryFile(suffix="_mq_job_conf.yml", mode="w", delete=False) as job_conf:
+            job_conf.write(job_conf_str)
+        config["job_config_file"] = job_conf.name
+        infrastructure_url = "http://localhost:$UWSGI_PORT"
+        config["galaxy_infrastructure_url"] = infrastructure_url
+
+
+instance = integration_util.integration_module_instance(EmbeddedMessageQueuePulsarIntegrationInstance)
+
+test_tools = integration_util.integration_tool_runner(["simple_constructs"])

From fc153737d1fa6414d845fa52abf8b02b335fdad9 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 24 Mar 2020 11:22:22 -0400
Subject: [PATCH 568/853] Fixing some lint errors

---
 lib/galaxy/objectstore/s3.py                   | 1 -
 test/integration/test_datatype_upload.py       | 1 +
 test/integration/test_datatype_upload_irods.py | 9 ++++++++-
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index a32f03113d85..a17294983915 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -742,4 +742,3 @@ def _configure_connection(self):
                                     port=self.port,
                                     calling_format=boto.s3.connection.OrdinaryCallingFormat(),
                                     path=self.conn_path)
-
diff --git a/test/integration/test_datatype_upload.py b/test/integration/test_datatype_upload.py
index e139c38c2f8b..71c14f43028e 100644
--- a/test/integration/test_datatype_upload.py
+++ b/test/integration/test_datatype_upload.py
@@ -63,6 +63,7 @@ def temp_file():
 def test_upload_datatype_auto(instance, test_data, temp_file):
     upload_datatype_helper(instance, test_data, temp_file)
 
+
 def upload_datatype_helper(instance, test_data, temp_file):
     is_compressed = False
     for is_method in (is_bz2, is_gzip, is_zip):
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index a0046b5b2873..14dba49453f7 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,10 +1,11 @@
 
+import os
 import pytest
+import tempfile
 
 from galaxy_test.driver import integration_util
 
 from .test_datatype_upload import (
-    temp_file,
     TEST_CASES,
     upload_datatype_helper,
     UploadTestDatatypeDataTestCase
@@ -26,6 +27,12 @@ def handle_galaxy_config_kwds(cls, config):
 instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
 
 
+@pytest.fixture
+def temp_file():
+    with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
+        yield fh
+
+
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
     upload_datatype_helper(instance, test_data, temp_file)

From 43780f0871017004ede8768097842565bc264033 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 24 Mar 2020 11:39:27 -0400
Subject: [PATCH 569/853] Fixed import orders/groupings

---
 lib/galaxy/objectstore/irods.py               | 22 +++++++------------
 .../integration/test_datatype_upload_irods.py | 10 ++++-----
 2 files changed, 12 insertions(+), 20 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 26af846bddbe..f707574cdef6 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -1,11 +1,17 @@
 """
 Object Store plugin for the Integrated Rule-Oriented Data Store (iRODS)
 """
-from datetime import datetime
 import logging
 import os
-from pathlib import Path
 import shutil
+from datetime import datetime
+from pathlib import Path
+
+from galaxy.exceptions import ObjectInvalid, ObjectNotFound
+from galaxy.util import directory_hash_id, umask_fix_perms
+from galaxy.util.path import safe_relpath
+
+from ..objectstore import DiskObjectStore
 
 try:
     import irods
@@ -17,18 +23,6 @@
 except ImportError:
     irods = None
 
-from galaxy.exceptions import (
-    ObjectInvalid,
-    ObjectNotFound
-)
-from galaxy.util import (
-    directory_hash_id,
-    umask_fix_perms,
-)
-from galaxy.util.path import safe_relpath
-from ..objectstore import (
-    DiskObjectStore,
-)
 
 IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this feature, please install it')
 
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 14dba49453f7..9a5196e629b5 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,15 +1,13 @@
 
 import os
-import pytest
 import tempfile
 
+import pytest
+
 from galaxy_test.driver import integration_util
 
-from .test_datatype_upload import (
-    TEST_CASES,
-    upload_datatype_helper,
-    UploadTestDatatypeDataTestCase
-)
+from .test_datatype_upload import (TEST_CASES, UploadTestDatatypeDataTestCase,
+                                   upload_datatype_helper)
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "irods_object_store_conf.xml")

From bf99baac2197853cf07f0a079ee53419a862eaab Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 24 Mar 2020 12:15:40 -0400
Subject: [PATCH 570/853] Fixing more import issues

---
 lib/galaxy/objectstore/irods.py                | 10 ++++------
 test/integration/test_datatype_upload_irods.py |  3 +--
 2 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index f707574cdef6..7d5ce9ea1878 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -7,12 +7,6 @@
 from datetime import datetime
 from pathlib import Path
 
-from galaxy.exceptions import ObjectInvalid, ObjectNotFound
-from galaxy.util import directory_hash_id, umask_fix_perms
-from galaxy.util.path import safe_relpath
-
-from ..objectstore import DiskObjectStore
-
 try:
     import irods
     import irods.keywords as kw
@@ -23,6 +17,10 @@
 except ImportError:
     irods = None
 
+from galaxy.exceptions import ObjectInvalid, ObjectNotFound
+from galaxy.util import directory_hash_id, umask_fix_perms
+from galaxy.util.path import safe_relpath
+from ..objectstore import DiskObjectStore
 
 IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this feature, please install it')
 
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 9a5196e629b5..6c94508bf0a5 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -6,8 +6,7 @@
 
 from galaxy_test.driver import integration_util
 
-from .test_datatype_upload import (TEST_CASES, UploadTestDatatypeDataTestCase,
-                                   upload_datatype_helper)
+from .test_datatype_upload import (TEST_CASES, upload_datatype_helper, UploadTestDatatypeDataTestCase)
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "irods_object_store_conf.xml")

From e4131c3e2666320bbf2d77ba7aeb7b378c59aeb7 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 24 Mar 2020 12:23:12 -0400
Subject: [PATCH 571/853] More fixes for imports

---
 test/integration/test_datatype_upload_irods.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 6c94508bf0a5..eb2751b72fe2 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -5,7 +5,6 @@
 import pytest
 
 from galaxy_test.driver import integration_util
-
 from .test_datatype_upload import (TEST_CASES, upload_datatype_helper, UploadTestDatatypeDataTestCase)
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))

From 05202d52f72144cd01f78d71c28a3e5f698cda07 Mon Sep 17 00:00:00 2001
From: Alexander OSTROVSKY <a.ostrovsky@mac.com>
Date: Tue, 24 Mar 2020 09:38:09 -0700
Subject: [PATCH 572/853] adding higlass IT from eu

---
 tools/interactive/interactivetool_higlass.xml | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 tools/interactive/interactivetool_higlass.xml

diff --git a/tools/interactive/interactivetool_higlass.xml b/tools/interactive/interactivetool_higlass.xml
new file mode 100644
index 000000000000..6d0510925da3
--- /dev/null
+++ b/tools/interactive/interactivetool_higlass.xml
@@ -0,0 +1,39 @@
+<tool id="interactive_tool_higlass" tool_type="interactive" name="HiGlass" version="1.8.0">
+    <description>an interactive Hi-C data visualizer</description>
+    <requirements>
+        <container type="docker">quay.io/bgruening/galaxy-higlass</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="HiGlass Visualisation on $matrix.display_name" requires_domain="True">
+            <port>80</port>
+        </entry_point>
+    </entry_points>
+    <command><![CDATA[
+        cp '$matrix' /tmp/matrix.cool &&
+        cd /home/higlass/projects &&
+        mkdir -p data/log/ &&
+        supervisord &&
+       	sleep 5 &&
+        python higlass-server/manage.py ingest_tileset --filename /tmp/matrix.cool --filetype cooler --datatype matrix &&
+        tail -f /var/log/supervisor/*
+    ]]>
+    </command>
+    <inputs>
+	<param name="matrix" type="data" format="mcool" label="Cool file with multiple resolutions"/>
+    </inputs>
+    <outputs>
+	<data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+    Interactive tool for visualising Hi-C data, works only for multi-cooler files which store multiple resolutions.
+    For a detailed documentaition please visit https://docs.higlass.io/.
+    </help>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/s13059-018-1486-1</citation>
+        </citations>
+    </xml>
+</tool>
+

From 2641c692e2ed6b19dbb45a53258a3dc327071407 Mon Sep 17 00:00:00 2001
From: Alexander OSTROVSKY <a.ostrovsky@mac.com>
Date: Tue, 24 Mar 2020 10:09:00 -0700
Subject: [PATCH 573/853] migrate ITs from EU

accidental files

more files

migrate ITs from EU

accidental files

more files

migrate ITs from EU

accidental files

more files

migrate ITs from EU

accidental files

more files
---
 default_notebook.ipynb                        |  53 --------
 interactivetool_askomics.xml                  |  70 -----------
 interactivetool_bam_iobio.xml                 |  47 --------
 interactivetool_cellxgene.xml                 | 114 ------------------
 interactivetool_ethercalc.xml                 |  63 ----------
 interactivetool_higlass.xml                   |  39 ------
 interactivetool_jupyter_notebook.xml          |  94 ---------------
 interactivetool_neo4j.xml                     |  41 -------
 interactivetool_phinch.xml                    |  39 ------
 interactivetool_rstudio.xml                   |  74 ------------
 interactivetool_wallace.xml                   |  67 ----------
 interactivetool_wilson.xml                    |  56 ---------
 .../interactivetool_climate_notebook.xml      |   0
 .../interactivetool_geoexplorer.xml           |   0
 .../interactivetool_guacamole_desktop.xml     |   0
 .../interactivetool_openrefine.xml            |   0
 .../interactive/interactivetool_panoply.xml   |   0
 .../interactive/interactivetool_paraview.xml  |   0
 .../interactive/interactivetool_pyiron.xml    |   0
 .../interactive/interactivetool_radiant.xml   |   0
 .../interactive/interactivetool_vcf_iobio.xml |   0
 21 files changed, 757 deletions(-)
 delete mode 100644 default_notebook.ipynb
 delete mode 100644 interactivetool_askomics.xml
 delete mode 100644 interactivetool_bam_iobio.xml
 delete mode 100644 interactivetool_cellxgene.xml
 delete mode 100644 interactivetool_ethercalc.xml
 delete mode 100644 interactivetool_higlass.xml
 delete mode 100644 interactivetool_jupyter_notebook.xml
 delete mode 100644 interactivetool_neo4j.xml
 delete mode 100644 interactivetool_phinch.xml
 delete mode 100644 interactivetool_rstudio.xml
 delete mode 100644 interactivetool_wallace.xml
 delete mode 100644 interactivetool_wilson.xml
 rename interactivetool_climate_notebook.xml => tools/interactive/interactivetool_climate_notebook.xml (100%)
 rename interactivetool_geoexplorer.xml => tools/interactive/interactivetool_geoexplorer.xml (100%)
 rename interactivetool_guacamole_desktop.xml => tools/interactive/interactivetool_guacamole_desktop.xml (100%)
 rename interactivetool_openrefine.xml => tools/interactive/interactivetool_openrefine.xml (100%)
 rename interactivetool_panoply.xml => tools/interactive/interactivetool_panoply.xml (100%)
 rename interactivetool_paraview.xml => tools/interactive/interactivetool_paraview.xml (100%)
 rename interactivetool_pyiron.xml => tools/interactive/interactivetool_pyiron.xml (100%)
 rename interactivetool_radiant.xml => tools/interactive/interactivetool_radiant.xml (100%)
 rename interactivetool_vcf_iobio.xml => tools/interactive/interactivetool_vcf_iobio.xml (100%)

diff --git a/default_notebook.ipynb b/default_notebook.ipynb
deleted file mode 100644
index e95737524789..000000000000
--- a/default_notebook.ipynb
+++ /dev/null
@@ -1,53 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Welcome to the interactive Galaxy IPython Notebook."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "You can access your data via the dataset number. Using a Python kernel, you can access dataset number 42 with ``handle = open(get(42), 'r')``.\n",
-    "To save data, write your data to a file, and then call ``put('filename.txt')``. The dataset will then be available in your galaxy history.\n<br>",
-    "When using a non-Python kernel, ``get`` and ``put`` are available as command-line tools, which can be accessed using system calls in R, Julia, and Ruby. For example, to read dataset number 42 into R, you can write ```handle <- file(system('get -i 42', intern = TRUE))```.\n",
-    "To save data in R, write the data to a file and then call ``system('put -p filename.txt')``.\n",
-    "Notebooks can be saved to Galaxy by clicking the large green button at the top right of the IPython interface.<br>\n",
-    "More help and informations can be found on the project [website](https://github.com/bgruening/docker-jupyter-notebook)."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 2",
-   "language": "python",
-   "name": "python2"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 2
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.10"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 0
-}
diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml
deleted file mode 100644
index 94cf111a2f35..000000000000
--- a/interactivetool_askomics.xml
+++ /dev/null
@@ -1,70 +0,0 @@
-<tool id="interactive_tool_askomics" tool_type="interactive" name="AskOmics" version="1.0">
-    <description>a visual SPARQL query builder</description>
-    <requirements>
-        <container type="docker">askomics/flaskomics-with-dependencies:3.2.0</container>
-    </requirements>
-    <entry_points>
-        <entry_point name="AskOmics instance on $infile.display_name" requires_domain="True">
-            <port>5000</port>
-            <url>/loginapikey/${__user_name__}</url>
-        </entry_point>
-    </entry_points>
-    <environment_variables>
-        <!-- AskOmics user -->
-        <environment_variable name="CREATE_USER">true</environment_variable>
-        <environment_variable name="USER_FIRST_NAME">${__user_name__}</environment_variable>
-        <environment_variable name="USER_LAST_NAME">Galaxy</environment_variable>
-        <environment_variable name="USER_USERNAME">${__user_name__}</environment_variable>
-        <environment_variable name="USER_EMAIL">${__user_email__}</environment_variable>
-        <environment_variable name="USER_APIKEY">${__user_name__}</environment_variable>
-        <!-- Galaxy info -->
-        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
-        <environment_variable name="GALAXY_API_KEY" inject="api_key" />
-        <!-- AskOmics config -->
-        <environment_variable name="DEPMODE">prod</environment_variable>
-        <environment_variable name="MAX_CELERY_QUEUE">1</environment_variable>
-        <environment_variable name="ASKO_askomics_subtitle">Galaxy</environment_variable>
-        <environment_variable name="ASKO_askomics_footer_message">AskOmics Interactive Tool for Galaxy</environment_variable>
-        <environment_variable name="ASKO_askomics_data_directory">/tmp/askomics-it</environment_variable>
-        <environment_variable name="ASKO_askomics_database_path">/tmp/askomics-it/database.db</environment_variable>
-        <environment_variable name="ASKO_triplestore_load_url">http://localhost:5000</environment_variable>
-        <!-- Virtuoso config -->
-        <environment_variable name="SPARQL_UPDATE">true</environment_variable>
-        <!-- 
-        Update the following environment variables according to how much memory you want to allow to virtuoso
-        see https://github.com/askomics/flaskomics-docker-compose#configure-virtuoso for help
-         -->
-        <environment_variable name="VIRT_Parameters_NumberOfBuffers">85000</environment_variable>
-        <environment_variable name="VIRT_Parameters_MaxDirtyBuffers">65000</environment_variable>
-    </environment_variables>
-    <command><![CDATA[
-        #import re
-
-        #set link_name = re.sub('[^\w_]', '_', $infile.element_identifier)
-        #if $infile.ext == 'tabular':
-            #set link_name = $link_name + '.tsv'
-        #elif $infile.ext == 'interval':
-            #set link_name = $link_name + '.bed'
-        #else:
-            #set link_name = $link_name + '.' + $infile.ext
-        #end if
-
-        mkdir -p /import &&
-        ln -s '$infile' '/import/$link_name' &&
-
-        /askomics/start_all.sh
-    ]]>
-    </command>
-    <inputs>
-        <param name="infile" type="data" optional="true" format="tabular,gff,gff3,interval" label="A dataset to load into AskOmics"/>
-    </inputs>
-    <outputs>
-        <data name="outfile" format="txt" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-        AskOmics is a visual SPARQL query interface supporting both intuitive data integration and
-        querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL.
-    </help>
-</tool>
diff --git a/interactivetool_bam_iobio.xml b/interactivetool_bam_iobio.xml
deleted file mode 100644
index 6c78eaa335b6..000000000000
--- a/interactivetool_bam_iobio.xml
+++ /dev/null
@@ -1,47 +0,0 @@
-<tool id="interactive_tool_bam_iobio" tool_type="interactive" name="BAM (iobio) Visualisation" version="0.1">
-    <requirements>
-        <container type="docker">qiaoy/iobio-bundle.bam-iobio:1.0-ondemand</container>
-    </requirements>
-    <entry_points>
-        <entry_point name="BAM io.bio visualisation of $infile.display_name" requires_domain="True">
-            <port>80</port>
-            <url><![CDATA[/?bam=http://localhost/tmp/bamfile.bam&region=1]]></url>
-        </entry_point>
-    </entry_points>
-    <command><![CDATA[
-    ## ToDo: websocket could not be found
-    ## WebSocket connection to 'ws://localhost/bamreaddepther/' failed: Error in connection establishment: net::ERR_CONNECTION_REFUSED
-
-    #set $PUB_HOSTNAME = 'localhost'
-    #set $PUB_HTTP_PORT = '80'
-
-    cd /var/www/html &&
-    sed -i "s@\"wss://services.iobio.io/samtools/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samtools/\"@" js/bam.iobio.js/bam.iobio.js &&
-    sed -i "s@\"wss://services.iobio.io/bamreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamreaddepther/\"@" js/bam.iobio.js/bam.iobio.js &&
-    sed -i "s@\"wss://services.iobio.io/bamstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamstatsalive/\"@" js/bam.iobio.js/bam.iobio.js &&
-    sed -i "s@\"wss://services.iobio.io/samheader/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samheader/\"@" js/bam.iobio.js/bam.iobio.js &&
-
-
-    sed -i 's/deny all;//g' /etc/nginx/nginx.conf &&
-
-        cp '${infile}' /input/bamfile.bam &&
-        cp '${infile.metadata.bam_index}' /input/bamfile.bam.bai &&
-        mkdir /var/log/supervisor/ &&
-        head -n -2  /etc/supervisor.d/app.conf > /tmp/app.conf &&
-        mv /tmp/app.conf /etc/supervisor.d/app.conf &&
-
-        /usr/bin/supervisord -c /etc/supervisord.conf
-    ]]>
-    </command>
-    <inputs>
-        <param name="infile" type="data" format="bam" label="BAM file"/>
-    </inputs>
-    <outputs>
-        <data name="outfile" format="txt" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-        BAM iobio visualisation.
-    </help>
-</tool>
diff --git a/interactivetool_cellxgene.xml b/interactivetool_cellxgene.xml
deleted file mode 100644
index 3c99f3a393b5..000000000000
--- a/interactivetool_cellxgene.xml
+++ /dev/null
@@ -1,114 +0,0 @@
-<tool id="interactive_tool_cellxgene" tool_type="interactive" name="Interactive CellXgene Environment" version="0.1">
-    <requirements>
-        <container type="docker">quay.io/galaxy/cellxgene-galaxy-ie:ie2</container>
-    </requirements>
-    <entry_points>
-        <entry_point name="Cellxgene Single Cell Visualization on $infile.display_name" requires_domain="True">
-            <port>80</port>
-        </entry_point>
-    </entry_points>
-    <command detect_errors="exit_code"><![CDATA[
-        #import re
-        #set $fancy_name = '/tmp/galaxy_cellxgene_' + re.sub('[^\w\-_]', '_', $infile.element_identifier) + '.h5ad'
-        cp '${infile}' '${fancy_name}'
-        &&
-        #set $experimental_annotations_file_tmp = '/tmp/galaxy_cellxgene_experimental_annotations.csv'
-        #if $experimental_annotations.experimental_annotations_select == 'enable':
-            #if $experimental_annotations.experimental_annotations_file:
-                cp '${experimental_annotations.experimental_annotations_file}' '${experimental_annotations_file_tmp}'
-            #else:
-                touch '${experimental_annotations_file_tmp}'
-            #end if
-            &&
-        #end if
-
-        cellxgene launch --host '0.0.0.0' --port 80 '${fancy_name}'
-
-        #if $diffexp.diffexp_select == 'enable'
-            --diffexp-lfc-cutoff '${diffexp.diffexp_lfc_cutoff}'
-        #else:
-            --disable-diffexp
-        #end if
-
-        #for $embedding in $embeddings:
-           --embedding '${embedding.embedding}'
-        #end for
-
-        #if $experimental_annotations.experimental_annotations_select == 'enable':
-            --experimental-annotations
-            --experimental-annotations-file '${experimental_annotations_file_tmp}'
-        #end if
-
-        --max-category-items '${max_category_items}'
-
-        #if str($title):
-            --title '${title}'
-        #end if
-
-        #if str($obs_names):
-            --obs-names '${obs_names}'
-        #end if
-
-        #if str($var_names):
-            --var-names '${var_names}'
-        #end if
-
-        ${backed}
-
-        #if $experimental_annotations.experimental_annotations_select == 'enable':
-            &&
-            cp '${experimental_annotations_file_tmp}' '${experimental_annotations_output}'
-        #end if
-    ]]>
-    </command>
-    <inputs>
-        <param name="infile" type="data" format="h5ad" label="AnnData Dataset" help="Requires layout"/>
-        <conditional name="diffexp">
-            <param name="diffexp_select" type="select" label="On demand differential expression">
-                <option value="enable" selected="True">Enable</option>
-                <option value="disable">Disable</option>
-            </param>
-            <when value="disable"/>
-            <when value="enable">
-                <param name="diffexp_lfc_cutoff" type="float" value="0.01" label="threshold for log fold change" help="Genes are only returned in differential expression if the effect size is above the specified threshold for log fold change. Defaults to 0.01" argument="--diffexp-lfc-cutoff"/>
-            </when>
-        </conditional>
-        <repeat name="embeddings" title="Embeddings">
-            <param name="embedding" type="text" value="" optional="false" label="Embedding name" help="eg, 'umap'; Defaults to all." argument="--embedding"/>
-        </repeat>
-        <conditional name="experimental_annotations">
-            <param name="experimental_annotations_select" type="select" label="Enable user annotation of data (experimental)">
-                <option value="enable">Enable</option>
-                <option value="disable" selected="True">Disable</option>
-            </param>
-            <when value="disable"/>
-            <when value="enable">
-                <param name="experimental_annotations_file" type="data" format="csv" optional="true" label="Annotations file" help="CSV file to initialize editing of existing annotations;" argument="--experimental-annotations-file"/>
-            </when>
-        </conditional>
-        <param name="max_category_items" type="integer" value="1000" label="Do not display categories with more distinct values than specified." help="Defaults to 1000" argument="--max-category-items"/>
-        <param name="title" type="text" value="" label="Title to display" help="If omitted will use file name." argument="--title"/>
-        <param name="obs_names" type="text" value="" label="Name of annotation field to use for observations" help="Leave empty to default to obs index" argument="--obs-names"/>
-        <param name="var_names" type="text" value="" label="Name of annotation to use for variables" help="Leave empty to default to var index" argument="--var-names"/>
-        <param name="backed" type="boolean" truevalue="--backed" falsevalue ="" checked="false" label="Load data in file-backed mode" help="This may save memory, but may result in slower overall performance." argument="--backed"/>
-    </inputs>
-    <outputs>
-        <data name="out_file1" format="txt" />
-        <data name="experimental_annotations_output" format="csv">
-            <filter>experimental_annotations['experimental_annotations_select'] == 'enable'</filter>
-        </data>
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-    An interactive explorer for single-cell transcriptomics (AnnData formatted) data
-
-    cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas. Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data.
-
-    Whether you need to visualize one thousand cells or one million, cellxgene helps you gain insight into your single-cell data.
-    https://github.com/chanzuckerberg/cellxgene
-    </help>
-    <citations>
-        <citation type="doi">10.5281/zenodo.3554576</citation>
-    </citations>
-</tool>
diff --git a/interactivetool_ethercalc.xml b/interactivetool_ethercalc.xml
deleted file mode 100644
index 88676c1e997d..000000000000
--- a/interactivetool_ethercalc.xml
+++ /dev/null
@@ -1,63 +0,0 @@
-<tool id="interactive_tool_ethercalc" tool_type="interactive" name="EtherCalc" version="0.1">
-    <requirements>
-        <container type="docker">shiltemann/ethercalc-galaxy-ie:17.05</container>
-    </requirements>
-    <entry_points>
-        <entry_point name="EtherCalc instance on $infile.display_name" requires_domain="True">
-            <port>8000</port>
-        </entry_point>
-    </entry_points>
-    <command><![CDATA[
-    
-        forever start `which ethercalc` --cors &
-        bash $wait_script
-        &&
-
-        curl --include --request POST --header "Content-Type: application/json" --data-binary "{ \"room\": \"galaxy\", \"snapshot\": \"...\"}" 'http://localhost:8000/_'
-        &&
-
-        ## put loading message into worksheet in case of large files
-        echo -e "Loading your,dataset\nThis may take, some time for, large files.." > loading.txt
-        &&
-        curl --include --request PUT --header "Content-Type: text/csv" --data-binary @loading.txt http://localhost:8000/_/galaxy
-        &&
-
-        ## remove dump file so this doesnt appear in audit trail
-        rm /dump.json
-        &&
-
-        ## load dataset into worksheet
-        curl --include --request PUT --header "Content-Type: text/csv" --data-binary @$infile http://localhost:8000/_/galaxy
-        &&
-
-        tail -f /etc/hosts
-
-    ]]>
-    </command>
-    <configfiles>
-        <configfile name="wait_script">
-<![CDATA[
-## make sure ethercalc has finished starting up
-STATUS=\$(curl --include 'http://localhost:8000/_/galaxy' 2>&1)
-while [[ \${STATUS} =~ "refused" ]]
-do
-  echo "waiting for ethercalc: \$STATUS \n"
-  STATUS=\$(curl --include 'http://localhost:8000/_/galaxy' 2>&1)
-  sleep 2
-done
-    ]]>
-        </configfile>
-    </configfiles>
-    <inputs>
-        <param name="infile" type="data" format="tabular,csv,tsv" label="Some tabular dataset"/>
-    </inputs>
-    <outputs>
-        <data name="outfile" format="txt" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-        EtherCalc is a web spreadsheet.
-        https://ethercalc.net
-    </help>
-</tool>
diff --git a/interactivetool_higlass.xml b/interactivetool_higlass.xml
deleted file mode 100644
index 6d0510925da3..000000000000
--- a/interactivetool_higlass.xml
+++ /dev/null
@@ -1,39 +0,0 @@
-<tool id="interactive_tool_higlass" tool_type="interactive" name="HiGlass" version="1.8.0">
-    <description>an interactive Hi-C data visualizer</description>
-    <requirements>
-        <container type="docker">quay.io/bgruening/galaxy-higlass</container>
-    </requirements>
-    <entry_points>
-        <entry_point name="HiGlass Visualisation on $matrix.display_name" requires_domain="True">
-            <port>80</port>
-        </entry_point>
-    </entry_points>
-    <command><![CDATA[
-        cp '$matrix' /tmp/matrix.cool &&
-        cd /home/higlass/projects &&
-        mkdir -p data/log/ &&
-        supervisord &&
-       	sleep 5 &&
-        python higlass-server/manage.py ingest_tileset --filename /tmp/matrix.cool --filetype cooler --datatype matrix &&
-        tail -f /var/log/supervisor/*
-    ]]>
-    </command>
-    <inputs>
-	<param name="matrix" type="data" format="mcool" label="Cool file with multiple resolutions"/>
-    </inputs>
-    <outputs>
-	<data name="outfile" format="txt" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-    Interactive tool for visualising Hi-C data, works only for multi-cooler files which store multiple resolutions.
-    For a detailed documentaition please visit https://docs.higlass.io/.
-    </help>
-    <xml name="citations">
-        <citations>
-            <citation type="doi">10.1186/s13059-018-1486-1</citation>
-        </citations>
-    </xml>
-</tool>
-
diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml
deleted file mode 100644
index c86717460df0..000000000000
--- a/interactivetool_jupyter_notebook.xml
+++ /dev/null
@@ -1,94 +0,0 @@
-<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive Jupyter Notebook" version="0.1">
-    <requirements>
-        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:ie2</container>
-    </requirements>
-    <entry_points>
-        <entry_point name="Jupyter Interactive Tool" requires_domain="True">
-            <port>8888</port>
-            <url>ipython/lab</url>
-        </entry_point>
-    </entry_points>
-    <environment_variables>
-        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
-        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
-        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
-        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
-        <environment_variable name="API_KEY" inject="api_key" />
-    </environment_variables>
-    <command detect_errors="aggressive"><![CDATA[
-        #import re
-        export GALAXY_WORKING_DIR=`pwd` &&
-        mkdir -p ./jupyter/outputs/ &&
-        mkdir -p ./jupyter/data &&
-
-        #if $input:
-            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
-            cp '$input' './jupyter/data/${cleaned_name}' &&
-        #end if
-        ## change into the directory where the notebooks are located
-        cd ./jupyter/ &&
-        export PATH=/home/jovyan/.local/bin:\$PATH &&
-
-        #if $mode.mode_select == 'scratch':
-            ## copy default notebook
-            cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
-            jupyter trust ./ipython_galaxy_notebook.ipynb &&
-            jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
-            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
-
-        #else:
-            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
-            cp '$mode.ipynb' ./${cleaned_name}.ipynb &&
-            jupyter trust ./${cleaned_name}.ipynb &&
-
-            #if $mode.run_it:
-                jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
-            #else:
-                jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
-            #end if
-            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
-        #end if
-    ]]>
-    </command>
-    <inputs>
-
-        <conditional name="mode">
-            <param name="mode_select" type="select" label="Do you already have a notebook?" help="If not, no problem we will provide you with a default one.">
-                <option value="scratch">Start with a fresh notebook</option>
-                <option value="previous">Load a previous notebook</option>
-            </param>
-            <when value="scratch"/>
-            <when value="previous">
-                <param name="ipynb" type="data" format="ipynb" label="IPython Notebook"/>
-                <param name="run_it" type="boolean" truevalue="true" falsevalue="false" label="Execute notebook and return a new one."
-                    help="This option is useful in workflows when you just want to execute a notebook and not dive into the webfrontend."/>
-            </when>
-        </conditional>
-        <param name="input" type="data" optional="true" label="Include data into the environment"/>
-
-    </inputs>
-    <outputs>
-        <data name="jupyter_notebook" format="ipynb" label="Executed Notebook"></data>
-    </outputs>
-    <tests>
-        <test expect_num_outputs="1">
-            <param name="mode" value="previous" />
-            <param name="ipynb" value="test.ipynb" />
-            <param name="run_it" value="true" />
-            <output name="jupyter_notebook" file="test.ipynb" ftype="ipynb"/>
-        </test>
-    </tests>
-    <help>
-    The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations,
-    visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization,
-    machine learning, and much more.
-
-    Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
-    do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter.
-
-    You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset.
-    If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history.
-
-    You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function.
-    </help>
-</tool>
diff --git a/interactivetool_neo4j.xml b/interactivetool_neo4j.xml
deleted file mode 100644
index 0b31a8b303e0..000000000000
--- a/interactivetool_neo4j.xml
+++ /dev/null
@@ -1,41 +0,0 @@
-<tool id="interactive_tool_neo4j" tool_type="interactive" name="Neo4j (Graph Database)" version="0.1">
-    <requirements>
-        <container type="docker">quay.io/sanbi-sa/neo_ie:3.1.9</container>
-    </requirements>
-    <entry_points>
-        <entry_point name="Neo4j on $infile.display_name" requires_domain="True">
-            <port>80</port>
-        </entry_point>
-        <!-- I get some web-socket error that 7687 is not reachable. 
-            but docker does not expose 7687?
-        -->
-    </entry_points>
-    <environment_variables>
-        <environment_variable name="USER_GID">2345</environment_variable>
-        <environment_variable name="USER_UID">2345</environment_variable>
-        <environment_variable name="MONITOR_TRAFFIC">false</environment_variable>
-    </environment_variables>
-    <command><![CDATA[
-        ##export USER_UID=2345 &&
-        ##export USER_GID=2345 &&
-        ##export MONITOR_TRAFFIC=false &&
-        mkdir -p /data/neo4jdb &&
-        unzip '$infile' -d /data/neo4jdb &&
-        ls -l /data/neo4jdb &&
-        sed -i.bak 's@/monitor_traffic.*@@g' /docker-entrypoint.sh &&
-        cd /opt/neo4j &&
-        bash /docker-entrypoint.sh neo4j
-    ]]>
-    </command>
-    <inputs>
-        <param name="infile" type="data" format="zip" label="Neo4J data store"/>
-    </inputs>
-    <outputs>
-        <data name="outfile" format="txt" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-        Neo4j is a highly scalable, robust native graph database.
-    </help>
-</tool>
diff --git a/interactivetool_phinch.xml b/interactivetool_phinch.xml
deleted file mode 100644
index 382cf32f0a9f..000000000000
--- a/interactivetool_phinch.xml
+++ /dev/null
@@ -1,39 +0,0 @@
-<tool id="interactive_tool_phinch" tool_type="interactive" name="Phinch Visualisation" version="0.1">
-    <requirements>
-        <container type="docker">shiltemann/docker-phinch-galaxy:16.04</container>
-    </requirements>
-    <entry_points>
-        <entry_point name="Phinch Visualisation of $infile.display_name" requires_domain="True">
-            <port>80</port>
-        </entry_point>
-    </entry_points>
-    <command><![CDATA[
-        ## ToDo nginx, proxy.conf etc can be removed from the container
-
-        #import os
-        #set $name = os.path.splitext(str($infile.display_name).replace(' ', '_'))[0]
-        ## in case someone names the data testdata.
-        rm /home/Phinch/data/testdata.biom | true &&
-        ln -s '$infile' '/home/Phinch/data/${name}.biom' &&
-        cd /home/Phinch/data &&
-        sed -i  "s/'REPLACE_ME'/'${name}.biom'/g" /home/Phinch/scripts/readFile.js &&
-        sed -i  "s/http/https/g" /home/Phinch/scripts/readFile.js &&
-
-        ## keep it running
-        cd /home/Phinch &&
-        php -S 0.0.0.0:80 2>&1 > /var/log/phinch.log
-
-    ]]>
-    </command>
-    <inputs>
-        <param name="infile" type="data" format="biom1" label="Biom1 dataset"/>
-    </inputs>
-    <outputs>
-        <data name="outfile" format="txt" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-        Interactive tool for visualising Biom data.
-    </help>
-</tool>
diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml
deleted file mode 100644
index 63e0eb3adb05..000000000000
--- a/interactivetool_rstudio.xml
+++ /dev/null
@@ -1,74 +0,0 @@
-<tool id="interactive_tool_rstudio" tool_type="interactive" name="RStudio" version="0.1">
-    <requirements>
-        <container type="docker">quay.io/erasche/docker-rstudio-notebook:19.09</container>
-    </requirements>
-    <entry_points>
-        <entry_point name="RStudio" requires_domain="True">
-            <port>80</port>
-            <url>rstudio/</url>
-        </entry_point>
-    </entry_points>
-    <environment_variables>
-        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($jupyter_notebook.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
-        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="DEBUG">true</environment_variable>
-        <environment_variable name="DISABLE_AUTH">true</environment_variable>
-        <environment_variable name="API_KEY" strip="True">
-            #if $__user__:
-                #for $api_key in $__user__.api_keys:
-                    ${api_key.key}
-                    #break
-                #end for
-            #end if
-        </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
-    </environment_variables>
-    <command detect_errors="aggressive"><![CDATA[
-        #import re
-        export GALAXY_WORKING_DIR=`pwd` &&
-        mkdir -p ./rstudio/outputs/ &&
-        mkdir -p ./rstudio/data &&
-
-        ## change into the directory where the notebooks are located
-        cd ./rstudio/ &&
-
-        sed -i 's|/monitor.*||g' /etc/services.d/nginx/run &&
-
-        /etc/init.d/syslog-ng start &&
-        /init &
-        ##rstudio-server start &&
-        sleep 5 &&
-
-        chmod 777 /tmp -R &&
-        tail -f /var/log/rstudio-server/rserver.log
-
-    ]]>
-    </command>
-    <inputs>
-        <!--<param name="input" type="data" optional="true" label="Include data into the environment"/>-->
-    </inputs>
-    <outputs>
-        <data name="jupyter_notebook" format="ipynb" label=""></data>
-    </outputs>
-    <tests>
-        <test expect_num_outputs="1">
-            <param name="mode" value="previous" />
-            <param name="ipynb" value="test.ipynb" />
-            <param name="run_it" value="true" />
-            <output name="jupyter_notebook" file="test.ipynb" ftype="ipynb"/>
-        </test>
-    </tests>
-    <help>
-    This familiar R analysis software suite will let you explore your
-    datasets in depth. Comes with ggplot2, RODBC, maps, shinyapps, knitr,
-    LaTeX, bioconductor, cummeRbund, and many more pre-installed packages.
-
-    Galaxy offers you to use RStudio directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
-    do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in RStudio.
-
-    The convenience functions gx_put() and gx_get() are available to you to interact with your current Galaxy history. You can save your workspace with gx_save().
-
-    For example, gx_get(42) will fetch dataset 42 from your history and return the file location
-    </help>
-</tool>
diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml
deleted file mode 100644
index 4d8e2c5353b0..000000000000
--- a/interactivetool_wallace.xml
+++ /dev/null
@@ -1,67 +0,0 @@
-<tool id="interactive_tool_wallace" tool_type="interactive" name="Wallace" version="0.1">
-    <description>Webbased Interactive modeling of species niches and distributions</description>
-    <requirements>
-        <container type="docker">ylebras/wallace-docker</container>
-    </requirements>
-    <entry_points>
-        <entry_point name="Wallace visualisation" requires_domain="True">
-            <port>3838</port>
-            <url>/sample-apps/SIG/wallace/shiny/</url>
-        </entry_point>
-    </entry_points>
-    <environment_variables>
-
-        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($outfile.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
-        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
-        <environment_variable name="API_KEY" strip="True">
-            #if $__user__:
-                #for $api_key in $__user__.api_keys:
-                    ${api_key.key}
-                    #break
-                #end for
-            #end if
-        </environment_variable> <!-- FIXME: We should have a better way to get user's API key -->
-    </environment_variables>
-    <command><![CDATA[
-
-        /usr/bin/shiny-server.sh
-
-    ]]>
-    </command>
-    <inputs>
-        <!--param name="infile" type="data" format="csv" label="csv file with for first columns: 'name', 'longitude', 'latitude' informations"/-->
-    </inputs>
-    <outputs>
-        <data name="outfile" format="txt" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-<![CDATA[
-
-
-
-
-`Wallace <https://wallaceecomod.github.io/>`_ is a flexible platform for reproducible modeling of species niches and distributions.
-
-.. class:: infomark
-
-Example input file (TAB separated)::
-
-  "name"	"longitude"	"latitude"	"countryCode"
-  Accipiter striatus Vieillot, 1808	-60.291838	46.328137	CA
-  Accipiter striatus Vieillot, 1808	-114.58927	35.022485	US
-  Accipiter striatus Vieillot, 1808	-93.37406	30.00586	US
-  Accipiter striatus Vieillot, 1808	-79.336288	43.682218	CA
-  Accipiter striatus Vieillot, 1808	-109.156024	31.904185	US
-  Accipiter striatus Vieillot, 1808	-71.098031	42.297408	US
-  Accipiter striatus Vieillot, 1808	-110.927215	32.18203	US
-
-]]>
-    </help>
-    <citations>
-        <citation type="doi">10.1111/2041-210X.12945</citation>
-    </citations>
-</tool>
diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml
deleted file mode 100644
index 7f575c43a636..000000000000
--- a/interactivetool_wilson.xml
+++ /dev/null
@@ -1,56 +0,0 @@
-<tool id="interactive_tool_wilson" tool_type="interactive" name="Wilson" version="0.1">
-    <description>Webbased Interactive Omics visualization</description>
-    <requirements>
-        <container type="docker">loosolab/wilson:2.1.1</container>
-    </requirements>
-    <entry_points>
-        <entry_point name="Wilson visualisation of $infile.display_name" requires_domain="True">
-            <port>3838</port>
-        </entry_point>
-    </entry_points>
-    <environment_variables>
-        <environment_variable name="WILSON_LANDING_PAGE">feature_selection</environment_variable>
-        <environment_variable name="WILSON_BLACKLIST_EXAMPLES">true</environment_variable>
-    </environment_variables>
-    <command><![CDATA[
-        mkdir -p /srv/shiny-server/external_data/ &&
-        echo "WILSON_LANDING_PAGE=\$WILSON_LANDING_PAGE" > /home/shiny/.Renviron &&
-        echo "WILSON_BLACKLIST_EXAMPLES=\$WILSON_BLACKLIST_EXAMPLES" >> /home/shiny/.Renviron &&
-        ln -s ${infile} /srv/shiny-server/external_data/input.clarion &&
-        exec shiny-server 2>&1
-    ]]>
-    </command>
-    <inputs>
-        <param name="infile" type="data" format="tabular,txt" label="Tabular in Clarion format"/>
-    </inputs>
-    <outputs>
-        <data name="outfile" format="txt" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-<![CDATA[
-
-`WIlsON: Webbased Interactive Omics visualizatioN <https://github.molgen.mpg.de/loosolab/wilson-apps/wiki>`_
-
-.. class:: infomark
-
-Wilson uses the CLARION file format, which is a generic file format for quantitative comparisons of high throughput screens.
-
-CLARION is a data format specially developed to be used with Wilson, which relies on a tab-delimited table with
-a metadata header to describe the following columns. It is based on the Summarized Experiment format and supports
-all types of data which can be reduced to features and their annotation (e.g. genes, transcripts, proteins, probes)
-with assigned numerical values (e.g. count, score, log2foldchange, z-score, p-value). Most result tables derived from RNA-Seq,
-ChIP/ATAC-Seq, Proteomics, Microarrays, and many other analyses can thus be easily reformatted to become compatible
-without having to modify the code of Wilson for each specific experiment.
-
-Please check the following link for details considering the `CLARION format <https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format>`_.
-
-
-
-]]>
-    </help>
-    <citations>
-        <citation type="doi">10.1093/bioinformatics/bty711</citation>
-    </citations>
-</tool>
diff --git a/interactivetool_climate_notebook.xml b/tools/interactive/interactivetool_climate_notebook.xml
similarity index 100%
rename from interactivetool_climate_notebook.xml
rename to tools/interactive/interactivetool_climate_notebook.xml
diff --git a/interactivetool_geoexplorer.xml b/tools/interactive/interactivetool_geoexplorer.xml
similarity index 100%
rename from interactivetool_geoexplorer.xml
rename to tools/interactive/interactivetool_geoexplorer.xml
diff --git a/interactivetool_guacamole_desktop.xml b/tools/interactive/interactivetool_guacamole_desktop.xml
similarity index 100%
rename from interactivetool_guacamole_desktop.xml
rename to tools/interactive/interactivetool_guacamole_desktop.xml
diff --git a/interactivetool_openrefine.xml b/tools/interactive/interactivetool_openrefine.xml
similarity index 100%
rename from interactivetool_openrefine.xml
rename to tools/interactive/interactivetool_openrefine.xml
diff --git a/interactivetool_panoply.xml b/tools/interactive/interactivetool_panoply.xml
similarity index 100%
rename from interactivetool_panoply.xml
rename to tools/interactive/interactivetool_panoply.xml
diff --git a/interactivetool_paraview.xml b/tools/interactive/interactivetool_paraview.xml
similarity index 100%
rename from interactivetool_paraview.xml
rename to tools/interactive/interactivetool_paraview.xml
diff --git a/interactivetool_pyiron.xml b/tools/interactive/interactivetool_pyiron.xml
similarity index 100%
rename from interactivetool_pyiron.xml
rename to tools/interactive/interactivetool_pyiron.xml
diff --git a/interactivetool_radiant.xml b/tools/interactive/interactivetool_radiant.xml
similarity index 100%
rename from interactivetool_radiant.xml
rename to tools/interactive/interactivetool_radiant.xml
diff --git a/interactivetool_vcf_iobio.xml b/tools/interactive/interactivetool_vcf_iobio.xml
similarity index 100%
rename from interactivetool_vcf_iobio.xml
rename to tools/interactive/interactivetool_vcf_iobio.xml

From b2ad091f6a5c323f5d0622b4cbfab64033284cb6 Mon Sep 17 00:00:00 2001
From: "jalili.vahid@gmail.com" <LetMeIn%#01>
Date: Tue, 24 Mar 2020 03:23:26 -0700
Subject: [PATCH 574/853] Do not declare methods as non-overridable, because
 ...

---
 lib/galaxy/objectstore/__init__.py | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index 52267e9397d6..c2552ca3334e 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -196,18 +196,7 @@ def get_store_by(self, obj):
         raise NotImplementedError()
 
 
-class NonOverridable(type):
-    def __new__(mcs, name, bases, dct):
-        # The following is a list of methods implemented in BaseObjectStore type, which shall not be overridden.
-        for method in ["exists", "create", "empty", "size", "delete", "get_data", "get_filename",
-                       "update_from_file", "get_object_url", "get_store_usage_percent", "get_store_by"]:
-            if bases and method in dct:
-                raise SyntaxError("Overriding {0} is not allowed".format(method))
-        return type.__new__(mcs, name, bases, dct)
-
-
 class BaseObjectStore(IObjectStore):
-    __metaclass__ = NonOverridable
 
     def __init__(self, config, config_dict=None, **kwargs):
         """

From fa1a87077055afdc56a97a26fadfde0d12f27900 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 24 Mar 2020 13:51:20 -0400
Subject: [PATCH 575/853] Fixed exception message in unit tests

---
 test/unit/objectstore/test_irods.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/unit/objectstore/test_irods.py b/test/unit/objectstore/test_irods.py
index d7c6f57fb38f..256a98383071 100644
--- a/test/unit/objectstore/test_irods.py
+++ b/test/unit/objectstore/test_irods.py
@@ -39,12 +39,12 @@ def test_parse_valid_config_xml():
 def test_parse_config_xml_no_extra_dir():
     tree = ET.parse(CONFIG_FILE_NO_EXTRA_DIR)
     root = tree.getroot()
-    with pytest.raises(Exception, match='No extra_dir element in XML tree'):
+    with pytest.raises(Exception, match='No extra_dir element in config XML tree'):
         parse_config_xml(root)
 
 
 def test_parse_config_xml_no_auth():
     tree = ET.parse(CONFIG_FILE_NO_AUTH)
     root = tree.getroot()
-    with pytest.raises(Exception, match='No auth element in XML tree'):
+    with pytest.raises(Exception, match='No auth element in config XML tree'):
         parse_config_xml(root)

From ed6312ffde89bd445a882fbd56c51d15f09c0893 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 24 Mar 2020 13:56:08 -0400
Subject: [PATCH 576/853] Fixed Python2 isue for pathlib import (Thanks to
 Marius)

---
 lib/galaxy/objectstore/irods.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 7d5ce9ea1878..24fb38dbdc03 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -5,7 +5,11 @@
 import os
 import shutil
 from datetime import datetime
-from pathlib import Path
+try:
+    from pathlib import Path
+except ImportError:
+    # Use backport on python 2
+    from pathlib2 import Path
 
 try:
     import irods

From 04027a89966f348c04f5a318283d1c3958f08066 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 25 Mar 2020 13:44:49 +0100
Subject: [PATCH 577/853] Hide LDDA when creating collection in library
 interface

Fixes https://github.com/galaxyproject/galaxy/issues/9435
---
 lib/galaxy/managers/collections.py | 2 +-
 lib/galaxy/model/__init__.py       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index 08cef87405b6..91b137c6ea7e 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -434,7 +434,7 @@ def __load_element(self, trans, element_identifier, hide_source_items, copy_elem
             self.tag_handler.apply_item_tags(user=trans.user, item=element, tags_str=tag_str)
         elif src_type == 'ldda':
             element = self.ldda_manager.get(trans, encoded_id, check_accessible=True)
-            element = element.to_history_dataset_association(trans.history, add_to_history=True)
+            element = element.to_history_dataset_association(trans.history, add_to_history=True, visible=not hide_source_items)
             self.tag_handler.apply_item_tags(user=trans.user, item=element, tags_str=tag_str)
         elif src_type == 'hdca':
             # TODO: Option to copy? Force copy? Copy or allow if not owned?
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 621124e9ccd6..d51b38cc2516 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3528,7 +3528,7 @@ def __init__(self,
         self.library_dataset = library_dataset
         self.user = user
 
-    def to_history_dataset_association(self, target_history, parent_id=None, add_to_history=False):
+    def to_history_dataset_association(self, target_history, parent_id=None, add_to_history=False, visible=None):
         sa_session = object_session(self)
         hda = HistoryDatasetAssociation(name=self.name,
                                         info=self.info,
@@ -3538,7 +3538,7 @@ def to_history_dataset_association(self, target_history, parent_id=None, add_to_
                                         extension=self.extension,
                                         dbkey=self.dbkey,
                                         dataset=self.dataset,
-                                        visible=self.visible,
+                                        visible=visible if visible is not None else self.visible,
                                         deleted=self.deleted,
                                         parent_id=parent_id,
                                         copied_from_library_dataset_dataset_association=self,

From 3b5a1a03d2f4b38c1ef9d0f8bc5955441b5fba51 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 25 Mar 2020 15:57:50 +0100
Subject: [PATCH 578/853] Add API tests library datasets as HDCA import

---
 lib/galaxy_test/api/test_libraries.py | 33 +++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/lib/galaxy_test/api/test_libraries.py b/lib/galaxy_test/api/test_libraries.py
index 2bfe863c01d3..8f0edbe60b78 100644
--- a/lib/galaxy_test/api/test_libraries.py
+++ b/lib/galaxy_test/api/test_libraries.py
@@ -319,6 +319,39 @@ def test_detect_datatype_of_dataset_in_folder(self):
         self._assert_has_keys(create_response.json(), "file_ext")
         assert create_response.json()["file_ext"] == "txt"
 
+    def test_ldda_collection_import_to_history(self):
+        self._import_to_history(visible=True)
+
+    def test_ldda_collection_import_to_history_hide_source(self):
+        self._import_to_history(visible=False)
+
+    def _import_to_history(self, visible=True):
+        ld = self._create_dataset_in_folder_in_library("ForHistoryImport").json()
+        history_id = self.dataset_populator.new_history()
+        url = "histories/%s/contents" % history_id
+        collection_name = 'new_collection_name'
+        element_identifer = 'new_element_identifier'
+        payload = {
+            "collection_type": "list",
+            "history_content_type": "dataset_collection",
+            "model_class": "HistoryDatasetCollectionAssociation",
+            "history_id": history_id,
+            "name": collection_name,
+            "hide_source_items": not visible,
+            "element_identifiers": json.dumps([{
+                "id": ld['id'],
+                "name": element_identifer,
+                "src": "ldda"}]),
+            "type": "dataset_collection",
+            "elements": []
+        }
+        new_collection = self._post(url, payload).json()
+        assert new_collection['name'] == collection_name
+        assert new_collection['element_count'] == 1
+        element = new_collection['elements'][0]
+        assert element['element_identifier'] == element_identifer
+        assert element['object']['visible'] == visible
+
     def test_create_datasets_in_library_from_collection(self):
         library = self.library_populator.new_private_library("ForCreateDatasetsFromCollection")
         folder_response = self._create_folder(library)

From 0ca974c0d5aaf922f9920caa16fa473ddb864a0e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 4 Mar 2020 12:04:18 +0100
Subject: [PATCH 579/853] Save integrated tool panel once on toolbox reload

This should make toolbox reloads work on main and other
large instances.
---
 lib/galaxy/config_watchers.py    | 13 ++++++++++++-
 lib/galaxy/queue_worker.py       |  6 +++---
 lib/galaxy/tools/toolbox/base.py |  5 +++--
 3 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/config_watchers.py b/lib/galaxy/config_watchers.py
index 23db380d6a2d..ddd1036644fa 100644
--- a/lib/galaxy/config_watchers.py
+++ b/lib/galaxy/config_watchers.py
@@ -1,3 +1,4 @@
+import logging
 from os.path import dirname
 
 from galaxy.queue_worker import job_rule_modules
@@ -7,6 +8,8 @@
 )
 from galaxy.util.watcher import get_watcher
 
+log = logging.getLogger(__name__)
+
 
 class ConfigWatchers(object):
     """Contains ToolConfWatcher, ToolWatcher and ToolDataWatcher objects."""
@@ -21,8 +24,16 @@ def __init__(self, app):
         # If there are multiple ToolConfWatcher objects for the same handler or web process a race condition occurs between the two cache_cleanup functions.
         # If the reload_data_managers callback wins, the cache will miss the tools that had been removed from the cache
         # and will be blind to further changes in these tools.
+
+        def reload_toolbox():
+            try:
+                self.app.queue_worker.send_local_control_task('reload_toolbox', get_response=True),
+            except Exception:
+                log.exception()
+            self.app.queue_worker.send_control_task('reload_toolbox', kwargs={'save_integrated_tool_panel': False}),
+
         self.tool_config_watcher = get_tool_conf_watcher(
-            reload_callback=lambda: self.app.queue_worker.send_control_task('reload_toolbox'),
+            reload_callback=reload_toolbox,
             tool_cache=self.app.tool_cache,
         )
         self.data_manager_config_watcher = get_tool_conf_watcher(
diff --git a/lib/galaxy/queue_worker.py b/lib/galaxy/queue_worker.py
index 593357260606..1c101bc2eff0 100644
--- a/lib/galaxy/queue_worker.py
+++ b/lib/galaxy/queue_worker.py
@@ -42,7 +42,7 @@ def send_local_control_task(app, task, get_response=False, kwargs=None):
     """
     if kwargs is None:
         kwargs = {}
-    log.info("Queuing async task %s for %s." % (task, app.config.server_name))
+    log.info("Queuing %s task %s for %s." % ("sync" if get_response else "async", task, app.config.server_name))
     payload = {'task': task,
                'kwargs': kwargs}
     routing_key = 'control.%s@%s' % (app.config.server_name, socket.gethostname())
@@ -352,8 +352,8 @@ def __init__(self, app, task_mapping=None):
     def send_control_task(self, task, noop_self=False, get_response=False, routing_key='control.*', kwargs=None):
         return send_control_task(app=self.app, task=task, noop_self=noop_self, get_response=get_response, routing_key=routing_key, kwargs=kwargs)
 
-    def send_local_control_task(self, task, kwargs=None):
-        return send_local_control_task(app=self.app, task=task, kwargs=kwargs)
+    def send_local_control_task(self, task, get_response=False, kwargs=None):
+        return send_local_control_task(app=self.app, get_response=get_response, task=task, kwargs=kwargs)
 
     @property
     def declare_queues(self):
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 60ed3c0e925d..f0af4bcbd97a 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -75,7 +75,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
     workflows optionally in labelled sections.
     """
 
-    def __init__(self, config_filenames, tool_root_dir, app):
+    def __init__(self, config_filenames, tool_root_dir, app, save_integrated_tool_panel=True):
         """
         Create a toolbox from the config files named by `config_filenames`, using
         `tool_root_dir` as the base directory for finding individual tool config files.
@@ -119,7 +119,8 @@ def __init__(self, config_filenames, tool_root_dir, app):
         if self.app.name == 'galaxy' and self._integrated_tool_panel_config_has_contents:
             # Load self._tool_panel based on the order in self._integrated_tool_panel.
             self._load_tool_panel()
-        self._save_integrated_tool_panel()
+        if save_integrated_tool_panel:
+            self._save_integrated_tool_panel()
 
     def create_tool(self, config_file, tool_shed_repository=None, guid=None, **kwds):
         raise NotImplementedError()

From 4a2ae58966c6bafc6f03ad9aa91153fce9a31c5c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 4 Mar 2020 12:45:27 +0100
Subject: [PATCH 580/853] Don't run toolbox reload twice on watcher

---
 lib/galaxy/config_watchers.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/config_watchers.py b/lib/galaxy/config_watchers.py
index ddd1036644fa..2e16735ee7f4 100644
--- a/lib/galaxy/config_watchers.py
+++ b/lib/galaxy/config_watchers.py
@@ -26,11 +26,15 @@ def __init__(self, app):
         # and will be blind to further changes in these tools.
 
         def reload_toolbox():
+            save_integrated_tool_panel = False
             try:
+                # Run and wait for toolbox reload on the process that watches the config files.
+                # The toolbpox reload will update the integrated_tool_panel_file
                 self.app.queue_worker.send_local_control_task('reload_toolbox', get_response=True),
             except Exception:
-                log.exception()
-            self.app.queue_worker.send_control_task('reload_toolbox', kwargs={'save_integrated_tool_panel': False}),
+                save_integrated_tool_panel = True
+                log.exception("Exception occured while reloading toolbox")
+            self.app.queue_worker.send_control_task('reload_toolbox', noop_self=True, kwargs={'save_integrated_tool_panel': save_integrated_tool_panel}),
 
         self.tool_config_watcher = get_tool_conf_watcher(
             reload_callback=reload_toolbox,

From a1ffcb6b30134f8a580bf9e4b4484465f429fda4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 4 Mar 2020 12:47:58 +0100
Subject: [PATCH 581/853] Log when writing tool panel config file

---
 lib/galaxy/tools/toolbox/integrated_panel.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/galaxy/tools/toolbox/integrated_panel.py b/lib/galaxy/tools/toolbox/integrated_panel.py
index 9e3020282bd8..fa1b7949b5ea 100644
--- a/lib/galaxy/tools/toolbox/integrated_panel.py
+++ b/lib/galaxy/tools/toolbox/integrated_panel.py
@@ -1,3 +1,4 @@
+import logging
 import os
 import shutil
 import string
@@ -11,6 +12,8 @@
     ToolPanelElements
 )
 
+log = logging.getLogger(__name__)
+
 INTEGRATED_TOOL_PANEL_DESCRIPTION = """
 This is Galaxy's integrated tool panel and should be modified directly only for
 reordering tools inside a section. Each time Galaxy starts up, this file is
@@ -52,6 +55,7 @@ def _write_integrated_tool_panel_config_file(self):
         use this file to manage the tool panel, we'll not use xml_to_string() since it doesn't write XML quite right.
         """
         destination = os.path.abspath(self._integrated_tool_panel_config)
+        log.debug("Writing integrated tool panel config file to '%s'", destination)
         tracking_directory = self._integrated_tool_panel_tracking_directory
         if tracking_directory:
             if not os.path.exists(tracking_directory):

From 173d19c23a7e027700488b8cc0deee25e3fcc006 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 4 Mar 2020 13:24:19 +0100
Subject: [PATCH 582/853] Pass save_integrated_tool_panel down the ToolBox

---
 lib/galaxy/queue_worker.py       | 8 ++++----
 lib/galaxy/tools/__init__.py     | 3 ++-
 lib/galaxy/tools/toolbox/base.py | 4 ++--
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/queue_worker.py b/lib/galaxy/queue_worker.py
index 1c101bc2eff0..da2538508e82 100644
--- a/lib/galaxy/queue_worker.py
+++ b/lib/galaxy/queue_worker.py
@@ -163,19 +163,19 @@ def reload_tool(app, **kwargs):
         log.error("Reload tool invoked without tool id.")
 
 
-def reload_toolbox(app, **kwargs):
+def reload_toolbox(app, save_integrated_tool_panel=True, **kwargs):
     reload_timer = util.ExecutionTimer()
     log.debug("Executing toolbox reload on '%s'", app.config.server_name)
     reload_count = app.toolbox._reload_count
     if hasattr(app, 'tool_cache'):
         app.tool_cache.cleanup()
-    _get_new_toolbox(app)
+    _get_new_toolbox(app, save_integrated_tool_panel)
     app.toolbox._reload_count = reload_count + 1
     send_local_control_task(app, 'rebuild_toolbox_search_index')
     log.debug("Toolbox reload %s", reload_timer)
 
 
-def _get_new_toolbox(app):
+def _get_new_toolbox(app, save_integrated_tool_panel=True):
     """
     Generate a new toolbox, by constructing a toolbox from the config files,
     and then adding pre-existing data managers from the old toolbox to the new toolbox.
@@ -186,7 +186,7 @@ def _get_new_toolbox(app):
         app.tool_shed_repository_cache.rebuild()
     tool_configs = app.config.tool_configs
 
-    new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)
+    new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app, save_integrated_tool_panel=save_integrated_tool_panel)
     new_toolbox.data_manager_tools = app.toolbox.data_manager_tools
     app.datatypes_registry.load_datatype_converters(new_toolbox, use_cached=True)
     app.datatypes_registry.load_external_metadata_tool(new_toolbox)
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 711b52c977bb..208fe5f5df4c 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -241,7 +241,7 @@ class ToolBox(BaseGalaxyToolBox):
     how to construct them, action types, dependency management, etc....
     """
 
-    def __init__(self, config_filenames, tool_root_dir, app):
+    def __init__(self, config_filenames, tool_root_dir, app, save_integrated_tool_panel=True):
         self._reload_count = 0
         self.tool_location_fetcher = ToolLocationFetcher()
         # This is here to deal with the old default value, which doesn't make
@@ -253,6 +253,7 @@ def __init__(self, config_filenames, tool_root_dir, app):
             config_filenames=config_filenames,
             tool_root_dir=tool_root_dir,
             app=app,
+            save_integrated_tool_panel=save_integrated_tool_panel,
         )
 
     def can_load_config_file(self, config_filename):
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index f0af4bcbd97a..a19a5f91b424 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -1190,8 +1190,8 @@ class BaseGalaxyToolBox(AbstractToolBox):
     shouldn't really depend on.
     """
 
-    def __init__(self, config_filenames, tool_root_dir, app):
-        super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app)
+    def __init__(self, config_filenames, tool_root_dir, app, save_integrated_tool_panel=True):
+        super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app, save_integrated_tool_panel)
         old_toolbox = getattr(app, 'toolbox', None)
         if old_toolbox:
             self.dependency_manager = old_toolbox.dependency_manager

From 1604f2ab28c6757d92a347e2c8b364b8f586c383 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 4 Mar 2020 16:16:05 +0100
Subject: [PATCH 583/853] Don't block forever if connection can't be acquired

---
 lib/galaxy/queue_worker.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/queue_worker.py b/lib/galaxy/queue_worker.py
index da2538508e82..87eeada1ecb5 100644
--- a/lib/galaxy/queue_worker.py
+++ b/lib/galaxy/queue_worker.py
@@ -114,7 +114,7 @@ def send_task(self, payload, routing_key, local=False, get_response=False, timeo
             callback_queue = [self.callback_queue]
             self.correlation_id = uuid()
         try:
-            with producers[self.connection].acquire(block=True) as producer:
+            with producers[self.connection].acquire(block=True, timeout=10) as producer:
                 producer.publish(
                     payload,
                     exchange=None if local else self.exchange,

From 7d110f1d71e4a00fb7a7e6cff594b45f61f52e0d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 17 Mar 2020 17:56:21 +0100
Subject: [PATCH 584/853] Exchange routing key needs to be wildcard ...

But why that wasn't a problem before is a mystery to me.
---
 lib/galaxy/queues.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/queues.py b/lib/galaxy/queues.py
index abb9b993027b..5b74c0e496d9 100644
--- a/lib/galaxy/queues.py
+++ b/lib/galaxy/queues.py
@@ -32,7 +32,7 @@ def control_queues_from_config(config):
     """
     hostname = socket.gethostname()
     process_name = "{server_name}@{hostname}".format(server_name=config.server_name, hostname=hostname)
-    exchange_queue = Queue("control.%s" % process_name, galaxy_exchange, routing_key='control.%s' % process_name)
+    exchange_queue = Queue("control.%s" % process_name, galaxy_exchange, routing_key='control.*')
     non_exchange_queue = Queue("control.%s" % process_name, routing_key='control.%s' % process_name)
     return exchange_queue, non_exchange_queue
 

From 9e48192ea97bac9a9960bb520d7b8d87b0799554 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 25 Mar 2020 17:20:07 +0100
Subject: [PATCH 585/853] Add right arrow

---
 .../components/Workflow/Editor/Node.vue       | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index d3d91f178869..a5ef377e1f4f 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -10,6 +10,16 @@
             >
                 <i class="fa fa-times" />
             </b-button>
+            <b-button 
+                v-if="isEnabled"
+                class="node-recommendations py-0 float-right"
+                variant="primary"
+                size="sm"
+                aria-label="tool recommendations"
+                @click="onGetRecommendations"
+            >
+                <i class="fa fa-arrow-right" />
+            </b-button>
             <b-button
                 v-if="canClone"
                 class="node-clone py-0 float-right"
@@ -36,6 +46,7 @@ import Vue from "vue";
 import BootstrapVue from "bootstrap-vue";
 import WorkflowIcons from "components/Workflow/icons";
 import LoadingSpan from "components/LoadingSpan";
+import { getGalaxyInstance } from "app";
 
 Vue.use(BootstrapVue);
 
@@ -70,6 +81,14 @@ export default {
         canClone() {
             return this.type != "subworkflow";
         },
+        isEnabled () {
+            const Galaxy = getGalaxyInstance();
+            const isRecommendationEnabled = Galaxy.config.enable_tool_recommendations;
+            if (isRecommendationEnabled === true || isRecommendationEnabled === "true") {
+                return true;
+            }
+            return false;
+        }
     },
     methods: {
         onDestroy() {
@@ -78,6 +97,9 @@ export default {
         onClone() {
             this.node.clone();
         },
+        onGetRecommendations() {
+            console.log("Clicked recommendations");
+        }
     },
 };
 </script>

From d99a932cde3f6b73bb6090aa04c570b2ea92ed40 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Wed, 25 Mar 2020 13:47:51 -0400
Subject: [PATCH 586/853] Start an iRODS instance when runing iRODS integration
 test.

---
 .../integration/test_datatype_upload_irods.py | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index eb2751b72fe2..dce0e51bde18 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,6 +1,7 @@
 
 import os
 import tempfile
+import subprocess
 
 import pytest
 
@@ -13,8 +14,36 @@
 IRODS_TEST_CASES = dict(list(TEST_CASES.items())[0:10])
 
 
+def start_irods(container_name):
+    minio_start_args = [
+        'docker',
+        'run',
+        '-p',
+        '1247:1247',
+        '-d',
+        '--name',
+        container_name,
+        'kxk302/irods-server:0.1']
+    subprocess.check_call(minio_start_args)
+
+
+def stop_irods(container_name):
+    subprocess.check_call(['docker', 'rm', '-f', container_name])
+
+
 class UploadTestDatatypeDataTestCase(UploadTestDatatypeDataTestCase):
 
+    @classmethod
+    def setUpClass(cls):
+        cls.container_name = "%s_container" % cls.__name__
+        start_irods(cls.container_name)
+        super(UploadTestDatatypeDataTestCase, cls).setUpClass()
+
+    @classmethod
+    def tearDownClass(cls):
+        stop_irods(cls.container_name)
+        super(UploadTestDatatypeDataTestCase, cls).tearDownClass()
+
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["object_store_config_file"] = OBJECT_STORE_CONFIG_FILE

From 824de841e05301e93670227a9ecf26a8596cbfa4 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Wed, 25 Mar 2020 13:52:11 -0400
Subject: [PATCH 587/853] Import in wrong order. Not sure why lint did not
 catch this locally.

---
 test/integration/test_datatype_upload_irods.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index dce0e51bde18..237879e36194 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,7 +1,7 @@
 
 import os
-import tempfile
 import subprocess
+import tempfile
 
 import pytest
 

From 6bc8cf329ee6806af6ff5f3c5dcfd1ed9cbc18b1 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 25 Mar 2020 19:18:56 +0100
Subject: [PATCH 588/853] Fetch path

---
 .../components/Workflow/Editor/Node.vue       |   3 +
 .../components/Workflow/Editor/utilities.js   | 136 ++++++++++++++++++
 2 files changed, 139 insertions(+)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index a5ef377e1f4f..7ddaddf95eb1 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -47,6 +47,7 @@ import BootstrapVue from "bootstrap-vue";
 import WorkflowIcons from "components/Workflow/icons";
 import LoadingSpan from "components/LoadingSpan";
 import { getGalaxyInstance } from "app";
+import { getToolRecommendations } from "./utilities";
 
 Vue.use(BootstrapVue);
 
@@ -99,6 +100,8 @@ export default {
         },
         onGetRecommendations() {
             console.log("Clicked recommendations");
+            console.log(this);
+            getToolRecommendations(this);
         }
     },
 };
diff --git a/client/galaxy/scripts/components/Workflow/Editor/utilities.js b/client/galaxy/scripts/components/Workflow/Editor/utilities.js
index dcd01b05aaf8..7e5395254962 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/utilities.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/utilities.js
@@ -206,3 +206,139 @@ export function saveAs(workflow) {
         Cancel: hide_modal,
     });
 }
+
+function getToolId(toolId) {
+    if (toolId !== undefined && toolId !== null && toolId.indexOf("/") > -1) {
+        let toolIdSlash = toolId.split("/");
+        toolId = toolIdSlash[toolIdSlash.length - 2];
+    }
+    return toolId;
+}
+
+function get_workflow_path(wf_steps, current_node_id, current_node_name) {
+        let steps = {};
+        let step_names = {};
+        for (let stp_idx in wf_steps.steps) {
+            let step = wf_steps.steps[stp_idx];
+            let input_connections = step.input_connections;
+            step_names[step.id] = getToolId(step.content_id);
+            for (let ic_idx in input_connections) {
+                let ic = input_connections[ic_idx];
+                if(ic !== null && ic !== undefined) {
+                    let prev_conn = [];
+                    for (let conn of ic) {
+                        prev_conn.push(conn.id.toString());
+                    }
+                    steps[step.id.toString()] = prev_conn;
+                }
+            }
+        }
+        // recursive call to determine path
+        function read_paths(node_id, ph) {
+            for (let st in steps) {
+                if (parseInt(st) === parseInt(node_id)) {
+                    let parent_id = parseInt(steps[st][0]);
+                    if (parent_id !== undefined && parent_id !== null) {
+                        ph.push(parent_id);
+                        if (steps[parent_id] !== undefined && steps[parent_id] !== null) {
+                            read_paths(parent_id, ph);
+                        }
+                    }
+                }
+            }
+            return ph;
+        }
+        let ph = [];
+        let step_names_list = [];
+        ph.push(current_node_id);
+        ph = read_paths(current_node_id, ph);
+        for (let s_idx of ph) {
+            let s_name = step_names[s_idx.toString()];
+            if (s_name !== undefined && s_name !== null) {
+                step_names_list.push(s_name);
+            }
+        }
+        return step_names_list.join(",");
+}
+
+export function getToolRecommendations(propsData) {
+        let workflow_simple = propsData.node.app.to_simple(), //window.workflow_globals.workflow.to_simple(),
+        node = propsData.node,
+        toolId = getToolId(node.content_id);
+        console.log(workflow_simple);
+        console.log(node);
+        let tool_sequence = get_workflow_path(workflow_simple, node.id, toolId);
+        console.log(tool_sequence);
+        // remove ui-modal if present
+        /*let $modal = $(".modal-tool-recommendation");
+        if ($modal.length > 0) {
+            $modal.remove();
+        }
+        // create new modal
+        let modal = new Modal.View({
+            title: "Recommended tools",
+            body: "<div> Loading tools ... </div>",
+            height: "230",
+            width: "250",
+            closing_events: true,
+            title_separator: true        
+        });
+        modal.$el.addClass("modal-tool-recommendation");
+        modal.$el.find(".modal-header").attr("title", "The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to have it on the workflow editor.");
+        modal.$el.find(".modal-body").css("overflow", "auto");
+        modal.show();
+        // fetch recommended tools
+        Utils.request({
+            type: "POST",
+            url: `${getAppRoot()}api/workflows/get_tool_predictions`,
+            data: {"tool_sequence": tool_sequence},
+            success: function(data) {
+                let predTemplate = "<div>";
+                let predictedData = data.predicted_data;
+                let outputDatatypes = predictedData["o_extensions"];
+                let predictedDataChildren = predictedData.children;
+                let noRecommendationsMessage = "No tool recommendations";
+                if (predictedDataChildren.length > 0) {
+                    let compatibleTools = {};
+                    // filter results based on datatype compatibility
+                    for (const [index, name_obj] of predictedDataChildren.entries()) {
+                        let inputDatatypes = name_obj["i_extensions"];
+                        for (const out_t of outputDatatypes.entries()) {
+                            for(const in_t of inputDatatypes.entries()) {
+                                if ((window.workflow_globals.app.isSubType(out_t[1], in_t[1]) === true) ||
+                                     out_t[1] === "input" ||
+                                     out_t[1] === "_sniff_" ||
+                                     out_t[1] === "input_collection") {
+                                    compatibleTools[name_obj["tool_id"]] = name_obj["name"];
+                                    break
+                                }
+                            }
+                        }
+                    }
+                    predTemplate += "<div>";
+                    if (Object.keys(compatibleTools).length > 0 && predictedData["is_deprecated"] === false) {
+                        for (let id in compatibleTools) {
+                            predTemplate += "<i class='fa mr-1 fa-wrench'></i><a href='#' title='Click to open the tool' class='pred-tool panel-header-button' id=" + "'" + id + "'" + ">" + compatibleTools[id];
+                            predTemplate += "</a></br>";
+                        }
+                    }
+                    else if (predictedData["is_deprecated"] === true) {
+                        predTemplate += predictedData["message"];
+                    }
+                    else {
+                        predTemplate += noRecommendationsMessage;
+                    }
+                    predTemplate += "</div>";
+                }
+                else {
+                    predTemplate += noRecommendationsMessage; 
+                }
+                predTemplate += "</div>";
+                modal.$body.html(predTemplate);
+                $(".pred-tool").click(e => {
+                    workflow_globals.app.add_node_for_tool(e.target.id, e.target.id);
+                    modal.hide();
+                });
+            }
+        });*/
+    }

From 3b294d08be575eefb89a2d9583da8df4d14b6217 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Wed, 25 Mar 2020 14:50:05 -0400
Subject: [PATCH 589/853] Added step to setup tmate

---
 .github/workflows/integration.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index eae99cebd440..53395915cab6 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -46,6 +46,8 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v2
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
       working-directory: 'galaxy root'

From f94365ef931ced126fdd5217e9da24162c566d40 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 25 Mar 2020 19:59:46 +0100
Subject: [PATCH 590/853] Add modal

---
 .../scripts/components/Workflow/Editor/utilities.js    | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/utilities.js b/client/galaxy/scripts/components/Workflow/Editor/utilities.js
index 7e5395254962..79c341000d83 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/utilities.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/utilities.js
@@ -7,6 +7,7 @@ import WorkflowIcons from "components/Workflow/icons";
 import { DefaultForm, ToolForm } from "mvc/workflow/workflow-forms";
 import { loadWorkflow } from "./services";
 import { hide_modal, show_message, show_modal } from "layout/modal";
+import Modal from "mvc/ui/ui-modal";
 
 export function copyIntoWorkflow(workflow, id = null, stepCount = null) {
     const _copy_into_workflow_ajax = () => {
@@ -262,15 +263,16 @@ function get_workflow_path(wf_steps, current_node_id, current_node_name) {
 }
 
 export function getToolRecommendations(propsData) {
-        let workflow_simple = propsData.node.app.to_simple(), //window.workflow_globals.workflow.to_simple(),
+        let workflow_simple = propsData.node.app.to_simple(),
         node = propsData.node,
         toolId = getToolId(node.content_id);
         console.log(workflow_simple);
         console.log(node);
         let tool_sequence = get_workflow_path(workflow_simple, node.id, toolId);
         console.log(tool_sequence);
+        
         // remove ui-modal if present
-        /*let $modal = $(".modal-tool-recommendation");
+        let $modal = $(".modal-tool-recommendation");
         if ($modal.length > 0) {
             $modal.remove();
         }
@@ -305,7 +307,7 @@ export function getToolRecommendations(propsData) {
                         let inputDatatypes = name_obj["i_extensions"];
                         for (const out_t of outputDatatypes.entries()) {
                             for(const in_t of inputDatatypes.entries()) {
-                                if ((window.workflow_globals.app.isSubType(out_t[1], in_t[1]) === true) ||
+                                if ((propsData.node.app.isSubType(out_t[1], in_t[1]) === true) ||
                                      out_t[1] === "input" ||
                                      out_t[1] === "_sniff_" ||
                                      out_t[1] === "input_collection") {
@@ -340,5 +342,5 @@ export function getToolRecommendations(propsData) {
                     modal.hide();
                 });
             }
-        });*/
+        });
     }

From d4f6089ccf6d4eeb6e5e55bd1e258b567e44b5fa Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Wed, 25 Mar 2020 15:37:42 -0400
Subject: [PATCH 591/853] Revised tmate step

---
 .github/workflows/integration.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 53395915cab6..2cfd173148bb 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -46,6 +46,7 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - uses: actions/checkout@v2
     - name: Setup tmate session
       uses: mxschmitt/action-tmate@v2
     - name: Run tests

From 20183bbc6669f805cdd302ddef86dc60c4ed581f Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Tue, 17 Mar 2020 18:44:13 +0100
Subject: [PATCH 592/853] implement visualization editor

intoduce webpack, remove ace-editor files from static

fix lint

build editor automatically

remove package lock
---
 client/gulpfile.js                            |  2 +-
 .../visualizations/editor/config/editor.xml   | 16 +++++
 .../visualizations/editor/package.json        | 21 ++++++
 .../visualizations/editor/src/index.js        |  4 ++
 .../editor/src/styles/style.css               | 41 +++++++++++
 .../editor/templates/editor.mako              | 72 +++++++++++++++++++
 .../visualizations/editor/webpack.config.js   | 39 ++++++++++
 7 files changed, 194 insertions(+), 1 deletion(-)
 create mode 100644 config/plugins/visualizations/editor/config/editor.xml
 create mode 100644 config/plugins/visualizations/editor/package.json
 create mode 100644 config/plugins/visualizations/editor/src/index.js
 create mode 100644 config/plugins/visualizations/editor/src/styles/style.css
 create mode 100755 config/plugins/visualizations/editor/templates/editor.mako
 create mode 100644 config/plugins/visualizations/editor/webpack.config.js

diff --git a/client/gulpfile.js b/client/gulpfile.js
index f31949a263cd..af0d5c6369ca 100644
--- a/client/gulpfile.js
+++ b/client/gulpfile.js
@@ -21,7 +21,7 @@ const paths = {
     //    "../config/plugins/{visualizations,interactive_environments}/*/*/package.json"
     //],
     plugin_build_dirs: [
-        "../config/plugins/visualizations/{annotate_image,hyphyvision,openlayers}/package.json",
+        "../config/plugins/visualizations/{annotate_image,hyphyvision,openlayers,editor}/package.json",
     ],
     lib_locs: {
         // This is a stepping stone towards having all this staged
diff --git a/config/plugins/visualizations/editor/config/editor.xml b/config/plugins/visualizations/editor/config/editor.xml
new file mode 100644
index 000000000000..94d863ddcb28
--- /dev/null
+++ b/config/plugins/visualizations/editor/config/editor.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="Editor">
+    <description>Manually edit text</description>
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <entry_point entry_point_type="mako">editor.mako</entry_point>
+</visualization>
\ No newline at end of file
diff --git a/config/plugins/visualizations/editor/package.json b/config/plugins/visualizations/editor/package.json
new file mode 100644
index 000000000000..bc92eebdc68a
--- /dev/null
+++ b/config/plugins/visualizations/editor/package.json
@@ -0,0 +1,21 @@
+{
+  "devDependencies": {
+    "css-loader": "^3.4.2",
+    "file-loader": "^5.0.2",
+    "mini-css-extract-plugin": "^0.9.0",
+    "style-loader": "^1.1.3",
+    "webpack": "^4.41.6",
+    "webpack-cli": "^3.3.11",
+    "extract-text-webpack-plugin": "^3.0.2"
+  },
+  "dependencies": {
+    "ace-builds": "^1.4.8"
+  },
+  "name": "galaxy-hyphy",
+  "version": "1.1.0",
+  "main": "index.js",
+  "license": "MIT",
+  "scripts": {
+    "build": "webpack --mode production"
+  }
+}
diff --git a/config/plugins/visualizations/editor/src/index.js b/config/plugins/visualizations/editor/src/index.js
new file mode 100644
index 000000000000..b9c17d7a2bbd
--- /dev/null
+++ b/config/plugins/visualizations/editor/src/index.js
@@ -0,0 +1,4 @@
+import './styles/style.css';
+import "ace-builds/src-noconflict/ace";
+import "ace-builds/src-noconflict/mode-powershell";
+import "ace-builds/src-noconflict/theme-textmate";
diff --git a/config/plugins/visualizations/editor/src/styles/style.css b/config/plugins/visualizations/editor/src/styles/style.css
new file mode 100644
index 000000000000..e187e15daace
--- /dev/null
+++ b/config/plugins/visualizations/editor/src/styles/style.css
@@ -0,0 +1,41 @@
+#editor {
+    position: absolute;
+    top: 0;
+    right: 0;
+    bottom: 0;
+    left: 0;
+}
+
+#export-btn {
+    position: relative;
+    z-index: 3;
+    left: 90%;
+}
+
+.transparent_btn {
+    display: inline-block;
+    padding: 10px 14px;
+    color: #FFF;
+    border: 1px solid #FFF;
+    text-decoration: none;
+    font-size: 14px;
+    line-height: 120%;
+    background-color: rgba(255, 255, 255, 0);
+    -webkit-border-radius: 4px;
+    -moz-border-radius: 4px;
+    border-radius: 4px;
+    -webkit-transition: 300ms ease;
+    -moz-transition:  300ms ease;
+    transition: 300ms ease;
+    cursor: pointer;
+}
+
+.transparent_btn.blue {
+    color: #aeddf5;
+    border-color: #aeddf5;
+}
+
+.transparent_btn.blue:hover {
+    color: #0062ff;
+    background-color: rgba(174, 221, 245, 0.3);
+}
diff --git a/config/plugins/visualizations/editor/templates/editor.mako b/config/plugins/visualizations/editor/templates/editor.mako
new file mode 100755
index 000000000000..385edbba6205
--- /dev/null
+++ b/config/plugins/visualizations/editor/templates/editor.mako
@@ -0,0 +1,72 @@
+<%
+    default_title = "JS Editor"
+
+    # Use root for resource loading.
+    root = h.url_for( '/static/' )
+    app_root    = root + "plugins/visualizations/editor/static/"
+%>
+## ----------------------------------------------------------------------------
+
+<!DOCTYPE HTML>
+<html>
+<head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+    <title> ${visualization_name}</title>
+    ${h.javascript_link( app_root + "script.js" )}
+    ${h.stylesheet_link( app_root + "main.css" )}
+</head>
+
+<body>
+<div id="editor">
+</div>
+<button onclick="exportData()" class="transparent_btn blue" id="export-btn">export</button>
+<script>
+    function httpGet(theUrl) {
+        var xmlHttp = new XMLHttpRequest();
+        xmlHttp.open("GET", theUrl, false);
+        xmlHttp.send(null);
+        return xmlHttp.responseText;
+    }
+
+    function exportData() {
+        ## Prepare data for export
+        const upload_data = {
+            tool_id: "upload1",
+            history_id: "${trans.security.encode_id(hda.history_id)}",
+            inputs: {
+                "file_count": 1,
+                "file_type": "auto",
+                "files_0|file_type": "auto",
+                "files_0|url_paste": editor.getValue(),
+                "files_0|NAME": "${ hda.name } (modified)"
+            }
+        };
+        ## upload data
+        const request = new XMLHttpRequest();
+        request.open("POST", "/api/tools");
+        request.setRequestHeader("Content-Type", "application/json");
+        request.send(JSON.stringify(upload_data));
+        request.onreadystatechange = function () {
+            if (request.readyState === XMLHttpRequest.DONE) {
+                var status = request.status;
+                if (status === 0 || (200 >= status && status < 400)) {
+                    top.location = "/"
+                } else {
+                    alert("something went wrong, please contact us!");
+                }
+            }
+        };
+    }
+
+    const hda_id = '${ trans.security.encode_id( hda.id ) }';
+
+    const ajax_url = "${h.url_for( controller='/datasets', action='index')}/" + hda_id + "/display";
+    const data = httpGet(ajax_url);
+    document.getElementById("editor").innerHTML = data;
+    var editor = ace.edit("editor", {
+        mode: "ace/mode/powershell",
+        theme: "ace/theme/textmate"
+    });
+</script>
+</body>
+</html>
diff --git a/config/plugins/visualizations/editor/webpack.config.js b/config/plugins/visualizations/editor/webpack.config.js
new file mode 100644
index 000000000000..0417541a1d02
--- /dev/null
+++ b/config/plugins/visualizations/editor/webpack.config.js
@@ -0,0 +1,39 @@
+const webpack = require("webpack");
+const path = require("path");
+const MiniCssExtractPlugin = require("mini-css-extract-plugin");
+
+module.exports = {
+    mode: 'production',
+    entry: path.resolve(__dirname, "src/index.js"),
+    output: {
+        filename: "script.js",
+        path: path.resolve(__dirname, "static")
+    },
+    plugins: [
+        new MiniCssExtractPlugin(),
+    ],
+    module: {
+        rules: [
+            {
+                test: /\.css$/i,
+                use: [MiniCssExtractPlugin.loader, 'css-loader'],
+            },
+            {
+                test: /\.(woff|woff2)(\?v=\d+\.\d+\.\d+)?$/,
+                loader: "url-loader",
+                options: {limit: 10000, mimetype: "application/font-woff"}
+            },
+            {
+                test: /\.ttf(\?v=\d+\.\d+\.\d+)?$/,
+                loader: "url-loader",
+                options: {limit: 10000, mimetype: "application/octet-stream"}
+            },
+            {test: /\.eot(\?v=\d+\.\d+\.\d+)?$/, loaders: "file-loader"},
+            {
+                test: /\.svg(\?v=\d+\.\d+\.\d+)?$/,
+                loaders: "url-loader",
+                options: {limit: 10000, mimetype: "image/svg+xml"}
+            }
+        ]
+    },
+};

From eb42ee88426d47747d30357117cd52ea4a6c0401 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 26 Mar 2020 00:59:41 +0100
Subject: [PATCH 593/853] Add utilities and vue

---
 .../components/Workflow/Editor/Node.vue       |   4 +-
 .../Editor/WorkflowRecommendationsVue.vue     |  66 ++++++++
 .../components/Workflow/Editor/utilities.js   | 137 ----------------
 .../Editor/workflowRecommendations.js         | 148 ++++++++++++++++++
 4 files changed, 215 insertions(+), 140 deletions(-)
 create mode 100644 client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
 create mode 100644 client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 7ddaddf95eb1..2f5c92c28c64 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -47,7 +47,7 @@ import BootstrapVue from "bootstrap-vue";
 import WorkflowIcons from "components/Workflow/icons";
 import LoadingSpan from "components/LoadingSpan";
 import { getGalaxyInstance } from "app";
-import { getToolRecommendations } from "./utilities";
+import { getToolRecommendations } from "./workflowRecommendations";
 
 Vue.use(BootstrapVue);
 
@@ -99,8 +99,6 @@ export default {
             this.node.clone();
         },
         onGetRecommendations() {
-            console.log("Clicked recommendations");
-            console.log(this);
             getToolRecommendations(this);
         }
     },
diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
new file mode 100644
index 000000000000..64b8b59690bc
--- /dev/null
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
@@ -0,0 +1,66 @@
+<template>
+    <div class="modal ui-modal modal-tool-recommendation" style="display: block;">
+        <div class="modal-backdrop fade in">
+        </div>
+        <div class="modal-dialog" style="width: 260px;">
+            <div class="modal-content">
+                <div class="modal-header" title="The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to have it on the workflow editor.">
+                    <h4 class="title" tabindex="0">Recommended tools</h4>
+                </div>
+                <div class="modal-body" style="height: 280px; overflow: auto;">
+                    <i class="fa mr-1 fa-wrench"></i>
+                    <a href="#" title="Click to open the tool" class="pred-tool panel-header-button" id="Grep1">Select (100%)</a>
+                        
+                    <i class="fa mr-1 fa-wrench"></i>
+                    <a href="#" title="Click to open the tool" class="pred-tool panel-header-button" id="Grep1">Select (100%)</a>
+                </div>
+                <div class="modal-footer">
+                    <div class="buttons">
+                        <button id="button-0">Close</button>&nbsp;
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+</template>
+
+<script>
+
+import { getAppRoot } from "onload/loadConfig";
+import axios from "axios";
+import _l from "utils/localization";
+
+export default {
+    props: {
+        workflowManager: {
+            type: Object,
+        },
+        toolSequence: {
+            type: String
+        }
+    },
+    data() {
+        return {
+        };
+    },
+    created() {
+        this.loadRecommendations();
+    },
+    computed: {
+    },
+    methods: {
+        loadRecommendations() {
+            console.log("loaded");
+            console.log(this.workflowManager);
+            console.log(this.toolSequence);
+            axios
+                .post(`${getAppRoot()}api/workflows/get_tool_predictions`, {
+                    tool_sequence: this.toolSequence,
+                })
+                .then((data) => {
+                    console.log(data);
+                });
+        },
+    },
+};
+</script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/utilities.js b/client/galaxy/scripts/components/Workflow/Editor/utilities.js
index 79c341000d83..dd705c7c5be7 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/utilities.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/utilities.js
@@ -207,140 +207,3 @@ export function saveAs(workflow) {
         Cancel: hide_modal,
     });
 }
-
-function getToolId(toolId) {
-    if (toolId !== undefined && toolId !== null && toolId.indexOf("/") > -1) {
-        let toolIdSlash = toolId.split("/");
-        toolId = toolIdSlash[toolIdSlash.length - 2];
-    }
-    return toolId;
-}
-
-function get_workflow_path(wf_steps, current_node_id, current_node_name) {
-        let steps = {};
-        let step_names = {};
-        for (let stp_idx in wf_steps.steps) {
-            let step = wf_steps.steps[stp_idx];
-            let input_connections = step.input_connections;
-            step_names[step.id] = getToolId(step.content_id);
-            for (let ic_idx in input_connections) {
-                let ic = input_connections[ic_idx];
-                if(ic !== null && ic !== undefined) {
-                    let prev_conn = [];
-                    for (let conn of ic) {
-                        prev_conn.push(conn.id.toString());
-                    }
-                    steps[step.id.toString()] = prev_conn;
-                }
-            }
-        }
-        // recursive call to determine path
-        function read_paths(node_id, ph) {
-            for (let st in steps) {
-                if (parseInt(st) === parseInt(node_id)) {
-                    let parent_id = parseInt(steps[st][0]);
-                    if (parent_id !== undefined && parent_id !== null) {
-                        ph.push(parent_id);
-                        if (steps[parent_id] !== undefined && steps[parent_id] !== null) {
-                            read_paths(parent_id, ph);
-                        }
-                    }
-                }
-            }
-            return ph;
-        }
-        let ph = [];
-        let step_names_list = [];
-        ph.push(current_node_id);
-        ph = read_paths(current_node_id, ph);
-        for (let s_idx of ph) {
-            let s_name = step_names[s_idx.toString()];
-            if (s_name !== undefined && s_name !== null) {
-                step_names_list.push(s_name);
-            }
-        }
-        return step_names_list.join(",");
-}
-
-export function getToolRecommendations(propsData) {
-        let workflow_simple = propsData.node.app.to_simple(),
-        node = propsData.node,
-        toolId = getToolId(node.content_id);
-        console.log(workflow_simple);
-        console.log(node);
-        let tool_sequence = get_workflow_path(workflow_simple, node.id, toolId);
-        console.log(tool_sequence);
-        
-        // remove ui-modal if present
-        let $modal = $(".modal-tool-recommendation");
-        if ($modal.length > 0) {
-            $modal.remove();
-        }
-        // create new modal
-        let modal = new Modal.View({
-            title: "Recommended tools",
-            body: "<div> Loading tools ... </div>",
-            height: "230",
-            width: "250",
-            closing_events: true,
-            title_separator: true        
-        });
-        modal.$el.addClass("modal-tool-recommendation");
-        modal.$el.find(".modal-header").attr("title", "The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to have it on the workflow editor.");
-        modal.$el.find(".modal-body").css("overflow", "auto");
-        modal.show();
-        // fetch recommended tools
-        Utils.request({
-            type: "POST",
-            url: `${getAppRoot()}api/workflows/get_tool_predictions`,
-            data: {"tool_sequence": tool_sequence},
-            success: function(data) {
-                let predTemplate = "<div>";
-                let predictedData = data.predicted_data;
-                let outputDatatypes = predictedData["o_extensions"];
-                let predictedDataChildren = predictedData.children;
-                let noRecommendationsMessage = "No tool recommendations";
-                if (predictedDataChildren.length > 0) {
-                    let compatibleTools = {};
-                    // filter results based on datatype compatibility
-                    for (const [index, name_obj] of predictedDataChildren.entries()) {
-                        let inputDatatypes = name_obj["i_extensions"];
-                        for (const out_t of outputDatatypes.entries()) {
-                            for(const in_t of inputDatatypes.entries()) {
-                                if ((propsData.node.app.isSubType(out_t[1], in_t[1]) === true) ||
-                                     out_t[1] === "input" ||
-                                     out_t[1] === "_sniff_" ||
-                                     out_t[1] === "input_collection") {
-                                    compatibleTools[name_obj["tool_id"]] = name_obj["name"];
-                                    break
-                                }
-                            }
-                        }
-                    }
-                    predTemplate += "<div>";
-                    if (Object.keys(compatibleTools).length > 0 && predictedData["is_deprecated"] === false) {
-                        for (let id in compatibleTools) {
-                            predTemplate += "<i class='fa mr-1 fa-wrench'></i><a href='#' title='Click to open the tool' class='pred-tool panel-header-button' id=" + "'" + id + "'" + ">" + compatibleTools[id];
-                            predTemplate += "</a></br>";
-                        }
-                    }
-                    else if (predictedData["is_deprecated"] === true) {
-                        predTemplate += predictedData["message"];
-                    }
-                    else {
-                        predTemplate += noRecommendationsMessage;
-                    }
-                    predTemplate += "</div>";
-                }
-                else {
-                    predTemplate += noRecommendationsMessage; 
-                }
-                predTemplate += "</div>";
-                modal.$body.html(predTemplate);
-                $(".pred-tool").click(e => {
-                    workflow_globals.app.add_node_for_tool(e.target.id, e.target.id);
-                    modal.hide();
-                });
-            }
-        });
-    }
diff --git a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
new file mode 100644
index 000000000000..ca4f46b652cd
--- /dev/null
+++ b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
@@ -0,0 +1,148 @@
+import _ from "underscore";
+import $ from "jquery";
+import Vue from "vue";
+import WorkflowToolRecommendations from "components/Workflow/Editor/WorkflowRecommendationsVue";
+
+function getToolId(toolId) {
+    if (toolId !== undefined && toolId !== null && toolId.indexOf("/") > -1) {
+        let toolIdSlash = toolId.split("/");
+        toolId = toolIdSlash[toolIdSlash.length - 2];
+    }
+    return toolId;
+}
+
+function getWorkflowPath(wf_steps, current_node_id, current_node_name) {
+        let steps = {};
+        let step_names = {};
+        for (let stp_idx in wf_steps.steps) {
+            let step = wf_steps.steps[stp_idx];
+            let input_connections = step.input_connections;
+            step_names[step.id] = getToolId(step.content_id);
+            for (let ic_idx in input_connections) {
+                let ic = input_connections[ic_idx];
+                if(ic !== null && ic !== undefined) {
+                    let prev_conn = [];
+                    for (let conn of ic) {
+                        prev_conn.push(conn.id.toString());
+                    }
+                    steps[step.id.toString()] = prev_conn;
+                }
+            }
+        }
+        // recursive call to determine path
+        function readPaths(node_id, ph) {
+            for (let st in steps) {
+                if (parseInt(st) === parseInt(node_id)) {
+                    let parent_id = parseInt(steps[st][0]);
+                    if (parent_id !== undefined && parent_id !== null) {
+                        ph.push(parent_id);
+                        if (steps[parent_id] !== undefined && steps[parent_id] !== null) {
+                            readPaths(parent_id, ph);
+                        }
+                    }
+                }
+            }
+            return ph;
+        }
+        let ph = [];
+        let step_names_list = [];
+        ph.push(current_node_id);
+        ph = readPaths(current_node_id, ph);
+        for (let s_idx of ph) {
+            let s_name = step_names[s_idx.toString()];
+            if (s_name !== undefined && s_name !== null) {
+                step_names_list.push(s_name);
+            }
+        }
+        return step_names_list.join(",");
+}
+
+export function getToolRecommendations(props) {
+        const workflowSimple = props.node.app.to_simple();
+        const node = props.node;
+        const toolId = getToolId(node.content_id);
+        const toolSequence = getWorkflowPath(workflowSimple, node.id, toolId);
+        
+        // show tool recommendations
+        const ToolRecommendationInstance = Vue.extend(WorkflowToolRecommendations);
+        const vm = document.createElement("div");
+        $("body").append(vm);
+        const instance = new ToolRecommendationInstance({
+             propsData: {
+                 workflowManager: props,
+                 toolSequence: toolSequence
+             },
+        });
+        instance.$mount(vm);
+        
+        // remove ui-modal if present
+        /*let $modal = $(".modal-tool-recommendation");
+        if ($modal.length > 0) {
+            $modal.remove();
+        }
+        // create new modal
+        let modal = new Modal.View({
+            title: "Recommended tools",
+            body: "<div> Loading tools ... </div>",
+            height: "230",
+            width: "250",
+            closing_events: true,
+            title_separator: true        
+        });
+        modal.$el.addClass("modal-tool-recommendation");
+        modal.$el.find(".modal-header").attr("title", "The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to have it on the workflow editor.");
+        modal.$el.find(".modal-body").css("overflow", "auto");
+        modal.show();
+        axios
+            .post(`${getAppRoot()}api/workflows/get_tool_predictions`, {
+                tool_sequence: toolSequence,
+            })
+            .then((data) => {
+                let predTemplate = "<div>";
+                let predictedData = data.predicted_data;
+                let outputDatatypes = predictedData["o_extensions"];
+                let predictedDataChildren = predictedData.children;
+                let noRecommendationsMessage = "No tool recommendations";
+                if (predictedDataChildren.length > 0) {
+                    let compatibleTools = {};
+                    // filter results based on datatype compatibility
+                    for (const [index, name_obj] of predictedDataChildren.entries()) {
+                        let inputDatatypes = name_obj["i_extensions"];
+                        for (const out_t of outputDatatypes.entries()) {
+                            for(const in_t of inputDatatypes.entries()) {
+                                if ((propsData.node.app.isSubType(out_t[1], in_t[1]) === true) ||
+                                     out_t[1] === "input" ||
+                                     out_t[1] === "_sniff_" ||
+                                     out_t[1] === "input_collection") {
+                                    compatibleTools[name_obj["tool_id"]] = name_obj["name"];
+                                    break
+                                }
+                            }
+                        }
+                    }
+                    predTemplate += "<div>";
+                    if (Object.keys(compatibleTools).length > 0 && predictedData["is_deprecated"] === false) {
+                        for (let id in compatibleTools) {
+                            predTemplate += "<i class='fa mr-1 fa-wrench'></i><a href='#' title='Click to open the tool' class='pred-tool panel-header-button' id=" + "'" + id + "'" + ">" + compatibleTools[id];
+                            predTemplate += "</a></br>";
+                        }
+                    }
+                    else if (predictedData["is_deprecated"] === true) {
+                        predTemplate += predictedData["message"];
+                    }
+                    else {
+                        predTemplate += noRecommendationsMessage;
+                    }
+                    predTemplate += "</div>";
+                }
+                else {
+                    predTemplate += noRecommendationsMessage; 
+                }
+                predTemplate += "</div>";
+                modal.$body.html(predTemplate);
+                $(".pred-tool").click(e => {
+                    workflow_globals.app.add_node_for_tool(e.target.id, e.target.id);
+                    modal.hide();
+                });
+            });*/
+    }

From 8fd03451c4300cfaac310c6f0f56d69f03838934 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 26 Mar 2020 12:00:20 +0100
Subject: [PATCH 594/853] Load data via ajax

---
 .../Editor/WorkflowRecommendationsVue.vue     | 84 +++++++++++++++----
 1 file changed, 67 insertions(+), 17 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
index 64b8b59690bc..dae2aa371280 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
@@ -1,22 +1,31 @@
 <template>
-    <div class="modal ui-modal modal-tool-recommendation" style="display: block;">
+    <div class="modal ui-modal tool-recommendation-view" style="display: block;">
         <div class="modal-backdrop fade in">
         </div>
         <div class="modal-dialog" style="width: 260px;">
             <div class="modal-content">
-                <div class="modal-header" title="The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to have it on the workflow editor.">
-                    <h4 class="title" tabindex="0">Recommended tools</h4>
+                <div class="modal-header" :title="modalHeaderToolTip">
+                    <h4 class="title" tabindex="0"> {{ modalHeaderTitle }}</h4>
                 </div>
                 <div class="modal-body" style="height: 280px; overflow: auto;">
-                    <i class="fa mr-1 fa-wrench"></i>
-                    <a href="#" title="Click to open the tool" class="pred-tool panel-header-button" id="Grep1">Select (100%)</a>
-                        
-                    <i class="fa mr-1 fa-wrench"></i>
-                    <a href="#" title="Click to open the tool" class="pred-tool panel-header-button" id="Grep1">Select (100%)</a>
+                    <div v-if="compatibleTools.length > 0 && !isDeprecated" >
+                        <span v-for="tool in compatibleTools">
+                            <i class="fa mr-1 fa-wrench"></i>
+                            <a href="#" title="Open tool" :id="tool.id" v-on:click="openTool(tool.id)"> {{ tool.name }} </a>
+                        </span>
+                        <br>
+                    </div>
+                    <div v-else-if="isDeprecated">
+                        {{ deprecatedMessage }}
+                    </div>
+                    <div v-else>
+                        {{ noRecommendationsMessage }}
+                    </div>
+                    
                 </div>
                 <div class="modal-footer">
                     <div class="buttons">
-                        <button id="button-0">Close</button>&nbsp;
+                        <button v-on:click="closeModal" title="Close">Close</button>
                     </div>
                 </div>
             </div>
@@ -41,6 +50,12 @@ export default {
     },
     data() {
         return {
+            modalHeaderTitle: _l("Tool Recommendations"),
+            modalHeaderToolTip: _l("The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to have it on the workflow editor."),
+            compatibleTools: [],
+            isDeprecated: false,
+            noRecommendationsMessage: "",
+            deprecatedMessage: "",
         };
     },
     created() {
@@ -49,18 +64,53 @@ export default {
     computed: {
     },
     methods: {
-        loadRecommendations() {
+        async loadRecommendations() {
             console.log("loaded");
             console.log(this.workflowManager);
             console.log(this.toolSequence);
-            axios
-                .post(`${getAppRoot()}api/workflows/get_tool_predictions`, {
-                    tool_sequence: this.toolSequence,
-                })
-                .then((data) => {
-                    console.log(data);
-                });
+            const response = await axios.post(`${getAppRoot()}api/workflows/get_tool_predictions`, {tool_sequence: this.toolSequence});
+            const predictedData = response.data.predicted_data;
+            const outputDatatypes = predictedData.o_extensions;
+            const predictedDataChildren = predictedData.children;
+            const app = this.workflowManager.node.app;
+            this.isDeprecated = predictedData.is_deprecated;
+            this.deprecatedMessage = predictedData.message;
+            console.log(predictedData);
+            if (predictedDataChildren.length > 0) {
+                let cTools = [];
+                // filter results based on datatype compatibility
+                for (const [index, name_obj] of predictedDataChildren.entries()) {
+                    let t = {};
+                    let inputDatatypes = name_obj.i_extensions;
+                    for (const out_t of outputDatatypes.entries()) {
+                        for(const in_t of inputDatatypes.entries()) {
+                            if ((app.isSubType(out_t[1], in_t[1]) === true) ||
+                                 out_t[1] === "input" ||
+                                 out_t[1] === "_sniff_" ||
+                                 out_t[1] === "input_collection") {
+                                t.id = name_obj.tool_id
+                                t.name = name_obj.name;
+                                cTools.push(t);
+                                    break
+                            }
+                        }
+                    }
+                }
+                console.log(cTools);
+                console.log(this);
+                this.compatibleTools = cTools;
+            }
+            else {
+                this.noRecommendationsMessage = "No tool recommendations";
+            }
         },
+        closeModal () {
+            this.$el.remove();
+        },
+        openTool (tId) {
+            console.log(tId);
+            this.closeModal();
+        }
     },
 };
 </script>

From 87b554ba9ec3f0c65722c761e5a40b0b6b845856 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 26 Mar 2020 12:34:47 +0100
Subject: [PATCH 595/853] Add new tool

---
 .../Editor/WorkflowRecommendationsVue.vue     | 22 +++---
 .../Editor/workflowRecommendations.js         | 71 -------------------
 2 files changed, 13 insertions(+), 80 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
index dae2aa371280..38a1bbe93d33 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
@@ -9,10 +9,10 @@
                 </div>
                 <div class="modal-body" style="height: 280px; overflow: auto;">
                     <div v-if="compatibleTools.length > 0 && !isDeprecated" >
-                        <span v-for="tool in compatibleTools">
+                        <div v-for="tool in compatibleTools">
                             <i class="fa mr-1 fa-wrench"></i>
                             <a href="#" title="Open tool" :id="tool.id" v-on:click="openTool(tool.id)"> {{ tool.name }} </a>
-                        </span>
+                        </div>
                         <br>
                     </div>
                     <div v-else-if="isDeprecated">
@@ -65,9 +65,6 @@ export default {
     },
     methods: {
         async loadRecommendations() {
-            console.log("loaded");
-            console.log(this.workflowManager);
-            console.log(this.toolSequence);
             const response = await axios.post(`${getAppRoot()}api/workflows/get_tool_predictions`, {tool_sequence: this.toolSequence});
             const predictedData = response.data.predicted_data;
             const outputDatatypes = predictedData.o_extensions;
@@ -75,13 +72,11 @@ export default {
             const app = this.workflowManager.node.app;
             this.isDeprecated = predictedData.is_deprecated;
             this.deprecatedMessage = predictedData.message;
-            console.log(predictedData);
             if (predictedDataChildren.length > 0) {
                 let cTools = [];
-                // filter results based on datatype compatibility
                 for (const [index, name_obj] of predictedDataChildren.entries()) {
                     let t = {};
-                    let inputDatatypes = name_obj.i_extensions;
+                    const inputDatatypes = name_obj.i_extensions;
                     for (const out_t of outputDatatypes.entries()) {
                         for(const in_t of inputDatatypes.entries()) {
                             if ((app.isSubType(out_t[1], in_t[1]) === true) ||
@@ -91,7 +86,7 @@ export default {
                                 t.id = name_obj.tool_id
                                 t.name = name_obj.name;
                                 cTools.push(t);
-                                    break
+                                break;
                             }
                         }
                     }
@@ -109,6 +104,15 @@ export default {
         },
         openTool (tId) {
             console.log(tId);
+            const app = this.workflowManager.node.app;
+            const toolData = {type: "tool", tool_id: tId, _: "true"};
+            const response = await axios.post(`${getAppRoot()}api/workflows/build_module`, toolData);
+            const tData = response.data;
+            console.log(tData);
+            let newTool = app.create_node(toolData.type, tData.name, tId);
+            newTool.init_field_data(tData);
+            newTool.update_field_data(newData);
+            app.activate_node(newTool);
             this.closeModal();
         }
     },
diff --git a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
index ca4f46b652cd..808316eb0608 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
@@ -74,75 +74,4 @@ export function getToolRecommendations(props) {
              },
         });
         instance.$mount(vm);
-        
-        // remove ui-modal if present
-        /*let $modal = $(".modal-tool-recommendation");
-        if ($modal.length > 0) {
-            $modal.remove();
-        }
-        // create new modal
-        let modal = new Modal.View({
-            title: "Recommended tools",
-            body: "<div> Loading tools ... </div>",
-            height: "230",
-            width: "250",
-            closing_events: true,
-            title_separator: true        
-        });
-        modal.$el.addClass("modal-tool-recommendation");
-        modal.$el.find(".modal-header").attr("title", "The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to have it on the workflow editor.");
-        modal.$el.find(".modal-body").css("overflow", "auto");
-        modal.show();
-        axios
-            .post(`${getAppRoot()}api/workflows/get_tool_predictions`, {
-                tool_sequence: toolSequence,
-            })
-            .then((data) => {
-                let predTemplate = "<div>";
-                let predictedData = data.predicted_data;
-                let outputDatatypes = predictedData["o_extensions"];
-                let predictedDataChildren = predictedData.children;
-                let noRecommendationsMessage = "No tool recommendations";
-                if (predictedDataChildren.length > 0) {
-                    let compatibleTools = {};
-                    // filter results based on datatype compatibility
-                    for (const [index, name_obj] of predictedDataChildren.entries()) {
-                        let inputDatatypes = name_obj["i_extensions"];
-                        for (const out_t of outputDatatypes.entries()) {
-                            for(const in_t of inputDatatypes.entries()) {
-                                if ((propsData.node.app.isSubType(out_t[1], in_t[1]) === true) ||
-                                     out_t[1] === "input" ||
-                                     out_t[1] === "_sniff_" ||
-                                     out_t[1] === "input_collection") {
-                                    compatibleTools[name_obj["tool_id"]] = name_obj["name"];
-                                    break
-                                }
-                            }
-                        }
-                    }
-                    predTemplate += "<div>";
-                    if (Object.keys(compatibleTools).length > 0 && predictedData["is_deprecated"] === false) {
-                        for (let id in compatibleTools) {
-                            predTemplate += "<i class='fa mr-1 fa-wrench'></i><a href='#' title='Click to open the tool' class='pred-tool panel-header-button' id=" + "'" + id + "'" + ">" + compatibleTools[id];
-                            predTemplate += "</a></br>";
-                        }
-                    }
-                    else if (predictedData["is_deprecated"] === true) {
-                        predTemplate += predictedData["message"];
-                    }
-                    else {
-                        predTemplate += noRecommendationsMessage;
-                    }
-                    predTemplate += "</div>";
-                }
-                else {
-                    predTemplate += noRecommendationsMessage; 
-                }
-                predTemplate += "</div>";
-                modal.$body.html(predTemplate);
-                $(".pred-tool").click(e => {
-                    workflow_globals.app.add_node_for_tool(e.target.id, e.target.id);
-                    modal.hide();
-                });
-            });*/
     }

From 4820ced582e93a9c3d1eb5903354137dfd9c0822 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 25 Mar 2020 21:18:43 +0100
Subject: [PATCH 596/853] OSX test

---
 .github/workflows/osx_startup.yaml | 33 ++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 .github/workflows/osx_startup.yaml

diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml
new file mode 100644
index 000000000000..0d215e97d857
--- /dev/null
+++ b/.github/workflows/osx_startup.yaml
@@ -0,0 +1,33 @@
+name: OSX
+on: [push, pull_request]
+jobs:
+
+  test:
+    name: Startup test
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: [3.7]
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        path: 'galaxy root'
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache pip dir
+      uses: actions/cache@v1
+      id: pip-cache
+      with:
+        path: ~/.cache/pip
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Install tox
+      run: pip install tox
+    - name: fetch migrations
+      run: |
+        wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite
+        mv db_gx_rev_0141.sqlite database/universe.sqlite
+      working-directory: 'galaxy root'
+    - name: run tests
+      run: tox -e mulled
+      working-directory: 'galaxy root'

From d709a4b9ba661d006dfe61566043e025320c64fc Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 25 Mar 2020 21:26:07 +0100
Subject: [PATCH 597/853] Test py37-first_startup

---
 .github/workflows/osx_startup.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml
index 0d215e97d857..8bd8a74b0f87 100644
--- a/.github/workflows/osx_startup.yaml
+++ b/.github/workflows/osx_startup.yaml
@@ -29,5 +29,5 @@ jobs:
         mv db_gx_rev_0141.sqlite database/universe.sqlite
       working-directory: 'galaxy root'
     - name: run tests
-      run: tox -e mulled
+      run: tox -e py37-first_startup
       working-directory: 'galaxy root'

From aa68c834361cfbab4c8d67e3bc288dc09d8b7034 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 26 Mar 2020 12:54:32 +0100
Subject: [PATCH 598/853] Drop .travis.yml

---
 .travis.yml | 29 -----------------------------
 1 file changed, 29 deletions(-)
 delete mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 0f690edec63f..000000000000
--- a/.travis.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-os: osx
-# No version of Python is available via virtualenv on OS X workers, see https://github.com/travis-ci/travis-ci/issues/2312
-language: generic
-
-env:
-  - TOX_ENV=py27-first_startup
-  - TOX_ENV=py37-first_startup
-
-install:
-  - set -e
-  - pip install tox
-  - |
-    if [ "$TOX_ENV" == "py27-first_startup" ]; then
-        # Use this job to test the latest migrations
-        wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite
-        mv db_gx_rev_0141.sqlite database/universe.sqlite
-    elif [ "$TOX_ENV" == "py37-first_startup" ]; then
-        # There is now a pre-installed python3 on osx Travis workers, but use this job to test using a conda environment
-        MINICONDA_URL="https://repo.anaconda.com/miniconda"
-        MINICONDA_FILE="Miniconda3-latest-MacOSX-x86_64.sh"
-        curl -L -O "${MINICONDA_URL}/${MINICONDA_FILE}"
-        bash $MINICONDA_FILE -b
-        . ~/miniconda3/bin/activate
-    fi
-
-script: tox -e $TOX_ENV
-
-notifications:
-  email: false

From cbe90b67a9c3803215b10fd0944e54fcbb1e83b0 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 26 Mar 2020 12:55:34 +0100
Subject: [PATCH 599/853] Keep osx-speicifc pip cache

---
 .github/workflows/osx_startup.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml
index 8bd8a74b0f87..b54e0ce7ddd0 100644
--- a/.github/workflows/osx_startup.yaml
+++ b/.github/workflows/osx_startup.yaml
@@ -20,7 +20,7 @@ jobs:
       id: pip-cache
       with:
         path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+        key: pip-cache-osx-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Install tox
       run: pip install tox
     - name: fetch migrations

From 611293a8ab459c1c4d11c20a5532cc934b8b98f5 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Thu, 26 Mar 2020 13:34:29 +0100
Subject: [PATCH 600/853] fix typo

---
 config/plugins/visualizations/editor/config/editor.xml | 2 +-
 config/plugins/visualizations/editor/package.json      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/plugins/visualizations/editor/config/editor.xml b/config/plugins/visualizations/editor/config/editor.xml
index 94d863ddcb28..48589917e998 100644
--- a/config/plugins/visualizations/editor/config/editor.xml
+++ b/config/plugins/visualizations/editor/config/editor.xml
@@ -13,4 +13,4 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <entry_point entry_point_type="mako">editor.mako</entry_point>
-</visualization>
\ No newline at end of file
+</visualization>
diff --git a/config/plugins/visualizations/editor/package.json b/config/plugins/visualizations/editor/package.json
index bc92eebdc68a..f10c514d6295 100644
--- a/config/plugins/visualizations/editor/package.json
+++ b/config/plugins/visualizations/editor/package.json
@@ -11,7 +11,7 @@
   "dependencies": {
     "ace-builds": "^1.4.8"
   },
-  "name": "galaxy-hyphy",
+  "name": "galaxy-vis-editor",
   "version": "1.1.0",
   "main": "index.js",
   "license": "MIT",

From 91794485e8a3fa2bf0ba8d98dc90b95674ad11cc Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Thu, 26 Mar 2020 14:33:23 +0100
Subject: [PATCH 601/853] Use correct location for OSX pip cache

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 .github/workflows/osx_startup.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml
index b54e0ce7ddd0..dfbf85ea7775 100644
--- a/.github/workflows/osx_startup.yaml
+++ b/.github/workflows/osx_startup.yaml
@@ -19,7 +19,7 @@ jobs:
       uses: actions/cache@v1
       id: pip-cache
       with:
-        path: ~/.cache/pip
+        path: ~/Library/Caches/pip
         key: pip-cache-osx-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Install tox
       run: pip install tox

From 6a0253499d781dfb352413f66e66390f81c63549 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 26 Mar 2020 09:39:39 -0400
Subject: [PATCH 602/853] Rebuild config.

---
 doc/source/admin/galaxy_options.rst        | 21 +++++++++++++++++++++
 lib/galaxy/config/sample/galaxy.yml.sample |  7 +++++++
 2 files changed, 28 insertions(+)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 619dd9b285f5..455e7b0e9a94 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -1344,6 +1344,27 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``interactivetools_proxy_host``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Proxy host - assumed to just be hosted on the same hostname and
+    port as Galaxy by default.
+:Default: ``None``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~
+``interactivetools_map``
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Map for interactivetool proxy.
+:Default: ``interactivetools_map.sqlite``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``visualizations_visible``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index acd9c1bd0a06..c07a4cfc80e0 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -747,6 +747,13 @@ galaxy:
   # Enable InteractiveTools.
   #interactivetools_enable: false
 
+  # Proxy host - assumed to just be hosted on the same hostname and port
+  # as Galaxy by default.
+  #interactivetools_proxy_host: null
+
+  # Map for interactivetool proxy.
+  #interactivetools_map: interactivetools_map.sqlite
+
   # Show visualization tab and list in masthead.
   #visualizations_visible: true
 

From 645ecf6f5d70c4bdf06d10518fc83eb203146aec Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 26 Mar 2020 10:04:58 -0400
Subject: [PATCH 603/853] Adding an empty continue file so tmate does not stop
 the workflow

---
 continue | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 continue

diff --git a/continue b/continue
new file mode 100644
index 000000000000..e69de29bb2d1

From 9df7aebae4da25f196d39722a51c9e6d022da6fe Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 26 Mar 2020 10:33:17 -0400
Subject: [PATCH 604/853] Fix in workflow yaml file

---
 .github/workflows/integration.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 2cfd173148bb..53395915cab6 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -46,7 +46,6 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - uses: actions/checkout@v2
     - name: Setup tmate session
       uses: mxschmitt/action-tmate@v2
     - name: Run tests

From cce6a2319cd0b720dc5c8eaa2278cd54f3d20969 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 26 Mar 2020 15:56:56 +0100
Subject: [PATCH 605/853] Fix indexing script

All indexed values need to be unicode
---
 lib/tool_shed/util/shed_index.py | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
index 206be3a3ce94..1862b103fd9f 100644
--- a/lib/tool_shed/util/shed_index.py
+++ b/lib/tool_shed/util/shed_index.py
@@ -147,20 +147,20 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
                     tools_in_dir = load_one_dir(os.path.join(root, dirname))
                     tools_list.extend(tools_in_dir)
 
-        yield (dict(id=repo_id,
-                    name=name,
-                    description=description,
-                    long_description=long_description,
-                    homepage_url=homepage_url,
-                    remote_repository_url=remote_repository_url,
-                    repo_owner_username=repo_owner_username,
-                    times_downloaded=times_downloaded,
-                    approved=approved,
-                    last_updated=last_updated,
-                    full_last_updated=full_last_updated,
+        yield (dict(id=unicodify(repo_id),
+                    name=unicodify(name),
+                    description=unicodify(description),
+                    long_description=unicodify(long_description),
+                    homepage_url=unicodify(homepage_url),
+                    remote_repository_url=unicodify(remote_repository_url),
+                    repo_owner_username=unicodify(repo_owner_username),
+                    times_downloaded=unicodify(times_downloaded),
+                    approved=unicodify(approved),
+                    last_updated=unicodify(last_updated),
+                    full_last_updated=unicodify(full_last_updated),
                     tools_list=tools_list,
-                    repo_lineage=repo_lineage,
-                    categories=categories))
+                    repo_lineage=unicodify(repo_lineage),
+                    categories=unicodify(categories)))
 
 
 def debug_handler(path, exc_info):

From d65a1be0aa752c1a86e40fb3c6e121599f57e190 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 26 Mar 2020 11:10:33 -0400
Subject: [PATCH 606/853] Dropped unnecessary steps

---
 .github/workflows/integration.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 53395915cab6..7324ef886133 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         python-version: [3.7]
-        subset: ['upload_datatype', 'extended_metadata', 'kubernetes', 'not (upload_datatype or extended_metadata or kubernetes)']
+        subset: ['upload_datatype']
     services:
       postgres:
         image: postgres:11

From 5d918c036f340a191155c9051cbaccd656d3e208 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 26 Mar 2020 16:31:36 +0100
Subject: [PATCH 607/853] Fix schema assertion

---
 lib/tool_shed/util/shed_index.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
index 1862b103fd9f..e424d7263deb 100644
--- a/lib/tool_shed/util/shed_index.py
+++ b/lib/tool_shed/util/shed_index.py
@@ -34,7 +34,7 @@ def _get_or_create_index(index_dir, schema):
     if index.exists_in(index_dir):
         idx = index.open_dir(index_dir)
         try:
-            assert idx.schema == repo_schema
+            assert idx.schema == schema
             return idx
         except AssertionError:
             log.warning("Index at '%s' uses outdated schema, creating new index", index_dir)

From 981d411aee24c9f92a5c8e99dd7e287368b32461 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 26 Mar 2020 16:43:16 +0100
Subject: [PATCH 608/853] Create new tools

---
 .../Editor/WorkflowRecommendationsVue.vue     | 31 +++++++++----------
 1 file changed, 15 insertions(+), 16 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
index 38a1bbe93d33..969b1283f1ae 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
@@ -11,7 +11,7 @@
                     <div v-if="compatibleTools.length > 0 && !isDeprecated" >
                         <div v-for="tool in compatibleTools">
                             <i class="fa mr-1 fa-wrench"></i>
-                            <a href="#" title="Open tool" :id="tool.id" v-on:click="openTool(tool.id)"> {{ tool.name }} </a>
+                            <a href="#" title="Open tool" :id="tool.id" v-on:click="createTool(tool.id)"> {{ tool.name }} </a>
                         </div>
                         <br>
                     </div>
@@ -37,6 +37,7 @@
 
 import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
+import { getModule } from "./services";
 import _l from "utils/localization";
 
 export default {
@@ -91,8 +92,6 @@ export default {
                         }
                     }
                 }
-                console.log(cTools);
-                console.log(this);
                 this.compatibleTools = cTools;
             }
             else {
@@ -102,19 +101,19 @@ export default {
         closeModal () {
             this.$el.remove();
         },
-        openTool (tId) {
-            console.log(tId);
-            const app = this.workflowManager.node.app;
-            const toolData = {type: "tool", tool_id: tId, _: "true"};
-            const response = await axios.post(`${getAppRoot()}api/workflows/build_module`, toolData);
-            const tData = response.data;
-            console.log(tData);
-            let newTool = app.create_node(toolData.type, tData.name, tId);
-            newTool.init_field_data(tData);
-            newTool.update_field_data(newData);
-            app.activate_node(newTool);
-            this.closeModal();
-        }
+        createTool (tId) {
+            const app = this.workflowManager.node.app;         
+            const requestData = {
+                type: "tool",
+                tool_id: tId,
+                _: "true",
+            };
+            getModule(requestData).then((response) => {
+                const node = app.create_node("tool", response.name, tId);
+                app.set_node(node, response);
+                this.closeModal();
+            });
+        },
     },
 };
 </script>

From 29f3f6403dd331146c2bee0d021dcc69f545a99d Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 26 Mar 2020 11:58:32 -0400
Subject: [PATCH 609/853] Changing iRODS port to see if the GitHub issue is
 fixed.

---
 test/integration/irods_object_store_conf.xml   | 2 +-
 test/integration/test_datatype_upload_irods.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/integration/irods_object_store_conf.xml b/test/integration/irods_object_store_conf.xml
index 778b42f4083e..5b78f498fc27 100644
--- a/test/integration/irods_object_store_conf.xml
+++ b/test/integration/irods_object_store_conf.xml
@@ -3,7 +3,7 @@
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
-    <connection host="localhost" port="1247"/>
+    <connection host="localhost" port="2020"/>
     <cache path="database/object_store_cache" size="1000" />
     <extra_dir type="job_work" path="database/job_working_directory_irods"/>
     <extra_dir type="temp" path="database/tmp_irods"/>
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 237879e36194..994dc0be9b2b 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -19,7 +19,7 @@ def start_irods(container_name):
         'docker',
         'run',
         '-p',
-        '1247:1247',
+        '2020:1247',
         '-d',
         '--name',
         container_name,

From 0d1025fbab9a62ffe43ba4d0c5d94ed6ed15dbfa Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 26 Mar 2020 12:21:46 -0400
Subject: [PATCH 610/853] Removed debugging tmate step

---
 .github/workflows/integration.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 7324ef886133..71694ddb289c 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -46,8 +46,6 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v2
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
       working-directory: 'galaxy root'

From 108774e6d4f9cf50d5697c438b792ec0634885c5 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 26 Mar 2020 17:26:28 +0100
Subject: [PATCH 611/853] update styles

---
 .../Editor/WorkflowRecommendationsVue.vue       | 17 +++++++++++------
 client/galaxy/style/scss/base.scss              | 15 +++++++++++++++
 2 files changed, 26 insertions(+), 6 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
index 969b1283f1ae..87b7497d59ba 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
@@ -1,13 +1,16 @@
 <template>
-    <div class="modal ui-modal tool-recommendation-view" style="display: block;">
+    <div class="modal ui-modal wf-recommendation-view">
         <div class="modal-backdrop fade in">
         </div>
-        <div class="modal-dialog" style="width: 260px;">
+        <div class="modal-dialog wf-tools-dialog">
             <div class="modal-content">
-                <div class="modal-header" :title="modalHeaderToolTip">
-                    <h4 class="title" tabindex="0"> {{ modalHeaderTitle }}</h4>
+                <div class="modal-header wf-tools-background" :title="modalHeaderToolTip">
+                    <h4> {{ modalHeaderTitle }}</h4>
                 </div>
-                <div class="modal-body" style="height: 280px; overflow: auto;">
+                <div class="modal-body wf-tools-body">
+                    <div>
+                        {{ loadingMessage }}
+                    </div>
                     <div v-if="compatibleTools.length > 0 && !isDeprecated" >
                         <div v-for="tool in compatibleTools">
                             <i class="fa mr-1 fa-wrench"></i>
@@ -25,7 +28,7 @@
                 </div>
                 <div class="modal-footer">
                     <div class="buttons">
-                        <button v-on:click="closeModal" title="Close">Close</button>
+                        <button v-on:click="closeModal" title="Cancel" class="wf-tools-background">Cancel</button>
                     </div>
                 </div>
             </div>
@@ -57,6 +60,7 @@ export default {
             isDeprecated: false,
             noRecommendationsMessage: "",
             deprecatedMessage: "",
+            loadingMessage: "Loading recommendations ..."
         };
     },
     created() {
@@ -92,6 +96,7 @@ export default {
                         }
                     }
                 }
+                this.loadingMessage = "";
                 this.compatibleTools = cTools;
             }
             else {
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index 05fdce4b8132..7b9b9174a4d3 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1684,3 +1684,18 @@ body.reports {
         stroke-width: 0.2rem;
     }
 }
+
+.wf-recommendation-view {
+    display: block;
+    .wf-tools-dialog {
+        width: 20%;
+    }
+    .wf-tools-body {
+        overflow: auto;
+        height: 50%;
+    }
+    .wf-tools-background {
+        background: $brand-primary;
+        color: $white;
+    }
+}

From 38475dcea373f63f92ceda24747ad2d1e644c4c8 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 26 Mar 2020 12:57:04 -0400
Subject: [PATCH 612/853] Re-named iRODS integration test.

---
 test/integration/test_datatype_upload_irods.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 994dc0be9b2b..014693c3684f 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -59,5 +59,5 @@ def temp_file():
 
 
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
-def test_upload_datatype_auto(instance, test_data, temp_file):
+def test_upload_datatype_irods(instance, test_data, temp_file):
     upload_datatype_helper(instance, test_data, temp_file)

From 73cfaae3ecc7764eb5684fa9350ee528b13e53ff Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 26 Mar 2020 18:00:36 +0100
Subject: [PATCH 613/853] Fix vars

---
 .../Editor/workflowRecommendations.js         | 61 +++++++++----------
 1 file changed, 29 insertions(+), 32 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
index 808316eb0608..a7ebf83551cf 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
@@ -1,4 +1,3 @@
-import _ from "underscore";
 import $ from "jquery";
 import Vue from "vue";
 import WorkflowToolRecommendations from "components/Workflow/Editor/WorkflowRecommendationsVue";
@@ -11,33 +10,33 @@ function getToolId(toolId) {
     return toolId;
 }
 
-function getWorkflowPath(wf_steps, current_node_id, current_node_name) {
+function getWorkflowPath(wfSteps, currentNodeId) {
         let steps = {};
-        let step_names = {};
-        for (let stp_idx in wf_steps.steps) {
-            let step = wf_steps.steps[stp_idx];
-            let input_connections = step.input_connections;
-            step_names[step.id] = getToolId(step.content_id);
-            for (let ic_idx in input_connections) {
-                let ic = input_connections[ic_idx];
+        let stepNames = {};
+        for (const stpIdx in wfSteps.steps) {
+            const step = wfSteps.steps[stpIdx];
+            const inputConnections = step.inputConnections;
+            stepNames[step.id] = getToolId(step.content_id);
+            for (const icIdx in inputConnections) {
+                const ic = inputConnections[icIdx];
                 if(ic !== null && ic !== undefined) {
-                    let prev_conn = [];
-                    for (let conn of ic) {
-                        prev_conn.push(conn.id.toString());
+                    let prevConn = [];
+                    for (const conn of ic) {
+                        prevConn.push(conn.id.toString());
                     }
-                    steps[step.id.toString()] = prev_conn;
+                    steps[step.id.toString()] = prevConn;
                 }
             }
         }
         // recursive call to determine path
-        function readPaths(node_id, ph) {
-            for (let st in steps) {
-                if (parseInt(st) === parseInt(node_id)) {
-                    let parent_id = parseInt(steps[st][0]);
-                    if (parent_id !== undefined && parent_id !== null) {
-                        ph.push(parent_id);
-                        if (steps[parent_id] !== undefined && steps[parent_id] !== null) {
-                            readPaths(parent_id, ph);
+        function readPaths(nodeId, ph) {
+            for (const st in steps) {
+                if (parseInt(st) === parseInt(nodeId)) {
+                    const parentId = parseInt(steps[st][0]);
+                    if (parentId !== undefined && parentId !== null) {
+                        ph.push(parentId);
+                        if (steps[parentId] !== undefined && steps[parentId] !== null) {
+                            readPaths(parentId, ph);
                         }
                     }
                 }
@@ -45,25 +44,23 @@ function getWorkflowPath(wf_steps, current_node_id, current_node_name) {
             return ph;
         }
         let ph = [];
-        let step_names_list = [];
-        ph.push(current_node_id);
-        ph = readPaths(current_node_id, ph);
-        for (let s_idx of ph) {
-            let s_name = step_names[s_idx.toString()];
-            if (s_name !== undefined && s_name !== null) {
-                step_names_list.push(s_name);
+        let stepNamesList = [];
+        ph.push(currentNodeId);
+        ph = readPaths(currentNodeId, ph);
+        for (const sIdx of ph) {
+            const sName = stepNames[sIdx.toString()];
+            if (sName !== undefined && sName !== null) {
+                stepNamesList.push(sName);
             }
         }
-        return step_names_list.join(",");
+        return stepNamesList.join(",");
 }
 
 export function getToolRecommendations(props) {
         const workflowSimple = props.node.app.to_simple();
         const node = props.node;
         const toolId = getToolId(node.content_id);
-        const toolSequence = getWorkflowPath(workflowSimple, node.id, toolId);
-        
-        // show tool recommendations
+        const toolSequence = getWorkflowPath(workflowSimple, node.id);
         const ToolRecommendationInstance = Vue.extend(WorkflowToolRecommendations);
         const vm = document.createElement("div");
         $("body").append(vm);

From 309e79a8f0b856c00eaa3abe0d294bfcac9092ee Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Thu, 26 Mar 2020 13:05:20 -0400
Subject: [PATCH 614/853] Check if path is set before joining

---
 lib/galaxy/config/__init__.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index a9cb031c201b..72a0b463fc48 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -246,16 +246,19 @@ def resolve(key):
             resolve(key)
 
     def _in_managed_config_dir(self, path):
-        return os.path.join(self.managed_config_dir, path)
+        return self._in_dir(self.managed_config_dir, path)
 
     def _in_config_dir(self, path):
-        return os.path.join(self.config_dir, path)
+        return self._in_dir(self.config_dir, path)
 
     def _in_sample_dir(self, path):
-        return os.path.join(self.sample_config_dir, path)
+        return self._in_dir(self.sample_config_dir, path)
 
     def _in_data_dir(self, path):
-        return os.path.join(self.data_dir, path)
+        return self._in_dir(self.data_dir, path)
+
+    def _in_dir(self, _dir, path):
+        return os.path.join(_dir, path) if path else _dir
 
     def _parse_config_file_options(self, defaults, listify_defaults, config_kwargs):
         for var, values in defaults.items():

From 4c18fc0a3424ba822adc989ed06a15420c0c11a3 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 26 Mar 2020 13:11:26 -0400
Subject: [PATCH 615/853] Just running iRODS integration test

---
 .github/workflows/integration.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 71694ddb289c..5759b6712ee2 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         python-version: [3.7]
-        subset: ['upload_datatype']
+        subset: ['upload_datatype_irods']
     services:
       postgres:
         image: postgres:11

From a52cca695b0c464056811e0e01ea5f55007024b3 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 26 Mar 2020 18:22:33 +0100
Subject: [PATCH 616/853] updat tool recommendations

---
 .../scripts/components/ToolRecommendation.vue | 89 +++++++++----------
 .../Editor/WorkflowRecommendationsVue.vue     |  2 +-
 client/galaxy/style/scss/base.scss            | 15 +---
 3 files changed, 47 insertions(+), 59 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 674f62f0e5e8..ade8bd1e05db 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -21,13 +21,13 @@ export default {
     props: {
         toolId: {
             type: String,
-            required: true,
-        },
+            required: true
+        }
     },
     data() {
         return {
             deprecated: null,
-            deprecatedMessage: "",
+            deprecatedMessage: ""
         };
     },
     created() {
@@ -41,7 +41,7 @@ export default {
                 toolId = toolIdSlash[toolIdSlash.length - 2];
             }
             return toolId;
-        },
+        }
     },
     methods: {
         loadRecommendations() {
@@ -49,10 +49,10 @@ export default {
             const url = `${getAppRoot()}api/workflows/get_tool_predictions`;
             axios
                 .post(url, {
-                    tool_sequence: toolId,
+                    tool_sequence: toolId
                 })
-                .then((response) => {
-                    axios.get(`${getAppRoot()}api/datatypes/mapping`).then((responseMapping) => {
+                .then(response => {
+                    axios.get(`${getAppRoot()}api/datatypes/mapping`).then(responseMapping => {
                         const predData = response.data.predicted_data;
                         const datatypesMapping = responseMapping.data;
                         const extToType = datatypesMapping.ext_to_class_name;
@@ -105,40 +105,39 @@ export default {
         },
         renderD3Tree(predictedTools) {
             const duration = 750;
-            const svg = d3.select("#tool-recommendation").append("svg").attr("class", "tree-size").append("g");
+            const svg = d3
+                .select("#tool-recommendation")
+                .append("svg")
+                .attr("class", "tree-size")
+                .append("g");
             let i = 0;
             let root = null;
-            let x = 0;
-            let y = 0;
             let translateX = 0;
 
             const gElem = svg[0][0];
             const svgElem = gElem.parentNode;
             const clientH = svgElem.clientHeight;
             const clientW = svgElem.clientWidth;
-            y = parseInt(clientH * 0.9);
-            x = parseInt(clientW * 0.6);
-            translateX = parseInt(clientW * 0.15);
+            translateX = parseInt(clientW * 0.33);
 
-            svgElem.setAttribute("viewBox", "0 0 " + x + " " + clientH);
-            svgElem.setAttribute("preserveAspectRatio", "xMinYMin");
-            gElem.setAttribute("transform", "translate(" + translateX + ", 5)");
+            svgElem.setAttribute("viewBox", -translateX + " 0 " + clientW + " " + clientH);
+            svgElem.setAttribute("preserveAspectRatio", "xMidYMid meet");
 
-            const tree = d3.layout.tree().size([y, x]);
+            const tree = d3.layout.tree().size([clientH, clientW]);
 
-            const diagonal = d3.svg.diagonal().projection((d) => {
+            const diagonal = d3.svg.diagonal().projection(d => {
                 return [d.y, d.x];
             });
-            const update = (source) => {
+            const update = source => {
                 // Compute the new tree layout.
                 const nodes = tree.nodes(root).reverse();
                 const links = tree.links(nodes);
                 // Normalize for fixed-depth.
-                nodes.forEach((d) => {
-                    d.y = d.depth * 180;
+                nodes.forEach(d => {
+                    d.y = d.depth * (clientW / 5);
                 });
-                // Update the nodes…
-                const node = svg.selectAll("g.node").data(nodes, (d) => {
+                // Update the nodes
+                const node = svg.selectAll("g.node").data(nodes, d => {
                     return d.id || (d.id = ++i);
                 });
                 // Enter any new nodes at the parent's previous position.
@@ -146,78 +145,76 @@ export default {
                     .enter()
                     .append("g")
                     .attr("class", "node")
-                    .attr("transform", (d) => {
+                    .attr("transform", d => {
                         return "translate(" + source.y0 + "," + source.x0 + ")";
                     })
                     .on("click", click);
                 nodeEnter.append("circle").attr("r", 1e-6);
                 nodeEnter
                     .append("text")
-                    .attr("x", (d) => {
+                    .attr("x", d => {
                         return d.children || d._children ? -10 : 10;
                     })
                     .attr("dy", ".35em")
-                    .attr("text-anchor", (d) => {
+                    .attr("text-anchor", d => {
                         return d.children || d._children ? "end" : "start";
                     })
-                    .text((d) => {
+                    .text(d => {
                         return d.name;
-                    })
-                    .attr("class", "node-enter");
-                nodeEnter.append("title").text((d) => {
+                    });
+                nodeEnter.append("title").text(d => {
                     return d.children || d._children ? "Click to collapse" : "Click to open tool definition";
                 });
                 // Transition nodes to their new position.
                 const nodeUpdate = node
                     .transition()
                     .duration(duration)
-                    .attr("transform", (d) => {
+                    .attr("transform", d => {
                         return "translate(" + d.y + "," + d.x + ")";
                     });
-                nodeUpdate.select("circle").attr("r", 4.5);
-                nodeUpdate.select("text").attr("class", "node-update");
+                nodeUpdate.select("circle").attr("r", 3.5);
                 // Transition exiting nodes to the parent's new position.
                 const nodeExit = node
                     .exit()
                     .transition()
                     .duration(duration)
-                    .attr("transform", (d) => {
+                    .attr("transform", d => {
                         return "translate(" + source.y + "," + source.x + ")";
                     })
                     .remove();
-                nodeExit.select("circle").attr("r", 1e-6);
-                nodeExit.select("text").attr("class", "node-enter");
                 // Update the links
-                const link = svg.selectAll("path.link").data(links, (d) => {
+                const link = svg.selectAll("path.link").data(links, d => {
                     return d.target.id;
                 });
                 // Enter any new links at the parent's previous position.
                 link.enter()
                     .insert("path", "g")
                     .attr("class", "link")
-                    .attr("d", (d) => {
+                    .attr("d", d => {
                         const o = { x: source.x0, y: source.y0 };
                         return diagonal({ source: o, target: o });
                     });
                 // Transition links to their new position.
-                link.transition().duration(duration).attr("d", diagonal);
+                link.transition()
+                    .duration(duration)
+                    .attr("d", diagonal);
                 // Transition exiting nodes to the parent's new position.
                 link.exit()
                     .transition()
                     .duration(duration)
-                    .attr("d", (d) => {
+                    .attr("d", d => {
                         const o = { x: source.x, y: source.y };
                         return diagonal({ source: o, target: o });
                     })
                     .remove();
                 // Stash the old positions for transition.
-                nodes.forEach((d) => {
+                nodes.forEach(d => {
                     d.x0 = d.x;
                     d.y0 = d.y;
                 });
             };
             // Toggle children on click.
-            const click = (d) => {
+            const click = d => {
                 if (d.children) {
                     d._children = d.children;
                     d.children = null;
@@ -231,7 +228,7 @@ export default {
                     document.location.href = `${getAppRoot()}tool_runner?tool_id=${tId}`;
                 }
             };
-            const collapse = (d) => {
+            const collapse = d => {
                 if (d.children) {
                     d._children = d.children;
                     d._children.forEach(collapse);
@@ -239,11 +236,11 @@ export default {
                 }
             };
             root = predictedTools;
-            root.x0 = y / 2;
+            root.x0 = clientH / 2;
             root.y0 = 0;
             root.children.forEach(collapse);
             update(root);
-        },
-    },
+        }
+    }
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
index 87b7497d59ba..e026de41cd22 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
@@ -3,7 +3,7 @@
         <div class="modal-backdrop fade in">
         </div>
         <div class="modal-dialog wf-tools-dialog">
-            <div class="modal-content">
+            <div class="modal-content wf-tool-content">
                 <div class="modal-header wf-tools-background" :title="modalHeaderToolTip">
                     <h4> {{ modalHeaderTitle }}</h4>
                 </div>
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index 7b9b9174a4d3..daf4e92b6908 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1658,19 +1658,7 @@ body.reports {
         circle {
             fill: lighten($brand-primary, 20%);
             stroke: lighten($brand-primary, 20%);
-            stroke-width: 0.1rem;
         }
-        text {
-            font: 0.4rem sans-serif;
-        }
-    }
-
-    .node-enter {
-        fill-opacity: 1e-6;
-    }
-
-    .node-update {
-        fill-opacity: 1;
     }
 
     .tree-size {
@@ -1698,4 +1686,7 @@ body.reports {
         background: $brand-primary;
         color: $white;
     }
+    .wf-tool-content {
+        border: solid 1px $brand-primary;
+    }
 }

From b309ac896607874cc279ce93114e1911ed8d5464 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 26 Mar 2020 18:25:09 +0100
Subject: [PATCH 617/853] Fix prettier

---
 .../Editor/WorkflowRecommendationsVue.vue     |  59 ++++++-----
 .../Editor/workflowRecommendations.js         | 100 +++++++++---------
 2 files changed, 81 insertions(+), 78 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
index e026de41cd22..a28545efd1eb 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
@@ -1,22 +1,23 @@
 <template>
     <div class="modal ui-modal wf-recommendation-view">
-        <div class="modal-backdrop fade in">
-        </div>
+        <div class="modal-backdrop fade in"></div>
         <div class="modal-dialog wf-tools-dialog">
             <div class="modal-content wf-tool-content">
                 <div class="modal-header wf-tools-background" :title="modalHeaderToolTip">
-                    <h4> {{ modalHeaderTitle }}</h4>
+                    <h4>{{ modalHeaderTitle }}</h4>
                 </div>
                 <div class="modal-body wf-tools-body">
                     <div>
                         {{ loadingMessage }}
                     </div>
-                    <div v-if="compatibleTools.length > 0 && !isDeprecated" >
+                    <div v-if="compatibleTools.length > 0 && !isDeprecated">
                         <div v-for="tool in compatibleTools">
                             <i class="fa mr-1 fa-wrench"></i>
-                            <a href="#" title="Open tool" :id="tool.id" v-on:click="createTool(tool.id)"> {{ tool.name }} </a>
+                            <a href="#" title="Open tool" :id="tool.id" v-on:click="createTool(tool.id)">
+                                {{ tool.name }}
+                            </a>
                         </div>
-                        <br>
+                        <br />
                     </div>
                     <div v-else-if="isDeprecated">
                         {{ deprecatedMessage }}
@@ -24,7 +25,6 @@
                     <div v-else>
                         {{ noRecommendationsMessage }}
                     </div>
-                    
                 </div>
                 <div class="modal-footer">
                     <div class="buttons">
@@ -37,7 +37,6 @@
 </template>
 
 <script>
-
 import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 import { getModule } from "./services";
@@ -46,7 +45,7 @@ import _l from "utils/localization";
 export default {
     props: {
         workflowManager: {
-            type: Object,
+            type: Object
         },
         toolSequence: {
             type: String
@@ -55,7 +54,9 @@ export default {
     data() {
         return {
             modalHeaderTitle: _l("Tool Recommendations"),
-            modalHeaderToolTip: _l("The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to have it on the workflow editor."),
+            modalHeaderToolTip: _l(
+                "The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to have it on the workflow editor."
+            ),
             compatibleTools: [],
             isDeprecated: false,
             noRecommendationsMessage: "",
@@ -66,11 +67,12 @@ export default {
     created() {
         this.loadRecommendations();
     },
-    computed: {
-    },
+    computed: {},
     methods: {
         async loadRecommendations() {
-            const response = await axios.post(`${getAppRoot()}api/workflows/get_tool_predictions`, {tool_sequence: this.toolSequence});
+            const response = await axios.post(`${getAppRoot()}api/workflows/get_tool_predictions`, {
+                tool_sequence: this.toolSequence
+            });
             const predictedData = response.data.predicted_data;
             const outputDatatypes = predictedData.o_extensions;
             const predictedDataChildren = predictedData.children;
@@ -83,12 +85,14 @@ export default {
                     let t = {};
                     const inputDatatypes = name_obj.i_extensions;
                     for (const out_t of outputDatatypes.entries()) {
-                        for(const in_t of inputDatatypes.entries()) {
-                            if ((app.isSubType(out_t[1], in_t[1]) === true) ||
-                                 out_t[1] === "input" ||
-                                 out_t[1] === "_sniff_" ||
-                                 out_t[1] === "input_collection") {
-                                t.id = name_obj.tool_id
+                        for (const in_t of inputDatatypes.entries()) {
+                            if (
+                                app.isSubType(out_t[1], in_t[1]) === true ||
+                                out_t[1] === "input" ||
+                                out_t[1] === "_sniff_" ||
+                                out_t[1] === "input_collection"
+                            ) {
+                                t.id = name_obj.tool_id;
                                 t.name = name_obj.name;
                                 cTools.push(t);
                                 break;
@@ -98,27 +102,26 @@ export default {
                 }
                 this.loadingMessage = "";
                 this.compatibleTools = cTools;
-            }
-            else {
+            } else {
                 this.noRecommendationsMessage = "No tool recommendations";
             }
         },
-        closeModal () {
+        closeModal() {
             this.$el.remove();
         },
-        createTool (tId) {
-            const app = this.workflowManager.node.app;         
+        createTool(tId) {
+            const app = this.workflowManager.node.app;
             const requestData = {
                 type: "tool",
                 tool_id: tId,
-                _: "true",
+                _: "true"
             };
-            getModule(requestData).then((response) => {
+            getModule(requestData).then(response => {
                 const node = app.create_node("tool", response.name, tId);
                 app.set_node(node, response);
                 this.closeModal();
             });
-        },
-    },
+        }
+    }
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
index a7ebf83551cf..5bca08a4d7e8 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
@@ -11,64 +11,64 @@ function getToolId(toolId) {
 }
 
 function getWorkflowPath(wfSteps, currentNodeId) {
-        let steps = {};
-        let stepNames = {};
-        for (const stpIdx in wfSteps.steps) {
-            const step = wfSteps.steps[stpIdx];
-            const inputConnections = step.inputConnections;
-            stepNames[step.id] = getToolId(step.content_id);
-            for (const icIdx in inputConnections) {
-                const ic = inputConnections[icIdx];
-                if(ic !== null && ic !== undefined) {
-                    let prevConn = [];
-                    for (const conn of ic) {
-                        prevConn.push(conn.id.toString());
-                    }
-                    steps[step.id.toString()] = prevConn;
+    let steps = {};
+    let stepNames = {};
+    for (const stpIdx in wfSteps.steps) {
+        const step = wfSteps.steps[stpIdx];
+        const inputConnections = step.inputConnections;
+        stepNames[step.id] = getToolId(step.content_id);
+        for (const icIdx in inputConnections) {
+            const ic = inputConnections[icIdx];
+            if (ic !== null && ic !== undefined) {
+                let prevConn = [];
+                for (const conn of ic) {
+                    prevConn.push(conn.id.toString());
                 }
+                steps[step.id.toString()] = prevConn;
             }
         }
-        // recursive call to determine path
-        function readPaths(nodeId, ph) {
-            for (const st in steps) {
-                if (parseInt(st) === parseInt(nodeId)) {
-                    const parentId = parseInt(steps[st][0]);
-                    if (parentId !== undefined && parentId !== null) {
-                        ph.push(parentId);
-                        if (steps[parentId] !== undefined && steps[parentId] !== null) {
-                            readPaths(parentId, ph);
-                        }
+    }
+    // recursive call to determine path
+    function readPaths(nodeId, ph) {
+        for (const st in steps) {
+            if (parseInt(st) === parseInt(nodeId)) {
+                const parentId = parseInt(steps[st][0]);
+                if (parentId !== undefined && parentId !== null) {
+                    ph.push(parentId);
+                    if (steps[parentId] !== undefined && steps[parentId] !== null) {
+                        readPaths(parentId, ph);
                     }
                 }
             }
-            return ph;
         }
-        let ph = [];
-        let stepNamesList = [];
-        ph.push(currentNodeId);
-        ph = readPaths(currentNodeId, ph);
-        for (const sIdx of ph) {
-            const sName = stepNames[sIdx.toString()];
-            if (sName !== undefined && sName !== null) {
-                stepNamesList.push(sName);
-            }
+        return ph;
+    }
+    let ph = [];
+    let stepNamesList = [];
+    ph.push(currentNodeId);
+    ph = readPaths(currentNodeId, ph);
+    for (const sIdx of ph) {
+        const sName = stepNames[sIdx.toString()];
+        if (sName !== undefined && sName !== null) {
+            stepNamesList.push(sName);
         }
-        return stepNamesList.join(",");
+    }
+    return stepNamesList.join(",");
 }
 
 export function getToolRecommendations(props) {
-        const workflowSimple = props.node.app.to_simple();
-        const node = props.node;
-        const toolId = getToolId(node.content_id);
-        const toolSequence = getWorkflowPath(workflowSimple, node.id);
-        const ToolRecommendationInstance = Vue.extend(WorkflowToolRecommendations);
-        const vm = document.createElement("div");
-        $("body").append(vm);
-        const instance = new ToolRecommendationInstance({
-             propsData: {
-                 workflowManager: props,
-                 toolSequence: toolSequence
-             },
-        });
-        instance.$mount(vm);
-    }
+    const workflowSimple = props.node.app.to_simple();
+    const node = props.node;
+    const toolId = getToolId(node.content_id);
+    const toolSequence = getWorkflowPath(workflowSimple, node.id);
+    const ToolRecommendationInstance = Vue.extend(WorkflowToolRecommendations);
+    const vm = document.createElement("div");
+    $("body").append(vm);
+    const instance = new ToolRecommendationInstance({
+        propsData: {
+            workflowManager: props,
+            toolSequence: toolSequence
+        }
+    });
+    instance.$mount(vm);
+}

From 62e5a11d1f335d1775e8530fac0d2c6658450d93 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 26 Mar 2020 13:42:16 -0400
Subject: [PATCH 618/853] Revert "Just running iRODS integration test"

This reverts commit 4c18fc0a3424ba822adc989ed06a15420c0c11a3.
---
 .github/workflows/integration.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 5759b6712ee2..71694ddb289c 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         python-version: [3.7]
-        subset: ['upload_datatype_irods']
+        subset: ['upload_datatype']
     services:
       postgres:
         image: postgres:11

From 00a9a5a5ea992b7a2360aebdb6350891d69e9db5 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 26 Mar 2020 19:01:31 +0100
Subject: [PATCH 619/853] Fix messages

---
 .../Workflow/Editor/WorkflowRecommendationsVue.vue | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
index a28545efd1eb..c8d290f66bd3 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
@@ -7,7 +7,7 @@
                     <h4>{{ modalHeaderTitle }}</h4>
                 </div>
                 <div class="modal-body wf-tools-body">
-                    <div>
+                    <div v-if="showLoading">
                         {{ loadingMessage }}
                     </div>
                     <div v-if="compatibleTools.length > 0 && !isDeprecated">
@@ -17,12 +17,11 @@
                                 {{ tool.name }}
                             </a>
                         </div>
-                        <br />
                     </div>
                     <div v-else-if="isDeprecated">
                         {{ deprecatedMessage }}
                     </div>
-                    <div v-else>
+                    <div v-if="compatibleTools.length === 0 && !showLoading">
                         {{ noRecommendationsMessage }}
                     </div>
                 </div>
@@ -59,9 +58,10 @@ export default {
             ),
             compatibleTools: [],
             isDeprecated: false,
-            noRecommendationsMessage: "",
+            noRecommendationsMessage: _l("No tool recommendations"),
             deprecatedMessage: "",
-            loadingMessage: "Loading recommendations ..."
+            loadingMessage: _l("Loading recommendations ..."),
+            showLoading: true
         };
     },
     created() {
@@ -100,11 +100,9 @@ export default {
                         }
                     }
                 }
-                this.loadingMessage = "";
                 this.compatibleTools = cTools;
-            } else {
-                this.noRecommendationsMessage = "No tool recommendations";
             }
+            this.showLoading = false;
         },
         closeModal() {
             this.$el.remove();

From 0d2b502669921e19124071c6baacf1334be50f73 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Thu, 26 Mar 2020 14:19:43 -0400
Subject: [PATCH 620/853] Putting tmate back in to see if it works now

---
 .github/workflows/integration.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 71694ddb289c..7324ef886133 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -46,6 +46,8 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v2
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
       working-directory: 'galaxy root'

From 4671e340dc8242e7778e478096653c9006d3412c Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 26 Mar 2020 19:31:31 +0100
Subject: [PATCH 621/853] Add brand color to D3 tree

---
 client/galaxy/style/scss/base.scss | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index daf4e92b6908..1710cbf181fd 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1656,8 +1656,8 @@ body.reports {
     .node {
         cursor: pointer;
         circle {
-            fill: lighten($brand-primary, 20%);
-            stroke: lighten($brand-primary, 20%);
+            fill: $brand-primary;
+            stroke: $brand-primary;
         }
     }
 
@@ -1668,8 +1668,8 @@ body.reports {
 
     .link {
         fill: none;
-        stroke: lighten($brand-primary, 20%);
-        stroke-width: 0.2rem;
+        stroke: $brand-primary;
+        stroke-width: 4;
     }
 }
 

From 12e202a1c51e5de31e6aff829d90652ac66dc85d Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 26 Mar 2020 19:59:07 +0100
Subject: [PATCH 622/853] Resize tool text

---
 client/galaxy/scripts/components/ToolRecommendation.vue | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index ade8bd1e05db..91814e194bf9 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -105,6 +105,7 @@ export default {
         },
         renderD3Tree(predictedTools) {
             const duration = 750;
+            const maxTextLength = 20;
             const svg = d3
                 .select("#tool-recommendation")
                 .append("svg")
@@ -160,10 +161,14 @@ export default {
                         return d.children || d._children ? "end" : "start";
                     })
                     .text(d => {
+                        let tName = d.name;
+                        if(tName.length > maxTextLength) {
+                            return tName.slice(0, maxTextLength) + "...";
+                        }
                         return d.name;
                     });
                 nodeEnter.append("title").text(d => {
-                    return d.children || d._children ? "Click to collapse" : "Click to open tool definition";
+                    return d.children || d._children ? "Click to collapse" : "Open tool - " + d.name;
                 });
                 // Transition nodes to their new position.
                 const nodeUpdate = node

From 08d9b94a42a013866ec3d55658df4efe8d7f784b Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Fri, 27 Mar 2020 01:40:46 +0100
Subject: [PATCH 623/853] Fix build

---
 .../scripts/components/ToolRecommendation.vue | 32 ++++-----
 .../Editor/WorkflowRecommendationsVue.vue     | 65 ++++++++++---------
 .../components/Workflow/Editor/utilities.js   |  1 -
 .../Editor/workflowRecommendations.js         | 11 ++--
 4 files changed, 55 insertions(+), 54 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 91814e194bf9..3b70b261deb3 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -1,6 +1,6 @@
 <template>
     <div id="tool-recommendation" class="tool-recommendation-view">
-        <div v-if="!deprecated" class="infomessagelarge">
+        <div v-if="!deprecated && showMessage" class="infomessagelarge">
             <h4>Tool recommendation</h4>
             You have used {{ getToolId }} tool. For further analysis, you could try using the following/recommended
             tools. The recommended tools are shown in the decreasing order of their scores predicted using machine
@@ -8,7 +8,9 @@
             tool than a tool with a lower score. Please click on one of the following/recommended tools to open its
             definition.
         </div>
-        <div v-else class="warningmessagelarge">You have used {{ getToolId }} tool. {{ deprecatedMessage }}</div>
+        <div v-else-if="deprecated" class="warningmessagelarge">
+            You have used {{ getToolId }} tool. {{ deprecatedMessage }}
+        </div>
     </div>
 </template>
 
@@ -26,8 +28,9 @@ export default {
     },
     data() {
         return {
-            deprecated: null,
-            deprecatedMessage: ""
+            deprecated: false,
+            deprecatedMessage: "",
+            showMessage: false
         };
     },
     created() {
@@ -58,7 +61,7 @@ export default {
                         const extToType = datatypesMapping.ext_to_class_name;
                         const typeToType = datatypesMapping.class_to_classes;
                         this.deprecated = predData.is_deprecated;
-
+                        this.deprecatedMessage = predData.message;
                         if (response.data !== null && predData.children.length > 0) {
                             const filteredData = {};
                             const compatibleTools = {};
@@ -67,15 +70,15 @@ export default {
                             const children = predData.children;
                             for (const nameObj of children.entries()) {
                                 const inputDatatypes = nameObj[1].i_extensions;
-                                for (const out_t of outputDatatypes.entries()) {
-                                    for (const in_t of inputDatatypes.entries()) {
-                                        const child = extToType[out_t[1]];
-                                        const parent = extToType[in_t[1]];
+                                for (const outT of outputDatatypes.entries()) {
+                                    for (const inTool of inputDatatypes.entries()) {
+                                        const child = extToType[outT[1]];
+                                        const parent = extToType[inTool[1]];
                                         if (
                                             (typeToType[child] && parent in typeToType[child]) === true ||
-                                            out_t[1] === "input" ||
-                                            out_t[1] === "_sniff_" ||
-                                            out_t[1] === "input_collection"
+                                            outT[1] === "input" ||
+                                            outT[1] === "_sniff_" ||
+                                            outT[1] === "input_collection"
                                         ) {
                                             compatibleTools[nameObj[1].tool_id] = nameObj[1].name;
                                             break;
@@ -95,9 +98,8 @@ export default {
                             filteredData.name = predData.name;
                             filteredData.children = filteredChildren;
                             if (filteredChildren.length > 0 && this.deprecated === false) {
+                                this.showMessage = true;
                                 this.renderD3Tree(filteredData);
-                            } else if (this.deprecated === true) {
-                                this.deprecatedMessage = predData.message;
                             }
                         }
                     });
@@ -162,7 +164,7 @@ export default {
                     })
                     .text(d => {
                         let tName = d.name;
-                        if(tName.length > maxTextLength) {
+                        if (tName.length > maxTextLength) {
                             return tName.slice(0, maxTextLength) + "...";
                         }
                         return d.name;
diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
index c8d290f66bd3..e59c455fd2a7 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
@@ -11,7 +11,7 @@
                         {{ loadingMessage }}
                     </div>
                     <div v-if="compatibleTools.length > 0 && !isDeprecated">
-                        <div v-for="tool in compatibleTools">
+                        <div v-for="tool in compatibleTools" :key="tool.id">
                             <i class="fa mr-1 fa-wrench"></i>
                             <a href="#" title="Open tool" :id="tool.id" v-on:click="createTool(tool.id)">
                                 {{ tool.name }}
@@ -69,40 +69,41 @@ export default {
     },
     computed: {},
     methods: {
-        async loadRecommendations() {
-            const response = await axios.post(`${getAppRoot()}api/workflows/get_tool_predictions`, {
-                tool_sequence: this.toolSequence
-            });
-            const predictedData = response.data.predicted_data;
-            const outputDatatypes = predictedData.o_extensions;
-            const predictedDataChildren = predictedData.children;
-            const app = this.workflowManager.node.app;
-            this.isDeprecated = predictedData.is_deprecated;
-            this.deprecatedMessage = predictedData.message;
-            if (predictedDataChildren.length > 0) {
-                let cTools = [];
-                for (const [index, name_obj] of predictedDataChildren.entries()) {
-                    let t = {};
-                    const inputDatatypes = name_obj.i_extensions;
-                    for (const out_t of outputDatatypes.entries()) {
-                        for (const in_t of inputDatatypes.entries()) {
-                            if (
-                                app.isSubType(out_t[1], in_t[1]) === true ||
-                                out_t[1] === "input" ||
-                                out_t[1] === "_sniff_" ||
-                                out_t[1] === "input_collection"
-                            ) {
-                                t.id = name_obj.tool_id;
-                                t.name = name_obj.name;
-                                cTools.push(t);
-                                break;
+        loadRecommendations() {
+            axios
+                .post(`${getAppRoot()}api/workflows/get_tool_predictions`, { tool_sequence: this.toolSequence })
+                .then(response => {
+                    const predictedData = response.data.predicted_data;
+                    const outputDatatypes = predictedData.o_extensions;
+                    const predictedDataChildren = predictedData.children;
+                    const app = this.workflowManager.node.app;
+                    this.isDeprecated = predictedData.is_deprecated;
+                    this.deprecatedMessage = predictedData.message;
+                    if (predictedDataChildren.length > 0) {
+                        const cTools = [];
+                        for (const nameObj of predictedDataChildren.entries()) {
+                            const t = {};
+                            const inputDatatypes = nameObj[1].i_extensions;
+                            for (const outT of outputDatatypes.entries()) {
+                                for (const inTool of inputDatatypes.entries()) {
+                                    if (
+                                        app.isSubType(outT[1], inTool[1]) === true ||
+                                        outT[1] === "input" ||
+                                        outT[1] === "_sniff_" ||
+                                        outT[1] === "input_collection"
+                                    ) {
+                                        t.id = nameObj[1].tool_id;
+                                        t.name = nameObj[1].name;
+                                        cTools.push(t);
+                                        break;
+                                    }
+                                }
                             }
                         }
+                        this.compatibleTools = cTools;
                     }
-                }
-                this.compatibleTools = cTools;
-            }
-            this.showLoading = false;
+                    this.showLoading = false;
+                });
         },
         closeModal() {
             this.$el.remove();
diff --git a/client/galaxy/scripts/components/Workflow/Editor/utilities.js b/client/galaxy/scripts/components/Workflow/Editor/utilities.js
index dd705c7c5be7..dcd01b05aaf8 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/utilities.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/utilities.js
@@ -7,7 +7,6 @@ import WorkflowIcons from "components/Workflow/icons";
 import { DefaultForm, ToolForm } from "mvc/workflow/workflow-forms";
 import { loadWorkflow } from "./services";
 import { hide_modal, show_message, show_modal } from "layout/modal";
-import Modal from "mvc/ui/ui-modal";
 
 export function copyIntoWorkflow(workflow, id = null, stepCount = null) {
     const _copy_into_workflow_ajax = () => {
diff --git a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
index 5bca08a4d7e8..2b0fcdd95dfa 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
@@ -4,15 +4,15 @@ import WorkflowToolRecommendations from "components/Workflow/Editor/WorkflowReco
 
 function getToolId(toolId) {
     if (toolId !== undefined && toolId !== null && toolId.indexOf("/") > -1) {
-        let toolIdSlash = toolId.split("/");
+        const toolIdSlash = toolId.split("/");
         toolId = toolIdSlash[toolIdSlash.length - 2];
     }
     return toolId;
 }
 
 function getWorkflowPath(wfSteps, currentNodeId) {
-    let steps = {};
-    let stepNames = {};
+    const steps = {};
+    const stepNames = {};
     for (const stpIdx in wfSteps.steps) {
         const step = wfSteps.steps[stpIdx];
         const inputConnections = step.inputConnections;
@@ -20,7 +20,7 @@ function getWorkflowPath(wfSteps, currentNodeId) {
         for (const icIdx in inputConnections) {
             const ic = inputConnections[icIdx];
             if (ic !== null && ic !== undefined) {
-                let prevConn = [];
+                const prevConn = [];
                 for (const conn of ic) {
                     prevConn.push(conn.id.toString());
                 }
@@ -44,7 +44,7 @@ function getWorkflowPath(wfSteps, currentNodeId) {
         return ph;
     }
     let ph = [];
-    let stepNamesList = [];
+    const stepNamesList = [];
     ph.push(currentNodeId);
     ph = readPaths(currentNodeId, ph);
     for (const sIdx of ph) {
@@ -59,7 +59,6 @@ function getWorkflowPath(wfSteps, currentNodeId) {
 export function getToolRecommendations(props) {
     const workflowSimple = props.node.app.to_simple();
     const node = props.node;
-    const toolId = getToolId(node.content_id);
     const toolSequence = getWorkflowPath(workflowSimple, node.id);
     const ToolRecommendationInstance = Vue.extend(WorkflowToolRecommendations);
     const vm = document.createElement("div");

From 0360d75cfbd3d7261873ef89f433c3a2f9dd1c0e Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Fri, 27 Mar 2020 11:08:28 +0100
Subject: [PATCH 624/853] Fix build

---
 client/galaxy/scripts/components/ToolRecommendation.vue   | 5 ++---
 .../components/Workflow/Editor/workflowRecommendations.js | 8 ++++----
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 3b70b261deb3..6562359a768d 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -163,7 +163,7 @@ export default {
                         return d.children || d._children ? "end" : "start";
                     })
                     .text(d => {
-                        let tName = d.name;
+                        const tName = d.name;
                         if (tName.length > maxTextLength) {
                             return tName.slice(0, maxTextLength) + "...";
                         }
@@ -181,8 +181,7 @@ export default {
                     });
                 nodeUpdate.select("circle").attr("r", 3.5);
                 // Transition exiting nodes to the parent's new position.
-                const nodeExit = node
-                    .exit()
+                node.exit()
                     .transition()
                     .duration(duration)
                     .attr("transform", d => {
diff --git a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
index 2b0fcdd95dfa..103909b6ea18 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
@@ -15,7 +15,7 @@ function getWorkflowPath(wfSteps, currentNodeId) {
     const stepNames = {};
     for (const stpIdx in wfSteps.steps) {
         const step = wfSteps.steps[stpIdx];
-        const inputConnections = step.inputConnections;
+        const inputConnections = step.input_connections;
         stepNames[step.id] = getToolId(step.content_id);
         for (const icIdx in inputConnections) {
             const ic = inputConnections[icIdx];
@@ -44,16 +44,16 @@ function getWorkflowPath(wfSteps, currentNodeId) {
         return ph;
     }
     let ph = [];
-    const stepNamesList = [];
+    const stepNameList = [];
     ph.push(currentNodeId);
     ph = readPaths(currentNodeId, ph);
     for (const sIdx of ph) {
         const sName = stepNames[sIdx.toString()];
         if (sName !== undefined && sName !== null) {
-            stepNamesList.push(sName);
+            stepNameList.push(sName);
         }
     }
-    return stepNamesList.join(",");
+    return stepNameList.join(",");
 }
 
 export function getToolRecommendations(props) {

From 29a6b93b7b78f333a9803250e03239adc2b94d01 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Fri, 27 Mar 2020 11:34:40 +0100
Subject: [PATCH 625/853] Fix prettier

---
 .../components/Workflow/Editor/Node.vue        | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 2f5c92c28c64..9d0cd6133276 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -10,7 +10,7 @@
             >
                 <i class="fa fa-times" />
             </b-button>
-            <b-button 
+            <b-button
                 v-if="isEnabled"
                 class="node-recommendations py-0 float-right"
                 variant="primary"
@@ -53,23 +53,23 @@ Vue.use(BootstrapVue);
 
 export default {
     components: {
-        LoadingSpan,
+        LoadingSpan
     },
     props: {
         id: {
-            type: String,
+            type: String
         },
         title: {
             type: String,
-            default: "title",
+            default: "title"
         },
         type: {
             type: String,
-            default: "tool",
+            default: "tool"
         },
         node: {
-            type: Object,
-        },
+            type: Object
+        }
     },
     computed: {
         iconClass() {
@@ -82,7 +82,7 @@ export default {
         canClone() {
             return this.type != "subworkflow";
         },
-        isEnabled () {
+        isEnabled() {
             const Galaxy = getGalaxyInstance();
             const isRecommendationEnabled = Galaxy.config.enable_tool_recommendations;
             if (isRecommendationEnabled === true || isRecommendationEnabled === "true") {
@@ -101,6 +101,6 @@ export default {
         onGetRecommendations() {
             getToolRecommendations(this);
         }
-    },
+    }
 };
 </script>

From f423a063202d463f6f2b1f7cc9c7263dea07179c Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 09:17:59 -0400
Subject: [PATCH 626/853] To start a new build

---
 CONTRIBUTORS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
index d6507a7be425..aab7c7c9accb 100644
--- a/CONTRIBUTORS.md
+++ b/CONTRIBUTORS.md
@@ -1,6 +1,6 @@
 # Contributors
 
-The following individuals have contributed code to Galaxy:
+The following individuals have contributed code to Galaxy: 
 
 * Enis Afgan <afgane@gmail.com>
 * Istvan Albert <istvan.albert@gmail.com>

From eaee6abcbe56af4f17abc956da0ec00371cccba5 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Fri, 27 Mar 2020 14:38:32 +0100
Subject: [PATCH 627/853] Add service calls

---
 .../scripts/components/ToolRecommendation.vue | 95 +++++++++----------
 .../Editor/WorkflowRecommendationsVue.vue     | 63 ++++++------
 .../components/Workflow/Editor/services.js    | 18 ++++
 3 files changed, 94 insertions(+), 82 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 6562359a768d..8fa5b0747d45 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -17,7 +17,7 @@
 <script>
 import * as d3 from "d3";
 import { getAppRoot } from "onload/loadConfig";
-import axios from "axios";
+import { getDatatypeMapping, getToolPredictions } from "components/Workflow/Editor/services";
 
 export default {
     props: {
@@ -49,61 +49,58 @@ export default {
     methods: {
         loadRecommendations() {
             const toolId = this.getToolId;
-            const url = `${getAppRoot()}api/workflows/get_tool_predictions`;
-            axios
-                .post(url, {
-                    tool_sequence: toolId
-                })
-                .then(response => {
-                    axios.get(`${getAppRoot()}api/datatypes/mapping`).then(responseMapping => {
-                        const predData = response.data.predicted_data;
-                        const datatypesMapping = responseMapping.data;
-                        const extToType = datatypesMapping.ext_to_class_name;
-                        const typeToType = datatypesMapping.class_to_classes;
-                        this.deprecated = predData.is_deprecated;
-                        this.deprecatedMessage = predData.message;
-                        if (response.data !== null && predData.children.length > 0) {
-                            const filteredData = {};
-                            const compatibleTools = {};
-                            const filteredChildren = [];
-                            const outputDatatypes = predData.o_extensions;
-                            const children = predData.children;
-                            for (const nameObj of children.entries()) {
-                                const inputDatatypes = nameObj[1].i_extensions;
-                                for (const outT of outputDatatypes.entries()) {
-                                    for (const inTool of inputDatatypes.entries()) {
-                                        const child = extToType[outT[1]];
-                                        const parent = extToType[inTool[1]];
-                                        if (
-                                            (typeToType[child] && parent in typeToType[child]) === true ||
-                                            outT[1] === "input" ||
-                                            outT[1] === "_sniff_" ||
-                                            outT[1] === "input_collection"
-                                        ) {
-                                            compatibleTools[nameObj[1].tool_id] = nameObj[1].name;
-                                            break;
-                                        }
-                                    }
-                                }
-                            }
-                            for (const id in compatibleTools) {
-                                for (const nameObj of children.entries()) {
-                                    if (nameObj[1].tool_id === id) {
-                                        filteredChildren.push(nameObj[1]);
+            const requestData = {
+                tool_sequence: toolId
+            };
+            getToolPredictions(requestData).then(responsePred => {
+                getDatatypeMapping().then(datatypesMapping => {
+                    const predData = responsePred.predicted_data;
+                    const extToType = datatypesMapping.ext_to_class_name;
+                    const typeToType = datatypesMapping.class_to_classes;
+                    this.deprecated = predData.is_deprecated;
+                    this.deprecatedMessage = predData.message;
+                    if (responsePred !== null && predData.children.length > 0) {
+                        const filteredData = {};
+                        const compatibleTools = {};
+                        const filteredChildren = [];
+                        const outputDatatypes = predData.o_extensions;
+                        const children = predData.children;
+                        for (const nameObj of children.entries()) {
+                            const inputDatatypes = nameObj[1].i_extensions;
+                            for (const outT of outputDatatypes.entries()) {
+                                for (const inTool of inputDatatypes.entries()) {
+                                    const child = extToType[outT[1]];
+                                    const parent = extToType[inTool[1]];
+                                    if (
+                                        (typeToType[child] && parent in typeToType[child]) === true ||
+                                        outT[1] === "input" ||
+                                        outT[1] === "_sniff_" ||
+                                        outT[1] === "input_collection"
+                                    ) {
+                                        compatibleTools[nameObj[1].tool_id] = nameObj[1].name;
                                         break;
                                     }
                                 }
                             }
-                            filteredData.o_extensions = predData.o_extensions;
-                            filteredData.name = predData.name;
-                            filteredData.children = filteredChildren;
-                            if (filteredChildren.length > 0 && this.deprecated === false) {
-                                this.showMessage = true;
-                                this.renderD3Tree(filteredData);
+                        }
+                        for (const id in compatibleTools) {
+                            for (const nameObj of children.entries()) {
+                                if (nameObj[1].tool_id === id) {
+                                    filteredChildren.push(nameObj[1]);
+                                    break;
+                                }
                             }
                         }
-                    });
+                        filteredData.o_extensions = predData.o_extensions;
+                        filteredData.name = predData.name;
+                        filteredData.children = filteredChildren;
+                        if (filteredChildren.length > 0 && this.deprecated === false) {
+                            this.showMessage = true;
+                            this.renderD3Tree(filteredData);
+                        }
+                    }
                 });
+            });
         },
         renderD3Tree(predictedTools) {
             const duration = 750;
diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
index e59c455fd2a7..d4cf7b55b42f 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
@@ -36,9 +36,7 @@
 </template>
 
 <script>
-import { getAppRoot } from "onload/loadConfig";
-import axios from "axios";
-import { getModule } from "./services";
+import { getModule, getToolPredictions } from "./services";
 import _l from "utils/localization";
 
 export default {
@@ -70,40 +68,39 @@ export default {
     computed: {},
     methods: {
         loadRecommendations() {
-            axios
-                .post(`${getAppRoot()}api/workflows/get_tool_predictions`, { tool_sequence: this.toolSequence })
-                .then(response => {
-                    const predictedData = response.data.predicted_data;
-                    const outputDatatypes = predictedData.o_extensions;
-                    const predictedDataChildren = predictedData.children;
-                    const app = this.workflowManager.node.app;
-                    this.isDeprecated = predictedData.is_deprecated;
-                    this.deprecatedMessage = predictedData.message;
-                    if (predictedDataChildren.length > 0) {
-                        const cTools = [];
-                        for (const nameObj of predictedDataChildren.entries()) {
-                            const t = {};
-                            const inputDatatypes = nameObj[1].i_extensions;
-                            for (const outT of outputDatatypes.entries()) {
-                                for (const inTool of inputDatatypes.entries()) {
-                                    if (
-                                        app.isSubType(outT[1], inTool[1]) === true ||
-                                        outT[1] === "input" ||
-                                        outT[1] === "_sniff_" ||
-                                        outT[1] === "input_collection"
-                                    ) {
-                                        t.id = nameObj[1].tool_id;
-                                        t.name = nameObj[1].name;
-                                        cTools.push(t);
-                                        break;
-                                    }
+            const requestData = { tool_sequence: this.toolSequence };
+            getToolPredictions(requestData).then(responsePred => {
+                const predictedData = responsePred.predicted_data;
+                const outputDatatypes = predictedData.o_extensions;
+                const predictedDataChildren = predictedData.children;
+                const app = this.workflowManager.node.app;
+                this.isDeprecated = predictedData.is_deprecated;
+                this.deprecatedMessage = predictedData.message;
+                if (predictedDataChildren.length > 0) {
+                    const cTools = [];
+                    for (const nameObj of predictedDataChildren.entries()) {
+                        const t = {};
+                        const inputDatatypes = nameObj[1].i_extensions;
+                        for (const outT of outputDatatypes.entries()) {
+                            for (const inTool of inputDatatypes.entries()) {
+                                if (
+                                    app.isSubType(outT[1], inTool[1]) === true ||
+                                    outT[1] === "input" ||
+                                    outT[1] === "_sniff_" ||
+                                    outT[1] === "input_collection"
+                                ) {
+                                    t.id = nameObj[1].tool_id;
+                                    t.name = nameObj[1].name;
+                                    cTools.push(t);
+                                    break;
                                 }
                             }
                         }
-                        this.compatibleTools = cTools;
                     }
-                    this.showLoading = false;
-                });
+                    this.compatibleTools = cTools;
+                }
+                this.showLoading = false;
+            });
         },
         closeModal() {
             this.$el.remove();
diff --git a/client/galaxy/scripts/components/Workflow/Editor/services.js b/client/galaxy/scripts/components/Workflow/Editor/services.js
index aeea83c9762e..4c89baa8601e 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/services.js
+++ b/client/galaxy/scripts/components/Workflow/Editor/services.js
@@ -67,3 +67,21 @@ export async function saveWorkflow(workflow, id) {
     }
     return {};
 }
+
+export async function getDatatypeMapping() {
+    try {
+        const mappingRequest = await axios.get(`${getAppRoot()}api/datatypes/mapping`);
+        return mappingRequest.data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}
+
+export async function getToolPredictions(requestData) {
+    try {
+        const response = await axios.post(`${getAppRoot()}api/workflows/get_tool_predictions`, requestData);
+        return response.data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}

From 1a90d85062fc581b7ecfcff9af83dfaf7d69ba40 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 09:41:04 -0400
Subject: [PATCH 628/853] Removing tmate step

---
 .github/workflows/integration.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 7324ef886133..71694ddb289c 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -46,8 +46,6 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v2
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
       working-directory: 'galaxy root'

From 4a68694ab2f17c13cb2b0001ee8000dddcfe7805 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 10:01:25 -0400
Subject: [PATCH 629/853] Only run irds test

---
 .github/workflows/integration.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 71694ddb289c..5759b6712ee2 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         python-version: [3.7]
-        subset: ['upload_datatype']
+        subset: ['upload_datatype_irods']
     services:
       postgres:
         image: postgres:11

From c2f09a3b64dcfc19ab8a12857d2970c7c140dd53 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 10:35:37 -0400
Subject: [PATCH 630/853] Putting tmate back in and renamed a variable

---
 .github/workflows/integration.yaml             | 2 ++
 test/integration/test_datatype_upload_irods.py | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 5759b6712ee2..5a990130a3f8 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -46,6 +46,8 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v2
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
       working-directory: 'galaxy root'
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 014693c3684f..cdbc115caacd 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -15,7 +15,7 @@
 
 
 def start_irods(container_name):
-    minio_start_args = [
+    irods_start_args = [
         'docker',
         'run',
         '-p',
@@ -24,7 +24,7 @@ def start_irods(container_name):
         '--name',
         container_name,
         'kxk302/irods-server:0.1']
-    subprocess.check_call(minio_start_args)
+    subprocess.check_call(irods_start_args)
 
 
 def stop_irods(container_name):

From 047acbc34053e25a81f237b89f271113c0f2252a Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 10:55:39 -0400
Subject: [PATCH 631/853] Usinf version 0.2 of iRODS server, where Postgres
 port is not exposed

---
 test/integration/test_datatype_upload_irods.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index cdbc115caacd..1107f23004cd 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -23,7 +23,7 @@ def start_irods(container_name):
         '-d',
         '--name',
         container_name,
-        'kxk302/irods-server:0.1']
+        'kxk302/irods-server:0.2']
     subprocess.check_call(irods_start_args)
 
 

From 02a564a7daba9f27e48f0b2bc1d5e88d3bb85279 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 11:01:24 -0400
Subject: [PATCH 632/853] REmoved tmate again

---
 .github/workflows/integration.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 5a990130a3f8..5759b6712ee2 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -46,8 +46,6 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v2
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
       working-directory: 'galaxy root'

From c0d7f9ed6b945902e5d2fe8857ab97781d946952 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 11:11:09 -0400
Subject: [PATCH 633/853] Using 0.0.0.0 instead of localhost in irods config
 file

---
 test/integration/irods_object_store_conf.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/irods_object_store_conf.xml b/test/integration/irods_object_store_conf.xml
index 5b78f498fc27..ca54ec6e33c7 100644
--- a/test/integration/irods_object_store_conf.xml
+++ b/test/integration/irods_object_store_conf.xml
@@ -3,7 +3,7 @@
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
-    <connection host="localhost" port="2020"/>
+    <connection host="0.0.0.0" port="2020"/>
     <cache path="database/object_store_cache" size="1000" />
     <extra_dir type="job_work" path="database/job_working_directory_irods"/>
     <extra_dir type="temp" path="database/tmp_irods"/>

From b6c64337c8572539dc1f2dcf58c2f8502a4b2089 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 11:25:32 -0400
Subject: [PATCH 634/853] Using 127.0.0.1 in iRODS config file

---
 test/integration/irods_object_store_conf.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/irods_object_store_conf.xml b/test/integration/irods_object_store_conf.xml
index ca54ec6e33c7..98be2362f357 100644
--- a/test/integration/irods_object_store_conf.xml
+++ b/test/integration/irods_object_store_conf.xml
@@ -3,7 +3,7 @@
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
-    <connection host="0.0.0.0" port="2020"/>
+    <connection host="127.0.0.1" port="2020"/>
     <cache path="database/object_store_cache" size="1000" />
     <extra_dir type="job_work" path="database/job_working_directory_irods"/>
     <extra_dir type="temp" path="database/tmp_irods"/>

From 52686ec3cc0d10d01cff6a521391b3938c3455dd Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 11:35:09 -0400
Subject: [PATCH 635/853] Changed host back to localhost in iRODS config

---
 test/integration/irods_object_store_conf.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/irods_object_store_conf.xml b/test/integration/irods_object_store_conf.xml
index 98be2362f357..5b78f498fc27 100644
--- a/test/integration/irods_object_store_conf.xml
+++ b/test/integration/irods_object_store_conf.xml
@@ -3,7 +3,7 @@
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
-    <connection host="127.0.0.1" port="2020"/>
+    <connection host="localhost" port="2020"/>
     <cache path="database/object_store_cache" size="1000" />
     <extra_dir type="job_work" path="database/job_working_directory_irods"/>
     <extra_dir type="temp" path="database/tmp_irods"/>

From 51b0112f480e67fe15f010177446f32ad61e9d43 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 27 Mar 2020 11:40:31 -0400
Subject: [PATCH 636/853] Do not assume a path should be set to parent

As per suggesion in code review
---
 lib/galaxy/config/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 72a0b463fc48..f2bd533ed910 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -258,7 +258,7 @@ def _in_data_dir(self, path):
         return self._in_dir(self.data_dir, path)
 
     def _in_dir(self, _dir, path):
-        return os.path.join(_dir, path) if path else _dir
+        return os.path.join(_dir, path) if path else None
 
     def _parse_config_file_options(self, defaults, listify_defaults, config_kwargs):
         for var, values in defaults.items():

From 0a047af4720f0eedd794a9083c7e001215fed388 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 11:41:49 -0400
Subject: [PATCH 637/853] Printing IP address of host (GitHub workers) for
 debugging purposes

---
 test/integration/test_datatype_upload_irods.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 1107f23004cd..9cd71dad0d73 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -25,6 +25,8 @@ def start_irods(container_name):
         container_name,
         'kxk302/irods-server:0.2']
     subprocess.check_call(irods_start_args)
+    hostIP = subprocess.check_output(['hostname', '-I'])
+    print('hostIP:', hostIP)
 
 
 def stop_irods(container_name):

From 03d571fc2819327ef918e9f118996aef2a48848c Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 12:10:46 -0400
Subject: [PATCH 638/853] To get more info on IP addresses

---
 test/integration/test_datatype_upload_irods.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 9cd71dad0d73..50618975687f 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -25,7 +25,7 @@ def start_irods(container_name):
         container_name,
         'kxk302/irods-server:0.2']
     subprocess.check_call(irods_start_args)
-    hostIP = subprocess.check_output(['hostname', '-I'])
+    hostIP = subprocess.check_output(['ip', 'a'])
     print('hostIP:', hostIP)
 
 

From 88b8787db6542f1948419434a7436fd5f0deb7d4 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 12:33:06 -0400
Subject: [PATCH 639/853] Directly using worker node's IP address as test

---
 test/integration/irods_object_store_conf.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/irods_object_store_conf.xml b/test/integration/irods_object_store_conf.xml
index 5b78f498fc27..81fd2e18728b 100644
--- a/test/integration/irods_object_store_conf.xml
+++ b/test/integration/irods_object_store_conf.xml
@@ -3,7 +3,7 @@
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
-    <connection host="localhost" port="2020"/>
+    <connection host="10.1.0.4" port="2020"/>
     <cache path="database/object_store_cache" size="1000" />
     <extra_dir type="job_work" path="database/job_working_directory_irods"/>
     <extra_dir type="temp" path="database/tmp_irods"/>

From cdafcc283d45a9e384c11570424e0f2ed8659531 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 12:41:43 -0400
Subject: [PATCH 640/853] Trying another IP address

---
 test/integration/irods_object_store_conf.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/irods_object_store_conf.xml b/test/integration/irods_object_store_conf.xml
index 81fd2e18728b..ec0f12cc3dcf 100644
--- a/test/integration/irods_object_store_conf.xml
+++ b/test/integration/irods_object_store_conf.xml
@@ -3,7 +3,7 @@
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
-    <connection host="10.1.0.4" port="2020"/>
+    <connection host="172.18.0.1" port="2020"/>
     <cache path="database/object_store_cache" size="1000" />
     <extra_dir type="job_work" path="database/job_working_directory_irods"/>
     <extra_dir type="temp" path="database/tmp_irods"/>

From f3cf3fcaaae2dfb2c2e6673915a74cba2dfec3e9 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 12:50:00 -0400
Subject: [PATCH 641/853] One final IP

---
 test/integration/irods_object_store_conf.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/irods_object_store_conf.xml b/test/integration/irods_object_store_conf.xml
index ec0f12cc3dcf..678914b2d27e 100644
--- a/test/integration/irods_object_store_conf.xml
+++ b/test/integration/irods_object_store_conf.xml
@@ -3,7 +3,7 @@
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
-    <connection host="172.18.0.1" port="2020"/>
+    <connection host="172.17.0.1" port="2020"/>
     <cache path="database/object_store_cache" size="1000" />
     <extra_dir type="job_work" path="database/job_working_directory_irods"/>
     <extra_dir type="temp" path="database/tmp_irods"/>

From bc181a668450e8358c0e450b71cf881714ad88ee Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 12:59:04 -0400
Subject: [PATCH 642/853] Switching back to localhost

---
 test/integration/irods_object_store_conf.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/irods_object_store_conf.xml b/test/integration/irods_object_store_conf.xml
index 678914b2d27e..5b78f498fc27 100644
--- a/test/integration/irods_object_store_conf.xml
+++ b/test/integration/irods_object_store_conf.xml
@@ -3,7 +3,7 @@
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
-    <connection host="172.17.0.1" port="2020"/>
+    <connection host="localhost" port="2020"/>
     <cache path="database/object_store_cache" size="1000" />
     <extra_dir type="job_work" path="database/job_working_directory_irods"/>
     <extra_dir type="temp" path="database/tmp_irods"/>

From b469e040ebb39548f0d7e72a45741afd5e56545e Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Fri, 27 Mar 2020 13:18:55 -0400
Subject: [PATCH 643/853] Update integration.yaml

Putting mate back in.
---
 .github/workflows/integration.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 5759b6712ee2..5a990130a3f8 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -46,6 +46,8 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v2
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
       working-directory: 'galaxy root'

From 99c2c1ac21327551365afa407ce30cd7d730c9a1 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 13:56:55 -0400
Subject: [PATCH 644/853] Removed debugging code. Using latest Docker image

---
 test/integration/test_datatype_upload_irods.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 50618975687f..f190bd45269f 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -23,10 +23,8 @@ def start_irods(container_name):
         '-d',
         '--name',
         container_name,
-        'kxk302/irods-server:0.2']
+        'kxk302/irods-server:0.3']
     subprocess.check_call(irods_start_args)
-    hostIP = subprocess.check_output(['ip', 'a'])
-    print('hostIP:', hostIP)
 
 
 def stop_irods(container_name):

From 2937f93870c76ea1bdc04c1738349784021ce502 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Fri, 27 Mar 2020 19:24:27 +0100
Subject: [PATCH 645/853] Fix review comments

---
 .../scripts/components/ToolRecommendation.vue |  2 +-
 .../components/Workflow/Editor/Node.vue       |  9 ++-
 ...onsVue.vue => WorkflowRecommendations.vue} | 61 ++++++++++++++--
 .../Editor/workflowRecommendations.js         | 73 -------------------
 4 files changed, 64 insertions(+), 81 deletions(-)
 rename client/galaxy/scripts/components/Workflow/Editor/{WorkflowRecommendationsVue.vue => WorkflowRecommendations.vue} (66%)
 delete mode 100644 client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 8fa5b0747d45..1e44dcb3308d 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -167,7 +167,7 @@ export default {
                         return d.name;
                     });
                 nodeEnter.append("title").text(d => {
-                    return d.children || d._children ? "Click to collapse" : "Open tool - " + d.name;
+                    return d.children || d._children ? d.name : "Open tool - " + d.name;
                 });
                 // Transition nodes to their new position.
                 const nodeUpdate = node
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 9d0cd6133276..97932e494327 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -47,7 +47,7 @@ import BootstrapVue from "bootstrap-vue";
 import WorkflowIcons from "components/Workflow/icons";
 import LoadingSpan from "components/LoadingSpan";
 import { getGalaxyInstance } from "app";
-import { getToolRecommendations } from "./workflowRecommendations";
+import WorkflowRecommendations from "components/Workflow/Editor/WorkflowRecommendations";
 
 Vue.use(BootstrapVue);
 
@@ -99,7 +99,12 @@ export default {
             this.node.clone();
         },
         onGetRecommendations() {
-            getToolRecommendations(this);
+            const component = Vue.extend(WorkflowRecommendations);
+            const instance = new component({ propsData: { workflowManager: this } });
+            const body = document.getElementsByTagName("body")[0];
+            const vm = document.createElement("div");
+            body.append(vm);
+            instance.$mount(vm);
         }
     }
 };
diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue
similarity index 66%
rename from client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
rename to client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue
index d4cf7b55b42f..8f8e2a4842ea 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendationsVue.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue
@@ -43,9 +43,6 @@ export default {
     props: {
         workflowManager: {
             type: Object
-        },
-        toolSequence: {
-            type: String
         }
     },
     data() {
@@ -65,10 +62,64 @@ export default {
     created() {
         this.loadRecommendations();
     },
-    computed: {},
     methods: {
+        getToolId(toolId) {
+            if (toolId !== undefined && toolId !== null && toolId.indexOf("/") > -1) {
+                const toolIdSlash = toolId.split("/");
+                toolId = toolIdSlash[toolIdSlash.length - 2];
+            }
+            return toolId;
+        },
+        getWorkflowPath(wfSteps, currentNodeId) {
+            const steps = {};
+            const stepNames = {};
+            for (const stpIdx in wfSteps.steps) {
+                const step = wfSteps.steps[stpIdx];
+                const inputConnections = step.input_connections;
+                stepNames[step.id] = this.getToolId(step.content_id);
+                for (const icIdx in inputConnections) {
+                    const ic = inputConnections[icIdx];
+                    if (ic !== null && ic !== undefined) {
+                        const prevConn = [];
+                        for (const conn of ic) {
+                            prevConn.push(conn.id.toString());
+                        }
+                        steps[step.id.toString()] = prevConn;
+                    }
+                }
+            }
+            // recursive call to determine path
+            function readPaths(nodeId, ph) {
+                for (const st in steps) {
+                    if (parseInt(st) === parseInt(nodeId)) {
+                        const parentId = parseInt(steps[st][0]);
+                        if (parentId !== undefined && parentId !== null) {
+                            ph.push(parentId);
+                            if (steps[parentId] !== undefined && steps[parentId] !== null) {
+                                readPaths(parentId, ph);
+                            }
+                        }
+                    }
+                }
+                return ph;
+            }
+            let ph = [];
+            const stepNameList = [];
+            ph.push(currentNodeId);
+            ph = readPaths(currentNodeId, ph);
+            for (const sIdx of ph) {
+                const sName = stepNames[sIdx.toString()];
+                if (sName !== undefined && sName !== null) {
+                    stepNameList.push(sName);
+                }
+            }
+            return stepNameList.join(",");
+        },
         loadRecommendations() {
-            const requestData = { tool_sequence: this.toolSequence };
+            const workflowSimple = this.workflowManager.node.app.to_simple();
+            const node = this.workflowManager.node;
+            const toolSequence = this.getWorkflowPath(workflowSimple, node.id);
+            const requestData = { tool_sequence: toolSequence };
             getToolPredictions(requestData).then(responsePred => {
                 const predictedData = responsePred.predicted_data;
                 const outputDatatypes = predictedData.o_extensions;
diff --git a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js b/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
deleted file mode 100644
index 103909b6ea18..000000000000
--- a/client/galaxy/scripts/components/Workflow/Editor/workflowRecommendations.js
+++ /dev/null
@@ -1,73 +0,0 @@
-import $ from "jquery";
-import Vue from "vue";
-import WorkflowToolRecommendations from "components/Workflow/Editor/WorkflowRecommendationsVue";
-
-function getToolId(toolId) {
-    if (toolId !== undefined && toolId !== null && toolId.indexOf("/") > -1) {
-        const toolIdSlash = toolId.split("/");
-        toolId = toolIdSlash[toolIdSlash.length - 2];
-    }
-    return toolId;
-}
-
-function getWorkflowPath(wfSteps, currentNodeId) {
-    const steps = {};
-    const stepNames = {};
-    for (const stpIdx in wfSteps.steps) {
-        const step = wfSteps.steps[stpIdx];
-        const inputConnections = step.input_connections;
-        stepNames[step.id] = getToolId(step.content_id);
-        for (const icIdx in inputConnections) {
-            const ic = inputConnections[icIdx];
-            if (ic !== null && ic !== undefined) {
-                const prevConn = [];
-                for (const conn of ic) {
-                    prevConn.push(conn.id.toString());
-                }
-                steps[step.id.toString()] = prevConn;
-            }
-        }
-    }
-    // recursive call to determine path
-    function readPaths(nodeId, ph) {
-        for (const st in steps) {
-            if (parseInt(st) === parseInt(nodeId)) {
-                const parentId = parseInt(steps[st][0]);
-                if (parentId !== undefined && parentId !== null) {
-                    ph.push(parentId);
-                    if (steps[parentId] !== undefined && steps[parentId] !== null) {
-                        readPaths(parentId, ph);
-                    }
-                }
-            }
-        }
-        return ph;
-    }
-    let ph = [];
-    const stepNameList = [];
-    ph.push(currentNodeId);
-    ph = readPaths(currentNodeId, ph);
-    for (const sIdx of ph) {
-        const sName = stepNames[sIdx.toString()];
-        if (sName !== undefined && sName !== null) {
-            stepNameList.push(sName);
-        }
-    }
-    return stepNameList.join(",");
-}
-
-export function getToolRecommendations(props) {
-    const workflowSimple = props.node.app.to_simple();
-    const node = props.node;
-    const toolSequence = getWorkflowPath(workflowSimple, node.id);
-    const ToolRecommendationInstance = Vue.extend(WorkflowToolRecommendations);
-    const vm = document.createElement("div");
-    $("body").append(vm);
-    const instance = new ToolRecommendationInstance({
-        propsData: {
-            workflowManager: props,
-            toolSequence: toolSequence
-        }
-    });
-    instance.$mount(vm);
-}

From b9dac3c485e31cad93bae616954c634c66c8bbfd Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 27 Mar 2020 15:28:38 +0000
Subject: [PATCH 646/853] Use osx_startup job to test using Python from a conda
 env

---
 .github/workflows/osx_startup.yaml | 21 ++++++++-------------
 tox.ini                            |  2 +-
 2 files changed, 9 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml
index dfbf85ea7775..f59525e812bd 100644
--- a/.github/workflows/osx_startup.yaml
+++ b/.github/workflows/osx_startup.yaml
@@ -5,29 +5,24 @@ jobs:
   test:
     name: Startup test
     runs-on: macos-latest
-    strategy:
-      matrix:
-        python-version: [3.7]
     steps:
     - uses: actions/checkout@v2
       with:
         path: 'galaxy root'
-    - uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
     - name: Cache pip dir
       uses: actions/cache@v1
       id: pip-cache
       with:
         path: ~/Library/Caches/pip
-        key: pip-cache-osx-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+        # scripts/common_startup.sh creates a conda env for Galaxy containing Python 3.6
+        key: pip-cache-3.6-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Install tox
       run: pip install tox
-    - name: fetch migrations
-      run: |
-        wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite
-        mv db_gx_rev_0141.sqlite database/universe.sqlite
-      working-directory: 'galaxy root'
+    - name: Install and activate miniconda  # use this job to test using Python from a conda environment
+      uses: goanpeca/setup-miniconda@v1
+      with:
+        activate-environment: ''
     - name: run tests
-      run: tox -e py37-first_startup
+      run: tox -e first_startup
+      shell: bash -l {0}  # need this to have CONDA_EXE set
       working-directory: 'galaxy root'
diff --git a/tox.ini b/tox.ini
index 65f753592933..0757e8e992a8 100644
--- a/tox.ini
+++ b/tox.ini
@@ -17,7 +17,7 @@ passenv = CI CONDA_EXE
 setenv =
     first_startup: GALAXY_PYTHON=python
     first_startup: GALAXY_CONFIG_DATABASE_AUTO_MIGRATE=true
-    py{35,36,37}-first_startup: GALAXY_VIRTUAL_ENV=.venv3
+    py{35,36,37,38}-first_startup: GALAXY_VIRTUAL_ENV=.venv3
     unit: GALAXY_VIRTUAL_ENV={envdir}
     unit: GALAXY_ENABLE_BETA_COMPRESSED_GENBANK_SNIFFING=1
     mulled: GALAXY_TEST_INCLUDE_SLOW=1

From a717ee05709ad014ac77e77dbff486cf229763c0 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 27 Mar 2020 15:49:28 -0400
Subject: [PATCH 647/853] Reverting to version 0.1 of irods server.

---
 test/integration/test_datatype_upload_irods.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index f190bd45269f..cdbc115caacd 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -23,7 +23,7 @@ def start_irods(container_name):
         '-d',
         '--name',
         container_name,
-        'kxk302/irods-server:0.3']
+        'kxk302/irods-server:0.1']
     subprocess.check_call(irods_start_args)
 
 

From fbd6abc92edb1e7426d469bb2a1cf86cbcf847a2 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 27 Mar 2020 16:38:25 -0400
Subject: [PATCH 648/853] Display recommendations in popover

---
 .../scripts/components/ToolRecommendation.vue | 62 +++++++--------
 .../components/Workflow/Editor/Node.vue       | 34 ++++----
 .../Editor/WorkflowRecommendations.vue        | 77 ++++++++-----------
 client/galaxy/style/scss/workflow.scss        |  3 +
 4 files changed, 81 insertions(+), 95 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 1e44dcb3308d..e9b8738eb6f1 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -23,14 +23,14 @@ export default {
     props: {
         toolId: {
             type: String,
-            required: true
-        }
+            required: true,
+        },
     },
     data() {
         return {
             deprecated: false,
             deprecatedMessage: "",
-            showMessage: false
+            showMessage: false,
         };
     },
     created() {
@@ -44,16 +44,16 @@ export default {
                 toolId = toolIdSlash[toolIdSlash.length - 2];
             }
             return toolId;
-        }
+        },
     },
     methods: {
         loadRecommendations() {
             const toolId = this.getToolId;
             const requestData = {
-                tool_sequence: toolId
+                tool_sequence: toolId,
             };
-            getToolPredictions(requestData).then(responsePred => {
-                getDatatypeMapping().then(datatypesMapping => {
+            getToolPredictions(requestData).then((responsePred) => {
+                getDatatypeMapping().then((datatypesMapping) => {
                     const predData = responsePred.predicted_data;
                     const extToType = datatypesMapping.ext_to_class_name;
                     const typeToType = datatypesMapping.class_to_classes;
@@ -105,11 +105,7 @@ export default {
         renderD3Tree(predictedTools) {
             const duration = 750;
             const maxTextLength = 20;
-            const svg = d3
-                .select("#tool-recommendation")
-                .append("svg")
-                .attr("class", "tree-size")
-                .append("g");
+            const svg = d3.select("#tool-recommendation").append("svg").attr("class", "tree-size").append("g");
             let i = 0;
             let root = null;
             let translateX = 0;
@@ -125,19 +121,19 @@ export default {
 
             const tree = d3.layout.tree().size([clientH, clientW]);
 
-            const diagonal = d3.svg.diagonal().projection(d => {
+            const diagonal = d3.svg.diagonal().projection((d) => {
                 return [d.y, d.x];
             });
-            const update = source => {
+            const update = (source) => {
                 // Compute the new tree layout.
                 const nodes = tree.nodes(root).reverse();
                 const links = tree.links(nodes);
                 // Normalize for fixed-depth.
-                nodes.forEach(d => {
+                nodes.forEach((d) => {
                     d.y = d.depth * (clientW / 5);
                 });
                 // Update the nodes
-                const node = svg.selectAll("g.node").data(nodes, d => {
+                const node = svg.selectAll("g.node").data(nodes, (d) => {
                     return d.id || (d.id = ++i);
                 });
                 // Enter any new nodes at the parent's previous position.
@@ -145,35 +141,35 @@ export default {
                     .enter()
                     .append("g")
                     .attr("class", "node")
-                    .attr("transform", d => {
+                    .attr("transform", (d) => {
                         return "translate(" + source.y0 + "," + source.x0 + ")";
                     })
                     .on("click", click);
                 nodeEnter.append("circle").attr("r", 1e-6);
                 nodeEnter
                     .append("text")
-                    .attr("x", d => {
+                    .attr("x", (d) => {
                         return d.children || d._children ? -10 : 10;
                     })
                     .attr("dy", ".35em")
-                    .attr("text-anchor", d => {
+                    .attr("text-anchor", (d) => {
                         return d.children || d._children ? "end" : "start";
                     })
-                    .text(d => {
+                    .text((d) => {
                         const tName = d.name;
                         if (tName.length > maxTextLength) {
                             return tName.slice(0, maxTextLength) + "...";
                         }
                         return d.name;
                     });
-                nodeEnter.append("title").text(d => {
+                nodeEnter.append("title").text((d) => {
                     return d.children || d._children ? d.name : "Open tool - " + d.name;
                 });
                 // Transition nodes to their new position.
                 const nodeUpdate = node
                     .transition()
                     .duration(duration)
-                    .attr("transform", d => {
+                    .attr("transform", (d) => {
                         return "translate(" + d.y + "," + d.x + ")";
                     });
                 nodeUpdate.select("circle").attr("r", 3.5);
@@ -181,43 +177,41 @@ export default {
                 node.exit()
                     .transition()
                     .duration(duration)
-                    .attr("transform", d => {
+                    .attr("transform", (d) => {
                         return "translate(" + source.y + "," + source.x + ")";
                     })
                     .remove();
                 // Update the links
-                const link = svg.selectAll("path.link").data(links, d => {
+                const link = svg.selectAll("path.link").data(links, (d) => {
                     return d.target.id;
                 });
                 // Enter any new links at the parent's previous position.
                 link.enter()
                     .insert("path", "g")
                     .attr("class", "link")
-                    .attr("d", d => {
+                    .attr("d", (d) => {
                         const o = { x: source.x0, y: source.y0 };
                         return diagonal({ source: o, target: o });
                     });
                 // Transition links to their new position.
-                link.transition()
-                    .duration(duration)
-                    .attr("d", diagonal);
+                link.transition().duration(duration).attr("d", diagonal);
                 // Transition exiting nodes to the parent's new position.
                 link.exit()
                     .transition()
                     .duration(duration)
-                    .attr("d", d => {
+                    .attr("d", (d) => {
                         const o = { x: source.x, y: source.y };
                         return diagonal({ source: o, target: o });
                     })
                     .remove();
                 // Stash the old positions for transition.
-                nodes.forEach(d => {
+                nodes.forEach((d) => {
                     d.x0 = d.x;
                     d.y0 = d.y;
                 });
             };
             // Toggle children on click.
-            const click = d => {
+            const click = (d) => {
                 if (d.children) {
                     d._children = d.children;
                     d.children = null;
@@ -231,7 +225,7 @@ export default {
                     document.location.href = `${getAppRoot()}tool_runner?tool_id=${tId}`;
                 }
             };
-            const collapse = d => {
+            const collapse = (d) => {
                 if (d.children) {
                     d._children = d.children;
                     d._children.forEach(collapse);
@@ -243,7 +237,7 @@ export default {
             root.y0 = 0;
             root.children.forEach(collapse);
             update(root);
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 97932e494327..d4875c7715b1 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -11,6 +11,7 @@
                 <i class="fa fa-times" />
             </b-button>
             <b-button
+                :id="popoverId"
                 v-if="isEnabled"
                 class="node-recommendations py-0 float-right"
                 variant="primary"
@@ -20,6 +21,9 @@
             >
                 <i class="fa fa-arrow-right" />
             </b-button>
+            <b-popover :target="popoverId" triggers="hover" placement="bottom">
+                <WorkflowRecommendations :node="node" />
+            </b-popover>
             <b-button
                 v-if="canClone"
                 class="node-clone py-0 float-right"
@@ -53,23 +57,26 @@ Vue.use(BootstrapVue);
 
 export default {
     components: {
-        LoadingSpan
+        LoadingSpan,
+        WorkflowRecommendations,
     },
     props: {
         id: {
-            type: String
+            type: String,
+            default: null,
         },
         title: {
             type: String,
-            default: "title"
+            default: "title",
         },
         type: {
             type: String,
-            default: "tool"
+            default: "tool",
         },
         node: {
-            type: Object
-        }
+            type: Object,
+            default: null,
+        },
     },
     computed: {
         iconClass() {
@@ -79,6 +86,9 @@ export default {
             }
             return null;
         },
+        popoverId() {
+            return `popover-${this.id}`;
+        },
         canClone() {
             return this.type != "subworkflow";
         },
@@ -89,7 +99,7 @@ export default {
                 return true;
             }
             return false;
-        }
+        },
     },
     methods: {
         onDestroy() {
@@ -98,14 +108,6 @@ export default {
         onClone() {
             this.node.clone();
         },
-        onGetRecommendations() {
-            const component = Vue.extend(WorkflowRecommendations);
-            const instance = new component({ propsData: { workflowManager: this } });
-            const body = document.getElementsByTagName("body")[0];
-            const vm = document.createElement("div");
-            body.append(vm);
-            instance.$mount(vm);
-        }
-    }
+    },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue
index 8f8e2a4842ea..5afc14f3af07 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue
@@ -1,49 +1,37 @@
 <template>
-    <div class="modal ui-modal wf-recommendation-view">
-        <div class="modal-backdrop fade in"></div>
-        <div class="modal-dialog wf-tools-dialog">
-            <div class="modal-content wf-tool-content">
-                <div class="modal-header wf-tools-background" :title="modalHeaderToolTip">
-                    <h4>{{ modalHeaderTitle }}</h4>
-                </div>
-                <div class="modal-body wf-tools-body">
-                    <div v-if="showLoading">
-                        {{ loadingMessage }}
-                    </div>
-                    <div v-if="compatibleTools.length > 0 && !isDeprecated">
-                        <div v-for="tool in compatibleTools" :key="tool.id">
-                            <i class="fa mr-1 fa-wrench"></i>
-                            <a href="#" title="Open tool" :id="tool.id" v-on:click="createTool(tool.id)">
-                                {{ tool.name }}
-                            </a>
-                        </div>
-                    </div>
-                    <div v-else-if="isDeprecated">
-                        {{ deprecatedMessage }}
-                    </div>
-                    <div v-if="compatibleTools.length === 0 && !showLoading">
-                        {{ noRecommendationsMessage }}
-                    </div>
-                </div>
-                <div class="modal-footer">
-                    <div class="buttons">
-                        <button v-on:click="closeModal" title="Cancel" class="wf-tools-background">Cancel</button>
-                    </div>
-                </div>
+    <div class="workflow-recommendations">
+        <LoadingSpan v-if="showLoading" message="Loading recommendations" />
+        <div v-if="compatibleTools.length > 0 && !isDeprecated">
+            <div v-for="tool in compatibleTools" :key="tool.id">
+                <i class="fa mr-1 fa-wrench"></i>
+                <a href="#" title="Open tool" :id="tool.id" @click="createTool(tool.id)">
+                    {{ tool.name }}
+                </a>
             </div>
         </div>
+        <div v-else-if="isDeprecated">
+            {{ deprecatedMessage }}
+        </div>
+        <div v-if="compatibleTools.length === 0 && !showLoading">
+            {{ noRecommendationsMessage }}
+        </div>
     </div>
 </template>
 
 <script>
 import { getModule, getToolPredictions } from "./services";
+import LoadingSpan from "components/LoadingSpan";
 import _l from "utils/localization";
 
 export default {
+    components: {
+        LoadingSpan,
+    },
     props: {
-        workflowManager: {
-            type: Object
-        }
+        node: {
+            type: Object,
+            required: true,
+        },
     },
     data() {
         return {
@@ -55,8 +43,7 @@ export default {
             isDeprecated: false,
             noRecommendationsMessage: _l("No tool recommendations"),
             deprecatedMessage: "",
-            loadingMessage: _l("Loading recommendations ..."),
-            showLoading: true
+            showLoading: true,
         };
     },
     created() {
@@ -116,15 +103,15 @@ export default {
             return stepNameList.join(",");
         },
         loadRecommendations() {
-            const workflowSimple = this.workflowManager.node.app.to_simple();
-            const node = this.workflowManager.node;
+            const workflowSimple = this.node.app.to_simple();
+            const node = this.node;
             const toolSequence = this.getWorkflowPath(workflowSimple, node.id);
             const requestData = { tool_sequence: toolSequence };
-            getToolPredictions(requestData).then(responsePred => {
+            getToolPredictions(requestData).then((responsePred) => {
                 const predictedData = responsePred.predicted_data;
                 const outputDatatypes = predictedData.o_extensions;
                 const predictedDataChildren = predictedData.children;
-                const app = this.workflowManager.node.app;
+                const app = this.node.app;
                 this.isDeprecated = predictedData.is_deprecated;
                 this.deprecatedMessage = predictedData.message;
                 if (predictedDataChildren.length > 0) {
@@ -157,18 +144,18 @@ export default {
             this.$el.remove();
         },
         createTool(tId) {
-            const app = this.workflowManager.node.app;
+            const app = this.node.app;
             const requestData = {
                 type: "tool",
                 tool_id: tId,
-                _: "true"
+                _: "true",
             };
-            getModule(requestData).then(response => {
+            getModule(requestData).then((response) => {
                 const node = app.create_node("tool", response.name, tId);
                 app.set_node(node, response);
                 this.closeModal();
             });
-        }
-    }
+        },
+    },
 };
 </script>
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index b89ca0bc69e7..b4ecd68b8545 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -7,6 +7,9 @@
         display: flex;
         flex-direction: column;
         flex-grow: 1;
+        .workflow-recommendations {
+            height: 30rem;
+        }
         .workflow-node {
             @extend .card;
             @extend .position-absolute;

From e6ef67047717b6b27c4cbaacb5a85925fd9a322d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 27 Mar 2020 17:54:16 -0400
Subject: [PATCH 649/853] Move recommended node creation to node component

---
 .../components/Workflow/Editor/Node.vue       | 20 +++++++++++++--
 .../Editor/WorkflowRecommendations.vue        | 25 ++-----------------
 2 files changed, 20 insertions(+), 25 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index d4875c7715b1..34668cdea523 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -17,12 +17,11 @@
                 variant="primary"
                 size="sm"
                 aria-label="tool recommendations"
-                @click="onGetRecommendations"
             >
                 <i class="fa fa-arrow-right" />
             </b-button>
             <b-popover :target="popoverId" triggers="hover" placement="bottom">
-                <WorkflowRecommendations :node="node" />
+                <WorkflowRecommendations :node="node" @onCreate="onCreate" />
             </b-popover>
             <b-button
                 v-if="canClone"
@@ -49,6 +48,7 @@
 import Vue from "vue";
 import BootstrapVue from "bootstrap-vue";
 import WorkflowIcons from "components/Workflow/icons";
+import { getModule } from "./services";
 import LoadingSpan from "components/LoadingSpan";
 import { getGalaxyInstance } from "app";
 import WorkflowRecommendations from "components/Workflow/Editor/WorkflowRecommendations";
@@ -60,6 +60,11 @@ export default {
         LoadingSpan,
         WorkflowRecommendations,
     },
+    data() {
+        return {
+            popoverShow: false,
+        };
+    },
     props: {
         id: {
             type: String,
@@ -108,6 +113,17 @@ export default {
         onClone() {
             this.node.clone();
         },
+        onCreate(toolId) {
+            const requestData = {
+                tool_id: toolId,
+                type: "tool",
+                _: "true",
+            };
+            getModule(requestData).then((response) => {
+                var node = this.node.app.create_node("tool", response.name, toolId);
+                this.node.app.set_node(node, response);
+            });
+        },
     },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue
index 5afc14f3af07..7c125f73c0a9 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue
@@ -3,8 +3,7 @@
         <LoadingSpan v-if="showLoading" message="Loading recommendations" />
         <div v-if="compatibleTools.length > 0 && !isDeprecated">
             <div v-for="tool in compatibleTools" :key="tool.id">
-                <i class="fa mr-1 fa-wrench"></i>
-                <a href="#" title="Open tool" :id="tool.id" @click="createTool(tool.id)">
+                <a href="#" title="Open tool" :id="tool.id" @click="$emit('onCreate', tool.id)">
                     {{ tool.name }}
                 </a>
             </div>
@@ -19,7 +18,7 @@
 </template>
 
 <script>
-import { getModule, getToolPredictions } from "./services";
+import { getToolPredictions } from "./services";
 import LoadingSpan from "components/LoadingSpan";
 import _l from "utils/localization";
 
@@ -35,10 +34,6 @@ export default {
     },
     data() {
         return {
-            modalHeaderTitle: _l("Tool Recommendations"),
-            modalHeaderToolTip: _l(
-                "The recommended tools are shown in the decreasing order of their scores predicted using machine learning analysis on workflows. A tool with a higher score (closer to 100%) may fit better as the following tool than a tool with a lower score. Please click on one of the following/recommended tools to have it on the workflow editor."
-            ),
             compatibleTools: [],
             isDeprecated: false,
             noRecommendationsMessage: _l("No tool recommendations"),
@@ -140,22 +135,6 @@ export default {
                 this.showLoading = false;
             });
         },
-        closeModal() {
-            this.$el.remove();
-        },
-        createTool(tId) {
-            const app = this.node.app;
-            const requestData = {
-                type: "tool",
-                tool_id: tId,
-                _: "true",
-            };
-            getModule(requestData).then((response) => {
-                const node = app.create_node("tool", response.name, tId);
-                app.set_node(node, response);
-                this.closeModal();
-            });
-        },
     },
 };
 </script>

From 5de2fa57e585f5deb6608e06bef942aa9ef310f1 Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Sat, 28 Mar 2020 08:06:39 -0400
Subject: [PATCH 650/853] Update integration.yaml

Tmate broken again.
---
 .github/workflows/integration.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 5a990130a3f8..5759b6712ee2 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -46,8 +46,6 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v2
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
       working-directory: 'galaxy root'

From edfe9dcbeb4650c135075a7e929b08c055aa4093 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 12 Mar 2020 18:10:20 +0000
Subject: [PATCH 651/853] Drop remaining Python 2.7 CircleCI tests

---
 .circleci/config.yml | 38 +++-----------------------------------
 1 file changed, 3 insertions(+), 35 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 3afbbc0bb985..b83111cc5753 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -81,23 +81,6 @@ jobs:
           key: v1-repo-{{ .Environment.CIRCLE_SHA1 }}
           paths:
             - ~/repo
-  py27_lint:
-    docker:
-      - image: circleci/python:2.7
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      - *install_tox
-      - run: tox -e py27-lint
-  py27_unit:
-    docker:
-      - image: circleci/python:2.7
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      # Ensure minimum virtualenv version due to https://github.com/pypa/virtualenv/issues/1670
-      - run: sudo pip install tox 'virtualenv>=20.0.8'
-      - run: tox -e py27-unit
   py35_docstring:
     docker:
       - image: circleci/python:3.5
@@ -106,14 +89,6 @@ jobs:
       - *restore_repo_cache
       - *install_tox
       - run: tox -e py35-lint_docstring_include_list
-  py27_first_startup:
-    docker:
-      - image: circleci/python:2.7
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      - *install_tox
-      - run: tox -e py27-first_startup
   py35_lint:
     docker:
       - image: circleci/python:3.5
@@ -136,10 +111,9 @@ jobs:
     <<: *set_workdir
     steps:
       - *restore_repo_cache
-      - run: sh scripts/common_startup.sh
-      - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite
-      - run: mv db_gx_rev_0127.sqlite database/universe.sqlite
-      - run: sh manage_db.sh -c ./config/galaxy.yml.sample upgrade
+      # Use this job to test the latest migrations
+      - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite
+      - run: mv db_gx_rev_0141.sqlite database/universe.sqlite
       - *install_tox
       - run: tox -e py35-first_startup
   validate_test_tools:
@@ -195,12 +169,6 @@ workflows:
   get_code_and_test:
     jobs:
       - get_code
-      - py27_lint:
-          <<: *requires_get_code
-      - py27_unit:
-          <<: *requires_get_code
-      - py27_first_startup:
-          <<: *requires_get_code
       - py35_docstring:
           <<: *requires_get_code
       - py35_lint:

From e7c0bdbcf1a9b0125822846554bedb114e85dfaa Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Sat, 28 Mar 2020 20:01:55 +0100
Subject: [PATCH 652/853] Remove percentage from predictions

---
 lib/galaxy/tools/recommendations.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/recommendations.py b/lib/galaxy/tools/recommendations.py
index c8df15f36a76..1b13547976b9 100644
--- a/lib/galaxy/tools/recommendations.py
+++ b/lib/galaxy/tools/recommendations.py
@@ -144,7 +144,7 @@ def filter_tool_predictions(self, trans, prediction_data, tool_ids, tool_scores,
                 if t_id == child and score > 0.0 and child in last_compatible_tools and child not in self.deprecated_tools:
                     full_tool_id = self.all_tools[t_id][0]
                     pred_input_extensions, _ = self.get_tool_extensions(trans, full_tool_id)
-                    c_dict["name"] = self.all_tools[t_id][1] + " (" + str(score) + "%)"
+                    c_dict["name"] = self.all_tools[t_id][1]
                     c_dict["tool_id"] = full_tool_id
                     c_dict["i_extensions"] = list(set(pred_input_extensions))
                     prediction_data["children"].append(c_dict)

From 8032d3e6632731807288e6ecfea4a4fb75589316 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Sun, 29 Mar 2020 19:25:28 +0200
Subject: [PATCH 653/853] fix > 20 tools, styles and filename

---
 .../scripts/components/ToolRecommendation.vue | 21 +++++++++----------
 .../components/Workflow/Editor/Node.vue       |  4 ++--
 ...ecommendations.vue => Recommendations.vue} |  0
 client/galaxy/style/scss/base.scss            |  6 ++++--
 4 files changed, 16 insertions(+), 15 deletions(-)
 rename client/galaxy/scripts/components/Workflow/Editor/{WorkflowRecommendations.vue => Recommendations.vue} (100%)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index e9b8738eb6f1..9af78aa2d57c 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -1,5 +1,5 @@
 <template>
-    <div id="tool-recommendation" class="tool-recommendation-view">
+    <div>
         <div v-if="!deprecated && showMessage" class="infomessagelarge">
             <h4>Tool recommendation</h4>
             You have used {{ getToolId }} tool. For further analysis, you could try using the following/recommended
@@ -11,6 +11,8 @@
         <div v-else-if="deprecated" class="warningmessagelarge">
             You have used {{ getToolId }} tool. {{ deprecatedMessage }}
         </div>
+        <div id="tool-recommendation" class="tool-recommendation-view">
+        </div>
     </div>
 </template>
 
@@ -103,24 +105,21 @@ export default {
             });
         },
         renderD3Tree(predictedTools) {
+            let i = 0;
+            let root = null;
             const duration = 750;
             const maxTextLength = 20;
             const svg = d3.select("#tool-recommendation").append("svg").attr("class", "tree-size").append("g");
-            let i = 0;
-            let root = null;
-            let translateX = 0;
-
             const gElem = svg[0][0];
             const svgElem = gElem.parentNode;
             const clientH = svgElem.clientHeight;
             const clientW = svgElem.clientWidth;
-            translateX = parseInt(clientW * 0.33);
+            const translateX = parseInt(clientW * 0.15);
 
-            svgElem.setAttribute("viewBox", -translateX + " 0 " + clientW + " " + clientH);
+            svgElem.setAttribute("viewBox", -translateX +  " 0 " + (0.5 * clientW) + " " + clientH);
             svgElem.setAttribute("preserveAspectRatio", "xMidYMid meet");
 
             const tree = d3.layout.tree().size([clientH, clientW]);
-
             const diagonal = d3.svg.diagonal().projection((d) => {
                 return [d.y, d.x];
             });
@@ -130,7 +129,7 @@ export default {
                 const links = tree.links(nodes);
                 // Normalize for fixed-depth.
                 nodes.forEach((d) => {
-                    d.y = d.depth * (clientW / 5);
+                    d.y = d.depth * (clientW / 10);
                 });
                 // Update the nodes
                 const node = svg.selectAll("g.node").data(nodes, (d) => {
@@ -172,7 +171,7 @@ export default {
                     .attr("transform", (d) => {
                         return "translate(" + d.y + "," + d.x + ")";
                     });
-                nodeUpdate.select("circle").attr("r", 3.5);
+                nodeUpdate.select("circle").attr("r", 2.5);
                 // Transition exiting nodes to the parent's new position.
                 node.exit()
                     .transition()
@@ -233,7 +232,7 @@ export default {
                 }
             };
             root = predictedTools;
-            root.x0 = clientH / 2;
+            root.x0 = parseInt(clientH / 2);
             root.y0 = 0;
             root.children.forEach(collapse);
             update(root);
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 34668cdea523..5a915cb87c06 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -51,7 +51,7 @@ import WorkflowIcons from "components/Workflow/icons";
 import { getModule } from "./services";
 import LoadingSpan from "components/LoadingSpan";
 import { getGalaxyInstance } from "app";
-import WorkflowRecommendations from "components/Workflow/Editor/WorkflowRecommendations";
+import WorkflowRecommendations from "components/Workflow/Editor/Recommendations";
 
 Vue.use(BootstrapVue);
 
@@ -100,7 +100,7 @@ export default {
         isEnabled() {
             const Galaxy = getGalaxyInstance();
             const isRecommendationEnabled = Galaxy.config.enable_tool_recommendations;
-            if (isRecommendationEnabled === true || isRecommendationEnabled === "true") {
+            if (isRecommendationEnabled === true) {
                 return true;
             }
             return false;
diff --git a/client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue b/client/galaxy/scripts/components/Workflow/Editor/Recommendations.vue
similarity index 100%
rename from client/galaxy/scripts/components/Workflow/Editor/WorkflowRecommendations.vue
rename to client/galaxy/scripts/components/Workflow/Editor/Recommendations.vue
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index 1710cbf181fd..bec0cac56980 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1659,17 +1659,19 @@ body.reports {
             fill: $brand-primary;
             stroke: $brand-primary;
         }
+        text {
+            font-size: 0.4rem;
+        }
     }
 
     .tree-size {
         width: 100%;
-        height: 50%;
     }
 
     .link {
         fill: none;
         stroke: $brand-primary;
-        stroke-width: 4;
+        stroke-width: 1;
     }
 }
 

From 6d6eade6f83364b5c641d1dcbf06c5041601f671 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 30 Mar 2020 00:13:02 +0200
Subject: [PATCH 654/853] Fix prettier

---
 client/galaxy/scripts/components/ToolRecommendation.vue | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/components/ToolRecommendation.vue b/client/galaxy/scripts/components/ToolRecommendation.vue
index 9af78aa2d57c..3e26c55e4fac 100644
--- a/client/galaxy/scripts/components/ToolRecommendation.vue
+++ b/client/galaxy/scripts/components/ToolRecommendation.vue
@@ -11,8 +11,7 @@
         <div v-else-if="deprecated" class="warningmessagelarge">
             You have used {{ getToolId }} tool. {{ deprecatedMessage }}
         </div>
-        <div id="tool-recommendation" class="tool-recommendation-view">
-        </div>
+        <div id="tool-recommendation" class="tool-recommendation-view"></div>
     </div>
 </template>
 
@@ -116,7 +115,7 @@ export default {
             const clientW = svgElem.clientWidth;
             const translateX = parseInt(clientW * 0.15);
 
-            svgElem.setAttribute("viewBox", -translateX +  " 0 " + (0.5 * clientW) + " " + clientH);
+            svgElem.setAttribute("viewBox", -translateX + " 0 " + 0.5 * clientW + " " + clientH);
             svgElem.setAttribute("preserveAspectRatio", "xMidYMid meet");
 
             const tree = d3.layout.tree().size([clientH, clientW]);

From e158231becb7b37e16829bdd73e5a74fc56d1f01 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 30 Mar 2020 00:14:53 +0200
Subject: [PATCH 655/853] Add header to popover

---
 client/galaxy/style/scss/base.scss | 18 ++++--------------
 1 file changed, 4 insertions(+), 14 deletions(-)

diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index bec0cac56980..8c0502e238fb 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -1675,20 +1675,10 @@ body.reports {
     }
 }
 
-.wf-recommendation-view {
+.workflow-recommendations {
     display: block;
-    .wf-tools-dialog {
-        width: 20%;
-    }
-    .wf-tools-body {
-        overflow: auto;
-        height: 50%;
-    }
-    .wf-tools-background {
-        background: $brand-primary;
-        color: $white;
-    }
-    .wf-tool-content {
-        border: solid 1px $brand-primary;
+    .header-background {
+        border-bottom: solid 1px $brand-primary;
+        margin-bottom: 0.5rem;
     }
 }

From 20f52f2a10d12924b8af294309acdc2911bf7c0a Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 30 Mar 2020 01:16:56 +0200
Subject: [PATCH 656/853] Add event

---
 client/galaxy/scripts/components/Workflow/Editor/Node.vue  | 5 ++++-
 .../scripts/components/Workflow/Editor/Recommendations.vue | 7 ++++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 5a915cb87c06..800730641be9 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -113,7 +113,9 @@ export default {
         onClone() {
             this.node.clone();
         },
-        onCreate(toolId) {
+        onCreate(toolId, event) {
+            console.log(toolId);
+            console.log(event);
             const requestData = {
                 tool_id: toolId,
                 type: "tool",
@@ -122,6 +124,7 @@ export default {
             getModule(requestData).then((response) => {
                 var node = this.node.app.create_node("tool", response.name, toolId);
                 this.node.app.set_node(node, response);
+                event.srcElement.getRootNode().remove();
             });
         },
     },
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Recommendations.vue b/client/galaxy/scripts/components/Workflow/Editor/Recommendations.vue
index 7c125f73c0a9..8f32d4492ae8 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Recommendations.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Recommendations.vue
@@ -1,9 +1,13 @@
 <template>
     <div class="workflow-recommendations">
+        <div class="header-background">
+            <h4> {{ popoverHeaderText }} </h4>
+        </div>
         <LoadingSpan v-if="showLoading" message="Loading recommendations" />
         <div v-if="compatibleTools.length > 0 && !isDeprecated">
             <div v-for="tool in compatibleTools" :key="tool.id">
-                <a href="#" title="Open tool" :id="tool.id" @click="$emit('onCreate', tool.id)">
+                <i class="fa mr-1 fa-wrench"></i>
+                <a href="#" title="Open tool" :id="tool.id" @click="$emit('onCreate', tool.id, $event)">
                     {{ tool.name }}
                 </a>
             </div>
@@ -36,6 +40,7 @@ export default {
         return {
             compatibleTools: [],
             isDeprecated: false,
+            popoverHeaderText: _l("Tool recommendations"),
             noRecommendationsMessage: _l("No tool recommendations"),
             deprecatedMessage: "",
             showLoading: true,

From 804dbaf7fdaa6c8a49af414d6199776d21fbfd03 Mon Sep 17 00:00:00 2001
From: Juan David Mendez Solano <juan.mendez@imtek.uni-freiburg.de>
Date: Mon, 30 Mar 2020 10:33:51 +0200
Subject: [PATCH 657/853] Creates a random password and checks that its not the
 same as default. Change the _get_random_password method to use all ASCII
 letters

---
 lib/galaxy/selenium/navigates_galaxy.py          | 5 ++++-
 lib/galaxy_test/selenium/test_change_password.py | 3 ++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index e9359560aa5c..aef773816718 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -389,8 +389,11 @@ def _get_random_email(self, username=None, domain=None):
         domain = domain or 'test.test'
         return self._get_random_name(prefix=username, suffix="@" + domain)
 
+    # Creates a random password of length len by creating an array with all ASCII letters and the numbers 0 to 9,
+    # then using the random number generator to pick one elemenent to concatinate it to the end of the password string until
+    # we have a password of length len.
     def _get_random_password(self, len=6):
-        return ''.join(random.SystemRandom().choice(string.ascii_uppercase + string.digits) for _ in range(len))
+        return ''.join(random.SystemRandom().choice(string.ascii_letters + string.digits) for _ in range(len))
 
     def submit_login(self, email, password=None, assert_valid=True, retries=0):
         if password is None:
diff --git a/lib/galaxy_test/selenium/test_change_password.py b/lib/galaxy_test/selenium/test_change_password.py
index c7bbedeef6e0..b8bc92578b61 100644
--- a/lib/galaxy_test/selenium/test_change_password.py
+++ b/lib/galaxy_test/selenium/test_change_password.py
@@ -36,7 +36,8 @@ def test_no_password_confirmation(self):
     def test_currect_password_incorrect(self):
         self.register_and_change_password()
         password = self._get_random_password()
-        self.fill_input_fields("4444444", password, password)
+        assert self.default_password != password
+        self.fill_input_fields(password, password, password)
         self.assert_error_message(contains='Invalid current password.')
 
     @selenium_test

From 28e70998f6cb4bf25f4127781f2261ffee533bfd Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 30 Mar 2020 12:08:04 +0200
Subject: [PATCH 658/853] Fix duplicate popover ids and close when clicked

---
 client/galaxy/scripts/components/Workflow/Editor/Node.vue | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 800730641be9..e89486d010a4 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -20,7 +20,7 @@
             >
                 <i class="fa fa-arrow-right" />
             </b-button>
-            <b-popover :target="popoverId" triggers="hover" placement="bottom">
+            <b-popover :target="popoverId" triggers="hover" placement="bottom" :show.sync="popoverShow">
                 <WorkflowRecommendations :node="node" @onCreate="onCreate" />
             </b-popover>
             <b-button
@@ -92,7 +92,7 @@ export default {
             return null;
         },
         popoverId() {
-            return `popover-${this.id}`;
+            return `popover-${this.id}-${this._uid}`;
         },
         canClone() {
             return this.type != "subworkflow";
@@ -114,8 +114,6 @@ export default {
             this.node.clone();
         },
         onCreate(toolId, event) {
-            console.log(toolId);
-            console.log(event);
             const requestData = {
                 tool_id: toolId,
                 type: "tool",
@@ -124,7 +122,7 @@ export default {
             getModule(requestData).then((response) => {
                 var node = this.node.app.create_node("tool", response.name, toolId);
                 this.node.app.set_node(node, response);
-                event.srcElement.getRootNode().remove();
+                this.popoverShow = false;
             });
         },
     },

From 3e7ae99d9c50be898969bd640f0fd75ad0fc7724 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 30 Mar 2020 13:06:14 +0200
Subject: [PATCH 659/853] Fix prettier

---
 .../scripts/components/Workflow/Editor/Recommendations.vue      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Recommendations.vue b/client/galaxy/scripts/components/Workflow/Editor/Recommendations.vue
index 8f32d4492ae8..fa51a3293308 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Recommendations.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Recommendations.vue
@@ -1,7 +1,7 @@
 <template>
     <div class="workflow-recommendations">
         <div class="header-background">
-            <h4> {{ popoverHeaderText }} </h4>
+            <h4>{{ popoverHeaderText }}</h4>
         </div>
         <LoadingSpan v-if="showLoading" message="Loading recommendations" />
         <div v-if="compatibleTools.length > 0 && !isDeprecated">

From 934ff35782823e041be6af49f15c44ffd2b541ed Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 30 Mar 2020 09:30:44 -0400
Subject: [PATCH 660/853] Update integration.yaml

---
 .github/workflows/integration.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 5759b6712ee2..5a990130a3f8 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -46,6 +46,8 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v2
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
       working-directory: 'galaxy root'

From 2b57b8772fdc3fefb8f3a190eaa5478945160285 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 30 Mar 2020 16:10:11 +0200
Subject: [PATCH 661/853] Catch exceptions

---
 lib/galaxy/tools/recommendations.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/recommendations.py b/lib/galaxy/tools/recommendations.py
index 1b13547976b9..1943dbb66d39 100644
--- a/lib/galaxy/tools/recommendations.py
+++ b/lib/galaxy/tools/recommendations.py
@@ -196,10 +196,18 @@ def compute_tool_prediction(self, trans, tool_sequence):
             for idx, tool_name in enumerate(tool_sequence):
                 if tool_name.find("/") > -1:
                     tool_name = tool_name.split("/")[-2]
-                sample[idx] = int(self.model_data_dictionary[tool_name])
+                try:
+                    sample[idx] = int(self.model_data_dictionary[tool_name])
+                except Exception:
+                    log.exception("Failed to find tool %s in model" % (tool_name))
+                    return prediction_data
             sample = np.reshape(sample, (1, max_seq_len))
             # predict next tools for a test path
-            prediction = self.loaded_model.predict(sample, verbose=0)
+            try:
+                prediction = self.loaded_model.predict_on_batch(sample)
+            except Exception as e:
+                log.exception(e)
+                return prediction_data
             prediction = np.reshape(prediction, (prediction.shape[1],))
             # boost the predicted scores using tools' usage
             weight_values = list(self.tool_weights_sorted.values())

From 3e5ff244ca017ec993ad417cc0be6c04d4a8cb2b Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 30 Mar 2020 11:08:52 -0400
Subject: [PATCH 662/853] Update integration.yaml

---
 .github/workflows/integration.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 5a990130a3f8..5759b6712ee2 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -46,8 +46,6 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v2
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
       working-directory: 'galaxy root'

From bd7da0b6cfd5ef7d1dce133daa1972182ff7b399 Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 30 Mar 2020 11:40:19 -0400
Subject: [PATCH 663/853] Update integration.yaml

---
 .github/workflows/integration.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 5759b6712ee2..e4641615abd0 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -49,3 +49,5 @@ jobs:
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
       working-directory: 'galaxy root'
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v2

From fa87cd0801f7af3e505889ed88a9fd9060794c17 Mon Sep 17 00:00:00 2001
From: Juan David Mendez Solano <mendezj@tf.uni-freiburg.de>
Date: Mon, 30 Mar 2020 17:54:06 +0200
Subject: [PATCH 664/853] Possible example of errors not showing

---
 lib/galaxy/selenium/navigation.yml        |  5 +++++
 lib/galaxy_test/selenium/test_sign_out.py | 17 ++++++++++++-----
 2 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index 9e4b125817fb..9ade81de4a29 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -89,6 +89,11 @@ change_user_address:
       type: xpath
       selector: '//span[contains(text(), "Insert Address")]'
 
+sign_out:
+  selectors:
+    cancel_button: '.modal-footer .buttons #button-0'
+    sign_out_button: '.modal-footer .buttons #button-0'
+
 history_panel:
   menu:
     labels:
diff --git a/lib/galaxy_test/selenium/test_sign_out.py b/lib/galaxy_test/selenium/test_sign_out.py
index 9a160bef9ac6..1fecc571f85e 100644
--- a/lib/galaxy_test/selenium/test_sign_out.py
+++ b/lib/galaxy_test/selenium/test_sign_out.py
@@ -1,3 +1,4 @@
+import time
 from .framework import (
     selenium_test,
     SeleniumTestCase
@@ -12,11 +13,17 @@ def test_sign_out(self):
         self.click_masthead_user()
         self.components.masthead.preferences.wait_for_and_click()
         self.components.preferences.sign_out.wait_for_and_click()
-        cancel_button = self.driver.find_element_by_xpath("//button[@id='button-0']")
-        cancel_button.click()
+        #Testing of the cancel button
+        time.sleep(5)
+        self.components.sign_out.cancel_button.wait_for_and_click()
+        time.sleep(10) #Giving time to click cancel and go back to user preferences (not happening, and no error)
         assert self.is_logged_in()
         new_email = self.driver.find_element_by_id("user-preferences-current-email").text
         self.assertTrue(email == new_email)
-        signout_button = self.driver.find_element_by_xpath("//button[@id='button-1']")
-        signout_button.click()
-        assert not self.is_logged_in()
+        #Testing of the sign out button
+        self.components.preferences.sign_out.wait_for_and_click()
+        time.sleep(5)
+        self.components.sign_out.sign_out_button.wait_for_and_click()
+        time.sleep(10) # Enough time to see a log out screen and redirection
+        # assert not self.is_logged_in() # Error only shows here, but should had been trigger in line 17
+        time.sleep(5)
\ No newline at end of file

From 2e31db8b49c27a74a8dbc1bb3bd56a899b985d9c Mon Sep 17 00:00:00 2001
From: Juan David Mendez Solano <mendezj@tf.uni-freiburg.de>
Date: Mon, 30 Mar 2020 18:34:41 +0200
Subject: [PATCH 665/853] Implementation of the Sign out from user preference
 selenium test

---
 lib/galaxy/selenium/navigation.yml        |  2 +-
 lib/galaxy_test/selenium/test_sign_out.py | 10 +---------
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index 9ade81de4a29..859250ea708a 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -92,7 +92,7 @@ change_user_address:
 sign_out:
   selectors:
     cancel_button: '.modal-footer .buttons #button-0'
-    sign_out_button: '.modal-footer .buttons #button-0'
+    sign_out_button: '.modal-footer .buttons #button-1'
 
 history_panel:
   menu:
diff --git a/lib/galaxy_test/selenium/test_sign_out.py b/lib/galaxy_test/selenium/test_sign_out.py
index 1fecc571f85e..928c61d23c12 100644
--- a/lib/galaxy_test/selenium/test_sign_out.py
+++ b/lib/galaxy_test/selenium/test_sign_out.py
@@ -1,4 +1,3 @@
-import time
 from .framework import (
     selenium_test,
     SeleniumTestCase
@@ -13,17 +12,10 @@ def test_sign_out(self):
         self.click_masthead_user()
         self.components.masthead.preferences.wait_for_and_click()
         self.components.preferences.sign_out.wait_for_and_click()
-        #Testing of the cancel button
-        time.sleep(5)
         self.components.sign_out.cancel_button.wait_for_and_click()
-        time.sleep(10) #Giving time to click cancel and go back to user preferences (not happening, and no error)
         assert self.is_logged_in()
         new_email = self.driver.find_element_by_id("user-preferences-current-email").text
         self.assertTrue(email == new_email)
-        #Testing of the sign out button
         self.components.preferences.sign_out.wait_for_and_click()
-        time.sleep(5)
         self.components.sign_out.sign_out_button.wait_for_and_click()
-        time.sleep(10) # Enough time to see a log out screen and redirection
-        # assert not self.is_logged_in() # Error only shows here, but should had been trigger in line 17
-        time.sleep(5)
\ No newline at end of file
+        assert not self.is_logged_in()
\ No newline at end of file

From e26e8d3c0b339a6a9a63baf9df9db47540ae4c0d Mon Sep 17 00:00:00 2001
From: Juan David Mendez Solano <mendezj@tf.uni-freiburg.de>
Date: Mon, 30 Mar 2020 18:34:41 +0200
Subject: [PATCH 666/853] Implementation of the Sign out from user preference
 selenium test

---
 lib/galaxy/selenium/navigation.yml        |  2 +-
 lib/galaxy_test/selenium/test_sign_out.py | 10 +---------
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index 9ade81de4a29..859250ea708a 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -92,7 +92,7 @@ change_user_address:
 sign_out:
   selectors:
     cancel_button: '.modal-footer .buttons #button-0'
-    sign_out_button: '.modal-footer .buttons #button-0'
+    sign_out_button: '.modal-footer .buttons #button-1'
 
 history_panel:
   menu:
diff --git a/lib/galaxy_test/selenium/test_sign_out.py b/lib/galaxy_test/selenium/test_sign_out.py
index 1fecc571f85e..928c61d23c12 100644
--- a/lib/galaxy_test/selenium/test_sign_out.py
+++ b/lib/galaxy_test/selenium/test_sign_out.py
@@ -1,4 +1,3 @@
-import time
 from .framework import (
     selenium_test,
     SeleniumTestCase
@@ -13,17 +12,10 @@ def test_sign_out(self):
         self.click_masthead_user()
         self.components.masthead.preferences.wait_for_and_click()
         self.components.preferences.sign_out.wait_for_and_click()
-        #Testing of the cancel button
-        time.sleep(5)
         self.components.sign_out.cancel_button.wait_for_and_click()
-        time.sleep(10) #Giving time to click cancel and go back to user preferences (not happening, and no error)
         assert self.is_logged_in()
         new_email = self.driver.find_element_by_id("user-preferences-current-email").text
         self.assertTrue(email == new_email)
-        #Testing of the sign out button
         self.components.preferences.sign_out.wait_for_and_click()
-        time.sleep(5)
         self.components.sign_out.sign_out_button.wait_for_and_click()
-        time.sleep(10) # Enough time to see a log out screen and redirection
-        # assert not self.is_logged_in() # Error only shows here, but should had been trigger in line 17
-        time.sleep(5)
\ No newline at end of file
+        assert not self.is_logged_in()
\ No newline at end of file

From fdce4d26b78a0bdf4980d8b867f9de87bc91b96d Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 30 Mar 2020 14:14:09 -0400
Subject: [PATCH 667/853] Adding a sleep call so iRODS instance is up and
 running before integration test starts (Thanks Marius)

---
 test/integration/test_datatype_upload_irods.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index cdbc115caacd..64802f1dc024 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,5 +1,6 @@
 
 import os
+import sleep
 import subprocess
 import tempfile
 
@@ -60,4 +61,6 @@ def temp_file():
 
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_irods(instance, test_data, temp_file):
+    # Sleep so integration test's iRODS instance is up and running
+    sleep(10)
     upload_datatype_helper(instance, test_data, temp_file)

From 24c1d00bbe98a88a97f7b77281c7944e07542afe Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 30 Mar 2020 14:15:39 -0400
Subject: [PATCH 668/853] Removed debug tmate step

---
 .github/workflows/integration.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index e4641615abd0..5759b6712ee2 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -49,5 +49,3 @@ jobs:
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
       working-directory: 'galaxy root'
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v2

From 4aee048b8c5f09a741443d0f745d4e604fd9ec67 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 30 Mar 2020 14:25:24 -0400
Subject: [PATCH 669/853] Fixed import errors

---
 test/integration/test_datatype_upload_irods.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 64802f1dc024..0a520333763c 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,8 +1,8 @@
 
 import os
-import sleep
 import subprocess
 import tempfile
+import time
 
 import pytest
 
@@ -62,5 +62,5 @@ def temp_file():
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_irods(instance, test_data, temp_file):
     # Sleep so integration test's iRODS instance is up and running
-    sleep(10)
+    time.sleep(10)
     upload_datatype_helper(instance, test_data, temp_file)

From 60547f2a804149b5f08ab1c96e72448c20df4f58 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 30 Mar 2020 14:57:08 -0400
Subject: [PATCH 670/853] Increase sleep time and re-used default iRODS port.

---
 test/integration/irods_object_store_conf.xml   | 2 +-
 test/integration/test_datatype_upload_irods.py | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/test/integration/irods_object_store_conf.xml b/test/integration/irods_object_store_conf.xml
index 5b78f498fc27..778b42f4083e 100644
--- a/test/integration/irods_object_store_conf.xml
+++ b/test/integration/irods_object_store_conf.xml
@@ -3,7 +3,7 @@
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
-    <connection host="localhost" port="2020"/>
+    <connection host="localhost" port="1247"/>
     <cache path="database/object_store_cache" size="1000" />
     <extra_dir type="job_work" path="database/job_working_directory_irods"/>
     <extra_dir type="temp" path="database/tmp_irods"/>
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 0a520333763c..dfc44c884122 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -20,13 +20,16 @@ def start_irods(container_name):
         'docker',
         'run',
         '-p',
-        '2020:1247',
+        '1247:1247',
         '-d',
         '--name',
         container_name,
         'kxk302/irods-server:0.1']
     subprocess.check_call(irods_start_args)
 
+    # Sleep so integration test's iRODS instance is up and running
+    time.sleep(20)
+
 
 def stop_irods(container_name):
     subprocess.check_call(['docker', 'rm', '-f', container_name])
@@ -61,6 +64,4 @@ def temp_file():
 
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_irods(instance, test_data, temp_file):
-    # Sleep so integration test's iRODS instance is up and running
-    time.sleep(10)
     upload_datatype_helper(instance, test_data, temp_file)

From 31dc09146dae7a5179b189897598cd9f0f97d42a Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 30 Mar 2020 15:35:25 -0400
Subject: [PATCH 671/853] Took space out of Galaxy root directory

---
 .github/workflows/integration.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 5759b6712ee2..2e014f3ae4b8 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -48,4 +48,4 @@ jobs:
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
-      working-directory: 'galaxy root'
+      working-directory: 'galaxy-root'

From c88981655dc3f4e7d353fe3a0a60488ef2dca94c Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 30 Mar 2020 16:08:52 -0400
Subject: [PATCH 672/853] Renamed root directory 'galaxy'

---
 .github/workflows/integration.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 2e014f3ae4b8..c233e794dea5 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -36,7 +36,7 @@ jobs:
         kubectl get pods
     - uses: actions/checkout@v2
       with:
-        path: 'galaxy root'
+        path: 'galaxy'
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
@@ -45,7 +45,7 @@ jobs:
       id: pip-cache
       with:
         path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy/requirements.txt') }}
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
-      working-directory: 'galaxy-root'
+      working-directory: 'galaxy'

From 4d6c3d28cfa244b35472bfbca1988c4094fa45f2 Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 30 Mar 2020 16:33:30 -0400
Subject: [PATCH 673/853] Renamed root folder.

---
 .github/workflows/converter_tests.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
index 8b20d095f3ae..8575a553a9f5 100644
--- a/.github/workflows/converter_tests.yaml
+++ b/.github/workflows/converter_tests.yaml
@@ -11,7 +11,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
-        path: 'galaxy root'
+        path: 'galaxy'
     - name: Clone galaxyproject/galaxy-test-data
       uses: actions/checkout@v2
       with:
@@ -25,10 +25,10 @@ jobs:
       id: pip-cache
       with:
         path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy/requirements.txt') }}
     - name: Move test data
-      run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/'
+      run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy/test-data/'
     - name: Install planemo
       run: pip install planemo
     - name: Run tests
-      run: planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' 'galaxy root'/lib/galaxy/datatypes/converters/*xml
+      run: planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy' 'galaxy'/lib/galaxy/datatypes/converters/*xml

From 0486b04dafe0cb9de7bf2dd2a1f389eafb191518 Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 30 Mar 2020 16:34:28 -0400
Subject: [PATCH 674/853] Renamed root directory

---
 .github/workflows/mulled.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/mulled.yaml b/.github/workflows/mulled.yaml
index 1bdcd1dfde06..2fea754e7d66 100644
--- a/.github/workflows/mulled.yaml
+++ b/.github/workflows/mulled.yaml
@@ -11,7 +11,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
-        path: 'galaxy root'
+        path: 'galaxy'
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
@@ -20,9 +20,9 @@ jobs:
       id: pip-cache
       with:
         path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy/requirements.txt') }}
     - name: Install tox
       run: pip install tox
     - name: run tests
       run: tox -e mulled
-      working-directory: 'galaxy root'
+      working-directory: 'galaxy'

From d02c908952e077f899d8ee233423697a5b79e74e Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 1 Apr 2020 00:03:35 +0200
Subject: [PATCH 675/853] make tensorflow graph and session consistent

---
 lib/galaxy/tools/recommendations.py | 47 +++++++++++++++++++----------
 1 file changed, 31 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/tools/recommendations.py b/lib/galaxy/tools/recommendations.py
index 1943dbb66d39..3576886096f0 100644
--- a/lib/galaxy/tools/recommendations.py
+++ b/lib/galaxy/tools/recommendations.py
@@ -23,6 +23,14 @@ def __init__(self):
         self.admin_tool_recommendations_path = None
         self.deprecated_tools = dict()
         self.admin_recommendations = dict()
+        self.model_data_dictionary = dict()
+        self.reverse_dictionary = dict()
+        self.all_tools = dict()
+        self.tool_weights_sorted = dict()
+        self.session = None
+        self.graph = None
+        self.loaded_model = None
+        self.compatible_tools = None
 
     def set_model(self, trans, remote_model_url):
         """
@@ -33,11 +41,11 @@ def set_model(self, trans, remote_model_url):
             # keras is not downloaded because of conditional requirement and Galaxy does not build
             try:
                 from keras.models import model_from_json
+                import tensorflow as tf
             except Exception:
                 trans.response.status = 400
                 return False
             self.tool_recommendation_model_path = self.download_model(remote_model_url)
-            self.all_tools = dict()
             model_weights = list()
             counter_layer_weights = 0
             # collect ids and names of all the installed tools
@@ -49,27 +57,32 @@ def set_model(self, trans, remote_model_url):
             # read the hdf5 attributes
             trained_model = h5py.File(self.tool_recommendation_model_path, 'r')
             model_config = json.loads(trained_model['model_config'][()])
-            self.loaded_model = model_from_json(model_config)
+            # set tensorflow's graph and session to maintain
+            # consistency between model load and predict methods
+            self.graph = tf.Graph()
+            with self.graph.as_default():
+                self.session = tf.Session(graph=self.graph)
+                with self.session.as_default():
+                    self.loaded_model = model_from_json(model_config)
+                    # iterate through all the attributes of the model to find weights of neural network layers
+                    for item in trained_model.keys():
+                        if "weight_" in item:
+                            d_key = "weight_" + str(counter_layer_weights)
+                            weights = trained_model[d_key][()]
+                            model_weights.append(weights)
+                            counter_layer_weights += 1
+                    # set the model weights
+                    self.loaded_model.set_weights(model_weights)
             # set the dictionary of tools
             self.model_data_dictionary = json.loads(trained_model['data_dictionary'][()])
             self.reverse_dictionary = dict((v, k) for k, v in self.model_data_dictionary.items())
             # set the list of compatible tools
             self.compatible_tools = json.loads(trained_model['compatible_tools'][()])
-            self.tool_weights = json.loads(trained_model['class_weights'][()])
-            self.tool_weights_sorted = dict()
+            tool_weights = json.loads(trained_model['class_weights'][()])
             # sort the tools' usage dictionary
-            tool_pos_sorted = [int(key) for key in self.tool_weights.keys()]
+            tool_pos_sorted = [int(key) for key in tool_weights.keys()]
             for k in tool_pos_sorted:
-                self.tool_weights_sorted[k] = self.tool_weights[str(k)]
-            # iterate through all the attributes of the model to find weights of neural network layers
-            for item in trained_model.keys():
-                if "weight_" in item:
-                    d_key = "weight_" + str(counter_layer_weights)
-                    weights = trained_model[d_key][()]
-                    model_weights.append(weights)
-                    counter_layer_weights += 1
-            # set the model weights
-            self.loaded_model.set_weights(model_weights)
+                self.tool_weights_sorted[k] = tool_weights[str(k)]
         return True
 
     def collect_admin_preferences(self, admin_path):
@@ -204,7 +217,9 @@ def compute_tool_prediction(self, trans, tool_sequence):
             sample = np.reshape(sample, (1, max_seq_len))
             # predict next tools for a test path
             try:
-                prediction = self.loaded_model.predict_on_batch(sample)
+                with self.graph.as_default():
+                    with self.session.as_default():
+                        prediction = self.loaded_model.predict(sample)
             except Exception as e:
                 log.exception(e)
                 return prediction_data

From 3fd4b71390905c7750e6656c62bcc3b2756e8c8d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 11:10:39 +0200
Subject: [PATCH 676/853] Avoid repeated calls to get_repo_for_repository

by creating the `hg_repo` property on the `Repository` object.  This is
only used in the toolshed, meaning we can move get_repo_for_repository
to lib/tool_shed/util/hg_util.py.

`get_repo_for_repository` takes up considerable time when hitting the
`/api/repositories/updates` route in the tool shed.  This is hit at
least whice per call
(https://gist.github.com/mvdbeek/6a58b5f4fe9489dd9a15109da74a0c86#file-gistfile1-txt-L7),
so making this a cached property should result in a nice speedup.
---
 .../tool_shed/metadata/metadata_generator.py  |  7 ++----
 lib/galaxy/tool_shed/util/hg_util.py          | 12 ----------
 lib/tool_shed/grids/repository_grids.py       |  2 +-
 .../grids/repository_review_grids.py          |  2 +-
 lib/tool_shed/grids/util.py                   |  4 ++--
 .../metadata/repository_metadata_manager.py   |  5 ++--
 lib/tool_shed/repository_types/metadata.py    |  6 ++---
 .../repository_suite_definition.py            |  7 ++----
 .../tool_dependency_definition.py             |  7 ++----
 lib/tool_shed/tools/tool_validator.py         |  2 +-
 lib/tool_shed/tools/tool_version_manager.py   |  2 +-
 lib/tool_shed/util/commit_util.py             |  2 +-
 lib/tool_shed/util/hg_util.py                 | 17 ++++++++++---
 lib/tool_shed/util/metadata_util.py           |  5 ++--
 lib/tool_shed/util/readme_util.py             |  2 +-
 lib/tool_shed/util/repository_content_util.py |  9 ++++---
 lib/tool_shed/util/review_util.py             |  4 ++--
 lib/tool_shed/util/shed_util_common.py        |  2 +-
 .../webapp/controllers/repository.py          | 24 +++++++++----------
 .../webapp/controllers/repository_review.py   | 10 ++++----
 lib/tool_shed/webapp/model/__init__.py        | 17 ++++++++-----
 21 files changed, 71 insertions(+), 77 deletions(-)

diff --git a/lib/galaxy/tool_shed/metadata/metadata_generator.py b/lib/galaxy/tool_shed/metadata/metadata_generator.py
index 7b2ab03864fe..6316e1275ea5 100644
--- a/lib/galaxy/tool_shed/metadata/metadata_generator.py
+++ b/lib/galaxy/tool_shed/metadata/metadata_generator.py
@@ -17,10 +17,7 @@
     tool_util,
 )
 from galaxy.tool_shed.util.basic_util import remove_dir, strip_path
-from galaxy.tool_shed.util.hg_util import (
-    get_config_from_disk,
-    get_repo_for_repository,
-)
+from galaxy.tool_shed.util.hg_util import get_config_from_disk
 from galaxy.tool_shed.util.metadata_util import get_updated_changeset_revisions_from_tool_shed
 from galaxy.tool_shed.util.repository_util import get_repository_for_dependency_relationship
 from galaxy.tool_util.loader_directory import looks_like_a_tool
@@ -989,7 +986,7 @@ def handle_repository_elem(self, repository_elem, only_if_compiling_contained_td
                     log.debug(error_message)
                     is_valid = False
                     return repository_dependency_tup, is_valid, error_message
-                repo = get_repo_for_repository(self.app, repository=repository)
+                repo = repository.hg_repo
 
                 # The received changeset_revision may be None since defining it in the dependency definition is optional.
                 # If this is the case, the default will be to set its value to the repository dependency tip revision.
diff --git a/lib/galaxy/tool_shed/util/hg_util.py b/lib/galaxy/tool_shed/util/hg_util.py
index 86046195b3e9..93e299aa72b4 100644
--- a/lib/galaxy/tool_shed/util/hg_util.py
+++ b/lib/galaxy/tool_shed/util/hg_util.py
@@ -107,17 +107,6 @@ def get_file_context_from_ctx(ctx, filename):
     return None
 
 
-def get_repo_for_repository(app, repository=None, repo_path=None):
-    # Import from mercurial here to let Galaxy start under Python 3
-    from mercurial import (
-        hg,
-        ui
-    )
-    if repository is not None:
-        return hg.repository(ui.ui(), repository.repo_path(app))
-    if repo_path is not None:
-        return hg.repository(ui.ui(), repo_path)
-
 
 def pull_repository(repo_path, repository_clone_url, ctx_rev):
     """Pull changes from a remote repository to a local one."""
@@ -199,7 +188,6 @@ def update_repository(repo_path, ctx_rev=None):
     'get_config_from_disk',
     'get_ctx_file_path_from_manifest',
     'get_file_context_from_ctx',
-    'get_repo_for_repository',
     'pull_repository',
     'reversed_lower_upper_bounded_changelog',
     'reversed_upper_bounded_changelog',
diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py
index c76b6210ae52..af7baa5bf24d 100644
--- a/lib/tool_shed/grids/repository_grids.py
+++ b/lib/tool_shed/grids/repository_grids.py
@@ -85,7 +85,7 @@ def __init__(self, col_name):
 
         def get_value(self, trans, grid, repository):
             """Display the current repository heads."""
-            repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+            repo = repository.hg_repo
             heads = hg_util.get_repository_heads(repo)
             multiple_heads = len(heads) > 1
             if multiple_heads:
diff --git a/lib/tool_shed/grids/repository_review_grids.py b/lib/tool_shed/grids/repository_review_grids.py
index 15c037ea7ee4..9ff94b879110 100644
--- a/lib/tool_shed/grids/repository_review_grids.py
+++ b/lib/tool_shed/grids/repository_review_grids.py
@@ -56,7 +56,7 @@ def get_value(self, trans, grid, repository):
             # Restrict to revisions that have been reviewed.
             if repository.reviews:
                 rval = ''
-                repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+                repo = repository.hg_repo
                 for review in repository.reviews:
                     changeset_revision = review.changeset_revision
                     rev, label = hg_util.get_rev_label_from_changeset_revision(repo, changeset_revision)
diff --git a/lib/tool_shed/grids/util.py b/lib/tool_shed/grids/util.py
index bfe6cd87e651..39b540894727 100644
--- a/lib/tool_shed/grids/util.py
+++ b/lib/tool_shed/grids/util.py
@@ -112,7 +112,7 @@ def get_latest_downloadable_repository_metadata(trans, repository):
      tool_dependency_definition.
     """
     encoded_repository_id = trans.security.encode_id(repository.id)
-    repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+    repo = repository.hg_repo
     tip_ctx = str(repo[repo.changelog.tip()])
     repository_metadata = None
     try:
@@ -151,7 +151,7 @@ def get_latest_repository_metadata(trans, repository):
      tool_dependency_definition.
     """
     encoded_repository_id = trans.security.encode_id(repository.id)
-    repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+    repo = repository.hg_repo
     tip_ctx = str(repo[repo.changelog.tip()])
     try:
         repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, encoded_repository_id, tip_ctx)
diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 599983bd078e..babbe4252e3b 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -735,7 +735,7 @@ def new_workflow_metadata_required(self, repository_metadata):
     def reset_all_metadata_on_repository_in_tool_shed(self):
         """Reset all metadata on a single repository in a tool shed."""
         log.debug("Resetting all metadata on repository: %s" % self.repository.name)
-        repo = hg_util.get_repo_for_repository(self.app, repository=self.repository)
+        repo = self.repository.hg_repo
         # The list of changeset_revisions refers to repository_metadata records that have been created
         # or updated.  When the following loop completes, we'll delete all repository_metadata records
         # for this repository that do not have a changeset_revision value in this list.
@@ -904,8 +904,7 @@ def set_repository_metadata(self, host, content_alert_str='', **kwd):
         message = ''
         status = 'done'
         encoded_id = self.app.security.encode_id(self.repository.id)
-        repo_dir = self.repository.repo_path(self.app)
-        repo = hg_util.get_repo_for_repository(self.app, repo_path=repo_dir)
+        repo = self.repository.hg_repo
         self.generate_metadata_for_changeset_revision()
         if self.metadata_dict:
             repository_metadata = None
diff --git a/lib/tool_shed/repository_types/metadata.py b/lib/tool_shed/repository_types/metadata.py
index f09c152441e2..97933df01dfd 100644
--- a/lib/tool_shed/repository_types/metadata.py
+++ b/lib/tool_shed/repository_types/metadata.py
@@ -1,7 +1,5 @@
 import logging
 
-from tool_shed.util import hg_util
-
 log = logging.getLogger(__name__)
 
 
@@ -11,7 +9,7 @@ def __init__(self):
         self.type = None
 
     def get_changesets_for_setting_metadata(self, app, repository):
-        repo = hg_util.get_repo_for_repository(app, repository=repository)
+        repo = repository.hg_repo
         return repo.changelog
 
     def is_valid_for_type(self, app, repository, revisions_to_check=None):
@@ -24,5 +22,5 @@ def __init__(self):
         self.type = None
 
     def get_changesets_for_setting_metadata(self, app, repository):
-        repo = hg_util.get_repo_for_repository(app, repository=repository)
+        repo = repository.hg_repo
         return [repo.changelog.tip()]
diff --git a/lib/tool_shed/repository_types/repository_suite_definition.py b/lib/tool_shed/repository_types/repository_suite_definition.py
index 9d82f7db6f79..4645653fd0b4 100644
--- a/lib/tool_shed/repository_types/repository_suite_definition.py
+++ b/lib/tool_shed/repository_types/repository_suite_definition.py
@@ -2,10 +2,7 @@
 
 import tool_shed.repository_types.util as rt_util
 from tool_shed.repository_types.metadata import TipOnly
-from tool_shed.util import (
-    basic_util,
-    hg_util
-)
+from tool_shed.util import basic_util
 
 log = logging.getLogger(__name__)
 
@@ -23,7 +20,7 @@ def is_valid_for_type(self, app, repository, revisions_to_check=None):
         the contents of this type.  If the received revisions_to_check is a list of changeset revisions,
         then inspection will be restricted to the revisions in the list.
         """
-        repo = hg_util.get_repo_for_repository(app, repository=repository)
+        repo = repository.hg_repo
         if revisions_to_check:
             changeset_revisions = revisions_to_check
         else:
diff --git a/lib/tool_shed/repository_types/tool_dependency_definition.py b/lib/tool_shed/repository_types/tool_dependency_definition.py
index 13db77ac12da..90b331f045fb 100644
--- a/lib/tool_shed/repository_types/tool_dependency_definition.py
+++ b/lib/tool_shed/repository_types/tool_dependency_definition.py
@@ -2,10 +2,7 @@
 
 import tool_shed.repository_types.util as rt_util
 from tool_shed.repository_types.metadata import TipOnly
-from tool_shed.util import (
-    basic_util,
-    hg_util
-)
+from tool_shed.util import basic_util
 
 log = logging.getLogger(__name__)
 
@@ -23,7 +20,7 @@ def is_valid_for_type(self, app, repository, revisions_to_check=None):
         If the received revisions_to_check is a list of changeset revisions, then inspection will be restricted to the revisions
         in the list.
         """
-        repo = hg_util.get_repo_for_repository(app, repository=repository)
+        repo = repository.hg_repo
         if revisions_to_check:
             changeset_revisions = revisions_to_check
         else:
diff --git a/lib/tool_shed/tools/tool_validator.py b/lib/tool_shed/tools/tool_validator.py
index cdef3885b141..40c538589942 100644
--- a/lib/tool_shed/tools/tool_validator.py
+++ b/lib/tool_shed/tools/tool_validator.py
@@ -183,7 +183,7 @@ def load_tool_from_changeset_revision(self, repository_id, changeset_revision, t
         """
         repository = repository_util.get_repository_in_tool_shed(self.app, repository_id)
         repo_files_dir = repository.repo_path(self.app)
-        repo = hg_util.get_repo_for_repository(self.app, repo_path=repo_files_dir)
+        repo = repository.hg_repo
         tool_config_filepath = repository_util.get_absolute_path_to_file_in_repository(repo_files_dir, tool_config_filename)
         work_dir = tempfile.mkdtemp(prefix="tmp-toolshed-ltfcr")
         can_use_disk_file = self.can_use_tool_config_disk_file(repository,
diff --git a/lib/tool_shed/tools/tool_version_manager.py b/lib/tool_shed/tools/tool_version_manager.py
index ccb05364533c..eedfdf376914 100644
--- a/lib/tool_shed/tools/tool_version_manager.py
+++ b/lib/tool_shed/tools/tool_version_manager.py
@@ -38,7 +38,7 @@ def get_version_lineage_for_tool(self, repository_id, repository_metadata, guid)
         is called only from the Tool Shed.
         """
         repository = repository_util.get_repository_by_id(self.app, repository_id)
-        repo = hg_util.get_repo_for_repository(self.app, repository=repository)
+        repo = hg_util.repository.hg_repo
         # Initialize the tool lineage
         version_lineage = [guid]
         # Get all ancestor guids of the received guid.
diff --git a/lib/tool_shed/util/commit_util.py b/lib/tool_shed/util/commit_util.py
index 642774180933..68f679a1717e 100644
--- a/lib/tool_shed/util/commit_util.py
+++ b/lib/tool_shed/util/commit_util.py
@@ -157,10 +157,10 @@ def handle_bz2(repository, uploaded_file_name):
 def handle_directory_changes(app, host, username, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar,
                              new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed):
     repo_path = repository.repo_path(app)
-    repo = hg_util.get_repo_for_repository(app, repo_path=repo_path)
     content_alert_str = ''
     files_to_remove = []
     filenames_in_archive = [os.path.join(full_path, name) for name in filenames_in_archive]
+    repo = repository.hg_repo
     if remove_repo_files_not_in_tar and not repository.is_new(app):
         # We have a repository that is not new (it contains files), so discover those files that are in the
         # repository, but not in the uploaded archive.
diff --git a/lib/tool_shed/util/hg_util.py b/lib/tool_shed/util/hg_util.py
index 686f51d1a429..cff03747997a 100644
--- a/lib/tool_shed/util/hg_util.py
+++ b/lib/tool_shed/util/hg_util.py
@@ -13,7 +13,6 @@
     get_config_from_disk,
     get_ctx_file_path_from_manifest,
     get_file_context_from_ctx,
-    get_repo_for_repository,
     pull_repository,
     reversed_lower_upper_bounded_changelog,
     reversed_upper_bounded_changelog,
@@ -121,6 +120,18 @@ def get_readable_ctx_date(ctx):
     return ctx_date
 
 
+def get_repo_for_repository(app, repository=None, repo_path=None):
+    # Import from mercurial here to let Galaxy start under Python 3
+    from mercurial import (
+        hg,
+        ui
+    )
+    if repository is not None:
+        return hg.repository(ui.ui(), repository.repo_path(app))
+    if repo_path is not None:
+        return hg.repository(ui.ui(), repo_path)
+
+
 def get_repository_heads(repo):
     """Return current repository heads, which are changesets with no child changesets."""
     heads = [repo[h] for h in repo.heads(None)]
@@ -140,7 +151,7 @@ def get_revision_label(app, repository, changeset_revision, include_date=True, i
     Return a string consisting of the human readable changeset rev and the changeset revision string
     which includes the revision date if the receive include_date is True.
     """
-    repo = get_repo_for_repository(app, repository=repository)
+    repo = repository.hg_repo
     ctx = get_changectx_for_changeset(repo, changeset_revision)
     if ctx:
         return get_revision_label_from_ctx(ctx, include_date=include_date, include_hash=include_hash)
@@ -155,7 +166,7 @@ def get_rev_label_changeset_revision_from_repository_metadata(app, repository_me
                                                               include_date=True, include_hash=True):
     if repository is None:
         repository = repository_metadata.repository
-    repo = get_repo_for_repository(app, repository=repository)
+    repo = repository.hg_repo
     changeset_revision = repository_metadata.changeset_revision
     ctx = get_changectx_for_changeset(repo, changeset_revision)
     if ctx:
diff --git a/lib/tool_shed/util/metadata_util.py b/lib/tool_shed/util/metadata_util.py
index 7be1eab8373d..8aaf5c9ed255 100644
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -4,7 +4,6 @@
 from sqlalchemy import and_
 
 from galaxy.tool_shed.util.hg_util import (
-    get_repo_for_repository,
     INITIAL_CHANGELOG_HASH,
     reversed_lower_upper_bounded_changelog,
 )
@@ -153,7 +152,7 @@ def get_next_downloadable_changeset_revision(app, repository, after_changeset_re
         if changeset_revision == after_changeset_revision:
             return after_changeset_revision
     found_after_changeset_revision = False
-    repo = get_repo_for_repository(app, repository=repository)
+    repo = repository.hg_repo
     for changeset in repo.changelog:
         changeset_revision = str(repo[changeset])
         if found_after_changeset_revision:
@@ -288,7 +287,7 @@ def get_updated_changeset_revisions(app, name, owner, changeset_revision):
     upper_bound_changeset_revision = get_next_downloadable_changeset_revision(app, repository, changeset_revision)
     # Build the list of changeset revision hashes defining each available update up to, but excluding
     # upper_bound_changeset_revision.
-    repo = get_repo_for_repository(app, repository=repository)
+    repo = repository.hg_repo
     changeset_hashes = []
     for changeset in reversed_lower_upper_bounded_changelog(repo, changeset_revision, upper_bound_changeset_revision):
         # Make sure to exclude upper_bound_changeset_revision.
diff --git a/lib/tool_shed/util/readme_util.py b/lib/tool_shed/util/readme_util.py
index 477e33e6de37..3b6b6cfea77a 100644
--- a/lib/tool_shed/util/readme_util.py
+++ b/lib/tool_shed/util/readme_util.py
@@ -68,7 +68,7 @@ def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_
                         readme_files_dict[readme_file_name] = text_of_reasonable_length
                 else:
                     # We must be in the tool shed and have an old changeset_revision, so we need to retrieve the file contents from the repository manifest.
-                    repo = hg_util.get_repo_for_repository(app, repository=repository)
+                    repo = repository.hg_repo
                     ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
                     if ctx:
                         fctx = hg_util.get_file_context_from_ctx(ctx, readme_file_name)
diff --git a/lib/tool_shed/util/repository_content_util.py b/lib/tool_shed/util/repository_content_util.py
index 0050a09fd49e..b062ea8e7d0d 100644
--- a/lib/tool_shed/util/repository_content_util.py
+++ b/lib/tool_shed/util/repository_content_util.py
@@ -2,14 +2,15 @@
 import shutil
 
 import tool_shed.repository_types.util as rt_util
-from tool_shed.util import commit_util, hg_util, xml_util
+from tool_shed.util import (
+    commit_util,
+    xml_util,
+)
 
 
 def upload_tar(trans, rdah, tdah, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar,
                commit_message, new_repo_alert):
     # Upload a tar archive of files.
-    repo_dir = repository.repo_path(trans.app)
-    hg_util.get_repo_for_repository(trans.app, repo_path=repo_dir)
     undesirable_dirs_removed = 0
     undesirable_files_removed = 0
     check_results = commit_util.check_archive(repository, tar)
@@ -20,6 +21,8 @@ def upload_tar(trans, rdah, tdah, repository, tar, uploaded_file, upload_point,
             ' '.join(check_results.errors), ', '.join(check_results.invalid))
         return False, message, [], '', undesirable_dirs_removed, undesirable_files_removed
     else:
+        repository.hg_repo
+        repo_dir = repository.repo_path(trans.app)
         if upload_point is not None:
             full_path = os.path.abspath(os.path.join(repo_dir, upload_point))
         else:
diff --git a/lib/tool_shed/util/review_util.py b/lib/tool_shed/util/review_util.py
index 992fe09ba7f9..876c34f79291 100644
--- a/lib/tool_shed/util/review_util.py
+++ b/lib/tool_shed/util/review_util.py
@@ -72,7 +72,7 @@ def get_previous_repository_reviews(app, repository, changeset_revision):
     Return an ordered dictionary of repository reviews up to and including the
     received changeset revision.
     """
-    repo = hg_util.get_repo_for_repository(app, repository=repository)
+    repo = repository.hg_repo
     reviewed_revision_hashes = [review.changeset_revision for review in repository.reviews]
     previous_reviews_dict = OrderedDict()
     for changeset in hg_util.reversed_upper_bounded_changelog(repo, changeset_revision):
@@ -122,7 +122,7 @@ def has_previous_repository_reviews(app, repository, changeset_revision):
     Determine if a repository has a changeset revision review prior to the
     received changeset revision.
     """
-    repo = hg_util.get_repo_for_repository(app, repository=repository)
+    repo = repository.hg_repo
     reviewed_revision_hashes = [review.changeset_revision for review in repository.reviews]
     for changeset in hg_util.reversed_upper_bounded_changelog(repo, changeset_revision):
         previous_changeset_revision = str(repo[changeset])
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index d67f87ab57db..cf3cb5986d2e 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -321,7 +321,7 @@ def handle_email_alerts(app, host, repository, content_alert_str='', new_repo_al
        that was included in the change set.
     """
     sa_session = app.model.context.current
-    repo = hg_util.get_repo_for_repository(app, repository=repository)
+    repo = repository.hg_repo
     sharable_link = repository_util.generate_sharable_link_for_repository_in_tool_shed(repository, changeset_revision=None)
     smtp_server = app.config.smtp_server
     if smtp_server and (new_repo_alert or repository.email_alerts):
diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index bfdacea8b58c..523793cfc76b 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -606,7 +606,7 @@ def check_for_updates(self, trans, **kwd):
         owner = kwd.get('owner', None)
         changeset_revision = kwd.get('changeset_revision', None)
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo = repository.hg_repo
         # Default to the current changeset revision.
         update_to_ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
         latest_changeset_revision = changeset_revision
@@ -1084,7 +1084,7 @@ def has_galaxy_utilities(repository_metadata):
         has_repository_dependencies_only_if_compiling_contained_td = \
             has_galaxy_utilities_dict['has_repository_dependencies_only_if_compiling_contained_td']
         includes_workflows = has_galaxy_utilities_dict['includes_workflows']
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo = repository.hg_repo
         # Default to the received changeset revision and ctx_rev.
         update_to_ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
         ctx_rev = str(update_to_ctx.rev())
@@ -1160,7 +1160,7 @@ def get_ctx_rev(self, trans, **kwd):
         repository_owner = kwd['owner']
         changeset_revision = kwd['changeset_revision']
         repository = repository_util.get_repository_by_name_and_owner(trans.app, repository_name, repository_owner)
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo = repository.hg_repo
         ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
         if ctx:
             return str(ctx.rev())
@@ -1372,7 +1372,7 @@ def get_tool_versions(self, trans, **kwd):
         owner = kwd['owner']
         changeset_revision = kwd['changeset_revision']
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo = repository.hg_repo
         tool_version_dicts = []
         for changeset in repo.changelog:
             current_changeset_revision = str(repo[changeset])
@@ -1645,7 +1645,7 @@ def manage_repository(self, trans, id, **kwd):
         status = kwd.get('status', 'done')
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
         repository_type = kwd.get('repository_type', str(repository.type))
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo = repository.hg_repo
         repo_name = kwd.get('repo_name', repository.name)
         changeset_revision = kwd.get('changeset_revision', repository.tip(trans.app))
         repository.share_url = repository_util.generate_sharable_link_for_repository_in_tool_shed(repository, changeset_revision=changeset_revision)
@@ -2040,7 +2040,7 @@ def previous_changeset_revisions(self, trans, from_tip=False, **kwd):
             else:
                 changeset_revision = kwd.get('changeset_revision', None)
             if changeset_revision is not None:
-                repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+                repo = repository.hg_repo
                 # Get the lower bound changeset revision.
                 lower_bound_changeset_revision = \
                     metadata_util.get_previous_metadata_changeset_revision(trans.app, repository, changeset_revision, downloadable=True)
@@ -2150,7 +2150,7 @@ def select_files_to_delete(self, trans, id, **kwd):
         commit_message = escape(kwd.get('commit_message', 'Deleted selected files'))
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
         repo_dir = repository.repo_path(trans.app)
-        repo = hg_util.get_repo_for_repository(trans.app, repo_path=repo_dir)
+        repo = repository.hg_repo
         selected_files_to_delete = kwd.get('selected_files_to_delete', '')
         if kwd.get('select_files_to_delete_button', False):
             if selected_files_to_delete:
@@ -2433,7 +2433,7 @@ def view_changelog(self, trans, id, **kwd):
         message = escape(kwd.get('message', ''))
         status = kwd.get('status', 'done')
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo = repository.hg_repo
         changesets = []
         for changeset in repo.changelog:
             ctx = repo[changeset]
@@ -2468,7 +2468,7 @@ def view_changeset(self, trans, id, ctx_str, **kwd):
         message = escape(kwd.get('message', ''))
         status = kwd.get('status', 'done')
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo = repository.hg_repo
         ctx = hg_util.get_changectx_for_changeset(repo, ctx_str)
         if ctx is None:
             message = "Repository does not include changeset revision '%s'." % str(ctx_str)
@@ -2560,7 +2560,7 @@ def view_repository(self, trans, id, **kwd):
         message = escape(kwd.get('message', ''))
         status = kwd.get('status', 'done')
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo = repository.hg_repo
         avg_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, repository, webapp_model=trans.model)
         changeset_revision = kwd.get('changeset_revision', repository.tip(trans.app))
         self.validate_changeset_revision(trans, changeset_revision, id)
@@ -2653,7 +2653,7 @@ def view_tool_metadata(self, trans, repository_id, changeset_revision, tool_id,
         render_repository_actions_for = kwd.get('render_repository_actions_for', 'tool_shed')
         repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
         repo_files_dir = repository.repo_path(trans.app)
-        repo = hg_util.get_repo_for_repository(trans.app, repo_path=repo_files_dir)
+        repo = repository.hg_repo
         tool_metadata_dict = {}
         tool_lineage = []
         tool = None
@@ -2729,7 +2729,7 @@ def validate_changeset_revision(self, trans, changeset_revision, repository_id):
         """In case changeset revision is invalid send them to the repository page"""
         if changeset_revision:
             repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
-            repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+            repo = repository.hg_repo
             if not hg_util.get_changectx_for_changeset(repo, changeset_revision):
                 message = 'Invalid changeset revision'
                 return trans.response.send_redirect(web.url_for(controller='repository',
diff --git a/lib/tool_shed/webapp/controllers/repository_review.py b/lib/tool_shed/webapp/controllers/repository_review.py
index 779c1f31353d..11769086b93c 100644
--- a/lib/tool_shed/webapp/controllers/repository_review.py
+++ b/lib/tool_shed/webapp/controllers/repository_review.py
@@ -82,7 +82,7 @@ def browse_review(self, trans, **kwd):
         status = kwd.get('status', 'done')
         review = review_util.get_review(trans.app, kwd['id'])
         repository = review.repository
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo = repository.hg_repo
         rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(repo, review.changeset_revision)
         return trans.fill_template('/webapps/tool_shed/repository_review/browse_review.mako',
                                    repository=repository,
@@ -244,7 +244,7 @@ def edit_review(self, trans, **kwd):
         for component in review_util.get_components(trans.app):
             components_dict[component.name] = dict(component=component, component_review=None)
         repository = review.repository
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo = repository.hg_repo
         for component_review in review.component_reviews:
             if component_review and component_review.component:
                 component_name = component_review.component.name
@@ -483,7 +483,7 @@ def manage_repository_reviews(self, trans, mine=False, **kwd):
         repository_id = kwd.get('id', None)
         if repository_id:
             repository = suc.get_repository_in_tool_shed(trans.app, repository_id)
-            repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+            repo = repository.hg_repo
             metadata_revision_hashes = [metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions]
             reviewed_revision_hashes = [review.changeset_revision for review in repository.reviews]
             reviews_dict = OrderedDict()
@@ -531,7 +531,7 @@ def manage_repository_reviews_of_revision(self, trans, **kwd):
         repository_id = kwd.get('id', None)
         changeset_revision = kwd.get('changeset_revision', None)
         repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo = repository.hg_repo
         installable = changeset_revision in [metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions]
         rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(repo, changeset_revision)
         reviews = review_util.get_reviews_by_repository_id_changeset_revision(trans.app,
@@ -594,7 +594,7 @@ def select_previous_review(self, trans, **kwd):
         status = kwd.get('status', 'done')
         repository = repository_util.get_repository_in_tool_shed(trans.app, kwd['id'])
         changeset_revision = kwd.get('changeset_revision', None)
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo = repository.hg_repo
         previous_reviews_dict = review_util.get_previous_repository_reviews(trans.app,
                                                                             repository,
                                                                             changeset_revision)
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 784618170679..e9d88a4935cf 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -190,6 +190,13 @@ def __init__(self, id=None, name=None, type=None, remote_repository_url=None, ho
         self.times_downloaded = times_downloaded
         self.deprecated = deprecated
         self.create_time = create_time
+        self._hg_repo = None
+
+    @property
+    def hg_repo(self):
+        if self._hg_repo is None:
+            self._hg_repo = hg_util.get_repo_for_repository(self)
+        return self._hg_repo
 
     @property
     def admin_role(self):
@@ -202,8 +209,7 @@ def admin_role(self):
                         (str(self.name), str(self.user.username)))
 
     def allow_push(self, app):
-        repo = hg_util.get_repo_for_repository(app, repository=self)
-        return repo.ui.config('web', 'allow_push')
+        return self.hg_repo.ui.config('web', 'allow_push')
 
     def can_change_type(self, app):
         # Allow changing the type only if the repository has no contents, has never been installed, or has
@@ -261,15 +267,14 @@ def installable_revisions(self, app, sort_revisions=True):
         return metadata_util.get_metadata_revisions(app, self, sort_revisions=sort_revisions)
 
     def is_new(self, app):
-        repo = hg_util.get_repo_for_repository(app, repository=self)
-        tip_rev = repo.changelog.tiprev()
+        tip_rev = self.hg_repo.changelog.tiprev()
         return tip_rev < 0
 
     def repo_path(self, app):
         return app.hgweb_config_manager.get_entry(os.path.join("repos", self.user.username, self.name))
 
     def revision(self, app):
-        repo = hg_util.get_repo_for_repository(app, repository=self)
+        repo = self.hg_repo
         tip_ctx = repo[repo.changelog.tip()]
         return "%s:%s" % (str(tip_ctx.rev()), str(tip_ctx))
 
@@ -296,7 +301,7 @@ def set_allow_push(self, app, usernames, remove_auth=''):
                     fh.write(line)
 
     def tip(self, app):
-        repo = hg_util.get_repo_for_repository(app, repository=self)
+        repo = self.hg_repo
         return str(repo[repo.changelog.tip()])
 
     def to_dict(self, view='collection', value_mapper=None):

From 4a43f1395512b3e0bce0d2dd7bc6603f197d5551 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 11:17:33 +0200
Subject: [PATCH 677/853] Only call repository.tip once in
 /api/repositories/updates

This also takes up considerable time in
https://gist.github.com/mvdbeek/6a58b5f4fe9489dd9a15109da74a0c86#file-gistfile1-txt-L6
---
 lib/tool_shed/webapp/api/repositories.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/tool_shed/webapp/api/repositories.py b/lib/tool_shed/webapp/api/repositories.py
index 396db8b041e7..8ac347af71e4 100644
--- a/lib/tool_shed/webapp/api/repositories.py
+++ b/lib/tool_shed/webapp/api/repositories.py
@@ -721,8 +721,9 @@ def updates(self, trans, **kwd):
             tool_shed_status_dict = {}
             # Handle repository deprecation.
             tool_shed_status_dict['repository_deprecated'] = str(repository.deprecated)
+            tip_revision = repository.tip(trans.app)
             # Handle latest installable revision.
-            if changeset_revision == repository.tip(trans.app):
+            if changeset_revision == tip_revision:
                 tool_shed_status_dict['latest_installable_revision'] = 'True'
             else:
                 next_installable_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository, changeset_revision)
@@ -737,7 +738,7 @@ def updates(self, trans, **kwd):
                     else:
                         tool_shed_status_dict['latest_installable_revision'] = 'True'
             # Handle revision updates.
-            if changeset_revision == repository.tip(trans.app):
+            if changeset_revision == tip_revision:
                 tool_shed_status_dict['revision_update'] = 'False'
             else:
                 if repository_metadata is None:

From f000232974cb4919aafd0879faa33468b67e5864 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 12:05:30 +0200
Subject: [PATCH 678/853] Drop workaround form when mercurial wasn't py3
 compatible

---
 lib/galaxy/tool_shed/util/hg_util.py |  1 -
 lib/tool_shed/util/hg_util.py        | 10 +++++-----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/tool_shed/util/hg_util.py b/lib/galaxy/tool_shed/util/hg_util.py
index 93e299aa72b4..a1426951ab3a 100644
--- a/lib/galaxy/tool_shed/util/hg_util.py
+++ b/lib/galaxy/tool_shed/util/hg_util.py
@@ -107,7 +107,6 @@ def get_file_context_from_ctx(ctx, filename):
     return None
 
 
-
 def pull_repository(repo_path, repository_clone_url, ctx_rev):
     """Pull changes from a remote repository to a local one."""
     try:
diff --git a/lib/tool_shed/util/hg_util.py b/lib/tool_shed/util/hg_util.py
index cff03747997a..556188f71249 100644
--- a/lib/tool_shed/util/hg_util.py
+++ b/lib/tool_shed/util/hg_util.py
@@ -5,6 +5,11 @@
 from datetime import datetime
 from time import gmtime
 
+from mercurial import (
+    hg,
+    ui
+)
+
 from galaxy.tool_shed.util import basic_util
 from galaxy.tool_shed.util.hg_util import (
     clone_repository,
@@ -121,11 +126,6 @@ def get_readable_ctx_date(ctx):
 
 
 def get_repo_for_repository(app, repository=None, repo_path=None):
-    # Import from mercurial here to let Galaxy start under Python 3
-    from mercurial import (
-        hg,
-        ui
-    )
     if repository is not None:
         return hg.repository(ui.ui(), repository.repo_path(app))
     if repo_path is not None:

From 0c43bb08aefac1ff0b97977b748c9d14965bc5ff Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 13:08:23 +0200
Subject: [PATCH 679/853] Work around sqlalchemy __init__ behavior

WEAK_HG_REPO_CACHE items will expire when Repository is garbage
collected.
---
 lib/tool_shed/webapp/model/__init__.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index e9d88a4935cf..5873003d6c1d 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -1,5 +1,6 @@
 import logging
 import os
+import weakref
 from datetime import (
     datetime,
     timedelta
@@ -20,6 +21,8 @@
 
 log = logging.getLogger(__name__)
 
+WEAK_HG_REPO_CACHE = weakref.WeakKeyDictionary()
+
 
 class APIKeys(object):
     pass
@@ -190,13 +193,12 @@ def __init__(self, id=None, name=None, type=None, remote_repository_url=None, ho
         self.times_downloaded = times_downloaded
         self.deprecated = deprecated
         self.create_time = create_time
-        self._hg_repo = None
 
     @property
     def hg_repo(self):
-        if self._hg_repo is None:
-            self._hg_repo = hg_util.get_repo_for_repository(self)
-        return self._hg_repo
+        if WEAK_HG_REPO_CACHE.get(self) is None:
+            WEAK_HG_REPO_CACH[self] = hg_util.get_repo_for_repository(self)
+        return WEAK_HG_REPO_CACH[self]
 
     @property
     def admin_role(self):

From 814b000e38993ae6bb5852df20861ac5f12732d7 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 13:21:25 +0200
Subject: [PATCH 680/853] Fix hg_repo access

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/tool_shed/tools/tool_version_manager.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/tools/tool_version_manager.py b/lib/tool_shed/tools/tool_version_manager.py
index eedfdf376914..95c2d01806d2 100644
--- a/lib/tool_shed/tools/tool_version_manager.py
+++ b/lib/tool_shed/tools/tool_version_manager.py
@@ -38,7 +38,7 @@ def get_version_lineage_for_tool(self, repository_id, repository_metadata, guid)
         is called only from the Tool Shed.
         """
         repository = repository_util.get_repository_by_id(self.app, repository_id)
-        repo = hg_util.repository.hg_repo
+        repo = repository.hg_repo
         # Initialize the tool lineage
         version_lineage = [guid]
         # Get all ancestor guids of the received guid.

From 3df849e467cd876bf2597447a3891526a1cd72ff Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 16:13:43 +0200
Subject: [PATCH 681/853] Use a global HgWebConfigManager instance

This avoids needing to pass app around.
---
 lib/tool_shed/test/base/twilltestcase.py        |  8 ++++++--
 lib/tool_shed/util/hg_util.py                   | 12 ------------
 lib/tool_shed/{webapp => }/util/hgweb_config.py |  3 +++
 lib/tool_shed/util/shed_index.py                |  4 ++--
 lib/tool_shed/webapp/app.py                     |  3 ++-
 lib/tool_shed/webapp/model/__init__.py          | 17 ++++++++++++-----
 lib/tool_shed/webapp/model/mapping.py           |  2 --
 7 files changed, 25 insertions(+), 24 deletions(-)
 rename lib/tool_shed/{webapp => }/util/hgweb_config.py (98%)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index d5f92adbe4bf..e7fbce33374e 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -31,7 +31,11 @@
 from galaxy.util import smart_str, unicodify
 from galaxy_test.base.api_util import get_master_api_key
 from galaxy_test.driver.testcase import FunctionalTestCase
-from tool_shed.util import hg_util, xml_util
+from tool_shed.util import (
+    hg_util,
+    xml_util,
+    hgweb_config
+)
 from . import common, test_db_util
 
 # Set a 10 minute timeout for repository installation.
@@ -54,7 +58,7 @@ def setUp(self):
         self.security = idencoding.IdEncodingHelper(id_secret='changethisinproductiontoo')
         self.history_id = None
         self.hgweb_config_dir = os.environ.get('TEST_HG_WEB_CONFIG_DIR')
-        self.hgweb_config_manager = tool_shed.webapp.util.hgweb_config.HgWebConfigManager()
+        self.hgweb_config_manager = hgweb_config.hgweb_config_manager
         self.hgweb_config_manager.hgweb_config_dir = self.hgweb_config_dir
         self.tool_shed_test_tmp_dir = os.environ.get('TOOL_SHED_TEST_TMP_DIR', None)
         self.host = os.environ.get('TOOL_SHED_TEST_HOST')
diff --git a/lib/tool_shed/util/hg_util.py b/lib/tool_shed/util/hg_util.py
index 556188f71249..39565cca8a8a 100644
--- a/lib/tool_shed/util/hg_util.py
+++ b/lib/tool_shed/util/hg_util.py
@@ -5,11 +5,6 @@
 from datetime import datetime
 from time import gmtime
 
-from mercurial import (
-    hg,
-    ui
-)
-
 from galaxy.tool_shed.util import basic_util
 from galaxy.tool_shed.util.hg_util import (
     clone_repository,
@@ -125,13 +120,6 @@ def get_readable_ctx_date(ctx):
     return ctx_date
 
 
-def get_repo_for_repository(app, repository=None, repo_path=None):
-    if repository is not None:
-        return hg.repository(ui.ui(), repository.repo_path(app))
-    if repo_path is not None:
-        return hg.repository(ui.ui(), repo_path)
-
-
 def get_repository_heads(repo):
     """Return current repository heads, which are changesets with no child changesets."""
     heads = [repo[h] for h in repo.heads(None)]
diff --git a/lib/tool_shed/webapp/util/hgweb_config.py b/lib/tool_shed/util/hgweb_config.py
similarity index 98%
rename from lib/tool_shed/webapp/util/hgweb_config.py
rename to lib/tool_shed/util/hgweb_config.py
index b38a72ff0dc1..03119dbf41a4 100644
--- a/lib/tool_shed/webapp/util/hgweb_config.py
+++ b/lib/tool_shed/util/hgweb_config.py
@@ -104,3 +104,6 @@ def write_config(self):
         config_file = open(self.hgweb_config, 'wb')
         self.in_memory_config.write(config_file)
         config_file.close
+
+
+hgweb_config_manager = HgWebConfigManager()
\ No newline at end of file
diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
index e424d7263deb..9e00b606bc4f 100644
--- a/lib/tool_shed/util/shed_index.py
+++ b/lib/tool_shed/util/shed_index.py
@@ -16,7 +16,7 @@
 from tool_shed.webapp import model
 from tool_shed.webapp.search.repo_search import schema as repo_schema
 from tool_shed.webapp.search.tool_search import schema as tool_schema
-from tool_shed.webapp.util.hgweb_config import HgWebConfigManager
+from tool_shed.util.hgweb_config import hgweb_config_manager
 
 log = logging.getLogger(__name__)
 
@@ -92,7 +92,7 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
     """
     Load repos from DB and included tools from .xml configs.
     """
-    hgwcm = HgWebConfigManager()
+    hgwcm = hgweb_config_manager
     hgwcm.hgweb_config_dir = hgweb_config_dir
     # Do not index deleted, deprecated, or "tool_dependency_definition" type repositories.
     q = sa_session.query(model.Repository).filter_by(deleted=False).filter_by(deprecated=False).order_by(model.Repository.update_time.desc())
diff --git a/lib/tool_shed/webapp/app.py b/lib/tool_shed/webapp/app.py
index c98ff24dc55d..77db4e3e2366 100644
--- a/lib/tool_shed/webapp/app.py
+++ b/lib/tool_shed/webapp/app.py
@@ -15,6 +15,7 @@
 from galaxy.util.dbkeys import GenomeBuilds
 from galaxy.web_stack import application_stack_instance
 from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
+from tool_shed.util.hgweb_config import hgweb_config_manager
 from . import config
 
 log = logging.getLogger(__name__)
@@ -73,7 +74,7 @@ def __init__(self, **kwd):
         # Initialize the baseline Tool Shed statistics component.
         self.shed_counter = self.model.shed_counter
         # Let the Tool Shed's HgwebConfigManager know where the hgweb.config file is located.
-        self.hgweb_config_manager = self.model.hgweb_config_manager
+        self.hgweb_config_manager = hgweb_config_manager
         self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
         # Initialize the repository registry.
         self.repository_registry = tool_shed.repository_registry.Registry(self)
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 5873003d6c1d..81eb74ea4d75 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -6,6 +6,11 @@
     timedelta
 )
 
+from mercurial import (
+    hg,
+    ui
+)
+
 import tool_shed.repository_types.util as rt_util
 from galaxy import util
 from galaxy.model.orm.now import now
@@ -18,6 +23,7 @@
     hg_util,
     metadata_util
 )
+from tool_shed.util.hgweb_config import hgweb_config_manager
 
 log = logging.getLogger(__name__)
 
@@ -197,8 +203,8 @@ def __init__(self, id=None, name=None, type=None, remote_repository_url=None, ho
     @property
     def hg_repo(self):
         if WEAK_HG_REPO_CACHE.get(self) is None:
-            WEAK_HG_REPO_CACH[self] = hg_util.get_repo_for_repository(self)
-        return WEAK_HG_REPO_CACH[self]
+            WEAK_HG_REPO_CACHE[self] = hg.repository(ui.ui(), self.repo_path())
+        return WEAK_HG_REPO_CACHE[self]
 
     @property
     def admin_role(self):
@@ -272,8 +278,9 @@ def is_new(self, app):
         tip_rev = self.hg_repo.changelog.tiprev()
         return tip_rev < 0
 
-    def repo_path(self, app):
-        return app.hgweb_config_manager.get_entry(os.path.join("repos", self.user.username, self.name))
+    def repo_path(self, app=None):
+        # Keep app argumen for compaibility with tool_shed_install Repository model
+        return hgweb_config_manager.get_entry(os.path.join("repos", self.user.username, self.name))
 
     def revision(self, app):
         repo = self.hg_repo
@@ -291,7 +298,7 @@ def set_allow_push(self, app, usernames, remove_auth=''):
         allow_push = '%s\n' % ','.join(allow_push)
         # Why doesn't the following work?
         # repo.ui.setconfig('web', 'allow_push', allow_push)
-        repo_dir = self.repo_path(app)
+        repo_dir = self.repo_path()
         hgrc_file = hg_util.get_hgrc_path(repo_dir)
         with open(hgrc_file, 'rb') as fh:
             lines = fh.readlines()
diff --git a/lib/tool_shed/webapp/model/mapping.py b/lib/tool_shed/webapp/model/mapping.py
index 599b259ccb8f..98bf309db388 100644
--- a/lib/tool_shed/webapp/model/mapping.py
+++ b/lib/tool_shed/webapp/model/mapping.py
@@ -8,7 +8,6 @@
 from sqlalchemy.orm import backref, mapper, relation
 
 import tool_shed.webapp.model
-import tool_shed.webapp.util.hgweb_config
 import tool_shed.webapp.util.shed_statistics as shed_statistics
 from galaxy.model.base import ModelMapping
 from galaxy.model.custom_types import JSONType, TrimmedString
@@ -328,5 +327,4 @@ def init(file_path, url, engine_options={}, create_tables=False):
     # Load local tool shed security policy
     result.security_agent = CommunityRBACAgent(result)
     result.shed_counter = shed_statistics.ShedCounter(result)
-    result.hgweb_config_manager = tool_shed.webapp.util.hgweb_config.HgWebConfigManager()
     return result

From fe86cb9181f9904c0bff06414c8c0c23ed71243f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 16:26:14 +0200
Subject: [PATCH 682/853] Don't need to pass app into Repository.tip

---
 .../tool_shed/metadata/metadata_generator.py  |  4 +--
 lib/galaxy/tool_shed/util/tool_util.py        |  2 +-
 .../metadata/repository_metadata_manager.py   |  6 ++--
 lib/tool_shed/repository_registry.py          |  6 ++--
 lib/tool_shed/tools/tool_validator.py         |  2 +-
 lib/tool_shed/tools/tool_version_manager.py   |  2 +-
 lib/tool_shed/util/metadata_util.py           |  4 +--
 lib/tool_shed/util/shed_util_common.py        |  2 +-
 lib/tool_shed/webapp/api/repositories.py      |  6 ++--
 lib/tool_shed/webapp/controllers/admin.py     |  2 +-
 .../webapp/controllers/repository.py          | 36 +++++++++----------
 lib/tool_shed/webapp/controllers/upload.py    |  4 +--
 lib/tool_shed/webapp/model/__init__.py        |  2 +-
 .../common/repository_actions_menu.mako       | 16 ++++-----
 .../repository/browse_repository.mako         |  2 +-
 .../repository/manage_repository.mako         |  4 +--
 .../preview_tools_in_changeset.mako           |  2 +-
 .../tool_shed/repository/view_repository.mako |  2 +-
 18 files changed, 52 insertions(+), 52 deletions(-)

diff --git a/lib/galaxy/tool_shed/metadata/metadata_generator.py b/lib/galaxy/tool_shed/metadata/metadata_generator.py
index 6316e1275ea5..21c5791c047e 100644
--- a/lib/galaxy/tool_shed/metadata/metadata_generator.py
+++ b/lib/galaxy/tool_shed/metadata/metadata_generator.py
@@ -74,7 +74,7 @@ def __init__(self, app, repository=None, changeset_revision=None, repository_clo
         else:
             # We're in the Tool Shed.
             if changeset_revision is None and self.repository is not None:
-                self.changeset_revision = self.repository.tip(self.app)
+                self.changeset_revision = self.repository.tip()
             else:
                 self.changeset_revision = changeset_revision
             if repository_clone_url is None and self.repository is not None:
@@ -1077,7 +1077,7 @@ def set_repository(self, repository, relative_install_dir=None, changeset_revisi
             if relative_install_dir is None and self.repository is not None:
                 relative_install_dir = repository.repo_path(self.app)
             if changeset_revision is None and self.repository is not None:
-                self.set_changeset_revision(self.repository.tip(self.app))
+                self.set_changeset_revision(self.repository.tip())
             else:
                 self.set_changeset_revision(changeset_revision)
             self.shed_config_dict = {}
diff --git a/lib/galaxy/tool_shed/util/tool_util.py b/lib/galaxy/tool_shed/util/tool_util.py
index 2ba625c7c4d3..aac1609dd2f6 100644
--- a/lib/galaxy/tool_shed/util/tool_util.py
+++ b/lib/galaxy/tool_shed/util/tool_util.py
@@ -97,7 +97,7 @@ def generate_message_for_invalid_tools(app, invalid_file_tups, repository, metad
     if app.name == 'galaxy':
         tip_rev = str(repository.changeset_revision)
     else:
-        tip_rev = str(repository.tip(app))
+        tip_rev = str(repository.tip())
     if not displaying_invalid_tool:
         if metadata_dict:
             message += "Metadata may have been defined for some items in revision '%s'.  " % tip_rev
diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index babbe4252e3b..3f08c7fd04e3 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -912,7 +912,7 @@ def set_repository_metadata(self, host, content_alert_str='', **kwd):
             tip_only = isinstance(repository_type_class, TipOnly)
             if not tip_only and self.new_metadata_required_for_utilities():
                 # Create a new repository_metadata table row.
-                repository_metadata = self.create_or_update_repository_metadata(self.repository.tip(self.app),
+                repository_metadata = self.create_or_update_repository_metadata(self.repository.tip(),
                                                                                 self.metadata_dict)
                 # If this is the first record stored for this repository, see if we need to send any email alerts.
                 if len(self.repository.downloadable_revisions) == 1:
@@ -961,7 +961,7 @@ def set_repository_metadata(self, host, content_alert_str='', **kwd):
                     self.sa_session.flush()
                 else:
                     # There are no metadata records associated with the repository.
-                    repository_metadata = self.create_or_update_repository_metadata(self.repository.tip(self.app),
+                    repository_metadata = self.create_or_update_repository_metadata(self.repository.tip(),
                                                                                     self.metadata_dict)
             if 'tools' in self.metadata_dict and repository_metadata and status != 'error':
                 # Set tool versions on the new downloadable change set.  The order of the list of changesets is
@@ -974,7 +974,7 @@ def set_repository_metadata(self, host, content_alert_str='', **kwd):
                 self.add_tool_versions(encoded_id, repository_metadata, changeset_revisions)
         elif len(repo) == 1 and not self.invalid_file_tups:
             message = "Revision <b>%s</b> includes no Galaxy utilities for which metadata can " % \
-                str(self.repository.tip(self.app))
+                str(self.repository.tip())
             message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."
             status = "error"
         if self.invalid_file_tups:
diff --git a/lib/tool_shed/repository_registry.py b/lib/tool_shed/repository_registry.py
index 35fcbfb92a17..d599233cb189 100644
--- a/lib/tool_shed/repository_registry.py
+++ b/lib/tool_shed/repository_registry.py
@@ -196,7 +196,7 @@ def load_certified_level_one_repository_and_suite_tuple(self, repository):
         # The received repository has been determined to be level one certified.
         name = str(repository.name)
         owner = str(repository.user.username)
-        tip_changeset_hash = repository.tip(self.app)
+        tip_changeset_hash = repository.tip()
         if tip_changeset_hash != hg_util.INITIAL_CHANGELOG_HASH:
             certified_level_one_tuple = (name, owner, tip_changeset_hash)
             if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION:
@@ -261,7 +261,7 @@ def load_viewable_repositories_and_suites_by_category(self):
                 if not repository.deleted and not repository.deprecated:
                     is_valid = self.is_valid(repository)
                     encoded_repository_id = self.app.security.encode_id(repository.id)
-                    tip_changeset_hash = repository.tip(self.app)
+                    tip_changeset_hash = repository.tip()
                     repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
                                                                                                       encoded_repository_id,
                                                                                                       tip_changeset_hash)
@@ -353,7 +353,7 @@ def unload_certified_level_one_repository_and_suite_tuple(self, repository):
         # The received repository has been determined to be level one certified.
         name = str(repository.name)
         owner = str(repository.user.username)
-        tip_changeset_hash = repository.tip(self.app)
+        tip_changeset_hash = repository.tip()
         if tip_changeset_hash != hg_util.INITIAL_CHANGELOG_HASH:
             certified_level_one_tuple = (name, owner, tip_changeset_hash)
             if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION:
diff --git a/lib/tool_shed/tools/tool_validator.py b/lib/tool_shed/tools/tool_validator.py
index 40c538589942..b392b253100d 100644
--- a/lib/tool_shed/tools/tool_validator.py
+++ b/lib/tool_shed/tools/tool_validator.py
@@ -29,7 +29,7 @@ def can_use_tool_config_disk_file(self, repository, repo, file_path, changeset_r
             # The file no longer exists on disk, so it must have been deleted at some previous
             # point in the change log.
             return False
-        if changeset_revision == repository.tip(self.app):
+        if changeset_revision == repository.tip():
             return True
         file_name = basic_util.strip_path(file_path)
         latest_version_of_file = \
diff --git a/lib/tool_shed/tools/tool_version_manager.py b/lib/tool_shed/tools/tool_version_manager.py
index 95c2d01806d2..6abab5dfc802 100644
--- a/lib/tool_shed/tools/tool_version_manager.py
+++ b/lib/tool_shed/tools/tool_version_manager.py
@@ -55,7 +55,7 @@ def get_version_lineage_for_tool(self, repository_id, repository_metadata, guid)
         current_parent_guid = guid
         for changeset in hg_util.reversed_lower_upper_bounded_changelog(repo,
                                                                         repository_metadata.changeset_revision,
-                                                                        repository.tip(self.app)):
+                                                                        repository.tip()):
             ctx = repo[changeset]
             rm = metadata_util.get_repository_metadata_by_changeset_revision(self.app, repository_id, str(ctx))
             if rm:
diff --git a/lib/tool_shed/util/metadata_util.py b/lib/tool_shed/util/metadata_util.py
index 8aaf5c9ed255..91a3b0b28811 100644
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -76,7 +76,7 @@ def get_dependencies_for_metadata_revision(app, metadata):
 
 
 def get_latest_changeset_revision(app, repository):
-    repository_tip = repository.tip(app)
+    repository_tip = repository.tip()
     repository_metadata = get_repository_metadata_by_changeset_revision(app,
                                                                         app.security.encode_id(repository.id),
                                                                         repository_tip)
@@ -89,7 +89,7 @@ def get_latest_changeset_revision(app, repository):
 
 
 def get_latest_downloadable_changeset_revision(app, repository):
-    repository_tip = repository.tip(app)
+    repository_tip = repository.tip()
     repository_metadata = get_repository_metadata_by_changeset_revision(app, app.security.encode_id(repository.id), repository_tip)
     if repository_metadata and repository_metadata.downloadable:
         return repository_tip
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index cf3cb5986d2e..b9f3f3f1d44f 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -250,7 +250,7 @@ def get_repository_from_refresh_on_change(app, **kwd):
         if k.startswith(changeset_revision_str):
             repository_id = app.security.encode_id(int(k.lstrip(changeset_revision_str)))
             repository = repository_util.get_repository_in_tool_shed(app, repository_id)
-            if repository.tip(app) != v:
+            if repository.tip() != v:
                 return v, repository
     # This should never be reached - raise an exception?
     return v, None
diff --git a/lib/tool_shed/webapp/api/repositories.py b/lib/tool_shed/webapp/api/repositories.py
index 8ac347af71e4..127d0e8cc7ac 100644
--- a/lib/tool_shed/webapp/api/repositories.py
+++ b/lib/tool_shed/webapp/api/repositories.py
@@ -721,7 +721,7 @@ def updates(self, trans, **kwd):
             tool_shed_status_dict = {}
             # Handle repository deprecation.
             tool_shed_status_dict['repository_deprecated'] = str(repository.deprecated)
-            tip_revision = repository.tip(trans.app)
+            tip_revision = repository.tip()
             # Handle latest installable revision.
             if changeset_revision == tip_revision:
                 tool_shed_status_dict['latest_installable_revision'] = 'True'
@@ -976,7 +976,7 @@ def create_changeset_revision(self, trans, id, payload, **kwd):
         repo_dir = repository.repo_path(self.app)
 
         upload_point = commit_util.get_upload_point(repository, **kwd)
-        tip = repository.tip(self.app)
+        tip = repository.tip()
 
         file_data = payload.get('file')
         # Code stolen from gx's upload_common.py
@@ -1026,7 +1026,7 @@ def create_changeset_revision(self, trans, id, payload, **kwd):
             # Update the repository files for browsing.
             hg_util.update_repository(repo_dir)
             # Get the new repository tip.
-            if tip == repository.tip(self.app):
+            if tip == repository.tip():
                 trans.response.status = 400
                 message = 'No changes to repository.'
                 ok = False
diff --git a/lib/tool_shed/webapp/controllers/admin.py b/lib/tool_shed/webapp/controllers/admin.py
index a5e2834d092a..0bb900a4aeaf 100644
--- a/lib/tool_shed/webapp/controllers/admin.py
+++ b/lib/tool_shed/webapp/controllers/admin.py
@@ -95,7 +95,7 @@ def browse_repositories(self, trans, **kwd):
             if k.startswith(changeset_revision_str):
                 repository_id = trans.security.encode_id(int(k.lstrip(changeset_revision_str)))
                 repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
-                if repository.tip(trans.app) != v:
+                if repository.tip() != v:
                     return trans.response.send_redirect(web.url_for(controller='repository',
                                                                     action='browse_repositories',
                                                                     operation='view_or_manage_repository',
diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index 523793cfc76b..42b678f73217 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -436,7 +436,7 @@ def browse_repository(self, trans, id, **kwd):
         repo_path = repository.repo_path(trans.app)
         # Update repository files for browsing.
         hg_util.update_repository(repo_path)
-        changeset_revision = repository.tip(trans.app)
+        changeset_revision = repository.tip()
         metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
                                                                                              id,
                                                                                              changeset_revision,
@@ -625,7 +625,7 @@ def check_for_updates(self, trans, **kwd):
             message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>.  ' % galaxy_url
             message += 'You may need to enable third-party cookies in your browser.  '
             return trans.show_error_message(message)
-        if changeset_revision == repository.tip(trans.app):
+        if changeset_revision == repository.tip():
             # If changeset_revision is the repository tip, there are no additional updates.
             if from_update_manager:
                 return no_update
@@ -649,7 +649,7 @@ def check_for_updates(self, trans, **kwd):
                     changeset_hash = str(repo[changeset])
                     hg_util.get_changectx_for_changeset(repo, changeset_hash)
                     if update_to_changeset_hash:
-                        if changeset_hash == repository.tip(trans.app):
+                        if changeset_hash == repository.tip():
                             update_to_ctx = hg_util.get_changectx_for_changeset(repo, changeset_hash)
                             latest_changeset_revision = changeset_hash
                             break
@@ -684,7 +684,7 @@ def contact_owner(self, trans, id, **kwd):
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
         metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
                                                                                              id,
-                                                                                             repository.tip(trans.app),
+                                                                                             repository.tip(),
                                                                                              metadata_only=True)
         if trans.user and trans.user.email:
             return trans.fill_template("/webapps/tool_shed/repository/contact_owner.mako",
@@ -1099,7 +1099,7 @@ def has_galaxy_utilities(repository_metadata):
                            has_repository_dependencies=has_repository_dependencies,
                            has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
                            includes_workflows=includes_workflows)
-        if changeset_revision == repository.tip(trans.app):
+        if changeset_revision == repository.tip():
             # If changeset_revision is the repository tip, there are no additional updates.
             return encoding_util.tool_shed_encode(update_dict)
         else:
@@ -1130,7 +1130,7 @@ def has_galaxy_utilities(repository_metadata):
                             has_repository_dependencies_only_if_compiling_contained_td = has_galaxy_utilities_dict['has_repository_dependencies_only_if_compiling_contained_td']
                             includes_workflows = has_galaxy_utilities_dict['includes_workflows']
                             # We found a RepositoryMetadata record.
-                            if changeset_hash == repository.tip(trans.app):
+                            if changeset_hash == repository.tip():
                                 # The current ctx is the repository tip, so use it.
                                 update_to_ctx = hg_util.get_changectx_for_changeset(repo, changeset_hash)
                                 latest_changeset_revision = changeset_hash
@@ -1356,7 +1356,7 @@ def get_tool_dependency_definition_metadata(self, trans, **kwd):
         repository_owner = kwd['owner']
         repository = repository_util.get_repository_by_name_and_owner(trans.app, repository_name, repository_owner)
         encoded_id = trans.app.security.encode_id(repository.id)
-        repository_tip = repository.tip(trans.app)
+        repository_tip = repository.tip()
         repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
                                                                                           encoded_id,
                                                                                           repository_tip)
@@ -1647,7 +1647,7 @@ def manage_repository(self, trans, id, **kwd):
         repository_type = kwd.get('repository_type', str(repository.type))
         repo = repository.hg_repo
         repo_name = kwd.get('repo_name', repository.name)
-        changeset_revision = kwd.get('changeset_revision', repository.tip(trans.app))
+        changeset_revision = kwd.get('changeset_revision', repository.tip())
         repository.share_url = repository_util.generate_sharable_link_for_repository_in_tool_shed(repository, changeset_revision=changeset_revision)
         repository.clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(trans.user, repository)
         remote_repository_url = kwd.get('remote_repository_url', repository.remote_repository_url)
@@ -1856,7 +1856,7 @@ def manage_repository_admins(self, trans, id, **kwd):
         message = escape(kwd.get('message', ''))
         status = kwd.get('status', 'done')
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
-        changeset_revision = kwd.get('changeset_revision', repository.tip(trans.app))
+        changeset_revision = kwd.get('changeset_revision', repository.tip())
         metadata = None
         if changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
             repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, id, changeset_revision)
@@ -1957,7 +1957,7 @@ def preview_tools_in_changeset(self, trans, repository_id, **kwd):
         message = escape(kwd.get('message', ''))
         status = kwd.get('status', 'done')
         repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
-        changeset_revision = kwd.get('changeset_revision', repository.tip(trans.app))
+        changeset_revision = kwd.get('changeset_revision', repository.tip())
         self.validate_changeset_revision(trans, changeset_revision, repository_id)
         repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_id, changeset_revision)
         if repository_metadata:
@@ -2036,7 +2036,7 @@ def previous_changeset_revisions(self, trans, from_tip=False, **kwd):
             repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
             from_tip = util.string_as_bool(from_tip)
             if from_tip:
-                changeset_revision = repository.tip(trans.app)
+                changeset_revision = repository.tip()
             else:
                 changeset_revision = kwd.get('changeset_revision', None)
             if changeset_revision is not None:
@@ -2068,7 +2068,7 @@ def rate_repository(self, trans, **kwd):
                                                             message='Select a repository to rate',
                                                             status='error'))
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
-        changeset_revision = repository.tip(trans.app)
+        changeset_revision = repository.tip()
         if repository.user == trans.user:
             return trans.response.send_redirect(web.url_for(controller='repository',
                                                             action='browse_repositories',
@@ -2156,7 +2156,7 @@ def select_files_to_delete(self, trans, id, **kwd):
             if selected_files_to_delete:
                 selected_files_to_delete = selected_files_to_delete.split(',')
                 # Get the current repository tip.
-                tip = repository.tip(trans.app)
+                tip = repository.tip()
                 for selected_file in selected_files_to_delete:
                     try:
                         hg_util.remove_file(repo_dir, selected_file, force=True)
@@ -2193,7 +2193,7 @@ def select_files_to_delete(self, trans, id, **kwd):
                 # Update the repository files for browsing.
                 hg_util.update_repository(repo_dir)
                 # Get the new repository tip.
-                if tip == repository.tip(trans.app):
+                if tip == repository.tip():
                     message += 'No changes to repository.  '
                 else:
                     rmm = repository_metadata_manager.RepositoryMetadataManager(app=trans.app,
@@ -2208,7 +2208,7 @@ def select_files_to_delete(self, trans, id, **kwd):
                 message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>."
                 status = "error"
         repository_type_select_field = rt_util.build_repository_type_select_field(trans, repository=repository)
-        changeset_revision = repository.tip(trans.app)
+        changeset_revision = repository.tip()
         metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
                                                                                              id,
                                                                                              changeset_revision,
@@ -2454,7 +2454,7 @@ def view_changelog(self, trans, id, **kwd):
             changesets.insert(0, change_dict)
         metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
                                                                                              id,
-                                                                                             repository.tip(trans.app),
+                                                                                             repository.tip(),
                                                                                              metadata_only=True)
         return trans.fill_template('/webapps/tool_shed/repository/view_changelog.mako',
                                    repository=repository,
@@ -2562,7 +2562,7 @@ def view_repository(self, trans, id, **kwd):
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
         repo = repository.hg_repo
         avg_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, repository, webapp_model=trans.model)
-        changeset_revision = kwd.get('changeset_revision', repository.tip(trans.app))
+        changeset_revision = kwd.get('changeset_revision', repository.tip())
         self.validate_changeset_revision(trans, changeset_revision, id)
         repository.share_url = repository_util.generate_sharable_link_for_repository_in_tool_shed(repository, changeset_revision=changeset_revision)
         repository.clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(trans.user, repository)
@@ -2614,7 +2614,7 @@ def view_repository(self, trans, id, **kwd):
                     status = 'warning'
         else:
             metadata = None
-        is_malicious = metadata_util.is_malicious(trans.app, id, repository.tip(trans.app))
+        is_malicious = metadata_util.is_malicious(trans.app, id, repository.tip())
         if is_malicious:
             if trans.app.security_agent.can_push(trans.app, trans.user, repository):
                 message += malicious_error_can_push
diff --git a/lib/tool_shed/webapp/controllers/upload.py b/lib/tool_shed/webapp/controllers/upload.py
index 8043b12a9836..ead68fa7124a 100644
--- a/lib/tool_shed/webapp/controllers/upload.py
+++ b/lib/tool_shed/webapp/controllers/upload.py
@@ -46,7 +46,7 @@ def upload(self, trans, **kwd):
         remove_repo_files_not_in_tar = util.string_as_bool(kwd.get('remove_repo_files_not_in_tar', 'true'))
         uploaded_file = None
         upload_point = commit_util.get_upload_point(repository, **kwd)
-        tip = repository.tip(trans.app)
+        tip = repository.tip()
         file_data = kwd.get('file_data', '')
         url = kwd.get('url', '')
         # Part of the upload process is sending email notification to those that have registered to
@@ -231,7 +231,7 @@ def upload(self, trans, **kwd):
                     # Update the repository files for browsing.
                     hg_util.update_repository(repo_dir)
                     # Get the new repository tip.
-                    if tip == repository.tip(trans.app):
+                    if tip == repository.tip():
                         message = 'No changes to repository.  '
                         status = 'warning'
                     else:
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 81eb74ea4d75..08fc37a61299 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -309,7 +309,7 @@ def set_allow_push(self, app, usernames, remove_auth=''):
                 else:
                     fh.write(line)
 
-    def tip(self, app):
+    def tip(self):
         repo = self.hg_repo
         return str(repo[repo.changelog.tip()])
 
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/common/repository_actions_menu.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/common/repository_actions_menu.mako
index 33e35125db46..008e9103a550 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/common/repository_actions_menu.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/common/repository_actions_menu.mako
@@ -22,12 +22,12 @@
         else:
             is_deprecated = False
 
-        if repository.is_new( trans.app ):
+        if repository.is_new():
             is_new = True
         else:
             is_new = False
 
-        if is_malicious( trans.app, trans.security.encode_id( repository.id ), repository.tip( trans.app ) ):
+        if is_malicious( trans.app, trans.security.encode_id( repository.id ), repository.tip() ):
             changeset_is_malicious = True
         else:
             changeset_is_malicious = False
@@ -102,7 +102,7 @@
             can_set_metadata = False
 
         if changeset_revision is not None:
-            if changeset_revision == repository.tip( trans.app ):
+            if changeset_revision == repository.tip():
                 changeset_revision_is_repository_tip = True
             else:
                 changeset_revision_is_repository_tip = False
@@ -148,9 +148,9 @@
                     <a class="action-button" target="galaxy_main" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
                 %endif
                 %if can_administer:
-                    <a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a>
+                    <a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip() )}">Manage repository</a>
                 %else:
-                    <a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a>
+                    <a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip() )}">View repository</a>
                 %endif
                 %if can_view_change_log:
                     <a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
@@ -180,9 +180,9 @@
                     %if metadata is not None and changeset_revision is not None:
                         <a class="action-button" href="${h.url_for( controller='repository', action='export', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Export this revision</a>
                     %endif
-                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a>
-                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='bz2' )}">Download as a .tar.bz2 file</a>
-                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='zip' )}">Download as a zip file</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip(), file_type='gz' )}">Download as a .tar.gz file</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip(), file_type='bz2' )}">Download as a .tar.bz2 file</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip(), file_type='zip' )}">Download as a zip file</a>
                 %endif
             </div>
         %endif
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/browse_repository.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/browse_repository.mako
index 12e9308673f4..5c35edef3a1a 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/browse_repository.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/browse_repository.mako
@@ -38,7 +38,7 @@ ${render_tool_shed_repository_actions( repository, metadata=metadata, changeset_
 
 %if can_browse_contents:
     <div class="toolForm">
-        <div class="toolFormTitle">Repository '${repository.name | h}' revision ${repository.tip( trans.app ) | h} (repository tip)</div>
+        <div class="toolFormTitle">Repository '${repository.name | h}' revision ${repository.tip() | h} (repository tip)</div>
         %if can_download:
             <div class="form-row">
                 <label>Clone this repository:</label>
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako
index 556456b2062e..9d3564def96e 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako
@@ -23,7 +23,7 @@
     else:
         is_deprecated = False
 
-    if is_malicious( trans.app, trans.security.encode_id( repository.id ), repository.tip( trans.app ) ):
+    if is_malicious( trans.app, trans.security.encode_id( repository.id ), repository.tip() ):
         changeset_is_malicious = True
     else:
         changeset_is_malicious = False
@@ -48,7 +48,7 @@
     else:
         can_set_metadata = False
 
-    if changeset_revision == repository.tip( trans.app ):
+    if changeset_revision == repository.tip():
         changeset_revision_is_repository_tip = True
     else:
         changeset_revision_is_repository_tip = False
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako
index 015bb91f2935..a83be362d108 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako
@@ -36,7 +36,7 @@ ${render_galaxy_repository_actions( repository=repository )}
             <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ) )}" method="post" >
                 <div class="form-row">
                     <%
-                        if changeset_revision == repository.tip( trans.app ):
+                        if changeset_revision == repository.tip():
                             tip_str = 'repository tip'
                         else:
                             tip_str = ''
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_repository.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_repository.mako
index 8063a03e74ef..aca6d66575ce 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_repository.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_repository.mako
@@ -15,7 +15,7 @@
     can_push = not is_deprecated and trans.app.security_agent.can_push( trans.app, trans.user, repository )
     can_download = not is_deprecated and not is_new and ( not is_malicious or can_push )
     can_view_change_log = trans.webapp.name == 'tool_shed' and not is_new
-    changeset_revision_is_repository_tip = changeset_revision == repository.tip( trans.app )
+    changeset_revision_is_repository_tip = changeset_revision == repository.tip()
 
     if changeset_revision_is_repository_tip:
         tip_str = 'repository tip'

From d3047110661d7634243160b8e7c545ef308f7328 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 16:28:18 +0200
Subject: [PATCH 683/853] Don't need to pass into Repository.is_new

---
 lib/tool_shed/repository_types/unrestricted.py                | 2 +-
 lib/tool_shed/util/commit_util.py                             | 2 +-
 lib/tool_shed/webapp/controllers/upload.py                    | 2 +-
 lib/tool_shed/webapp/model/__init__.py                        | 4 ++--
 .../webapps/tool_shed/repository/browse_repository.mako       | 2 +-
 .../webapps/tool_shed/repository/manage_repository.mako       | 2 +-
 .../webapps/tool_shed/repository/rate_repository.mako         | 2 +-
 .../webapp/templates/webapps/tool_shed/repository/upload.mako | 4 ++--
 .../webapps/tool_shed/repository/view_changelog.mako          | 2 +-
 .../webapps/tool_shed/repository/view_changeset.mako          | 2 +-
 .../webapps/tool_shed/repository/view_repository.mako         | 2 +-
 .../webapps/tool_shed/repository/view_tool_metadata.mako      | 2 +-
 12 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/lib/tool_shed/repository_types/unrestricted.py b/lib/tool_shed/repository_types/unrestricted.py
index 87496cecd90a..0409a1c1c62a 100644
--- a/lib/tool_shed/repository_types/unrestricted.py
+++ b/lib/tool_shed/repository_types/unrestricted.py
@@ -14,7 +14,7 @@ def __init__(self):
 
     def is_valid_for_type(self, app, repository, revisions_to_check=None):
         """A repository's type can only be changed to the unrestricted type if it is new or has never been installed."""
-        if repository.is_new(app):
+        if repository.is_new():
             return True
         if repository.times_downloaded == 0:
             return True
diff --git a/lib/tool_shed/util/commit_util.py b/lib/tool_shed/util/commit_util.py
index 68f679a1717e..2f287a9f8ebf 100644
--- a/lib/tool_shed/util/commit_util.py
+++ b/lib/tool_shed/util/commit_util.py
@@ -161,7 +161,7 @@ def handle_directory_changes(app, host, username, repository, full_path, filenam
     files_to_remove = []
     filenames_in_archive = [os.path.join(full_path, name) for name in filenames_in_archive]
     repo = repository.hg_repo
-    if remove_repo_files_not_in_tar and not repository.is_new(app):
+    if remove_repo_files_not_in_tar and not repository.is_new():
         # We have a repository that is not new (it contains files), so discover those files that are in the
         # repository, but not in the uploaded archive.
         for root, dirs, files in os.walk(full_path):
diff --git a/lib/tool_shed/webapp/controllers/upload.py b/lib/tool_shed/webapp/controllers/upload.py
index ead68fa7124a..0a972b62e5b5 100644
--- a/lib/tool_shed/webapp/controllers/upload.py
+++ b/lib/tool_shed/webapp/controllers/upload.py
@@ -52,7 +52,7 @@ def upload(self, trans, **kwd):
         # Part of the upload process is sending email notification to those that have registered to
         # receive them.  One scenario occurs when the first change set is produced for the repository.
         # See the suc.handle_email_alerts() method for the definition of the scenarios.
-        new_repo_alert = repository.is_new(trans.app)
+        new_repo_alert = repository.is_new()
         uploaded_directory = None
         if kwd.get('upload_button', False):
             if file_data == '' and url == '':
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 08fc37a61299..357845f9e67e 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -222,7 +222,7 @@ def allow_push(self, app):
     def can_change_type(self, app):
         # Allow changing the type only if the repository has no contents, has never been installed, or has
         # never been changed from the default type.
-        if self.is_new(app):
+        if self.is_new():
             return True
         if self.times_downloaded == 0:
             return True
@@ -274,7 +274,7 @@ def get_tool_dependencies(self, app, changeset_revision):
     def installable_revisions(self, app, sort_revisions=True):
         return metadata_util.get_metadata_revisions(app, self, sort_revisions=sort_revisions)
 
-    def is_new(self, app):
+    def is_new(self):
         tip_rev = self.hg_repo.changelog.tiprev()
         return tip_rev < 0
 
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/browse_repository.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/browse_repository.mako
index 5c35edef3a1a..6eaf1455d468 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/browse_repository.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/browse_repository.mako
@@ -24,7 +24,7 @@
 </%def>
 
 <%
-    is_new = repository.is_new( trans.app )
+    is_new = repository.is_new()
     can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository )
     can_download = not is_new and ( not is_malicious or can_push )
     can_browse_contents = not is_new
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako
index 9d3564def96e..66e19e6c2b69 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako
@@ -16,7 +16,7 @@
         has_metadata = False
 
     is_admin = trans.user_is_admin
-    is_new = repository.is_new( trans.app )
+    is_new = repository.is_new()
 
     if repository.deprecated:
         is_deprecated = True
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/rate_repository.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/rate_repository.mako
index 68b926150c76..72e49ca9535b 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/rate_repository.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/rate_repository.mako
@@ -5,7 +5,7 @@
 
 <%
     from galaxy.web.framework.helpers import time_ago
-    is_new = repository.is_new( trans.app )
+    is_new = repository.is_new()
     can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository )
     can_download = not is_new and ( not is_malicious or can_push )
 %>
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/upload.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/upload.mako
index fa93af64552f..e2fc5dd43069 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/upload.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/upload.mako
@@ -3,7 +3,7 @@
 <%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_tool_shed_repository_actions" />
 
 <%
-    is_new = repository.is_new( trans.app )
+    is_new = repository.is_new()
 %>
 
 <%!
@@ -138,7 +138,7 @@ ${render_tool_shed_repository_actions( repository=repository)}
                 </div>
                 <div style="clear: both"></div>
             </div>
-            %if not repository.is_new( trans.app ):
+            %if not repository.is_new():
                 <div class="form-row" >
                     <label>Contents:</label>
                     <div id="tree" >
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_changelog.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_changelog.mako
index bcbe001c1136..2b9e4f23c446 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_changelog.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_changelog.mako
@@ -5,7 +5,7 @@
 <%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_tool_shed_repository_actions" />
 
 <%
-    is_new = repository.is_new( trans.app )
+    is_new = repository.is_new()
     can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository )
     can_download = not is_new and ( not is_malicious or can_push )
 %>
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_changeset.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_changeset.mako
index d5080052f280..15f34e1c889d 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_changeset.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_changeset.mako
@@ -5,7 +5,7 @@
 <%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_tool_shed_repository_actions" />
 
 <%
-    is_new = repository.is_new( trans.app )
+    is_new = repository.is_new()
     can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository )
     can_download = not is_new and ( not is_malicious or can_push )
 %>
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_repository.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_repository.mako
index aca6d66575ce..d07644ff0faf 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_repository.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_repository.mako
@@ -8,7 +8,7 @@
     from galaxy.web.framework.helpers import time_ago
     from tool_shed.util.basic_util import to_html_string
 
-    is_new = repository.is_new( trans.app )
+    is_new = repository.is_new()
     is_deprecated = repository.deprecated
 
     can_browse_contents = trans.webapp.name == 'tool_shed' and not is_new
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_tool_metadata.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_tool_metadata.mako
index a84993a49c6a..fad4e51e0363 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_tool_metadata.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_tool_metadata.mako
@@ -5,7 +5,7 @@
 <%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="*" />
 
 <%
-    is_new = repository.is_new( trans.app )
+    is_new = repository.is_new()
 
     can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository )
     can_download = not is_new and ( not is_malicious or can_push )

From 5e0f481a0ebcd7460955bdc1d47526e7d6ac08f3 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 16:28:41 +0200
Subject: [PATCH 684/853] Missed one tip() instance

---
 lib/tool_shed/webapp/controllers/repository.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index 42b678f73217..9107f59bb0cb 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -1751,7 +1751,7 @@ def manage_repository(self, trans, id, **kwd):
                                                                                            selected_value=changeset_revision,
                                                                                            add_id_to_name=False,
                                                                                            downloadable=False)
-        revision_label = hg_util.get_revision_label(trans.app, repository, repository.tip(trans.app), include_date=False)
+        revision_label = hg_util.get_revision_label(trans.app, repository, repository.tip(), include_date=False)
         repository_metadata = None
         metadata = None
         is_malicious = False

From 59dfff23d97656d8460780df2c64588092a7e1ec Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 16:39:40 +0200
Subject: [PATCH 685/853] allow_push doesn't need app

---
 lib/tool_shed/grids/repository_grids.py               | 6 +++---
 lib/tool_shed/metadata/repository_metadata_manager.py | 2 +-
 lib/tool_shed/webapp/controllers/repository.py        | 4 ++--
 lib/tool_shed/webapp/model/__init__.py                | 7 ++++---
 lib/tool_shed/webapp/security/__init__.py             | 2 +-
 5 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py
index af7baa5bf24d..1a1bdb8e3369 100644
--- a/lib/tool_shed/grids/repository_grids.py
+++ b/lib/tool_shed/grids/repository_grids.py
@@ -418,7 +418,7 @@ def build_initial_query(self, trans, **kwd):
         for repository in trans.sa_session.query(model.Repository) \
                                           .filter(and_(model.Repository.table.c.deprecated == false(),
                                                        model.Repository.table.c.deleted == false())):
-            allow_push = repository.allow_push(trans.app)
+            allow_push = repository.allow_push
             if allow_push:
                 allow_push_usernames = allow_push.split(',')
                 if username in allow_push_usernames:
@@ -710,7 +710,7 @@ def build_initial_query(self, trans, **kwd):
         for repository in trans.sa_session.query(model.Repository) \
                                           .filter(and_(model.Repository.table.c.deprecated == false(),
                                                        model.Repository.table.c.deleted == false())):
-            allow_push = repository.allow_push(trans.app)
+            allow_push = repository.allow_push
             if allow_push:
                 allow_push_usernames = allow_push.split(',')
                 if username in allow_push_usernames:
@@ -849,7 +849,7 @@ def build_initial_query(self, trans, **kwd):
         for repository in trans.sa_session.query(model.Repository) \
                                           .filter(and_(model.Repository.table.c.deprecated == false(),
                                                        model.Repository.table.c.deleted == false())):
-            allow_push = repository.allow_push(trans.app)
+            allow_push = repository.allow_push
             if allow_push:
                 allow_push_usernames = allow_push.split(',')
                 if username in allow_push_usernames:
diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 3f08c7fd04e3..1a832ec42b27 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -438,7 +438,7 @@ def get_query_for_setting_metadata_on_repositories(self, my_writable=False, orde
                 if repository.type in [rt_util.REPOSITORY_SUITE_DEFINITION, rt_util.TOOL_DEPENDENCY_DEFINITION]:
                     clause_list.append(self.app.model.Repository.table.c.id == repository.id)
                 else:
-                    allow_push = repository.allow_push(self.app)
+                    allow_push = repository.allow_push
                     if allow_push:
                         # Include all repositories that are writable by the current user.
                         allow_push_usernames = allow_push.split(',')
diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index 9107f59bb0cb..3875babb2883 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -1710,7 +1710,7 @@ def manage_repository(self, trans, id, **kwd):
                         user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id))
                         usernames.append(user.username)
                     usernames = ','.join(usernames)
-                repository.set_allow_push(trans.app, usernames, remove_auth=remove_auth)
+                repository.set_allow_push(usernames, remove_auth=remove_auth)
             message = "The repository information has been updated."
         elif kwd.get('receive_email_alerts_button', False):
             flush_needed = False
@@ -1732,7 +1732,7 @@ def manage_repository(self, trans, id, **kwd):
             status = 'error'
         allow_push_select_field = SelectField(name='allow_push',
                                               multiple=True)
-        current_allow_push = repository.allow_push(trans.app)
+        current_allow_push = repository.allow_push
         if current_allow_push:
             current_allow_push_list = current_allow_push.split(',')
         else:
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 357845f9e67e..979c62baf8e1 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -216,7 +216,8 @@ def admin_role(self):
         raise Exception('Repository %s owned by %s is not associated with a required administrative role.' %
                         (str(self.name), str(self.user.username)))
 
-    def allow_push(self, app):
+    @property
+    def allow_push(self):
         return self.hg_repo.ui.config('web', 'allow_push')
 
     def can_change_type(self, app):
@@ -287,8 +288,8 @@ def revision(self, app):
         tip_ctx = repo[repo.changelog.tip()]
         return "%s:%s" % (str(tip_ctx.rev()), str(tip_ctx))
 
-    def set_allow_push(self, app, usernames, remove_auth=''):
-        allow_push = util.listify(self.allow_push(app))
+    def set_allow_push(self, usernames, remove_auth=''):
+        allow_push = util.listify(self.allow_push)
         if remove_auth:
             allow_push.remove(remove_auth)
         else:
diff --git a/lib/tool_shed/webapp/security/__init__.py b/lib/tool_shed/webapp/security/__init__.py
index b212e674e6e2..3cdc040226b0 100644
--- a/lib/tool_shed/webapp/security/__init__.py
+++ b/lib/tool_shed/webapp/security/__init__.py
@@ -214,7 +214,7 @@ def set_entity_user_associations(self, users=None, roles=None, groups=None, dele
 
     def can_push(self, app, user, repository):
         if user:
-            return user.username in listify(repository.allow_push(app))
+            return user.username in listify(repository.allow_push)
         return False
 
     def user_can_administer_repository(self, user, repository):

From aa6feca9f60d2089b53bd43275121f299c12fdd2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 16:40:47 +0200
Subject: [PATCH 686/853] can_change_type doesn't need app

---
 lib/tool_shed/webapp/model/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 979c62baf8e1..abba8e76b6a0 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -220,7 +220,7 @@ def admin_role(self):
     def allow_push(self):
         return self.hg_repo.ui.config('web', 'allow_push')
 
-    def can_change_type(self, app):
+    def can_change_type(self):
         # Allow changing the type only if the repository has no contents, has never been installed, or has
         # never been changed from the default type.
         if self.is_new():
@@ -234,7 +234,7 @@ def can_change_type(self, app):
     def can_change_type_to(self, app, new_type_label):
         if self.type == new_type_label:
             return False
-        if self.can_change_type(app):
+        if self.can_change_type():
             new_type = app.repository_types_registry.get_class_by_label(new_type_label)
             if new_type.is_valid_for_type(app, self):
                 return True

From 1ceca3b620222c8ac2dd1537e360e4b69ad80556 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 16:46:10 +0200
Subject: [PATCH 687/853] Repository.revision doesn't need app access

---
 lib/tool_shed/grids/repository_grids.py | 2 +-
 lib/tool_shed/webapp/model/__init__.py  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py
index 1a1bdb8e3369..a03d67ef2a1f 100644
--- a/lib/tool_shed/grids/repository_grids.py
+++ b/lib/tool_shed/grids/repository_grids.py
@@ -140,7 +140,7 @@ def __init__(self, col_name):
 
         def get_value(self, trans, grid, repository):
             """Display the repository tip revision label."""
-            return escape_html(repository.revision(trans.app))
+            return escape_html(repository.revision())
 
     class DescriptionColumn(grids.TextColumn):
 
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index abba8e76b6a0..6b14dcd19323 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -283,7 +283,7 @@ def repo_path(self, app=None):
         # Keep app argumen for compaibility with tool_shed_install Repository model
         return hgweb_config_manager.get_entry(os.path.join("repos", self.user.username, self.name))
 
-    def revision(self, app):
+    def revision(self):
         repo = self.hg_repo
         tip_ctx = repo[repo.changelog.tip()]
         return "%s:%s" % (str(tip_ctx.rev()), str(tip_ctx))

From b9e902704c1e06ee0ccb60819a815b13408b8d43 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 16:48:03 +0200
Subject: [PATCH 688/853] is_valid_for_type doesn't need app

---
 lib/tool_shed/repository_types/metadata.py                    | 2 +-
 lib/tool_shed/repository_types/repository_suite_definition.py | 2 +-
 lib/tool_shed/repository_types/tool_dependency_definition.py  | 2 +-
 lib/tool_shed/repository_types/unrestricted.py                | 2 +-
 lib/tool_shed/repository_types/util.py                        | 2 +-
 lib/tool_shed/webapp/model/__init__.py                        | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/tool_shed/repository_types/metadata.py b/lib/tool_shed/repository_types/metadata.py
index 97933df01dfd..58d1135cd394 100644
--- a/lib/tool_shed/repository_types/metadata.py
+++ b/lib/tool_shed/repository_types/metadata.py
@@ -12,7 +12,7 @@ def get_changesets_for_setting_metadata(self, app, repository):
         repo = repository.hg_repo
         return repo.changelog
 
-    def is_valid_for_type(self, app, repository, revisions_to_check=None):
+    def is_valid_for_type(self, repository, revisions_to_check=None):
         raise Exception("Unimplemented Method")
 
 
diff --git a/lib/tool_shed/repository_types/repository_suite_definition.py b/lib/tool_shed/repository_types/repository_suite_definition.py
index 4645653fd0b4..b45e3946c746 100644
--- a/lib/tool_shed/repository_types/repository_suite_definition.py
+++ b/lib/tool_shed/repository_types/repository_suite_definition.py
@@ -14,7 +14,7 @@ def __init__(self):
         self.label = 'Repository suite definition'
         self.valid_file_names = ['repository_dependencies.xml']
 
-    def is_valid_for_type(self, app, repository, revisions_to_check=None):
+    def is_valid_for_type(self, repository, revisions_to_check=None):
         """
         Inspect the received repository's contents to determine if they abide by the rules defined for
         the contents of this type.  If the received revisions_to_check is a list of changeset revisions,
diff --git a/lib/tool_shed/repository_types/tool_dependency_definition.py b/lib/tool_shed/repository_types/tool_dependency_definition.py
index 90b331f045fb..11ffead4297b 100644
--- a/lib/tool_shed/repository_types/tool_dependency_definition.py
+++ b/lib/tool_shed/repository_types/tool_dependency_definition.py
@@ -14,7 +14,7 @@ def __init__(self):
         self.label = 'Tool dependency definition'
         self.valid_file_names = ['tool_dependencies.xml']
 
-    def is_valid_for_type(self, app, repository, revisions_to_check=None):
+    def is_valid_for_type(self, repository, revisions_to_check=None):
         """
         Inspect the received repository's contents to determine if they abide by the rules defined for the contents of this type.
         If the received revisions_to_check is a list of changeset revisions, then inspection will be restricted to the revisions
diff --git a/lib/tool_shed/repository_types/unrestricted.py b/lib/tool_shed/repository_types/unrestricted.py
index 0409a1c1c62a..9ccb55568cca 100644
--- a/lib/tool_shed/repository_types/unrestricted.py
+++ b/lib/tool_shed/repository_types/unrestricted.py
@@ -12,7 +12,7 @@ def __init__(self):
         self.type = rt_util.UNRESTRICTED
         self.label = 'Unrestricted'
 
-    def is_valid_for_type(self, app, repository, revisions_to_check=None):
+    def is_valid_for_type(self, repository, revisions_to_check=None):
         """A repository's type can only be changed to the unrestricted type if it is new or has never been installed."""
         if repository.is_new():
             return True
diff --git a/lib/tool_shed/repository_types/util.py b/lib/tool_shed/repository_types/util.py
index 974141d496c2..2cd7fccc9f5d 100644
--- a/lib/tool_shed/repository_types/util.py
+++ b/lib/tool_shed/repository_types/util.py
@@ -30,7 +30,7 @@ def build_repository_type_select_field(trans, repository=None, name='repository_
         if repository:
             if repository.type == option_value:
                 repository_type_select_field.add_option(option_label, option_value, selected=selected)
-            elif type_class.is_valid_for_type(trans.app, repository):
+            elif type_class.is_valid_for_type(repository):
                 repository_type_select_field.add_option(option_label, option_value, selected=selected)
         else:
             repository_type_select_field.add_option(option_label, option_value, selected=selected)
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 6b14dcd19323..42b6b64a6a3b 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -236,7 +236,7 @@ def can_change_type_to(self, app, new_type_label):
             return False
         if self.can_change_type():
             new_type = app.repository_types_registry.get_class_by_label(new_type_label)
-            if new_type.is_valid_for_type(app, self):
+            if new_type.is_valid_for_type(self):
                 return True
         return False
 

From 6d79c917e7f54855880580b651e7b9c90d4541d7 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 16:50:04 +0200
Subject: [PATCH 689/853] Tweak weakreaf check

---
 lib/tool_shed/webapp/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 42b6b64a6a3b..1da1ad15243e 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -202,7 +202,7 @@ def __init__(self, id=None, name=None, type=None, remote_repository_url=None, ho
 
     @property
     def hg_repo(self):
-        if WEAK_HG_REPO_CACHE.get(self) is None:
+        if not WEAK_HG_REPO_CACHE.get(self):
             WEAK_HG_REPO_CACHE[self] = hg.repository(ui.ui(), self.repo_path())
         return WEAK_HG_REPO_CACHE[self]
 

From f356c98e2b5b0d555780d8ccfa65cd46d33a338e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 1 Apr 2020 16:53:40 +0200
Subject: [PATCH 690/853] Lint fixes

---
 lib/tool_shed/test/base/twilltestcase.py | 3 +--
 lib/tool_shed/util/hg_util.py            | 1 -
 lib/tool_shed/util/hgweb_config.py       | 2 +-
 lib/tool_shed/util/shed_index.py         | 2 +-
 lib/tool_shed/webapp/model/__init__.py   | 2 +-
 5 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index e7fbce33374e..65a6614d2fc2 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -26,15 +26,14 @@
 
 import galaxy.model.tool_shed_install as galaxy_model
 import galaxy.util
-import tool_shed.webapp.util.hgweb_config
 from galaxy.security import idencoding
 from galaxy.util import smart_str, unicodify
 from galaxy_test.base.api_util import get_master_api_key
 from galaxy_test.driver.testcase import FunctionalTestCase
 from tool_shed.util import (
     hg_util,
+    hgweb_config,
     xml_util,
-    hgweb_config
 )
 from . import common, test_db_util
 
diff --git a/lib/tool_shed/util/hg_util.py b/lib/tool_shed/util/hg_util.py
index 39565cca8a8a..b113b656a16c 100644
--- a/lib/tool_shed/util/hg_util.py
+++ b/lib/tool_shed/util/hg_util.py
@@ -263,7 +263,6 @@ def changeset2rev(repo_path, changeset_revision):
     'get_file_context_from_ctx',
     'get_named_tmpfile_from_ctx',
     'get_readable_ctx_date',
-    'get_repo_for_repository',
     'get_repository_heads',
     'get_reversed_changelog_changesets',
     'get_revision_label',
diff --git a/lib/tool_shed/util/hgweb_config.py b/lib/tool_shed/util/hgweb_config.py
index 03119dbf41a4..b0171562aa14 100644
--- a/lib/tool_shed/util/hgweb_config.py
+++ b/lib/tool_shed/util/hgweb_config.py
@@ -106,4 +106,4 @@ def write_config(self):
         config_file.close
 
 
-hgweb_config_manager = HgWebConfigManager()
\ No newline at end of file
+hgweb_config_manager = HgWebConfigManager()
diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
index 9e00b606bc4f..5e537304b61b 100644
--- a/lib/tool_shed/util/shed_index.py
+++ b/lib/tool_shed/util/shed_index.py
@@ -13,10 +13,10 @@
     pretty_print_time_interval,
     unicodify
 )
+from tool_shed.util.hgweb_config import hgweb_config_manager
 from tool_shed.webapp import model
 from tool_shed.webapp.search.repo_search import schema as repo_schema
 from tool_shed.webapp.search.tool_search import schema as tool_schema
-from tool_shed.util.hgweb_config import hgweb_config_manager
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 1da1ad15243e..73b2ef76ee40 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -280,7 +280,7 @@ def is_new(self):
         return tip_rev < 0
 
     def repo_path(self, app=None):
-        # Keep app argumen for compaibility with tool_shed_install Repository model
+        # Keep app argument for compaibility with tool_shed_install Repository model
         return hgweb_config_manager.get_entry(os.path.join("repos", self.user.username, self.name))
 
     def revision(self):

From 41448d220cfc29de6f9eaf61f847f0e348bb08eb Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Sun, 16 Feb 2020 23:17:51 -0500
Subject: [PATCH 691/853] Remove obvious duplication from TS config

---
 lib/tool_shed/webapp/config.py | 49 ++++------------------------------
 1 file changed, 5 insertions(+), 44 deletions(-)

diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index dc4292c0a7ef..3dfcc856393e 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -51,10 +51,7 @@ def _resolve_paths(self, paths_to_resolve):
         pass  # Intentionally does nothing. To enable, remove + call base __init__().
 
     def __init__(self, **kwargs):
-        self.config_dict = kwargs
-        self.root = kwargs.get('root_dir', '.')
-
-        self._set_config_base(kwargs)
+        super(ToolShedAppConfiguration, self).__init__(**kwargs)
 
         # Resolve paths of other config files
         self.parse_config_file_options(kwargs)
@@ -66,34 +63,16 @@ def __init__(self, **kwargs):
         self.version_major = VERSION_MAJOR
         self.version = VERSION
         # Database related configuration
-        self.database_connection = kwargs.get("database_connection", False)
         self.database_connection = kwargs.get("database_connection",
                                               "sqlite:///%s?isolation_level=IMMEDIATE" % resolve_path("community.sqlite", self.data_dir))
         self.database_engine_options = get_database_engine_options(kwargs)
         self.database_create_tables = string_as_bool(kwargs.get("database_create_tables", "True"))
-        # Repository and Tool search API
-        self.toolshed_search_on = string_as_bool(kwargs.get("toolshed_search_on", True))
-        self.whoosh_index_dir = kwargs.get("whoosh_index_dir", 'database/toolshed_whoosh_indexes')
-        self.repo_name_boost = kwargs.get("repo_name_boost", 0.9)
-        self.repo_description_boost = kwargs.get("repo_description_boost", 0.6)
-        self.repo_long_description_boost = kwargs.get("repo_long_description_boost", 0.5)
-        self.repo_homepage_url_boost = kwargs.get("repo_homepage_url_boost", 0.3)
-        self.repo_remote_repository_url_boost = kwargs.get("repo_remote_repository_url_boost", 0.2)
-        self.repo_owner_username_boost = kwargs.get("repo_owner_username_boost", 0.3)
-        self.tool_name_boost = kwargs.get("tool_name_boost", 1.2)
-        self.tool_description_boost = kwargs.get("tool_description_boost", 0.6)
-        self.tool_help_boost = kwargs.get("tool_help_boost", 0.4)
-        self.tool_repo_owner_username = kwargs.get("tool_repo_owner_username", 0.3)
-        # Analytics
-        self.ga_code = kwargs.get("ga_code", None)
-        self.session_duration = int(kwargs.get('session_duration', 0))
         # Where dataset files are stored
-        self.file_path = resolve_path(kwargs.get("file_path", "database/community_files"), self.root)
-        self.new_file_path = resolve_path(kwargs.get("new_file_path", "database/tmp"), self.root)
+        self.file_path = resolve_path(self.file_path, self.root)
+        self.new_file_path = resolve_path(self.new_file_path, self.root)
         self.cookie_path = kwargs.get("cookie_path", None)
         self.cookie_domain = kwargs.get("cookie_domain", None)
         self.enable_quotas = string_as_bool(kwargs.get('enable_quotas', False))
-        self.id_secret = kwargs.get("id_secret", "changethisinproductiontoo")
         # Tool stuff
         self.tool_path = resolve_path(kwargs.get("tool_path", "tools"), self.root)
         self.tool_secret = kwargs.get("tool_secret", "")
@@ -105,11 +84,8 @@ def __init__(self, **kwargs):
         self.ftp_upload_dir = kwargs.get('ftp_upload_dir', None)
         self.update_integrated_tool_panel = False
         # Galaxy flavor Docker Image
-        self.enable_galaxy_flavor_docker_image = string_as_bool(kwargs.get("enable_galaxy_flavor_docker_image", "False"))
-        self.use_remote_user = string_as_bool(kwargs.get("use_remote_user", "False"))
         self.user_activation_on = None
         self.registration_warning_message = kwargs.get('registration_warning_message', None)
-        self.terms_url = kwargs.get('terms_url', None)
         self.blacklist_location = kwargs.get('blacklist_file', None)
         self.blacklist_content = None
         self.whitelist_location = kwargs.get('whitelist_file', None)
@@ -118,41 +94,26 @@ def __init__(self, **kwargs):
         self.remote_user_header = kwargs.get("remote_user_header", 'HTTP_REMOTE_USER')
         self.remote_user_logout_href = kwargs.get("remote_user_logout_href", None)
         self.remote_user_secret = kwargs.get("remote_user_secret", None)
-        self.require_login = string_as_bool(kwargs.get("require_login", "False"))
-        self.allow_user_creation = string_as_bool(kwargs.get("allow_user_creation", "True"))
-        self.allow_user_deletion = string_as_bool(kwargs.get("allow_user_deletion", "False"))
         self.template_path = templates_path
         self.template_cache_path = resolve_path(kwargs.get("template_cache_path", "database/compiled_templates/community"), self.root)
-        self.admin_users = kwargs.get("admin_users", "")
         self.admin_users_list = [u.strip() for u in self.admin_users.split(',') if u]
-        self.mailing_join_addr = kwargs.get('mailing_join_addr', "galaxy-announce-join@bx.psu.edu")
         self.error_email_to = kwargs.get('error_email_to', None)
         self.smtp_server = kwargs.get('smtp_server', None)
-        self.smtp_username = kwargs.get('smtp_username', None)
-        self.smtp_password = kwargs.get('smtp_password', None)
         self.smtp_ssl = kwargs.get('smtp_ssl', None)
         self.email_from = kwargs.get('email_from', None)
         self.nginx_upload_path = kwargs.get('nginx_upload_path', False)
         self.log_actions = string_as_bool(kwargs.get('log_actions', 'False'))
-        self.brand = kwargs.get('brand', None)
-        self.pretty_datetime_format = expand_pretty_datetime_format(kwargs.get('pretty_datetime_format', '$locale (UTC)'))
+        self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format)
         # Configuration for the message box directly below the masthead.
-        self.message_box_visible = string_as_bool(kwargs.get('message_box_visible', False))
-        self.message_box_content = kwargs.get('message_box_content', None)
-        self.message_box_class = kwargs.get('message_box_class', 'info')
-        self.support_url = kwargs.get('support_url', 'https://galaxyproject.org/support')
         self.wiki_url = kwargs.get('wiki_url', 'https://galaxyproject.org/')
         self.blog_url = kwargs.get('blog_url', None)
         self.screencasts_url = kwargs.get('screencasts_url', None)
         self.log_events = False
         self.cloud_controller_instance = False
         self.server_name = ''
-        # Error logging with sentry
-        self.sentry_dsn = kwargs.get('sentry_dsn', None)
         # Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory.
-        self.hgweb_config_dir = resolve_path(kwargs.get('hgweb_config_dir', ''), self.root)
+        self.hgweb_config_dir = resolve_path(self.hgweb_config_dir, self.root)
         # Proxy features
-        self.apache_xsendfile = kwargs.get('apache_xsendfile', False)
         self.nginx_x_accel_redirect_base = kwargs.get('nginx_x_accel_redirect_base', False)
         self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script', None)
         # Parse global_conf and save the parser

From 78daace8adc9b57b9c04f4104ff4bf764381a922 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Sat, 14 Mar 2020 22:26:44 -0400
Subject: [PATCH 692/853] Rebase; remove stub methods: let base do the work

---
 lib/tool_shed/webapp/config.py | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index 3dfcc856393e..5d529650fbb8 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -41,15 +41,6 @@ class ToolShedAppConfiguration(BaseAppConfiguration):
     def _load_schema(self):
         return AppSchema(TOOLSHED_CONFIG_SCHEMA_PATH, TOOLSHED_APP_NAME)
 
-    def _update_raw_config_from_kwargs(self, kwargs):
-        pass  # Intentionally does nothing. To enable, remove + call base __init__().
-
-    def _create_attributes_from_raw_config(self):
-        pass  # Intentionally does nothing. To enable, remove + call base __init__().
-
-    def _resolve_paths(self, paths_to_resolve):
-        pass  # Intentionally does nothing. To enable, remove + call base __init__().
-
     def __init__(self, **kwargs):
         super(ToolShedAppConfiguration, self).__init__(**kwargs)
 

From 2fe7f4d335724ce23adf71ea4c3f60af4451b44b Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Sat, 14 Mar 2020 22:48:15 -0400
Subject: [PATCH 693/853] Remove mics. duplication from config

---
 lib/galaxy/config/__init__.py | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index d10da18e85f1..738b32c7651d 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -325,7 +325,6 @@ def _process_config(self, kwargs):
         self.database_engine_options = get_database_engine_options(kwargs)
         self.database_create_tables = string_as_bool(kwargs.get('database_create_tables', 'True'))
         self.database_encoding = kwargs.get('database_encoding')  # Create new databases with this encoding
-        self.database_log_query_counts = string_as_bool(kwargs.get("database_log_query_counts", 'False'))
         self.thread_local_log = None
         if self.enable_per_request_sql_debugging:
             self.thread_local_log = threading.local()
@@ -340,7 +339,7 @@ def _process_config(self, kwargs):
         self.tool_path = os.path.join(self.root, self.tool_path)
         self.tool_data_path = os.path.join(self.root, self.tool_data_path)
         if not running_from_source and kwargs.get("tool_data_path") is None:
-            self.tool_data_path = os.path.join(self.data_dir, "tool-data")
+            self.tool_data_path = self._in_data_dir(self.schema.defaults['tool_data_path'])
         self.builds_file_path = os.path.join(self.tool_data_path, self.builds_file_path)
         self.len_file_path = os.path.join(self.tool_data_path, self.len_file_path)
         # Galaxy OIDC settings.
@@ -528,17 +527,15 @@ def _process_config(self, kwargs):
         self.object_store = kwargs.get('object_store', 'disk')
         self.object_store_check_old_style = string_as_bool(kwargs.get('object_store_check_old_style', False))
         self.object_store_cache_path = self.resolve_path(kwargs.get("object_store_cache_path", os.path.join(self.data_dir, "object_store_cache")))
-        object_store_store_by = kwargs.get('object_store_store_by', None)
-        if object_store_store_by is None:
+        if self.object_store_store_by is None:
             if not self.file_path_set:
                 if self.file_path.endswith('objects'):
-                    object_store_store_by = 'uuid'
+                    self.object_store_store_by = 'uuid'
                 else:
-                    object_store_store_by = 'id'
+                    self.object_store_store_by = 'id'
             else:
-                object_store_store_by = 'id'
-        assert object_store_store_by in ['id', 'uuid'], "Invalid value for object_store_store_by [%s]" % object_store_store_by
-        self.object_store_store_by = object_store_store_by
+                self.object_store_store_by = 'id'
+        assert self.object_store_store_by in ['id', 'uuid'], "Invalid value for object_store_store_by [%s]" % self.object_store_store_by
         # Handle AWS-specific config options for backward compatibility
         if kwargs.get('aws_access_key') is not None:
             self.os_access_key = kwargs.get('aws_access_key')
@@ -620,7 +617,6 @@ def _process_config(self, kwargs):
         # This is for testing new library browsing capabilities.
         self.new_lib_browse = string_as_bool(kwargs.get('new_lib_browse', False))
         # Logging configuration with logging.config.configDict:
-        self.logging = kwargs.get('logging')
         # Statistics and profiling with statsd
         self.statsd_host = kwargs.get('statsd_host', '')
 

From 67c799fd0015988fd792e8f23b2cdb5180bb0aee Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Sat, 14 Mar 2020 22:50:27 -0400
Subject: [PATCH 694/853] Trim some boolean logic.

---
 lib/galaxy/config/__init__.py | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 738b32c7651d..952bbfe9a0be 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -528,13 +528,9 @@ def _process_config(self, kwargs):
         self.object_store_check_old_style = string_as_bool(kwargs.get('object_store_check_old_style', False))
         self.object_store_cache_path = self.resolve_path(kwargs.get("object_store_cache_path", os.path.join(self.data_dir, "object_store_cache")))
         if self.object_store_store_by is None:
-            if not self.file_path_set:
-                if self.file_path.endswith('objects'):
-                    self.object_store_store_by = 'uuid'
-                else:
-                    self.object_store_store_by = 'id'
-            else:
-                self.object_store_store_by = 'id'
+            self.object_store_store_by = 'id'
+            if not self.file_path_set and self.file_path.endswith('objects'):
+                self.object_store_store_by = 'uuid'
         assert self.object_store_store_by in ['id', 'uuid'], "Invalid value for object_store_store_by [%s]" % self.object_store_store_by
         # Handle AWS-specific config options for backward compatibility
         if kwargs.get('aws_access_key') is not None:

From a303b1e0e5ef3b09f45ebe5b6edd478be8260fe4 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Sun, 15 Mar 2020 20:54:44 -0400
Subject: [PATCH 695/853] Move resolve_path to base class; use _in_root
 internally

Prerequisite for getting rid of more duplication in TS config. Makes
things consistent in galaxy config.
---
 lib/galaxy/config/__init__.py | 35 ++++++++++++++++-------------------
 1 file changed, 16 insertions(+), 19 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 952bbfe9a0be..0c44246580da 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -118,6 +118,10 @@ def __init__(self, **kwargs):
         self._create_attributes_from_raw_config()  # Create attributes based on raw_config
         self._resolve_paths()  # Overwrite attribute values with resolved paths
 
+    def resolve_path(self, path):
+        """Resolve a path relative to Galaxy's root."""
+        return self._in_root_dir(path)
+
     def _set_config_base(self, config_kwargs):
 
         def _set_global_conf():
@@ -245,6 +249,9 @@ def resolve(key):
         for key in self.schema.paths_to_resolve:
             resolve(key)
 
+    def _in_root_dir(self, path):
+        return os.path.join(self.root, path)
+
     def _in_managed_config_dir(self, path):
         return self._in_dir(self.managed_config_dir, path)
 
@@ -402,7 +409,7 @@ def _process_config(self, kwargs):
         ]
         self.template_path = os.path.join(self.root, kwargs.get("template_path", "templates"))
         self.job_queue_cleanup_interval = int(kwargs.get("job_queue_cleanup_interval", "5"))
-        self.cluster_files_directory = self.resolve_path(self.cluster_files_directory)
+        self.cluster_files_directory = self._in_root_dir(self.cluster_files_directory)
 
         # Fall back to legacy job_working_directory config variable if set.
         self.jobs_directory = os.path.join(self.data_dir, kwargs.get("jobs_directory", self.job_working_directory))
@@ -414,7 +421,7 @@ def _process_config(self, kwargs):
         # should probably drop the backward compatiblity to save the path check.
         self.container_image_cache_path = os.path.join(self.data_dir, kwargs.get("container_image_cache_path", "container_images"))
         if not os.path.exists(self.container_image_cache_path):
-            self.container_image_cache_path = self.resolve_path(kwargs.get("container_image_cache_path", os.path.join(self.data_dir, "container_cache")))
+            self.container_image_cache_path = self._in_root_dir(kwargs.get("container_image_cache_path", os.path.join(self.data_dir, "container_cache")))
         self.output_size_limit = int(kwargs.get('output_size_limit', 0))
         # activation_email was used until release_15.03
         activation_email = kwargs.get('activation_email')
@@ -451,7 +458,7 @@ def _process_config(self, kwargs):
             workflow_resource_params_mapper = None
         elif ":" not in workflow_resource_params_mapper:
             # Assume it is not a Python function, so a file
-            workflow_resource_params_mapper = self.resolve_path(workflow_resource_params_mapper)
+            workflow_resource_params_mapper = self._in_root_dir(workflow_resource_params_mapper)
         # else: a Python a function!
         self.workflow_resource_params_mapper = workflow_resource_params_mapper
 
@@ -526,7 +533,7 @@ def _process_config(self, kwargs):
             self.nginx_upload_store = os.path.abspath(self.nginx_upload_store)
         self.object_store = kwargs.get('object_store', 'disk')
         self.object_store_check_old_style = string_as_bool(kwargs.get('object_store_check_old_style', False))
-        self.object_store_cache_path = self.resolve_path(kwargs.get("object_store_cache_path", os.path.join(self.data_dir, "object_store_cache")))
+        self.object_store_cache_path = self._in_root_dir(kwargs.get("object_store_cache_path", os.path.join(self.data_dir, "object_store_cache")))
         if self.object_store_store_by is None:
             self.object_store_store_by = 'id'
             if not self.file_path_set and self.file_path.endswith('objects'):
@@ -625,7 +632,7 @@ def _process_config(self, kwargs):
         self.manage_dynamic_proxy = self.dynamic_proxy_manage  # Set to false if being launched externally
 
         # InteractiveTools propagator mapping file
-        self.interactivetools_map = self.resolve_path(kwargs.get("interactivetools_map", os.path.join(self.data_dir, "interactivetools_map.sqlite")))
+        self.interactivetools_map = self._in_root_dir(kwargs.get("interactivetools_map", os.path.join(self.data_dir, "interactivetools_map.sqlite")))
         self.interactivetool_prefix = kwargs.get("interactivetools_prefix", "interactivetool")
         self.interactivetool_proxy_host = kwargs.get("interactivetool_proxy_host", None)
 
@@ -728,9 +735,7 @@ def sentry_dsn_public(self):
             return None
 
     def parse_config_file_options(self, kwargs):
-        """
-        Backwards compatibility for config files moved to the config/ dir.
-        """
+        """Backwards compatibility for config files moved to the config/ dir."""
         defaults = dict(
             auth_config_file=[self._in_config_dir('auth_conf.xml')],
             build_sites_config_file=[self._in_config_dir('build_sites.yml'), self._in_sample_dir('build_sites.yml.sample')],
@@ -843,11 +848,6 @@ def is_admin_user(self, user):
         """
         return user is not None and user.email in self.admin_users_list
 
-    def resolve_path(self, path):
-        """ Resolve a path relative to Galaxy's root.
-        """
-        return os.path.join(self.root, path)
-
     @staticmethod
     def _parse_allowed_origin_hostnames(kwargs):
         """
@@ -873,7 +873,7 @@ def parse(string):
 
 
 def reload_config_options(current_config):
-    """ Reload modified reloadable config options """
+    """Reload modified reloadable config options."""
     modified_config = read_properties_from_file(current_config.config_file)
     for option in current_config.schema.reloadable_options:
         if option in modified_config:
@@ -974,8 +974,7 @@ def configure_logging(config):
 
 
 class ConfiguresGalaxyMixin(object):
-    """ Shared code for configuring Galaxy-like app objects.
-    """
+    """Shared code for configuring Galaxy-like app objects."""
 
     def _configure_genome_builds(self, data_table_name="__dbkeys__", load_old_style=True):
         self.genome_builds = GenomeBuilds(self, data_table_name=data_table_name, load_old_style=load_old_style)
@@ -1112,9 +1111,7 @@ def _configure_tool_shed_registry(self):
             self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry()
 
     def _configure_models(self, check_migrate_databases=False, check_migrate_tools=False, config_file=None):
-        """
-        Preconditions: object_store must be set on self.
-        """
+        """Preconditions: object_store must be set on self."""
         db_url = get_database_url(self.config)
         install_db_url = self.config.install_database_connection
         # TODO: Consider more aggressive check here that this is not the same

From 281b854998e34b1126362ccd8b8347b55c980d49 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Sun, 15 Mar 2020 21:49:34 -0400
Subject: [PATCH 696/853] Get rid of path_resolve in TS config

Same as identical method in galaxy config's that was removed in 8646.
See rationale in commit message: https://github.com/galaxyproject/galaxy/pull/8646/commits/4518d803f2e17b6e930b9426aa888d80d1ee7e6f
---
 lib/tool_shed/webapp/config.py | 33 +++++++++++++--------------------
 1 file changed, 13 insertions(+), 20 deletions(-)

diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index 5d529650fbb8..c8aa10a4b26f 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -24,13 +24,6 @@
 TOOLSHED_CONFIG_SCHEMA_PATH = 'lib/tool_shed/webapp/config_schema.yml'
 
 
-def resolve_path(path, root):
-    """If 'path' is relative make absolute by prepending 'root'"""
-    if not(os.path.isabs(path)):
-        path = os.path.join(root, path)
-    return path
-
-
 class ConfigurationError(Exception):
     pass
 
@@ -54,24 +47,24 @@ def __init__(self, **kwargs):
         self.version_major = VERSION_MAJOR
         self.version = VERSION
         # Database related configuration
-        self.database_connection = kwargs.get("database_connection",
-                                              "sqlite:///%s?isolation_level=IMMEDIATE" % resolve_path("community.sqlite", self.data_dir))
+        if not self.database_connection:  # Provide default if not supplied by user
+            self.database_connection = 'sqlite:///%s?isolation_level=IMMEDIATE' % self._in_data_dir('community.sqlite')
         self.database_engine_options = get_database_engine_options(kwargs)
         self.database_create_tables = string_as_bool(kwargs.get("database_create_tables", "True"))
         # Where dataset files are stored
-        self.file_path = resolve_path(self.file_path, self.root)
-        self.new_file_path = resolve_path(self.new_file_path, self.root)
+        self.file_path = self._in_root_dir(self.file_path)
+        self.new_file_path = self._in_root_dir(self.new_file_path)
         self.cookie_path = kwargs.get("cookie_path", None)
         self.cookie_domain = kwargs.get("cookie_domain", None)
         self.enable_quotas = string_as_bool(kwargs.get('enable_quotas', False))
         # Tool stuff
-        self.tool_path = resolve_path(kwargs.get("tool_path", "tools"), self.root)
+        self.tool_path = self._in_root_dir(kwargs.get("tool_path", "tools"))
         self.tool_secret = kwargs.get("tool_secret", "")
-        self.tool_data_path = resolve_path(kwargs.get("tool_data_path", "shed-tool-data"), os.getcwd())
+        self.tool_data_path = os.path.join(os.getcwd(), kwargs.get("tool_data_path", "shed-tool-data"))
         self.tool_data_table_config_path = None
-        self.integrated_tool_panel_config = resolve_path(kwargs.get('integrated_tool_panel_config', 'integrated_tool_panel.xml'), self.root)
-        self.builds_file_path = resolve_path(kwargs.get("builds_file_path", os.path.join(self.tool_data_path, 'shared', 'ucsc', 'builds.txt')), self.root)
-        self.len_file_path = resolve_path(kwargs.get("len_file_path", os.path.join(self.tool_data_path, 'shared', 'ucsc', 'chrom')), self.root)
+        self.integrated_tool_panel_config = self._in_root_dir(kwargs.get('integrated_tool_panel_config', 'integrated_tool_panel.xml'))
+        self.builds_file_path = self._in_root_dir(kwargs.get("builds_file_path", os.path.join(self.tool_data_path, 'shared', 'ucsc', 'builds.txt')))
+        self.len_file_path = self._in_root_dir(kwargs.get("len_file_path", os.path.join(self.tool_data_path, 'shared', 'ucsc', 'chrom')))
         self.ftp_upload_dir = kwargs.get('ftp_upload_dir', None)
         self.update_integrated_tool_panel = False
         # Galaxy flavor Docker Image
@@ -86,7 +79,7 @@ def __init__(self, **kwargs):
         self.remote_user_logout_href = kwargs.get("remote_user_logout_href", None)
         self.remote_user_secret = kwargs.get("remote_user_secret", None)
         self.template_path = templates_path
-        self.template_cache_path = resolve_path(kwargs.get("template_cache_path", "database/compiled_templates/community"), self.root)
+        self.template_cache_path = self._in_root_dir(kwargs.get("template_cache_path", "database/compiled_templates/community"))
         self.admin_users_list = [u.strip() for u in self.admin_users.split(',') if u]
         self.error_email_to = kwargs.get('error_email_to', None)
         self.smtp_server = kwargs.get('smtp_server', None)
@@ -103,7 +96,7 @@ def __init__(self, **kwargs):
         self.cloud_controller_instance = False
         self.server_name = ''
         # Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory.
-        self.hgweb_config_dir = resolve_path(self.hgweb_config_dir, self.root)
+        self.hgweb_config_dir = self._in_root_dir(self.hgweb_config_dir)
         # Proxy features
         self.nginx_x_accel_redirect_base = kwargs.get('nginx_x_accel_redirect_base', False)
         self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script', None)
@@ -115,8 +108,8 @@ def __init__(self, **kwargs):
             global_conf_parser.read(global_conf['__file__'])
         self.running_functional_tests = string_as_bool(kwargs.get('running_functional_tests', False))
         self.citation_cache_type = kwargs.get("citation_cache_type", "file")
-        self.citation_cache_data_dir = resolve_path(kwargs.get("citation_cache_data_dir", "database/tool_shed_citations/data"), self.root)
-        self.citation_cache_lock_dir = resolve_path(kwargs.get("citation_cache_lock_dir", "database/tool_shed_citations/locks"), self.root)
+        self.citation_cache_data_dir = self._in_root_dir(kwargs.get("citation_cache_data_dir", "database/tool_shed_citations/data"))
+        self.citation_cache_lock_dir = self._in_root_dir(kwargs.get("citation_cache_lock_dir", "database/tool_shed_citations/locks"))
         self.password_expiration_period = timedelta(days=int(kwargs.get("password_expiration_period", 0)))
 
         # Security/Policy Compliance

From 4c94eab50a4520c05d5481d7941c7f0934d912ad Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Sun, 15 Mar 2020 22:47:09 -0400
Subject: [PATCH 697/853] Use dedicated helpers instead of os.path.join

(_in_data_dir, _in_root_dir, etc.)
---
 lib/galaxy/config/__init__.py | 45 ++++++++++++++++-------------------
 1 file changed, 21 insertions(+), 24 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 0c44246580da..1e9df2632ef7 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -327,7 +327,7 @@ def _process_config(self, kwargs):
         # Database related configuration
         self.check_migrate_databases = kwargs.get('check_migrate_databases', True)
         if not self.database_connection:  # Provide default if not supplied by user
-            db_path = os.path.join(self.data_dir, 'universe.sqlite')
+            db_path = self._in_data_dir('universe.sqlite')
             self.database_connection = 'sqlite:///%s?isolation_level=IMMEDIATE' % db_path
         self.database_engine_options = get_database_engine_options(kwargs)
         self.database_create_tables = string_as_bool(kwargs.get('database_create_tables', 'True'))
@@ -343,8 +343,8 @@ def _process_config(self, kwargs):
             tempfile.tempdir = self.new_file_path
         self.shared_home_dir = kwargs.get("shared_home_dir")
         self.cookie_path = kwargs.get("cookie_path")
-        self.tool_path = os.path.join(self.root, self.tool_path)
-        self.tool_data_path = os.path.join(self.root, self.tool_data_path)
+        self.tool_path = self._in_root_dir(self.tool_path)
+        self.tool_data_path = self._in_root_dir(self.tool_data_path)
         if not running_from_source and kwargs.get("tool_data_path") is None:
             self.tool_data_path = self._in_data_dir(self.schema.defaults['tool_data_path'])
         self.builds_file_path = os.path.join(self.tool_data_path, self.builds_file_path)
@@ -356,7 +356,7 @@ def _process_config(self, kwargs):
         self.integrated_tool_panel_config = self._in_managed_config_dir(self.integrated_tool_panel_config)
         integrated_tool_panel_tracking_directory = kwargs.get('integrated_tool_panel_tracking_directory')
         if integrated_tool_panel_tracking_directory:
-            self.integrated_tool_panel_tracking_directory = os.path.join(self.root, integrated_tool_panel_tracking_directory)
+            self.integrated_tool_panel_tracking_directory = self._in_root_dir(integrated_tool_panel_tracking_directory)
         else:
             self.integrated_tool_panel_tracking_directory = None
         self.toolbox_filter_base_modules = listify(self.toolbox_filter_base_modules)
@@ -372,7 +372,7 @@ def _process_config(self, kwargs):
         self.password_expiration_period = timedelta(days=int(self.password_expiration_period))
 
         if self.shed_tool_data_path:
-            self.shed_tool_data_path = os.path.join(self.root, self.shed_tool_data_path)
+            self.shed_tool_data_path = self._in_root_dir(self.shed_tool_data_path)
         else:
             self.shed_tool_data_path = self.tool_data_path
 
@@ -407,21 +407,21 @@ def _process_config(self, kwargs):
             for ip in kwargs.get("fetch_url_whitelist", "").split(',')
             if len(ip.strip()) > 0
         ]
-        self.template_path = os.path.join(self.root, kwargs.get("template_path", "templates"))
+        self.template_path = self._in_root_dir(kwargs.get("template_path", "templates"))
         self.job_queue_cleanup_interval = int(kwargs.get("job_queue_cleanup_interval", "5"))
         self.cluster_files_directory = self._in_root_dir(self.cluster_files_directory)
 
         # Fall back to legacy job_working_directory config variable if set.
-        self.jobs_directory = os.path.join(self.data_dir, kwargs.get("jobs_directory", self.job_working_directory))
+        self.jobs_directory = self._in_data_dir(kwargs.get("jobs_directory", self.job_working_directory))
         if self.preserve_python_environment not in ["legacy_only", "legacy_and_local", "always"]:
             log.warning("preserve_python_environment set to unknown value [%s], defaulting to legacy_only")
             self.preserve_python_environment = "legacy_only"
         self.nodejs_path = kwargs.get("nodejs_path")
         # Older default container cache path, I don't think anyone is using it anymore and it wasn't documented - we
         # should probably drop the backward compatiblity to save the path check.
-        self.container_image_cache_path = os.path.join(self.data_dir, kwargs.get("container_image_cache_path", "container_images"))
+        self.container_image_cache_path = self._in_data_dir(kwargs.get("container_image_cache_path", "container_images"))
         if not os.path.exists(self.container_image_cache_path):
-            self.container_image_cache_path = self._in_root_dir(kwargs.get("container_image_cache_path", os.path.join(self.data_dir, "container_cache")))
+            self.container_image_cache_path = self._in_root_dir(kwargs.get("container_image_cache_path", self._in_data_dir("container_cache")))
         self.output_size_limit = int(kwargs.get('output_size_limit', 0))
         # activation_email was used until release_15.03
         activation_email = kwargs.get('activation_email')
@@ -430,7 +430,7 @@ def _process_config(self, kwargs):
         #  Get the disposable email domains blacklist file and its contents
         self.blacklist_content = None
         if self.blacklist_file:
-            self.blacklist_file = os.path.join(self.root, self.blacklist_file)
+            self.blacklist_file = self._in_root_dir(self.blacklist_file)
             try:
                 with open(self.blacklist_file) as f:
                     self.blacklist_content = [line.rstrip() for line in f]
@@ -469,7 +469,7 @@ def _process_config(self, kwargs):
 
         _sanitize_whitelist_path = self._in_managed_config_dir(self.sanitize_whitelist_file)
         if not os.path.isfile(_sanitize_whitelist_path):  # then check old default location
-            deprecated = os.path.join(self.root, 'config/sanitize_whitelist.txt')
+            deprecated = self._in_root_dir('config/sanitize_whitelist.txt')
             if os.path.isfile(deprecated):
                 log.warning("The path '%s' for the 'sanitize_whitelist_file' config option is "
                     "deprecated and will be no longer checked in a future release. Please consult "
@@ -497,29 +497,26 @@ def _process_config(self, kwargs):
         # not needed on production systems but useful if running many functional tests.
         self.index_tool_help = string_as_bool(kwargs.get("index_tool_help", True))
         self.tool_labels_boost = kwargs.get("tool_labels_boost", 1)
-        default_tool_test_data_directories = os.environ.get("GALAXY_TEST_FILE_DIR", os.path.join(self.root, "test-data"))
+        default_tool_test_data_directories = os.environ.get("GALAXY_TEST_FILE_DIR", self._in_root_dir("test-data"))
         self.tool_test_data_directories = kwargs.get("tool_test_data_directories", default_tool_test_data_directories)
         # Deployers may either specify a complete list of mapping files or get the default for free and just
         # specify a local mapping file to adapt and extend the default one.
         if "conda_mapping_files" not in kwargs:
-            conda_mapping_files = [
-                self.local_conda_mapping_file,
-                os.path.join(self.root, "lib", "galaxy", "tool_util", "deps", "resolvers", "default_conda_mapping.yml"),
-            ]
+            _default_mapping = self._in_root_dir(os.path.join("lib", "galaxy", "tool_util", "deps", "resolvers", "default_conda_mapping.yml"))
             # dependency resolution options are consumed via config_dict - so don't populate
             # self, populate config_dict
-            self.config_dict["conda_mapping_files"] = conda_mapping_files
+            self.config_dict["conda_mapping_files"] = [self.local_conda_mapping_file, _default_mapping]
 
         if self.containers_resolvers_config_file:
-            self.containers_resolvers_config_file = os.path.join(self.config_dir, self.containers_resolvers_config_file)
+            self.containers_resolvers_config_file = self._in_config_dir(self.containers_resolvers_config_file)
 
         # tool_dependency_dir can be "none" (in old configs). If so, set it to None
         if self.tool_dependency_dir and self.tool_dependency_dir.lower() == 'none':
             self.tool_dependency_dir = None
         if self.involucro_path is None:
             target_dir = self.tool_dependency_dir or self.schema.defaults['tool_dependency_dir']
-            self.involucro_path = os.path.join(self.data_dir, target_dir, "involucro")
-        self.involucro_path = os.path.join(self.root, self.involucro_path)
+            self.involucro_path = self._in_data_dir(os.path.join(target_dir, "involucro"))
+        self.involucro_path = self._in_root_dir(self.involucro_path)
         if self.mulled_channels:
             self.mulled_channels = [c.strip() for c in self.mulled_channels.split(',')]
 
@@ -533,7 +530,7 @@ def _process_config(self, kwargs):
             self.nginx_upload_store = os.path.abspath(self.nginx_upload_store)
         self.object_store = kwargs.get('object_store', 'disk')
         self.object_store_check_old_style = string_as_bool(kwargs.get('object_store_check_old_style', False))
-        self.object_store_cache_path = self._in_root_dir(kwargs.get("object_store_cache_path", os.path.join(self.data_dir, "object_store_cache")))
+        self.object_store_cache_path = self._in_root_dir(kwargs.get("object_store_cache_path", self._in_data_dir("object_store_cache")))
         if self.object_store_store_by is None:
             self.object_store_store_by = 'id'
             if not self.file_path_set and self.file_path.endswith('objects'):
@@ -557,7 +554,7 @@ def _process_config(self, kwargs):
         self.object_store_cache_size = float(kwargs.get('object_store_cache_size', -1))
         self.distributed_object_store_config_file = kwargs.get('distributed_object_store_config_file')
         if self.distributed_object_store_config_file is not None:
-            self.distributed_object_store_config_file = os.path.join(self.root, self.distributed_object_store_config_file)
+            self.distributed_object_store_config_file = self._in_root_dir(self.distributed_object_store_config_file)
         self.irods_root_collection_path = kwargs.get('irods_root_collection_path')
         self.irods_default_resource = kwargs.get('irods_default_resource')
         # Heartbeat log file name override
@@ -603,7 +600,7 @@ def _process_config(self, kwargs):
         elif 'database_connection' in kwargs:
             self.amqp_internal_connection = "sqlalchemy+" + self.database_connection
         else:
-            self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % os.path.join(self.data_dir, "control.sqlite")
+            self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % self._in_data_dir("control.sqlite")
         self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format)
         try:
             with open(self.user_preferences_extra_conf_path, 'r') as stream:
@@ -632,7 +629,7 @@ def _process_config(self, kwargs):
         self.manage_dynamic_proxy = self.dynamic_proxy_manage  # Set to false if being launched externally
 
         # InteractiveTools propagator mapping file
-        self.interactivetools_map = self._in_root_dir(kwargs.get("interactivetools_map", os.path.join(self.data_dir, "interactivetools_map.sqlite")))
+        self.interactivetools_map = self._in_root_dir(kwargs.get("interactivetools_map", self._in_data_dir("interactivetools_map.sqlite")))
         self.interactivetool_prefix = kwargs.get("interactivetools_prefix", "interactivetool")
         self.interactivetool_proxy_host = kwargs.get("interactivetool_proxy_host", None)
 

From a92323e53d13eb4ad86d8897fc81548685686aa0 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 16 Mar 2020 00:38:44 -0400
Subject: [PATCH 698/853] Use mixin for common config settings

- Create mixin
- Factor out admin_user settings and initialization into mixin
---
 lib/galaxy/config/__init__.py  | 43 +++++++++++++++++-----------------
 lib/tool_shed/webapp/config.py | 12 ++--------
 2 files changed, 23 insertions(+), 32 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 1e9df2632ef7..9593a8515c82 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -301,7 +301,27 @@ def _parse_config_file_options(self, defaults, listify_defaults, config_kwargs):
             setattr(self, var, [os.path.join(self.root, x) for x in paths])
 
 
-class GalaxyAppConfiguration(BaseAppConfiguration):
+class CommonConfigurationMixin(object):
+    """Shared configuration settings code for Galaxy and ToolShed."""
+
+    @property
+    def admin_users(self):
+        return self._admin_users
+
+    @admin_users.setter
+    def admin_users(self, value):
+        self._admin_users = value
+        if value:
+            self.admin_users_list = [u.strip() for u in value.split(',') if u]
+        else:  # provide empty list for convenience (check membership, etc.)
+            self.admin_users_list = []
+
+    def is_admin_user(self, user):
+        """Determine if the provided user is listed in `admin_users`."""
+        return user is not None and user.email in self.admin_users_list
+
+
+class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     deprecated_options = ('database_file', 'track_jobs_in_database')
     default_config_file_name = 'galaxy.yml'
     deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
@@ -708,18 +728,6 @@ def _set_galaxy_infrastructure_url(self, kwargs):
                 'UWSGI_PORT': port
             })
 
-    @property
-    def admin_users(self):
-        return self._admin_users
-
-    @admin_users.setter
-    def admin_users(self, value):
-        self._admin_users = value
-        if value:
-            self.admin_users_list = [u.strip() for u in value.split(',') if u]
-        else:  # provide empty list for convenience (check membership, etc.)
-            self.admin_users_list = []
-
     @property
     def sentry_dsn_public(self):
         """
@@ -836,15 +844,6 @@ def check(self):
             if key in self.deprecated_options:
                 log.warning("Config option '%s' is deprecated and will be removed in a future release.  Please consult the latest version of the sample configuration file." % key)
 
-    def is_admin_user(self, user):
-        """
-        Determine if the provided user is listed in `admin_users`.
-
-        NOTE: This is temporary, admin users will likely be specified in the
-              database in the future.
-        """
-        return user is not None and user.email in self.admin_users_list
-
     @staticmethod
     def _parse_allowed_origin_hostnames(kwargs):
         """
diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index c8aa10a4b26f..7a4012306fec 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -9,7 +9,7 @@
 
 from six.moves import configparser
 
-from galaxy.config import BaseAppConfiguration
+from galaxy.config import BaseAppConfiguration, CommonConfigurationMixin
 from galaxy.config.schema import AppSchema
 from galaxy.util import string_as_bool
 from galaxy.version import VERSION, VERSION_MAJOR
@@ -28,7 +28,7 @@ class ConfigurationError(Exception):
     pass
 
 
-class ToolShedAppConfiguration(BaseAppConfiguration):
+class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     default_config_file_name = 'tool_shed.yml'
 
     def _load_schema(self):
@@ -80,7 +80,6 @@ def __init__(self, **kwargs):
         self.remote_user_secret = kwargs.get("remote_user_secret", None)
         self.template_path = templates_path
         self.template_cache_path = self._in_root_dir(kwargs.get("template_cache_path", "database/compiled_templates/community"))
-        self.admin_users_list = [u.strip() for u in self.admin_users.split(',') if u]
         self.error_email_to = kwargs.get('error_email_to', None)
         self.smtp_server = kwargs.get('smtp_server', None)
         self.smtp_ssl = kwargs.get('smtp_ssl', None)
@@ -183,13 +182,6 @@ def check(self):
         if not os.path.isfile(self.datatypes_config):
             raise ConfigurationError("File not found: %s" % self.datatypes_config)
 
-    def is_admin_user(self, user):
-        """
-        Determine if the provided user is listed in `admin_users`.
-        """
-        admin_users = self.get("admin_users", "").split(",")
-        return user is not None and user.email in admin_users
-
 
 Configuration = ToolShedAppConfiguration
 

From 9f78181b228677ca1039c83039b91c0a54f2a2f7 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 30 Mar 2020 10:54:44 -0400
Subject: [PATCH 699/853] Apply _in_dir helper to _in_root()

_in_dir helper was added in #9568
---
 lib/galaxy/config/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 9593a8515c82..ac903ba583a8 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -250,7 +250,7 @@ def resolve(key):
             resolve(key)
 
     def _in_root_dir(self, path):
-        return os.path.join(self.root, path)
+        return self._in_dir(self.root, path)
 
     def _in_managed_config_dir(self, path):
         return self._in_dir(self.managed_config_dir, path)

From acf4404270574150add5620ba375e98f914f16b3 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 30 Mar 2020 11:02:38 -0400
Subject: [PATCH 700/853] Set hgweb_config_dir to root if null

There is no way to specify self.root as the default in the schema right
now. There should be.
---
 lib/tool_shed/webapp/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index 7a4012306fec..ecc25a7e6712 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -95,7 +95,7 @@ def __init__(self, **kwargs):
         self.cloud_controller_instance = False
         self.server_name = ''
         # Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory.
-        self.hgweb_config_dir = self._in_root_dir(self.hgweb_config_dir)
+        self.hgweb_config_dir = self._in_root_dir(self.hgweb_config_dir) or self.root
         # Proxy features
         self.nginx_x_accel_redirect_base = kwargs.get('nginx_x_accel_redirect_base', False)
         self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script', None)

From 19bb6e38f2a43d06fe7721eec2037ea10edf4bda Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 30 Mar 2020 15:39:37 -0400
Subject: [PATCH 701/853] Move sentry_dsn_public to mixin

---
 lib/galaxy/config/__init__.py  | 20 +++++++++-----------
 lib/tool_shed/webapp/config.py | 14 --------------
 2 files changed, 9 insertions(+), 25 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index ac903ba583a8..5d51b1af1cf4 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -320,6 +320,15 @@ def is_admin_user(self, user):
         """Determine if the provided user is listed in `admin_users`."""
         return user is not None and user.email in self.admin_users_list
 
+    @property
+    def sentry_dsn_public(self):
+        """
+        Sentry URL with private key removed for use in client side scripts,
+        sentry server will need to be configured to accept events
+        """
+        if self.sentry_dsn:
+            return re.sub(r"^([^:/?#]+:)?//(\w+):(\w+)", r"\1//\2", self.sentry_dsn)
+
 
 class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     deprecated_options = ('database_file', 'track_jobs_in_database')
@@ -728,17 +737,6 @@ def _set_galaxy_infrastructure_url(self, kwargs):
                 'UWSGI_PORT': port
             })
 
-    @property
-    def sentry_dsn_public(self):
-        """
-        Sentry URL with private key removed for use in client side scripts,
-        sentry server will need to be configured to accept events
-        """
-        if self.sentry_dsn:
-            return re.sub(r"^([^:/?#]+:)?//(\w+):(\w+)", r"\1//\2", self.sentry_dsn)
-        else:
-            return None
-
     def parse_config_file_options(self, kwargs):
         """Backwards compatibility for config files moved to the config/ dir."""
         defaults = dict(
diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index ecc25a7e6712..806df4f7de71 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -4,7 +4,6 @@
 import logging
 import logging.config
 import os
-import re
 from datetime import timedelta
 
 from six.moves import configparser
@@ -126,19 +125,6 @@ def __init__(self, **kwargs):
     def shed_tool_data_path(self):
         return self.tool_data_path
 
-    @property
-    def sentry_dsn_public(self):
-        """
-        Sentry URL with private key removed for use in client side scripts,
-        sentry server will need to be configured to accept events
-        """
-        # TODO refactor this to a common place between toolshed/galaxy config, along
-        # with other duplicated methods.
-        if self.sentry_dsn:
-            return re.sub(r"^([^:/?#]+:)?//(\w+):(\w+)", r"\1//\2", self.sentry_dsn)
-        else:
-            return None
-
     def parse_config_file_options(self, kwargs):
         defaults = dict(
             auth_config_file=[self._in_config_dir('config/auth_conf.xml')],

From cbd1b0b9998b0ad236b1ceb4c49f2dbd6399a109 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 16 Mar 2020 01:09:56 -0400
Subject: [PATCH 702/853] Move get, get_bool into mixin

---
 lib/galaxy/config/__init__.py  | 20 +++++++++++---------
 lib/tool_shed/webapp/config.py |  9 ---------
 2 files changed, 11 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 5d51b1af1cf4..77b22c4be80a 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -329,6 +329,17 @@ def sentry_dsn_public(self):
         if self.sentry_dsn:
             return re.sub(r"^([^:/?#]+:)?//(\w+):(\w+)", r"\1//\2", self.sentry_dsn)
 
+    def get_bool(self, key, default):  
+        # Warning: the value of self.config_dict['foo'] may be different from self.foo
+        if key in self.config_dict:
+            return string_as_bool(self.config_dict[key])
+        else:
+            return default
+
+    def get(self, key, default=None):
+        # Warning: the value of self.config_dict['foo'] may be different from self.foo
+        return self.config_dict.get(key, default)
+
 
 class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     deprecated_options = ('database_file', 'track_jobs_in_database')
@@ -796,15 +807,6 @@ def reload_sanitize_whitelist(self, explicit=True):
             if explicit:
                 log.warning("Sanitize log file explicitly specified as '%s' but does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
 
-    def get(self, key, default=None):
-        return self.config_dict.get(key, default)
-
-    def get_bool(self, key, default):
-        if key in self.config_dict:
-            return string_as_bool(self.config_dict[key])
-        else:
-            return default
-
     def ensure_tempdir(self):
         self._ensure_directory(self.new_file_path)
 
diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index 806df4f7de71..1a0b2cf6556c 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -137,15 +137,6 @@ def parse_config_file_options(self, kwargs):
         # Backwards compatibility for names used in too many places to fix
         self.datatypes_config = self.datatypes_config_file
 
-    def get(self, key, default=None):
-        return self.config_dict.get(key, default)
-
-    def get_bool(self, key, default):
-        if key in self.config_dict:
-            return string_as_bool(self.config_dict[key])
-        else:
-            return default
-
     def check(self):
         # Check that required directories exist.
         paths_to_check = [self.root, self.file_path, self.hgweb_config_dir, self.tool_data_path, self.template_path]

From 93def38be1e0070444748bc7593b263d81f8b57a Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 30 Mar 2020 15:46:00 -0400
Subject: [PATCH 703/853] Do not check if exists or try to create self.root

---
 lib/tool_shed/webapp/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index 1a0b2cf6556c..c1f23b11f2c4 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -139,7 +139,7 @@ def parse_config_file_options(self, kwargs):
 
     def check(self):
         # Check that required directories exist.
-        paths_to_check = [self.root, self.file_path, self.hgweb_config_dir, self.tool_data_path, self.template_path]
+        paths_to_check = [self.file_path, self.hgweb_config_dir, self.tool_data_path, self.template_path]
         for path in paths_to_check:
             if path not in [None, False] and not os.path.isdir(path):
                 try:

From c40bec9966b67c9750f53307d1428510688b7c5c Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 30 Mar 2020 15:49:47 -0400
Subject: [PATCH 704/853] Do not redefine get_database_options in TS: use base

---
 lib/galaxy/config/__init__.py  |  2 +-
 lib/tool_shed/webapp/config.py | 34 +++++-----------------------------
 2 files changed, 6 insertions(+), 30 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 77b22c4be80a..ccc1c4a08e4d 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -329,7 +329,7 @@ def sentry_dsn_public(self):
         if self.sentry_dsn:
             return re.sub(r"^([^:/?#]+:)?//(\w+):(\w+)", r"\1//\2", self.sentry_dsn)
 
-    def get_bool(self, key, default):  
+    def get_bool(self, key, default):
         # Warning: the value of self.config_dict['foo'] may be different from self.foo
         if key in self.config_dict:
             return string_as_bool(self.config_dict[key])
diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index c1f23b11f2c4..40572c13d180 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -8,7 +8,11 @@
 
 from six.moves import configparser
 
-from galaxy.config import BaseAppConfiguration, CommonConfigurationMixin
+from galaxy.config import (
+    BaseAppConfiguration,
+    CommonConfigurationMixin,
+    get_database_engine_options,
+)
 from galaxy.config.schema import AppSchema
 from galaxy.util import string_as_bool
 from galaxy.version import VERSION, VERSION_MAJOR
@@ -161,31 +165,3 @@ def check(self):
 
 
 Configuration = ToolShedAppConfiguration
-
-
-def get_database_engine_options(kwargs):
-    """
-    Allow options for the SQLAlchemy database engine to be passed by using
-    the prefix "database_engine_option".
-    """
-    conversions = {
-        'convert_unicode': string_as_bool,
-        'pool_timeout': int,
-        'echo': string_as_bool,
-        'echo_pool': string_as_bool,
-        'pool_recycle': int,
-        'pool_size': int,
-        'max_overflow': int,
-        'pool_threadlocal': string_as_bool,
-        'server_side_cursors': string_as_bool
-    }
-    prefix = "database_engine_option_"
-    prefix_len = len(prefix)
-    rval = {}
-    for key, value in kwargs.items():
-        if key.startswith(prefix):
-            key = key[prefix_len:]
-            if key in conversions:
-                value = conversions[key](value)
-            rval[key] = value
-    return rval

From 9d4423a2af460f012f9f192e1f101e140b9b950f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 2 Apr 2020 11:29:59 +0200
Subject: [PATCH 705/853] Fix cached repo usage

---
 lib/tool_shed/metadata/repository_metadata_manager.py | 2 +-
 lib/tool_shed/webapp/model/__init__.py                | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 1a832ec42b27..81f8a6b2adcd 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -930,7 +930,7 @@ def set_repository_metadata(self, host, content_alert_str='', **kwd):
                 if repository_metadata:
                     downloadable = metadata_util.is_downloadable(self.metadata_dict)
                     # Update the last saved repository_metadata table row.
-                    repository_metadata.changeset_revision = self.repository.tip(self.app)
+                    repository_metadata.changeset_revision = self.repository.tip()
                     repository_metadata.metadata = self.metadata_dict
                     repository_metadata.downloadable = downloadable
                     if 'datatypes' in self.metadata_dict:
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 73b2ef76ee40..367444f5abf4 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -203,8 +203,8 @@ def __init__(self, id=None, name=None, type=None, remote_repository_url=None, ho
     @property
     def hg_repo(self):
         if not WEAK_HG_REPO_CACHE.get(self):
-            WEAK_HG_REPO_CACHE[self] = hg.repository(ui.ui(), self.repo_path())
-        return WEAK_HG_REPO_CACHE[self]
+            WEAK_HG_REPO_CACHE[self] = hg.cachedlocalrepo(hg.repository(ui.ui(), self.repo_path().encode('utf-8')))
+        return WEAK_HG_REPO_CACHE[self].fetch()[0]
 
     @property
     def admin_role(self):

From c2af862d124c18eb56a6010e065816b5a8e2acb8 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 2 Apr 2020 11:33:18 +0200
Subject: [PATCH 706/853] Make allow_push regular function again

---
 lib/tool_shed/grids/repository_grids.py               | 6 +++---
 lib/tool_shed/metadata/repository_metadata_manager.py | 2 +-
 lib/tool_shed/webapp/controllers/repository.py        | 2 +-
 lib/tool_shed/webapp/model/__init__.py                | 3 +--
 lib/tool_shed/webapp/security/__init__.py             | 2 +-
 5 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py
index a03d67ef2a1f..55d4c4744ca2 100644
--- a/lib/tool_shed/grids/repository_grids.py
+++ b/lib/tool_shed/grids/repository_grids.py
@@ -418,7 +418,7 @@ def build_initial_query(self, trans, **kwd):
         for repository in trans.sa_session.query(model.Repository) \
                                           .filter(and_(model.Repository.table.c.deprecated == false(),
                                                        model.Repository.table.c.deleted == false())):
-            allow_push = repository.allow_push
+            allow_push = repository.allow_push()
             if allow_push:
                 allow_push_usernames = allow_push.split(',')
                 if username in allow_push_usernames:
@@ -710,7 +710,7 @@ def build_initial_query(self, trans, **kwd):
         for repository in trans.sa_session.query(model.Repository) \
                                           .filter(and_(model.Repository.table.c.deprecated == false(),
                                                        model.Repository.table.c.deleted == false())):
-            allow_push = repository.allow_push
+            allow_push = repository.allow_push()
             if allow_push:
                 allow_push_usernames = allow_push.split(',')
                 if username in allow_push_usernames:
@@ -849,7 +849,7 @@ def build_initial_query(self, trans, **kwd):
         for repository in trans.sa_session.query(model.Repository) \
                                           .filter(and_(model.Repository.table.c.deprecated == false(),
                                                        model.Repository.table.c.deleted == false())):
-            allow_push = repository.allow_push
+            allow_push = repository.allow_push()
             if allow_push:
                 allow_push_usernames = allow_push.split(',')
                 if username in allow_push_usernames:
diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 81f8a6b2adcd..f5afcf5ecc23 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -438,7 +438,7 @@ def get_query_for_setting_metadata_on_repositories(self, my_writable=False, orde
                 if repository.type in [rt_util.REPOSITORY_SUITE_DEFINITION, rt_util.TOOL_DEPENDENCY_DEFINITION]:
                     clause_list.append(self.app.model.Repository.table.c.id == repository.id)
                 else:
-                    allow_push = repository.allow_push
+                    allow_push = repository.allow_push()
                     if allow_push:
                         # Include all repositories that are writable by the current user.
                         allow_push_usernames = allow_push.split(',')
diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index 3875babb2883..f9f168a3fa3e 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -1732,7 +1732,7 @@ def manage_repository(self, trans, id, **kwd):
             status = 'error'
         allow_push_select_field = SelectField(name='allow_push',
                                               multiple=True)
-        current_allow_push = repository.allow_push
+        current_allow_push = repository.allow_push()
         if current_allow_push:
             current_allow_push_list = current_allow_push.split(',')
         else:
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 367444f5abf4..a60e445b4d5b 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -216,7 +216,6 @@ def admin_role(self):
         raise Exception('Repository %s owned by %s is not associated with a required administrative role.' %
                         (str(self.name), str(self.user.username)))
 
-    @property
     def allow_push(self):
         return self.hg_repo.ui.config('web', 'allow_push')
 
@@ -289,7 +288,7 @@ def revision(self):
         return "%s:%s" % (str(tip_ctx.rev()), str(tip_ctx))
 
     def set_allow_push(self, usernames, remove_auth=''):
-        allow_push = util.listify(self.allow_push)
+        allow_push = util.listify(self.allow_push())
         if remove_auth:
             allow_push.remove(remove_auth)
         else:
diff --git a/lib/tool_shed/webapp/security/__init__.py b/lib/tool_shed/webapp/security/__init__.py
index 3cdc040226b0..29b88fc835b9 100644
--- a/lib/tool_shed/webapp/security/__init__.py
+++ b/lib/tool_shed/webapp/security/__init__.py
@@ -214,7 +214,7 @@ def set_entity_user_associations(self, users=None, roles=None, groups=None, dele
 
     def can_push(self, app, user, repository):
         if user:
-            return user.username in listify(repository.allow_push)
+            return user.username in listify(repository.allow_push())
         return False
 
     def user_can_administer_repository(self, user, repository):

From 015ce348025b6b182c7e02ba0af5917362657244 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 2 Apr 2020 11:35:06 +0200
Subject: [PATCH 707/853] Typo fix (thx Nicola)

---
 lib/tool_shed/webapp/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index a60e445b4d5b..d801a3874c47 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -279,7 +279,7 @@ def is_new(self):
         return tip_rev < 0
 
     def repo_path(self, app=None):
-        # Keep app argument for compaibility with tool_shed_install Repository model
+        # Keep app argument for compatibility with tool_shed_install Repository model
         return hgweb_config_manager.get_entry(os.path.join("repos", self.user.username, self.name))
 
     def revision(self):

From e2f1680597f57ae751c8dcf2a76119df9342a441 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 2 Apr 2020 13:19:13 +0200
Subject: [PATCH 708/853] eagerload downloadable revisions

---
 lib/galaxy/tool_shed/util/repository_util.py | 26 +++++++++++++-------
 lib/tool_shed/webapp/api/repositories.py     |  2 +-
 2 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/tool_shed/util/repository_util.py b/lib/galaxy/tool_shed/util/repository_util.py
index 12f53e6ca935..68deb9a8cf92 100644
--- a/lib/galaxy/tool_shed/util/repository_util.py
+++ b/lib/galaxy/tool_shed/util/repository_util.py
@@ -5,7 +5,12 @@
 
 from markupsafe import escape
 from six.moves.urllib.error import HTTPError
-from sqlalchemy import and_, false, or_
+from sqlalchemy import (
+    and_,
+    false,
+    or_,
+)
+from sqlalchemy.orm import joinedload
 
 from galaxy import util
 from galaxy import web
@@ -307,7 +312,7 @@ def get_repository_by_id(app, id):
         return sa_session.query(app.model.Repository).get(app.security.decode_id(id))
 
 
-def get_repository_by_name_and_owner(app, name, owner):
+def get_repository_by_name_and_owner(app, name, owner, eagerload_columns=None):
     """Get a repository from the database via name and owner"""
     repository_query = get_repository_query(app)
     if is_tool_shed_client(app):
@@ -316,13 +321,16 @@ def get_repository_by_name_and_owner(app, name, owner):
                          app.install_model.ToolShedRepository.table.c.owner == owner)) \
             .first()
     # We're in the tool shed.
-    user = common_util.get_user_by_username(app, owner)
-    if user:
-        return repository_query \
-            .filter(and_(app.model.Repository.table.c.name == name,
-                         app.model.Repository.table.c.user_id == user.id)) \
-            .first()
-    return None
+    q = repository_query.filter(
+        and_(
+            app.model.Repository.table.c.name == name,
+            app.model.User.table.c.username == owner,
+            app.model.Repository.table.c.user_id == app.model.User.table.c.id
+        )
+    )
+    if eagerload_columns:
+        q = q.options(joinedload(*eagerload_columns))
+    return q.first()
 
 
 def get_repository_by_name(app, name):
diff --git a/lib/tool_shed/webapp/api/repositories.py b/lib/tool_shed/webapp/api/repositories.py
index 127d0e8cc7ac..6c046716fc22 100644
--- a/lib/tool_shed/webapp/api/repositories.py
+++ b/lib/tool_shed/webapp/api/repositories.py
@@ -713,7 +713,7 @@ def updates(self, trans, **kwd):
         owner = kwd.get('owner', None)
         changeset_revision = kwd.get('changeset_revision', None)
         hexlify_this = util.asbool(kwd.get('hexlify', True))
-        repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
+        repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner, eagerload_column=['downloadable_revisions'])
         if repository:
             repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
                                                                                               trans.security.encode_id(repository.id),

From ed22beb17b85b4dcefbafd84fed67abe87d9e451 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 2 Apr 2020 14:19:36 +0200
Subject: [PATCH 709/853] eagerload downloadable_revisions where appropriate

Where appropriate means iteration over
repository.downloadable_revisions.
---
 lib/galaxy/tool_shed/util/repository_util.py |  7 +++++--
 lib/tool_shed/webapp/api/repositories.py     | 13 +++++++------
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/tool_shed/util/repository_util.py b/lib/galaxy/tool_shed/util/repository_util.py
index 68deb9a8cf92..f851a06b8188 100644
--- a/lib/galaxy/tool_shed/util/repository_util.py
+++ b/lib/galaxy/tool_shed/util/repository_util.py
@@ -462,9 +462,12 @@ def get_repository_ids_requiring_prior_import_or_install(app, tsr_ids, repositor
     return prior_tsr_ids
 
 
-def get_repository_in_tool_shed(app, id):
+def get_repository_in_tool_shed(app, id, eagerload_columns=None):
     """Get a repository on the tool shed side from the database via id."""
-    return get_repository_query(app).get(app.security.decode_id(id))
+    q = get_repository_query(app)
+    if eagerload_columns:
+        q = q.options(joinedload(*eagerload_columns))
+    return q.get(app.security.decode_id(id))
 
 
 def get_repository_owner(cleaned_repository_url):
diff --git a/lib/tool_shed/webapp/api/repositories.py b/lib/tool_shed/webapp/api/repositories.py
index 6c046716fc22..d37d0d3507e4 100644
--- a/lib/tool_shed/webapp/api/repositories.py
+++ b/lib/tool_shed/webapp/api/repositories.py
@@ -111,14 +111,15 @@ def get_ordered_installable_revisions(self, trans, name=None, owner=None, **kwd)
         if owner is None:
             owner = kwd.get('owner', None)
         tsr_id = kwd.get('tsr_id', None)
+        eagerload_columns = ['downloadable_revisions']
         if None not in [name, owner]:
             # Get the repository information.
-            repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner)
+            repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner, eagerload_columns=eagerload_columns)
             if repository is None:
                 trans.response.status = 404
                 return {'status': 'error', 'message': 'No repository named %s found with owner %s' % (name, owner)}
         elif tsr_id is not None:
-            repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id)
+            repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id, eagerload_columns=eagerload_columns)
         else:
             error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
             error_message += "invalid parameters received."
@@ -197,7 +198,7 @@ def get_repository_revision_install_info(self, trans, name, owner, changeset_rev
         # http://<xyz>/api/repositories/get_repository_revision_install_info?name=<n>&owner=<o>&changeset_revision=<cr>
         if name and owner and changeset_revision:
             # Get the repository information.
-            repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner)
+            repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner, eagerload_columns=['downloadable_revisions'])
             if repository is None:
                 log.debug('Cannot locate repository %s owned by %s' % (str(name), str(owner)))
                 return {}, {}, {}
@@ -263,7 +264,7 @@ def get_installable_revisions(self, trans, **kwd):
         # Example URL: http://localhost:9009/api/repositories/get_installable_revisions?tsr_id=9d37e53072ff9fa4
         tsr_id = kwd.get('tsr_id', None)
         if tsr_id is not None:
-            repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id)
+            repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id, eagerload_columns=['downloadable_revisions'])
         else:
             error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
             error_message += "missing or invalid parameter received."
@@ -713,7 +714,7 @@ def updates(self, trans, **kwd):
         owner = kwd.get('owner', None)
         changeset_revision = kwd.get('changeset_revision', None)
         hexlify_this = util.asbool(kwd.get('hexlify', True))
-        repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner, eagerload_column=['downloadable_revisions'])
+        repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner, eagerload_columns=['downloadable_revisions'])
         if repository:
             repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
                                                                                               trans.security.encode_id(repository.id),
@@ -802,7 +803,7 @@ def metadata(self, trans, id, **kwd):
             raise MalformedId('The given id is invalid.')
         recursive = util.asbool(kwd.get('recursive', 'True'))
         all_metadata = {}
-        repository = repository_util.get_repository_in_tool_shed(self.app, id)
+        repository = repository_util.get_repository_in_tool_shed(self.app, id, eagerload_columns=['downloadable_revisions'])
         for changeset, changehash in repository.installable_revisions(self.app):
             metadata = metadata_util.get_current_repository_metadata_for_changeset_revision(self.app, repository, changehash)
             if metadata is None:

From 78f2a3736ce2a4b083cf8cf7bdd2f85bb657afc3 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 2 Apr 2020 15:18:03 +0200
Subject: [PATCH 710/853] Use latest downloadable revision instead of
 repository.tip()

There should be no need to hit the disk in the updates route now.
We might eventually miss some local modifications that did not
create a new MetdataRevision, but I don't think managing this should
be a concern for the `updates` route.
---
 lib/tool_shed/webapp/api/repositories.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/tool_shed/webapp/api/repositories.py b/lib/tool_shed/webapp/api/repositories.py
index d37d0d3507e4..d1bd82918665 100644
--- a/lib/tool_shed/webapp/api/repositories.py
+++ b/lib/tool_shed/webapp/api/repositories.py
@@ -715,14 +715,14 @@ def updates(self, trans, **kwd):
         changeset_revision = kwd.get('changeset_revision', None)
         hexlify_this = util.asbool(kwd.get('hexlify', True))
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner, eagerload_columns=['downloadable_revisions'])
-        if repository:
+        if repository and repository.downloadable_revisions:
             repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
                                                                                               trans.security.encode_id(repository.id),
                                                                                               changeset_revision)
             tool_shed_status_dict = {}
             # Handle repository deprecation.
             tool_shed_status_dict['repository_deprecated'] = str(repository.deprecated)
-            tip_revision = repository.tip()
+            tip_revision = repository.downloadable_revisions[0]
             # Handle latest installable revision.
             if changeset_revision == tip_revision:
                 tool_shed_status_dict['latest_installable_revision'] = 'True'

From c920372befa848121208a244a30c4f3a7f307454 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <jos.to.new@gmail.com>
Date: Thu, 2 Apr 2020 17:20:34 +0200
Subject: [PATCH 711/853] Vuefy Job Destination Parameters

---
 client/galaxy/scripts/bundleEntries.js        |  2 +
 .../JobDestinationParams.vue                  | 66 +++++++++++++++++++
 .../components/JobDestinationParams/index.js  |  3 +
 .../components/JobDestinationParams/mount.js  | 13 ++++
 client/galaxy/scripts/store/index.js          |  2 +
 .../store/jobDestinationParametersStore.js    | 33 ++++++++++
 lib/galaxy/managers/jobs.py                   | 16 +++++
 lib/galaxy/webapps/galaxy/api/jobs.py         | 16 +++++
 lib/galaxy/webapps/galaxy/buildapp.py         |  1 +
 templates/show_params.mako                    | 23 +------
 10 files changed, 155 insertions(+), 20 deletions(-)
 create mode 100644 client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
 create mode 100644 client/galaxy/scripts/components/JobDestinationParams/index.js
 create mode 100644 client/galaxy/scripts/components/JobDestinationParams/mount.js
 create mode 100644 client/galaxy/scripts/store/jobDestinationParametersStore.js

diff --git a/client/galaxy/scripts/bundleEntries.js b/client/galaxy/scripts/bundleEntries.js
index 2818689602fb..c544bbd08bab 100644
--- a/client/galaxy/scripts/bundleEntries.js
+++ b/client/galaxy/scripts/bundleEntries.js
@@ -95,6 +95,8 @@ export { mountJobMetrics } from "components/JobMetrics";
 export { mountJobParameters } from "components/JobParameters";
 export { mountWorkflowEditor } from "components/Workflow/Editor/mount";
 export { mountPageDisplay } from "components/PageDisplay";
+export { mountDestinationParams } from "components/JobDestinationParams";
+
 
 // Used in common.mako
 export { default as store } from "storemodern";
diff --git a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
new file mode 100644
index 000000000000..b028e55ec82e
--- /dev/null
+++ b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
@@ -0,0 +1,66 @@
+<template>
+    <div>
+        <table class="tabletip info_data_table">
+            <tbody>
+            <tr v-for="(value, title) in destinationParams">
+                <td>{{ title }}</td>
+                <td>{{ value }}</td>
+            </tr>
+            </tbody>
+        </table>
+    </div>
+</template>
+
+<script>
+    import {mapCacheActions} from "vuex-cache";
+    import {mapGetters} from "vuex";
+
+    export default {
+        props: {
+            jobId: {
+                type: String,
+            },
+            datasetId: {
+                type: String,
+            },
+            datasetType: {
+                type: String,
+                default: "hda",
+            },
+            includeTitle: {
+                type: Boolean,
+                default: true,
+            },
+        },
+        data() {
+            return {};
+        },
+        created: function () {
+            this.fetchJobDestinationParams(this.jobId);
+        },
+        computed: {
+            ...mapGetters(["getJobDestinationParams"]),
+            jobDestinationParams: function () {
+                return this.getJobDestinationParams(this.jobId);
+            },
+            destinationParams: function () {
+                const params = this.jobDestinationParams;
+                const special_parameters = {
+                    'runner_name': 'Runner',
+                    'runner_external_id': 'Runner Job ID',
+                    'handler': 'Handler'
+                };
+
+                Object.keys(params).forEach((title) => {
+                    if (title in special_parameters) {
+                        params[title] = special_parameters[title]
+                    }
+                });
+                return params;
+            }
+        },
+        methods: {
+            ...mapCacheActions(["fetchJobDestinationParams"]),
+        },
+    };
+</script>
diff --git a/client/galaxy/scripts/components/JobDestinationParams/index.js b/client/galaxy/scripts/components/JobDestinationParams/index.js
new file mode 100644
index 000000000000..d7e3a3045779
--- /dev/null
+++ b/client/galaxy/scripts/components/JobDestinationParams/index.js
@@ -0,0 +1,3 @@
+export { default as JobDestinationParams } from "./JobDestinationParams";
+
+export { mountDestinationParams } from "./mount";
diff --git a/client/galaxy/scripts/components/JobDestinationParams/mount.js b/client/galaxy/scripts/components/JobDestinationParams/mount.js
new file mode 100644
index 000000000000..271db1a40b91
--- /dev/null
+++ b/client/galaxy/scripts/components/JobDestinationParams/mount.js
@@ -0,0 +1,13 @@
+/**
+ * Endpoint for mounting job metrics from non-Vue environment.
+ */
+import $ from "jquery";
+import JobDestinationParams from "./JobDestinationParams.vue";
+import { mountVueComponent } from "utils/mountVueComponent";
+
+export const mountDestinationParams = (propsData = {}) => {
+    $(".job-destination-parameters").each((index, el) => {
+        propsData.jobId = $(el).attr("job_id");
+        mountVueComponent(JobDestinationParams)(propsData, el);
+    });
+};
diff --git a/client/galaxy/scripts/store/index.js b/client/galaxy/scripts/store/index.js
index ecdde654cbab..fe51b2e5680f 100644
--- a/client/galaxy/scripts/store/index.js
+++ b/client/galaxy/scripts/store/index.js
@@ -9,6 +9,7 @@ import createCache from "vuex-cache";
 import { gridSearchStore } from "./gridSearchStore";
 import { tagStore } from "./tagStore";
 import { jobMetricsStore } from "./jobMetricsStore";
+import { jobDestinationParametersStore } from "./jobDestinationParametersStore";
 import { invocationStore } from "./invocationStore";
 import { historyStore } from "./historyStore";
 import { userStore } from "./userStore";
@@ -31,6 +32,7 @@ export function createStore() {
             histories: historyStore,
             tags: tagStore,
             jobMetrics: jobMetricsStore,
+            DestinationParameters: jobDestinationParametersStore,
             invocations: invocationStore,
             user: userStore,
             config: configStore,
diff --git a/client/galaxy/scripts/store/jobDestinationParametersStore.js b/client/galaxy/scripts/store/jobDestinationParametersStore.js
new file mode 100644
index 000000000000..12d439a25476
--- /dev/null
+++ b/client/galaxy/scripts/store/jobDestinationParametersStore.js
@@ -0,0 +1,33 @@
+export const state = {
+    jobDestinationParametersByJobId: {},
+};
+
+import Vue from "vue";
+import { getAppRoot } from "onload/loadConfig";
+import axios from "axios";
+
+const getters = {
+    getJobDestinationParams: (state) => (jobId) => {
+        return state.jobDestinationParametersByJobId[jobId] || [];
+    },
+};
+
+const actions = {
+    fetchJobDestinationParams: async ({ commit }, jobId) => {
+        const { data } = await axios.get(`${getAppRoot()}api/jobs/${jobId}/destination_params`);
+        commit("saveJobDestinationParamsForJobId", { jobId, jobDestinationParams: data });
+    },
+};
+
+const mutations = {
+    saveJobDestinationParamsForJobId: (state, { jobId, jobDestinationParams }) => {
+        Vue.set(state.jobDestinationParametersByJobId, jobId, jobDestinationParams);
+    },
+};
+
+export const jobDestinationParametersStore = {
+    state,
+    getters,
+    actions,
+    mutations,
+};
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 54b119f9033a..fde61e71d43e 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -497,6 +497,22 @@ def metric_to_dict(metric):
     metrics = [m for m in job.metrics if m.plugin != 'env' or trans.user_is_admin]
     return list(map(metric_to_dict, metrics))
 
+def summarize_destination_params(trans, job):
+    """Produce a dict-ified version of job destination parameters ready for tabular rendering.
+
+    Precondition: the caller has verified the job is accessible to the user
+    represented by the trans parameter.
+    """
+    if not trans.user_is_admin:
+        return []
+
+    else:
+        destination_params = job.destination_params
+        destination_params['runner_name'] = job.job_runner_name
+        destination_params['runner_external_id'] = job.job_runner_external_id
+        destination_params['handler'] = job.handler
+        return destination_params
+
 
 def summarize_job_parameters(trans, job):
     """Produce a dict-ified version of job parameters ready for tabular rendering.
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index 20448c65260a..32698825a5db 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -16,6 +16,7 @@
     JobManager,
     JobSearch,
     summarize_job_metrics,
+    summarize_destination_params,
     summarize_job_parameters,
 )
 from galaxy.web import (
@@ -283,6 +284,21 @@ def metrics(self, trans, **kwd):
         job = self.__get_job(trans, **kwd)
         return summarize_job_metrics(trans, job)
 
+    @expose_api_anonymous
+    def destination_params(self, trans, **kwd):
+        """
+        * GET /api/jobs/{job_id}/destination_params
+            Return destination parameters for specified job.
+
+        :type   job_id: string
+        :param  job_id: Encoded job id
+
+        :rtype:     list
+        :returns:   list containing job destination parameters
+        """
+        job = self.__get_job(trans, **kwd)
+        return summarize_destination_params(trans, job)
+
     @expose_api_anonymous
     def parameters_display(self, trans, **kwd):
         """
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 5438ee12b663..9df4eb0ad505 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -946,6 +946,7 @@ def connect_invocation_endpoint(endpoint_name, endpoint_suffix, action, conditio
     webapp.mapper.connect('common_problems', '/api/jobs/{id}/common_problems', controller='jobs', action='common_problems', conditions=dict(method=['GET']))
     # Job metrics and parameters by job id or dataset id (for slightly different accessibility checking)
     webapp.mapper.connect('metrics', '/api/jobs/{job_id}/metrics', controller='jobs', action='metrics', conditions=dict(method=['GET']))
+    webapp.mapper.connect('destination_params', '/api/jobs/{job_id}/destination_params', controller='jobs', action='destination_params', conditions=dict(method=['GET']))
     webapp.mapper.connect('show_job_lock', '/api/job_lock', controller='jobs', action='show_job_lock', conditions=dict(method=['GET']))
     webapp.mapper.connect('update_job_lock', '/api/job_lock', controller='jobs', action='update_job_lock', conditions=dict(method=['PUT']))
     webapp.mapper.connect('dataset_metrics', '/api/datasets/{dataset_id}/metrics', controller='jobs', action='metrics', conditions=dict(method=['GET']))
diff --git a/templates/show_params.mako b/templates/show_params.mako
index 2a4e8f3549c9..17e02f87ce12 100644
--- a/templates/show_params.mako
+++ b/templates/show_params.mako
@@ -119,26 +119,8 @@ ${ job.command_line | h }</pre>
 
 %if trans.user_is_admin:
 <h3>Destination Parameters</h3>
-    <table class="tabletip">
-        <tbody>
-            <tr><th scope="row">Runner</th><td>${ job.job_runner_name }</td></tr>
-            <tr><th scope="row">Runner Job ID</th><td>${ job.job_runner_external_id }</td></tr>
-            <tr><th scope="row">Handler</th><td>${ job.handler }</td></tr>
-            %if job.destination_params:
-            %for (k, v) in job.destination_params.items():
-                <tr><th scope="row">${ k | h }</th>
-                    <td>
-                        %if str(k) in ('nativeSpecification', 'rank', 'requirements'):
-                        <pre style="white-space: pre-wrap; word-wrap: break-word;">${ v | h }</pre>
-                        %else:
-                        ${ v | h }
-                        %endif
-                    </td>
-                </tr>
-            %endfor
-            %endif
-        </tbody>
-    </table>
+<div class="job-destination-parameters" job_id="${trans.security.encode_id(job.id)}">
+</div>
 %endif
 
 %if job and job.dependencies:
@@ -193,5 +175,6 @@ $(function(){
     })
     window.bundleEntries.mountJobMetrics();
     window.bundleEntries.mountJobParameters();
+    window.bundleEntries.mountDestinationParams();
 });
 </script>

From 3100009fc65159368105d21dddf654e6c3bd7154 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 2 Apr 2020 16:08:33 +0200
Subject: [PATCH 712/853] Log node state if history doesn't finish

---
 test/integration/test_kubernetes_runner.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/test/integration/test_kubernetes_runner.py b/test/integration/test_kubernetes_runner.py
index 000b10297370..09b325b92b04 100644
--- a/test/integration/test_kubernetes_runner.py
+++ b/test/integration/test_kubernetes_runner.py
@@ -12,7 +12,10 @@
 import pytest
 
 from galaxy.util import unicodify
-from galaxy_test.base.populators import skip_without_tool
+from galaxy_test.base.populators import (
+    DatasetPopulator,
+    skip_without_tool,
+)
 from galaxy_test.driver import integration_util
 from .test_containerized_jobs import MulledJobTestCases
 from .test_job_environments import BaseJobEnvironmentIntegrationTestCase
@@ -151,11 +154,22 @@ def job_config(jobs_directory):
     return Config(job_conf.name)
 
 
+class KubernetesDatasetPopulator(DatasetPopulator):
+
+    def wait_for_history(self, *args, **kwargs):
+        try:
+            super(KubernetesDatasetPopulator, self).wait_for_history(*args, **kwargs)
+        except AssertionError:
+            print("Kubernetes status:\n %s" % unicodify(subprocess.check_output(['kubectl', 'describe', 'nodes'])))
+            raise
+
+
 @integration_util.skip_unless_kubernetes()
 class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, MulledJobTestCases):
 
     def setUp(self):
         super(BaseKubernetesIntegrationTestCase, self).setUp()
+        self.dataset_populator = KubernetesDatasetPopulator(self.galaxy_interactor)
         self.history_id = self.dataset_populator.new_history()
 
     @classmethod

From e9549ebe8d41136da4b17520fe3db63b168385da Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 2 Apr 2020 19:53:59 +0200
Subject: [PATCH 713/853] Delete 15G dotnet folder, use minikube 1.9.0

---
 .github/workflows/integration.yaml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 7e72077fbb26..3bd0aaf4d697 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -27,10 +27,15 @@ jobs:
     steps:
     - name: Prune unused docker image, volumes and containers
       run: docker system prune -a -f
+    - name: Clean dotnet folder for space
+      if: matrix.subset == 'kubernetes'
+      run: rm -Rf /usr/share/dotnet
     - name: Setup Minikube
       if: matrix.subset == 'kubernetes'
       id: minikube
-      uses: CodingNagger/minikube-setup-action@v1.0.2
+      uses: CodingNagger/minikube-setup-action@v1.0.3
+      with:
+        minikube-version: "1.9.0-0_amd64"
     - name: Launch Minikube
       if: matrix.subset == 'kubernetes'
       run: eval ${{ steps.minikube.outputs.launcher }}

From 375be4d8512e4ac84c265d6f4658fa4e4bca3805 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 3 Apr 2020 11:35:31 -0400
Subject: [PATCH 714/853] Removed config file and put configuration in test.

---
 test/integration/irods_object_store_conf.xml  | 10 -----
 .../integration/test_datatype_upload_irods.py | 42 ++++++++++++++++++-
 2 files changed, 40 insertions(+), 12 deletions(-)
 delete mode 100644 test/integration/irods_object_store_conf.xml

diff --git a/test/integration/irods_object_store_conf.xml b/test/integration/irods_object_store_conf.xml
deleted file mode 100644
index 778b42f4083e..000000000000
--- a/test/integration/irods_object_store_conf.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0"?>
-<object_store type="irods"> 
-    <auth username="rods" password="rods" />
-    <resource name="demoResc" />
-    <zone name="tempZone" />
-    <connection host="localhost" port="1247"/>
-    <cache path="database/object_store_cache" size="1000" />
-    <extra_dir type="job_work" path="database/job_working_directory_irods"/>
-    <extra_dir type="temp" path="database/tmp_irods"/>
-</object_store>
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index dfc44c884122..cce074610e67 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -1,5 +1,6 @@
 
 import os
+import string
 import subprocess
 import tempfile
 import time
@@ -10,9 +11,25 @@
 from .test_datatype_upload import (TEST_CASES, upload_datatype_helper, UploadTestDatatypeDataTestCase)
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-OBJECT_STORE_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "irods_object_store_conf.xml")
 # Run test for only the first 10 test files
 IRODS_TEST_CASES = dict(list(TEST_CASES.items())[0:10])
+OBJECT_STORE_HOST = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_HOST', 'localhost')
+OBJECT_STORE_PORT = int(os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_PORT', 1247))
+OBJECT_STORE_USERNAME = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_USERNAME', 'rods')
+OBJECT_STORE_PASSWORD = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_PASSWORD', 'rods')
+OBJECT_STORE_RESOURCE = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_RESOURCE', 'demoResc')
+OBJECT_STORE_ZONE = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_ZONE', 'tempZone')
+OBJECT_STORE_CONFIG = string.Template("""
+<object_store type="irods">
+    <auth username="${username}" password="${password}"/>
+    <resource name="${resource}"/>
+    <zone name="${zone}"/>
+    <connection host="${host}" port="${port}"/>
+    <cache path="${temp_directory}/object_store_cache" size="1000"/>
+    <extra_dir type="job_work" path="${temp_directory}/job_working_directory_irods"/>
+    <extra_dir type="temp" path="${temp_directory}/tmp_irods"/>
+</object_store>
+""")
 
 
 def start_irods(container_name):
@@ -50,7 +67,28 @@ def tearDownClass(cls):
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
-        config["object_store_config_file"] = OBJECT_STORE_CONFIG_FILE
+        temp_directory = cls._test_driver.mkdtemp()
+        cls.object_stores_parent = temp_directory
+        config_path = os.path.join(temp_directory, "object_store_conf.xml")
+        # This doesn't quite work yet, fails with extra_files_path
+        # config["metadata_strategy"] = "extended"
+        config["outpus_to_working_dir"] = True
+        config["retry_metadata_internally"] = False
+        with open(config_path, "w") as f:
+            f.write(
+                OBJECT_STORE_CONFIG.safe_substitute(
+                    {
+                        "temp_directory": temp_directory,
+                        "host": OBJECT_STORE_HOST,
+                        "port": OBJECT_STORE_PORT,
+                        "username": OBJECT_STORE_USERNAME,
+                        "password": OBJECT_STORE_PASSWORD,
+                        "resource": OBJECT_STORE_RESOURCE,
+                        "zone": OBJECT_STORE_ZONE,
+                    }
+                )
+            )
+        config["object_store_config_file"] = config_path
 
 
 instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)

From a97d81d61895cd296b5b7c4937995640e7ac33d1 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Fri, 3 Apr 2020 13:05:41 -0400
Subject: [PATCH 715/853] Added connection timeout for iRODS

---
 lib/galaxy/objectstore/irods.py                           | 8 ++++++++
 test/integration/test_datatype_upload_irods.py            | 4 +++-
 test/unit/objectstore/irods_object_store_conf.xml         | 2 +-
 test/unit/objectstore/irods_object_store_conf_no_auth.xml | 2 +-
 .../objectstore/irods_object_store_conf_no_extra_dir.xml  | 2 +-
 test/unit/objectstore/test_irods.py                       | 1 +
 6 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 24fb38dbdc03..bf0e1f83b38e 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -64,6 +64,7 @@ def parse_config_xml(config_xml):
             _config_xml_error('connection')
         host = c_xml[0].get('host', None)
         port = int(c_xml[0].get('port', 0))
+        timeout = int(c_xml[0].get('timeout', 30))
 
         c_xml = config_xml.findall('cache')
         if not c_xml:
@@ -91,6 +92,7 @@ def parse_config_xml(config_xml):
             'connection': {
                 'host': host,
                 'port': port,
+                'timeout': timeout
             },
             'cache': {
                 'size': cache_size,
@@ -121,6 +123,7 @@ def _config_to_dict(self):
             'connection': {
                 'host': self.host,
                 'port': self.port,
+                'timeout': self.timeout,
             },
             'cache': {
                 'size': self.cache_size,
@@ -174,6 +177,9 @@ def __init__(self, config, config_dict):
         self.port = connection_dict.get('port')
         if self.port is None:
             _config_dict_error('connection->port')
+        self.timeout = connection_dict.get('timeout')
+        if self.timeout is None:
+            _config_dict_error('connection->timeout')
 
         cache_dict = config_dict['cache']
         if cache_dict is None:
@@ -205,6 +211,8 @@ def _initialize(self):
 
     def _configure_connection(self, host='localhost', port='1247', user='rods', password='rods', zone='tempZone'):
         with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
+            # Set connection timeout
+            session.connection_timeout = self.timeout
             # Throws NetworkException if connection fails
             try:
                 session.pool.get_connection()
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index cce074610e67..5ea2248b9829 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -15,6 +15,7 @@
 IRODS_TEST_CASES = dict(list(TEST_CASES.items())[0:10])
 OBJECT_STORE_HOST = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_HOST', 'localhost')
 OBJECT_STORE_PORT = int(os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_PORT', 1247))
+OBJECT_STORE_TIMEOUT = int(os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_TIMEOUT', 30))
 OBJECT_STORE_USERNAME = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_USERNAME', 'rods')
 OBJECT_STORE_PASSWORD = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_PASSWORD', 'rods')
 OBJECT_STORE_RESOURCE = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_RESOURCE', 'demoResc')
@@ -24,7 +25,7 @@
     <auth username="${username}" password="${password}"/>
     <resource name="${resource}"/>
     <zone name="${zone}"/>
-    <connection host="${host}" port="${port}"/>
+    <connection host="${host}" port="${port}" timeout="${timeout}"/>
     <cache path="${temp_directory}/object_store_cache" size="1000"/>
     <extra_dir type="job_work" path="${temp_directory}/job_working_directory_irods"/>
     <extra_dir type="temp" path="${temp_directory}/tmp_irods"/>
@@ -81,6 +82,7 @@ def handle_galaxy_config_kwds(cls, config):
                         "temp_directory": temp_directory,
                         "host": OBJECT_STORE_HOST,
                         "port": OBJECT_STORE_PORT,
+                        "timeout": OBJECT_STORE_TIMEOUT,
                         "username": OBJECT_STORE_USERNAME,
                         "password": OBJECT_STORE_PASSWORD,
                         "resource": OBJECT_STORE_RESOURCE,
diff --git a/test/unit/objectstore/irods_object_store_conf.xml b/test/unit/objectstore/irods_object_store_conf.xml
index 778b42f4083e..275ef682ad5d 100644
--- a/test/unit/objectstore/irods_object_store_conf.xml
+++ b/test/unit/objectstore/irods_object_store_conf.xml
@@ -3,7 +3,7 @@
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
-    <connection host="localhost" port="1247"/>
+    <connection host="localhost" port="1247" timeout="30"/>
     <cache path="database/object_store_cache" size="1000" />
     <extra_dir type="job_work" path="database/job_working_directory_irods"/>
     <extra_dir type="temp" path="database/tmp_irods"/>
diff --git a/test/unit/objectstore/irods_object_store_conf_no_auth.xml b/test/unit/objectstore/irods_object_store_conf_no_auth.xml
index 7388b11fe358..787f6161a383 100644
--- a/test/unit/objectstore/irods_object_store_conf_no_auth.xml
+++ b/test/unit/objectstore/irods_object_store_conf_no_auth.xml
@@ -3,7 +3,7 @@
     <!--<auth username="rods" password="rods" />-->
     <resource name="demoResc" />
     <zone name="tempZone" />
-    <connection host="localhost" port="1247"/>
+    <connection host="localhost" port="1247" timeout="30"/>
     <cache path="database/object_store_cache" size="1000" />
     <extra_dir type="job_work" path="database/job_working_directory_irods"/>
     <extra_dir type="temp" path="database/tmp_irods"/>
diff --git a/test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml b/test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml
index d2c07a428ac0..54bc01592795 100644
--- a/test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml
+++ b/test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml
@@ -3,7 +3,7 @@
     <auth username="rods" password="rods" />
     <resource name="demoResc" />
     <zone name="tempZone" />
-    <connection host="localhost" port="1247"/>
+    <connection host="localhost" port="1247" timeout="30"/>
     <cache path="database/object_store_cache" size="1000" />
     <!--<extra_dir type="job_work" path="database/job_working_directory_irods"/>-->
     <!--<extra_dir type="temp" path="database/tmp_irods"/>-->
diff --git a/test/unit/objectstore/test_irods.py b/test/unit/objectstore/test_irods.py
index 256a98383071..b721f3ac9472 100644
--- a/test/unit/objectstore/test_irods.py
+++ b/test/unit/objectstore/test_irods.py
@@ -28,6 +28,7 @@ def test_parse_valid_config_xml():
     assert config['zone']['name'] == 'tempZone'
     assert config['connection']['host'] == 'localhost'
     assert config['connection']['port'] == 1247
+    assert config['connection']['timeout'] == 30
     assert config['cache']['path'] == 'database/object_store_cache'
     assert config['cache']['size'] == 1000
     assert config['extra_dirs'][0]['type'] == 'job_work'

From c0b3a59b52fbaf280a74f9caffa1034c099f801a Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <jos.to.new@gmail.com>
Date: Fri, 3 Apr 2020 19:04:33 +0200
Subject: [PATCH 716/853] fix order & lint

---
 client/galaxy/scripts/bundleEntries.js        |  1 -
 .../JobDestinationParams.vue                  | 79 ++++++++-----------
 lib/galaxy/managers/jobs.py                   | 10 +--
 lib/galaxy/webapps/galaxy/api/jobs.py         |  2 +-
 4 files changed, 38 insertions(+), 54 deletions(-)

diff --git a/client/galaxy/scripts/bundleEntries.js b/client/galaxy/scripts/bundleEntries.js
index c544bbd08bab..8e6efed234d8 100644
--- a/client/galaxy/scripts/bundleEntries.js
+++ b/client/galaxy/scripts/bundleEntries.js
@@ -97,6 +97,5 @@ export { mountWorkflowEditor } from "components/Workflow/Editor/mount";
 export { mountPageDisplay } from "components/PageDisplay";
 export { mountDestinationParams } from "components/JobDestinationParams";
 
-
 // Used in common.mako
 export { default as store } from "storemodern";
diff --git a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
index b028e55ec82e..dda05013eae2 100644
--- a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
+++ b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
@@ -2,10 +2,10 @@
     <div>
         <table class="tabletip info_data_table">
             <tbody>
-            <tr v-for="(value, title) in destinationParams">
-                <td>{{ title }}</td>
-                <td>{{ value }}</td>
-            </tr>
+                <tr v-for="(value, title) in jobDestinationParams">
+                    <td>{{ title }}</td>
+                    <td>{{ value }}</td>
+                </tr>
             </tbody>
         </table>
     </div>
@@ -16,51 +16,36 @@
     import {mapGetters} from "vuex";
 
     export default {
-        props: {
-            jobId: {
-                type: String,
-            },
-            datasetId: {
-                type: String,
-            },
-            datasetType: {
-                type: String,
-                default: "hda",
-            },
-            includeTitle: {
-                type: Boolean,
-                default: true,
-            },
+    props: {
+        jobId: {
+            type: String,
         },
-        data() {
-            return {};
+        datasetId: {
+            type: String,
         },
-        created: function () {
-            this.fetchJobDestinationParams(this.jobId);
+        datasetType: {
+            type: String,
+            default: "hda",
         },
-        computed: {
-            ...mapGetters(["getJobDestinationParams"]),
-            jobDestinationParams: function () {
-                return this.getJobDestinationParams(this.jobId);
-            },
-            destinationParams: function () {
-                const params = this.jobDestinationParams;
-                const special_parameters = {
-                    'runner_name': 'Runner',
-                    'runner_external_id': 'Runner Job ID',
-                    'handler': 'Handler'
-                };
-
-                Object.keys(params).forEach((title) => {
-                    if (title in special_parameters) {
-                        params[title] = special_parameters[title]
-                    }
-                });
-                return params;
-            }
-        },
-        methods: {
-            ...mapCacheActions(["fetchJobDestinationParams"]),
+        includeTitle: {
+            type: Boolean,
+            default: true,
         },
-    };
+    },
+    data() {
+        return {};
+    },
+    created: function () {
+        this.fetchJobDestinationParams(this.jobId);
+    },
+    computed: {
+        ...mapGetters(["getJobDestinationParams"]),
+        jobDestinationParams: function () {
+            return this.getJobDestinationParams(this.jobId);
+        }
+    },
+    methods: {
+        ...mapCacheActions(["fetchJobDestinationParams"]),
+    },
+};
 </script>
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index fde61e71d43e..18465d9424ce 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -497,6 +497,7 @@ def metric_to_dict(metric):
     metrics = [m for m in job.metrics if m.plugin != 'env' or trans.user_is_admin]
     return list(map(metric_to_dict, metrics))
 
+
 def summarize_destination_params(trans, job):
     """Produce a dict-ified version of job destination parameters ready for tabular rendering.
 
@@ -505,12 +506,11 @@ def summarize_destination_params(trans, job):
     """
     if not trans.user_is_admin:
         return []
-
     else:
-        destination_params = job.destination_params
-        destination_params['runner_name'] = job.job_runner_name
-        destination_params['runner_external_id'] = job.job_runner_external_id
-        destination_params['handler'] = job.handler
+        destination_params = {'Runner': job.job_runner_name,
+                              'Runner Job ID': job.job_runner_external_id,
+                              'Handler': job.handler}
+        destination_params.update(job.destination_params)
         return destination_params
 
 
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index 32698825a5db..317747ee7cf6 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -15,8 +15,8 @@
 from galaxy.managers.jobs import (
     JobManager,
     JobSearch,
-    summarize_job_metrics,
     summarize_destination_params,
+    summarize_job_metrics,
     summarize_job_parameters,
 )
 from galaxy.web import (

From 5c50da45e01e3fba53bbd09b0a4f13e3df9377b2 Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 6 Apr 2020 14:10:58 -0400
Subject: [PATCH 717/853] Update test/integration/test_datatype_upload_irods.py

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 test/integration/test_datatype_upload_irods.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 5ea2248b9829..9fe404b65ac7 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -96,12 +96,6 @@ def handle_galaxy_config_kwds(cls, config):
 instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
 
 
-@pytest.fixture
-def temp_file():
-    with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
-        yield fh
-
-
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_irods(instance, test_data, temp_file):
     upload_datatype_helper(instance, test_data, temp_file)

From c0722e3acb00247b432f0a8b1df29c363452792a Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 6 Apr 2020 14:12:30 -0400
Subject: [PATCH 718/853] Update test/integration/test_datatype_upload_irods.py

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 test/integration/test_datatype_upload_irods.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 9fe404b65ac7..d6f9b1fa70ad 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -8,7 +8,12 @@
 import pytest
 
 from galaxy_test.driver import integration_util
-from .test_datatype_upload import (TEST_CASES, upload_datatype_helper, UploadTestDatatypeDataTestCase)
+from .test_datatype_upload import (
+    temp_file
+    TEST_CASES,
+    upload_datatype_helper, 
+    UploadTestDatatypeDataTestCase
+)
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 # Run test for only the first 10 test files

From 0395f23189b93863ec638c23884d5d9a1a2841cb Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 6 Apr 2020 14:45:10 -0400
Subject: [PATCH 719/853] Revert "Renamed root folder."

This reverts commit 4d6c3d28cfa244b35472bfbca1988c4094fa45f2.
---
 .github/workflows/converter_tests.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
index 8575a553a9f5..8b20d095f3ae 100644
--- a/.github/workflows/converter_tests.yaml
+++ b/.github/workflows/converter_tests.yaml
@@ -11,7 +11,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
-        path: 'galaxy'
+        path: 'galaxy root'
     - name: Clone galaxyproject/galaxy-test-data
       uses: actions/checkout@v2
       with:
@@ -25,10 +25,10 @@ jobs:
       id: pip-cache
       with:
         path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy/requirements.txt') }}
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Move test data
-      run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy/test-data/'
+      run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/'
     - name: Install planemo
       run: pip install planemo
     - name: Run tests
-      run: planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy' 'galaxy'/lib/galaxy/datatypes/converters/*xml
+      run: planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' 'galaxy root'/lib/galaxy/datatypes/converters/*xml

From 62412a4e72b02dbdf2de7da1800142e4762f0aae Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 6 Apr 2020 14:46:38 -0400
Subject: [PATCH 720/853] Revert "Renamed root directory 'galaxy'"

This reverts commit c88981655dc3f4e7d353fe3a0a60488ef2dca94c.
---
 .github/workflows/integration.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index c233e794dea5..2e014f3ae4b8 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -36,7 +36,7 @@ jobs:
         kubectl get pods
     - uses: actions/checkout@v2
       with:
-        path: 'galaxy'
+        path: 'galaxy root'
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
@@ -45,7 +45,7 @@ jobs:
       id: pip-cache
       with:
         path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy/requirements.txt') }}
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
-      working-directory: 'galaxy'
+      working-directory: 'galaxy-root'

From 757142124094961fd9cffc6754be394210245b5e Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 6 Apr 2020 14:48:16 -0400
Subject: [PATCH 721/853] Revert "Renamed root directory"

This reverts commit 0486b04dafe0cb9de7bf2dd2a1f389eafb191518.
---
 .github/workflows/mulled.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/mulled.yaml b/.github/workflows/mulled.yaml
index 2fea754e7d66..1bdcd1dfde06 100644
--- a/.github/workflows/mulled.yaml
+++ b/.github/workflows/mulled.yaml
@@ -11,7 +11,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
-        path: 'galaxy'
+        path: 'galaxy root'
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
@@ -20,9 +20,9 @@ jobs:
       id: pip-cache
       with:
         path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy/requirements.txt') }}
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Install tox
       run: pip install tox
     - name: run tests
       run: tox -e mulled
-      working-directory: 'galaxy'
+      working-directory: 'galaxy root'

From b65faf2ce6821d15133b925ea41a53865388939f Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Mon, 6 Apr 2020 14:49:00 -0400
Subject: [PATCH 722/853] Apply suggestions from code review

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 CONTRIBUTORS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
index aab7c7c9accb..d6507a7be425 100644
--- a/CONTRIBUTORS.md
+++ b/CONTRIBUTORS.md
@@ -1,6 +1,6 @@
 # Contributors
 
-The following individuals have contributed code to Galaxy: 
+The following individuals have contributed code to Galaxy:
 
 * Enis Afgan <afgane@gmail.com>
 * Istvan Albert <istvan.albert@gmail.com>

From 601b5a2c384cc6bb464e9e050b834ad7e8480cfd Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Mon, 6 Apr 2020 15:18:36 -0400
Subject: [PATCH 723/853] Some code review changes. And fixed a lint issue

---
 .github/workflows/integration.yaml            |  3 ---
 lib/galaxy/objectstore/irods.py               | 22 -------------------
 .../integration/test_datatype_upload_irods.py |  4 +---
 3 files changed, 1 insertion(+), 28 deletions(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 2e014f3ae4b8..a2ac1f5df8e8 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -35,8 +35,6 @@ jobs:
       run: |
         kubectl get pods
     - uses: actions/checkout@v2
-      with:
-        path: 'galaxy root'
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
@@ -48,4 +46,3 @@ jobs:
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
-      working-directory: 'galaxy-root'
diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index bf0e1f83b38e..3841bf0909e2 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -313,28 +313,6 @@ def _in_cache(self, rel_path):
         """ Check if the given dataset is in the local cache and return True if so. """
         cache_path = self._get_cache_path(rel_path)
         return os.path.exists(cache_path)
-        # TODO: Part of checking if a file is in cache should be to ensure the
-        # size of the cached file matches that on S3. Once the upload tool explicitly
-        # creates, this check sould be implemented- in the mean time, it's not
-        # looking likely to be implementable reliably.
-        # if os.path.exists(cache_path):
-        #     # print("***1 %s exists" % cache_path)
-        #     if self._key_exists(rel_path):
-        #         # print("***2 %s exists in S3" % rel_path)
-        #         # Make sure the size in cache is available in its entirety
-        #         # print("File '%s' cache size: %s, S3 size: %s" % (cache_path, os.path.getsize(cache_path), self._get_size_in_s3(rel_path)))
-        #         if os.path.getsize(cache_path) == self._get_size_in_s3(rel_path):
-        #             # print("***2.1 %s exists in S3 and the size is the same as in cache (in_cache=True)" % rel_path)
-        #             exists = True
-        #         else:
-        #             # print("***2.2 %s exists but differs in size from cache (in_cache=False)" % cache_path)
-        #             exists = False
-        #     else:
-        #         # Although not perfect decision making, this most likely means
-        #         # that the file is currently being uploaded
-        #         # print("***3 %s found in cache but not in S3 (in_cache=True)" % cache_path)
-        #         exists = True
-        # else:
 
     def _pull_into_cache(self, rel_path):
         # Ensure the cache directory structure exists (e.g., dataset_#_files/)
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index d6f9b1fa70ad..3001da5d3a13 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -2,16 +2,14 @@
 import os
 import string
 import subprocess
-import tempfile
 import time
 
 import pytest
 
 from galaxy_test.driver import integration_util
 from .test_datatype_upload import (
-    temp_file
     TEST_CASES,
-    upload_datatype_helper, 
+    upload_datatype_helper,
     UploadTestDatatypeDataTestCase
 )
 

From cdb9f50d2043beb4579c544fec3138c002cb99f4 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 7 Apr 2020 09:26:16 -0400
Subject: [PATCH 724/853] Read/write files in chunks

---
 lib/galaxy/objectstore/irods.py | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 3841bf0909e2..d26b6610697d 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -1,6 +1,7 @@
 """
 Object Store plugin for the Integrated Rule-Oriented Data Store (iRODS)
 """
+from functool import partial
 import logging
 import os
 import shutil
@@ -27,7 +28,8 @@
 from ..objectstore import DiskObjectStore
 
 IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this feature, please install it')
-
+# 1 MB
+CHUNK_SIZE = 2**20
 log = logging.getLogger(__name__)
 
 
@@ -349,8 +351,8 @@ def _download(self, rel_path):
         log.debug("Pulled data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
 
         with data_obj.open('r') as data_obj_fp, open(self._get_cache_path(rel_path), "wb") as cache_fp:
-            content = data_obj_fp.read()
-            cache_fp.write(content)
+            for chunk in iter(partial(data_obj_fp.read, CHUNK_SIZE), b''):
+                cache_fp.write(chunk)
         return True
 
     def _push_to_irods(self, rel_path, source_file=None, from_string=None):
@@ -388,15 +390,12 @@ def _push_to_irods(self, rel_path, source_file=None, from_string=None):
 
                 # Create sub-collection first
                 self.session.collections.create(collection_path, recurse=True)
-
-                file_content = None
-                with open(source_file, 'rb') as content_file:
-                    file_content = content_file.read()
+                data_obj = self.session.data_objects.create(data_object_path, self.resource, **options)
 
                 # Write to file in subcollection created above
-                data_obj = self.session.data_objects.create(data_object_path, self.resource, **options)
-                with data_obj.open('w') as data_obj_fp:
-                    data_obj_fp.write(file_content)
+                with open(source_file, 'rb') as content_file, data_obj.open('w') as data_obj_fp:
+                    for chunk in iter(partial(content_file.read, CHUNK_SIZE), b''):
+                        data_obj_fp.write(chunk)
 
                 end_time = datetime.now()
                 log.debug("Pushed cache file '%s' to collection '%s' (%s bytes transfered in %s sec)",

From 501ab2c018448e8c5c5a7ddada1e8df75c6155b7 Mon Sep 17 00:00:00 2001
From: kxk302 <kxk302@gmail.com>
Date: Tue, 7 Apr 2020 10:00:20 -0400
Subject: [PATCH 725/853] Apply suggestions from code review

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 .../dependencies/pipfiles/default/pinned-dev-requirements.txt   | 1 -
 lib/galaxy/objectstore/irods.py                                 | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index 8bf9fe43e9a9..13e8e7864c78 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -64,4 +64,3 @@ watchdog==0.10.2
 wcwidth==0.1.8
 wrapt==1.12.0
 zipp==1.2.0
-
diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index d26b6610697d..06d49254a847 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -1,11 +1,11 @@
 """
 Object Store plugin for the Integrated Rule-Oriented Data Store (iRODS)
 """
-from functool import partial
 import logging
 import os
 import shutil
 from datetime import datetime
+from functools import partial
 try:
     from pathlib import Path
 except ImportError:

From c4d43ff745dc43a80bfa26244f7a4c1a2ab5cfce Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 7 Apr 2020 10:18:56 -0400
Subject: [PATCH 726/853] Added fixture back as tests were failing

---
 test/integration/test_datatype_upload_irods.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 3001da5d3a13..8a78f5a79b2e 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -2,6 +2,7 @@
 import os
 import string
 import subprocess
+import tempfile
 import time
 
 import pytest
@@ -99,6 +100,12 @@ def handle_galaxy_config_kwds(cls, config):
 instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
 
 
+@pytest.fixture
+def temp_file():
+    with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
+        yield fh
+
+
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_irods(instance, test_data, temp_file):
     upload_datatype_helper(instance, test_data, temp_file)

From b482d835b20d737e89cd442b1201ee830e81ae3d Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 7 Apr 2020 11:33:02 -0400
Subject: [PATCH 727/853] Reverted change to integration.yaml file

---
 .github/workflows/integration.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index a2ac1f5df8e8..bb9db9522f0d 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         python-version: [3.7]
-        subset: ['upload_datatype_irods']
+        subset: ['upload_datatype', 'extended_metadata', 'kubernetes', 'not (upload_datatype or extended_metadata or kubernetes)']
     services:
       postgres:
         image: postgres:11

From e269bf75efaf47af7c7de5f1d767fc070cc267c1 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 7 Apr 2020 13:36:37 -0400
Subject: [PATCH 728/853] Restored integration.yaml. Moved common integration
 test fixture into conftest.py.

---
 .github/workflows/integration.yaml             | 16 ++++++++++++++--
 test/integration/conftest.py                   | 10 ++++++++++
 test/integration/test_datatype_upload.py       |  7 -------
 test/integration/test_datatype_upload_irods.py |  7 -------
 4 files changed, 24 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index bb9db9522f0d..3bd0aaf4d697 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -2,8 +2,8 @@ name: Integration
 on: [push, pull_request]
 env:
   GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_AMQP_URL: 'amqp://localhost:5672//'
 jobs:
-
   test:
     name: Test
     runs-on: ubuntu-18.04
@@ -20,13 +20,22 @@ jobs:
           POSTGRES_DB: postgres
         ports:
           - 5432:5432
+      rabbitmq:
+        image: rabbitmq
+        ports:
+          - 5672:5672
     steps:
     - name: Prune unused docker image, volumes and containers
       run: docker system prune -a -f
+    - name: Clean dotnet folder for space
+      if: matrix.subset == 'kubernetes'
+      run: rm -Rf /usr/share/dotnet
     - name: Setup Minikube
       if: matrix.subset == 'kubernetes'
       id: minikube
-      uses: CodingNagger/minikube-setup-action@v1.0.2
+      uses: CodingNagger/minikube-setup-action@v1.0.3
+      with:
+        minikube-version: "1.9.0-0_amd64"
     - name: Launch Minikube
       if: matrix.subset == 'kubernetes'
       run: eval ${{ steps.minikube.outputs.launcher }}
@@ -35,6 +44,8 @@ jobs:
       run: |
         kubectl get pods
     - uses: actions/checkout@v2
+      with:
+        path: 'galaxy root'
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
@@ -46,3 +57,4 @@ jobs:
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Run tests
       run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
+      working-directory: 'galaxy root'
diff --git a/test/integration/conftest.py b/test/integration/conftest.py
index 57000428c9e1..91c4ace1ef67 100644
--- a/test/integration/conftest.py
+++ b/test/integration/conftest.py
@@ -1,3 +1,7 @@
+import pytest
+import tempfile
+
+
 def pytest_unconfigure(config):
     try:
         # This needs to be run if no test were run.
@@ -6,3 +10,9 @@ def pytest_unconfigure(config):
         print("Galaxy test driver shutdown succesfull")
     except Exception:
         pass
+
+
+@pytest.fixture
+def temp_file():
+    with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
+        yield fh
diff --git a/test/integration/test_datatype_upload.py b/test/integration/test_datatype_upload.py
index 71c14f43028e..0250d3d3a6dd 100644
--- a/test/integration/test_datatype_upload.py
+++ b/test/integration/test_datatype_upload.py
@@ -1,6 +1,5 @@
 import collections
 import os
-import tempfile
 
 import pytest
 
@@ -48,12 +47,6 @@ class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance):
 instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
 
 
-@pytest.fixture
-def temp_file():
-    with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
-        yield fh
-
-
 registry = Registry()
 registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG)
 TEST_CASES = collect_test_data(registry)
diff --git a/test/integration/test_datatype_upload_irods.py b/test/integration/test_datatype_upload_irods.py
index 8a78f5a79b2e..3001da5d3a13 100644
--- a/test/integration/test_datatype_upload_irods.py
+++ b/test/integration/test_datatype_upload_irods.py
@@ -2,7 +2,6 @@
 import os
 import string
 import subprocess
-import tempfile
 import time
 
 import pytest
@@ -100,12 +99,6 @@ def handle_galaxy_config_kwds(cls, config):
 instance = integration_util.integration_module_instance(UploadTestDatatypeDataTestCase)
 
 
-@pytest.fixture
-def temp_file():
-    with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
-        yield fh
-
-
 @pytest.mark.parametrize('test_data', IRODS_TEST_CASES.values(), ids=list(IRODS_TEST_CASES.keys()))
 def test_upload_datatype_irods(instance, test_data, temp_file):
     upload_datatype_helper(instance, test_data, temp_file)

From f4b537bf2fa6616c5a773b6fa31b97849dec3641 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 7 Apr 2020 13:51:25 -0400
Subject: [PATCH 729/853] Fixed import order

---
 test/integration/conftest.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/integration/conftest.py b/test/integration/conftest.py
index 91c4ace1ef67..35317ac3d38c 100644
--- a/test/integration/conftest.py
+++ b/test/integration/conftest.py
@@ -1,6 +1,7 @@
-import pytest
 import tempfile
 
+import pytest
+
 
 def pytest_unconfigure(config):
     try:

From d79ae912a73b8b893b6537ac73466e7a68858733 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 8 Apr 2020 01:55:25 +0100
Subject: [PATCH 730/853] Add PAF datatype

---
 .../config/sample/datatypes_conf.xml.sample   |   2 +
 lib/galaxy/datatypes/test/A-3105.paf          | 245 ++++++++++++++++++
 lib/galaxy/datatypes/text.py                  |  34 +++
 3 files changed, 281 insertions(+)
 create mode 100644 lib/galaxy/datatypes/test/A-3105.paf

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 053a1fb9a412..e8a0f3d4c2b3 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -17,6 +17,7 @@
     <datatype extension="anvio_structure_db" type="galaxy.datatypes.anvio:AnvioStructureDB" display_in_upload="false" />
     <datatype extension="anvio_variability" type="galaxy.datatypes.tabular:TSV" display_in_upload="false" subclass="true" />
     <datatype extension="arff" type="galaxy.datatypes.text:Arff" mimetype="text/plain" display_in_upload="true"/>
+    <datatype extension="paf" type="galaxy.datatypes.text:Paf" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format.  Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines.  Blocks are separated from one another by blank lines.  The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
@@ -876,6 +877,7 @@
     <sniffer type="galaxy.datatypes.interval:Gff"/>
     <sniffer type="galaxy.datatypes.interval:Gff3"/>
     <sniffer type="galaxy.datatypes.tabular:Pileup"/>
+    <sniffer type="galaxy.datatypes.text:Paf"/>
     <sniffer type="galaxy.datatypes.interval:Interval"/>
     <sniffer type="galaxy.datatypes.tabular:Sam"/>
     <sniffer type="galaxy.datatypes.data:Newick"/>
diff --git a/lib/galaxy/datatypes/test/A-3105.paf b/lib/galaxy/datatypes/test/A-3105.paf
new file mode 100644
index 000000000000..2d338e4f1b6e
--- /dev/null
+++ b/lib/galaxy/datatypes/test/A-3105.paf
@@ -0,0 +1,245 @@
+gi|568815454:1200216-1203631	3416	0	3416	+	gi|568815529:1421891-1425306	3416	0	3416	3416	3416	0	NM:i:0	ms:i:6832	AS:i:6832	nn:i:0	tp:A:S	cm:i:637	s1:i:3404	de:f:0	rl:i:0	cg:Z:3416M
+gi|568815454:1200216-1203631	3416	0	3416	+	gi|568815592:29942469-29945883	3415	0	3415	3371	3416	0	NM:i:45	ms:i:6560	AS:i:6560	nn:i:0	tp:A:S	cm:i:540	s1:i:3085	de:f:0.0132	rl:i:0	cg:Z:1212M1I2203M
+gi|568815454:1200216-1203631	3416	0	3411	+	gi|568815567:1196244-1200852	4609	1184	4609	3297	3432	0	NM:i:135	ms:i:6090	AS:i:6090	nn:i:0	tp:A:S	cm:i:381	s1:i:2452	de:f:0.0329	rl:i:0	cg:Z:1339M4D149M17D495M3I183M1I238M3I1000M
+gi|568815454:1200216-1203631	3416	0	3411	+	gi|568815551:1197321-1201446	4126	701	4126	3289	3432	0	NM:i:143	ms:i:6038	AS:i:6038	nn:i:0	tp:A:S	cm:i:385	s1:i:2485	de:f:0.0355	rl:i:0	cg:Z:1343M3D1M1D144M17D495M3I183M1I238M3I1000M
+gi|568815454:1200216-1203631	3416	0	3411	+	gi|568815561:1196951-1200436	3486	60	3486	3290	3434	0	NM:i:144	ms:i:6038	AS:i:6038	nn:i:0	tp:A:S	cm:i:371	s1:i:2447	de:f:0.0352	rl:i:0	cg:Z:175M1I1163M4D149M17D495M3I165M2D18M1I238M3I1000M
+gi|568815454:1200216-1203631	3416	5	3411	+	gi|568815569:1240288-1243708	3421	0	3421	3284	3429	0	NM:i:145	ms:i:6022	AS:i:6022	nn:i:0	tp:A:S	cm:i:383	s1:i:2483	de:f:0.0355	rl:i:0	cg:Z:170M1I1163M4D149M17D495M3I165M2D18M1I238M3I1000M
+gi|568815454:1200216-1203631	3416	92	3411	+	gi|568815564:1286641-1289973	3333	0	3333	3198	3340	0	NM:i:142	ms:i:5860	AS:i:5860	nn:i:0	tp:A:S	cm:i:372	s1:i:2412	de:f:0.0362	rl:i:0	cg:Z:1251M3D1M1D144M17D495M3I183M1I238M3I1000M
+gi|568815529:1421891-1425306	3416	0	3416	+	gi|568815592:29942469-29945883	3415	0	3415	3371	3416	0	NM:i:45	ms:i:6560	AS:i:6560	nn:i:0	tp:A:S	cm:i:540	s1:i:3085	de:f:0.0132	rl:i:0	cg:Z:1212M1I2203M
+gi|568815529:1421891-1425306	3416	0	3411	+	gi|568815567:1196244-1200852	4609	1184	4609	3297	3432	0	NM:i:135	ms:i:6090	AS:i:6090	nn:i:0	tp:A:S	cm:i:381	s1:i:2452	de:f:0.0329	rl:i:0	cg:Z:1339M4D149M17D495M3I183M1I238M3I1000M
+gi|568815529:1421891-1425306	3416	0	3411	+	gi|568815561:1196951-1200436	3486	60	3486	3290	3434	0	NM:i:144	ms:i:6038	AS:i:6038	nn:i:0	tp:A:S	cm:i:371	s1:i:2447	de:f:0.0352	rl:i:0	cg:Z:175M1I1163M4D149M17D495M3I165M2D18M1I238M3I1000M
+gi|568815529:1421891-1425306	3416	0	3411	+	gi|568815551:1197321-1201446	4126	701	4126	3289	3432	0	NM:i:143	ms:i:6038	AS:i:6038	nn:i:0	tp:A:S	cm:i:385	s1:i:2485	de:f:0.0355	rl:i:0	cg:Z:1343M3D1M1D144M17D495M3I183M1I238M3I1000M
+gi|568815529:1421891-1425306	3416	5	3411	+	gi|568815569:1240288-1243708	3421	0	3421	3284	3429	0	NM:i:145	ms:i:6022	AS:i:6022	nn:i:0	tp:A:S	cm:i:383	s1:i:2483	de:f:0.0355	rl:i:0	cg:Z:170M1I1163M4D149M17D495M3I165M2D18M1I238M3I1000M
+gi|568815529:1421891-1425306	3416	92	3411	+	gi|568815564:1286641-1289973	3333	0	3333	3198	3340	0	NM:i:142	ms:i:5860	AS:i:5860	nn:i:0	tp:A:S	cm:i:372	s1:i:2412	de:f:0.0362	rl:i:0	cg:Z:1251M3D1M1D144M17D495M3I183M1I238M3I1000M
+gi|568815551:1197321-1201446	4126	0	4126	+	gi|568815567:1196244-1200852	4609	483	4609	4061	4126	0	NM:i:65	ms:i:7862	AS:i:7862	nn:i:0	tp:A:S	cm:i:604	s1:i:3595	de:f:0.0158	rl:i:0	cg:Z:4126M
+gi|568815551:1197321-1201446	4126	793	4126	+	gi|568815564:1286641-1289973	3333	0	3333	3333	3333	0	NM:i:0	ms:i:6666	AS:i:6666	nn:i:0	tp:A:S	cm:i:615	s1:i:3324	de:f:0	rl:i:0	cg:Z:3333M
+gi|568815551:1197321-1201446	4126	641	4126	+	gi|568815561:1196951-1200436	3486	0	3486	3409	3487	0	NM:i:78	ms:i:6504	AS:i:6504	nn:i:0	tp:A:S	cm:i:456	s1:i:2855	de:f:0.0221	rl:i:0	cg:Z:235M1I1996M2D1253M
+gi|568815551:1197321-1201446	4126	706	4126	+	gi|568815569:1240288-1243708	3421	0	3421	3343	3422	0	NM:i:79	ms:i:6368	AS:i:6368	nn:i:0	tp:A:S	cm:i:455	s1:i:2819	de:f:0.0228	rl:i:0	cg:Z:170M1I1996M2D1253M
+gi|568815551:1197321-1201446	4126	701	4126	+	gi|568815592:29942469-29945883	3415	0	3410	3296	3432	0	NM:i:136	ms:i:6078	AS:i:6078	nn:i:0	tp:A:S	cm:i:381	s1:i:2471	de:f:0.0334	rl:i:0	cg:Z:1212M1I130M3I1M1I144M17I495M3D183M1D238M3D1000M
+gi|568815561:1196951-1200436	3486	65	3486	+	gi|568815569:1240288-1243708	3421	0	3421	3398	3421	0	NM:i:23	ms:i:6704	AS:i:6704	nn:i:0	tp:A:S	cm:i:574	s1:i:3257	de:f:0.0067	rl:i:0	cg:Z:3421M
+gi|568815561:1196951-1200436	3486	0	3486	+	gi|568815567:1196244-1200852	4609	1124	4609	3435	3487	0	NM:i:52	ms:i:6660	AS:i:6660	nn:i:0	tp:A:S	cm:i:518	s1:i:3068	de:f:0.0146	rl:i:0	cg:Z:235M1D1996M2I1253M
+gi|568815561:1196951-1200436	3486	152	3486	+	gi|568815564:1286641-1289973	3333	0	3333	3257	3335	0	NM:i:78	ms:i:6200	AS:i:6200	nn:i:0	tp:A:S	cm:i:426	s1:i:2708	de:f:0.0231	rl:i:0	cg:Z:83M1D1996M2I1253M
+gi|568815561:1196951-1200436	3486	60	3486	+	gi|568815592:29942469-29945883	3415	0	3410	3298	3434	0	NM:i:136	ms:i:6084	AS:i:6084	nn:i:0	tp:A:S	cm:i:380	s1:i:2501	de:f:0.0328	rl:i:0	cg:Z:175M1D1036M1I126M4I149M17I495M3D165M2I18M1D238M3D1000M
+gi|568815564:1286641-1289973	3333	0	3333	+	gi|568815567:1196244-1200852	4609	1276	4609	3271	3333	0	NM:i:62	ms:i:6294	AS:i:6294	nn:i:0	tp:A:S	cm:i:459	s1:i:2836	de:f:0.0186	rl:i:0	cg:Z:3333M
+gi|568815564:1286641-1289973	3333	0	3333	+	gi|568815569:1240288-1243708	3421	87	3421	3256	3335	0	NM:i:79	ms:i:6194	AS:i:6194	nn:i:0	tp:A:S	cm:i:439	s1:i:2735	de:f:0.0234	rl:i:0	cg:Z:83M1I1996M2D1253M
+gi|568815564:1286641-1289973	3333	0	3333	+	gi|568815592:29942469-29945883	3415	92	3410	3206	3340	0	NM:i:134	ms:i:5906	AS:i:5906	nn:i:0	tp:A:S	cm:i:370	s1:i:2404	de:f:0.0338	rl:i:0	cg:Z:1120M1I130M3I1M1I144M17I495M3D183M1D238M3D1000M
+gi|568815567:1196244-1200852	4609	1189	4609	+	gi|568815569:1240288-1243708	3421	0	3421	3368	3422	0	NM:i:54	ms:i:6518	AS:i:6518	nn:i:0	tp:A:S	cm:i:514	s1:i:3034	de:f:0.0155	rl:i:0	cg:Z:170M1I1996M2D1253M
+gi|568815567:1196244-1200852	4609	1184	4609	+	gi|568815592:29942469-29945883	3415	0	3410	3293	3432	0	NM:i:139	ms:i:6064	AS:i:6064	nn:i:0	tp:A:S	cm:i:374	s1:i:2444	de:f:0.0340	rl:i:0	cg:Z:1212M1I126M4I149M17I495M3D183M1D238M3D1000M
+gi|568815569:1240288-1243708	3421	0	3421	+	gi|568815592:29942469-29945883	3415	5	3410	3289	3429	0	NM:i:140	ms:i:6050	AS:i:6050	nn:i:0	tp:A:S	cm:i:388	s1:i:2487	de:f:0.0341	rl:i:0	cg:Z:170M1D1036M1I126M4I149M17I495M3D165M2I18M1D238M3D1000M
+gi|342187237:5004-8419	3416	0	3416	+	gi|568815529:1421891-1425306	3416	0	3416	3416	3416	0	NM:i:0	ms:i:6832	AS:i:6832	nn:i:0	tp:A:S	cm:i:637	s1:i:3404	de:f:0	rl:i:0	cg:Z:3416M
+gi|342187237:5004-8419	3416	0	3416	+	gi|568815454:1200216-1203631	3416	0	3416	3416	3416	0	NM:i:0	ms:i:6832	AS:i:6832	nn:i:0	tp:A:S	cm:i:637	s1:i:3404	de:f:0	rl:i:0	cg:Z:3416M
+gi|342187237:5004-8419	3416	0	3416	+	gi|568815592:29942469-29945883	3415	0	3415	3371	3416	0	NM:i:45	ms:i:6560	AS:i:6560	nn:i:0	tp:A:S	cm:i:540	s1:i:3085	de:f:0.0132	rl:i:0	cg:Z:1212M1I2203M
+gi|342187237:5004-8419	3416	0	3411	+	gi|568815567:1196244-1200852	4609	1184	4609	3297	3432	0	NM:i:135	ms:i:6090	AS:i:6090	nn:i:0	tp:A:S	cm:i:381	s1:i:2452	de:f:0.0329	rl:i:0	cg:Z:1339M4D149M17D495M3I183M1I238M3I1000M
+gi|342187237:5004-8419	3416	0	3416	+	gi|528476637:29857558-29915771	58214	54784	58214	3296	3437	0	NM:i:141	ms:i:6060	AS:i:6060	nn:i:0	tp:A:S	cm:i:389	s1:i:2505	de:f:0.0348	rl:i:0	cg:Z:1343M3D1M1D144M17D495M3I183M1I238M3I1005M
+gi|342187237:5004-8419	3416	0	3411	+	gi|568815551:1197321-1201446	4126	701	4126	3289	3432	0	NM:i:143	ms:i:6038	AS:i:6038	nn:i:0	tp:A:S	cm:i:385	s1:i:2485	de:f:0.0355	rl:i:0	cg:Z:1343M3D1M1D144M17D495M3I183M1I238M3I1000M
+gi|342187237:5004-8419	3416	0	3411	+	gi|568815561:1196951-1200436	3486	60	3486	3290	3434	0	NM:i:144	ms:i:6038	AS:i:6038	nn:i:0	tp:A:S	cm:i:371	s1:i:2447	de:f:0.0352	rl:i:0	cg:Z:175M1I1163M4D149M17D495M3I165M2D18M1I238M3I1000M
+gi|342187237:5004-8419	3416	5	3411	+	gi|568815569:1240288-1243708	3421	0	3421	3284	3429	0	NM:i:145	ms:i:6022	AS:i:6022	nn:i:0	tp:A:S	cm:i:383	s1:i:2483	de:f:0.0355	rl:i:0	cg:Z:170M1I1163M4D149M17D495M3I165M2D18M1I238M3I1000M
+gi|342187237:5004-8419	3416	92	3411	+	gi|568815564:1286641-1289973	3333	0	3333	3198	3340	0	NM:i:142	ms:i:5860	AS:i:5860	nn:i:0	tp:A:S	cm:i:372	s1:i:2412	de:f:0.0362	rl:i:0	cg:Z:1251M3D1M1D144M17D495M3I183M1I238M3I1000M
+gi|342187237:5004-8419	3416	0	3416	+	gi|528476637:29857558-29915771	58214	0	3428	3142	3464	0	NM:i:322	ms:i:5064	AS:i:5064	nn:i:0	tp:A:S	cm:i:215	s1:i:1596	de:f:0.0772	rl:i:0	cg:Z:185M2I2M4I224M1D3M1I61M1I5M1D108M3D13M1I118M1I486M12I112M4D22M19D127M17D296M1I433M2I589M1I40M1D33M1I37M1I48M1I57M1D1M2I31M4I96M1D88M1I165M
+gi|342187237:5004-8419	3416	3	3416	+	gi|528476637:29857558-29915771	58214	38484	41952	3039	3493	0	NM:i:454	ms:i:4320	AS:i:4320	nn:i:0	tp:A:S	cm:i:107	s1:i:1001	de:f:0.1130	rl:i:0	cg:Z:34M1D52M1I123M2I1M1D255M1I4M1D11M1I21M1D12M4I3M1D2M1D4M2D59M3D33M3D38M1I3M2D60M1I25M1D277M1I327M1D132M16D164M5D6M2D207M2I74M7D52M20D363M1D41M3D90M1I103M6I96M1D6M1I117M1D2M1I208M1I132M2D26M4D60M1I165M
+gi|342187237:5004-8419	3416	1488	3158	+	gi|528476637:29857558-29915771	58214	8636	10269	1295	1729	0	NM:i:434	ms:i:964	AS:i:970	nn:i:0	tp:A:S	cm:i:10	s1:i:118	de:f:0.2026	rl:i:0	cg:Z:35M1I414M1D3M1I7M1I12M3D44M20D84M3I2M2I2M10I42M1D3M1I9M3I2M4I21M1D24M2I2M4I11M9D11M1D1M1D11M4I8M1D4M1D8M4I60M3I11M1D6M1D17M2I8M1D5M2D38M2D4M1D3M1I39M2I15M26I105M2D1M5D59M1I108M1I2M1D47M2I71M2I47M1D6M7I3M3I40M2I3M1D19M1D7M1D37M3I12M1I41M
+gi|342187237:5004-8419	3416	891	1307	+	gi|528476637:29857558-29915771	58214	44457	44873	392	416	0	NM:i:24	ms:i:688	AS:i:688	nn:i:0	tp:A:S	cm:i:36	s1:i:238	de:f:0.0577	rl:i:0	cg:Z:416M
+gi|528476637:29857558-29915771	58214	53600	58209	+	gi|568815567:1196244-1200852	4609	0	4609	4559	4609	0	NM:i:50	ms:i:8918	AS:i:8918	nn:i:0	tp:A:S	cm:i:729	s1:i:4180	de:f:0.0108	rl:i:25	cg:Z:4609M
+gi|528476637:29857558-29915771	58214	33375	41952	+	gi|528476637:29857558-29915771	58214	49822	58214	7180	8967	0	NM:i:1787	ms:i:8814	AS:i:9504	nn:i:0	tp:A:S	cm:i:225	s1:i:2063	de:f:0.1118	rl:i:25	cg:Z:24M4D11M3I103M2I43M2I32M3D51M1D139M5D1M1D573M3I3M2I49M1D3M1D13M2D5M1I189M1D36M17D448M1I3M1D215M3I35M4I263M8I23M1D91M1D279M1I137M310D48M4I225M6I3M1D3M350I6M2I46M1D379M1I54M1I85M2I21M1I6M90I167M1I74M1D1M2D236M1D10M4D48M19I109M4D346M1I52M1D125M1D271M1D21M1I12M4D3M1I2M1I4M2I57M2I3M1I32M3I40M1I62M1D25M1I277M1D311M3D2M1D14M1I148M1D170M7I207M2D66M2I5M6I2M1D39M3I10M20I173M1I189M1I41M3I8M3I79M1D103M6D96M1I6M1D328M1D132M2I26M4I60M1D165M
+gi|528476637:29857558-29915771	58214	49822	58214	+	gi|528476637:29857558-29915771	58214	33375	41952	7180	8967	0	NM:i:1787	ms:i:8814	AS:i:9504	nn:i:0	tp:A:S	cm:i:225	s1:i:2063	de:f:0.1118	rl:i:25	cg:Z:24M4I11M3D103M2D43M2D32M3I51M1I139M5I1M1I573M3D3M2D49M1I3M1I13M2I5M1D189M1I36M17I448M1D3M1I215M3D35M4D263M8D23M1I91M1I279M1D137M310I48M4D225M6D3M1I3M350D6M2D46M1I379M1D54M1D85M2D21M1D6M90D167M1D74M1I1M2I236M1I10M4I48M19D109M4I346M1D52M1I125M1I271M1I21M1D12M4I3M1D2M1D4M2D57M2D3M1D32M3D40M1D62M1I25M1D277M1I311M3I2M1I14M1D148M1I170M7D207M2I66M2D5M6D2M1I39M3D10M20D173M1D189M1D41M3D8M3D79M1I103M6I96M1D6M1I328M1I132M2D26M4D60M1I165M
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+gi|528476637:29857558-29915771	58214	54876	58209	+	gi|568815564:1286641-1289973	3333	0	3333	3317	3333	0	NM:i:16	ms:i:6570	AS:i:6570	nn:i:0	tp:A:S	cm:i:578	s1:i:3203	de:f:0.0048	rl:i:25	cg:Z:3333M
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+gi|528476637:29857558-29915771	58214	54789	58209	+	gi|568815569:1240288-1243708	3421	0	3421	3347	3422	0	NM:i:75	ms:i:6392	AS:i:6392	nn:i:0	tp:A:S	cm:i:462	s1:i:2853	de:f:0.0216	rl:i:25	cg:Z:170M1I1996M2D1253M
+gi|528476637:29857558-29915771	58214	54784	58214	+	gi|568815592:29942469-29945883	3415	0	3415	3305	3437	0	NM:i:132	ms:i:6112	AS:i:6112	nn:i:0	tp:A:S	cm:i:393	s1:i:2554	de:f:0.0322	rl:i:25	cg:Z:1212M1I130M3I1M1I144M17I495M3D183M1D238M3D1005M
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+gi|528476637:29857558-29915771	58214	0	3428	+	gi|568815529:1421891-1425306	3416	0	3416	3142	3464	0	NM:i:322	ms:i:5064	AS:i:5064	nn:i:0	tp:A:S	cm:i:215	s1:i:1596	de:f:0.0772	rl:i:25	cg:Z:185M2D2M4D224M1I3M1D61M1D5M1I108M3I13M1D118M1D486M12D112M4I22M19I127M17I296M1D433M2D589M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D165M
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+gi|528476637:29857558-29915771	58214	0	3423	+	gi|568815561:1196951-1200436	3486	60	3486	3144	3463	0	NM:i:319	ms:i:5042	AS:i:5042	nn:i:0	tp:A:S	cm:i:188	s1:i:1556	de:f:0.0799	rl:i:25	cg:Z:172M1D2M2I9M2D2M4D225M1I2M1D61M1D5M1I108M3I13M1D118M1D486M12D138M19I440M1D198M3I168M2D16M1I47M2D188M3I398M1D40M1I33M1D37M1D11M1D3M1I33M1D57M1I1M2D31M4D96M1I88M1D160M
+gi|528476637:29857558-29915771	58214	0	3423	+	gi|568815551:1197321-1201446	4126	701	4126	3137	3459	0	NM:i:322	ms:i:5022	AS:i:5022	nn:i:0	tp:A:S	cm:i:196	s1:i:1569	de:f:0.0814	rl:i:25	cg:Z:185M2D2M4D225M1I2M1D61M1D5M1I108M3I13M1D118M1D486M12D138M19I440M1D198M3I184M1I47M2D188M3I398M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D160M
+gi|528476637:29857558-29915771	58214	0	3428	+	gi|568815592:29942469-29945883	3415	0	3415	3134	3463	0	NM:i:329	ms:i:5014	AS:i:5014	nn:i:0	tp:A:S	cm:i:206	s1:i:1582	de:f:0.0799	rl:i:25	cg:Z:185M2D2M4D225M1I2M1D61M1D5M1I108M3I13M1D118M1D485M10D1M1D112M4I22M19I127M17I296M1D433M2D589M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D165M
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+gi|528476637:29857558-29915771	58214	38484	42085	+	gi|528476637:29857558-29915771	58214	3	3561	3171	3642	0	NM:i:471	ms:i:4520	AS:i:4520	nn:i:0	tp:A:S	cm:i:135	s1:i:1107	de:f:0.1103	rl:i:25	cg:Z:34M1I52M1D95M2I2M4I22M1D202M1D2M1I67M1D19M1I104M1I9M3I47M1I87M1I277M1D106M1D7M2I2M1D68M12I114M1D2M3D20M17D1M1D142M1D164M5I6M2I120M1I86M2D74M7I58M14I6M5I1M1I209M2I139M1I42M2I1M1I88M1D103M6D96M1I6M1D106M1I40M1D33M1I37M1I52M1I84M4I101M1I26M4I358M
+gi|528476637:29857558-29915771	58214	3	3561	+	gi|528476637:29857558-29915771	58214	38484	42085	3171	3642	0	NM:i:471	ms:i:4520	AS:i:4520	nn:i:0	tp:A:S	cm:i:135	s1:i:1107	de:f:0.1103	rl:i:25	cg:Z:34M1D52M1I95M2D2M4D22M1I202M1I2M1D67M1I19M1D104M1D9M3D47M1D87M1D277M1I106M1I7M2D2M1I68M12D114M1I2M3I20M17I1M1I142M1I164M5D6M2D120M1D86M2I74M7D58M14D6M5D1M1D209M2D139M1D42M2D1M1D88M1I103M6I96M1D6M1I106M1D40M1I33M1D37M1D52M1D84M4D101M1D26M4D358M
+gi|528476637:29857558-29915771	58214	38421	41947	+	gi|568815561:1196951-1200436	3486	0	3486	3090	3555	0	NM:i:465	ms:i:4352	AS:i:4352	nn:i:0	tp:A:S	cm:i:95	s1:i:919	de:f:0.1166	rl:i:25	cg:Z:97M1I52M1D81M1I43M1D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I57M2I3M1I32M3I40M1I62M1D25M1I277M1D311M1D2M3D14M1I148M1D170M7I207M2D74M7I39M3I10M20I158M2D15M1I189M1I41M3I8M3I79M1D103M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
+gi|528476637:29857558-29915771	58214	38484	41952	+	gi|568815592:29942469-29945883	3415	3	3415	3041	3495	0	NM:i:454	ms:i:4326	AS:i:4326	nn:i:0	tp:A:S	cm:i:110	s1:i:990	de:f:0.1121	rl:i:25	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I40M1I62M1D25M1I222M3D4M3I48M1D180M1I146M1I132M16I164M5I6M2I207M2D74M7I52M20I363M1I41M3I90M1D103M6D96M1I6M1D117M1I2M1D208M1D132M2I26M4I60M1D165M
+gi|528476637:29857558-29915771	58214	38484	41952	+	gi|568815454:1200216-1203631	3416	3	3416	3039	3493	0	NM:i:454	ms:i:4320	AS:i:4320	nn:i:0	tp:A:S	cm:i:107	s1:i:1001	de:f:0.1130	rl:i:25	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I38M1D3M2I60M1D25M1I277M1D327M1I132M16I164M5I6M2I207M2D74M7I52M20I363M1I41M3I90M1D103M6D96M1I6M1D117M1I2M1D208M1D132M2I26M4I60M1D165M
+gi|528476637:29857558-29915771	58214	38484	41952	+	gi|568815529:1421891-1425306	3416	3	3416	3039	3493	0	NM:i:454	ms:i:4320	AS:i:4320	nn:i:0	tp:A:S	cm:i:107	s1:i:1001	de:f:0.1130	rl:i:25	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I38M1D3M2I60M1D25M1I277M1D327M1I132M16I164M5I6M2I207M2D74M7I52M20I363M1I41M3I90M1D103M6D96M1I6M1D117M1I2M1D208M1D132M2I26M4I60M1D165M
+gi|528476637:29857558-29915771	58214	38486	41947	+	gi|568815569:1240288-1243708	3421	0	3421	3037	3486	0	NM:i:449	ms:i:4310	AS:i:4310	nn:i:0	tp:A:S	cm:i:97	s1:i:949	de:f:0.1154	rl:i:25	cg:Z:32M1I52M1D81M1I43M1D255M1D4M1I11M1D21M1I82M2I3M1I32M3I40M1I62M1D25M1I277M1D311M1D2M3D14M1I148M1D170M7I207M2D74M7I39M3I10M20I158M2D15M1I189M1I41M3I8M3I79M1D103M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
+gi|528476637:29857558-29915771	58214	38573	41947	+	gi|568815564:1286641-1289973	3333	0	3333	2962	3402	0	NM:i:440	ms:i:4198	AS:i:4198	nn:i:0	tp:A:S	cm:i:100	s1:i:935	de:f:0.1145	rl:i:25	cg:Z:121M1I1M2D254M1D5M1I11M1D21M1I12M4D3M1I2M1I4M2I57M2I3M1I32M3I40M1I62M1D25M1I277M1D311M3D2M1D14M1I148M1D170M7I207M2D66M2I5M6I2M1D39M3I10M20I173M1I189M1I41M3I8M3I79M1D103M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
+gi|528476637:29857558-29915771	58214	3555	4654	+	gi|528476637:29857558-29915771	58214	43020	44118	982	1103	0	NM:i:121	ms:i:1478	AS:i:1478	nn:i:0	tp:A:S	cm:i:30	s1:i:230	de:f:0.1065	rl:i:25	cg:Z:156M1I416M3D62M3I27M1I156M1D277M
+gi|528476637:29857558-29915771	58214	43020	44118	+	gi|528476637:29857558-29915771	58214	3555	4654	982	1103	0	NM:i:121	ms:i:1478	AS:i:1478	nn:i:0	tp:A:S	cm:i:30	s1:i:230	de:f:0.1065	rl:i:25	cg:Z:156M1D416M3I62M3D27M1D156M1I277M
+gi|528476637:29857558-29915771	58214	48998	49823	+	gi|528476637:29857558-29915771	58214	31581	32408	735	834	0	NM:i:99	ms:i:1062	AS:i:1062	nn:i:0	tp:A:S	cm:i:17	s1:i:194	de:f:0.1134	rl:i:25	cg:Z:9M2D100M1I166M1I2M1D93M1D142M1D28M2D3M2D113M1I3M3I4M1I155M
+gi|528476637:29857558-29915771	58214	31581	32408	+	gi|528476637:29857558-29915771	58214	48998	49823	735	834	0	NM:i:99	ms:i:1062	AS:i:1062	nn:i:0	tp:A:S	cm:i:17	s1:i:194	de:f:0.1134	rl:i:25	cg:Z:9M2I100M1D166M1D2M1I93M1I142M1I28M2I3M2I113M1D3M3D4M1D155M
+gi|528476637:29857558-29915771	58214	1488	3170	+	gi|528476637:29857558-29915771	58214	8615	10269	1320	1753	0	NM:i:433	ms:i:1012	AS:i:1018	nn:i:0	tp:A:S	cm:i:12	s1:i:120	de:f:0.1961	rl:i:25	cg:Z:11M2I45M1I260M1D153M1D3M1I7M1I12M3D41M14D4M6D78M3I6M5I3M7I55M5I2M2I21M1D26M2D2M6D11M1I6M2I5M2D11M4I8M1D4M1D8M4I59M3I12M1D6M1D17M2I8M1D5M2D38M2D47M2I15M26I22M1I7M1D75M2D1M5D22M1I5M1I6M1I3M3D20M1I115M1D44M5I3M1D1M1D17M1D41M1D2M2I7M1I3M1D36M2D6M7I3M3I63M1D3M5D37M3I2M2I9M1D41M
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+gi|528476637:29857558-29915771	58214	8629	10269	+	gi|568815569:1240288-1243708	3421	1496	3168	1284	1736	0	NM:i:452	ms:i:868	AS:i:874	nn:i:0	tp:A:S	cm:i:10	s1:i:116	de:f:0.2118	rl:i:25	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I79M3D3M4D3M8D48M2D10M3D2M3D21M1I30M6I11M1D6M2D7M4I4M1I3M7D7M1I4M1I8M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
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+gi|528476637:29857558-29915771	58214	4739	5908	+	gi|528476637:29857558-29915771	58214	27052	28249	925	1207	0	NM:i:282	ms:i:726	AS:i:726	nn:i:0	tp:A:S	cm:i:8	s1:i:95	de:f:0.2174	rl:i:25	cg:Z:100M1I5M1D139M7D13M1D133M7D80M1I58M1D6M1I70M1D31M2I5M1D15M1D3M1D17M1I2M1D168M9D2M1D48M2D113M2I73M2I4M2D15M1D23M1D36M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815569:1240288-1243708	3421	885	1301	398	416	0	NM:i:18	ms:i:724	AS:i:724	nn:i:0	tp:A:S	cm:i:39	s1:i:284	de:f:0.0433	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815567:1196244-1200852	4609	2075	2491	398	416	0	NM:i:18	ms:i:724	AS:i:724	nn:i:0	tp:A:S	cm:i:39	s1:i:295	de:f:0.0433	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815592:29942469-29945883	3415	891	1306	398	416	0	NM:i:18	ms:i:722	AS:i:722	nn:i:0	tp:A:S	cm:i:42	s1:i:282	de:f:0.0433	rl:i:25	cg:Z:321M1I94M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815561:1196951-1200436	3486	950	1366	397	416	0	NM:i:19	ms:i:718	AS:i:718	nn:i:0	tp:A:S	cm:i:36	s1:i:274	de:f:0.0457	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	55675	56091	+	gi|528476637:29857558-29915771	58214	44457	44873	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:37	s1:i:254	de:f:0.0481	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815551:1197321-1201446	4126	1592	2008	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:37	s1:i:254	de:f:0.0481	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815564:1286641-1289973	3333	799	1215	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:37	s1:i:254	de:f:0.0481	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|528476637:29857558-29915771	58214	55675	56091	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:37	s1:i:254	de:f:0.0481	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815454:1200216-1203631	3416	891	1307	392	416	0	NM:i:24	ms:i:688	AS:i:688	nn:i:0	tp:A:S	cm:i:36	s1:i:238	de:f:0.0577	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815529:1421891-1425306	3416	891	1307	392	416	0	NM:i:24	ms:i:688	AS:i:688	nn:i:0	tp:A:S	cm:i:36	s1:i:238	de:f:0.0577	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	886	1289	+	gi|528476637:29857558-29915771	58214	44457	44872	368	415	0	NM:i:47	ms:i:568	AS:i:568	nn:i:0	tp:A:S	cm:i:17	s1:i:133	de:f:0.0891	rl:i:25	cg:Z:324M12D79M
+gi|528476637:29857558-29915771	58214	44457	44872	+	gi|528476637:29857558-29915771	58214	886	1289	368	415	0	NM:i:47	ms:i:568	AS:i:568	nn:i:0	tp:A:S	cm:i:17	s1:i:133	de:f:0.0891	rl:i:25	cg:Z:324M12I79M
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+gi|528476637:29857558-29915771	58214	28378	28643	-	gi|528476637:29857558-29915771	58214	29092	29357	236	265	31	NM:i:29	ms:i:356	AS:i:356	nn:i:0	tp:A:P	cm:i:4	s1:i:46	s2:i:0	de:f:0.1094	zd:i:2	rl:i:25	cg:Z:265M
+gi|528476637:29857558-29915771	58214	45137	45465	-	gi|528476637:29857558-29915771	58214	14421	14731	269	329	0	NM:i:60	ms:i:318	AS:i:318	nn:i:0	tp:A:S	cm:i:3	s1:i:42	de:f:0.1433	rl:i:25	cg:Z:35M1D115M1I2M14I113M1I28M3I16M
+gi|528476637:29857558-29915771	58214	14421	14731	-	gi|528476637:29857558-29915771	58214	45137	45465	269	329	0	NM:i:60	ms:i:318	AS:i:318	nn:i:0	tp:A:S	cm:i:3	s1:i:42	de:f:0.1433	rl:i:25	cg:Z:14M3D30M1D113M14D2M1D114M1I36M
+gi|528476637:29857558-29915771	58214	6307	7004	-	gi|528476637:29857558-29915771	58214	6307	7004	528	727	0	NM:i:199	ms:i:272	AS:i:272	nn:i:0	tp:A:S	cm:i:4	s1:i:44	de:f:0.2392	rl:i:25	cg:Z:11M1D155M1I43M2D64M2I1M1I6M3I5M2I1M2I6M1D9M2I3M3D6M8I5M1I8M1I5M1I10M1D5M1D5M1D8M8D5M3I4M2D3M2D13M2D7M5D70M2I43M1D154M1I12M
+gi|528476637:29857558-29915771	58214	8056	8300	+	gi|528476637:29857558-29915771	58214	8056	8376	225	321	0	NM:i:96	ms:i:258	AS:i:271	nn:i:0	tp:A:S	cm:i:7	s1:i:51	de:f:0.0816	rl:i:25	cg:Z:129M77D89M1I25M
+gi|528476637:29857558-29915771	58214	8056	8376	+	gi|528476637:29857558-29915771	58214	8056	8300	225	321	0	NM:i:96	ms:i:258	AS:i:271	nn:i:0	tp:A:S	cm:i:7	s1:i:51	de:f:0.0816	rl:i:25	cg:Z:129M77I89M1D25M
+gi|528476637:29857558-29915771	58214	17754	17858	+	gi|528476637:29857558-29915771	58214	17845	17947	98	104	0	NM:i:6	ms:i:172	AS:i:172	nn:i:0	tp:A:S	cm:i:8	s1:i:52	de:f:0.0485	rl:i:25	cg:Z:13M2I89M
+gi|528476637:29857558-29915771	58214	17845	17947	+	gi|528476637:29857558-29915771	58214	17754	17858	98	104	0	NM:i:6	ms:i:172	AS:i:172	nn:i:0	tp:A:S	cm:i:8	s1:i:52	de:f:0.0485	rl:i:25	cg:Z:13M2D89M
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+gi|157734152:29655295-29712160	56866	12900	22956	+	gi|528476637:29857558-29915771	58214	12858	22836	9939	10067	0	NM:i:128	ms:i:19554	AS:i:19623	nn:i:0	tp:A:S	cm:i:5	s1:i:51	de:f:0.0031	rl:i:96	cg:Z:1820M9D806M2D2415M89I4926M
+gi|157734152:29655295-29712160	56866	47082	56866	+	gi|528476637:29857558-29915771	58214	48429	58214	9630	9801	0	NM:i:171	ms:i:18606	AS:i:18606	nn:i:0	tp:A:S	cm:i:1505	s1:i:8643	de:f:0.0150	rl:i:96	cg:Z:179M2D335M1D587M2D3229M2I161M13I113M1I180M8D563M1D518M3D3903M
+gi|157734152:29655295-29712160	56866	48470	56866	+	gi|528476637:29857558-29915771	58214	33375	41952	7179	8982	60	NM:i:1803	ms:i:8784	AS:i:9498	nn:i:0	tp:A:P	cm:i:223	s1:i:1956	s2:i:0	de:f:0.1112	zd:i:2	rl:i:96	cg:Z:24M4I11M3D103M2D43M2D32M3I51M1I139M5I1M1I573M3D3M2D49M1I3M1I13M2I5M1D189M1I36M17I448M1D3M1I215M3D35M4D263M8D23M1I91M1I279M1D133M325I52M4D50M1I175M6D3M359D48M1I379M1D54M1D84M3D21M1D6M90D168M1D72M2I2M1I236M1I10M1I48M19D109M4I346M1D52M1I123M2I1M1D254M1I5M1D11M1I21M1D12M4I3M1D2M1D4M2D57M2D3M1D32M3D40M1D62M1I25M1D277M1I311M3I2M1I14M1D148M1I170M7D207M2I66M2D5M6D2M1I39M3D10M20D173M1D189M1D41M3D8M3D79M1I103M6I96M1D6M1I117M1D2M1I208M1I132M2D26M4D60M1I165M
+gi|157734152:29655295-29712160	56866	33497	42074	+	gi|528476637:29857558-29915771	58214	49822	58214	7174	8964	0	NM:i:1790	ms:i:8766	AS:i:9456	nn:i:0	tp:A:S	cm:i:227	s1:i:2051	de:f:0.1132	rl:i:96	cg:Z:24M4D11M3I103M1I43M2I32M3D51M1D139M5D1M1D573M3I3M2I49M1D3M1D13M2D5M1I189M1D36M17D448M1I3M1D215M3I35M4I263M8I23M1D91M1D279M1I137M310D48M4I225M6I3M1D3M350I6M2I46M1D379M1I54M1I85M2I21M1I6M90I167M1I74M1D1M2D247M4D48M19I109M4D346M1I52M1D125M1D271M1D21M1I12M4D3M1I2M1I4M2I57M2I3M1I32M3I40M1I62M1D25M1I277M1D307M4D20M1I148M1D172M2I2M1I271M1I3M1I2M1I2M4I40M3I10M20I173M1I189M1I41M3I8M3I79M1D17M1D3M1I9M1I1M1I72M6D96M1I6M1D328M1D132M2I26M4I60M1D165M
+gi|157734152:29655295-29712160	56866	33497	42074	+	gi|157734152:29655295-29712160	56866	48470	56866	7171	8978	60	NM:i:1807	ms:i:8732	AS:i:9446	nn:i:0	tp:A:P	cm:i:226	s1:i:1962	s2:i:0	de:f:0.1127	zd:i:2	rl:i:96	cg:Z:24M4D11M3I103M1I43M2I32M3D51M1D139M5D1M1D573M3I3M2I49M1D3M1D13M2D5M1I189M1D36M17D448M1I3M1D215M3I35M4I263M8I23M1D91M1D279M1I133M325D52M4I50M1D175M6I3M359I48M1D379M1I54M1I84M3I21M1I6M90I168M1I72M2D2M1D236M1D59M19I109M4D346M1I52M1D123M1I1M2D254M1D5M1I11M1D21M1I12M4D3M1I2M1I4M2I57M2I3M1I32M3I40M1I62M1D25M1I277M1D307M4D20M1I148M1D172M2I2M1I271M1I3M1I2M1I2M4I40M3I10M20I173M1I189M1I41M3I8M3I79M1D30M1I1M1I72M6D96M1I6M1D116M1I3M1D208M1D132M2I26M4I60M1D165M
+gi|157734152:29655295-29712160	56866	48470	56866	+	gi|157734152:29655295-29712160	56866	33497	42074	7171	8978	60	NM:i:1807	ms:i:8732	AS:i:9446	nn:i:0	tp:A:P	cm:i:226	s1:i:1962	s2:i:0	de:f:0.1127	zd:i:2	rl:i:96	cg:Z:24M4I11M3D103M1D43M2D32M3I51M1I139M5I1M1I573M3D3M2D49M1I3M1I13M2I5M1D189M1I36M17I448M1D3M1I215M3D35M4D263M8D23M1I91M1I279M1D133M325I52M4D50M1I175M6D3M359D48M1I379M1D54M1D84M3D21M1D6M90D168M1D72M2I2M1I236M1I59M19D109M4I346M1D52M1I123M2I1M1D254M1I5M1D11M1I21M1D12M4I3M1D2M1D4M2D57M2D3M1D32M3D40M1D62M1I25M1D277M1I307M4I20M1D148M1I172M2D2M1D271M1D3M1D2M1D2M4D40M3D10M20D173M1D189M1D41M3D8M3D79M1I30M1D1M1D72M6I96M1D6M1I116M1D3M1I208M1I132M2D26M4D60M1I165M
+gi|157734152:29655295-29712160	56866	52256	56861	+	gi|568815567:1196244-1200852	4609	0	4609	4503	4609	0	NM:i:106	ms:i:8582	AS:i:8582	nn:i:0	tp:A:S	cm:i:628	s1:i:3840	de:f:0.0226	rl:i:96	cg:Z:189M1D518M3D3898M
+gi|157734152:29655295-29712160	56866	52738	56861	+	gi|568815551:1197321-1201446	4126	0	4126	4100	4126	0	NM:i:26	ms:i:8098	AS:i:8098	nn:i:0	tp:A:S	cm:i:722	s1:i:3930	de:f:0.0058	rl:i:96	cg:Z:225M3D3898M
+gi|157734152:29655295-29712160	56866	53528	56861	+	gi|568815564:1286641-1289973	3333	0	3333	3317	3333	0	NM:i:16	ms:i:6570	AS:i:6570	nn:i:0	tp:A:S	cm:i:585	s1:i:3212	de:f:0.0048	rl:i:96	cg:Z:3333M
+gi|157734152:29655295-29712160	56866	53376	56861	+	gi|568815561:1196951-1200436	3486	0	3486	3397	3487	0	NM:i:90	ms:i:6432	AS:i:6432	nn:i:0	tp:A:S	cm:i:442	s1:i:2777	de:f:0.0255	rl:i:96	cg:Z:235M1I1996M2D1253M
+gi|157734152:29655295-29712160	56866	53441	56861	+	gi|568815569:1240288-1243708	3421	0	3421	3331	3422	0	NM:i:91	ms:i:6296	AS:i:6296	nn:i:0	tp:A:S	cm:i:441	s1:i:2741	de:f:0.0263	rl:i:96	cg:Z:170M1I1996M2D1253M
+gi|157734152:29655295-29712160	56866	53436	56866	+	gi|342187237:5004-8419	3416	0	3416	3310	3437	0	NM:i:127	ms:i:6144	AS:i:6144	nn:i:0	tp:A:S	cm:i:427	s1:i:2612	de:f:0.0307	rl:i:96	cg:Z:1343M3I1M1I144M17I495M3D183M1D238M3D1005M
+gi|157734152:29655295-29712160	56866	53436	56866	+	gi|568815454:1200216-1203631	3416	0	3416	3310	3437	0	NM:i:127	ms:i:6144	AS:i:6144	nn:i:0	tp:A:S	cm:i:427	s1:i:2612	de:f:0.0307	rl:i:96	cg:Z:1343M3I1M1I144M17I495M3D183M1D238M3D1005M
+gi|157734152:29655295-29712160	56866	53436	56866	+	gi|568815529:1421891-1425306	3416	0	3416	3310	3437	0	NM:i:127	ms:i:6144	AS:i:6144	nn:i:0	tp:A:S	cm:i:427	s1:i:2612	de:f:0.0307	rl:i:96	cg:Z:1343M3I1M1I144M17I495M3D183M1D238M3D1005M
+gi|157734152:29655295-29712160	56866	53436	56866	+	gi|568815592:29942469-29945883	3415	0	3415	3305	3437	0	NM:i:132	ms:i:6112	AS:i:6112	nn:i:0	tp:A:S	cm:i:396	s1:i:2527	de:f:0.0322	rl:i:96	cg:Z:1212M1I130M3I1M1I144M17I495M3D183M1D238M3D1005M
+gi|157734152:29655295-29712160	56866	37319	42069	+	gi|568815567:1196244-1200852	4609	4	4609	4082	4789	0	NM:i:707	ms:i:5566	AS:i:5636	nn:i:0	tp:A:S	cm:i:119	s1:i:1112	de:f:0.1165	rl:i:96	cg:Z:48M1I54M1I85M2I21M1I6M90I167M1I74M1D1M2D247M4D48M19I109M4D346M1I52M1D125M1D271M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I40M1I62M1D25M1I217M3D9M3I48M1D307M4D20M1I148M1D169M3I276M1I3M1I2M1I2M4I40M3I10M20I173M1I189M1I41M3I8M3I79M1D17M1D3M1I9M1I1M1I72M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
+gi|157734152:29655295-29712160	56866	43615	46576	+	gi|157734152:29655295-29712160	56866	43615	46614	2915	3042	0	NM:i:127	ms:i:5546	AS:i:5600	nn:i:0	tp:A:S	cm:i:16	s1:i:120	de:f:0.0031	rl:i:96	cg:Z:1340M41D41I1438M32D17M6D6M2D100M2I17M
+gi|157734152:29655295-29712160	56866	43615	46614	+	gi|157734152:29655295-29712160	56866	43615	46576	2915	3042	0	NM:i:127	ms:i:5546	AS:i:5600	nn:i:0	tp:A:S	cm:i:16	s1:i:120	de:f:0.0031	rl:i:96	cg:Z:1340M41I41D1438M32I17M6I6M2I100M2D17M
+gi|157734152:29655295-29712160	56866	0	3406	+	gi|528476637:29857558-29915771	58214	54784	58214	3161	3445	0	NM:i:284	ms:i:5194	AS:i:5194	nn:i:0	tp:A:S	cm:i:208	s1:i:1674	de:f:0.0746	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D112M4D20M1I442M1D198M3I184M1I47M2D188M3I398M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D165M
+gi|157734152:29655295-29712160	56866	0	3401	+	gi|568815567:1196244-1200852	4609	1184	4609	3157	3441	0	NM:i:284	ms:i:5182	AS:i:5182	nn:i:0	tp:A:S	cm:i:194	s1:i:1592	de:f:0.0747	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D112M4D20M1I442M1D198M3I184M1I47M2D188M3I398M1D40M1I33M1D37M1D11M1D3M1I33M1D57M1I1M2D31M4D96M1I88M1D160M
+gi|157734152:29655295-29712160	56866	5	3401	+	gi|568815569:1240288-1243708	3421	0	3421	3152	3439	0	NM:i:287	ms:i:5158	AS:i:5158	nn:i:0	tp:A:S	cm:i:196	s1:i:1628	de:f:0.0751	rl:i:96	cg:Z:167M1D2M2I9M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D112M4D20M1I442M1D198M3I168M2D16M1I47M2D188M3I398M1D40M1I33M1D37M1D11M1D3M1I33M1D57M1I1M2D31M4D96M1I88M1D160M
+gi|157734152:29655295-29712160	56866	0	3406	+	gi|568815529:1421891-1425306	3416	0	3416	3143	3441	0	NM:i:298	ms:i:5126	AS:i:5126	nn:i:0	tp:A:S	cm:i:206	s1:i:1579	de:f:0.0764	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D132M1I129M17I296M1D433M2D589M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D165M
+gi|157734152:29655295-29712160	56866	0	3406	+	gi|342187237:5004-8419	3416	0	3416	3143	3441	0	NM:i:298	ms:i:5126	AS:i:5126	nn:i:0	tp:A:S	cm:i:206	s1:i:1579	de:f:0.0764	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D132M1I129M17I296M1D433M2D589M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D165M
+gi|157734152:29655295-29712160	56866	0	3406	+	gi|568815454:1200216-1203631	3416	0	3416	3143	3441	0	NM:i:298	ms:i:5126	AS:i:5126	nn:i:0	tp:A:S	cm:i:206	s1:i:1579	de:f:0.0764	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D132M1I129M17I296M1D433M2D589M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D165M
+gi|157734152:29655295-29712160	56866	37891	42069	+	gi|568815551:1197321-1201446	4126	0	4126	3654	4213	0	NM:i:559	ms:i:5120	AS:i:5120	nn:i:0	tp:A:S	cm:i:117	s1:i:1076	de:f:0.1174	rl:i:96	cg:Z:227M4D48M19I109M4D346M1I52M1D123M1I1M2D254M1D5M1I11M1D21M1I12M4D3M1I2M1I4M2I57M2I3M1I32M3I40M1I62M1D25M1I277M1D307M4D20M1I148M1D172M2I2M1I271M1I3M1I2M1I2M4I40M3I10M20I173M1I189M1I41M3I8M3I79M1D17M1D3M1I9M1I1M1I72M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
+gi|157734152:29655295-29712160	56866	0	3401	+	gi|568815561:1196951-1200436	3486	60	3486	3149	3444	0	NM:i:295	ms:i:5120	AS:i:5120	nn:i:0	tp:A:S	cm:i:189	s1:i:1603	de:f:0.0774	rl:i:96	cg:Z:172M1D2M2I9M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D112M4D20M1I442M1D198M3I168M2D16M1I47M2D188M3I398M1D40M1I33M1D37M1D11M1D3M1I33M1D57M1I1M2D31M4D96M1I88M1D160M
+gi|157734152:29655295-29712160	56866	0	3406	+	gi|568815592:29942469-29945883	3415	0	3415	3142	3440	0	NM:i:298	ms:i:5118	AS:i:5118	nn:i:0	tp:A:S	cm:i:207	s1:i:1610	de:f:0.0770	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D485M10D1M1D132M1I129M17I296M1D433M2D589M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D165M
+gi|157734152:29655295-29712160	56866	0	3401	+	gi|568815551:1197321-1201446	4126	701	4126	3142	3440	0	NM:i:298	ms:i:5100	AS:i:5100	nn:i:0	tp:A:S	cm:i:198	s1:i:1597	de:f:0.0789	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D112M4D20M1I442M1D198M3I184M1I47M2D188M3I398M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D160M
+gi|157734152:29655295-29712160	56866	53436	56866	+	gi|157734152:29655295-29712160	56866	0	3406	3142	3445	0	NM:i:303	ms:i:5080	AS:i:5080	nn:i:0	tp:A:S	cm:i:193	s1:i:1577	de:f:0.0802	rl:i:96	cg:Z:185M2I2M4I289M1I5M1D108M3D13M1I118M1I486M12I112M4I20M1D442M1I198M3D184M1D47M2I188M3D398M1I40M1D33M1I37M1I48M1I57M1D1M2I31M4I96M1D88M1I165M
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+gi|157734152:29655295-29712160	56866	38606	42207	+	gi|157734152:29655295-29712160	56866	3	3539	3166	3622	0	NM:i:456	ms:i:4550	AS:i:4550	nn:i:0	tp:A:S	cm:i:135	s1:i:1116	de:f:0.1102	rl:i:96	cg:Z:34M1I52M1D95M2I2M4I22M1D272M1D19M1I104M1I9M3I47M1I87M1I222M5D3M5I47M1D106M1D7M2I2M1D68M12I279M1D169M3I121M1I162M7I58M14I6M5I1M1I209M2I139M1I42M2I1M1I88M1D30M1I1M1I72M6D96M1I6M1D106M1I40M1D33M1I37M1I52M1I85M4I100M1I26M4I358M
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+gi|157734152:29655295-29712160	56866	38606	42207	+	gi|528476637:29857558-29915771	58214	3	3561	3162	3640	0	NM:i:478	ms:i:4470	AS:i:4470	nn:i:0	tp:A:S	cm:i:132	s1:i:1092	de:f:0.1130	rl:i:96	cg:Z:34M1I52M1D95M2I2M4I22M1D202M1D2M1I67M1D19M1I104M1I9M3I47M1I87M1I277M1D106M1D7M2I2M1D68M12I110M4D26M17D1M1D142M1D169M3I121M1I162M7I58M14I6M5I1M1I209M2I139M1I42M2I1M1I88M1D30M1I1M1I72M6D96M1I6M1D106M1I40M1D33M1I37M1I52M1I85M4I100M1I26M4I358M
+gi|157734152:29655295-29712160	56866	38543	42069	+	gi|568815561:1196951-1200436	3486	0	3486	3089	3554	0	NM:i:465	ms:i:4338	AS:i:4338	nn:i:0	tp:A:S	cm:i:95	s1:i:925	de:f:0.1177	rl:i:96	cg:Z:97M1I52M1D81M1I43M1D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I57M2I3M1I32M3I40M1I62M1D25M1I277M1D307M4D20M1I148M1D169M3I284M7I39M3I10M20I158M2D15M1I189M1I41M3I8M3I79M1D17M1D3M1I9M1I1M1I72M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
+gi|157734152:29655295-29712160	56866	38606	42074	+	gi|568815592:29942469-29945883	3415	3	3415	3036	3493	0	NM:i:457	ms:i:4300	AS:i:4300	nn:i:0	tp:A:S	cm:i:112	s1:i:1008	de:f:0.1138	rl:i:96	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I40M1I62M1D25M1I222M3D4M3I48M1D180M1I146M1I132M16I169M3I284M7I52M20I363M1I41M3I90M1D29M2I74M6D96M1I6M1D116M1I3M1D208M1D132M2I26M4I60M1D165M
+gi|157734152:29655295-29712160	56866	38606	42074	+	gi|342187237:5004-8419	3416	3	3416	3034	3491	0	NM:i:457	ms:i:4294	AS:i:4294	nn:i:0	tp:A:S	cm:i:108	s1:i:1013	de:f:0.1147	rl:i:96	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I38M1D3M2I60M1D25M1I277M1D327M1I132M16I169M3I284M7I52M20I363M1I41M3I90M1D29M2I74M6D96M1I6M1D116M1I3M1D208M1D132M2I26M4I60M1D165M
+gi|157734152:29655295-29712160	56866	38606	42074	+	gi|568815454:1200216-1203631	3416	3	3416	3034	3491	0	NM:i:457	ms:i:4294	AS:i:4294	nn:i:0	tp:A:S	cm:i:108	s1:i:1013	de:f:0.1147	rl:i:96	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I38M1D3M2I60M1D25M1I277M1D327M1I132M16I169M3I284M7I52M20I363M1I41M3I90M1D29M2I74M6D96M1I6M1D116M1I3M1D208M1D132M2I26M4I60M1D165M
+gi|157734152:29655295-29712160	56866	38606	42074	+	gi|568815529:1421891-1425306	3416	3	3416	3034	3491	0	NM:i:457	ms:i:4294	AS:i:4294	nn:i:0	tp:A:S	cm:i:108	s1:i:1013	de:f:0.1147	rl:i:96	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I38M1D3M2I60M1D25M1I277M1D327M1I132M16I169M3I284M7I52M20I363M1I41M3I90M1D29M2I74M6D96M1I6M1D116M1I3M1D208M1D132M2I26M4I60M1D165M
+gi|157734152:29655295-29712160	56866	38608	42069	+	gi|568815569:1240288-1243708	3421	0	3421	3034	3485	0	NM:i:451	ms:i:4284	AS:i:4284	nn:i:0	tp:A:S	cm:i:97	s1:i:955	de:f:0.1170	rl:i:96	cg:Z:32M1I52M1D81M1I43M1D255M1D4M1I11M1D21M1I82M2I3M1I32M3I40M1I62M1D25M1I277M1D307M4D20M1I148M1D169M3I284M7I39M3I10M20I158M2D15M1I189M1I41M3I8M3I79M1D17M1D3M1I9M1I1M1I72M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
+gi|157734152:29655295-29712160	56866	38697	42069	+	gi|568815564:1286641-1289973	3333	2	3333	2959	3398	0	NM:i:439	ms:i:4172	AS:i:4172	nn:i:0	tp:A:S	cm:i:98	s1:i:923	de:f:0.1165	rl:i:96	cg:Z:119M1I1M2D254M1D5M1I11M1D21M1I12M4D3M1I2M1I4M2I57M2I3M1I32M3I40M1I62M1D25M1I277M1D307M4D20M1I148M1D172M2I2M1I271M1I3M1I2M1I2M4I40M3I10M20I173M1I189M1I41M3I8M3I79M1D17M1D3M1I9M1I1M1I72M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
+gi|157734152:29655295-29712160	56866	3533	4632	+	gi|528476637:29857558-29915771	58214	43020	44118	979	1103	0	NM:i:124	ms:i:1460	AS:i:1460	nn:i:0	tp:A:S	cm:i:27	s1:i:217	de:f:0.1092	rl:i:96	cg:Z:156M1I416M3D62M3I27M1I156M1D277M
+gi|157734152:29655295-29712160	56866	43143	44241	+	gi|528476637:29857558-29915771	58214	3555	4654	977	1103	0	NM:i:126	ms:i:1448	AS:i:1448	nn:i:0	tp:A:S	cm:i:31	s1:i:245	de:f:0.1110	rl:i:96	cg:Z:156M1D416M3I62M3D27M1D156M1I277M
+gi|157734152:29655295-29712160	56866	43143	44241	+	gi|157734152:29655295-29712160	56866	3533	4632	975	1103	0	NM:i:128	ms:i:1436	AS:i:1436	nn:i:0	tp:A:S	cm:i:28	s1:i:232	de:f:0.1128	rl:i:96	cg:Z:156M1D416M3I62M3D27M1D156M1I277M
+gi|157734152:29655295-29712160	56866	3533	4632	+	gi|157734152:29655295-29712160	56866	43143	44241	975	1103	0	NM:i:128	ms:i:1436	AS:i:1436	nn:i:0	tp:A:S	cm:i:28	s1:i:232	de:f:0.1128	rl:i:96	cg:Z:156M1I416M3D62M3I27M1I156M1D277M
+gi|157734152:29655295-29712160	56866	47648	48471	+	gi|528476637:29857558-29915771	58214	31581	32408	734	834	0	NM:i:100	ms:i:1064	AS:i:1064	nn:i:0	tp:A:S	cm:i:19	s1:i:213	de:f:0.1114	rl:i:96	cg:Z:9M2D100M1I166M1I2M1D93M1D142M1D29M6D113M2I3M2I4M1I155M
+gi|157734152:29655295-29712160	56866	31699	32530	+	gi|528476637:29857558-29915771	58214	48998	49823	733	838	0	NM:i:105	ms:i:1046	AS:i:1046	nn:i:0	tp:A:S	cm:i:17	s1:i:193	de:f:0.1147	rl:i:96	cg:Z:9M2I100M1D166M1D2M1I93M1I142M1I31M8I113M1D3M3D4M1D155M
+gi|157734152:29655295-29712160	56866	47648	48471	+	gi|157734152:29655295-29712160	56866	31699	32530	732	838	0	NM:i:106	ms:i:1044	AS:i:1044	nn:i:0	tp:A:S	cm:i:19	s1:i:213	de:f:0.1138	rl:i:96	cg:Z:9M2D100M1I166M1I2M1D93M1D142M1D29M10D113M2I3M2I4M1I155M
+gi|157734152:29655295-29712160	56866	31699	32530	+	gi|157734152:29655295-29712160	56866	47648	48471	732	838	0	NM:i:106	ms:i:1044	AS:i:1044	nn:i:0	tp:A:S	cm:i:19	s1:i:213	de:f:0.1138	rl:i:96	cg:Z:9M2I100M1D166M1D2M1I93M1I142M1I29M10I113M2D3M2D4M1D155M
+gi|157734152:29655295-29712160	56866	8694	10348	+	gi|528476637:29857558-29915771	58214	1488	3170	1320	1753	0	NM:i:433	ms:i:1012	AS:i:1018	nn:i:0	tp:A:S	cm:i:12	s1:i:120	de:f:0.1961	rl:i:96	cg:Z:11M2D45M1D260M1I153M1I3M1D7M1D12M3I41M14I4M6I78M3D6M5D3M7D55M5D2M2D21M1I26M2I2M6I11M1D6M2D5M2I11M4D8M1I4M1I8M4D59M3D12M1I6M1I17M2D8M1I5M2I38M2I47M2D15M26D22M1D7M1I75M2I1M5I22M1D5M1D6M1D3M3I20M1D115M1I44M5D3M1I1M1I17M1I41M1I2M2D7M1D3M1I36M2I6M7D3M3D63M1I3M5I37M3D2M2D9M1I41M
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+gi|157734152:29655295-29712160	56866	8694	10345	+	gi|528476637:29857558-29915771	58214	39969	41686	1323	1759	0	NM:i:436	ms:i:974	AS:i:981	nn:i:0	tp:A:S	cm:i:11	s1:i:113	de:f:0.2059	rl:i:96	cg:Z:11M2D12M1I32M1D131M1D1M5D6M1D202M2I69M4D9M1D2M3D15M3I162M15D32M1D5M6D31M1I26M2I1M4I14M1D6M2D5M2I11M4D8M1I4M1I8M4D55M3D23M1I17M2D54M2I4M1I3M1D43M1D23M27D1M1I51M5I1M1I33M2I1M2I6M3I55M2D6M1I39M1I3M1D24M1D5M1I74M1D6M1I2M1D1M1D61M2D49M1D7M5D3M3D63M1I3M1I41M3D2M2D9M1I38M
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+gi|157734152:29655295-29712160	56866	8715	10348	+	gi|568815529:1421891-1425306	3416	1488	3158	1295	1726	0	NM:i:431	ms:i:964	AS:i:970	nn:i:0	tp:A:S	cm:i:10	s1:i:118	de:f:0.2041	rl:i:96	cg:Z:35M1D414M1I3M1D7M1D12M3I44M20I84M3D2M2D2M10D42M1I3M1D9M3D2M4D21M1I30M6I7M1D3M2D11M1I1M1I11M4D8M1I4M1I8M4D60M3D11M1I6M1I17M2D8M1I5M2I38M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D71M2D47M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
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+gi|157734152:29655295-29712160	56866	8708	10348	+	gi|568815561:1196951-1200436	3486	1561	3233	1285	1737	0	NM:i:452	ms:i:874	AS:i:880	nn:i:0	tp:A:S	cm:i:10	s1:i:116	de:f:0.2107	rl:i:96	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I78M14D4M2D2M1I48M2D10M3D2M3D21M1I30M6I11M1D6M2D7M4I4M1I3M7D7M1I4M1I8M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	8708	10348	+	gi|568815567:1196244-1200852	4609	2686	4356	1284	1732	0	NM:i:448	ms:i:868	AS:i:874	nn:i:0	tp:A:S	cm:i:9	s1:i:100	de:f:0.2132	rl:i:96	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I79M3D3M4D2M3D1M5D58M3D2M3D21M1I30M6I11M1D6M2D7M4I4M1I3M1D1M1D11M1D2M2D7M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	8708	10348	+	gi|568815569:1240288-1243708	3421	1496	3168	1284	1736	0	NM:i:452	ms:i:868	AS:i:874	nn:i:0	tp:A:S	cm:i:10	s1:i:116	de:f:0.2118	rl:i:96	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I79M3D3M4D3M8D48M2D10M3D2M3D21M1I30M6I11M1D6M2D7M4I4M1I3M7D7M1I4M1I8M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
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+gi|157734152:29655295-29712160	56866	46634	47073	+	gi|528476637:29857558-29915771	58214	45882	46332	428	450	0	NM:i:22	ms:i:782	AS:i:782	nn:i:0	tp:A:S	cm:i:56	s1:i:327	de:f:0.0295	rl:i:96	cg:Z:393M10D38M1D8M
+gi|157734152:29655295-29712160	56866	4717	5886	+	gi|528476637:29857558-29915771	58214	27052	28249	926	1207	0	NM:i:281	ms:i:732	AS:i:732	nn:i:0	tp:A:S	cm:i:8	s1:i:95	de:f:0.2166	rl:i:96	cg:Z:100M1I5M1D139M7D13M1D133M7D80M1I58M1D6M1I70M1D31M2I5M1D15M1D3M1D17M1I2M1D168M9D2M1D48M2D113M2I73M2I4M2D15M1D23M1D36M
+gi|157734152:29655295-29712160	56866	27171	28370	+	gi|157734152:29655295-29712160	56866	4717	5886	925	1208	0	NM:i:283	ms:i:722	AS:i:722	nn:i:0	tp:A:S	cm:i:8	s1:i:95	de:f:0.2181	rl:i:96	cg:Z:100M1D5M1I139M9I13M1I133M7I80M1D58M1I6M1D70M1I31M2D5M1I15M1I3M1I16M1I3M1D168M9I2M1I48M2I113M2D73M1I5M1D15M1I23M1I36M
+gi|157734152:29655295-29712160	56866	4717	5886	+	gi|157734152:29655295-29712160	56866	27171	28370	925	1209	0	NM:i:284	ms:i:722	AS:i:722	nn:i:0	tp:A:S	cm:i:8	s1:i:95	de:f:0.2174	rl:i:96	cg:Z:100M1I5M1D139M9D13M1D133M7D80M1I58M1D6M1I70M1D31M2I5M1D15M1D3M1D17M1I2M1D168M9D2M1D48M2D113M2I73M2I4M2D15M1D23M1D36M
+gi|157734152:29655295-29712160	56866	27171	28370	+	gi|528476637:29857558-29915771	58214	4739	5908	924	1208	0	NM:i:284	ms:i:716	AS:i:716	nn:i:0	tp:A:S	cm:i:8	s1:i:95	de:f:0.2189	rl:i:96	cg:Z:100M1D5M1I139M9I13M1I133M7I80M1D58M1I6M1D70M1I31M2D5M1I15M1I3M1I16M1I3M1D168M9I2M1I48M2I113M2D73M1I5M1D15M1I23M1I36M
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+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815569:1240288-1243708	3421	885	1301	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:32	s1:i:246	de:f:0.0481	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815567:1196244-1200852	4609	2075	2491	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:32	s1:i:257	de:f:0.0481	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815592:29942469-29945883	3415	891	1306	396	416	0	NM:i:20	ms:i:710	AS:i:710	nn:i:0	tp:A:S	cm:i:35	s1:i:244	de:f:0.0481	rl:i:96	cg:Z:321M1I94M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815561:1196951-1200436	3486	950	1366	395	416	0	NM:i:21	ms:i:706	AS:i:706	nn:i:0	tp:A:S	cm:i:29	s1:i:236	de:f:0.0505	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|528476637:29857558-29915771	58214	55675	56091	393	416	0	NM:i:23	ms:i:694	AS:i:694	nn:i:0	tp:A:S	cm:i:30	s1:i:216	de:f:0.0553	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815551:1197321-1201446	4126	1592	2008	393	416	0	NM:i:23	ms:i:694	AS:i:694	nn:i:0	tp:A:S	cm:i:30	s1:i:216	de:f:0.0553	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815564:1286641-1289973	3333	799	1215	393	416	0	NM:i:23	ms:i:694	AS:i:694	nn:i:0	tp:A:S	cm:i:30	s1:i:216	de:f:0.0553	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|157734152:29655295-29712160	56866	54327	54743	393	416	0	NM:i:23	ms:i:694	AS:i:694	nn:i:0	tp:A:S	cm:i:30	s1:i:216	de:f:0.0553	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	54327	54743	+	gi|157734152:29655295-29712160	56866	44580	44996	393	416	0	NM:i:23	ms:i:694	AS:i:694	nn:i:0	tp:A:S	cm:i:30	s1:i:216	de:f:0.0553	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815529:1421891-1425306	3416	891	1307	390	416	0	NM:i:26	ms:i:676	AS:i:676	nn:i:0	tp:A:S	cm:i:29	s1:i:188	de:f:0.0625	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815454:1200216-1203631	3416	891	1307	390	416	0	NM:i:26	ms:i:676	AS:i:676	nn:i:0	tp:A:S	cm:i:29	s1:i:188	de:f:0.0625	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|342187237:5004-8419	3416	891	1307	390	416	0	NM:i:26	ms:i:676	AS:i:676	nn:i:0	tp:A:S	cm:i:29	s1:i:188	de:f:0.0625	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	886	1289	+	gi|528476637:29857558-29915771	58214	44457	44872	370	415	0	NM:i:45	ms:i:580	AS:i:580	nn:i:0	tp:A:S	cm:i:16	s1:i:142	de:f:0.0842	rl:i:96	cg:Z:324M12D79M
+gi|157734152:29655295-29712160	56866	46651	47139	+	gi|528476637:29857558-29915771	58214	31111	31578	418	497	0	NM:i:79	ms:i:570	AS:i:573	nn:i:0	tp:A:S	cm:i:18	s1:i:159	de:f:0.1011	rl:i:96	cg:Z:196M7D1M2D3M1I15M2I1M1I138M3I30M23I74M
+gi|157734152:29655295-29712160	56866	44580	44995	+	gi|157734152:29655295-29712160	56866	886	1289	368	415	0	NM:i:47	ms:i:568	AS:i:568	nn:i:0	tp:A:S	cm:i:11	s1:i:116	de:f:0.0891	rl:i:96	cg:Z:324M12I79M
+gi|157734152:29655295-29712160	56866	886	1289	+	gi|157734152:29655295-29712160	56866	44580	44995	368	415	0	NM:i:47	ms:i:568	AS:i:568	nn:i:0	tp:A:S	cm:i:11	s1:i:116	de:f:0.0891	rl:i:96	cg:Z:324M12D79M
+gi|157734152:29655295-29712160	56866	31228	31696	+	gi|157734152:29655295-29712160	56866	46651	47139	418	497	0	NM:i:79	ms:i:560	AS:i:560	nn:i:0	tp:A:S	cm:i:16	s1:i:161	de:f:0.1068	rl:i:96	cg:Z:47M1D148M7I1M2I3M1D15M2D1M1D138M3D25M8D7M13D74M
+gi|157734152:29655295-29712160	56866	46651	47139	+	gi|157734152:29655295-29712160	56866	31228	31696	418	497	0	NM:i:79	ms:i:560	AS:i:560	nn:i:0	tp:A:S	cm:i:16	s1:i:161	de:f:0.1068	rl:i:96	cg:Z:47M1I148M7D1M2D3M1I15M2I1M1I138M3I25M8I7M13I74M
+gi|157734152:29655295-29712160	56866	44580	44995	+	gi|528476637:29857558-29915771	58214	886	1289	366	415	0	NM:i:49	ms:i:556	AS:i:556	nn:i:0	tp:A:S	cm:i:12	s1:i:107	de:f:0.0941	rl:i:96	cg:Z:324M12I79M
+gi|157734152:29655295-29712160	56866	44580	44995	+	gi|528476637:29857558-29915771	58214	39378	39792	363	418	0	NM:i:55	ms:i:508	AS:i:508	nn:i:0	tp:A:S	cm:i:7	s1:i:93	de:f:0.1232	rl:i:96	cg:Z:85M3I4M3D48M1I274M
+gi|157734152:29655295-29712160	56866	44580	44995	+	gi|157734152:29655295-29712160	56866	39500	39914	362	418	0	NM:i:56	ms:i:502	AS:i:502	nn:i:0	tp:A:S	cm:i:6	s1:i:78	de:f:0.1256	rl:i:96	cg:Z:85M3I4M3D48M1I274M
+gi|157734152:29655295-29712160	56866	39500	39914	+	gi|157734152:29655295-29712160	56866	44580	44995	362	418	0	NM:i:56	ms:i:502	AS:i:502	nn:i:0	tp:A:S	cm:i:6	s1:i:78	de:f:0.1256	rl:i:96	cg:Z:85M3D4M3I48M1D274M
+gi|157734152:29655295-29712160	56866	39500	39914	+	gi|528476637:29857558-29915771	58214	44457	44872	360	418	0	NM:i:58	ms:i:490	AS:i:490	nn:i:0	tp:A:S	cm:i:6	s1:i:78	de:f:0.1304	rl:i:96	cg:Z:85M3D4M3I48M1D274M
+gi|157734152:29655295-29712160	56866	7021	7639	+	gi|528476637:29857558-29915771	58214	49208	49824	489	643	0	NM:i:154	ms:i:370	AS:i:370	nn:i:0	tp:A:S	cm:i:5	s1:i:47	de:f:0.2049	rl:i:96	cg:Z:26M4D20M1I64M2D7M1I1M1I39M9I5M2I5M4I75M2D8M1I4M2D25M1D11M1I5M1I2M2D4M1I4M1I7M5D7M1D133M1D49M1D29M4D5M3I3M1I53M
+gi|157734152:29655295-29712160	56866	7021	7639	+	gi|157734152:29655295-29712160	56866	47858	48472	488	641	0	NM:i:153	ms:i:364	AS:i:364	nn:i:0	tp:A:S	cm:i:5	s1:i:48	de:f:0.2078	rl:i:96	cg:Z:26M4D20M1I64M2D7M1I1M1I39M9I5M2I5M4I75M2D9M1I3M2D25M1D11M1I5M1I3M1D8M1I7M3D7M1D90M1I5M1D37M1D49M1D30M4D4M3I3M1I53M
+gi|157734152:29655295-29712160	56866	47858	48472	+	gi|528476637:29857558-29915771	58214	7043	7661	488	641	0	NM:i:153	ms:i:364	AS:i:364	nn:i:0	tp:A:S	cm:i:5	s1:i:48	de:f:0.2078	rl:i:96	cg:Z:26M4I20M1D64M2I7M1D1M1D39M9D5M2D5M4D75M2I9M1D3M2I25M1I11M1D5M1D3M1I8M1D7M3I7M1I90M1D5M1I37M1I49M1I30M4I4M3D3M1D53M
+gi|157734152:29655295-29712160	56866	47858	48472	+	gi|157734152:29655295-29712160	56866	7021	7639	488	641	0	NM:i:153	ms:i:364	AS:i:364	nn:i:0	tp:A:S	cm:i:5	s1:i:48	de:f:0.2078	rl:i:96	cg:Z:26M4I20M1D64M2I7M1D1M1D39M9D5M2D5M4D75M2I9M1D3M2I25M1I11M1D5M1D3M1I8M1D7M3I7M1I90M1D5M1I37M1I49M1I30M4I4M3D3M1D53M
+gi|157734152:29655295-29712160	56866	28499	28764	-	gi|528476637:29857558-29915771	58214	29092	29357	235	265	41	NM:i:30	ms:i:350	AS:i:350	nn:i:0	tp:A:P	cm:i:4	s1:i:46	s2:i:0	de:f:0.1132	zd:i:2	rl:i:96	cg:Z:265M
+gi|157734152:29655295-29712160	56866	14465	14764	-	gi|528476637:29857558-29915771	58214	45149	45463	266	316	0	NM:i:50	ms:i:350	AS:i:350	nn:i:0	tp:A:S	cm:i:3	s1:i:40	de:f:0.1192	rl:i:96	cg:Z:5M1I26M2D116M14D2M1D114M1I34M
+gi|157734152:29655295-29712160	56866	29213	29478	-	gi|528476637:29857558-29915771	58214	28378	28643	234	265	0	NM:i:31	ms:i:344	AS:i:344	nn:i:0	tp:A:S	cm:i:4	s1:i:46	de:f:0.1170	zd:i:1	rl:i:96	cg:Z:265M
+gi|157734152:29655295-29712160	56866	28499	28764	-	gi|157734152:29655295-29712160	56866	29213	29478	233	265	40	NM:i:32	ms:i:338	AS:i:338	nn:i:0	tp:A:P	cm:i:4	s1:i:46	s2:i:0	de:f:0.1208	zd:i:2	rl:i:96	cg:Z:265M
+gi|157734152:29655295-29712160	56866	29213	29478	-	gi|157734152:29655295-29712160	56866	28499	28764	233	265	0	NM:i:32	ms:i:338	AS:i:338	nn:i:0	tp:A:S	cm:i:4	s1:i:46	de:f:0.1208	zd:i:1	rl:i:96	cg:Z:265M
+gi|157734152:29655295-29712160	56866	17792	17978	+	gi|157734152:29655295-29712160	56866	17883	18067	176	186	0	NM:i:10	ms:i:312	AS:i:312	nn:i:0	tp:A:S	cm:i:11	s1:i:86	de:f:0.0486	rl:i:96	cg:Z:6M2I178M
+gi|157734152:29655295-29712160	56866	17883	18067	+	gi|157734152:29655295-29712160	56866	17792	17978	176	186	0	NM:i:10	ms:i:312	AS:i:312	nn:i:0	tp:A:S	cm:i:11	s1:i:86	de:f:0.0486	rl:i:96	cg:Z:6M2D178M
+gi|157734152:29655295-29712160	56866	6285	6982	-	gi|528476637:29857558-29915771	58214	6307	7004	528	727	0	NM:i:199	ms:i:272	AS:i:272	nn:i:0	tp:A:S	cm:i:4	s1:i:44	de:f:0.2392	rl:i:96	cg:Z:11M1D155M1I43M2D64M2I1M1I6M3I5M2I1M2I6M1D9M2I3M3D6M8I5M1I8M1I5M1I9M1D6M1D5M1D8M8D5M3I4M2D3M2D13M2D7M5D70M2I43M1D154M1I12M
+gi|157734152:29655295-29712160	56866	6285	6982	-	gi|157734152:29655295-29712160	56866	6285	6982	528	723	0	NM:i:195	ms:i:272	AS:i:272	nn:i:0	tp:A:S	cm:i:4	s1:i:44	de:f:0.2436	rl:i:96	cg:Z:11M1D155M1I43M2D64M2I1M1I6M3I5M2I1M2I6M1D9M2I3M3D6M1I7M2D2M2I3M2D26M2I3M2D2M2I7M1D5M3I4M2D3M2D13M2D7M5D70M2I43M1D154M1I12M
+gi|157734152:29655295-29712160	56866	8039	8361	+	gi|157734152:29655295-29712160	56866	8039	8285	228	323	0	NM:i:95	ms:i:262	AS:i:281	nn:i:0	tp:A:S	cm:i:8	s1:i:53	de:f:0.0769	rl:i:96	cg:Z:131M77I89M1D25M
+gi|157734152:29655295-29712160	56866	8039	8285	+	gi|157734152:29655295-29712160	56866	8039	8361	228	323	0	NM:i:95	ms:i:262	AS:i:281	nn:i:0	tp:A:S	cm:i:8	s1:i:53	de:f:0.0769	rl:i:96	cg:Z:131M77D89M1I25M
+gi|157734152:29655295-29712160	56866	46497	46603	-	gi|157734152:29655295-29712160	56866	46497	46603	92	106	0	NM:i:14	ms:i:128	AS:i:128	nn:i:0	tp:A:S	cm:i:4	s1:i:54	de:f:0.1321	rl:i:96	cg:Z:106M
+gi|157734152:29655295-29712160	56866	8206	8392	+	gi|157734152:29655295-29712160	56866	8003	8199	154	201	0	NM:i:47	ms:i:116	AS:i:116	nn:i:0	tp:A:S	cm:i:5	s1:i:41	de:f:0.1979	rl:i:96	cg:Z:14M3D43M2I1M1I28M1D2M2D3M1D14M1D11M2D3M2D5M2I5M3D52M
+gi|157734152:29655295-29712160	56866	8003	8199	+	gi|157734152:29655295-29712160	56866	8206	8392	154	201	0	NM:i:47	ms:i:116	AS:i:116	nn:i:0	tp:A:S	cm:i:5	s1:i:41	de:f:0.1979	rl:i:96	cg:Z:14M3I43M2D1M1D28M1I2M2I3M1I14M1I11M2I3M2I5M2D5M3I52M
+gi|157734152:29655295-29712160	56866	46537	46603	-	gi|157734152:29655295-29712160	56866	46537	46603	60	66	0	NM:i:6	ms:i:96	AS:i:96	nn:i:0	tp:A:S	cm:i:4	s1:i:48	de:f:0.0909	rl:i:96	cg:Z:66M
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index cbb82492cfdc..4e70191fe06b 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -730,3 +730,37 @@ def sniff_prefix(self, file_prefix):
         False
         """
         return file_prefix.startswith("IQ-TREE")
+
+
+@build_sniff_from_prefix
+class Paf(Text):
+    """
+    PAF: a Pairwise mApping Format
+
+    https://github.com/lh3/miniasm/blob/master/PAF.md
+    """
+    file_ext = "paf"
+
+    def sniff_prefix(self, file_prefix):
+        """
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('A-3105.paf')
+        >>> Paf().sniff(fname)
+        True
+        """
+        found_valid_lines = False
+        for line in iter_headers(file_prefix, "\t"):
+            if len(line) < 12:
+                return False
+            for i in (1, 2, 3, 6, 7, 8, 9, 10, 11):
+                int(line[i])
+            if line[4] not in ('+', '-'):
+                return False
+            if not (0 <= int(line[11]) <= 255):
+                return False
+            # Check that the optional columns after the 12th contain SAM-like typed key-value pairs
+            for i in range(12, len(line)):
+                if len(line[i].split(':')) != 3:
+                    return False
+            found_valid_lines = True
+        return found_valid_lines

From 6954e3467850278686cbc72b619ca97fb550edb6 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 8 Apr 2020 03:06:17 +0100
Subject: [PATCH 731/853] Add GFA 1.0 datatype

---
 .../config/sample/datatypes_conf.xml.sample   |   1 +
 lib/galaxy/datatypes/test/big.gfa1            | 137 ++++++++++++++++++
 lib/galaxy/datatypes/text.py                  |  47 ++++++
 3 files changed, 185 insertions(+)
 create mode 100644 lib/galaxy/datatypes/test/big.gfa1

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index e8a0f3d4c2b3..00e6fd165ea5 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -18,6 +18,7 @@
     <datatype extension="anvio_variability" type="galaxy.datatypes.tabular:TSV" display_in_upload="false" subclass="true" />
     <datatype extension="arff" type="galaxy.datatypes.text:Arff" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="paf" type="galaxy.datatypes.text:Paf" mimetype="text/plain" display_in_upload="true"/>
+    <datatype extension="gfa1" type="galaxy.datatypes.text:Gfa1" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format.  Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines.  Blocks are separated from one another by blank lines.  The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
diff --git a/lib/galaxy/datatypes/test/big.gfa1 b/lib/galaxy/datatypes/test/big.gfa1
new file mode 100644
index 000000000000..b2d1b27910b9
--- /dev/null
+++ b/lib/galaxy/datatypes/test/big.gfa1
@@ -0,0 +1,137 @@
+# Downloaded from https://github.com/sjackman/gfalint/blob/master/examples/big1.gfa
+H	VN:Z:1.0
+S	3	*	LN:i:5376	KC:i:485841
+S	5	*	LN:i:124	KC:i:6306
+S	7	*	LN:i:3602	KC:i:327981
+S	8	*	LN:i:52	KC:i:2218
+S	9	*	LN:i:48	KC:i:154
+S	10	*	LN:i:144	KC:i:4604
+S	11	*	LN:i:6491	KC:i:611916
+S	13	*	LN:i:10648	KC:i:1023627
+S	14	*	LN:i:48	KC:i:16
+S	15	*	LN:i:5930	KC:i:599587
+S	17	*	LN:i:9404	KC:i:991226
+S	18	*	LN:i:2206	KC:i:240150
+S	19	*	LN:i:893	KC:i:82277
+S	20	*	LN:i:12201	KC:i:1351219
+S	21	*	LN:i:49	KC:i:300
+S	22	*	LN:i:11669	KC:i:1131776
+S	23	*	LN:i:7665	KC:i:766424
+S	27	*	LN:i:48	KC:i:35
+S	28	*	LN:i:1597	KC:i:142681
+S	30	*	LN:i:48	KC:i:7874
+S	31	*	LN:i:94	KC:i:805
+S	32	*	LN:i:3065	KC:i:275287
+S	33	*	LN:i:70	KC:i:5123
+S	34	*	LN:i:49	KC:i:23
+S	36	*	LN:i:12335	KC:i:1315304
+S	37	*	LN:i:130	KC:i:5258
+S	38	*	LN:i:4516	KC:i:440430
+S	39	*	LN:i:59	KC:i:4094
+S	41	*	LN:i:215	KC:i:11423
+S	42	*	LN:i:146	KC:i:3161
+S	43	*	LN:i:50	KC:i:563
+S	44	*	LN:i:3913	KC:i:434585
+S	46	*	LN:i:2710	KC:i:268203
+S	47	*	LN:i:49	KC:i:200
+S	49	*	LN:i:61	KC:i:3442
+S	50	*	LN:i:5010	KC:i:532820
+S	51	*	LN:i:9644	KC:i:950549
+S	52	*	LN:i:417	KC:i:16750
+S	54	*	LN:i:50	KC:i:600
+S	55	*	LN:i:69	KC:i:11532
+S	56	*	LN:i:1550	KC:i:141042
+S	57	*	LN:i:346	KC:i:12512
+S	58	*	LN:i:3825	KC:i:349334
+S	59	*	LN:i:11508	KC:i:1237494
+S	60	*	LN:i:720	KC:i:72448
+S	61	*	LN:i:1086	KC:i:83405
+S	62	*	LN:i:4818	KC:i:464490
+S	63	*	LN:i:8207	KC:i:822244
+S	65	*	LN:i:67	KC:i:2088
+S	66	*	LN:i:4375	KC:i:421128
+S	67	*	LN:i:5063	KC:i:530425
+S	68	*	LN:i:78	KC:i:10057
+S	69	*	LN:i:10204	KC:i:1039066
+S	71	*	LN:i:789	KC:i:65350
+S	72	*	LN:i:95	KC:i:6170
+S	73	*	LN:i:48	KC:i:14
+S	76	*	LN:i:54	KC:i:1373
+S	77	*	LN:i:4167	KC:i:460259
+S	78	*	LN:i:49	KC:i:925
+S	79	*	LN:i:95	KC:i:5402
+S	83	*	LN:i:15015	KC:i:1487985
+S	84	*	LN:i:9811	KC:i:1021233
+S	85	*	LN:i:3483	KC:i:365113
+S	86	*	LN:i:7953	KC:i:722908
+L	3	+	65	-	47M
+L	3	-	76	-	47M
+L	5	+	47	-	47M
+L	5	-	22	-	47M
+L	5	-	32	+	47M
+L	7	+	49	-	47M
+L	8	+	33	-	47M
+L	8	+	55	-	36M
+L	8	-	78	+	47M
+L	8	-	79	+	47M
+L	9	+	37	-	47M
+L	9	+	47	+	46M
+L	9	-	67	-	47M
+L	9	-	69	-	47M
+L	10	+	47	+	47M
+L	11	-	43	-	47M
+L	14	+	30	+	47M
+L	14	+	31	+	47M
+L	14	+	73	-	47M
+L	17	+	21	-	47M
+L	18	+	78	-	47M
+L	19	+	76	+	47M
+L	19	-	76	-	47M
+L	20	-	76	+	47M
+L	21	+	51	-	47M
+L	21	-	32	-	47M
+L	21	-	66	+	47M
+L	22	+	63	+	47M
+L	23	+	68	-	47M
+L	27	+	30	+	47M
+L	27	+	31	+	47M
+L	27	+	73	-	47M
+L	27	-	31	-	47M
+L	27	-	83	+	47M
+L	28	+	43	+	47M
+L	30	+	30	+	47M
+L	30	+	31	+	47M
+L	30	+	73	-	47M
+L	30	-	34	-	47M
+L	31	-	34	-	47M
+L	32	-	63	+	47M
+L	33	+	72	-	47M
+L	33	-	44	-	47M
+L	33	-	55	-	16M
+L	34	+	73	-	47M
+L	36	-	63	-	47M
+L	36	-	85	+	47M
+L	37	-	49	+	47M
+L	39	+	56	+	47M
+L	39	+	67	+	47M
+L	39	-	71	-	47M
+L	39	-	65	+	14M
+L	41	+	43	+	47M
+L	42	+	65	-	47M
+L	43	+	60	+	47M
+L	47	+	59	+	47M
+L	49	+	71	+	47M
+L	49	-	84	+	47M
+L	52	-	65	+	47M
+L	54	+	77	-	47M
+L	54	+	54	+	46M
+L	54	-	58	-	47M
+L	55	+	72	-	36M
+L	55	-	79	-	47M
+L	55	-	78	-	44M
+L	57	+	63	-	47M
+L	57	+	85	+	47M
+L	61	+	68	+	47M
+L	68	+	68	+	26M
+L	72	-	78	+	47M
+L	72	-	79	+	47M
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index 4e70191fe06b..820363665aec 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -764,3 +764,50 @@ def sniff_prefix(self, file_prefix):
                     return False
             found_valid_lines = True
         return found_valid_lines
+
+
+@build_sniff_from_prefix
+class Gfa1(Text):
+    """
+    Graphical Fragment Assembly (GFA) 1.0
+
+    http://gfa-spec.github.io/GFA-spec/GFA1.html
+    """
+    file_ext = "gfa1"
+
+    def sniff_prefix(self, file_prefix):
+        """
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('big.gfa1')
+        >>> Gfa1().sniff(fname)
+        True
+        """
+        found_valid_lines = False
+        for line in iter_headers(file_prefix, "\t"):
+            if line[0].startswith('#'):
+                continue
+            if line[0] == 'H':
+                return len(line) == 2 and line[1] == 'VN:Z:1.0'
+            elif line[0] == 'S':
+                if len(line) < 3:
+                    return False
+            elif line[0] == 'L':
+                if len(line) < 6:
+                    return False
+                for i in (2, 4):
+                    if line[i] not in ('+', '-'):
+                        return False
+            elif line[0] == 'C':
+                if len(line) < 7:
+                    return False
+                for i in (2, 4):
+                    if line[i] not in ('+', '-'):
+                        return False
+                int(line[5])
+            elif line[0] == 'P':
+                if len(line) < 4:
+                    return False
+            else:
+                return False
+            found_valid_lines = True
+        return found_valid_lines

From 8aa5520817cb3622e2e414a0a26ba8237d062592 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 8 Apr 2020 08:46:56 +0200
Subject: [PATCH 732/853] add odgi as well

needed for https://github.com/galaxyproject/tools-iuc/pull/2956
---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 00e6fd165ea5..2fe8cf2afddc 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -378,6 +378,7 @@
       <display file="igb/wig.xml"/>
     </datatype>
     <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="true"/>
+    <datatype extension="odgi" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs self index used by odgi."/>
     <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">

From f0868b937d22f81c72ce5548774970aacf9da820 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Wed, 8 Apr 2020 10:00:36 -0400
Subject: [PATCH 733/853] More code change per code review comments

---
 continue                            | 0
 lib/galaxy/dependencies/__init__.py | 3 +++
 2 files changed, 3 insertions(+)
 delete mode 100644 continue

diff --git a/continue b/continue
deleted file mode 100644
index e69de29bb2d1..000000000000
diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index 328e553cb73a..dc8bbab484ad 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -175,6 +175,9 @@ def check_azure_storage(self):
     def check_kamaki(self):
         return 'pithos' in self.object_stores
 
+    def check_python_irodsclient(self):
+        return 'irods' in self.object_stores
+
     def check_watchdog(self):
         install_set = {'auto', 'True', 'true', 'polling'}
         return (self.config['watch_tools'] in install_set or

From aafb8b07bb6e51214eee8d5114d3ae27d2b9e98c Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Wed, 8 Apr 2020 18:15:58 +0200
Subject: [PATCH 734/853] implement testing for Vue version of destination
 params

---
 .../JobDestinationParams.test.js              | 67 +++++++++++++++++++
 .../JobDestinationParams.vue                  | 10 +--
 .../testData/jobDestinationResponse.json      | 12 ++++
 3 files changed, 84 insertions(+), 5 deletions(-)
 create mode 100644 client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.test.js
 create mode 100644 client/galaxy/scripts/components/JobDestinationParams/testData/jobDestinationResponse.json

diff --git a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.test.js b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.test.js
new file mode 100644
index 000000000000..1a0eb75321a7
--- /dev/null
+++ b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.test.js
@@ -0,0 +1,67 @@
+import Vuex from "vuex";
+import axios from "axios";
+import MockAdapter from "axios-mock-adapter";
+import { mount, createLocalVue } from "@vue/test-utils";
+import { createStore } from "../../store";
+import flushPromises from "flush-promises";
+import JobDestinationParams from "./JobDestinationParams";
+import jobDestinationResponse from "./testData/jobDestinationResponse";
+
+const JOB_ID = "foo_job_id";
+
+describe("JobDestinationParams/JobDestinationParams.vue", () => {
+    const localVue = createLocalVue();
+    localVue.use(Vuex);
+
+    const responseKeys = Object.keys(jobDestinationResponse);
+
+    let testStore, axiosMock, wrapper;
+
+    beforeEach(async () => {
+        axiosMock = new MockAdapter(axios);
+        testStore = createStore();
+        const propsData = {
+            jobId: JOB_ID,
+        };
+        axiosMock.onGet(`/api/jobs/${JOB_ID}/destination_params`).reply(200, jobDestinationResponse);
+        wrapper = mount(JobDestinationParams, {
+            store: testStore,
+            propsData,
+            localVue,
+        });
+        await flushPromises();
+        assert(responseKeys.length > 0, "test data is invalid!");
+    });
+
+    afterEach(() => {
+        axiosMock.restore();
+    });
+
+    it("destination parameters should exist", async () => {
+        expect(Object.keys(wrapper.vm.jobDestinationParams).length).to.equals(responseKeys.length);
+        expect(wrapper.vm.jobId).to.equals(JOB_ID);
+        expect(wrapper.vm.jobDestinationParams["docker_net"]).to.equals("bridge");
+        expect(wrapper.vm.jobDestinationParams["docker_set_user"]).to.equals(null);
+    });
+
+    it("destination parameters should be rendered", async () => {
+        console.log(wrapper.html());
+        const paramsTable = wrapper.find("#destination_parameters");
+        expect(paramsTable.isVisible()).to.equals(true);
+        const params = paramsTable.findAll("tbody > tr");
+        expect(params.length).to.equals(responseKeys.length);
+
+        for (let counter = 0; counter < responseKeys.length - 1; counter++) {
+            const parameter = params.at(counter).findAll("td");
+            const parameterTitle = parameter.at(0).text();
+            const parameterValue = parameter.at(1).text();
+
+            assert(responseKeys.includes(parameterTitle), "rendered parameter should exist in test data!");
+            // since we render null as an empty string, rendered empty string should always equal null in test data
+            assert(
+                jobDestinationResponse[parameterTitle] === (parameterValue === "" ? null : parameterValue),
+                "parameter value is not equal to test data!"
+            );
+        }
+    });
+});
diff --git a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
index dda05013eae2..a0c6deb85eed 100644
--- a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
+++ b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <table class="tabletip info_data_table">
+        <table id="destination_parameters" class="tabletip info_data_table">
             <tbody>
                 <tr v-for="(value, title) in jobDestinationParams">
                     <td>{{ title }}</td>
@@ -12,10 +12,10 @@
 </template>
 
 <script>
-    import {mapCacheActions} from "vuex-cache";
-    import {mapGetters} from "vuex";
+import { mapCacheActions } from "vuex-cache";
+import { mapGetters } from "vuex";
 
-    export default {
+export default {
     props: {
         jobId: {
             type: String,
@@ -42,7 +42,7 @@
         ...mapGetters(["getJobDestinationParams"]),
         jobDestinationParams: function () {
             return this.getJobDestinationParams(this.jobId);
-        }
+        },
     },
     methods: {
         ...mapCacheActions(["fetchJobDestinationParams"]),
diff --git a/client/galaxy/scripts/components/JobDestinationParams/testData/jobDestinationResponse.json b/client/galaxy/scripts/components/JobDestinationParams/testData/jobDestinationResponse.json
new file mode 100644
index 000000000000..42070b6f77ef
--- /dev/null
+++ b/client/galaxy/scripts/components/JobDestinationParams/testData/jobDestinationResponse.json
@@ -0,0 +1,12 @@
+{
+  "Runner": "local",
+  "Runner Job ID": "23027",
+  "Handler": "main.web.1",
+  "docker_auto_rm": "true",
+  "docker_enabled": "true",
+  "docker_net": "bridge",
+  "docker_set_user": null,
+  "docker_sudo": "false",
+  "docker_volumes": "$galaxy_root:ro,$tool_directory:ro,$job_directory:rw,$working_directory:rw,$default_file_path:ro",
+  "require_container": "true"
+}

From 8416e56685f68bbfd1b1a2a24359c0eb0d3a7799 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Wed, 8 Apr 2020 19:01:16 +0200
Subject: [PATCH 735/853] fix eslint test

---
 .../components/JobDestinationParams/JobDestinationParams.vue    | 2 +-
 client/galaxy/scripts/store/index.js                            | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
index a0c6deb85eed..ad50ec8911ac 100644
--- a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
+++ b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
@@ -2,7 +2,7 @@
     <div>
         <table id="destination_parameters" class="tabletip info_data_table">
             <tbody>
-                <tr v-for="(value, title) in jobDestinationParams">
+                <tr v-for="(value, title) in jobDestinationParams" :key="title">
                     <td>{{ title }}</td>
                     <td>{{ value }}</td>
                 </tr>
diff --git a/client/galaxy/scripts/store/index.js b/client/galaxy/scripts/store/index.js
index fe51b2e5680f..0f89419a996a 100644
--- a/client/galaxy/scripts/store/index.js
+++ b/client/galaxy/scripts/store/index.js
@@ -32,7 +32,7 @@ export function createStore() {
             histories: historyStore,
             tags: tagStore,
             jobMetrics: jobMetricsStore,
-            DestinationParameters: jobDestinationParametersStore,
+            destinationParameters: jobDestinationParametersStore,
             invocations: invocationStore,
             user: userStore,
             config: configStore,

From def7c6b25c9356265ac5ca79d82849068b788ea4 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Wed, 8 Apr 2020 20:52:51 +0200
Subject: [PATCH 736/853] add xg,vg,protobuf datatypes

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 0480a651f4b4..0b901b26b334 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -382,6 +382,10 @@
     </datatype>
     <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="odgi" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs self index used by odgi."/>
+    <datatype extension="vg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs."/>
+    <datatype extension="xg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs with vg index."/>
+    <datatype extension="protobuf2" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data."/>
+    <datatype extension="protobuf3" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data."/>
     <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">

From 524ea09f7cbc42f407a75030ca27b25942866d0f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 9 Apr 2020 09:29:20 +0200
Subject: [PATCH 737/853] add display_in_upload

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 0b901b26b334..9ebea36a237f 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -381,9 +381,9 @@
       <display file="igb/wig.xml"/>
     </datatype>
     <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="true"/>
-    <datatype extension="odgi" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs self index used by odgi."/>
-    <datatype extension="vg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs."/>
-    <datatype extension="xg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs with vg index."/>
+    <datatype extension="odgi" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs self index used by odgi." display_in_upload="true"/>
+    <datatype extension="vg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs." display_in_upload="true"/>
+    <datatype extension="xg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs with vg index." display_in_upload="true"/>
     <datatype extension="protobuf2" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data."/>
     <datatype extension="protobuf3" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data."/>
     <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="true"/>

From 2549abc67f98c912b1677478fd1020c3d7e30676 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?=
 <lecorguille@users.noreply.github.com>
Date: Thu, 9 Apr 2020 11:23:28 +0200
Subject: [PATCH 738/853] Upload - deal with multifile zip file

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 lib/galaxy/datatypes/binary.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 1f464bbdc9f0..a4a651807c76 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -249,6 +249,16 @@ def display_peek(self, dataset):
         except Exception:
             return "Compressed zip file (%s)" % (nice_size(dataset.get_size()))
 
+    def sniff(self, filename):
+        with zipfile.ZipFile(filename) as zf:
+            zf_files = zf.infolist()
+            count = 0
+            for f in zf_files:
+                if f.file_size > 0 and not f.filename.startswith('__MACOSX/') and not f.filename.endswith('.DS_Store'):
+                    count += 1
+                if count > 1:
+                    return True
+
 
 class GenericAsn1Binary(Binary):
     """Class for generic ASN.1 binary format"""

From add34b583abdf578c01a3b1b462658989fd6a0c8 Mon Sep 17 00:00:00 2001
From: lecorguille <gildas.le.corguille@gmail.com>
Date: Fri, 10 Apr 2020 15:57:21 +0200
Subject: [PATCH 739/853] Upload - deal with multifile zip file - sniff order

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 403a24856b3d..8c6199731197 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -843,6 +843,8 @@
     <sniffer type="galaxy.datatypes.binary:Cpt"/>
     <sniffer type="galaxy.datatypes.binary:Edr"/>
     <sniffer type="galaxy.datatypes.binary:Vel"/>
+    <sniffer type="galaxy.datatypes.binary:Xlsx"/>
+    <sniffer type="galaxy.datatypes.binary:CompressedZipArchive"/>
     <sniffer type="galaxy.datatypes.annotation:Augustus"/>
     <sniffer type="galaxy.datatypes.triples:Rdf"/>
     <sniffer type="galaxy.datatypes.blast:BlastXml"/>

From 18fb6b0b8990689476117349e383b3784a8d121c Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Fri, 10 Apr 2020 16:36:50 +0200
Subject: [PATCH 740/853] Refactor enabled

---
 client/galaxy/scripts/components/Workflow/Editor/Node.vue | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 625cfed21832..caacaa8d8d77 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -98,12 +98,7 @@ export default {
             return this.type != "subworkflow";
         },
         isEnabled() {
-            const Galaxy = getGalaxyInstance();
-            const isRecommendationEnabled = Galaxy.config.enable_tool_recommendations;
-            if (isRecommendationEnabled === true) {
-                return true;
-            }
-            return false;
+            return getGalaxyInstance().config.enable_tool_recommendations;
         },
     },
     methods: {

From eec5aa516582591c51776dee7b540e99765cad4e Mon Sep 17 00:00:00 2001
From: "jalili.vahid@gmail.com" <LetMeIn%#01>
Date: Fri, 10 Apr 2020 09:33:35 -0700
Subject: [PATCH 741/853] Refactor IObjectStore to ObjectStore.

---
 lib/galaxy/objectstore/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index c2552ca3334e..5a6eb180625a 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -39,7 +39,7 @@
 log = logging.getLogger(__name__)
 
 
-class IObjectStore(object):
+class ObjectStore(object):
     __metaclass__ = abc.ABCMeta
 
     """ObjectStore interface.
@@ -196,7 +196,7 @@ def get_store_by(self, obj):
         raise NotImplementedError()
 
 
-class BaseObjectStore(IObjectStore):
+class BaseObjectStore(ObjectStore):
 
     def __init__(self, config, config_dict=None, **kwargs):
         """

From 1b0d8fe28ed3e7c45df5f9651a0ff3e1be7798ca Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 10 Apr 2020 15:08:10 -0400
Subject: [PATCH 742/853] Fix removal of workflow outputs from workflow nodes
 in editor by removing dom element

---
 client/galaxy/scripts/mvc/workflow/workflow-node.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js
index fcdc22080e9d..6fe45f1f9f2d 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js
@@ -274,7 +274,7 @@ export class Node {
                     x.destroy(); // Removes the noodle connectors
                 }
             });
-            nodeView.outputViews[unused_output].remove(); // removes the rendered output
+            nodeView.outputViews[unused_output].$el.remove(); // removes the rendered output
             delete nodeView.outputViews[unused_output]; // removes the reference to the output
             delete node.output_terminals[unused_output]; // removes the output terminal
         });

From 88b9493b7be0a089495e146610fe2fe657696d1f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 10 Mar 2020 15:43:46 +0100
Subject: [PATCH 743/853] Get basic TS functionality working on python 3

---
 lib/tool_shed/util/hgweb_config.py     | 10 ++++------
 lib/tool_shed/webapp/model/__init__.py | 11 ++++++++---
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/lib/tool_shed/util/hgweb_config.py b/lib/tool_shed/util/hgweb_config.py
index b0171562aa14..76a389b63655 100644
--- a/lib/tool_shed/util/hgweb_config.py
+++ b/lib/tool_shed/util/hgweb_config.py
@@ -80,9 +80,8 @@ def hgweb_config(self):
             # raise Exception( "Required file %s does not exist - check config setting for hgweb_config_dir." % hgweb_config )
             # ...but now we just log the missing file and create a new empty one.
             log.debug("Required file %s does not exist, so creating a new, empty file.  Check your config setting for hgweb_config_dir." % hgweb_config)
-            hgweb_config_file = open(hgweb_config, 'wb')
-            hgweb_config_file.write(new_hgweb_config_template)
-            hgweb_config_file.close()
+            with open(hgweb_config, 'w') as hgweb_config_file:
+                hgweb_config_file.write(new_hgweb_config_template)
         return os.path.abspath(hgweb_config)
 
     def make_backup(self):
@@ -101,9 +100,8 @@ def read_config(self, force_read=False):
 
     def write_config(self):
         """Writing the in-memory configuration to the hgweb.config file on disk."""
-        config_file = open(self.hgweb_config, 'wb')
-        self.in_memory_config.write(config_file)
-        config_file.close
+        with open(self.hgweb_config, 'wb') as config_file:
+            self.in_memory_config.write(config_file)
 
 
 hgweb_config_manager = HgWebConfigManager()
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index d801a3874c47..6b0f856be3c4 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -217,7 +217,12 @@ def admin_role(self):
                         (str(self.name), str(self.user.username)))
 
     def allow_push(self):
-        return self.hg_repo.ui.config('web', 'allow_push')
+        hgrc_file = hg_util.get_hgrc_path(self.repo_path())
+        with open(hgrc_file, 'r') as fh:
+            for line in fh:
+                if line.startswith('allow_push = '):
+                    return line[len('allow_push = '):]
+        return ''
 
     def can_change_type(self):
         # Allow changing the type only if the repository has no contents, has never been installed, or has
@@ -300,9 +305,9 @@ def set_allow_push(self, usernames, remove_auth=''):
         # repo.ui.setconfig('web', 'allow_push', allow_push)
         repo_dir = self.repo_path()
         hgrc_file = hg_util.get_hgrc_path(repo_dir)
-        with open(hgrc_file, 'rb') as fh:
+        with open(hgrc_file, 'r') as fh:
             lines = fh.readlines()
-        with open(hgrc_file, 'wb') as fh:
+        with open(hgrc_file, 'w') as fh:
             for line in lines:
                 if line.startswith('allow_push'):
                     fh.write('allow_push = %s' % allow_push)

From 48b8d8e6f95e7631d254bc97e59ad2a03b9a7417 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 10 Mar 2020 17:06:50 +0100
Subject: [PATCH 744/853] Strip newlines

---
 lib/tool_shed/webapp/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 6b0f856be3c4..d1981ed661aa 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -219,7 +219,7 @@ def admin_role(self):
     def allow_push(self):
         hgrc_file = hg_util.get_hgrc_path(self.repo_path())
         with open(hgrc_file, 'r') as fh:
-            for line in fh:
+            for line in fh.read().splitlines():
                 if line.startswith('allow_push = '):
                     return line[len('allow_push = '):]
         return ''

From a248fee4656ec26ce31d6836b1079105e9219672 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 11 Mar 2020 09:52:29 +0100
Subject: [PATCH 745/853] Minor twilltestcase fixes

---
 lib/tool_shed/test/base/twilltestcase.py | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 188be16c6981..fb07832cfefa 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -13,16 +13,15 @@
 # imported by twill.
 import pyparsing  # noqa: F401
 import requests
-import twill
-import twill.commands as tc
+import twill3.commands as tc
 from mercurial import commands, hg, ui
-from six import string_types, StringIO
+from six import string_types
 from six.moves.urllib.parse import (
     quote_plus,
     urlencode,
     urlparse
 )
-from twill.other_packages._mechanize_dist import ClientForm
+from twill3.other_packages._mechanize_dist import ClientForm
 
 import galaxy.model.tool_shed_install as galaxy_model
 import galaxy.util
@@ -41,8 +40,6 @@
 repository_installation_timeout = 600
 
 # Force twill to log to a buffer -- FIXME: Should this go to stdout and be captured by nose?
-buffer = StringIO()
-twill.set_output(buffer)
 tc.config('use_tidy', 0)
 
 # Dial ClientCookie logging down (very noisy)
@@ -253,7 +250,7 @@ def login(self, email='test@bx.psu.edu', password='testuser', username='admin-us
     def logout(self):
         self.visit_url("%s/user/logout" % self.url)
         self.check_page_for_string("You have been logged out")
-        tc.browser.cj.clear()
+        tc.clear_cookies()
 
     def showforms(self):
         """Shows form, helpful for debugging new tests"""
@@ -944,7 +941,7 @@ def galaxy_login(self, email='test@bx.psu.edu', password='testuser', username='a
 
     def galaxy_logout(self):
         self.visit_galaxy_url("/user/logout", params=dict(session_csrf_token=self.galaxy_token()))
-        tc.browser.cj.clear()
+        tc.browser.clear_cookies()
 
     def generate_complex_dependency_xml(self, filename, filepath, repository_tuples, package, version):
         file_path = os.path.join(filepath, filename)

From 17cf06fc49827a8f4c654fa64e7cd80734648d06 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 11 Mar 2020 10:20:25 +0100
Subject: [PATCH 746/853] Fix test setup

---
 lib/tool_shed/test/functional_tests.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/test/functional_tests.py b/lib/tool_shed/test/functional_tests.py
index 2356a15c469a..bfa419a08ee0 100644
--- a/lib/tool_shed/test/functional_tests.py
+++ b/lib/tool_shed/test/functional_tests.py
@@ -132,7 +132,7 @@ def setup(self):
             os.environ['GALAXY_TEST_SHED_TOOL_CONF'] = galaxy_shed_tool_conf_file
             # Generate shed_data_manager_conf.xml
             if not os.environ.get('GALAXY_SHED_DATA_MANAGER_CONF'):
-                open(galaxy_shed_data_manager_conf_file, 'wb').write(shed_data_manager_conf_xml_template)
+                open(galaxy_shed_data_manager_conf_file, 'w').write(shed_data_manager_conf_xml_template)
             kwargs = dict(migrated_tools_config=galaxy_migrated_tool_conf_file,
                           shed_data_manager_config_file=galaxy_shed_data_manager_conf_file,
                           shed_tool_path=galaxy_shed_tool_path,

From bb5f4bb1b6d4cba1cdabba5397fa7133093d930c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 11 Mar 2020 11:50:28 +0100
Subject: [PATCH 747/853] Write in text mode

---
 lib/tool_shed/util/hgweb_config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/util/hgweb_config.py b/lib/tool_shed/util/hgweb_config.py
index 76a389b63655..dcc5ca2b92be 100644
--- a/lib/tool_shed/util/hgweb_config.py
+++ b/lib/tool_shed/util/hgweb_config.py
@@ -100,7 +100,7 @@ def read_config(self, force_read=False):
 
     def write_config(self):
         """Writing the in-memory configuration to the hgweb.config file on disk."""
-        with open(self.hgweb_config, 'wb') as config_file:
+        with open(self.hgweb_config, 'w') as config_file:
             self.in_memory_config.write(config_file)
 
 

From d0481e3ea5872f81acae79132074b9e8ff3549f9 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 11 Mar 2020 12:57:42 +0100
Subject: [PATCH 748/853] WIP trying to figure out why login doesn't work

---
 lib/tool_shed/test/base/twilltestcase.py | 141 ++++++++++++-----------
 1 file changed, 71 insertions(+), 70 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index fb07832cfefa..253add3c7759 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -124,21 +124,21 @@ def create(self, cntrller='user', email='test@bx.psu.edu', password='testuser',
         invalid_username = False
         try:
             self.check_page_for_string("Created new user account")
-        except Exception:
+        except AssertionError:
             try:
                 # May have created the account in a previous test run...
                 self.check_page_for_string("User with email '%s' already exists." % email)
                 previously_created = True
-            except Exception:
+            except AssertionError:
                 try:
                     self.check_page_for_string('Public name is taken; please choose another')
                     username_taken = True
-                except Exception:
+                except AssertionError:
+                    # Note that we're only checking if the usr name is >< 4 chars here...
                     try:
-                        # Note that we're only checking if the usr name is >< 4 chars here...
                         self.check_page_for_string('Public name must be at least 4 characters in length')
                         invalid_username = True
-                    except Exception:
+                    except AssertionError:
                         pass
         return previously_created, username_taken, invalid_username
 
@@ -147,7 +147,7 @@ def get_all_history_ids_from_api(self):
 
     def get_form_controls(self, form):
         formcontrols = []
-        for i, control in enumerate(form.controls):
+        for i, control in enumerate(form.inputs):
             formcontrols.append("control %d: %s" % (i, str(control)))
         return formcontrols
 
@@ -265,11 +265,11 @@ def submit_form(self, form_no=0, button="runtool_btn", **kwd):
             if i == form_no:
                 break
         # To help with debugging a tool, print out the form controls when the test fails
-        print("form '%s' contains the following controls ( note the values )" % f.name)
+        # print("form '%s' contains the following controls ( note the values )" % f.get('name'))
         controls = {}
         formcontrols = self.get_form_controls(f)
         hc_prefix = '<HiddenControl('
-        for i, control in enumerate(f.controls):
+        for i, control in enumerate(f.inputs):
             if hc_prefix not in str(control):
                 try:
                     # check if a repeat element needs to be added
@@ -296,7 +296,7 @@ def submit_form(self, form_no=0, button="runtool_btn", **kwd):
                             control.clear()
                             # kwd[control.name] should be a singlelist
                             for elem in kwd[control.name]:
-                                tc.fv(f.name, control.name, str(elem))
+                                tc.fv(f.get('name'), control.name, str(elem))
                             # Create a new submit control, allows form to refresh, instead of going to next page
                             control = ClientForm.SubmitControl('SubmitControl', '___refresh_grouping___', {'name': 'refresh_grouping'})
                             control.add_to_form(f)
@@ -317,71 +317,72 @@ def submit_form(self, form_no=0, button="runtool_btn", **kwd):
             if not isinstance(control_value, list):
                 control_value = [control_value]
             control = controls[control_name]
-            control.clear()
-            if control.is_of_kind("text"):
-                tc.fv(f.name, control.name, ",".join(control_value))
-            elif control.is_of_kind("list"):
-                try:
-                    if control.is_of_kind("multilist"):
-                        if control.type == "checkbox":
-                            def is_checked(value):
-                                # Copied from form_builder.CheckboxField
-                                if value is True:
-                                    return True
-                                if isinstance(value, list):
-                                    value = value[0]
-                                return isinstance(value, string_types) and value.lower() in ("yes", "true", "on")
-                            try:
-                                checkbox = control.get()
-                                checkbox.selected = is_checked(control_value)
-                            except Exception as e1:
-                                print("Attempting to set checkbox selected value threw exception: ", e1)
-                                # if there's more than one checkbox, probably should use the behaviour for
-                                # ClientForm.ListControl ( see twill code ), but this works for now...
+            control_type = getattr(control, "type", None)
+            if control_type:
+                if control_type in ("text", "textfield", "submit"):
+                    tc.fv(f.get('name'), control.name, ",".join(control_value))
+                elif control.type == "list":
+                    try:
+                        if control.type in ("multilist", "checkbox"):
+                            if control.type == "checkbox":
+                                def is_checked(value):
+                                    # Copied from form_builder.CheckboxField
+                                    if value is True:
+                                        return True
+                                    if isinstance(value, list):
+                                        value = value[0]
+                                    return isinstance(value, string_types) and value.lower() in ("yes", "true", "on")
+                                try:
+                                    checkbox = control.get()
+                                    checkbox.selected = is_checked(control_value)
+                                except Exception as e1:
+                                    print("Attempting to set checkbox selected value threw exception: ", e1)
+                                    # if there's more than one checkbox, probably should use the behaviour for
+                                    # ClientForm.ListControl ( see twill code ), but this works for now...
+                                    for elem in control_value:
+                                        control.get(name=elem).selected = True
+                            else:
                                 for elem in control_value:
-                                    control.get(name=elem).selected = True
-                        else:
+                                    try:
+                                        # Doubt this case would ever work, but want
+                                        # to preserve backward compat.
+                                        control.get(name=elem).selected = True
+                                    except Exception:
+                                        # ... anyway this is really what we want to
+                                        # do, probably even want to try the len(
+                                        # elem ) > 30 check below.
+                                        control.get(label=elem).selected = True
+                        else:  # control.is_of_kind( "singlelist" )
                             for elem in control_value:
                                 try:
-                                    # Doubt this case would ever work, but want
-                                    # to preserve backward compat.
-                                    control.get(name=elem).selected = True
+                                    tc.fv(f.get('name'), control.name, str(elem))
                                 except Exception:
-                                    # ... anyway this is really what we want to
-                                    # do, probably even want to try the len(
-                                    # elem ) > 30 check below.
-                                    control.get(label=elem).selected = True
-                    else:  # control.is_of_kind( "singlelist" )
-                        for elem in control_value:
-                            try:
-                                tc.fv(f.name, control.name, str(elem))
-                            except Exception:
-                                try:
-                                    # Galaxy truncates long file names in the dataset_collector in galaxy/tools/parameters/basic.py
-                                    if len(elem) > 30:
-                                        elem_name = '%s..%s' % (elem[:17], elem[-11:])
-                                        tc.fv(f.name, control.name, str(elem_name))
-                                        pass
-                                    else:
+                                    try:
+                                        # Galaxy truncates long file names in the dataset_collector in galaxy/tools/parameters/basic.py
+                                        if len(elem) > 30:
+                                            elem_name = '%s..%s' % (elem[:17], elem[-11:])
+                                            tc.fv(f.get('name'), control.name, str(elem_name))
+                                            pass
+                                        else:
+                                            raise
+                                    except Exception:
                                         raise
                                 except Exception:
-                                    raise
-                            except Exception:
-                                for formcontrol in formcontrols:
-                                    log.debug(formcontrol)
-                                log.exception("Attempting to set control '%s' to value '%s' (also tried '%s') threw exception.", control.name, elem, elem_name)
-                                pass
-                except Exception as exc:
-                    for formcontrol in formcontrols:
-                        log.debug(formcontrol)
-                    errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % (control_name, str(control_value), f.name, str(exc))
-                    errmsg += "control: %s\n" % str(control)
-                    errmsg += "If the above control is a DataToolparameter whose data type class does not include a sniff() method,\n"
-                    errmsg += "make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.\n"
-                    raise AssertionError(errmsg)
-            else:
-                # Add conditions for other control types here when necessary.
-                pass
+                                    for formcontrol in formcontrols:
+                                        log.debug(formcontrol)
+                                    log.exception("Attempting to set control '%s' to value '%s' (also tried '%s') threw exception.", control.name, elem, elem_name)
+                                    pass
+                    except Exception as exc:
+                        for formcontrol in formcontrols:
+                            log.debug(formcontrol)
+                        errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % (control.name, str(control_value), f.get('name'), str(exc))
+                        errmsg += "control: %s\n" % str(control)
+                        errmsg += "If the above control is a DataToolparameter whose data type class does not include a sniff() method,\n"
+                        errmsg += "make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.\n"
+                        raise AssertionError(errmsg)
+                else:
+                    # Add conditions for other control types here when necessary.
+                    pass
         tc.submit(button)
 
     def visit_url(self, url, params=None, doseq=False, allowed_codes=[200]):
@@ -1503,7 +1504,7 @@ def set_form_value(self, form, kwd, field_name, field_value):
         the field does not exist in the provided form, return a dict without that index.
         '''
         form_id = form.attrs.get('id')
-        controls = [control for control in form.controls if str(control.name) == field_name]
+        controls = [control for control in form.inputs if str(control.name) == field_name]
         if len(controls) > 0:
             log.debug('Setting field %s of form %s to %s.' % (field_name, form_id, str(field_value)))
             tc.formvalue(form_id, field_name, str(field_value))
@@ -1534,7 +1535,7 @@ def set_skip_tool_tsts_flag(self, repository, flag_value, reason, changeset_revi
         self.display_manage_repository_page(repository, changeset_revision=changeset_revision)
         form = tc.browser.get_form('skip_tool_tests')
         assert form is not None, 'Could not find form skip_tool_tests.'
-        for control in form.controls:
+        for control in form.inputs:
             control_name = str(control.name)
             if control_name == 'skip_tool_tests' and control.type == 'checkbox':
                 checkbox = control.get()

From 86f8328490aa3f77a61231742e2d5e503dceae39 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 13 Mar 2020 17:56:11 +0100
Subject: [PATCH 749/853] More Python 3 fixes for TS

---
 lib/galaxy/tool_shed/util/hg_util.py                        | 4 ++--
 .../repository_types/repository_suite_definition.py         | 3 ++-
 .../repository_types/tool_dependency_definition.py          | 3 ++-
 lib/tool_shed/tools/tool_validator.py                       | 5 +++--
 lib/tool_shed/util/hg_util.py                               | 2 +-
 lib/tool_shed/util/readme_util.py                           | 5 ++---
 lib/tool_shed/util/repository_util.py                       | 2 +-
 lib/tool_shed/webapp/controllers/hg.py                      | 2 +-
 lib/tool_shed/webapp/controllers/repository.py              | 6 ++++--
 .../webapp/templates/webapps/tool_shed/common/common.mako   | 2 +-
 10 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/lib/galaxy/tool_shed/util/hg_util.py b/lib/galaxy/tool_shed/util/hg_util.py
index a1426951ab3a..3d6ddd9e7319 100644
--- a/lib/galaxy/tool_shed/util/hg_util.py
+++ b/lib/galaxy/tool_shed/util/hg_util.py
@@ -77,7 +77,7 @@ def get_ctx_file_path_from_manifest(filename, repo, changeset_revision):
     for changeset in reversed_upper_bounded_changelog(repo, changeset_revision):
         manifest_ctx = repo[changeset]
         for ctx_file in manifest_ctx.files():
-            ctx_file_name = basic_util.strip_path(ctx_file)
+            ctx_file_name = basic_util.strip_path(unicodify(ctx_file))
             if ctx_file_name == stripped_filename:
                 return manifest_ctx, ctx_file
     return None, None
@@ -93,7 +93,7 @@ def get_file_context_from_ctx(ctx, filename):
     deleted = False
     filename = basic_util.strip_path(filename)
     for ctx_file in ctx.files():
-        ctx_file_name = basic_util.strip_path(ctx_file)
+        ctx_file_name = basic_util.strip_path(unicodify(ctx_file))
         if filename == ctx_file_name:
             try:
                 # If the file was moved, its destination will be returned here.
diff --git a/lib/tool_shed/repository_types/repository_suite_definition.py b/lib/tool_shed/repository_types/repository_suite_definition.py
index b45e3946c746..a891d4605b42 100644
--- a/lib/tool_shed/repository_types/repository_suite_definition.py
+++ b/lib/tool_shed/repository_types/repository_suite_definition.py
@@ -1,6 +1,7 @@
 import logging
 
 import tool_shed.repository_types.util as rt_util
+from galaxy.util import unicodify
 from tool_shed.repository_types.metadata import TipOnly
 from tool_shed.util import basic_util
 
@@ -31,7 +32,7 @@ def is_valid_for_type(self, repository, revisions_to_check=None):
             # is named repository_dependencies.xml.
             files_changed_in_changeset = ctx.files()
             for file_path in files_changed_in_changeset:
-                file_name = basic_util.strip_path(file_path)
+                file_name = basic_util.strip_path(unicodify(file_path))
                 if file_name not in self.valid_file_names:
                     return False
         return True
diff --git a/lib/tool_shed/repository_types/tool_dependency_definition.py b/lib/tool_shed/repository_types/tool_dependency_definition.py
index 11ffead4297b..52e30e302525 100644
--- a/lib/tool_shed/repository_types/tool_dependency_definition.py
+++ b/lib/tool_shed/repository_types/tool_dependency_definition.py
@@ -1,6 +1,7 @@
 import logging
 
 import tool_shed.repository_types.util as rt_util
+from galaxy.util import unicodify
 from tool_shed.repository_types.metadata import TipOnly
 from tool_shed.util import basic_util
 
@@ -30,7 +31,7 @@ def is_valid_for_type(self, repository, revisions_to_check=None):
             # Inspect all files in the changeset (in sorted order) to make sure there is only one and it is named tool_dependencies.xml.
             files_changed_in_changeset = ctx.files()
             for file_path in files_changed_in_changeset:
-                file_name = basic_util.strip_path(file_path)
+                file_name = basic_util.strip_path(unicodify(file_path))
                 if file_name not in self.valid_file_names:
                     return False
         return True
diff --git a/lib/tool_shed/tools/tool_validator.py b/lib/tool_shed/tools/tool_validator.py
index b392b253100d..f3ed34b80deb 100644
--- a/lib/tool_shed/tools/tool_validator.py
+++ b/lib/tool_shed/tools/tool_validator.py
@@ -5,6 +5,7 @@
 
 from galaxy.tool_shed.tools.tool_validator import ToolValidator as GalaxyToolValidator
 from galaxy.tools import Tool
+from galaxy.util import unicodify
 from tool_shed.util import (
     basic_util,
     hg_util,
@@ -79,7 +80,7 @@ def get_latest_tool_config_revision_from_repository_manifest(self, repo, filenam
         for changeset in hg_util.reversed_upper_bounded_changelog(repo, changeset_revision):
             manifest_ctx = repo[changeset]
             for ctx_file in manifest_ctx.files():
-                ctx_file_name = basic_util.strip_path(ctx_file)
+                ctx_file_name = basic_util.strip_path(unicodify(ctx_file))
                 if ctx_file_name == stripped_filename:
                     try:
                         fctx = manifest_ctx[ctx_file]
@@ -111,7 +112,7 @@ def get_list_of_copied_sample_files(self, repo, changeset_revision, dir):
         for changeset in hg_util.reversed_upper_bounded_changelog(repo, changeset_revision):
             changeset_ctx = repo[changeset]
             for ctx_file in changeset_ctx.files():
-                ctx_file_name = basic_util.strip_path(ctx_file)
+                ctx_file_name = basic_util.strip_path(unicodify(ctx_file))
                 # If we decide in the future that files deleted later in the changelog should
                 # not be used, we can use the following if statement. if ctx_file_name.endswith( '.sample' )
                 # and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files:
diff --git a/lib/tool_shed/util/hg_util.py b/lib/tool_shed/util/hg_util.py
index b113b656a16c..4108c9aab966 100644
--- a/lib/tool_shed/util/hg_util.py
+++ b/lib/tool_shed/util/hg_util.py
@@ -92,7 +92,7 @@ def get_named_tmpfile_from_ctx(ctx, filename, dir):
     """
     filename = basic_util.strip_path(filename)
     for ctx_file in ctx.files():
-        ctx_file_name = basic_util.strip_path(ctx_file)
+        ctx_file_name = basic_util.strip_path(unicodify(ctx_file))
         if filename == ctx_file_name:
             try:
                 # If the file was moved, its destination file contents will be returned here.
diff --git a/lib/tool_shed/util/readme_util.py b/lib/tool_shed/util/readme_util.py
index 3b6b6cfea77a..fa80a198b444 100644
--- a/lib/tool_shed/util/readme_util.py
+++ b/lib/tool_shed/util/readme_util.py
@@ -39,9 +39,8 @@ def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_
                         full_path_to_readme_file = os.path.abspath(relative_path_to_readme_file)
                     text = None
                     try:
-                        f = open(full_path_to_readme_file, 'r')
-                        text = unicodify(f.read())
-                        f.close()
+                        with open(full_path_to_readme_file, 'rb') as f:
+                            text = unicodify(f.read())
                     except Exception:
                         log.exception("Error reading README file '%s' from disk", relative_path_to_readme_file)
                         text = None
diff --git a/lib/tool_shed/util/repository_util.py b/lib/tool_shed/util/repository_util.py
index 6f6533c26534..091423e223ba 100644
--- a/lib/tool_shed/util/repository_util.py
+++ b/lib/tool_shed/util/repository_util.py
@@ -406,7 +406,7 @@ def change_repository_name_in_hgrc_file(hgrc_file, new_name):
     config = configparser.ConfigParser()
     config.read(hgrc_file)
     config.set('web', 'name', new_name)
-    with open(hgrc_file, 'wb') as fh:
+    with open(hgrc_file, 'w') as fh:
         config.write(fh)
 
 
diff --git a/lib/tool_shed/webapp/controllers/hg.py b/lib/tool_shed/webapp/controllers/hg.py
index 1501550e138b..89abf6677861 100644
--- a/lib/tool_shed/webapp/controllers/hg.py
+++ b/lib/tool_shed/webapp/controllers/hg.py
@@ -19,7 +19,7 @@ def handle_request(self, trans, **kwd):
         cmd = kwd.get('cmd', None)
 
         def make_web_app():
-            hgwebapp = hgwebdir(hgweb_config)
+            hgwebapp = hgwebdir(hgweb_config.encode('utf-8'))
             return hgwebapp
         wsgi_app = wsgiapplication(make_web_app)
         if cmd == 'getbundle':
diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index 9671916ce8e3..58f940c272c4 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -61,7 +61,7 @@ def get_mercurial_default_options_dict(command):
         possible = possible[0]
     if len(possible) != 1:
         raise Exception('unable to find mercurial command "%s"' % command)
-    return dict((r[1].replace('-', '_'), r[2]) for r in next(iter(possible.values()))[1][1])
+    return dict((r[1].replace(b'-', b'_'), r[2]) for r in next(iter(possible.values()))[1][1])
 
 
 class RepositoryController(BaseUIController, ratings_util.ItemRatings):
@@ -2480,9 +2480,10 @@ def view_changeset(self, trans, id, ctx_str, **kwd):
         else:
             ctx_child = None
         diffs = []
-        options_dict = get_mercurial_default_options_dict('diff')
+        options_dict = get_mercurial_default_options_dict(b"diff")
         # Not quite sure if the following settings make any difference, but with a combination of them and the size check on each
         # diff, we don't run out of memory when viewing the changelog of the cisortho2 repository on the test tool shed.
+        options_dict = {util.unicodify(k): util.unicodify(v) for k, v in options_dict.items()}
         options_dict['maxfile'] = basic_util.MAXDIFFSIZE
         options_dict['maxtotal'] = basic_util.MAXDIFFSIZE
         diffopts = mdiff.diffopts(**options_dict)
@@ -2492,6 +2493,7 @@ def view_changeset(self, trans, id, ctx_str, **kwd):
             diffs.append(basic_util.to_html_string(diff))
         modified, added, removed, deleted, unknown, ignored, clean = repo.status(node1=ctx_parent.node(), node2=ctx.node())
         anchors = modified + added + removed + deleted + unknown + ignored + clean
+        anchors = util.unicodify(anchors)
         metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
                                                                                              id,
                                                                                              ctx_str,
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/common/common.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/common/common.mako
index 5603b65e6888..ecf9fd706393 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/common/common.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/common/common.mako
@@ -111,7 +111,7 @@
         html = ''
         for index in range( 1, 6 ):
             html += '<input name="%s" type="radio" class="star" value="%s" %s' % ( str( name ), str( index ), disabled_str )
-            if rating > ( index - 0.5 ) and rating < ( index + 0.5 ):
+            if rating or 0 > ( index - 0.5 ) and rating or 0 < ( index + 0.5 ):
                 html += ' checked="checked"'
             html += '/>'
     %>

From 405597b1797d4f2dd3a0545299791a28c086dc5a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 13 Mar 2020 18:00:22 +0100
Subject: [PATCH 750/853] Various hacks and debug statements for python3 twill
 tests

---
 lib/tool_shed/test/base/twilltestcase.py | 158 ++++++++++++-----------
 1 file changed, 85 insertions(+), 73 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 253add3c7759..19f1de673193 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -74,12 +74,20 @@ def setUp(self):
     """Class of FunctionalTestCase geared toward HTML interactions using the Twill library."""
 
     def check_for_strings(self, strings_displayed=[], strings_not_displayed=[]):
-        if strings_displayed:
-            for check_str in strings_displayed:
-                self.check_page_for_string(check_str)
-        if strings_not_displayed:
-            for check_str in strings_not_displayed:
-                self.check_string_not_in_page(check_str)
+        try:
+            if strings_displayed:
+                for check_str in strings_displayed:
+                    self.check_page_for_string(check_str)
+        except AssertionError:
+            log.error("%s not found in page", check_str)
+            raise
+        try:
+            if strings_not_displayed:
+                for check_str in strings_not_displayed:
+                    self.check_string_not_in_page(check_str)
+        except AssertionError:
+            log.error("%s found in page", check_str)
+            raise
 
     def check_page(self, strings_displayed, strings_displayed_count, strings_not_displayed):
         """Checks a page for strings displayed, not displayed and number of occurrences of a string"""
@@ -237,10 +245,10 @@ def login(self, email='test@bx.psu.edu', password='testuser', username='admin-us
         # test@bx.psu.edu is configured as an admin user
         previously_created, username_taken, invalid_username = \
             self.create(email=email, password=password, username=username, redirect=redirect)
+        # The acount has previously been created, so just login.
+        # HACK: don't use panels because late_javascripts() messes up the twill browser and it
+        # can't find form fields (and hence user can't be logged in).
         if previously_created:
-            # The acount has previously been created, so just login.
-            # HACK: don't use panels because late_javascripts() messes up the twill browser and it
-            # can't find form fields (and hence user can't be logged in).
             params = {
                 'use_panels': False
             }
@@ -248,7 +256,7 @@ def login(self, email='test@bx.psu.edu', password='testuser', username='admin-us
             self.submit_form('login', 'login_button', login=email, redirect=redirect, password=password)
 
     def logout(self):
-        self.visit_url("%s/user/logout" % self.url)
+        self.visit_url("/user/logout")
         self.check_page_for_string("You have been logged out")
         tc.clear_cookies()
 
@@ -315,74 +323,78 @@ def submit_form(self, form_no=0, button="runtool_btn", **kwd):
             if control_name not in controls:
                 continue  # these cannot be handled safely - cause the test to barf out
             if not isinstance(control_value, list):
-                control_value = [control_value]
+                control_value = [str(control_value)]
             control = controls[control_name]
             control_type = getattr(control, "type", None)
-            if control_type:
-                if control_type in ("text", "textfield", "submit"):
-                    tc.fv(f.get('name'), control.name, ",".join(control_value))
-                elif control.type == "list":
-                    try:
-                        if control.type in ("multilist", "checkbox"):
-                            if control.type == "checkbox":
-                                def is_checked(value):
-                                    # Copied from form_builder.CheckboxField
-                                    if value is True:
-                                        return True
-                                    if isinstance(value, list):
-                                        value = value[0]
-                                    return isinstance(value, string_types) and value.lower() in ("yes", "true", "on")
-                                try:
-                                    checkbox = control.get()
-                                    checkbox.selected = is_checked(control_value)
-                                except Exception as e1:
-                                    print("Attempting to set checkbox selected value threw exception: ", e1)
-                                    # if there's more than one checkbox, probably should use the behaviour for
-                                    # ClientForm.ListControl ( see twill code ), but this works for now...
-                                    for elem in control_value:
-                                        control.get(name=elem).selected = True
-                            else:
+            try:
+                log.debug("Control type: %s, Control: %s, value: %s", control_type, control_name, ",".join(control_value))
+            except Exception:
+                pass
+            if control_type in ("text", "textfield", "submit", "password", "TextareaElement", "checkbox", "radio", None):
+                tc.fv(f.get('name'), control.name, ",".join(control_value))
+            elif control_type in ("list", "multilist, checkbox"):
+                try:
+                    if control_type in ("multilist", "checkbox"):
+                        if control_type == "checkbox":
+                            def is_checked(value):
+                                # Copied from form_builder.CheckboxField
+                                if value is True:
+                                    return True
+                                if isinstance(value, list):
+                                    value = value[0]
+                                return isinstance(value, string_types) and value.lower() in ("yes", "true", "on")
+                            try:
+                                checkbox = control.get()
+                                checkbox.selected = is_checked(control_value)
+                            except Exception as e1:
+                                log.exception(e1)
+                                print("Attempting to set checkbox selected value threw exception: ", e1)
+                                # if there's more than one checkbox, probably should use the behaviour for
+                                # ClientForm.ListControl ( see twill code ), but this works for now...
                                 for elem in control_value:
-                                    try:
-                                        # Doubt this case would ever work, but want
-                                        # to preserve backward compat.
-                                        control.get(name=elem).selected = True
-                                    except Exception:
-                                        # ... anyway this is really what we want to
-                                        # do, probably even want to try the len(
-                                        # elem ) > 30 check below.
-                                        control.get(label=elem).selected = True
-                        else:  # control.is_of_kind( "singlelist" )
+                                    control.get(name=elem).selected = True
+                        else:
                             for elem in control_value:
                                 try:
-                                    tc.fv(f.get('name'), control.name, str(elem))
+                                    # Doubt this case would ever work, but want
+                                    # to preserve backward compat.
+                                    control.get(name=elem).selected = True
                                 except Exception:
-                                    try:
-                                        # Galaxy truncates long file names in the dataset_collector in galaxy/tools/parameters/basic.py
-                                        if len(elem) > 30:
-                                            elem_name = '%s..%s' % (elem[:17], elem[-11:])
-                                            tc.fv(f.get('name'), control.name, str(elem_name))
-                                            pass
-                                        else:
-                                            raise
-                                    except Exception:
+                                    # ... anyway this is really what we want to
+                                    # do, probably even want to try the len(
+                                    # elem ) > 30 check below.
+                                    control.get(label=elem).selected = True
+                    else:  # control.is_of_kind( "singlelist" )
+                        for elem in control_value:
+                            try:
+                                tc.fv(f.get('name'), control.name, str(elem))
+                            except Exception:
+                                try:
+                                    # Galaxy truncates long file names in the dataset_collector in galaxy/tools/parameters/basic.py
+                                    if len(elem) > 30:
+                                        elem_name = '%s..%s' % (elem[:17], elem[-11:])
+                                        tc.fv(f.get('name'), control.name, str(elem_name))
+                                        pass
+                                    else:
                                         raise
                                 except Exception:
-                                    for formcontrol in formcontrols:
-                                        log.debug(formcontrol)
-                                    log.exception("Attempting to set control '%s' to value '%s' (also tried '%s') threw exception.", control.name, elem, elem_name)
-                                    pass
-                    except Exception as exc:
-                        for formcontrol in formcontrols:
-                            log.debug(formcontrol)
-                        errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % (control.name, str(control_value), f.get('name'), str(exc))
-                        errmsg += "control: %s\n" % str(control)
-                        errmsg += "If the above control is a DataToolparameter whose data type class does not include a sniff() method,\n"
-                        errmsg += "make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.\n"
-                        raise AssertionError(errmsg)
-                else:
-                    # Add conditions for other control types here when necessary.
-                    pass
+                                    raise
+                            except Exception:
+                                for formcontrol in formcontrols:
+                                    log.debug(formcontrol)
+                                log.exception("Attempting to set control '%s' to value '%s' (also tried '%s') threw exception.", control.name, elem, elem_name)
+                                pass
+                except Exception as exc:
+                    for formcontrol in formcontrols:
+                        log.debug(formcontrol)
+                    errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % (control.name, str(control_value), f.get('name'), str(exc))
+                    errmsg += "control: %s\n" % str(control)
+                    errmsg += "If the above control is a DataToolparameter whose data type class does not include a sniff() method,\n"
+                    errmsg += "make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.\n"
+                    raise AssertionError(errmsg)
+            else:
+                # Add conditions for other control types here when necessary.
+                pass
         tc.submit(button)
 
     def visit_url(self, url, params=None, doseq=False, allowed_codes=[200]):
@@ -732,8 +744,8 @@ def delete_files_from_repository(self, repository, filenames=[], strings_display
                 files_to_delete.append(os.path.join(basepath, filename))
         self.browse_repository(repository)
         # Twill sets hidden form fields to read-only by default. We need to write to this field.
-        form = tc.browser.get_form('select_files_to_delete')
-        form.find_control("selected_files_to_delete").readonly = False
+        # form = tc.browser.get_form('select_files_to_delete')
+        # form.find_control("selected_files_to_delete").readonly = False
         tc.fv("2", "selected_files_to_delete", ','.join(files_to_delete))
         tc.submit('select_files_to_delete_button')
         self.check_for_strings(strings_displayed, strings_not_displayed)
@@ -1022,7 +1034,7 @@ def get_filename(self, filename, filepath=None):
             return os.path.abspath(os.path.join(self.file_dir, filename))
 
     def get_hg_repo(self, path):
-        return hg.repository(ui.ui(), path)
+        return hg.repository(ui.ui(), path.encode('utf-8'))
 
     def get_last_reviewed_revision_by_user(self, user, repository):
         changelog_tuples = self.get_repository_changelog_tuples(repository)

From 2fe76198b2b1d9a5c5f17cce811dd1a05522b740 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 15 Mar 2020 11:42:14 +0100
Subject: [PATCH 751/853] Fix bytestring handling when logging package
 installation steps

---
 .../recipe/asynchronous_reader.py             |  2 +-
 .../recipe/install_environment.py             | 40 +++++++++----------
 2 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
index 3e9d26decf65..66a579d817c5 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
@@ -20,7 +20,7 @@ def run(self):
         """Read lines and put them on the queue."""
         thread_lock = threading.Lock()
         thread_lock.acquire()
-        for line in iter(self._fd.readline, ''):
+        for line in iter(self._fd.readline, b''):
             stripped_line = line.rstrip()
             self.lines.append(stripped_line)
             self._queue.put(stripped_line)
diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
index 3221dad2b847..a74cc7682669 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
@@ -19,7 +19,8 @@
     DATABASE_MAX_STRING_SIZE,
     DATABASE_MAX_STRING_SIZE_PRETTY,
     shrink_string_by_size,
-    unicodify
+    smart_str,
+    unicodify,
 )
 
 log = logging.getLogger(__name__)
@@ -78,12 +79,12 @@ def enqueue_output(self, stdout, stdout_queue, stderr, stderr_queue):
         """
         stdout_logger = logging.getLogger('install_environment.STDOUT')
         stderr_logger = logging.getLogger('install_environment.STDERR')
-        for line in iter(stdout.readline, ''):
+        for line in iter(stdout.readline, b''):
             output = line.rstrip()
             stdout_logger.debug(output)
             stdout_queue.put(output)
         stdout_queue.put(None)
-        for line in iter(stderr.readline, ''):
+        for line in iter(stderr.readline, b''):
             output = line.rstrip()
             stderr_logger.debug(output)
             stderr_queue.put(output)
@@ -232,11 +233,11 @@ def handle_complex_command(self, command, job_name=""):
         # Close subprocess' file descriptors.
         self.close_file_descriptor(process_handle.stdout)
         self.close_file_descriptor(process_handle.stderr)
-        stdout = '\n'.join(stdout_reader.lines)
-        stderr = '\n'.join(stderr_reader.lines)
+        stdout = b'\n'.join(stdout_reader.lines)
+        stderr = b'\n'.join(stderr_reader.lines)
         # Handle error condition (deal with stdout being None, too)
-        output = _AttributeString(stdout.strip() if stdout else "")
-        errors = _AttributeString(stderr.strip() if stderr else "")
+        output = _AttributeString(stdout.strip() if stdout else b"")
+        errors = _AttributeString(stderr.strip() if stderr else b"")
         # Make sure the process has finished.
         process_handle.poll()
         output.return_code = process_handle.returncode
@@ -245,19 +246,18 @@ def handle_complex_command(self, command, job_name=""):
 
     def log_results(self, command, fabric_AttributeString, file_path):
         """Write attributes of fabric.operations._AttributeString to a specified log file."""
-        if os.path.exists(file_path):
-            logfile = open(file_path, 'ab')
-        else:
-            logfile = open(file_path, 'wb')
-        logfile.write("\n#############################################\n")
-        logfile.write('%s\nSTDOUT\n' % command)
-        logfile.write(str(fabric_AttributeString.stdout))
-        logfile.write("\n#############################################\n")
-        logfile.write("\n#############################################\n")
-        logfile.write('%s\nSTDERR\n' % command)
-        logfile.write(str(fabric_AttributeString.stderr))
-        logfile.write("\n#############################################\n")
-        logfile.close()
+        mode = 'ab' if os.path.exists(file_path) else 'wb'
+        with open(file_path, mode) as logfile:
+            logfile.write(b"\n#############################################\n")
+            logfile.write(smart_str(command))
+            logfile.write(b'\nSTDOUT\n')
+            logfile.write(smart_str(fabric_AttributeString.stdout))
+            logfile.write(b"\n#############################################\n")
+            logfile.write(b"\n#############################################\n")
+            logfile.write(smart_str(command))
+            logfile.write(b'\nSTDERR\n')
+            logfile.write(smart_str(fabric_AttributeString.stderr))
+            logfile.write(b"\n#############################################\n")
 
     @contextmanager
     def use_tmp_dir(self):

From 37bf822186d30997de6bfa336e0622870fdc89b0 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 15 Mar 2020 11:44:04 +0100
Subject: [PATCH 752/853] Fix form handling in prepare_for_install twill test

---
 lib/tool_shed/test/base/twilltestcase.py | 52 ++++++++++++++++--------
 1 file changed, 36 insertions(+), 16 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 19f1de673193..26c6748bf0b4 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -22,6 +22,7 @@
     urlparse
 )
 from twill3.other_packages._mechanize_dist import ClientForm
+from twill3.utils import ResultWrapper
 
 import galaxy.model.tool_shed_install as galaxy_model
 import galaxy.util
@@ -258,20 +259,26 @@ def login(self, email='test@bx.psu.edu', password='testuser', username='admin-us
     def logout(self):
         self.visit_url("/user/logout")
         self.check_page_for_string("You have been logged out")
-        tc.clear_cookies()
+        try:
+            del tc.browser._session.cookies['galaxycommunitysession']
+        except KeyError:
+            log.exception('Error removing toolshed session cookie')
 
     def showforms(self):
         """Shows form, helpful for debugging new tests"""
         return tc.showforms()
 
-    def submit_form(self, form_no=0, button="runtool_btn", **kwd):
+    def submit_form(self, form_no=0, button="runtool_btn", form=None, **kwd):
         """Populates and submits a form from the keyword arguments."""
         # An HTMLForm contains a sequence of Controls.  Supported control classes are:
         # TextControl, FileControl, ListControl, RadioControl, CheckboxControl, SelectControl,
         # SubmitControl, ImageControl
-        for i, f in enumerate(self.showforms()):
-            if i == form_no:
-                break
+        if form:
+            f = form
+        else:
+            for i, f in enumerate(self.showforms()):
+                if i == form_no:
+                    break
         # To help with debugging a tool, print out the form controls when the test fails
         # print("form '%s' contains the following controls ( note the values )" % f.get('name'))
         controls = {}
@@ -1266,21 +1273,34 @@ def install_repository(self, name, owner, category_name, install_resolver_depend
         }
         self.visit_url('/repository/install_repositories_by_revision', params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
-        # This section is tricky, due to the way twill handles form submission. The tool dependency checkbox needs to
-        # be hacked in through tc.browser, putting the form field in kwd doesn't work.
         form = tc.browser.get_form('select_tool_panel_section')
         if form is None:
             form = tc.browser.get_form('select_shed_tool_panel_config')
         assert form is not None, 'Could not find form select_shed_tool_panel_config or select_tool_panel_section.'
-        kwd = self.set_form_value(form, kwd, 'install_tool_dependencies', install_tool_dependencies)
-        kwd = self.set_form_value(form, kwd, 'install_repository_dependencies', install_repository_dependencies)
-        kwd = self.set_form_value(form, kwd, 'install_resolver_dependencies', install_resolver_dependencies)
-        kwd = self.set_form_value(form, kwd, 'shed_tool_conf', self.shed_tool_conf)
+        kwds = {
+            'install_tool_dependencies': install_tool_dependencies,
+            'install_repository_dependencies': install_repository_dependencies,
+            'install_resolver_dependencies': install_resolver_dependencies,
+            'shed_tool_conf': self.shed_tool_conf,
+        }
         if new_tool_panel_section_label is not None:
-            kwd = self.set_form_value(form, kwd, 'new_tool_panel_section_label', new_tool_panel_section_label)
-        submit_button_control = form.find_control(type='submit')
-        assert submit_button_control is not None, 'No submit button found for form %s.' % form.attrs.get('id')
-        self.submit_form(form.attrs.get('id'), str(submit_button_control.name), **kwd)
+            kwds['new_tool_panel_section_label'] = new_tool_panel_section_label
+        submit_button = [inp.name for inp in form.inputs if getattr(inp, 'type', None) == 'submit']
+        if len(submit_button) == 0:
+            # TODO: refactor, use regular TS install API
+            submit_kwargs = {inp.name: inp.value for inp in tc.browser.get_all_forms()[0].inputs if getattr(inp, 'type', None) == 'submit'}
+            payload = {_: form.inputs[_].value for _ in form.fields.keys()}
+            payload.update(kwds)
+            payload.update(submit_kwargs)
+            r = tc.browser._session.post(
+                self.galaxy_url + form.action,
+                data=payload,
+            )
+            tc.browser.result = ResultWrapper(r)
+        else:
+            assert len(submit_button) == 1, 'Expected to find a single submit button, found %s (%s)' % (len(submit_button), ','.join(submit_button))
+            submit_button = submit_button[0]
+            self.submit_form(form=form, button=submit_button, **kwds)
         self.check_for_strings(post_submit_strings_displayed, strings_not_displayed)
         repository_ids = self.initiate_installation_process(new_tool_panel_section_label=new_tool_panel_section_label)
         log.debug('Waiting for the installation of repository IDs: %s' % str(repository_ids))
@@ -1515,7 +1535,7 @@ def set_form_value(self, form, kwd, field_name, field_value):
         Set the form field field_name to field_value if it exists, and return the provided dict containing that value. If
         the field does not exist in the provided form, return a dict without that index.
         '''
-        form_id = form.attrs.get('id')
+        form_id = form.attrib.get('id')
         controls = [control for control in form.inputs if str(control.name) == field_name]
         if len(controls) > 0:
             log.debug('Setting field %s of form %s to %s.' % (field_name, form_id, str(field_value)))

From 28679ed11eeda1ba5476b670bdd96d52cac3e682 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 15 Mar 2020 19:59:44 +0100
Subject: [PATCH 753/853] Purge a lot of unused ShedTwillTestCase methods

---
 lib/tool_shed/test/base/twilltestcase.py | 204 +----------------------
 1 file changed, 3 insertions(+), 201 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 26c6748bf0b4..785733ac5980 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -7,7 +7,6 @@
 import tempfile
 import time
 from json import loads
-from xml.etree import ElementTree
 
 # Be sure to use Galaxy's vanilla pyparsing instead of the older version
 # imported by twill.
@@ -15,13 +14,11 @@
 import requests
 import twill3.commands as tc
 from mercurial import commands, hg, ui
-from six import string_types
 from six.moves.urllib.parse import (
     quote_plus,
     urlencode,
     urlparse
 )
-from twill3.other_packages._mechanize_dist import ClientForm
 from twill3.utils import ResultWrapper
 
 import galaxy.model.tool_shed_install as galaxy_model
@@ -151,84 +148,6 @@ def create(self, cntrller='user', email='test@bx.psu.edu', password='testuser',
                         pass
         return previously_created, username_taken, invalid_username
 
-    def get_all_history_ids_from_api(self):
-        return [history['id'] for history in self.json_from_url('/api/histories')]
-
-    def get_form_controls(self, form):
-        formcontrols = []
-        for i, control in enumerate(form.inputs):
-            formcontrols.append("control %d: %s" % (i, str(control)))
-        return formcontrols
-
-    def get_hids_in_history(self, history_id):
-        """Returns the list of hid values for items in a history"""
-        hids = []
-        api_url = '/api/histories/%s/contents' % history_id
-        hids = [history_item['hid'] for history_item in self.json_from_url(api_url)]
-        return hids
-
-    def get_history_as_data_list(self, show_deleted=False):
-        """Returns the data elements of a history"""
-        tree = self.history_as_xml_tree(show_deleted=show_deleted)
-        data_list = [elem for elem in tree.findall("data")]
-        return data_list
-
-    def get_history_from_api(self, encoded_history_id=None, show_deleted=None, show_details=False):
-        if encoded_history_id is None:
-            history = self.get_latest_history()
-            encoded_history_id = history['id']
-        params = dict()
-        if show_deleted is not None:
-            params['deleted'] = show_deleted
-        api_url = '/api/histories/%s/contents' % encoded_history_id
-        json_data = self.json_from_url(api_url, params=params)
-        if show_deleted is not None:
-            hdas = []
-            for hda in json_data:
-                if show_deleted:
-                    hdas.append(hda)
-                else:
-                    if not hda['deleted']:
-                        hdas.append(hda)
-            json_data = hdas
-        if show_details:
-            params['details'] = ','.join(hda['id'] for hda in json_data)
-            api_url = '/api/histories/%s/contents' % encoded_history_id
-            json_data = self.json_from_url(api_url, params=params)
-        return json_data
-
-    def get_latest_history(self):
-        return self.json_from_url('/api/histories')[0]
-
-    def get_running_datasets(self):
-        self.visit_url('/api/histories')
-        history_id = loads(self.last_page())[0]['id']
-        self.visit_url('/api/histories/%s' % history_id)
-        jsondata = loads(self.last_page())
-        return jsondata['state'] in ['queued', 'running']
-
-    def history_as_xml_tree(self, show_deleted=False):
-        """Returns a parsed xml object of a history"""
-        params = {
-            'as_xml': True,
-            'show_deleted': show_deleted
-        }
-        self.visit_url('/history', params=params)
-        xml = self.last_page()
-        tree = ElementTree.fromstring(xml)
-        return tree
-
-    def is_history_empty(self):
-        """
-        Uses history page JSON to determine whether this history is empty
-        (i.e. has no undeleted datasets).
-        """
-        return len(self.get_history_from_api()) == 0
-
-    def json_from_url(self, url, params={}):
-        self.visit_url(url, params)
-        return loads(self.last_page())
-
     def last_page(self):
         """
         Return the last visited page (usually HTML, but can binary data as
@@ -259,14 +178,11 @@ def login(self, email='test@bx.psu.edu', password='testuser', username='admin-us
     def logout(self):
         self.visit_url("/user/logout")
         self.check_page_for_string("You have been logged out")
-        try:
-            del tc.browser._session.cookies['galaxycommunitysession']
-        except KeyError:
-            log.exception('Error removing toolshed session cookie')
+        tc.browser.clear_cookies()
 
     def showforms(self):
         """Shows form, helpful for debugging new tests"""
-        return tc.showforms()
+        return tc.browser.get_all_forms()
 
     def submit_form(self, form_no=0, button="runtool_btn", form=None, **kwd):
         """Populates and submits a form from the keyword arguments."""
@@ -279,53 +195,7 @@ def submit_form(self, form_no=0, button="runtool_btn", form=None, **kwd):
             for i, f in enumerate(self.showforms()):
                 if i == form_no:
                     break
-        # To help with debugging a tool, print out the form controls when the test fails
-        # print("form '%s' contains the following controls ( note the values )" % f.get('name'))
-        controls = {}
-        formcontrols = self.get_form_controls(f)
-        hc_prefix = '<HiddenControl('
-        for i, control in enumerate(f.inputs):
-            if hc_prefix not in str(control):
-                try:
-                    # check if a repeat element needs to be added
-                    if control.name is not None:
-                        if control.name not in kwd and control.name.endswith('_add'):
-                            # control name doesn't exist, could be repeat
-                            repeat_startswith = control.name[0:-4]
-                            if repeat_startswith and not [c_name for c_name in controls.keys() if c_name.startswith(repeat_startswith)] and [c_name for c_name in kwd.keys() if c_name.startswith(repeat_startswith)]:
-                                tc.browser.clicked(f, control)
-                                tc.submit(control.name)
-                                return self.submit_form(form_no=form_no, button=button, **kwd)
-                    # Check for refresh_on_change attribute, submit a change if required
-                    if hasattr(control, 'attrs') and 'refresh_on_change' in control.attrs.keys():
-                        changed = False
-                        # For DataToolParameter, control.value is the HDA id, but kwd contains the filename.
-                        # This loop gets the filename/label for the selected values.
-                        item_labels = [item.attrs['label'] for item in control.get_items() if item.selected]
-                        for value in kwd[control.name]:
-                            if value not in control.value and True not in [value in item_label for item_label in item_labels]:
-                                changed = True
-                                break
-                        if changed:
-                            # Clear Control and set to proper value
-                            control.clear()
-                            # kwd[control.name] should be a singlelist
-                            for elem in kwd[control.name]:
-                                tc.fv(f.get('name'), control.name, str(elem))
-                            # Create a new submit control, allows form to refresh, instead of going to next page
-                            control = ClientForm.SubmitControl('SubmitControl', '___refresh_grouping___', {'name': 'refresh_grouping'})
-                            control.add_to_form(f)
-                            control.fixup()
-                            # Submit for refresh
-                            tc.submit('___refresh_grouping___')
-                            return self.submit_form(form_no=form_no, button=button, **kwd)
-                except Exception:
-                    log.exception("In submit_form, continuing, but caught exception.")
-                    for formcontrol in formcontrols:
-                        log.debug(formcontrol)
-                    continue
-                controls[control.name] = control
-        # No refresh_on_change attribute found in current form, so process as usual
+        controls = {c.name: c for c in f.inputs}
         for control_name, control_value in kwd.items():
             if control_name not in controls:
                 continue  # these cannot be handled safely - cause the test to barf out
@@ -333,72 +203,8 @@ def submit_form(self, form_no=0, button="runtool_btn", form=None, **kwd):
                 control_value = [str(control_value)]
             control = controls[control_name]
             control_type = getattr(control, "type", None)
-            try:
-                log.debug("Control type: %s, Control: %s, value: %s", control_type, control_name, ",".join(control_value))
-            except Exception:
-                pass
             if control_type in ("text", "textfield", "submit", "password", "TextareaElement", "checkbox", "radio", None):
                 tc.fv(f.get('name'), control.name, ",".join(control_value))
-            elif control_type in ("list", "multilist, checkbox"):
-                try:
-                    if control_type in ("multilist", "checkbox"):
-                        if control_type == "checkbox":
-                            def is_checked(value):
-                                # Copied from form_builder.CheckboxField
-                                if value is True:
-                                    return True
-                                if isinstance(value, list):
-                                    value = value[0]
-                                return isinstance(value, string_types) and value.lower() in ("yes", "true", "on")
-                            try:
-                                checkbox = control.get()
-                                checkbox.selected = is_checked(control_value)
-                            except Exception as e1:
-                                log.exception(e1)
-                                print("Attempting to set checkbox selected value threw exception: ", e1)
-                                # if there's more than one checkbox, probably should use the behaviour for
-                                # ClientForm.ListControl ( see twill code ), but this works for now...
-                                for elem in control_value:
-                                    control.get(name=elem).selected = True
-                        else:
-                            for elem in control_value:
-                                try:
-                                    # Doubt this case would ever work, but want
-                                    # to preserve backward compat.
-                                    control.get(name=elem).selected = True
-                                except Exception:
-                                    # ... anyway this is really what we want to
-                                    # do, probably even want to try the len(
-                                    # elem ) > 30 check below.
-                                    control.get(label=elem).selected = True
-                    else:  # control.is_of_kind( "singlelist" )
-                        for elem in control_value:
-                            try:
-                                tc.fv(f.get('name'), control.name, str(elem))
-                            except Exception:
-                                try:
-                                    # Galaxy truncates long file names in the dataset_collector in galaxy/tools/parameters/basic.py
-                                    if len(elem) > 30:
-                                        elem_name = '%s..%s' % (elem[:17], elem[-11:])
-                                        tc.fv(f.get('name'), control.name, str(elem_name))
-                                        pass
-                                    else:
-                                        raise
-                                except Exception:
-                                    raise
-                            except Exception:
-                                for formcontrol in formcontrols:
-                                    log.debug(formcontrol)
-                                log.exception("Attempting to set control '%s' to value '%s' (also tried '%s') threw exception.", control.name, elem, elem_name)
-                                pass
-                except Exception as exc:
-                    for formcontrol in formcontrols:
-                        log.debug(formcontrol)
-                    errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % (control.name, str(control_value), f.get('name'), str(exc))
-                    errmsg += "control: %s\n" % str(control)
-                    errmsg += "If the above control is a DataToolparameter whose data type class does not include a sniff() method,\n"
-                    errmsg += "make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.\n"
-                    raise AssertionError(errmsg)
             else:
                 # Add conditions for other control types here when necessary.
                 pass
@@ -424,10 +230,6 @@ def visit_url(self, url, params=None, doseq=False, allowed_codes=[200]):
             (return_code, ', '.join(str(code) for code in allowed_codes))
         return new_url
 
-    def wait(self, **kwds):
-        """Waits for the tools to finish"""
-        return self.wait_for(lambda: self.get_running_datasets(), **kwds)
-
     def write_temp_file(self, content, suffix='.html'):
         with tempfile.NamedTemporaryFile(suffix=suffix, prefix='twilltestcase-', delete=False) as fh:
             fh.write(smart_str(content))

From eaa8c5b26c348733bf338885e564b6f869d4790b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 16 Mar 2020 08:58:53 +0100
Subject: [PATCH 754/853] Use with statements to open files

---
 lib/tool_shed/test/functional_tests.py | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/lib/tool_shed/test/functional_tests.py b/lib/tool_shed/test/functional_tests.py
index bfa419a08ee0..e77f0465ac91 100644
--- a/lib/tool_shed/test/functional_tests.py
+++ b/lib/tool_shed/test/functional_tests.py
@@ -95,9 +95,11 @@ def setup(self):
                       use_heartbeat=False)
         kwargs.update(toolshed_database_conf)
         # Generate the tool_data_table_conf.xml file.
-        open(default_tool_data_table_config_path, 'w').write(tool_data_table_conf_xml_template)
+        with open(default_tool_data_table_config_path, 'w') as fh:
+            fh.write(tool_data_table_conf_xml_template)
         # Generate the shed_tool_data_table_conf.xml file.
-        open(shed_tool_data_table_conf_file, 'w').write(tool_data_table_conf_xml_template)
+        with open(shed_tool_data_table_conf_file, 'w') as fh:
+            fh.write(tool_data_table_conf_xml_template)
         os.environ['TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF'] = shed_tool_data_table_conf_file
         # ---- Build Tool Shed Application --------------------------------------------------
         toolshedapp = driver_util.build_shed_app(kwargs)
@@ -121,18 +123,22 @@ def setup(self):
             # Generate the shed_tool_conf.xml file.
             tool_sheds_conf_template_parser = string.Template(tool_sheds_conf_xml_template)
             tool_sheds_conf_xml = tool_sheds_conf_template_parser.safe_substitute(shed_url=tool_shed_test_host, shed_port=tool_shed_test_port)
-            open(galaxy_tool_sheds_conf_file, 'w').write(tool_sheds_conf_xml)
+            with open(galaxy_tool_sheds_conf_file, 'w') as fh:
+                fh.write(tool_sheds_conf_xml)
             # Generate the tool_sheds_conf.xml file.
             shed_tool_conf_template_parser = string.Template(shed_tool_conf_xml_template)
             shed_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute(shed_tool_path=galaxy_shed_tool_path)
-            open(galaxy_shed_tool_conf_file, 'w').write(shed_tool_conf_xml)
+            with open(galaxy_shed_tool_conf_file, 'w') as fh:
+                fh.write(shed_tool_conf_xml)
             # Generate the migrated_tool_conf.xml file.
             migrated_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute(shed_tool_path=galaxy_migrated_tool_path)
-            open(galaxy_migrated_tool_conf_file, 'w').write(migrated_tool_conf_xml)
+            with open(galaxy_migrated_tool_conf_file, 'w') as fh:
+                fh.write(migrated_tool_conf_xml)
             os.environ['GALAXY_TEST_SHED_TOOL_CONF'] = galaxy_shed_tool_conf_file
             # Generate shed_data_manager_conf.xml
             if not os.environ.get('GALAXY_SHED_DATA_MANAGER_CONF'):
-                open(galaxy_shed_data_manager_conf_file, 'w').write(shed_data_manager_conf_xml_template)
+                with open(galaxy_shed_data_manager_conf_file, 'w') as fh:
+                    fh.write(shed_data_manager_conf_xml_template)
             kwargs = dict(migrated_tools_config=galaxy_migrated_tool_conf_file,
                           shed_data_manager_config_file=galaxy_shed_data_manager_conf_file,
                           shed_tool_path=galaxy_shed_tool_path,

From 1924a651c634b99e7cc43ccf5f76573b2ee411dc Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 16 Mar 2020 18:13:14 +0100
Subject: [PATCH 755/853] Switch back to twill namespace

---
 lib/tool_shed/test/base/twilltestcase.py      |  6 +--
 .../test_1400_review_migration_stages.py      | 41 -------------------
 2 files changed, 3 insertions(+), 44 deletions(-)
 delete mode 100644 lib/tool_shed/test/functional/test_1400_review_migration_stages.py

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 785733ac5980..e93b21e1353b 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -12,14 +12,14 @@
 # imported by twill.
 import pyparsing  # noqa: F401
 import requests
-import twill3.commands as tc
+import twill.commands as tc
 from mercurial import commands, hg, ui
 from six.moves.urllib.parse import (
     quote_plus,
     urlencode,
     urlparse
 )
-from twill3.utils import ResultWrapper
+from twill.utils import ResultWrapper
 
 import galaxy.model.tool_shed_install as galaxy_model
 import galaxy.util
@@ -189,7 +189,7 @@ def submit_form(self, form_no=0, button="runtool_btn", form=None, **kwd):
         # An HTMLForm contains a sequence of Controls.  Supported control classes are:
         # TextControl, FileControl, ListControl, RadioControl, CheckboxControl, SelectControl,
         # SubmitControl, ImageControl
-        if form:
+        if form is not None:
             f = form
         else:
             for i, f in enumerate(self.showforms()):
diff --git a/lib/tool_shed/test/functional/test_1400_review_migration_stages.py b/lib/tool_shed/test/functional/test_1400_review_migration_stages.py
deleted file mode 100644
index 8413101d43b4..000000000000
--- a/lib/tool_shed/test/functional/test_1400_review_migration_stages.py
+++ /dev/null
@@ -1,41 +0,0 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
-
-
-class TestToolMigrationStages(ShedTwillTestCase):
-    '''Verify that the migration stages display correctly.'''
-
-    def test_0000_initiate_users(self):
-        """Create necessary user accounts and login as an admin user."""
-        self.login(email=common.admin_email, username=common.admin_username)
-        admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
-        self.test_db_util.get_private_role(admin_user)
-        self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
-        self.test_db_util.get_private_role(admin_user)
-
-    def test_0005_load_migration_stages_page(self):
-        '''Load the migration page and check for the appropriate migration stages.'''
-        stages = []
-        migration_message_strings = ['The&nbsp;Emboss&nbsp;5.0.0&nbsp;tools&nbsp;have&nbsp;been&nbsp;eliminated',
-                                     'The&nbsp;freebayes&nbsp;tool&nbsp;has&nbsp;been&nbsp;eliminated',
-                                     'The&nbsp;NCBI&nbsp;BLAST+&nbsp;tools',
-                                     'The&nbsp;tools&nbsp;&#34;Map&nbsp;with&nbsp;BWA&nbsp;for&nbsp;Illumina&#34;',
-                                     'FASTQ&nbsp;to&nbsp;BAM,&nbsp;SAM&nbsp;to&nbsp;FASTQ,&nbsp;BAM&nbsp;',
-                                     'Map&nbsp;with&nbsp;Bowtie&nbsp;for&nbsp;Illumina,&nbsp;',
-                                     'BAM-to-SAM&nbsp;converts&nbsp;BAM&nbsp;format']
-        migrated_repository_names = ['emboss_5', 'emboss_datatypes', 'freebayes', 'ncbi_blast_plus',
-                                     'blast_datatypes', 'bwa_wrappers', 'picard', 'lastz',
-                                     'lastz_paired_reads', 'bowtie_color_wrappers', 'bowtie_wrappers',
-                                     'xy_plot', 'bam_to_sam']
-        migrated_tool_dependencies = ['emboss', '5.0.0', 'freebayes', '0.9.4_a46483351fd0196637614121868fb5c386612b55',
-                                      'samtools', '0.1.18', 'blast+', '2.2.26+', 'bwa', '0.5.9', 'picard', '1.56.0',
-                                      'lastz', '1.02.00', 'bowtie', '0.12.7', 'FreeBayes requires g++', 'ncurses', 'zlib',
-                                      'blast.ncbi.nlm.nih.gov', 'fastx_toolkit', '0.0.13', 'samtools', '0.1.16', 'cufflinks',
-                                      '2.1.1', 'R', '2.11.0']
-        migration_scripts = ['0002_tools.sh', '0003_tools.sh', '0004_tools.sh', '0005_tools.sh', '0006_tools.sh',
-                             '0007_tools.sh', '0008_tools.sh']
-        stages.extend(migration_scripts + migrated_tool_dependencies + migrated_repository_names)
-        stages.extend(migration_message_strings)
-        self.load_galaxy_tool_migrations_page(strings_displayed=stages)

From a6cf584ae6668bc32813320d40770973c5746e29 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 16 Mar 2020 18:14:06 +0100
Subject: [PATCH 756/853] Don't create comma-separated lists for form values

---
 lib/tool_shed/test/base/twilltestcase.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index e93b21e1353b..17af4c0ed009 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -204,7 +204,8 @@ def submit_form(self, form_no=0, button="runtool_btn", form=None, **kwd):
             control = controls[control_name]
             control_type = getattr(control, "type", None)
             if control_type in ("text", "textfield", "submit", "password", "TextareaElement", "checkbox", "radio", None):
-                tc.fv(f.get('name'), control.name, ",".join(control_value))
+                for cv in control_value:
+                    tc.fv(form_name, control.name, cv)
             else:
                 # Add conditions for other control types here when necessary.
                 pass

From 413f8cee135c2d05a5b44344926cc174287f8437 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 16 Mar 2020 18:48:41 +0100
Subject: [PATCH 757/853] Use new twill 2.0 release

---
 lib/galaxy/dependencies/pipfiles/default/Pipfile                | 2 +-
 .../dependencies/pipfiles/default/pinned-dev-requirements.txt   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/lib/galaxy/dependencies/pipfiles/default/Pipfile
index bf8281d506c7..0b669e32aaa3 100644
--- a/lib/galaxy/dependencies/pipfiles/default/Pipfile
+++ b/lib/galaxy/dependencies/pipfiles/default/Pipfile
@@ -25,7 +25,7 @@ Sphinx = "*"
 sphinx_markdown_tables = "*"
 sphinx_rtd_theme = "*"
 testfixtures = "*"
-twill = {version = "==0.9.1", markers = "python_version < '3'"}
+twill = "*"
 watchdog = "*"
 python-irodsclient = "*"
 
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index 13e8e7864c78..a66925ec2f3d 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -57,7 +57,7 @@ sphinx-rtd-theme==0.4.3
 sphinx==1.8.5
 sphinxcontrib-websupport==1.1.2
 testfixtures==6.14.0
-twill==0.9.1 ; python_version < '3'
+twill==2.0
 typing==3.7.4.1 ; python_version < '3.5'
 urllib3==1.25.8
 watchdog==0.10.2

From 313098e1469f4b9f9b3104caea6a275a50cdb666 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 16 Mar 2020 18:50:28 +0100
Subject: [PATCH 758/853] Add python3 toolshed test

---
 .github/workflows/toolshed.yaml | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 .github/workflows/toolshed.yaml

diff --git a/.github/workflows/toolshed.yaml b/.github/workflows/toolshed.yaml
new file mode 100644
index 000000000000..b33a65eafd99
--- /dev/null
+++ b/.github/workflows/toolshed.yaml
@@ -0,0 +1,25 @@
+name: Toolshed
+on: [push, pull_request]
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        python-version: [3.7]
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        path: 'galaxy root'
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache pip dir
+      uses: actions/cache@v1
+      id: pip-cache
+      with:
+        path: ~/.cache/pip
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Run tests
+      run: './run_tests.sh -toolshed'
+      working-directory: 'galaxy root'

From f16855c19ab9dd44c95c7bedece9104c74679fc0 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 16 Mar 2020 18:55:54 +0100
Subject: [PATCH 759/853] Need form_name

---
 lib/tool_shed/test/base/twilltestcase.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 17af4c0ed009..e860767baf78 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -196,6 +196,7 @@ def submit_form(self, form_no=0, button="runtool_btn", form=None, **kwd):
                 if i == form_no:
                     break
         controls = {c.name: c for c in f.inputs}
+        form_name = f.get('name')
         for control_name, control_value in kwd.items():
             if control_name not in controls:
                 continue  # these cannot be handled safely - cause the test to barf out

From 80c67e4aa4f840ee2238edf4b863d4b4413c6c79 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 17 Mar 2020 10:39:00 +0100
Subject: [PATCH 760/853] Update TwillTestCase for twill refactorings

---
 lib/tool_shed/test/base/twilltestcase.py | 22 +++++++++-------------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index e860767baf78..4af38ca15419 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -37,12 +37,10 @@
 # Set a 10 minute timeout for repository installation.
 repository_installation_timeout = 600
 
-# Force twill to log to a buffer -- FIXME: Should this go to stdout and be captured by nose?
-tc.config('use_tidy', 0)
-
 # Dial ClientCookie logging down (very noisy)
 logging.getLogger("ClientCookie.cookies").setLevel(logging.WARNING)
 log = logging.getLogger(__name__)
+tc.options['equiv_refresh_interval'] = 0
 
 
 class ShedTwillTestCase(FunctionalTestCase):
@@ -153,10 +151,10 @@ def last_page(self):
         Return the last visited page (usually HTML, but can binary data as
         well).
         """
-        return tc.browser.get_html()
+        return tc.browser.html
 
     def last_url(self):
-        return tc.browser.get_url()
+        return tc.browser.url
 
     def login(self, email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='', logout_first=True):
         # Clear cookies.
@@ -178,11 +176,10 @@ def login(self, email='test@bx.psu.edu', password='testuser', username='admin-us
     def logout(self):
         self.visit_url("/user/logout")
         self.check_page_for_string("You have been logged out")
-        tc.browser.clear_cookies()
 
     def showforms(self):
         """Shows form, helpful for debugging new tests"""
-        return tc.browser.get_all_forms()
+        return tc.browser.forms
 
     def submit_form(self, form_no=0, button="runtool_btn", form=None, **kwd):
         """Populates and submits a form from the keyword arguments."""
@@ -227,7 +224,7 @@ def visit_url(self, url, params=None, doseq=False, allowed_codes=[200]):
         if params:
             url += '?%s' % urlencode(params, doseq=doseq)
         new_url = tc.go(url)
-        return_code = tc.browser.get_code()
+        return_code = tc.browser.code
         assert return_code in allowed_codes, 'Invalid HTTP return code %s, allowed codes: %s' % \
             (return_code, ', '.join(str(code) for code in allowed_codes))
         return new_url
@@ -765,7 +762,6 @@ def galaxy_login(self, email='test@bx.psu.edu', password='testuser', username='a
 
     def galaxy_logout(self):
         self.visit_galaxy_url("/user/logout", params=dict(session_csrf_token=self.galaxy_token()))
-        tc.browser.clear_cookies()
 
     def generate_complex_dependency_xml(self, filename, filepath, repository_tuples, package, version):
         file_path = os.path.join(filepath, filename)
@@ -1077,9 +1073,9 @@ def install_repository(self, name, owner, category_name, install_resolver_depend
         }
         self.visit_url('/repository/install_repositories_by_revision', params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
-        form = tc.browser.get_form('select_tool_panel_section')
+        form = tc.browser.form('select_tool_panel_section')
         if form is None:
-            form = tc.browser.get_form('select_shed_tool_panel_config')
+            form = tc.browser.form('select_shed_tool_panel_config')
         assert form is not None, 'Could not find form select_shed_tool_panel_config or select_tool_panel_section.'
         kwds = {
             'install_tool_dependencies': install_tool_dependencies,
@@ -1092,7 +1088,7 @@ def install_repository(self, name, owner, category_name, install_resolver_depend
         submit_button = [inp.name for inp in form.inputs if getattr(inp, 'type', None) == 'submit']
         if len(submit_button) == 0:
             # TODO: refactor, use regular TS install API
-            submit_kwargs = {inp.name: inp.value for inp in tc.browser.get_all_forms()[0].inputs if getattr(inp, 'type', None) == 'submit'}
+            submit_kwargs = {inp.name: inp.value for inp in tc.browser.forms[0].inputs if getattr(inp, 'type', None) == 'submit'}
             payload = {_: form.inputs[_].value for _ in form.fields.keys()}
             payload.update(kwds)
             payload.update(submit_kwargs)
@@ -1369,7 +1365,7 @@ def set_skip_tool_tsts_flag(self, repository, flag_value, reason, changeset_revi
         if changeset_revision is None:
             changeset_revision = self.get_repository_tip(repository)
         self.display_manage_repository_page(repository, changeset_revision=changeset_revision)
-        form = tc.browser.get_form('skip_tool_tests')
+        form = tc.browser.form('skip_tool_tests')
         assert form is not None, 'Could not find form skip_tool_tests.'
         for control in form.inputs:
             control_name = str(control.name)

From 377902406a9b4d34618d00139f71ade0013c0bed Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 17 Mar 2020 12:33:00 +0100
Subject: [PATCH 761/853] Need to send back something to browser

---
 lib/galaxy/webapps/galaxy/controllers/user.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index 817bfb9d6bcb..9afea0a96324 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -237,6 +237,7 @@ def logout(self, trans, logout_all=False, **kwd):
         # Since logging an event requires a session, we'll log prior to ending the session
         trans.log_event("User logged out")
         trans.handle_user_logout(logout_all=logout_all)
+        return {"message": "Success."}
 
     @expose_api_anonymous_and_sessionless
     def create(self, trans, payload={}, **kwd):

From a400cb628d33032dcac1de2bb6696e540d10caeb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 20 Mar 2020 10:03:03 +0100
Subject: [PATCH 762/853] Drop more debug statements, remove commented code

---
 lib/tool_shed/test/base/twilltestcase.py | 29 ++++++++----------------
 1 file changed, 9 insertions(+), 20 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 4af38ca15419..6f9be3bab079 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -70,20 +70,12 @@ def setUp(self):
     """Class of FunctionalTestCase geared toward HTML interactions using the Twill library."""
 
     def check_for_strings(self, strings_displayed=[], strings_not_displayed=[]):
-        try:
-            if strings_displayed:
-                for check_str in strings_displayed:
-                    self.check_page_for_string(check_str)
-        except AssertionError:
-            log.error("%s not found in page", check_str)
-            raise
-        try:
-            if strings_not_displayed:
-                for check_str in strings_not_displayed:
-                    self.check_string_not_in_page(check_str)
-        except AssertionError:
-            log.error("%s found in page", check_str)
-            raise
+        if strings_displayed:
+            for check_str in strings_displayed:
+                self.check_page_for_string(check_str)
+        if strings_not_displayed:
+            for check_str in strings_not_displayed:
+                self.check_string_not_in_page(check_str)
 
     def check_page(self, strings_displayed, strings_displayed_count, strings_not_displayed):
         """Checks a page for strings displayed, not displayed and number of occurrences of a string"""
@@ -163,10 +155,10 @@ def login(self, email='test@bx.psu.edu', password='testuser', username='admin-us
         # test@bx.psu.edu is configured as an admin user
         previously_created, username_taken, invalid_username = \
             self.create(email=email, password=password, username=username, redirect=redirect)
-        # The acount has previously been created, so just login.
-        # HACK: don't use panels because late_javascripts() messes up the twill browser and it
-        # can't find form fields (and hence user can't be logged in).
         if previously_created:
+            # The acount has previously been created, so just login.
+            # HACK: don't use panels because late_javascripts() messes up the twill browser and it
+            # can't find form fields (and hence user can't be logged in).
             params = {
                 'use_panels': False
             }
@@ -551,9 +543,6 @@ def delete_files_from_repository(self, repository, filenames=[], strings_display
             if filename in filenames:
                 files_to_delete.append(os.path.join(basepath, filename))
         self.browse_repository(repository)
-        # Twill sets hidden form fields to read-only by default. We need to write to this field.
-        # form = tc.browser.get_form('select_files_to_delete')
-        # form.find_control("selected_files_to_delete").readonly = False
         tc.fv("2", "selected_files_to_delete", ','.join(files_to_delete))
         tc.submit('select_files_to_delete_button')
         self.check_for_strings(strings_displayed, strings_not_displayed)

From c55a2a9a015816bde4caf085de143894bc31d8ee Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 2 Apr 2020 21:49:39 +0200
Subject: [PATCH 763/853] Fix rating logic

---
 .../webapp/templates/webapps/tool_shed/common/common.mako      | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/common/common.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/common/common.mako
index ecf9fd706393..37b90a5b3034 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/common/common.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/common/common.mako
@@ -109,9 +109,10 @@
         else:
             disabled_str = ''
         html = ''
+        rating = rating or 0
         for index in range( 1, 6 ):
             html += '<input name="%s" type="radio" class="star" value="%s" %s' % ( str( name ), str( index ), disabled_str )
-            if rating or 0 > ( index - 0.5 ) and rating or 0 < ( index + 0.5 ):
+            if rating > ( index - 0.5 ) and rating < ( index + 0.5 ):
                 html += ' checked="checked"'
             html += '/>'
     %>

From 8e1c2fd70a08343740fc8e2124c1edd9ba6549ee Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 3 Apr 2020 12:11:36 +0200
Subject: [PATCH 764/853] Raise exception if form not found

---
 lib/tool_shed/test/base/twilltestcase.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 6f9be3bab079..569b70b7cdd6 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -178,14 +178,13 @@ def submit_form(self, form_no=0, button="runtool_btn", form=None, **kwd):
         # An HTMLForm contains a sequence of Controls.  Supported control classes are:
         # TextControl, FileControl, ListControl, RadioControl, CheckboxControl, SelectControl,
         # SubmitControl, ImageControl
-        if form is not None:
-            f = form
-        else:
-            for i, f in enumerate(self.showforms()):
+        if form is None:
+            for i, form in enumerate(self.showforms()):
                 if i == form_no:
                     break
-        controls = {c.name: c for c in f.inputs}
-        form_name = f.get('name')
+        assert form, "No form to submit found"
+        controls = {c.name: c for c in form.inputs}
+        form_name = form.get('name')
         for control_name, control_value in kwd.items():
             if control_name not in controls:
                 continue  # these cannot be handled safely - cause the test to barf out

From ac2b22a545baf4a669aea971e9f32677d611b78f Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sun, 12 Apr 2020 01:29:30 +0100
Subject: [PATCH 765/853] Fix typo

---
 lib/tool_shed/metadata/repository_metadata_manager.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index f5afcf5ecc23..85b8dca45d34 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -752,7 +752,7 @@ def reset_all_metadata_on_repository_in_tool_shed(self):
             log.debug("Cloning repository changeset revision: %s", str(ctx.rev()))
             cloned_ok, error_message = hg_util.clone_repository(self.repository_clone_url, work_dir, str(ctx.rev()))
             if cloned_ok:
-                log.debug("Generating metadata for changset revision: %s", str(ctx.rev()))
+                log.debug("Generating metadata for changeset revision: %s", str(ctx.rev()))
                 self.set_changeset_revision(str(ctx))
                 self.set_repository_files_dir(work_dir)
                 self.generate_metadata_for_changeset_revision()

From fffd8ba86b4cb429bb1f13c7822ef34db6054606 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sun, 12 Apr 2020 00:06:36 +0100
Subject: [PATCH 766/853] Unicodify line-by-line

---
 .../recipe/asynchronous_reader.py             |  4 +-
 .../recipe/install_environment.py             | 40 ++++++++++---------
 2 files changed, 24 insertions(+), 20 deletions(-)

diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
index 66a579d817c5..eff83c4d2d75 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
@@ -1,6 +1,8 @@
 import logging
 import threading
 
+from galaxy.util import unicodify
+
 log = logging.getLogger(__name__)
 
 
@@ -21,7 +23,7 @@ def run(self):
         thread_lock = threading.Lock()
         thread_lock.acquire()
         for line in iter(self._fd.readline, b''):
-            stripped_line = line.rstrip()
+            stripped_line = unicodify(line).rstrip()
             self.lines.append(stripped_line)
             self._queue.put(stripped_line)
         thread_lock.release()
diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
index a74cc7682669..0f1c4068bd5c 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
@@ -13,13 +13,15 @@
 from six.moves import queue
 
 from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe import asynchronous_reader
-from galaxy.tool_shed.util.basic_util import INSTALLATION_LOG, NO_OUTPUT_TIMEOUT
+from galaxy.tool_shed.util.basic_util import (
+    INSTALLATION_LOG,
+    NO_OUTPUT_TIMEOUT,
+)
 from galaxy.tool_shed.util.tool_dependency_util import set_tool_dependency_attributes
 from galaxy.util import (
     DATABASE_MAX_STRING_SIZE,
     DATABASE_MAX_STRING_SIZE_PRETTY,
     shrink_string_by_size,
-    smart_str,
     unicodify,
 )
 
@@ -80,12 +82,12 @@ def enqueue_output(self, stdout, stdout_queue, stderr, stderr_queue):
         stdout_logger = logging.getLogger('install_environment.STDOUT')
         stderr_logger = logging.getLogger('install_environment.STDERR')
         for line in iter(stdout.readline, b''):
-            output = line.rstrip()
+            output = unicodify(line).rstrip()
             stdout_logger.debug(output)
             stdout_queue.put(output)
         stdout_queue.put(None)
         for line in iter(stderr.readline, b''):
-            output = line.rstrip()
+            output = unicodify(line).rstrip()
             stderr_logger.debug(output)
             stderr_queue.put(output)
         stderr_queue.put(None)
@@ -233,11 +235,11 @@ def handle_complex_command(self, command, job_name=""):
         # Close subprocess' file descriptors.
         self.close_file_descriptor(process_handle.stdout)
         self.close_file_descriptor(process_handle.stderr)
-        stdout = b'\n'.join(stdout_reader.lines)
-        stderr = b'\n'.join(stderr_reader.lines)
+        stdout = '\n'.join(stdout_reader.lines)
+        stderr = '\n'.join(stderr_reader.lines)
         # Handle error condition (deal with stdout being None, too)
-        output = _AttributeString(stdout.strip() if stdout else b"")
-        errors = _AttributeString(stderr.strip() if stderr else b"")
+        output = _AttributeString(stdout.strip() if stdout else "")
+        errors = _AttributeString(stderr.strip() if stderr else "")
         # Make sure the process has finished.
         process_handle.poll()
         output.return_code = process_handle.returncode
@@ -246,18 +248,18 @@ def handle_complex_command(self, command, job_name=""):
 
     def log_results(self, command, fabric_AttributeString, file_path):
         """Write attributes of fabric.operations._AttributeString to a specified log file."""
-        mode = 'ab' if os.path.exists(file_path) else 'wb'
+        mode = 'a' if os.path.exists(file_path) else 'w'
         with open(file_path, mode) as logfile:
-            logfile.write(b"\n#############################################\n")
-            logfile.write(smart_str(command))
-            logfile.write(b'\nSTDOUT\n')
-            logfile.write(smart_str(fabric_AttributeString.stdout))
-            logfile.write(b"\n#############################################\n")
-            logfile.write(b"\n#############################################\n")
-            logfile.write(smart_str(command))
-            logfile.write(b'\nSTDERR\n')
-            logfile.write(smart_str(fabric_AttributeString.stderr))
-            logfile.write(b"\n#############################################\n")
+            logfile.write("\n#############################################\n")
+            logfile.write(command)
+            logfile.write('\nSTDOUT\n')
+            logfile.write(fabric_AttributeString.stdout)
+            logfile.write("\n#############################################\n")
+            logfile.write("\n#############################################\n")
+            logfile.write(command)
+            logfile.write('\nSTDERR\n')
+            logfile.write(fabric_AttributeString.stderr)
+            logfile.write("\n#############################################\n")
 
     @contextmanager
     def use_tmp_dir(self):

From 5d2ae892945ca10a2edaee56730006f7f035a683 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sun, 12 Apr 2020 01:49:55 +0100
Subject: [PATCH 767/853] Use `io.open()` to read Unicode file

---
 .../test/test_data/filtering/readme.txt       |  4 ++--
 lib/tool_shed/util/readme_util.py             | 23 ++++++++++++-------
 2 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/lib/tool_shed/test/test_data/filtering/readme.txt b/lib/tool_shed/test/test_data/filtering/readme.txt
index 291b190d703b..ce3ff7330feb 100644
--- a/lib/tool_shed/test/test_data/filtering/readme.txt
+++ b/lib/tool_shed/test/test_data/filtering/readme.txt
@@ -1,2 +1,2 @@
-These characters should not result in a unicode decoding error: ®Ãâ�âèÃ
-....
\ No newline at end of file
+These characters should not result in a unicode decoding error: cómpl�c�tëd strĩñg
+....
diff --git a/lib/tool_shed/util/readme_util.py b/lib/tool_shed/util/readme_util.py
index fa80a198b444..927ee061b3c2 100644
--- a/lib/tool_shed/util/readme_util.py
+++ b/lib/tool_shed/util/readme_util.py
@@ -1,3 +1,4 @@
+import io
 import json
 import logging
 import os
@@ -6,12 +7,18 @@
 
 import tool_shed.util.shed_util_common as suc
 from galaxy import web
-from galaxy.util import rst_to_html, unicodify, url_get
-from tool_shed.util import basic_util
-from tool_shed.util import common_util
-from tool_shed.util import hg_util
-from tool_shed.util import metadata_util
-from tool_shed.util import repository_util
+from galaxy.util import (
+    rst_to_html,
+    unicodify,
+    url_get,
+)
+from tool_shed.util import (
+    basic_util,
+    common_util,
+    hg_util,
+    metadata_util,
+    repository_util,
+)
 
 log = logging.getLogger(__name__)
 
@@ -39,8 +46,8 @@ def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_
                         full_path_to_readme_file = os.path.abspath(relative_path_to_readme_file)
                     text = None
                     try:
-                        with open(full_path_to_readme_file, 'rb') as f:
-                            text = unicodify(f.read())
+                        with io.open(full_path_to_readme_file, 'r', encoding='utf-8') as f:
+                            text = f.read()
                     except Exception:
                         log.exception("Error reading README file '%s' from disk", relative_path_to_readme_file)
                         text = None

From 46124ba52c5d5f3426e0e0c3fbf6af1a80805d66 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 12 Apr 2020 11:44:46 +0200
Subject: [PATCH 768/853] Run tests against postgres

---
 .github/workflows/toolshed.yaml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/.github/workflows/toolshed.yaml b/.github/workflows/toolshed.yaml
index b33a65eafd99..38628962cea1 100644
--- a/.github/workflows/toolshed.yaml
+++ b/.github/workflows/toolshed.yaml
@@ -1,5 +1,8 @@
 name: Toolshed
 on: [push, pull_request]
+env:
+  GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  TOOL_SHED_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/toolshed?client_encoding=utf8'
 jobs:
   test:
     name: Test
@@ -7,6 +10,15 @@ jobs:
     strategy:
       matrix:
         python-version: [3.7]
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
     steps:
     - uses: actions/checkout@v2
       with:

From dd63ce043d48083bc40a2a96ebfa4ef74e8963af Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 12 Apr 2020 12:20:44 +0200
Subject: [PATCH 769/853] Auto-create database for TS and install database

---
 lib/galaxy/model/tool_shed_install/migrate/check.py | 9 +++++++++
 lib/tool_shed/webapp/model/migrate/check.py         | 9 +++++++++
 2 files changed, 18 insertions(+)

diff --git a/lib/galaxy/model/tool_shed_install/migrate/check.py b/lib/galaxy/model/tool_shed_install/migrate/check.py
index a7fffd7381a1..0888d192579d 100644
--- a/lib/galaxy/model/tool_shed_install/migrate/check.py
+++ b/lib/galaxy/model/tool_shed_install/migrate/check.py
@@ -12,6 +12,10 @@
     Table
 )
 from sqlalchemy.exc import NoSuchTableError
+from sqlalchemy_utils import (
+    create_database,
+    database_exists,
+)
 
 from galaxy.model.tool_shed_install import mapping
 
@@ -27,6 +31,11 @@ def create_or_verify_database(url, engine_options={}, app=None):
     """
     """
     # Create engine and metadata
+    if not database_exists(url):
+        message = "Creating database for URI [%s]" % url
+        log.info(message)
+        create_database(url)
+
     engine = create_engine(url, **engine_options)
 
     def migrate():
diff --git a/lib/tool_shed/webapp/model/migrate/check.py b/lib/tool_shed/webapp/model/migrate/check.py
index 95780f995df1..dbd97242bf12 100644
--- a/lib/tool_shed/webapp/model/migrate/check.py
+++ b/lib/tool_shed/webapp/model/migrate/check.py
@@ -5,6 +5,10 @@
 from migrate.versioning import repository, schema
 from sqlalchemy import create_engine, MetaData, Table
 from sqlalchemy.exc import NoSuchTableError
+from sqlalchemy_utils import (
+    create_database,
+    database_exists,
+)
 
 log = logging.getLogger(__name__)
 
@@ -26,6 +30,11 @@ def create_or_verify_database(url, engine_options={}):
 
     """
     # Create engine and metadata
+    if not database_exists(url):
+        message = "Creating database for URI [%s]" % url
+        log.info(message)
+        create_database(url)
+
     engine = create_engine(url, **engine_options)
     meta = MetaData(bind=engine)
     # Try to load dataset table

From 92ff3193245ed1a8b3678ea4daa8e2a9ac66cc8d Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 16 Mar 2020 22:18:39 +0000
Subject: [PATCH 770/853] Full Python dependencies update

using `make update-dependencies`.
---
 .../default/pinned-dev-requirements.txt       | 18 +++---
 .../pipfiles/default/pinned-requirements.txt  | 58 +++++++++----------
 .../pipfiles/flake8/pinned-requirements.txt   |  2 +-
 3 files changed, 40 insertions(+), 38 deletions(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index a66925ec2f3d..5d27d5abf3d6 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -4,20 +4,20 @@ alabaster==0.7.12
 atomicwrites==1.3.0
 attrs==19.3.0
 babel==2.8.0
-certifi==2019.11.28
+certifi==2020.4.5.1
 chardet==3.0.4
 commonmark==0.9.1
 configparser==4.0.2 ; python_version < '3.2'
 contextlib2==0.6.0.post1 ; python_version < '3.5'
-coverage==5.0.3
-deprecated==1.2.7
+coverage==5.0.4
+deprecated==1.2.9
 docutils==0.15.2
 funcsigs==1.0.2 ; python_version < '3.3'
 future==0.18.2
 gunicorn==19.10.0
 idna==2.9
 imagesize==1.2.0
-importlib-metadata==1.5.0 ; python_version < '3.8'
+importlib-metadata==1.6.0 ; python_version < '3.8'
 jinja2==2.11.1
 lxml==4.5.0
 markdown==3.1.1
@@ -27,17 +27,18 @@ mock==3.0.5
 more-itertools==5.0.0
 nose==1.3.7
 nosehtml==0.4.5
-packaging==20.1
+packaging==20.3
 pathlib2==2.3.5 ; python_version < '3.6'
 pathtools==0.1.2
 pluggy==0.13.1
 port-for==0.4
+prettytable==0.7.2
 psutil==5.7.0
 py==1.8.1
 pygithub==1.45
 pygments==2.5.2
 pyjwt==1.7.1
-pyparsing==2.4.6
+pyparsing==2.4.7
 pytest-cov==2.8.1
 pytest-html==1.22.1
 pytest-metadata==1.8.0
@@ -61,6 +62,7 @@ twill==2.0
 typing==3.7.4.1 ; python_version < '3.5'
 urllib3==1.25.8
 watchdog==0.10.2
-wcwidth==0.1.8
-wrapt==1.12.0
+wcwidth==0.1.9
+wrapt==1.12.1
+xmlrunner==1.7.7
 zipp==1.2.0
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 0d47bdffdc26..ba38a4adb57f 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -23,8 +23,8 @@ bcrypt==3.1.7
 bdbag==1.5.6
 beaker==1.11.0
 bioblend==0.13.0
-bleach==3.1.1
-boltons==20.0.0
+bleach==3.1.4
+boltons==20.1.0
 boto3==1.9.114
 boto==2.49.0
 botocore==1.12.253
@@ -32,7 +32,7 @@ bx-python==0.8.8
 bz2file==0.98 ; python_version < '3.3'
 cachecontrol==0.11.7
 cachetools==3.1.1
-certifi==2019.11.28
+certifi==2020.4.5.1
 cffi==1.14.0
 chardet==3.0.4
 cheetah3==3.2.4
@@ -43,18 +43,18 @@ cmd2==0.8.9
 coloredlogs==14.0
 configparser==4.0.2 ; python_version < '3.2'
 contextlib2==0.6.0.post1 ; python_version < '3.5'
-cryptography==2.8
+cryptography==2.9
 cwltool==1.0.20191225192155
 debtcollector==1.22.0
 decorator==4.4.2
-deprecated==1.2.7
+deprecated==1.2.9
 deprecation==2.0.7
 dictobj==0.4
 docopt==0.6.2
 docutils==0.15.2
 dogpile.cache==0.9.0
 ecdsa==0.15
-enum34==1.1.9 ; python_version < '3.4'
+enum34==1.1.10 ; python_version < '3.4'
 fabric3==1.14.post1
 funcsigs==1.0.2 ; python_version < '3.3'
 functools32==3.2.3.post2 ; python_version < '3.2'
@@ -63,13 +63,13 @@ futures==3.3.0 ; python_version == '2.6' or python_version == '2.7'
 galaxy-sequence-utils==1.1.5
 google-api-python-client==1.7.8
 google-auth-httplib2==0.0.3
-google-auth==1.11.2
-gxformat2==0.10.1
+google-auth==1.13.1
+gxformat2==0.11.1
 h5py==2.10.0
-httplib2==0.17.0
-humanfriendly==7.1.1
+httplib2==0.17.2
+humanfriendly==8.1
 idna==2.9
-importlib-metadata==1.5.0 ; python_version < '3.8'
+importlib-metadata==1.6.0 ; python_version < '3.8'
 ipaddress==1.0.23 ; python_version < '3.3'
 isa-rwval==0.10.7
 iso8601==0.1.12
@@ -78,14 +78,14 @@ jmespath==0.9.5
 jsonpatch==1.25
 jsonpointer==2.0
 jsonschema==3.2.0
-keystoneauth1==3.18.0
-kombu==4.6.7
+keystoneauth1==4.0.0
+kombu==4.6.8
 lockfile==0.12.2
 lxml==4.5.0
-mako==1.1.1
+mako==1.1.2
 markdown==3.1.1
 markupsafe==1.1.1
-mercurial==5.3
+mercurial==5.3.2
 mistune==0.8.4
 monotonic==1.5
 msgpack==1.0.0
@@ -102,7 +102,7 @@ numpy==1.16.6
 oauth2client==4.1.3
 oauthlib==3.1.0
 openstacksdk==0.17.0
-os-client-config==2.0.0
+os-client-config==2.1.0
 os-service-types==1.7.0
 osc-lib==2.0.0
 oslo.config==7.0.0
@@ -111,21 +111,21 @@ oslo.i18n==3.25.1
 oslo.log==3.45.2
 oslo.serialization==2.29.2
 oslo.utils==3.42.1
-packaging==20.1
+packaging==20.3
 paramiko==2.7.1
 parsley==1.3
 paste==3.4.0
 pastedeploy==2.1.0
 pastescript==3.2.0
 pathlib2==2.3.5 ; python_version < '3.6'
-pbr==5.4.4
+pbr==5.4.5
 prettytable==0.7.2
 prov==1.5.1
 psutil==5.7.0
 pulsar-galaxy-lib==0.14.0.dev1
 pyasn1-modules==0.2.8
 pyasn1==0.4.8
-pycparser==2.19
+pycparser==2.20
 pycryptodome==3.9.7
 pyeventsystem==0.1.0
 pyinotify==0.9.6 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
@@ -133,9 +133,9 @@ pyjwt==1.7.1
 pykwalify==1.7.0
 pynacl==1.3.0
 pyopenssl==19.1.0
-pyparsing==2.4.6
-pyperclip==1.7.0
-pyrsistent==0.15.7
+pyparsing==2.4.7
+pyperclip==1.8.0
+pyrsistent==0.16.0
 pysam==0.15.2
 pysftp==0.2.9
 python-cinderclient==4.0.0
@@ -149,7 +149,7 @@ python-openid==2.2.5 ; python_version < '3.0'
 python-swiftclient==3.6.0
 pytz==2019.3
 pyuwsgi==2.0.18.post0
-pyyaml==5.3
+pyyaml==5.3.1
 rdflib-jsonld==0.4.0
 rdflib==4.2.2
 repoze.lru==0.7
@@ -157,7 +157,7 @@ requests-oauthlib==1.3.0
 requests-toolbelt==0.9.1
 requests==2.23.0
 requestsexceptions==1.4.0
-rfc3986==1.3.2
+rfc3986==1.4.0
 routes==2.4.1
 rsa==4.0
 ruamel.ordereddict==0.4.14 ; platform_python_implementation == 'CPython' and python_version <= '2.7'
@@ -172,15 +172,15 @@ simplejson==3.17.0
 six==1.11.0
 social-auth-core[openidconnect]==3.1.0+gx0
 sqlalchemy-migrate==0.13.0
-sqlalchemy-utils==0.36.1
-sqlalchemy==1.3.13
+sqlalchemy-utils==0.36.3
+sqlalchemy==1.3.16
 sqlparse==0.3.1
 stevedore==1.32.0
 subprocess32==3.5.4 ; python_version < '3.0'
 svgwrite==1.3.1
 tempita==0.5.2
 tenacity==4.12.0
-typing-extensions==3.7.4.1
+typing-extensions==3.7.4.2
 typing==3.7.4.1 ; python_version < '3.5'
 tzlocal==2.0.0
 unicodecsv==0.14.1 ; python_version < '3.0'
@@ -188,9 +188,9 @@ uritemplate==3.0.1
 urllib3==1.25.8
 vine==1.3.0
 warlock==1.3.3
-wcwidth==0.1.8
+wcwidth==0.1.9
 webencodings==0.5.1
 webob==1.8.6
 whoosh==2.7.4
-wrapt==1.12.0
+wrapt==1.12.1
 zipp==1.2.0
diff --git a/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
index 0a1aafdbde5a..aa48e32250eb 100644
--- a/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
@@ -1,7 +1,7 @@
 -i https://pypi.python.org/simple
 configparser==4.0.2 ; python_version < '3.2'
 entrypoints==0.3
-enum34==1.1.9 ; python_version < '3.4'
+enum34==1.1.10 ; python_version < '3.4'
 flake8-import-order==0.18.1
 flake8==3.7.9
 functools32==3.2.3.post2 ; python_version < '3.2'

From 1b1aa4a9e84a1140307c7608a308d533cbfb5607 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 17 Mar 2020 07:43:06 -0400
Subject: [PATCH 771/853] Fix test_fail_job_tool_unavailable.py for updated
 gxformat2 syntax.

---
 test/integration/test_fail_job_tool_unavailable.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/test/integration/test_fail_job_tool_unavailable.py b/test/integration/test_fail_job_tool_unavailable.py
index 1b53845441a3..da638369e255 100644
--- a/test/integration/test_fail_job_tool_unavailable.py
+++ b/test/integration/test_fail_job_tool_unavailable.py
@@ -27,20 +27,21 @@ def test_fail_job_when_tool_unavailable(self):
         self.workflow_populator.run_workflow("""
 class: GalaxyWorkflow
 steps:
-  - label: sleep
+  sleep:
     run:
       class: GalaxyTool
       command: sleep 20s && echo 'hello world 2' > '$output1'
       outputs:
         output1:
           format: txt
-  - tool_id: cat1
+  cat:
+    tool_id: cat1
     state:
       input1:
-        $link: sleep#output1
+        $link: sleep/output1
       queries:
         input2:
-          $link: sleep#output1
+          $link: sleep/output1
 """, history_id=self.history_id, assert_ok=False, wait=False)
         # Wait until workflow is fully scheduled, otherwise can't test effect of removing tool from queued job
         time.sleep(10)

From 74a27f3de0a2b7a83472cc07cc42e0f1382ac8b7 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 17 Mar 2020 15:14:33 +0100
Subject: [PATCH 772/853] Move docker image build to ubuntu 18.04, drop unused
 stuff

---
 .ci/jenkins/api-py3/run_tests.sh         |  3 ---
 .ci/jenkins/framework-py3/run_tests.sh   |  3 ---
 .ci/jenkins/integration-py3/run_tests.sh |  3 ---
 .ci/jenkins/main-tools-py3/run_tests.sh  |  3 ---
 .ci/jenkins/selenium-py3/run_tests.sh    | 26 ---------------------
 run_tests.sh                             |  4 ++--
 test/docker/base/Dockerfile              | 29 ++++--------------------
 test/docker/base/ansible_vars.yml        |  3 ++-
 test/docker/base/run_test_wrapper.sh     |  2 +-
 9 files changed, 9 insertions(+), 67 deletions(-)
 delete mode 100755 .ci/jenkins/api-py3/run_tests.sh
 delete mode 100755 .ci/jenkins/framework-py3/run_tests.sh
 delete mode 100755 .ci/jenkins/integration-py3/run_tests.sh
 delete mode 100755 .ci/jenkins/main-tools-py3/run_tests.sh
 delete mode 100755 .ci/jenkins/selenium-py3/run_tests.sh

diff --git a/.ci/jenkins/api-py3/run_tests.sh b/.ci/jenkins/api-py3/run_tests.sh
deleted file mode 100755
index 24790d0b7206..000000000000
--- a/.ci/jenkins/api-py3/run_tests.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --skip_flakey_fails -api "$@"
diff --git a/.ci/jenkins/framework-py3/run_tests.sh b/.ci/jenkins/framework-py3/run_tests.sh
deleted file mode 100755
index f8bfe97335d6..000000000000
--- a/.ci/jenkins/framework-py3/run_tests.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --framework "$@"
diff --git a/.ci/jenkins/integration-py3/run_tests.sh b/.ci/jenkins/integration-py3/run_tests.sh
deleted file mode 100755
index ffc6c87e98cf..000000000000
--- a/.ci/jenkins/integration-py3/run_tests.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-DOCKER_RUN_EXTRA_ARGS="--privileged" ./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --integration "$@"
diff --git a/.ci/jenkins/main-tools-py3/run_tests.sh b/.ci/jenkins/main-tools-py3/run_tests.sh
deleted file mode 100755
index 442b15cdf2d2..000000000000
--- a/.ci/jenkins/main-tools-py3/run_tests.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc -main "$@"
diff --git a/.ci/jenkins/selenium-py3/run_tests.sh b/.ci/jenkins/selenium-py3/run_tests.sh
deleted file mode 100755
index 827151835f64..000000000000
--- a/.ci/jenkins/selenium-py3/run_tests.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/bin/bash
-
-# Enable retries on tests to reduce chances of transient failures.
-: ${GALAXY_TEST_SELENIUM_RETRIES:=1}
-
-# If in Jenkins environment, use it for artifacts.
-if [ -n "$BUILD_NUMBER" ];
-then
-    : ${GALAXY_TEST_ERRORS_DIRECTORY:=${BUILD_NUMBER}-test-errors}
-    : ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=${BUILD_NUMBER}-test-screenshots}
-else
-    : ${GALAXY_TEST_ERRORS_DIRECTORY:=database/test-errors}
-    : ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=database/test-screenshots}
-fi
-
-mkdir -p "$GALAXY_TEST_ERRORS_DIRECTORY"
-mkdir -p "$GALAXY_TEST_SCREENSHOTS_DIRECTORY"
-
-mkdir -p ~/.jenkins-yarn-cache
-YARN_CACHE_FOLDER=~/.jenkins-yarn-cache
-
-# Start Selenium server in the test Docker container.
-DOCKER_RUN_EXTRA_ARGS="${DOCKER_RUN_EXTRA_ARGS} --shm-size=2g -v $YARN_CACHE_FOLDER:$YARN_CACHE_FOLDER -e YARN_CACHE_FOLDER=$YARN_CACHE_FOLDER -e USE_SELENIUM=1 -e GALAXY_TEST_SELENIUM_RETRIES=${GALAXY_TEST_SELENIUM_RETRIES} -e GALAXY_TEST_ERRORS_DIRECTORY=${GALAXY_TEST_ERRORS_DIRECTORY} -e GALAXY_TEST_SCREENSHOTS_DIRECTORY=${GALAXY_TEST_SCREENSHOTS_DIRECTORY}"
-export DOCKER_RUN_EXTRA_ARGS
-
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --skip_flakey_fails --selenium "$@"
diff --git a/run_tests.sh b/run_tests.sh
index 7e6bdb798f2b..1a1336346a75 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -269,7 +269,7 @@ exists() {
     type "$1" >/dev/null 2>/dev/null
 }
 
-DOCKER_DEFAULT_IMAGE='galaxy/testing-base:19.05.0'
+DOCKER_DEFAULT_IMAGE='galaxy/testing-base:20.05.00'
 
 test_script="./scripts/functional_tests.py"
 report_file="run_functional_tests.html"
@@ -312,7 +312,7 @@ then
     echo "Docker version:"
     docker --version
     echo "Launching docker container for testing with extra args ${DOCKER_RUN_EXTRA_ARGS}..."
-    name=$(python -c 'import re; import uuid; print re.sub("-", "", str(uuid.uuid4()))')
+    name=$(python -c 'import re; import uuid; print(re.sub("-", "", str(uuid.uuid4())))')
     # Create a cache dir for pip, so it has the right owner
     DOCKER_PIP_CACHE_DIR="$HOME"/.cache/docker_galaxy_pip
     mkdir -p "$DOCKER_PIP_CACHE_DIR"
diff --git a/test/docker/base/Dockerfile b/test/docker/base/Dockerfile
index af8c07fc0307..758ccad7c9b4 100644
--- a/test/docker/base/Dockerfile
+++ b/test/docker/base/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:16.04
+FROM ubuntu:18.04
 LABEL maintainer="John Chilton <jmchilton@gmail.com>"
 
 ARG CHROME_VERSION="google-chrome-beta"
@@ -11,8 +11,6 @@ ENV DEBIAN_FRONTEND=noninteractive \
     POSTGRES_MAJOR=9.5 \
     GALAXY_ROOT=/galaxy \
     GALAXY_VIRTUAL_ENV=/galaxy_venv \
-    GALAXY_VIRTUAL_ENV_2=/galaxy_venv \
-    GALAXY_VIRTUAL_ENV_3=/galaxy_venv3 \
     LC_ALL=C.UTF-8
 
 # Pre-install a bunch of packages to speed up ansible steps.
@@ -20,13 +18,10 @@ RUN apt-get update -y && apt-get install -y software-properties-common apt-trans
     apt-add-repository -y ppa:ansible/ansible && \
     curl -s https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add - && \
     echo "deb http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google-chrome.list && \
-    curl -s http://neuro.debian.net/lists/xenial.us-ca.full > /etc/apt/sources.list.d/neurodebian.sources.list && \
-    apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 && \
     apt-get update -y && \
     apt-get install -y --no-install-recommends postgresql postgresql-client ansible wget \
             python3-dev \
             git-core \
-            python-prettytable python-virtualenv python-pip \
             rsync swig sysstat unzip \
             openssl \
             bzip2 \
@@ -37,9 +32,6 @@ RUN apt-get update -y && apt-get install -y software-properties-common apt-trans
             locales \
             xvfb \
             ${CHROME_VERSION:-google-chrome-stable} \
-            ffmpeg \
-            bcftools \
-            singularity-container \
             libnss3 libgconf-2-4 && \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
@@ -69,24 +61,11 @@ RUN mkdir /etc/galaxy && cd /tmp/ansible && mkdir roles && \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 RUN cd $GALAXY_ROOT && \
-    virtualenv -p /usr/bin/python3 $GALAXY_VIRTUAL_ENV_3 && \
-    for VENV in $GALAXY_VIRTUAL_ENV_2 $GALAXY_VIRTUAL_ENV_3; do \
-        GALAXY_VIRTUAL_ENV=$VENV ./scripts/common_startup.sh --dev-wheels && \
-        $VENV/bin/pip install psycopg2-binary; done && \
+    virtualenv -p /usr/bin/python3 $GALAXY_VIRTUAL_ENV && \
+        ./scripts/common_startup.sh --dev-wheels && \
+        $GALAXY_VIRTUAL_ENV/bin/pip install psycopg2-binary && \
     rm -rf ~/.cache/pip
 
-RUN cd $GALAXY_ROOT && \
-    echo "Prepopulating postgres database" && \
-    su -c '/usr/lib/postgresql/${POSTGRES_MAJOR}/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres && \
-    sleep 3 && \
-    GALAXY_CONFIG_DATABASE_CONNECTION="postgresql://root@localhost:5930/galaxy" bash create_db.sh && \
-    echo "Prepopulating sqlite database" && \
-    GALAXY_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/galaxy.sqlite" bash create_db.sh && \
-    echo "Prepopulating toolshed postgres database" && \
-    TOOL_SHED_CONFIG_DATABASE_CONNECTION="postgresql://root@localhost:5930/toolshed" bash create_db.sh tool_shed && \
-    echo "Prepopulating toolshed sqlite database" && \
-    TOOL_SHED_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/toolshed.sqlite" bash create_db.sh tool_shed
-
 #========================================
 # Add Selenium user with passwordless sudo
 #========================================
diff --git a/test/docker/base/ansible_vars.yml b/test/docker/base/ansible_vars.yml
index d92d87f6f419..027365d086ed 100644
--- a/test/docker/base/ansible_vars.yml
+++ b/test/docker/base/ansible_vars.yml
@@ -17,7 +17,7 @@ galaxy_db_log: /tmp/pSQL.log
 psql_galaxyftp_password: ignoredthis
 galaxy_config_file: "{{ galaxy_server_dir }}/config/galaxy.ini"
 configure_docker: no
-postgresql_bin_dir: /usr/lib/postgresql/9.5/bin
+postgresql_bin_dir: /usr/lib/postgresql/10/bin
 galaxy_manage_database: no
 # avoid some packages unneeded packages install by ansible-galaxy-os
 install_maintainance_packages: false
@@ -25,6 +25,7 @@ galaxy_user_name: "root"
 galaxy_extras_install_packages: true
 galaxy_job_conf_path: "/etc/galaxy/job_conf.xml"
 galaxy_build_client: no
+galaxy_virtualenv_python: python3
 
 galaxy_web_processes: 1
 galaxy_handler_processes: 2
diff --git a/test/docker/base/run_test_wrapper.sh b/test/docker/base/run_test_wrapper.sh
index 46295549ef0d..4fb5e770ed35 100644
--- a/test/docker/base/run_test_wrapper.sh
+++ b/test/docker/base/run_test_wrapper.sh
@@ -25,7 +25,7 @@ chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "${GALAXY_VIRTUAL_ENV:-/galaxy_venv
 if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ];
 then
     echo "Starting postgres and then sleeping for 3 seconds"
-    su -c '/usr/lib/postgresql/9.5/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres
+    su -c '/usr/lib/postgresql/10/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres
     sleep 3
     GALAXY_TEST_INSTALL_DB_MERGED="true"
     GALAXY_TEST_DBURI="postgresql://root@localhost:5930/galaxy?client_encoding=utf8"

From 780bc0560cd61fff7d7e61bc56feb8ffab6c8f7e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 17 Mar 2020 18:46:20 +0100
Subject: [PATCH 773/853] Add temporary symlinks, need to update jenkins after
 merging the PR

---
 .ci/jenkins/api-py3         | 1 +
 .ci/jenkins/framework-py3   | 1 +
 .ci/jenkins/integration-py3 | 1 +
 .ci/jenkins/main-tools-py3  | 1 +
 .ci/jenkins/selenium-py3    | 1 +
 5 files changed, 5 insertions(+)
 create mode 120000 .ci/jenkins/api-py3
 create mode 120000 .ci/jenkins/framework-py3
 create mode 120000 .ci/jenkins/integration-py3
 create mode 120000 .ci/jenkins/main-tools-py3
 create mode 120000 .ci/jenkins/selenium-py3

diff --git a/.ci/jenkins/api-py3 b/.ci/jenkins/api-py3
new file mode 120000
index 000000000000..9e5bfb42d239
--- /dev/null
+++ b/.ci/jenkins/api-py3
@@ -0,0 +1 @@
+api
\ No newline at end of file
diff --git a/.ci/jenkins/framework-py3 b/.ci/jenkins/framework-py3
new file mode 120000
index 000000000000..e3939d229ced
--- /dev/null
+++ b/.ci/jenkins/framework-py3
@@ -0,0 +1 @@
+framework
\ No newline at end of file
diff --git a/.ci/jenkins/integration-py3 b/.ci/jenkins/integration-py3
new file mode 120000
index 000000000000..c0bfe0d4f942
--- /dev/null
+++ b/.ci/jenkins/integration-py3
@@ -0,0 +1 @@
+integration
\ No newline at end of file
diff --git a/.ci/jenkins/main-tools-py3 b/.ci/jenkins/main-tools-py3
new file mode 120000
index 000000000000..49589fdd3a88
--- /dev/null
+++ b/.ci/jenkins/main-tools-py3
@@ -0,0 +1 @@
+main-tools
\ No newline at end of file
diff --git a/.ci/jenkins/selenium-py3 b/.ci/jenkins/selenium-py3
new file mode 120000
index 000000000000..954f0db0bc08
--- /dev/null
+++ b/.ci/jenkins/selenium-py3
@@ -0,0 +1 @@
+selenium
\ No newline at end of file

From 0a2ed24a9df3f69c9a2b235d3ff3fe0cd8435549 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 17 Mar 2020 20:30:59 +0100
Subject: [PATCH 774/853] Skip migrations

---
 test/docker/base/run_test_wrapper.sh | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/test/docker/base/run_test_wrapper.sh b/test/docker/base/run_test_wrapper.sh
index 4fb5e770ed35..0d648759c670 100644
--- a/test/docker/base/run_test_wrapper.sh
+++ b/test/docker/base/run_test_wrapper.sh
@@ -16,10 +16,9 @@ echo "Creating galaxy group with gid $GALAXY_TEST_UID - it may already exist and
 groupadd -r galaxy -g "$GALAXY_TEST_UID" | true
 echo "Creating galaxy user with uid $GALAXY_TEST_UID - it may already exist and this is fine."
 useradd -u $GALAXY_TEST_UID -r -g galaxy -d /home/galaxy -c "Galaxy User" galaxy -s /bin/bash | true
-mkdir -p /home/galaxy/.singularity
 echo "Setting galaxy user password - the operation may fail."
 echo "galaxy:galaxy" | chpasswd | true
-chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "${GALAXY_VIRTUAL_ENV:-/galaxy_venv}" /home/galaxy/
+chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "${GALAXY_VIRTUAL_ENV:-/galaxy_venv}"
 
 : ${GALAXY_TEST_DATABASE_TYPE:-"postgres"}
 if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ];
@@ -49,16 +48,9 @@ cd /galaxy
 
 : ${GALAXY_VIRTUAL_ENV:=.venv}
 
-HOME=/home/galaxy
-
 echo "Running common startup for updated dependencies (if any)"
 sudo -E -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh --dev-wheels || { echo "common_startup.sh failed"; exit 1; }
 
-echo "Upgrading test database..."
-sudo -E -u "#${GALAXY_TEST_UID}" GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI" sh manage_db.sh upgrade
-echo "Upgrading tool shed database... $TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION"
-sudo -E -u "#${GALAXY_TEST_UID}" TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION="$TOOL_SHED_TEST_DBURI" sh manage_db.sh upgrade tool_shed
-
 # Ensure Selenium is running before starting tests.
 if [ ! -z "$USE_SELENIUM" ];
 then

From a5c9b82edc6e916187fe53ffd341feffc249b18b Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 23 Mar 2020 00:30:56 +0000
Subject: [PATCH 775/853] Fix API tests for updated gxformat2 syntax

---
 lib/galaxy_test/api/embed_test_1.gxwf.yml     |  4 +-
 .../api/test_workflow_extraction.py           | 12 +--
 lib/galaxy_test/api/test_workflows.py         | 76 +++++--------------
 .../api/test_workflows_from_yaml.py           |  4 +-
 lib/galaxy_test/base/workflow_fixtures.py     |  8 +-
 5 files changed, 31 insertions(+), 73 deletions(-)

diff --git a/lib/galaxy_test/api/embed_test_1.gxwf.yml b/lib/galaxy_test/api/embed_test_1.gxwf.yml
index 76461dff6fd2..e43f9426582e 100644
--- a/lib/galaxy_test/api/embed_test_1.gxwf.yml
+++ b/lib/galaxy_test/api/embed_test_1.gxwf.yml
@@ -14,7 +14,7 @@ steps:
   - tool_id: cat1
     state:
       input1:
-        $link: first_cat#out_file1
+        $link: first_cat/out_file1
       queries:
         - input2:
-            $link: embed1#output1
+            $link: embed1/output1
diff --git a/lib/galaxy_test/api/test_workflow_extraction.py b/lib/galaxy_test/api/test_workflow_extraction.py
index 048f20aa237d..6e94c1839d2b 100644
--- a/lib/galaxy_test/api/test_workflow_extraction.py
+++ b/lib/galaxy_test/api/test_workflow_extraction.py
@@ -228,7 +228,7 @@ def test_subcollection_mapping(self):
   - tool_id: cat_collection
     state:
       input1:
-        $link: noop#out_file1
+        $link: noop/out_file1
 test_data:
   text_input1:
     type: "list:paired"
@@ -274,11 +274,11 @@ def test_extract_workflow_with_output_collections(self):
     tool_id: collection_split_on_column
     state:
       input1:
-        $link: cat_inputs#out_file1
+        $link: cat_inputs/out_file1
   - tool_id: cat_list
     state:
       input1:
-        $link: split_up#split_output
+        $link: split_up/split_output
 test_data:
   text_input1: "samp1\t10.0\nsamp2\t20.0\n"
   text_input2: "samp1\t30.0\nsamp2\t40.0\n"
@@ -316,16 +316,16 @@ def test_extract_with_mapped_output_collections(self):
     tool_id: collection_creates_pair
     state:
       input1:
-        $link: cat_inputs#out_file1
+        $link: cat_inputs/out_file1
   - label: cat_pairs
     tool_id: cat_collection
     state:
       input1:
-        $link: pair_off#paired_output
+        $link: pair_off/paired_output
   - tool_id: cat_list
     state:
       input1:
-        $link: cat_pairs#out_file1
+        $link: cat_pairs/out_file1
 test_data:
   text_input1:
     type: list
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index bb0a662896a1..d4e2359c8de6 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -40,47 +40,6 @@
 from ._framework import ApiTestCase
 
 
-NESTED_WORKFLOW_AUTO_LABELS_LEGACY_SYNTAX = """
-class: GalaxyWorkflow
-inputs:
-  outer_input: data
-outputs:
-  outer_output:
-    outputSource: second_cat/out_file1
-steps:
-  first_cat:
-    tool_id: cat1
-    in:
-      input1: outer_input
-  nested_workflow:
-    run:
-      class: GalaxyWorkflow
-      inputs:
-        - id: inner_input
-      outputs:
-        - source: 1#out_file1
-      steps:
-        random:
-          tool_id: random_lines1
-          state:
-            num_lines: 1
-            input:
-              $link: inner_input
-            seed_source:
-              seed_source_selector: set_seed
-              seed: asdf
-    in:
-      inner_input: first_cat/out_file1
-  second_cat:
-    tool_id: cat1
-    state:
-      input1:
-        $link: nested_workflow#1:out_file1
-      queries:
-        - input2:
-            $link: nested_workflow#1:out_file1
-"""
-
 NESTED_WORKFLOW_AUTO_LABELS_MODERN_SYNTAX = """
 class: GalaxyWorkflow
 inputs:
@@ -487,10 +446,10 @@ def test_import_export_dynamic(self):
   - tool_id: cat1
     state:
       input1:
-        $link: first_cat#out_file1
+        $link: first_cat/out_file1
       queries:
         input2:
-          $link: embed1#output1
+          $link: embed1/output1
 test_data:
   input1: "hello world"
 """)
@@ -832,12 +791,12 @@ def test_workflow_resume_from_failed_step(self):
         inner_cond:
           cond_param_inner: true
           input1:
-            $link: 0#out_file1
+            $link: 0/out_file1
   cat:
     tool_id: cat1
     in:
-      input1: identifier#output1
-      queries_0|input2: identifier#output1
+      input1: identifier/output1
+      queries_0|input2: identifier/output1
 """)
         with self.dataset_populator.test_history() as history_id:
             invocation_id = self.__invoke_workflow(history_id, workflow_id)
@@ -873,11 +832,11 @@ def test_workflow_resume_from_failed_step_with_hdca_input(self):
   list_in_list_out:
     tool_id: collection_creates_list
     in:
-      input1: job_props#list_output
+      input1: job_props/list_output
   identifier:
     tool_id: identifier_collection
     in:
-      input1: list_in_list_out#list_output
+      input1: list_in_list_out/list_output
 """)
         with self.dataset_populator.test_history() as history_id:
             invocation_id = self.__invoke_workflow(history_id, workflow_id)
@@ -1220,8 +1179,7 @@ def run_test(workflow_text):
                     "chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n",
                     content)
 
-        for workflow_text in [NESTED_WORKFLOW_AUTO_LABELS_LEGACY_SYNTAX, NESTED_WORKFLOW_AUTO_LABELS_MODERN_SYNTAX]:
-            run_test(workflow_text)
+        run_test(NESTED_WORKFLOW_AUTO_LABELS_MODERN_SYNTAX)
 
     @skip_without_tool("cat1")
     @skip_without_tool("collection_paired_test")
@@ -1274,7 +1232,7 @@ def test_workflow_flatten(self):
     tool_id: '__FLATTEN__'
     state:
       input:
-        $link: nested#list_output
+        $link: nested/list_output
       join_identifier: '-'
 """, test_data={}, history_id=history_id)
             details = self.dataset_populator.get_history_collection_details(history_id, hid=14)
@@ -1400,7 +1358,7 @@ def test_filter_failed_mapping(self):
     tool_id: "__FILTER_FAILED_DATASETS__"
     state:
       input:
-        $link: mixed_collection#out_file1
+        $link: mixed_collection/out_file1
 
   cat:
     tool_id: cat1
@@ -1870,7 +1828,7 @@ def test_empty_list_mapping(self):
     state:
       num_lines: 2
       input:
-        $link: empty_list#output
+        $link: empty_list/output
       seed_source:
         seed_source_selector: set_seed
         seed: asdf
@@ -1953,7 +1911,7 @@ def test_empty_list_reduction(self):
     state:
       num_lines: 2
       input:
-        $link: empty_list#output
+        $link: empty_list/output
       seed_source:
         seed_source_selector: set_seed
         seed: asdf
@@ -2388,7 +2346,7 @@ def test_run_with_numeric_input_connection(self):
   state:
     floattest: 3.14
     inttest:
-      $link: forty_two#out1
+      $link: forty_two/out1
 test_data: {}
 """, history_id=history_id)
 
@@ -2417,7 +2375,7 @@ def test_expression_tool_map_over(self):
 - label: consume_expression_parameter
   tool_id: validation_default
   in:
-    input1: param_out#text_param
+    input1: param_out/text_param
   outputs:
     out_file1:
       rename: "replaced_param_collection"
@@ -3272,7 +3230,7 @@ def test_run_remove_tag_on_collection_output(self):
   create_pair:
     tool_id: collection_creates_pair
     in:
-      input1: first_cat#out_file1
+      input1: first_cat/out_file1
     outputs:
       paired_output:
         remove_tags:
@@ -4103,10 +4061,10 @@ def test_import_export_dynamic_tools(self):
   - tool_id: cat1
     state:
       input1:
-        $link: first_cat#out_file1
+        $link: first_cat/out_file1
       queries:
       - input2:
-          $link: embed1#output1
+          $link: embed1/output1
 test_data:
   input1: "hello world"
 """)
diff --git a/lib/galaxy_test/api/test_workflows_from_yaml.py b/lib/galaxy_test/api/test_workflows_from_yaml.py
index 73e0c101af6c..c8dfe57c8b29 100644
--- a/lib/galaxy_test/api/test_workflows_from_yaml.py
+++ b/lib/galaxy_test/api/test_workflows_from_yaml.py
@@ -296,10 +296,10 @@ def test_workflow_embed_tool(self):
   - tool_id: cat1
     state:
       input1:
-        $link: first_cat#out_file1
+        $link: first_cat/out_file1
       queries:
         - input2:
-            $link: embed1#output1
+            $link: embed1/output1
 test_data:
   input1: "hello world"
 """, history_id=history_id)
diff --git a/lib/galaxy_test/base/workflow_fixtures.py b/lib/galaxy_test/base/workflow_fixtures.py
index 33651b93ace6..f51af2b98e7d 100644
--- a/lib/galaxy_test/base/workflow_fixtures.py
+++ b/lib/galaxy_test/base/workflow_fixtures.py
@@ -143,11 +143,11 @@
   - tool_id: collection_paired_test
     state:
       f1:
-        $link: 1#paired_output
+        $link: 1/paired_output
   - tool_id: cat_list
     state:
       input1:
-        $link: 2#out1
+        $link: 2/out1
 """
 
 
@@ -175,7 +175,7 @@
     state:
       num_lines: 1
       input:
-        $link: apply#output
+        $link: apply/output
       seed_source:
         seed_source_selector: set_seed
         seed: asdf
@@ -279,7 +279,7 @@
         inner_input: data
       outputs:
         workflow_output:
-          outputSource: random_lines#out_file1
+          outputSource: random_lines/out_file1
       steps:
         - tool_id: random_lines1
           label: random_lines

From 38f93ba318df4636b33aac244aa8d65aa792a443 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sun, 12 Apr 2020 22:02:15 +0100
Subject: [PATCH 776/853] Remove unnecessary pyparsing import

Not needed any more after commit 413f8cee135c2d05a5b44344926cc174287f8437 .
---
 lib/tool_shed/test/base/twilltestcase.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 569b70b7cdd6..3786eb2dfa34 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -8,9 +8,6 @@
 import time
 from json import loads
 
-# Be sure to use Galaxy's vanilla pyparsing instead of the older version
-# imported by twill.
-import pyparsing  # noqa: F401
 import requests
 import twill.commands as tc
 from mercurial import commands, hg, ui

From 9eae2c58cf771294da776834a6caf6882767cdb9 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 13 Apr 2020 00:51:11 +0100
Subject: [PATCH 777/853] Always set HOME to the target user's dir when calling
 `sudo -E`

---
 .ci/jenkins/selenium-compose/run_galaxy.bash | 5 ++---
 test/docker/base/run_test_wrapper.sh         | 6 +++---
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/.ci/jenkins/selenium-compose/run_galaxy.bash b/.ci/jenkins/selenium-compose/run_galaxy.bash
index aaf10b77401a..c16901324c14 100755
--- a/.ci/jenkins/selenium-compose/run_galaxy.bash
+++ b/.ci/jenkins/selenium-compose/run_galaxy.bash
@@ -20,8 +20,7 @@ virtualenv "$GALAXY_VIRTUAL_ENV"
 chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "$GALAXY_VIRTUAL_ENV"
 
 cd /galaxy
-HOME=/galaxy
-sudo -E -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
+sudo -E -H -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
 
 echo "Waiting for postgres to become available"
 while ! nc -z postgres 5432;
@@ -34,7 +33,7 @@ echo "Creating postgres database for Galaxy"
 createdb -w -U postgres -h postgres galaxy
 
 echo "Starting and waiting for Galaxy daemon(s)"
-sudo -E -u "#${GALAXY_TEST_UID}" GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait
+sudo -E -H -u "#${GALAXY_TEST_UID}" GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait
 
 echo "Galaxy daemon ready, monitoring Galaxy logs"
 tail -f "$GALAXY_ROOT/main.log"
diff --git a/test/docker/base/run_test_wrapper.sh b/test/docker/base/run_test_wrapper.sh
index 0d648759c670..4ac43222424f 100644
--- a/test/docker/base/run_test_wrapper.sh
+++ b/test/docker/base/run_test_wrapper.sh
@@ -4,7 +4,7 @@ set -e
 if [ ! -z "$USE_SELENIUM" ];
 then
     # Start Selenium.
-    sudo -H -E -u seluser /opt/bin/entry_point.sh &
+    sudo -E -H -u seluser /opt/bin/entry_point.sh &
 fi
 
 echo "Deleting galaxy user - it may not exist and this is fine."
@@ -49,7 +49,7 @@ cd /galaxy
 : ${GALAXY_VIRTUAL_ENV:=.venv}
 
 echo "Running common startup for updated dependencies (if any)"
-sudo -E -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh --dev-wheels || { echo "common_startup.sh failed"; exit 1; }
+sudo -E -H -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh --dev-wheels || { echo "common_startup.sh failed"; exit 1; }
 
 # Ensure Selenium is running before starting tests.
 if [ ! -z "$USE_SELENIUM" ];
@@ -70,7 +70,7 @@ fi
 
 if [ -z "$GALAXY_NO_TESTS" ];
 then
-    sudo -E -u "#${GALAXY_TEST_UID}" sh run_tests.sh --skip-common-startup $@
+    sudo -E -H -u "#${GALAXY_TEST_UID}" sh run_tests.sh --skip-common-startup $@
 else
     GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI"
     TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION="$TOOL_SHED_TEST_DBURI"

From cbc84dda0daeabeaa6f8124bc5e5038d479c74b3 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 13 Apr 2020 13:12:22 +0200
Subject: [PATCH 778/853] Use popover counter

---
 client/galaxy/scripts/components/Workflow/Editor/Node.vue | 6 +++++-
 client/galaxy/scripts/mvc/workflow/workflow-manager.js    | 3 +++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index caacaa8d8d77..0acf23edeb73 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -82,6 +82,10 @@ export default {
             type: Object,
             default: null,
         },
+        nodeId: {
+            type: String,
+            default: "",
+        },
     },
     computed: {
         iconClass() {
@@ -92,7 +96,7 @@ export default {
             return null;
         },
         popoverId() {
-            return `popover-${this.id}-${this._uid}`;
+            return `popover-${this.nodeId}`;
         },
         canClone() {
             return this.type != "subworkflow";
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index 1bbcc0f94aa8..1ec548ff0b13 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -18,6 +18,7 @@ class Workflow extends EventEmitter {
         this.has_changes = false;
         this.workflowOutputLabels = {};
         this.workflow_version = 0;
+        this.popover_counter = 0;
 
         // Canvas overview management
         this.canvas_manager = new WorkflowCanvas(this, $("#canvas-viewport"), $("#overview-container"));
@@ -142,8 +143,10 @@ class Workflow extends EventEmitter {
             type: type,
             title: title_text,
             node: node,
+            nodeId: this.popover_counter
         });
 
+        this.popover_counter++;
         // Set initial scroll position
         $f.css("left", $(window).scrollLeft() + 20);
         $f.css("top", $(window).scrollTop() + 20);

From 060d83294f05a40bad86955262347bd2c86a7bc4 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Mon, 13 Apr 2020 13:33:23 +0200
Subject: [PATCH 779/853] Fix prettier

---
 client/galaxy/scripts/mvc/workflow/workflow-manager.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index 1ec548ff0b13..241b9646f81f 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -143,7 +143,7 @@ class Workflow extends EventEmitter {
             type: type,
             title: title_text,
             node: node,
-            nodeId: this.popover_counter
+            nodeId: this.popover_counter,
         });
 
         this.popover_counter++;

From 51c383453f682363ea8b0d01c7f2b4b50bc93469 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Tue, 7 Jan 2020 16:33:33 -0500
Subject: [PATCH 780/853] add basic data source tool for SRA testing

---
 tools/data_source/sra.xml | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 tools/data_source/sra.xml

diff --git a/tools/data_source/sra.xml b/tools/data_source/sra.xml
new file mode 100644
index 000000000000..dae4a089c738
--- /dev/null
+++ b/tools/data_source/sra.xml
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<!--
+    If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
+    the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
+    initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
+-->
+
+<tool name="SRA" id="sra_source" tool_type="data_source" version="1.0.0">
+    <description>server</description>
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <inputs action="https://www.ncbi.nlm.nih.gov/Traces/study" check_values="false" method="get">
+        <display>go to SRA server $GALAXY_URL</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=sra_source" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
+        <request_param galaxy_name="URL" remote_name="URL" missing="" />
+        <request_param galaxy_name="name" remote_name="name" missing="SRA query" />
+        <request_param galaxy_name="info" remote_name="info" missing="SRA TEST" />
+        <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
+        </request_param>
+    </request_param_translation>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+    <citations>
+        <citation type="doi">10.1093/database/bar011</citation>
+        <citation type="doi">10.1101/gr.229102</citation>
+    </citations>
+</tool>
+

From e367681ce00d76ff60a7f438ebd88a963c79c624 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 14 Apr 2020 15:20:04 +0200
Subject: [PATCH 781/853] Update url for sra tool to
 https://www.ncbi.nlm.nih.gov/sra

---
 tools/data_source/sra.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/data_source/sra.xml b/tools/data_source/sra.xml
index dae4a089c738..d0c5fd5fed97 100644
--- a/tools/data_source/sra.xml
+++ b/tools/data_source/sra.xml
@@ -8,7 +8,7 @@
 <tool name="SRA" id="sra_source" tool_type="data_source" version="1.0.0">
     <description>server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
-    <inputs action="https://www.ncbi.nlm.nih.gov/Traces/study" check_values="false" method="get">
+    <inputs action="https://www.ncbi.nlm.nih.gov/sra" check_values="false" method="get">
         <display>go to SRA server $GALAXY_URL</display>
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=sra_source" />
     </inputs>

From 2994f515652f23ce439a03d95e8f595e3d839390 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 14 Apr 2020 15:33:02 +0200
Subject: [PATCH 782/853] Drop unnecessary parameters, quote tool, modernize

---
 tools/data_source/sra.xml | 23 +++--------------------
 1 file changed, 3 insertions(+), 20 deletions(-)

diff --git a/tools/data_source/sra.xml b/tools/data_source/sra.xml
index d0c5fd5fed97..f0b791ef1664 100644
--- a/tools/data_source/sra.xml
+++ b/tools/data_source/sra.xml
@@ -1,28 +1,12 @@
-<?xml version="1.0"?>
-<!--
-    If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
-    the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
-    initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
--->
-
-<tool name="SRA" id="sra_source" tool_type="data_source" version="1.0.0">
+<tool name="SRA" id="sra_source" tool_type="data_source" version="1.0.0" profile="16.04">
     <description>server</description>
-    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <command>python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit</command>
     <inputs action="https://www.ncbi.nlm.nih.gov/sra" check_values="false" method="get">
         <display>go to SRA server $GALAXY_URL</display>
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=sra_source" />
     </inputs>
-    <request_param_translation>
-        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
-        <request_param galaxy_name="URL" remote_name="URL" missing="" />
-        <request_param galaxy_name="name" remote_name="name" missing="SRA query" />
-        <request_param galaxy_name="info" remote_name="info" missing="SRA TEST" />
-        <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
-        </request_param>
-    </request_param_translation>
-    <uihints minwidth="800"/>
     <outputs>
-        <data name="output" format="txt" />
+        <data name="output" format="csv" />
     </outputs>
     <options sanitize="False" refresh="True"/>
     <citations>
@@ -30,4 +14,3 @@
         <citation type="doi">10.1101/gr.229102</citation>
     </citations>
 </tool>
-

From 409bab500993cdc8819614788a4dc09fc6b3e66f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 14 Apr 2020 15:35:37 +0200
Subject: [PATCH 783/853] Enable sra tool by default

---
 lib/galaxy/config/sample/tool_conf.xml.sample | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/config/sample/tool_conf.xml.sample b/lib/galaxy/config/sample/tool_conf.xml.sample
index fd6f80066f57..286a0c9f1c2d 100644
--- a/lib/galaxy/config/sample/tool_conf.xml.sample
+++ b/lib/galaxy/config/sample/tool_conf.xml.sample
@@ -5,6 +5,7 @@
     <tool file="data_source/ucsc_tablebrowser.xml" />
     <!-- <tool file="data_source/ucsc_tablebrowser_test.xml" /> -->
     <tool file="data_source/ucsc_tablebrowser_archaea.xml" />
+    <tool file="data_source/sra.xml" />
     <tool file="data_source/ebi_sra.xml" />
     <tool file="data_source/fly_modencode.xml" />
     <tool file="data_source/intermine.xml" />

From 5a1df10230d17f7de646644278b1931e79ddaa7e Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Wed, 15 Apr 2020 10:30:31 -0400
Subject: [PATCH 784/853] Add IDs to admin links and selenium navigation.

---
 client/galaxy/scripts/entry/panels/admin-panel.js | 7 +++++++
 lib/galaxy/selenium/navigation.yml                | 8 ++++++++
 2 files changed, 15 insertions(+)

diff --git a/client/galaxy/scripts/entry/panels/admin-panel.js b/client/galaxy/scripts/entry/panels/admin-panel.js
index c44603784d89..f972914eed31 100644
--- a/client/galaxy/scripts/entry/panels/admin-panel.js
+++ b/client/galaxy/scripts/entry/panels/admin-panel.js
@@ -87,6 +87,7 @@ const AdminPanel = Backbone.View.extend({
                         title: _l("Forms"),
                         url: "admin/forms",
                         target: "__use_router__",
+                        id: "admin-link-forms",
                     },
                 ],
             },
@@ -97,17 +98,20 @@ const AdminPanel = Backbone.View.extend({
                         title: _l("Install and Uninstall"),
                         url: "admin/toolshed",
                         target: "__use_router__",
+                        id: "admin-link-toolshed",
                         enabled: this.settings.is_tool_shed_installed,
                     },
                     {
                         title: _l("Manage Metadata"),
                         url: "admin/reset_metadata",
+                        id: "admin-link-metadata",
                         enabled: this.settings.is_repo_installed,
                         target: "__use_router__",
                     },
                     {
                         title: _l("Manage Whitelist"),
                         url: "admin/sanitize_whitelist",
+                        id: "admin-link-whitelist",
                     },
                     {
                         title: _l("Manage Dependencies"),
@@ -123,14 +127,17 @@ const AdminPanel = Backbone.View.extend({
                         title: _l("View Lineage"),
                         url: "admin/tool_versions",
                         target: "__use_router__",
+                        id: "admin-link-tool-versions",
                     },
                     {
                         title: _l("View Migration Stages"),
                         url: "admin/review_tool_migration_stages",
+                        id: "admin-link-migrations",
                     },
                     {
                         title: _l("View Error Logs"),
                         url: "admin/error_stack",
+                        id: "admin-link-error-stack",
                         target: "__use_router__",
                     },
                 ],
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index f35dab23a0ba..f5619a118cb3 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -356,15 +356,23 @@ admin:
   index:
     selectors:
       datatypes: '#admin-link-datatypes'
+      dependencies: '#admin-link-manage-dependencies'
       data_tables: '#admin-link-data-tables'
       display_applications: '#admin-link-display-applications'
+      errors: '#admin-link-error-stack'
+      forms: '#admin-link-forms'
       jobs: '#admin-link-jobs'
       local_data: '#admin-link-local-data'
+      metadata: '#admin-link-metadata'
+      migrations: '#admin-link-migrations'
+      tool_versions: '#admin-link-tool-versions'
+      toolshed: '#admin-link-toolshed'
       users: '#admin-link-users'
       quotas: '#admin-link-quotas'
       groups: '#admin-link-groups'
       roles: '#admin-link-roles'
       impersonate: '#admin-link-impersonate'
+      whitelist: '#admin-link-whitelist'
 
   selectors:
     # TODO: place betters IDS or something on this in these grids in the DOM

From 253901a90959a6b6c288a75a8d9f61da54148058 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 15 Apr 2020 13:47:14 -0400
Subject: [PATCH 785/853] Drop unused properties for JobDestinationParms
 component

---
 .../JobDestinationParams/JobDestinationParams.vue         | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
index ad50ec8911ac..8910e2eeec6a 100644
--- a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
+++ b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
@@ -23,14 +23,6 @@ export default {
         datasetId: {
             type: String,
         },
-        datasetType: {
-            type: String,
-            default: "hda",
-        },
-        includeTitle: {
-            type: Boolean,
-            default: true,
-        },
     },
     data() {
         return {};

From b378fd54358c02a82ffc3055ddd61ddf15c82703 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 15 Apr 2020 13:48:22 -0400
Subject: [PATCH 786/853] Drop empty/unused local data.

---
 .../components/JobDestinationParams/JobDestinationParams.vue   | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
index 8910e2eeec6a..5e7281ccf1cf 100644
--- a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
+++ b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
@@ -24,9 +24,6 @@ export default {
             type: String,
         },
     },
-    data() {
-        return {};
-    },
     created: function () {
         this.fetchJobDestinationParams(this.jobId);
     },

From cf65e1339bbfccf84152b4bdcc828fc84113b7da Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 15 Apr 2020 14:48:35 -0400
Subject: [PATCH 787/853] Minor refactoring/simplification of vuex usage.

---
 .../components/JobDestinationParams/JobDestinationParams.vue   | 3 +--
 client/galaxy/scripts/store/jobDestinationParametersStore.js   | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
index 5e7281ccf1cf..6f62297dfd66 100644
--- a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
+++ b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
@@ -28,9 +28,8 @@ export default {
         this.fetchJobDestinationParams(this.jobId);
     },
     computed: {
-        ...mapGetters(["getJobDestinationParams"]),
         jobDestinationParams: function () {
-            return this.getJobDestinationParams(this.jobId);
+            return this.$store.getters.jobDestinationParams(this.jobId);
         },
     },
     methods: {
diff --git a/client/galaxy/scripts/store/jobDestinationParametersStore.js b/client/galaxy/scripts/store/jobDestinationParametersStore.js
index 12d439a25476..4503f15cb178 100644
--- a/client/galaxy/scripts/store/jobDestinationParametersStore.js
+++ b/client/galaxy/scripts/store/jobDestinationParametersStore.js
@@ -7,7 +7,7 @@ import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 
 const getters = {
-    getJobDestinationParams: (state) => (jobId) => {
+    jobDestinationParams: (state) => (jobId) => {
         return state.jobDestinationParametersByJobId[jobId] || [];
     },
 };

From 4e0cf47e408ed23b1253478af9c122205d7fe3da Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 15 Apr 2020 14:49:26 -0400
Subject: [PATCH 788/853] Drop unused datasetId from JobDestinationParams

---
 .../components/JobDestinationParams/JobDestinationParams.vue   | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
index 6f62297dfd66..48447b53781a 100644
--- a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
+++ b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
@@ -20,9 +20,6 @@ export default {
         jobId: {
             type: String,
         },
-        datasetId: {
-            type: String,
-        },
     },
     created: function () {
         this.fetchJobDestinationParams(this.jobId);

From 4cde46b48b1cf75a53b9300dfa39eb13ad49bf49 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 15 Apr 2020 14:52:24 -0400
Subject: [PATCH 789/853] require job id for destination params block

---
 .../components/JobDestinationParams/JobDestinationParams.vue     | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
index 48447b53781a..82dedaf5c81c 100644
--- a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
+++ b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
@@ -19,6 +19,7 @@ export default {
     props: {
         jobId: {
             type: String,
+            required: true,
         },
     },
     created: function () {

From e38c4a764beaecfe2d455de6c009152bf9d5ebbf Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 15 Apr 2020 14:53:54 -0400
Subject: [PATCH 790/853] Drop unused import

---
 .../components/JobDestinationParams/JobDestinationParams.vue     | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
index 82dedaf5c81c..7732edf8b904 100644
--- a/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
+++ b/client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue
@@ -13,7 +13,6 @@
 
 <script>
 import { mapCacheActions } from "vuex-cache";
-import { mapGetters } from "vuex";
 
 export default {
     props: {

From db103e759fab0ba6e5e1850197e713d5c116b855 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <jos.to.new@gmail.com>
Date: Wed, 15 Apr 2020 21:47:16 +0200
Subject: [PATCH 791/853] add @require_admin to destination parameters API

---
 lib/galaxy/managers/jobs.py           | 14 ++++++--------
 lib/galaxy/webapps/galaxy/api/jobs.py |  3 ++-
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 18465d9424ce..f1c24ed75678 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -504,14 +504,12 @@ def summarize_destination_params(trans, job):
     Precondition: the caller has verified the job is accessible to the user
     represented by the trans parameter.
     """
-    if not trans.user_is_admin:
-        return []
-    else:
-        destination_params = {'Runner': job.job_runner_name,
-                              'Runner Job ID': job.job_runner_external_id,
-                              'Handler': job.handler}
-        destination_params.update(job.destination_params)
-        return destination_params
+
+    destination_params = {'Runner': job.job_runner_name,
+                          'Runner Job ID': job.job_runner_external_id,
+                          'Handler': job.handler}
+    destination_params.update(job.destination_params)
+    return destination_params
 
 
 def summarize_job_parameters(trans, job):
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index 317747ee7cf6..21714f8dd577 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -284,7 +284,8 @@ def metrics(self, trans, **kwd):
         job = self.__get_job(trans, **kwd)
         return summarize_job_metrics(trans, job)
 
-    @expose_api_anonymous
+    @require_admin
+    @expose_api
     def destination_params(self, trans, **kwd):
         """
         * GET /api/jobs/{job_id}/destination_params

From ff0a08054077f0c1c6f42d61723ef6ebc0c12f9b Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 16 Apr 2020 01:37:18 +0200
Subject: [PATCH 792/853] Add graph consistency

---
 lib/galaxy/tools/recommendations.py | 33 ++++++++++++++++-------------
 1 file changed, 18 insertions(+), 15 deletions(-)

diff --git a/lib/galaxy/tools/recommendations.py b/lib/galaxy/tools/recommendations.py
index 3576886096f0..35bb6e03305a 100644
--- a/lib/galaxy/tools/recommendations.py
+++ b/lib/galaxy/tools/recommendations.py
@@ -31,12 +31,13 @@ def __init__(self):
         self.graph = None
         self.loaded_model = None
         self.compatible_tools = None
+        self.max_seq_len = 25
 
     def set_model(self, trans, remote_model_url):
         """
         Create model and associated dictionaries for recommendations
         """
-        if not self.tool_recommendation_model_path:
+        if not self.graph:
             # import moves from the top of file: in case the tool recommendation feature is disabled,
             # keras is not downloaded because of conditional requirement and Galaxy does not build
             try:
@@ -45,23 +46,19 @@ def set_model(self, trans, remote_model_url):
             except Exception:
                 trans.response.status = 400
                 return False
-            self.tool_recommendation_model_path = self.download_model(remote_model_url)
+            # set graph and session only once
+            if self.graph is None:
+                self.graph = tf.Graph()
+                self.session = tf.Session(graph=self.graph)
             model_weights = list()
             counter_layer_weights = 0
-            # collect ids and names of all the installed tools
-            for tool_id, tool in trans.app.toolbox.tools():
-                t_id_renamed = tool_id
-                if t_id_renamed.find("/") > -1:
-                    t_id_renamed = t_id_renamed.split("/")[-2]
-                self.all_tools[t_id_renamed] = (tool_id, tool.name)
+            self.tool_recommendation_model_path = self.download_model(remote_model_url)
             # read the hdf5 attributes
             trained_model = h5py.File(self.tool_recommendation_model_path, 'r')
             model_config = json.loads(trained_model['model_config'][()])
             # set tensorflow's graph and session to maintain
             # consistency between model load and predict methods
-            self.graph = tf.Graph()
             with self.graph.as_default():
-                self.session = tf.Session(graph=self.graph)
                 with self.session.as_default():
                     self.loaded_model = model_from_json(model_config)
                     # iterate through all the attributes of the model to find weights of neural network layers
@@ -72,7 +69,7 @@ def set_model(self, trans, remote_model_url):
                             model_weights.append(weights)
                             counter_layer_weights += 1
                     # set the model weights
-                    self.loaded_model.set_weights(model_weights)
+                    self.loaded_model.set_weights(model_weights)      
             # set the dictionary of tools
             self.model_data_dictionary = json.loads(trained_model['data_dictionary'][()])
             self.reverse_dictionary = dict((v, k) for k, v in self.model_data_dictionary.items())
@@ -83,6 +80,12 @@ def set_model(self, trans, remote_model_url):
             tool_pos_sorted = [int(key) for key in tool_weights.keys()]
             for k in tool_pos_sorted:
                 self.tool_weights_sorted[k] = tool_weights[str(k)]
+            # collect ids and names of all the installed tools
+            for tool_id, tool in trans.app.toolbox.tools():
+                t_id_renamed = tool_id
+                if t_id_renamed.find("/") > -1:
+                    t_id_renamed = t_id_renamed.split("/")[-2]
+                self.all_tools[t_id_renamed] = (tool_id, tool.name)
         return True
 
     def collect_admin_preferences(self, admin_path):
@@ -192,7 +195,6 @@ def compute_tool_prediction(self, trans, tool_sequence):
         Return a payload with the tool sequences and recommended tools
         Return an empty payload with just the tool sequence if anything goes wrong within the try block
         """
-        max_seq_len = 25
         topk = trans.app.config.topk_recommendations
         prediction_data = dict()
         tool_sequence = tool_sequence.split(",")[::-1]
@@ -201,7 +203,7 @@ def compute_tool_prediction(self, trans, tool_sequence):
         last_tool_name = tool_sequence[-1]
         # do prediction only if the last is present in the collections of tools
         if last_tool_name in self.model_data_dictionary:
-            sample = np.zeros(max_seq_len)
+            sample = np.zeros(self.max_seq_len)
             # get the list of datatype extensions of the last tool of the tool sequence
             _, last_output_extensions = self.get_tool_extensions(trans, self.all_tools[last_tool_name][0])
             prediction_data["o_extensions"] = list(set(last_output_extensions))
@@ -214,12 +216,13 @@ def compute_tool_prediction(self, trans, tool_sequence):
                 except Exception:
                     log.exception("Failed to find tool %s in model" % (tool_name))
                     return prediction_data
-            sample = np.reshape(sample, (1, max_seq_len))
+            sample = np.reshape(sample, (1, self.max_seq_len))
             # predict next tools for a test path
             try:
+                # use the same graph and session to predict
                 with self.graph.as_default():
                     with self.session.as_default():
-                        prediction = self.loaded_model.predict(sample)
+                        prediction = self.loaded_model.predict_on_batch(sample)
             except Exception as e:
                 log.exception(e)
                 return prediction_data

From 712790539eedc695d861c3d59ac003970a71234e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?=
 <lecorguille@users.noreply.github.com>
Date: Thu, 16 Apr 2020 10:05:48 +0200
Subject: [PATCH 793/853] Fix ELIXIR AAI

---
 lib/galaxy/authnz/psa_authnz.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/authnz/psa_authnz.py b/lib/galaxy/authnz/psa_authnz.py
index b6a5ad8eea3e..2dbce80d66b8 100644
--- a/lib/galaxy/authnz/psa_authnz.py
+++ b/lib/galaxy/authnz/psa_authnz.py
@@ -114,8 +114,9 @@ def __init__(self, provider, oidc_config, oidc_backend_config):
 
         # Secondary AuthZ with Google identities is currently supported
         if provider != "google":
-            del self.config["SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER"]
-            del self.config["SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT"]
+            if 'SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER' in self.config:
+                del self.config["SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER"]
+                del self.config["SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT"]
 
     def _setup_idp(self, oidc_backend_config):
         self.config[setting_name('AUTH_EXTRA_ARGUMENTS')] = {'access_type': 'offline'}

From eeddaeb1cee60346c9962383b9709392a77ccfae Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?=
 <lecorguille@users.noreply.github.com>
Date: Thu, 16 Apr 2020 11:11:33 +0200
Subject: [PATCH 794/853] Fix ELIXIR AAI - fix

---
 lib/galaxy/authnz/psa_authnz.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/authnz/psa_authnz.py b/lib/galaxy/authnz/psa_authnz.py
index 2dbce80d66b8..61c12f54ff0f 100644
--- a/lib/galaxy/authnz/psa_authnz.py
+++ b/lib/galaxy/authnz/psa_authnz.py
@@ -116,6 +116,7 @@ def __init__(self, provider, oidc_config, oidc_backend_config):
         if provider != "google":
             if 'SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER' in self.config:
                 del self.config["SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER"]
+            if 'SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT' in self.config:
                 del self.config["SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT"]
 
     def _setup_idp(self, oidc_backend_config):

From c8fc93d29473da5a69d154852dfa3bcc5dd1f662 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 16 Apr 2020 13:05:59 +0200
Subject: [PATCH 795/853] Refactor

---
 lib/galaxy/tools/recommendations.py        | 36 +++++++++++++++-------
 lib/galaxy/webapps/galaxy/api/workflows.py | 17 ++--------
 2 files changed, 28 insertions(+), 25 deletions(-)

diff --git a/lib/galaxy/tools/recommendations.py b/lib/galaxy/tools/recommendations.py
index 35bb6e03305a..8ae33d28b00c 100644
--- a/lib/galaxy/tools/recommendations.py
+++ b/lib/galaxy/tools/recommendations.py
@@ -33,7 +33,21 @@ def __init__(self):
         self.compatible_tools = None
         self.max_seq_len = 25
 
-    def set_model(self, trans, remote_model_url):
+    def get_predictions(self, trans, tool_sequence, remote_model_url):
+        """
+        Compute tool predictions
+        """
+        recommended_tools = dict()
+        self.__collect_admin_preferences(trans.app.config.admin_tool_recommendations_path)
+        is_set = self.__set_model(trans, remote_model_url)
+        if is_set is True:
+            # get the recommended tools for a tool sequence
+            recommended_tools = self.__compute_tool_prediction(trans, tool_sequence)
+        else:
+            tool_sequence = ""
+        return tool_sequence, recommended_tools
+
+    def __set_model(self, trans, remote_model_url):
         """
         Create model and associated dictionaries for recommendations
         """
@@ -52,7 +66,7 @@ def set_model(self, trans, remote_model_url):
                 self.session = tf.Session(graph=self.graph)
             model_weights = list()
             counter_layer_weights = 0
-            self.tool_recommendation_model_path = self.download_model(remote_model_url)
+            self.tool_recommendation_model_path = self.__download_model(remote_model_url)
             # read the hdf5 attributes
             trained_model = h5py.File(self.tool_recommendation_model_path, 'r')
             model_config = json.loads(trained_model['model_config'][()])
@@ -69,7 +83,7 @@ def set_model(self, trans, remote_model_url):
                             model_weights.append(weights)
                             counter_layer_weights += 1
                     # set the model weights
-                    self.loaded_model.set_weights(model_weights)      
+                    self.loaded_model.set_weights(model_weights)
             # set the dictionary of tools
             self.model_data_dictionary = json.loads(trained_model['data_dictionary'][()])
             self.reverse_dictionary = dict((v, k) for k, v in self.model_data_dictionary.items())
@@ -88,7 +102,7 @@ def set_model(self, trans, remote_model_url):
                 self.all_tools[t_id_renamed] = (tool_id, tool.name)
         return True
 
-    def collect_admin_preferences(self, admin_path):
+    def __collect_admin_preferences(self, admin_path):
         """
         Collect preferences for recommendations of tools
         set by admins as dictionaries of deprecated tools and
@@ -108,7 +122,7 @@ def collect_admin_preferences(self, admin_path):
                                 if tool_id not in self.admin_recommendations:
                                     self.admin_recommendations[tool_id] = tool_info
 
-    def download_model(self, model_url, download_local='database/'):
+    def __download_model(self, model_url, download_local='database/'):
         """
         Download the model from remote server
         """
@@ -120,7 +134,7 @@ def download_model(self, model_url, download_local='database/'):
             model_file.write(model_binary.content)
             return local_dir
 
-    def get_tool_extensions(self, trans, tool_id):
+    def __get_tool_extensions(self, trans, tool_id):
         """
         Get the input and output extensions of a tool
         """
@@ -142,7 +156,7 @@ def get_tool_extensions(self, trans, tool_id):
             output_extensions.extend(o_ext['extensions'])
         return input_extensions, output_extensions
 
-    def filter_tool_predictions(self, trans, prediction_data, tool_ids, tool_scores, last_tool_name):
+    def __filter_tool_predictions(self, trans, prediction_data, tool_ids, tool_scores, last_tool_name):
         """
         Filter tool predictions based on datatype compatibility and tool connections.
         Add admin preferences to recommendations.
@@ -159,7 +173,7 @@ def filter_tool_predictions(self, trans, prediction_data, tool_ids, tool_scores,
                 # select the name and tool id if it is installed in Galaxy
                 if t_id == child and score > 0.0 and child in last_compatible_tools and child not in self.deprecated_tools:
                     full_tool_id = self.all_tools[t_id][0]
-                    pred_input_extensions, _ = self.get_tool_extensions(trans, full_tool_id)
+                    pred_input_extensions, _ = self.__get_tool_extensions(trans, full_tool_id)
                     c_dict["name"] = self.all_tools[t_id][1]
                     c_dict["tool_id"] = full_tool_id
                     c_dict["i_extensions"] = list(set(pred_input_extensions))
@@ -189,7 +203,7 @@ def filter_tool_predictions(self, trans, prediction_data, tool_ids, tool_scores,
                 break
         return prediction_data
 
-    def compute_tool_prediction(self, trans, tool_sequence):
+    def __compute_tool_prediction(self, trans, tool_sequence):
         """
         Compute the predicted tools for a tool sequences
         Return a payload with the tool sequences and recommended tools
@@ -205,7 +219,7 @@ def compute_tool_prediction(self, trans, tool_sequence):
         if last_tool_name in self.model_data_dictionary:
             sample = np.zeros(self.max_seq_len)
             # get the list of datatype extensions of the last tool of the tool sequence
-            _, last_output_extensions = self.get_tool_extensions(trans, self.all_tools[last_tool_name][0])
+            _, last_output_extensions = self.__get_tool_extensions(trans, self.all_tools[last_tool_name][0])
             prediction_data["o_extensions"] = list(set(last_output_extensions))
             # get tool names without slashes and create a sequence vector
             for idx, tool_name in enumerate(tool_sequence):
@@ -241,5 +255,5 @@ def compute_tool_prediction(self, trans, tool_sequence):
             # read tool names using reverse dictionary
             pred_tool_ids = [self.reverse_dictionary[int(tool_pos)] for tool_pos in topk_prediction_pos]
             predicted_scores = [int(prediction[pos] * 100) for pos in topk_prediction_pos]
-            prediction_data = self.filter_tool_predictions(trans, prediction_data, pred_tool_ids[::-1], predicted_scores[::-1], last_tool_name)
+            prediction_data = self.__filter_tool_predictions(trans, prediction_data, pred_tool_ids[::-1], predicted_scores[::-1], last_tool_name)
         return prediction_data
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 9cfe322b53fb..13a59170d2a3 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -643,22 +643,11 @@ def get_tool_predictions(self, trans, payload, **kwd):
                          'tool_sequence' - comma separated sequence of tool ids
                          'remote_model_url' - (optional) path to the deep learning model
         """
-        remote_model_url = payload.get('remote_model_url', None)
-        if remote_model_url is None:
-            remote_model_url = trans.app.config.tool_recommendation_model_path
+        remote_model_url = payload.get('remote_model_url', trans.app.config.tool_recommendation_model_path)
+        tool_sequence = payload.get('tool_sequence', "")
         if 'tool_sequence' not in payload or remote_model_url is None:
             return
-        is_model_set = True
-        recommended_tools = dict()
-        tool_sequence = ""
-        # collect tool recommendation preferences if set by admin
-        self.tool_recommendations.collect_admin_preferences(trans.app.config.admin_tool_recommendations_path)
-        # recreate the neural network model to be used for prediction
-        is_model_set = self.tool_recommendations.set_model(trans, remote_model_url)
-        if is_model_set is True:
-            # get the recommended tools for a tool sequence
-            tool_sequence = payload.get('tool_sequence', "")
-            recommended_tools = self.tool_recommendations.compute_tool_prediction(trans, tool_sequence)
+        tool_sequence, recommended_tools = self.tool_recommendations.get_predictions(trans, tool_sequence, remote_model_url)
         return {
             "current_tool": tool_sequence,
             "predicted_data": recommended_tools

From b6669c31cf29a7306d20200d844e1047ff20261b Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 16 Apr 2020 15:55:45 +0200
Subject: [PATCH 796/853] Add predict

---
 lib/galaxy/tools/recommendations.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/recommendations.py b/lib/galaxy/tools/recommendations.py
index 8ae33d28b00c..715878e4b2ca 100644
--- a/lib/galaxy/tools/recommendations.py
+++ b/lib/galaxy/tools/recommendations.py
@@ -236,7 +236,7 @@ def __compute_tool_prediction(self, trans, tool_sequence):
                 # use the same graph and session to predict
                 with self.graph.as_default():
                     with self.session.as_default():
-                        prediction = self.loaded_model.predict_on_batch(sample)
+                        prediction = self.loaded_model.predict(sample)
             except Exception as e:
                 log.exception(e)
                 return prediction_data

From b182ec09638ae631ca9203db88b61bc7fc1f70ea Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Wed, 15 Apr 2020 18:44:54 +0200
Subject: [PATCH 797/853] implement AWS estimate

---
 .../components/JobMetrics/JobMetrics.vue      |  46 +++
 .../scripts/components/JobMetrics/ec2.json    | 306 ++++++++++++++++++
 .../scripts/components/JobMetrics/mount.js    |   2 +
 doc/source/admin/galaxy_options.rst           |  10 +
 lib/galaxy/config/sample/galaxy.yml.sample    |   3 +
 lib/galaxy/managers/configuration.py          |   1 +
 lib/galaxy/webapps/galaxy/config_schema.yml   |   7 +
 templates/show_params.mako                    |   2 +-
 8 files changed, 376 insertions(+), 1 deletion(-)
 create mode 100644 client/galaxy/scripts/components/JobMetrics/ec2.json

diff --git a/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue b/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue
index f0bcd2702588..8bd64ae7b3f4 100644
--- a/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue
+++ b/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue
@@ -12,12 +12,22 @@
                 </tbody>
             </table>
         </div>
+
+        <div v-if="isAwsEstimate && awsEstimate">
+            <h3>AWS estimate</h3>
+            <b>{{ awsEstimate.price }} USD</b><br />
+            This job requested {{ awsEstimate.vcpus }} cores and {{ awsEstimate.memory }} Gb. Given this, the smallest
+            EC2 machine we could find is {{ awsEstimate.instance.name }} ({{ awsEstimate.instance.mem }} GB /
+            {{ awsEstimate.instance.vcpus }} vCPUs / {{ awsEstimate.instance.cpu }}). That instance is priced at
+            {{ awsEstimate.instance.price }} USD/hour.
+        </div>
     </div>
 </template>
 
 <script>
 import { mapCacheActions } from "vuex-cache";
 import { mapGetters } from "vuex";
+import ec2 from "./ec2.json";
 
 export default {
     props: {
@@ -27,6 +37,9 @@ export default {
         datasetId: {
             type: String,
         },
+        aws_estimate: {
+            type: String,
+        },
         datasetType: {
             type: String,
             default: "hda",
@@ -48,6 +61,39 @@ export default {
     },
     computed: {
         ...mapGetters(["getJobMetricsByDatasetId", "getJobMetricsByJobId"]),
+        isAwsEstimate: function () {
+            return this.aws_estimate && this.aws_estimate.toUpperCase() === "true".toUpperCase();
+        },
+        awsEstimate: function () {
+            if (!this.isAwsEstimate) return;
+
+            const aws = {};
+            this.jobMetrics.forEach((metric) => {
+                switch (metric.name) {
+                    case "galaxy_memory_mb":
+                        aws.memory = parseInt(metric.raw_value);
+                        break;
+                    case "galaxy_slots":
+                        aws.vcpus = parseInt(metric.raw_value);
+                        break;
+                    case "runtime_seconds":
+                        aws.seconds = parseInt(metric.raw_value);
+                        break;
+                    default:
+                }
+            });
+
+            if (aws.memory) aws.memory /= 1024;
+            // if memory was not specified, assign the smallest amount (we judge based on CPU-count only)
+            else aws.memory = 0.5;
+
+            // ec2 is already pre-sorted
+            aws.instance = ec2.find((ec) => {
+                return ec.mem >= aws.memory && ec.vcpus >= aws.vcpus;
+            });
+            aws.price = ((aws.seconds * aws.instance.price) / 3600).toFixed(2);
+            return aws;
+        },
         jobMetrics: function () {
             if (this.jobId) {
                 return this.getJobMetricsByJobId(this.jobId);
diff --git a/client/galaxy/scripts/components/JobMetrics/ec2.json b/client/galaxy/scripts/components/JobMetrics/ec2.json
new file mode 100644
index 000000000000..541f25528675
--- /dev/null
+++ b/client/galaxy/scripts/components/JobMetrics/ec2.json
@@ -0,0 +1,306 @@
+[
+  {
+    "name": "t2.nano",
+    "mem": 0.5,
+    "price": 0.0067,
+    "priceunit": "Hrs",
+    "vcpus": 1,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "t3.nano",
+    "mem": 0.5,
+    "price": 0.006,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "t2.micro",
+    "mem": 1,
+    "price": 0.0134,
+    "priceunit": "Hrs",
+    "vcpus": 1,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "t3.micro",
+    "mem": 1,
+    "price": 0.012,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "t2.small",
+    "mem": 2,
+    "price": 0.0268,
+    "priceunit": "Hrs",
+    "vcpus": 1,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "t3.small",
+    "mem": 2,
+    "price": 0.024,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "m3.medium",
+    "mem": 3.75,
+    "price": 0.079,
+    "priceunit": "Hrs",
+    "vcpus": 1,
+    "cpu": "Intel Xeon E5-2670 v2 (Ivy Bridge/Sandy Bridge)"
+  },
+  {
+    "name": "t2.medium",
+    "mem": 4,
+    "price": 0.0536,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "t3.medium",
+    "mem": 4,
+    "price": 0.048,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "m3.large",
+    "mem": 7.5,
+    "price": 0.158,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Xeon E5-2670 v2 (Ivy Bridge/Sandy Bridge)"
+  },
+  {
+    "name": "t2.large",
+    "mem": 8,
+    "price": 0.1072,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "t3.large",
+    "mem": 8,
+    "price": 0.096,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "m5.large",
+    "mem": 8,
+    "price": 0.115,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m5d.large",
+    "mem": 8,
+    "price": 0.136,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m4.large",
+    "mem": 8,
+    "price": 0.12,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Xeon E5-2676 v3 (Haswell)"
+  },
+  {
+    "name": "m3.xlarge",
+    "mem": 15,
+    "price": 0.315,
+    "priceunit": "Hrs",
+    "vcpus": 4,
+    "cpu": "Intel Xeon E5-2670 v2 (Ivy Bridge/Sandy Bridge)"
+  },
+  {
+    "name": "m5.xlarge",
+    "mem": 16,
+    "price": 0.23,
+    "priceunit": "Hrs",
+    "vcpus": 4,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m4.xlarge",
+    "mem": 16,
+    "price": 0.24,
+    "priceunit": "Hrs",
+    "vcpus": 4,
+    "cpu": "Intel Xeon E5-2676 v3 (Haswell)"
+  },
+  {
+    "name": "t3.xlarge",
+    "mem": 16,
+    "price": 0.192,
+    "priceunit": "Hrs",
+    "vcpus": 4,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "t2.xlarge",
+    "mem": 16,
+    "price": 0.2144,
+    "priceunit": "Hrs",
+    "vcpus": 4,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "m5d.xlarge",
+    "mem": 16,
+    "price": 0.272,
+    "priceunit": "Hrs",
+    "vcpus": 4,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m3.2xlarge",
+    "mem": 30,
+    "price": 0.632,
+    "priceunit": "Hrs",
+    "vcpus": 8,
+    "cpu": "Intel Xeon E5-2670 v2 (Ivy Bridge/Sandy Bridge)"
+  },
+  {
+    "name": "m5d.2xlarge",
+    "mem": 32,
+    "price": 0.544,
+    "priceunit": "Hrs",
+    "vcpus": 8,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m5.2xlarge",
+    "mem": 32,
+    "price": 0.46,
+    "priceunit": "Hrs",
+    "vcpus": 8,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m4.2xlarge",
+    "mem": 32,
+    "price": 0.48,
+    "priceunit": "Hrs",
+    "vcpus": 8,
+    "cpu": "Intel Xeon E5-2676 v3 (Haswell)"
+  },
+  {
+    "name": "t3.2xlarge",
+    "mem": 32,
+    "price": 0.384,
+    "priceunit": "Hrs",
+    "vcpus": 8,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "t2.2xlarge",
+    "mem": 32,
+    "price": 0.4288,
+    "priceunit": "Hrs",
+    "vcpus": 8,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "m5d.4xlarge",
+    "mem": 64,
+    "price": 1.088,
+    "priceunit": "Hrs",
+    "vcpus": 16,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m4.4xlarge",
+    "mem": 64,
+    "price": 0.96,
+    "priceunit": "Hrs",
+    "vcpus": 16,
+    "cpu": "Intel Xeon E5-2676 v3 (Haswell)"
+  },
+  {
+    "name": "m5.4xlarge",
+    "mem": 64,
+    "price": 0.92,
+    "priceunit": "Hrs",
+    "vcpus": 16,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m4.10xlarge",
+    "mem": 160,
+    "price": 2.4,
+    "priceunit": "Hrs",
+    "vcpus": 40,
+    "cpu": "Intel Xeon E5-2676 v3 (Haswell)"
+  },
+  {
+    "name": "m5d.12xlarge",
+    "mem": 192,
+    "price": 3.264,
+    "priceunit": "Hrs",
+    "vcpus": 48,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m5.12xlarge",
+    "mem": 192,
+    "price": 2.76,
+    "priceunit": "Hrs",
+    "vcpus": 48,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m4.16xlarge",
+    "mem": 256,
+    "price": 3.84,
+    "priceunit": "Hrs",
+    "vcpus": 64,
+    "cpu": "Intel Xeon E5-2686 v4 (Broadwell)"
+  },
+  {
+    "name": "m5d.metal",
+    "mem": 384,
+    "price": 6.528,
+    "priceunit": "Hrs",
+    "vcpus": 96,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m5.metal",
+    "mem": 384,
+    "price": 5.52,
+    "priceunit": "Hrs",
+    "vcpus": 96,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m5d.24xlarge",
+    "mem": 384,
+    "price": 6.528,
+    "priceunit": "Hrs",
+    "vcpus": 96,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m5.24xlarge",
+    "mem": 384,
+    "price": 5.52,
+    "priceunit": "Hrs",
+    "vcpus": 96,
+    "cpu": "Intel Xeon Platinum 8175"
+  }
+]
diff --git a/client/galaxy/scripts/components/JobMetrics/mount.js b/client/galaxy/scripts/components/JobMetrics/mount.js
index 04b1bfe0c578..1ef820abd693 100644
--- a/client/galaxy/scripts/components/JobMetrics/mount.js
+++ b/client/galaxy/scripts/components/JobMetrics/mount.js
@@ -8,11 +8,13 @@ import { mountVueComponent } from "utils/mountVueComponent";
 export const mountJobMetrics = (propsData = {}) => {
     $(".job-metrics").each((index, el) => {
         const jobId = $(el).attr("job_id");
+        const aws_estimate = $(el).attr("aws_estimate");
         const datasetId = $(el).attr("dataset_id");
         const datasetType = $(el).attr("dataset_type") || "hda";
         propsData.jobId = jobId;
         propsData.datasetId = datasetId;
         propsData.datasetType = datasetType;
+        propsData.aws_estimate = aws_estimate;
         mountVueComponent(JobMetrics)(propsData, el);
     });
 };
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 736869828f18..182a7c01da75 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -1376,6 +1376,16 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~
+``aws_estimate``
+~~~~~~~~~~~~~~~~
+
+:Description:
+    Enable AWS estimate.
+:Default: ``false``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``interactivetools_proxy_host``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index ec01788720a0..c54a00559f8f 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -761,6 +761,9 @@ galaxy:
   # Enable InteractiveTools.
   #interactivetools_enable: false
 
+  # Enable AWS estimate.
+  #aws_estimate: false
+
   # Proxy host - assumed to just be hosted on the same hostname and port
   # as Galaxy by default.
   #interactivetools_proxy_host: null
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index 4812e33091fb..a34c21ccd518 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -91,6 +91,7 @@ def _use_config(config, key, **context):
             'inactivity_box_content'            : _use_config,
             'visualizations_visible'            : _use_config,
             'interactivetools_enable'           : _use_config,
+            'aws_estimate'                      : _use_config,
             'message_box_content'               : _use_config,
             'message_box_visible'               : _use_config,
             'message_box_class'                 : _use_config,
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 788b992ca024..be52780d085f 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -1026,6 +1026,13 @@ mapping:
         desc: |
           Enable InteractiveTools.
 
+      aws_estimate:
+        type: bool
+        default: false
+        required: false
+        desc: |
+          Enable AWS estimate.
+
       interactivetools_proxy_host:
         type: str
         desc: |
diff --git a/templates/show_params.mako b/templates/show_params.mako
index 2a4e8f3549c9..295707827ba8 100644
--- a/templates/show_params.mako
+++ b/templates/show_params.mako
@@ -113,7 +113,7 @@ ${ job.command_line | h }</pre>
 %endif
 
 %if job and (trans.user_is_admin or trans.app.config.expose_potentially_sensitive_job_metrics):
-<div class="job-metrics" dataset_id="${encoded_hda_id}" dataset_type="hda">
+<div class="job-metrics" dataset_id="${encoded_hda_id}" aws_estimate="${trans.app.config.aws_estimate}" dataset_type="hda">
 </div>
 %endif
 

From 573654c2da82f974c08e34394b1472165fa29de8 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 16 Apr 2020 18:32:46 +0200
Subject: [PATCH 798/853] Fix tensorflow graph issue

---
 lib/galaxy/tools/recommendations.py | 24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/tools/recommendations.py b/lib/galaxy/tools/recommendations.py
index 715878e4b2ca..4d8f59aa0c1a 100644
--- a/lib/galaxy/tools/recommendations.py
+++ b/lib/galaxy/tools/recommendations.py
@@ -74,16 +74,20 @@ def __set_model(self, trans, remote_model_url):
             # consistency between model load and predict methods
             with self.graph.as_default():
                 with self.session.as_default():
-                    self.loaded_model = model_from_json(model_config)
-                    # iterate through all the attributes of the model to find weights of neural network layers
-                    for item in trained_model.keys():
-                        if "weight_" in item:
-                            d_key = "weight_" + str(counter_layer_weights)
-                            weights = trained_model[d_key][()]
-                            model_weights.append(weights)
-                            counter_layer_weights += 1
-                    # set the model weights
-                    self.loaded_model.set_weights(model_weights)
+                    try:
+                        # iterate through all the attributes of the model to find weights of neural network layers
+                        for item in trained_model.keys():
+                            if "weight_" in item:
+                                key = "weight_{}".format(str(counter_layer_weights))
+                                weight = trained_model[key][()]
+                                model_weights.append(weight)
+                                counter_layer_weights += 1
+                        self.loaded_model = model_from_json(model_config)
+                        self.loaded_model.set_weights(model_weights)
+                    except Exception as e:
+                        log.exception(e)
+                        trans.response.status = 400
+                        return False
             # set the dictionary of tools
             self.model_data_dictionary = json.loads(trained_model['data_dictionary'][()])
             self.reverse_dictionary = dict((v, k) for k, v in self.model_data_dictionary.items())

From 6d3db7d283cfcf3944de3eb90190aff9c3747a06 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Thu, 16 Apr 2020 19:10:37 +0200
Subject: [PATCH 799/853] Update str

---
 lib/galaxy/tools/recommendations.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/recommendations.py b/lib/galaxy/tools/recommendations.py
index 4d8f59aa0c1a..533d3fb160bd 100644
--- a/lib/galaxy/tools/recommendations.py
+++ b/lib/galaxy/tools/recommendations.py
@@ -78,8 +78,7 @@ def __set_model(self, trans, remote_model_url):
                         # iterate through all the attributes of the model to find weights of neural network layers
                         for item in trained_model.keys():
                             if "weight_" in item:
-                                key = "weight_{}".format(str(counter_layer_weights))
-                                weight = trained_model[key][()]
+                                weight = trained_model["weight_" + str(counter_layer_weights)][()]
                                 model_weights.append(weight)
                                 counter_layer_weights += 1
                         self.loaded_model = model_from_json(model_config)

From fd1a5c21eb7babc0f81b136691afda46fa87c450 Mon Sep 17 00:00:00 2001
From: Assunta DeSanto <adesanto@lhup.edu>
Date: Wed, 8 Apr 2020 17:39:48 -0400
Subject: [PATCH 800/853] refactored components of Rule Collection into
 separate vue files

---
 .../components/RuleBuilder/ColumnSelector.vue | 134 +++++++
 .../RuleBuilder/IdentifierDisplay.vue         |  50 +++
 .../RuleBuilder/RegularExpressionInput.vue    |  32 ++
 .../components/RuleBuilder/RuleComponent.vue  |  46 +++
 .../components/RuleBuilder/RuleDisplay.vue    |  51 +++
 .../RuleBuilder/RuleTargetComponent.vue       |  25 ++
 .../components/RuleCollectionBuilder.vue      | 329 +-----------------
 7 files changed, 346 insertions(+), 321 deletions(-)
 create mode 100644 client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue
 create mode 100644 client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
 create mode 100644 client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue
 create mode 100644 client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue
 create mode 100644 client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue
 create mode 100644 client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue

diff --git a/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue b/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue
new file mode 100644
index 000000000000..764ab9690bbb
--- /dev/null
+++ b/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue
@@ -0,0 +1,134 @@
+<template>
+    <div class="rule-column-selector" v-if="!multiple || !ordered">
+        <label class="d-flex justify-content-end align-items-center">
+            <span class="mr-auto" v-b-tooltip.hover :title="help">{{ label }}</span>
+            <div class="mr-1" v-b-tooltip.hover :title="title"><select2 :value="target" @input="handleInput" :multiple="multiple">
+                <option v-for="(col, index) in colHeaders" :value="index">{{ col }}</option>
+            </select2></div>
+            <slot></slot>
+        </label>
+    </div>
+    <div class="rule-column-selector" v-else>
+        <span>{{ label }}</span>
+        <slot></slot>
+        <ol>
+            <li v-for="(targetEl, index) in target"
+                v-bind:index="index"
+                v-bind:key="targetEl"
+                class="rule-column-selector-target">
+                {{ colHeaders[targetEl] }}
+                <span class="fa fa-times rule-column-selector-target-remove" @click="handleRemove(index)"></span>
+                <span class="fa fa-arrow-up rule-column-selector-up" v-if="index !== 0" @click="moveUp(index)"></span>
+                <span class="fa fa-arrow-down rule-column-selector-down" v-if="index < target.length - 1" @click="moveUp(index + 1)"></span>
+            </li>
+            <li v-if="this.target.length < this.colHeaders.length">
+                <span class="rule-column-selector-target-add" v-if="!orderedEdit">
+                    <i @click="$emit('update:orderedEdit', true)">... {{ l("Assign Another Column") }}</i>
+                </span>
+                <span class="rule-column-selector-target-select" v-else>
+                    <select2 @input="handleAdd" placeholder="Select a column">
+                        <option /><!-- empty option selection for placeholder -->
+                        <option v-for="(col, index) in remainingHeaders" :value="index">{{ col }}</option>
+                    </select2>
+                </span>
+            </li>
+        </ol>
+    </div>
+</template>
+
+<script>
+import _l from "utils/localization";
+import Select2 from "components/Select2";
+export default {
+    components: {
+        Select2,
+    },
+    data: function () {
+        return {
+            l: _l,
+        };
+    },
+    props: {
+        target: {
+            required: true,
+        },
+        label: {
+            required: false,
+            type: String,
+            default: _l("From Column"),
+        },
+        help: {
+            required: false,
+        },
+        colHeaders: {
+            type: Array,
+            required: true,
+        },
+        multiple: {
+            type: Boolean,
+            required: false,
+            default: false,
+        },
+        ordered: {
+            type: Boolean,
+            required: false,
+            default: false,
+        },
+        valueAsList: {
+            type: Boolean,
+            required: false,
+            default: false,
+        },
+        orderedEdit: {
+            type: Boolean,
+            required: false,
+            default: false,
+        },
+    },
+    computed: {
+        remainingHeaders() {
+            const colHeaders = this.colHeaders;
+            if (!this.multiple) {
+                return colHeaders;
+            }
+            const remaining = {};
+            for (const key in colHeaders) {
+                if (this.target.indexOf(parseInt(key)) === -1) {
+                    remaining[key] = colHeaders[key];
+                }
+            }
+            return remaining;
+        },
+        title() {
+            return _l("Select a column");
+        },
+    },
+    methods: {
+        handleInput(value) {
+            if (this.multiple) {
+                // https://stackoverflow.com/questions/262427/why-does-parseint-yield-nan-with-arraymap
+                const val = value.map((idx) => parseInt(idx));
+                this.$emit("update:target", val);
+            } else {
+                let val = parseInt(value);
+                if (this.valueAsList) {
+                    val = [val];
+                }
+                this.$emit("update:target", val);
+            }
+        },
+        handleAdd(value) {
+            this.target.push(parseInt(value));
+            this.$emit("update:orderedEdit", false);
+        },
+        handleRemove(index) {
+            this.target.splice(index, 1);
+        },
+        moveUp(value) {
+            const swapVal = this.target[value - 1];
+            Vue.set(this.target, value - 1, this.target[value]);
+            Vue.set(this.target, value, swapVal);
+        },
+    }
+}
+</script> 
\ No newline at end of file
diff --git a/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue b/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
new file mode 100644
index 000000000000..fd5659c73be4
--- /dev/null
+++ b/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
@@ -0,0 +1,50 @@
+<template>
+    <li class="rule">
+        <span v-b-tooltip.hover :title="help">Set {{ columnsLabel }} as {{ typeDisplay }}</span>
+        <span v-b-tooltip.hover :title="titleEdit" class="fa fa-edit" @click="edit"></span>
+        <span v-b-tooltip.hover :title="titleRemove" class="fa fa-times" @click="remove"></span>
+    </li>
+</template>
+
+<script>
+export default{
+    props: {
+        type: {
+            type: String,
+            required: true,
+        },
+        columns: {
+            required: true,
+        },
+        colHeaders: {
+            type: Array,
+            required: true,
+        },
+    },
+    methods: {
+        remove() {
+            this.$emit("remove");
+        },
+        edit() {
+            this.$emit("edit");
+        },
+    },
+    computed: {
+        typeDisplay() {
+            return MAPPING_TARGETS[this.type].label;
+        },
+        help() {
+            return MAPPING_TARGETS[this.type].help || "";
+        },
+        titleEdit() {
+            return _l("Edit column definition");
+        },
+        titleRemove() {
+            return _l("Remove this column definition");
+        },
+        columnsLabel() {
+            return RuleDefs.columnDisplay(this.columns, this.colHeaders);
+        },
+    }
+}
+</script>
\ No newline at end of file
diff --git a/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue b/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue
new file mode 100644
index 000000000000..9437edae40cf
--- /dev/null
+++ b/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue
@@ -0,0 +1,32 @@
+<template>
+    <div>
+        <label for="regular_expression" v-b-tooltip.hover :title="title">{{ label }}</label>
+        <span v-b-popover.html="popoverContent" :title="popoverTitle" class="fa fa-question"></span>
+        <input v-b-tooltip.hover.left :title="title" name="regular_expression" class="rule-regular-expression" type="text" :value="target" @input="$emit('update:target', $event.target.value)" />
+    </div>
+</template>
+
+<script>
+export default {
+    props: {
+        target: {
+            required: true,
+        },
+    },
+    computed: {
+        label() {
+            return _l("Regular Expression");
+        },
+        title() {
+            return _l("Enter a regular expression.");
+        },
+        popoverTitle() {
+            return _l("Regular Expressions");
+        },
+        popoverContent() {
+            return _l(
+                `Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in <a href="https://pythonforbiologists.com/regular-expressions/">this Python for Biologists tutorial</a>.`
+            );
+        }
+}
+</script> 
\ No newline at end of file
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue b/client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue
new file mode 100644
index 000000000000..826c0fda1c02
--- /dev/null
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue
@@ -0,0 +1,46 @@
+<template>
+    <div v-if="ruleType == displayRuleType" class="rule-editor" :class="typeToClass">
+        <slot></slot>
+        <div class="buttons rule-edit-buttons d-flex justify-content-end">
+           <button type="button" class="btn rule-editor-cancel mr-1" @click="cancel">{{ cancelLabel }}</button>
+           <button type="button" class="btn btn-primary rule-editor-ok" @click="okay">{{ applyLabel }}</button>
+        </div>
+    </div>
+</template>
+
+<script>
+export default {
+    data: function () {
+        return {
+            applyLabel: _l("Apply"),
+            cancelLabel: _l("Cancel"),
+        };
+    },
+    props: {
+        ruleType: {
+            type: String,
+            required: true,
+        },
+        displayRuleType: {
+            required: true,
+        },
+        builder: {
+            required: true,
+        },
+    },
+    methods: {
+        cancel() {
+            this.builder.displayRuleType = null;
+        },
+        okay() {
+            this.builder.handleRuleSave(this.ruleType);
+            this.cancel();
+        },
+    },
+    computed: {
+        typeToClass() {
+            return "rule-edit-" + this.ruleType.replace(/_/g, "-");
+        },
+    },
+}
+</script>
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue b/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue
new file mode 100644
index 000000000000..c51377581f81
--- /dev/null
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue
@@ -0,0 +1,51 @@
+
+<template>
+    <li class="rule">
+        <span class="rule-display">
+            <span class="mr-1">{{ title }}</span>
+            <span v-b-tooltip.hover :title="editTitle" class="fa fa-edit mr-1" @click="edit"></span>
+            <span v-b-tooltip.hover :title="removeTitle" class="fa fa-times map" @click="remove"></span>
+        </span>
+        <span class="rule-warning" v-if="rule.warn">
+            {{ rule.warn }}
+        </span>
+        <span class="rule-error" v-if="rule.error">
+            <span class="alert-message">{{ rule.error }}</span>
+        </span>
+    </li>
+</template>
+
+<script>
+export default {
+    props: {
+        rule: {
+            required: true,
+            type: Object,
+        },
+        colHeaders: {
+            type: Array,
+            required: true,
+        },
+    },
+    computed: {
+        title() {
+            const ruleType = this.rule.type;
+            return RULES[ruleType].display(this.rule, this.colHeaders);
+        },
+        editTitle() {
+            return _l("Edit this rule.");
+        },
+        removeTitle() {
+            return _l("Remove this rule.");
+        },
+    },
+    methods: {
+        edit() {
+            this.$emit("edit");
+        },
+        remove() {
+            this.$emit("remove");
+        },
+    }
+}
+</script>
\ No newline at end of file
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue b/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
new file mode 100644
index 000000000000..ec3e7dd890d3
--- /dev/null
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
@@ -0,0 +1,25 @@
+<template>
+    template: `<a class="rule-link dropdown-item" href="javascript:void(0)" :class="linkClassName" @click="builder.addNewRule(ruleType)">{{title}}</a>`,
+</template>
+
+<script>
+export default {
+    props: {
+        ruleType: {
+            type: String,
+            required: true,
+        },
+        builder: {
+            required: true,
+        },
+    },
+    computed: {
+        linkClassName() {
+            return "rule-link-" + this.ruleType.replace(/_/g, "-");
+        },
+        title() {
+            return RULES[this.ruleType].title;
+        },
+    },
+}
+</script>
\ No newline at end of file
diff --git a/client/galaxy/scripts/components/RuleCollectionBuilder.vue b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
index d4d99436d373..60e5ed92e537 100644
--- a/client/galaxy/scripts/components/RuleCollectionBuilder.vue
+++ b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
@@ -576,332 +576,19 @@ import RuleDefs from "mvc/rules/rule-definitions";
 import Vue from "vue";
 import BootstrapVue from "bootstrap-vue";
 import Select2 from "components/Select2";
+import ColumnSelector from "components/RuleBuilder/ColumnSelector";
+import RegularExpressionInput from "components/RuleBuilder/RegularExpressionInput";
+import RuleDisplay from "components/RuleBuilder/RuleDisplay";
+import IdentifierDisplay from "components/RuleBuilder/IdentifierDisplay";
+import RuleTargetComponent from "components/RuleBuilder/RuleTargetComponent";
+import RuleComponent from "components/RuleBuilder/RuleComponent";
+
 
 Vue.use(BootstrapVue);
 
 const RULES = RuleDefs.RULES;
 const MAPPING_TARGETS = RuleDefs.MAPPING_TARGETS;
-
-const ColumnSelector = {
-    template: `
-        <div class="rule-column-selector" v-if="!multiple || !ordered">
-            <label class="d-flex justify-content-end align-items-center">
-                <span class="mr-auto" v-b-tooltip.hover :title="help">{{ label }}</span>
-                <div class="mr-1" v-b-tooltip.hover :title="title"><select2 :value="target" @input="handleInput" :multiple="multiple">
-                    <option v-for="(col, index) in colHeaders" :value="index">{{ col }}</option>
-                </select2></div>
-                <slot></slot>
-            </label>
-        </div>
-        <div class="rule-column-selector" v-else>
-            <span>{{ label }}</span>
-            <slot></slot>
-            <ol>
-                <li v-for="(targetEl, index) in target"
-                    v-bind:index="index"
-                    v-bind:key="targetEl"
-                    class="rule-column-selector-target">
-                    {{ colHeaders[targetEl] }}
-                    <span class="fa fa-times rule-column-selector-target-remove" @click="handleRemove(index)"></span>
-                    <span class="fa fa-arrow-up rule-column-selector-up" v-if="index !== 0" @click="moveUp(index)"></span>
-                    <span class="fa fa-arrow-down rule-column-selector-down" v-if="index < target.length - 1" @click="moveUp(index + 1)"></span>
-                </li>
-                <li v-if="this.target.length < this.colHeaders.length">
-                    <span class="rule-column-selector-target-add" v-if="!orderedEdit">
-                        <i @click="$emit('update:orderedEdit', true)">... {{ l("Assign Another Column") }}</i>
-                    </span>
-                    <span class="rule-column-selector-target-select" v-else>
-                        <select2 @input="handleAdd" placeholder="Select a column">
-                            <option /><!-- empty option selection for placeholder -->
-                            <option v-for="(col, index) in remainingHeaders" :value="index">{{ col }}</option>
-                        </select2>
-                    </span>
-                </li>
-            </ol>
-        </div>
-    `,
-    data: function () {
-        return {
-            l: _l,
-        };
-    },
-    props: {
-        target: {
-            required: true,
-        },
-        label: {
-            required: false,
-            type: String,
-            default: _l("From Column"),
-        },
-        help: {
-            required: false,
-        },
-        colHeaders: {
-            type: Array,
-            required: true,
-        },
-        multiple: {
-            type: Boolean,
-            required: false,
-            default: false,
-        },
-        ordered: {
-            type: Boolean,
-            required: false,
-            default: false,
-        },
-        valueAsList: {
-            type: Boolean,
-            required: false,
-            default: false,
-        },
-        orderedEdit: {
-            type: Boolean,
-            required: false,
-            default: false,
-        },
-    },
-    computed: {
-        remainingHeaders() {
-            const colHeaders = this.colHeaders;
-            if (!this.multiple) {
-                return colHeaders;
-            }
-            const remaining = {};
-            for (const key in colHeaders) {
-                if (this.target.indexOf(parseInt(key)) === -1) {
-                    remaining[key] = colHeaders[key];
-                }
-            }
-            return remaining;
-        },
-        title() {
-            return _l("Select a column");
-        },
-    },
-    methods: {
-        handleInput(value) {
-            if (this.multiple) {
-                // https://stackoverflow.com/questions/262427/why-does-parseint-yield-nan-with-arraymap
-                const val = value.map((idx) => parseInt(idx));
-                this.$emit("update:target", val);
-            } else {
-                let val = parseInt(value);
-                if (this.valueAsList) {
-                    val = [val];
-                }
-                this.$emit("update:target", val);
-            }
-        },
-        handleAdd(value) {
-            this.target.push(parseInt(value));
-            this.$emit("update:orderedEdit", false);
-        },
-        handleRemove(index) {
-            this.target.splice(index, 1);
-        },
-        moveUp(value) {
-            const swapVal = this.target[value - 1];
-            Vue.set(this.target, value - 1, this.target[value]);
-            Vue.set(this.target, value, swapVal);
-        },
-    },
-    components: {
-        Select2,
-    },
-};
-
-const RegularExpressionInput = {
-    template: `
-        <div>
-            <label for="regular_expression" v-b-tooltip.hover :title="title">{{ label }}</label>
-            <span v-b-popover.html="popoverContent" :title="popoverTitle" class="fa fa-question"></span>
-            <input v-b-tooltip.hover.left :title="title" name="regular_expression" class="rule-regular-expression" type="text" :value="target" @input="$emit('update:target', $event.target.value)" />
-        </div>
-    `,
-    props: {
-        target: {
-            required: true,
-        },
-    },
-    computed: {
-        label() {
-            return _l("Regular Expression");
-        },
-        title() {
-            return _l("Enter a regular expression.");
-        },
-        popoverTitle() {
-            return _l("Regular Expressions");
-        },
-        popoverContent() {
-            return _l(
-                `Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in <a href="https://pythonforbiologists.com/regular-expressions/">this Python for Biologists tutorial</a>.`
-            );
-        },
-    },
-};
-
-const RuleDisplay = {
-    template: `
-        <li class="rule">
-            <span class="rule-display">
-                <span class="mr-1">{{ title }}</span>
-                <span v-b-tooltip.hover :title="editTitle" class="fa fa-edit mr-1" @click="edit"></span>
-                <span v-b-tooltip.hover :title="removeTitle" class="fa fa-times map" @click="remove"></span>
-            </span>
-            <span class="rule-warning" v-if="rule.warn">
-                {{ rule.warn }}
-            </span>
-            <span class="rule-error" v-if="rule.error">
-                <span class="alert-message">{{ rule.error }}</span>
-            </span>
-        </li>
-    `,
-    props: {
-        rule: {
-            required: true,
-            type: Object,
-        },
-        colHeaders: {
-            type: Array,
-            required: true,
-        },
-    },
-    computed: {
-        title() {
-            const ruleType = this.rule.type;
-            return RULES[ruleType].display(this.rule, this.colHeaders);
-        },
-        editTitle() {
-            return _l("Edit this rule.");
-        },
-        removeTitle() {
-            return _l("Remove this rule.");
-        },
-    },
-    methods: {
-        edit() {
-            this.$emit("edit");
-        },
-        remove() {
-            this.$emit("remove");
-        },
-    },
-};
-
-const IdentifierDisplay = {
-    template: `
-      <li class="rule">
-        <span v-b-tooltip.hover :title="help">Set {{ columnsLabel }} as {{ typeDisplay }}</span>
-        <span v-b-tooltip.hover :title="titleEdit" class="fa fa-edit" @click="edit"></span>
-        <span v-b-tooltip.hover :title="titleRemove" class="fa fa-times" @click="remove"></span>
-      </li>
-    `,
-    props: {
-        type: {
-            type: String,
-            required: true,
-        },
-        columns: {
-            required: true,
-        },
-        colHeaders: {
-            type: Array,
-            required: true,
-        },
-    },
-    methods: {
-        remove() {
-            this.$emit("remove");
-        },
-        edit() {
-            this.$emit("edit");
-        },
-    },
-    computed: {
-        typeDisplay() {
-            return MAPPING_TARGETS[this.type].label;
-        },
-        help() {
-            return MAPPING_TARGETS[this.type].help || "";
-        },
-        titleEdit() {
-            return _l("Edit column definition");
-        },
-        titleRemove() {
-            return _l("Remove this column definition");
-        },
-        columnsLabel() {
-            return RuleDefs.columnDisplay(this.columns, this.colHeaders);
-        },
-    },
-};
-
-const RuleTargetComponent = {
-    template: `<a class="rule-link dropdown-item" href="javascript:void(0)" :class="linkClassName" @click="builder.addNewRule(ruleType)">{{title}}</a>`,
-    props: {
-        ruleType: {
-            type: String,
-            required: true,
-        },
-        builder: {
-            required: true,
-        },
-    },
-    computed: {
-        linkClassName() {
-            return "rule-link-" + this.ruleType.replace(/_/g, "-");
-        },
-        title() {
-            return RULES[this.ruleType].title;
-        },
-    },
-};
-
-const RuleComponent = {
-    template: `
-    <div v-if="ruleType == displayRuleType" class="rule-editor" :class="typeToClass">
-        <slot></slot>
-        <div class="buttons rule-edit-buttons d-flex justify-content-end">
-           <button type="button" class="btn rule-editor-cancel mr-1" @click="cancel">{{ cancelLabel }}</button>
-           <button type="button" class="btn btn-primary rule-editor-ok" @click="okay">{{ applyLabel }}</button>
-        </div>
-    </div>`,
-    data: function () {
-        return {
-            applyLabel: _l("Apply"),
-            cancelLabel: _l("Cancel"),
-        };
-    },
-    props: {
-        ruleType: {
-            type: String,
-            required: true,
-        },
-        displayRuleType: {
-            required: true,
-        },
-        builder: {
-            required: true,
-        },
-    },
-    methods: {
-        cancel() {
-            this.builder.displayRuleType = null;
-        },
-        okay() {
-            this.builder.handleRuleSave(this.ruleType);
-            this.cancel();
-        },
-    },
-    computed: {
-        typeToClass() {
-            return "rule-edit-" + this.ruleType.replace(/_/g, "-");
-        },
-    },
-};
+     
 
 const StateDiv = {
     template: `

From 379ceee29ca9bdbea6fcaf220044185667ba20c7 Mon Sep 17 00:00:00 2001
From: Assunta DeSanto <adesanto@lhup.edu>
Date: Wed, 8 Apr 2020 18:11:55 -0400
Subject: [PATCH 801/853] fixing a typo

---
 .../scripts/components/RuleBuilder/RuleTargetComponent.vue      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue b/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
index ec3e7dd890d3..d7358ce8a518 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
@@ -1,5 +1,5 @@
 <template>
-    template: `<a class="rule-link dropdown-item" href="javascript:void(0)" :class="linkClassName" @click="builder.addNewRule(ruleType)">{{title}}</a>`,
+    <a class="rule-link dropdown-item" href="javascript:void(0)" :class="linkClassName" @click="builder.addNewRule(ruleType)">{{title}}</a>
 </template>
 
 <script>

From 86266dfccab6f30ea8ed71ee8520cbf8ab43329c Mon Sep 17 00:00:00 2001
From: Assunta DeSanto <adesanto@lhup.edu>
Date: Thu, 9 Apr 2020 10:23:43 -0400
Subject: [PATCH 802/853] refactored additional classes

---
 .../RuleBuilder/RuleModalFooter.vue           | 10 ++++++
 .../RuleBuilder/RuleModalHeader.vue           |  3 ++
 .../RuleBuilder/RuleModalMiddle.vue           |  3 ++
 .../components/RuleBuilder/StateDiv.vue       |  5 +++
 .../components/RuleCollectionBuilder.vue      | 32 +++----------------
 5 files changed, 25 insertions(+), 28 deletions(-)
 create mode 100644 client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue
 create mode 100644 client/galaxy/scripts/components/RuleBuilder/RuleModalHeader.vue
 create mode 100644 client/galaxy/scripts/components/RuleBuilder/RuleModalMiddle.vue
 create mode 100644 client/galaxy/scripts/components/RuleBuilder/StateDiv.vue

diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue b/client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue
new file mode 100644
index 000000000000..6cbf2db28c49
--- /dev/null
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue
@@ -0,0 +1,10 @@
+<template>
+    <div class="rule-footer footer flex-row no-flex">
+        <slot name="inputs"></slot>
+        <div class="actions clear vertically-spaced">
+            <div class="main-options float-right">
+                <slot></slot>
+            </div>
+        </div>
+    </div>`,
+</template>
\ No newline at end of file
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleModalHeader.vue b/client/galaxy/scripts/components/RuleBuilder/RuleModalHeader.vue
new file mode 100644
index 000000000000..ccd1c57734f9
--- /dev/null
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleModalHeader.vue
@@ -0,0 +1,3 @@
+<template>
+    <div class="header flex-row no-flex"><slot></slot></div>
+</template>
\ No newline at end of file
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleModalMiddle.vue b/client/galaxy/scripts/components/RuleBuilder/RuleModalMiddle.vue
new file mode 100644
index 000000000000..745fa17ceffd
--- /dev/null
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleModalMiddle.vue
@@ -0,0 +1,3 @@
+<template>
+    <div class="middle flex-row flex-row-container"><slot></slot></div>
+</template>
\ No newline at end of file
diff --git a/client/galaxy/scripts/components/RuleBuilder/StateDiv.vue b/client/galaxy/scripts/components/RuleBuilder/StateDiv.vue
new file mode 100644
index 000000000000..c7cc9eb12923
--- /dev/null
+++ b/client/galaxy/scripts/components/RuleBuilder/StateDiv.vue
@@ -0,0 +1,5 @@
+<template>
+    <div class="rule-collection-creator collection-creator flex-row-container">
+        <slot></slot>
+    </div>
+</template>
\ No newline at end of file
diff --git a/client/galaxy/scripts/components/RuleCollectionBuilder.vue b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
index 60e5ed92e537..5f4098da3e62 100644
--- a/client/galaxy/scripts/components/RuleCollectionBuilder.vue
+++ b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
@@ -582,40 +582,16 @@ import RuleDisplay from "components/RuleBuilder/RuleDisplay";
 import IdentifierDisplay from "components/RuleBuilder/IdentifierDisplay";
 import RuleTargetComponent from "components/RuleBuilder/RuleTargetComponent";
 import RuleComponent from "components/RuleBuilder/RuleComponent";
+import RuleModalHeader from "components/RuleBuilder/RuleModalHeader";
+import RuleModalMiddle from "components/RuleBuilder/RuleModalMiddle";
+import RuleModalFooter from "components/RuleBuilder/RuleModalFooter";
+import StateDiv from "components/RuleBuilder/StateDiv";
 
 
 Vue.use(BootstrapVue);
 
 const RULES = RuleDefs.RULES;
 const MAPPING_TARGETS = RuleDefs.MAPPING_TARGETS;
-     
-
-const StateDiv = {
-    template: `
-        <div class="rule-collection-creator collection-creator flex-row-container">
-            <slot></slot>
-        </div>`,
-};
-
-const RuleModalHeader = {
-    template: `<div class="header flex-row no-flex"><slot></slot></div>`,
-};
-
-const RuleModalMiddle = {
-    template: `<div class="middle flex-row flex-row-container"><slot></slot></div>`,
-};
-
-const RuleModalFooter = {
-    template: `
-        <div class="rule-footer footer flex-row no-flex">
-            <slot name="inputs"></slot>
-            <div class="actions clear vertically-spaced">
-                <div class="main-options float-right">
-                    <slot></slot>
-                </div>
-            </div>
-        </div>`,
-};
 
 export default {
     data: function () {

From 34111c5ffe1f916bf6b55f6d7bf62cb5d23491a9 Mon Sep 17 00:00:00 2001
From: Assunta DeSanto <adesanto@lhup.edu>
Date: Thu, 9 Apr 2020 11:03:03 -0400
Subject: [PATCH 803/853] fixing a typo

---
 .../scripts/components/RuleBuilder/RegularExpressionInput.vue    | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue b/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue
index 9437edae40cf..f5f453a8fd41 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue
@@ -28,5 +28,6 @@ export default {
                 `Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in <a href="https://pythonforbiologists.com/regular-expressions/">this Python for Biologists tutorial</a>.`
             );
         }
+    }
 }
 </script> 
\ No newline at end of file

From d0821eea321b05067549b6f1f234521728b4d149 Mon Sep 17 00:00:00 2001
From: Assunta DeSanto <adesanto@lhup.edu>
Date: Thu, 9 Apr 2020 11:32:02 -0400
Subject: [PATCH 804/853] fixing another typo. This is why you shouldn't copy
 and paste

---
 .../galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue   | 2 +-
 .../scripts/components/RuleBuilder/RuleTargetComponent.vue      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue b/client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue
index 6cbf2db28c49..1cf35a95eb88 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue
@@ -6,5 +6,5 @@
                 <slot></slot>
             </div>
         </div>
-    </div>`,
+    </div>
 </template>
\ No newline at end of file
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue b/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
index d7358ce8a518..601d12387b01 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
@@ -20,6 +20,6 @@ export default {
         title() {
             return RULES[this.ruleType].title;
         },
-    },
+    }
 }
 </script>
\ No newline at end of file

From ae48ebe8660f38fb3ce3b18fd2eac94ebc125b32 Mon Sep 17 00:00:00 2001
From: Assunta DeSanto <adesanto@lhup.edu>
Date: Mon, 13 Apr 2020 09:40:34 -0400
Subject: [PATCH 805/853] adding in imports that were causing an error

---
 .../scripts/components/RuleBuilder/IdentifierDisplay.vue       | 3 +++
 client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue   | 3 +++
 .../scripts/components/RuleBuilder/RuleTargetComponent.vue     | 3 +++
 3 files changed, 9 insertions(+)

diff --git a/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue b/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
index fd5659c73be4..7c821e2ae5eb 100644
--- a/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
@@ -7,6 +7,9 @@
 </template>
 
 <script>
+import RuleDefs from "mvc/rules/rule-definitions";
+MAPPING_TARGETS = RuleDefs.MAPPING_TARGETS;
+
 export default{
     props: {
         type: {
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue b/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue
index c51377581f81..f0d4501abafe 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue
@@ -16,6 +16,9 @@
 </template>
 
 <script>
+import RuleDefs from "mvc/rules/rule-definitions";
+const RULES = RuleDefs.RULES;
+
 export default {
     props: {
         rule: {
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue b/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
index 601d12387b01..d81805c26e89 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
@@ -3,6 +3,9 @@
 </template>
 
 <script>
+import RuleDefs from "mvc/rules/rule-definitions";
+const RULES = RuleDefs.RULES;
+
 export default {
     props: {
         ruleType: {

From a982cf4034fa713ca0fbdfa50c711184f86c3614 Mon Sep 17 00:00:00 2001
From: Assunta DeSanto <adesanto@lhup.edu>
Date: Mon, 13 Apr 2020 10:08:41 -0400
Subject: [PATCH 806/853] forgot to declare type

---
 .../galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue b/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
index 7c821e2ae5eb..9f0b103dc5dd 100644
--- a/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
@@ -8,7 +8,7 @@
 
 <script>
 import RuleDefs from "mvc/rules/rule-definitions";
-MAPPING_TARGETS = RuleDefs.MAPPING_TARGETS;
+const MAPPING_TARGETS = RuleDefs.MAPPING_TARGETS;
 
 export default{
     props: {

From 5e544790af2a12a3a88ac1d5caceb1478ce952a6 Mon Sep 17 00:00:00 2001
From: Assunta DeSanto <adesanto@lhup.edu>
Date: Thu, 16 Apr 2020 10:40:17 -0400
Subject: [PATCH 807/853] adding _l and Vue imports where they js_lint
 indicated errors

---
 client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue | 1 +
 .../galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue | 1 +
 .../scripts/components/RuleBuilder/RegularExpressionInput.vue   | 2 ++
 client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue  | 2 ++
 client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue    | 1 +
 .../scripts/components/RuleBuilder/RuleTargetComponent.vue      | 2 +-
 6 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue b/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue
index 764ab9690bbb..a23a929a6398 100644
--- a/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue
@@ -37,6 +37,7 @@
 </template>
 
 <script>
+import Vue from "vue";
 import _l from "utils/localization";
 import Select2 from "components/Select2";
 export default {
diff --git a/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue b/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
index 9f0b103dc5dd..9cfb211924e3 100644
--- a/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
@@ -7,6 +7,7 @@
 </template>
 
 <script>
+import _l from "utils/localization";
 import RuleDefs from "mvc/rules/rule-definitions";
 const MAPPING_TARGETS = RuleDefs.MAPPING_TARGETS;
 
diff --git a/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue b/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue
index f5f453a8fd41..2cd375bc95db 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue
@@ -7,6 +7,8 @@
 </template>
 
 <script>
+import _l from "utils/localization";
+
 export default {
     props: {
         target: {
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue b/client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue
index 826c0fda1c02..cbeacf299773 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue
@@ -9,6 +9,8 @@
 </template>
 
 <script>
+import _l from "utils/localization";
+
 export default {
     data: function () {
         return {
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue b/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue
index f0d4501abafe..d3188159d6c7 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue
@@ -16,6 +16,7 @@
 </template>
 
 <script>
+import _l from "utils/localization";
 import RuleDefs from "mvc/rules/rule-definitions";
 const RULES = RuleDefs.RULES;
 
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue b/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
index d81805c26e89..ef622ae0b282 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
@@ -1,5 +1,5 @@
 <template>
-    <a class="rule-link dropdown-item" href="javascript:void(0)" :class="linkClassName" @click="builder.addNewRule(ruleType)">{{title}}</a>
+    <a class="rule-link dropdown-item" href="javascript:void(0)" :class="linkClassName" @click="builder.addNewRule(ruleType)">{{ title }}</a>
 </template>
 
 <script>

From fe23ee0affaf5ca0880a91da7578d00288aaf017 Mon Sep 17 00:00:00 2001
From: assuntad23 <assuntad@localhost.localdomain>
Date: Fri, 17 Apr 2020 09:35:50 -0400
Subject: [PATCH 808/853] fixed v-for issue on js_lint

---
 .../scripts/components/RuleBuilder/ColumnSelector.vue     | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue b/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue
index a23a929a6398..45773eb356d9 100644
--- a/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue
@@ -3,7 +3,7 @@
         <label class="d-flex justify-content-end align-items-center">
             <span class="mr-auto" v-b-tooltip.hover :title="help">{{ label }}</span>
             <div class="mr-1" v-b-tooltip.hover :title="title"><select2 :value="target" @input="handleInput" :multiple="multiple">
-                <option v-for="(col, index) in colHeaders" :value="index">{{ col }}</option>
+                <option v-for="(col, index) in colHeaders" :value="index" :key="col">{{ col }}</option>
             </select2></div>
             <slot></slot>
         </label>
@@ -13,8 +13,8 @@
         <slot></slot>
         <ol>
             <li v-for="(targetEl, index) in target"
-                v-bind:index="index"
-                v-bind:key="targetEl"
+                :index="index"
+                :key="targetEl"
                 class="rule-column-selector-target">
                 {{ colHeaders[targetEl] }}
                 <span class="fa fa-times rule-column-selector-target-remove" @click="handleRemove(index)"></span>
@@ -28,7 +28,7 @@
                 <span class="rule-column-selector-target-select" v-else>
                     <select2 @input="handleAdd" placeholder="Select a column">
                         <option /><!-- empty option selection for placeholder -->
-                        <option v-for="(col, index) in remainingHeaders" :value="index">{{ col }}</option>
+                        <option v-for="(col, index) in remainingHeaders" :value="index" :key="col">{{ col }}</option>
                     </select2>
                 </span>
             </li>

From 3b52d61ee652ad2c37257096f4829e882f94a9b1 Mon Sep 17 00:00:00 2001
From: assuntad23 <assuntad@localhost.localdomain>
Date: Fri, 17 Apr 2020 09:50:07 -0400
Subject: [PATCH 809/853] Fixed minor formatting issues

---
 .../components/RuleBuilder/ColumnSelector.vue | 25 +++++++++++--------
 .../RuleBuilder/IdentifierDisplay.vue         |  8 +++---
 .../RuleBuilder/RegularExpressionInput.vue    | 18 +++++++++----
 .../components/RuleBuilder/RuleComponent.vue  |  6 ++---
 .../components/RuleBuilder/RuleDisplay.vue    |  7 +++---
 .../RuleBuilder/RuleModalFooter.vue           |  2 +-
 .../RuleBuilder/RuleModalHeader.vue           |  2 +-
 .../RuleBuilder/RuleModalMiddle.vue           |  2 +-
 .../RuleBuilder/RuleTargetComponent.vue       | 14 ++++++++---
 .../components/RuleBuilder/StateDiv.vue       |  2 +-
 .../components/RuleCollectionBuilder.vue      |  1 -
 11 files changed, 51 insertions(+), 36 deletions(-)

diff --git a/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue b/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue
index 45773eb356d9..195d777edc3b 100644
--- a/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue
@@ -2,9 +2,11 @@
     <div class="rule-column-selector" v-if="!multiple || !ordered">
         <label class="d-flex justify-content-end align-items-center">
             <span class="mr-auto" v-b-tooltip.hover :title="help">{{ label }}</span>
-            <div class="mr-1" v-b-tooltip.hover :title="title"><select2 :value="target" @input="handleInput" :multiple="multiple">
-                <option v-for="(col, index) in colHeaders" :value="index" :key="col">{{ col }}</option>
-            </select2></div>
+            <div class="mr-1" v-b-tooltip.hover :title="title">
+                <select2 :value="target" @input="handleInput" :multiple="multiple">
+                    <option v-for="(col, index) in colHeaders" :value="index" :key="col">{{ col }}</option>
+                </select2>
+            </div>
             <slot></slot>
         </label>
     </div>
@@ -12,14 +14,15 @@
         <span>{{ label }}</span>
         <slot></slot>
         <ol>
-            <li v-for="(targetEl, index) in target"
-                :index="index"
-                :key="targetEl"
-                class="rule-column-selector-target">
+            <li v-for="(targetEl, index) in target" :index="index" :key="targetEl" class="rule-column-selector-target">
                 {{ colHeaders[targetEl] }}
                 <span class="fa fa-times rule-column-selector-target-remove" @click="handleRemove(index)"></span>
                 <span class="fa fa-arrow-up rule-column-selector-up" v-if="index !== 0" @click="moveUp(index)"></span>
-                <span class="fa fa-arrow-down rule-column-selector-down" v-if="index < target.length - 1" @click="moveUp(index + 1)"></span>
+                <span
+                    class="fa fa-arrow-down rule-column-selector-down"
+                    v-if="index < target.length - 1"
+                    @click="moveUp(index + 1)"
+                ></span>
             </li>
             <li v-if="this.target.length < this.colHeaders.length">
                 <span class="rule-column-selector-target-add" v-if="!orderedEdit">
@@ -130,6 +133,6 @@ export default {
             Vue.set(this.target, value - 1, this.target[value]);
             Vue.set(this.target, value, swapVal);
         },
-    }
-}
-</script> 
\ No newline at end of file
+    },
+};
+</script>
diff --git a/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue b/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
index 9cfb211924e3..54f1ce1ca4b4 100644
--- a/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue
@@ -11,7 +11,7 @@ import _l from "utils/localization";
 import RuleDefs from "mvc/rules/rule-definitions";
 const MAPPING_TARGETS = RuleDefs.MAPPING_TARGETS;
 
-export default{
+export default {
     props: {
         type: {
             type: String,
@@ -49,6 +49,6 @@ export default{
         columnsLabel() {
             return RuleDefs.columnDisplay(this.columns, this.colHeaders);
         },
-    }
-}
-</script>
\ No newline at end of file
+    },
+};
+</script>
diff --git a/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue b/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue
index 2cd375bc95db..36f65600040d 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue
@@ -2,7 +2,15 @@
     <div>
         <label for="regular_expression" v-b-tooltip.hover :title="title">{{ label }}</label>
         <span v-b-popover.html="popoverContent" :title="popoverTitle" class="fa fa-question"></span>
-        <input v-b-tooltip.hover.left :title="title" name="regular_expression" class="rule-regular-expression" type="text" :value="target" @input="$emit('update:target', $event.target.value)" />
+        <input
+            v-b-tooltip.hover.left
+            :title="title"
+            name="regular_expression"
+            class="rule-regular-expression"
+            type="text"
+            :value="target"
+            @input="$emit('update:target', $event.target.value)"
+        />
     </div>
 </template>
 
@@ -29,7 +37,7 @@ export default {
             return _l(
                 `Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in <a href="https://pythonforbiologists.com/regular-expressions/">this Python for Biologists tutorial</a>.`
             );
-        }
-    }
-}
-</script> 
\ No newline at end of file
+        },
+    },
+};
+</script>
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue b/client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue
index cbeacf299773..474e6cbc4a4a 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue
@@ -2,8 +2,8 @@
     <div v-if="ruleType == displayRuleType" class="rule-editor" :class="typeToClass">
         <slot></slot>
         <div class="buttons rule-edit-buttons d-flex justify-content-end">
-           <button type="button" class="btn rule-editor-cancel mr-1" @click="cancel">{{ cancelLabel }}</button>
-           <button type="button" class="btn btn-primary rule-editor-ok" @click="okay">{{ applyLabel }}</button>
+            <button type="button" class="btn rule-editor-cancel mr-1" @click="cancel">{{ cancelLabel }}</button>
+            <button type="button" class="btn btn-primary rule-editor-ok" @click="okay">{{ applyLabel }}</button>
         </div>
     </div>
 </template>
@@ -44,5 +44,5 @@ export default {
             return "rule-edit-" + this.ruleType.replace(/_/g, "-");
         },
     },
-}
+};
 </script>
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue b/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue
index d3188159d6c7..1d52daf80119 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue
@@ -1,4 +1,3 @@
-
 <template>
     <li class="rule">
         <span class="rule-display">
@@ -50,6 +49,6 @@ export default {
         remove() {
             this.$emit("remove");
         },
-    }
-}
-</script>
\ No newline at end of file
+    },
+};
+</script>
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue b/client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue
index 1cf35a95eb88..fc2a3bfe7390 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue
@@ -7,4 +7,4 @@
             </div>
         </div>
     </div>
-</template>
\ No newline at end of file
+</template>
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleModalHeader.vue b/client/galaxy/scripts/components/RuleBuilder/RuleModalHeader.vue
index ccd1c57734f9..9ea12aefa61d 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleModalHeader.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleModalHeader.vue
@@ -1,3 +1,3 @@
 <template>
     <div class="header flex-row no-flex"><slot></slot></div>
-</template>
\ No newline at end of file
+</template>
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleModalMiddle.vue b/client/galaxy/scripts/components/RuleBuilder/RuleModalMiddle.vue
index 745fa17ceffd..35fca19d00ad 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleModalMiddle.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleModalMiddle.vue
@@ -1,3 +1,3 @@
 <template>
     <div class="middle flex-row flex-row-container"><slot></slot></div>
-</template>
\ No newline at end of file
+</template>
diff --git a/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue b/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
index ef622ae0b282..aeb4d07d1df8 100644
--- a/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue
@@ -1,5 +1,11 @@
 <template>
-    <a class="rule-link dropdown-item" href="javascript:void(0)" :class="linkClassName" @click="builder.addNewRule(ruleType)">{{ title }}</a>
+    <a
+        class="rule-link dropdown-item"
+        href="javascript:void(0)"
+        :class="linkClassName"
+        @click="builder.addNewRule(ruleType)"
+        >{{ title }}</a
+    >
 </template>
 
 <script>
@@ -23,6 +29,6 @@ export default {
         title() {
             return RULES[this.ruleType].title;
         },
-    }
-}
-</script>
\ No newline at end of file
+    },
+};
+</script>
diff --git a/client/galaxy/scripts/components/RuleBuilder/StateDiv.vue b/client/galaxy/scripts/components/RuleBuilder/StateDiv.vue
index c7cc9eb12923..2f06d8daf7fb 100644
--- a/client/galaxy/scripts/components/RuleBuilder/StateDiv.vue
+++ b/client/galaxy/scripts/components/RuleBuilder/StateDiv.vue
@@ -2,4 +2,4 @@
     <div class="rule-collection-creator collection-creator flex-row-container">
         <slot></slot>
     </div>
-</template>
\ No newline at end of file
+</template>
diff --git a/client/galaxy/scripts/components/RuleCollectionBuilder.vue b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
index 5f4098da3e62..ee2162d7cb8b 100644
--- a/client/galaxy/scripts/components/RuleCollectionBuilder.vue
+++ b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
@@ -587,7 +587,6 @@ import RuleModalMiddle from "components/RuleBuilder/RuleModalMiddle";
 import RuleModalFooter from "components/RuleBuilder/RuleModalFooter";
 import StateDiv from "components/RuleBuilder/StateDiv";
 
-
 Vue.use(BootstrapVue);
 
 const RULES = RuleDefs.RULES;

From 7bcd617c9f8558f5292ca369da596b329a4db306 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sat, 28 Mar 2020 14:38:38 -0400
Subject: [PATCH 810/853] Change session timeout redirect URL to login
 entrypoint.

---
 lib/galaxy/web/framework/webapp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py
index d77b230a2752..179e6bd41f0c 100644
--- a/lib/galaxy/web/framework/webapp.py
+++ b/lib/galaxy/web/framework/webapp.py
@@ -251,7 +251,7 @@ def __init__(self, environ, app, webapp, session_cookie=None):
                         self.user = None
                         self.galaxy_session = None
                     else:
-                        self.response.send_redirect(url_for(controller='user',
+                        self.response.send_redirect(url_for(controller='root',
                                                      action='login',
                                                      message="You have been logged out due to inactivity.  Please log in again to continue using Galaxy.",
                                                      status='info',

From 5ca5d015c944ba5694ebc1c95c5b73e70333bfb9 Mon Sep 17 00:00:00 2001
From: assuntad23 <assuntad@localhost.localdomain>
Date: Fri, 17 Apr 2020 12:47:43 -0400
Subject: [PATCH 811/853] Changed CSS overflow property from scroll to hidden
 to make table scrollable

---
 .../galaxy/scripts/components/RuleCollectionBuilder.vue   | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/client/galaxy/scripts/components/RuleCollectionBuilder.vue b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
index d4d99436d373..f8bb6d6696d7 100644
--- a/client/galaxy/scripts/components/RuleCollectionBuilder.vue
+++ b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
@@ -446,7 +446,7 @@
                         :data="hotData.data"
                         :col-headers="colHeadersDisplay"
                         :read-only="true"
-                        stretch-h="all"
+                        :stretch-h="all"
                     >
                     </hot-table>
                 </div>
@@ -1977,19 +1977,19 @@ export default {
 <style>
 .table-column {
     width: 100%;
-    /* overflow: scroll; */
+    overflow: hidden;
 }
 .select2-container {
     min-width: 60px;
 }
 .vertical #hot-table {
     width: 100%;
-    overflow: scroll;
+    overflow: hidden;
     height: 400px;
 }
 .horizontal #hot-table {
     width: 100%;
-    overflow: scroll;
+    overflow: hidden;
     height: 250px;
 }
 .rule-builder-body {

From c5084f4f37d61b24feab0d777be50508a3fd8cf0 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <jos.to.new@gmail.com>
Date: Fri, 17 Apr 2020 19:19:09 +0200
Subject: [PATCH 812/853] implent tests

---
 .../components/JobMetrics/JobMetrics.test.js  | 60 +++++++++++++++++++
 .../components/JobMetrics/JobMetrics.vue      | 14 +++--
 doc/source/admin/galaxy_options.rst           |  4 +-
 3 files changed, 73 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/components/JobMetrics/JobMetrics.test.js b/client/galaxy/scripts/components/JobMetrics/JobMetrics.test.js
index 0a97c76206ea..ccf5122e8028 100644
--- a/client/galaxy/scripts/components/JobMetrics/JobMetrics.test.js
+++ b/client/galaxy/scripts/components/JobMetrics/JobMetrics.test.js
@@ -5,6 +5,7 @@ import { mount, createLocalVue } from "@vue/test-utils";
 import { createStore } from "../../store";
 import flushPromises from "flush-promises";
 import JobMetrics from "./JobMetrics";
+import ec2 from "./ec2.json";
 
 const JOB_ID = "moo";
 
@@ -65,4 +66,63 @@ describe("JobMetrics/JobMetrics.vue", () => {
         expect(metricsTables.at(1).find(".metrics_plugin_title").text()).to.equals("extended");
         expect(metricsTables.at(1).findAll("tr").length).to.equals(1);
     });
+
+    it("should render correct AWS Estimates", async () => {
+        let deriveRenderedAwsEstimate = async (cores, seconds, memory) => {
+            const JOB_ID = Math.random().toString(36).substring(2);
+            const propsData = {
+                jobId: JOB_ID,
+                aws_estimate: "True",
+            };
+            const metricsResponse = [
+                { plugin: "core", name: "galaxy_slots", raw_value: cores },
+                { plugin: "core", name: "runtime_seconds", raw_value: seconds },
+                { plugin: "core", name: "galaxy_memory_mb", raw_value: memory },
+            ];
+            axiosMock.onGet(`/api/jobs/${JOB_ID}/metrics`).reply(200, metricsResponse);
+            const wrapper = mount(JobMetrics, {
+                store: testStore,
+                propsData,
+                localVue,
+            });
+            // Wait for axios and rendering.
+            await flushPromises();
+
+            const estimates = {};
+
+            if (!wrapper.find("#aws-estimate").exists()) return false;
+
+            estimates.cost = wrapper.find("#aws-estimate > b").text();
+            estimates.vcpus = wrapper.find("#aws_vcpus").text();
+            estimates.cpu = wrapper.find("#aws_cpu").text();
+            estimates.mem = wrapper.find("#aws_mem").text();
+            estimates.name = wrapper.find("#aws_name").text();
+
+            return estimates;
+        };
+        let assertAwsInstance = (estimates) => {
+            const instance = ec2.find((instance) => estimates.name === instance.name);
+            expect(estimates.mem).to.equals(instance.mem.toString());
+            expect(estimates.vcpus).to.equals(instance.vcpus.toString());
+            expect(estimates.cpu).to.equals(instance.cpu.toString());
+        };
+
+        let estimates_small = await deriveRenderedAwsEstimate("1.0000000", "9.0000000", "2048.0000000");
+
+        expect(estimates_small.name).to.equals("t2.small");
+        expect(estimates_small.cost).to.equals("0.00 USD");
+        assertAwsInstance(estimates_small);
+
+        let estimates_large = await deriveRenderedAwsEstimate("40.0000000", "18000.0000000", "194560.0000000");
+        expect(estimates_large.name).to.equals("m5d.12xlarge");
+        expect(estimates_large.cost).to.equals("16.32 USD");
+        assertAwsInstance(estimates_large);
+
+        let estimates_not_available = await deriveRenderedAwsEstimate(
+            "99999.0000000",
+            "18000.0000000",
+            "99999.0000000"
+        );
+        expect(estimates_not_available).to.equals(false);
+    });
 });
diff --git a/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue b/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue
index 8bd64ae7b3f4..9e148322c302 100644
--- a/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue
+++ b/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue
@@ -13,13 +13,18 @@
             </table>
         </div>
 
-        <div v-if="isAwsEstimate && awsEstimate">
+        <div id="aws-estimate" v-if="isAwsEstimate && awsEstimate">
             <h3>AWS estimate</h3>
             <b>{{ awsEstimate.price }} USD</b><br />
             This job requested {{ awsEstimate.vcpus }} cores and {{ awsEstimate.memory }} Gb. Given this, the smallest
-            EC2 machine we could find is {{ awsEstimate.instance.name }} ({{ awsEstimate.instance.mem }} GB /
-            {{ awsEstimate.instance.vcpus }} vCPUs / {{ awsEstimate.instance.cpu }}). That instance is priced at
-            {{ awsEstimate.instance.price }} USD/hour.
+            EC2 machine we could find is <span id="aws_name">{{ awsEstimate.instance.name }}</span> (<span
+                id="aws_mem"
+                >{{ awsEstimate.instance.mem }}</span
+            >
+            GB / <span id="aws_vcpus">{{ awsEstimate.instance.vcpus }}</span> vCPUs /
+            <span id="aws_cpu">{{ awsEstimate.instance.cpu }}</span
+            >). That instance is priced at {{ awsEstimate.instance.price }} USD/hour.<br />
+            Please note, that those numbers are only estimates, all jobs are always free of charge for all users.
         </div>
     </div>
 </template>
@@ -91,6 +96,7 @@ export default {
             aws.instance = ec2.find((ec) => {
                 return ec.mem >= aws.memory && ec.vcpus >= aws.vcpus;
             });
+            if (aws.instance === undefined) return;
             aws.price = ((aws.seconds * aws.instance.price) / 3600).toFixed(2);
             return aws;
         },
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 182a7c01da75..f20e111ced85 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -1381,7 +1381,9 @@
 ~~~~~~~~~~~~~~~~
 
 :Description:
-    Enable AWS estimate.
+    This flag enables an AWS cost estimate for every job based on their runtime matrices.
+    CPU, RAM and runtime usage is mapped against AWS pricing table.
+    Please note, that those numbers are only estimates.
 :Default: ``false``
 :Type: bool
 

From 8e4dd10baedcf88a5f559f80cf4f9dd9c34114db Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Fri, 17 Apr 2020 15:12:14 -0400
Subject: [PATCH 813/853] Add test for admin toolshed operations.

- Search
- Install
- Uninstall

Also adds some selectors in navigation.yml and element IDs where
appropriate to make it a little easier for the tests to find the right
DOM elements.
---
 .../scripts/components/Toolshed/Index.vue     |  1 +
 .../InstallationSettings.vue                  |  2 +-
 .../Toolshed/SearchList/Repositories.vue      |  2 +-
 lib/galaxy/selenium/navigates_galaxy.py       |  4 +++
 lib/galaxy/selenium/navigation.yml            |  5 +++
 lib/galaxy_test/selenium/test_admin_app.py    | 35 +++++++++++++++++++
 6 files changed, 47 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/Toolshed/Index.vue b/client/galaxy/scripts/components/Toolshed/Index.vue
index 81506b3f3482..6c3e97acdfdf 100644
--- a/client/galaxy/scripts/components/Toolshed/Index.vue
+++ b/client/galaxy/scripts/components/Toolshed/Index.vue
@@ -4,6 +4,7 @@
         <div v-else>
             <b-input-group class="mb-3">
                 <b-input
+                    id="toolshed-repo-search"
                     placeholder="Search Repositories"
                     v-model="queryInput"
                     @input="delayQuery"
diff --git a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.vue b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.vue
index cca78c921c9e..abb45ac90bef 100644
--- a/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.vue
+++ b/client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.vue
@@ -1,5 +1,5 @@
 <template>
-    <b-modal :static="modalStatic" v-model="modalShow" @ok="onOk" @hide="onHide">
+    <b-modal id="repo-install-settings" :static="modalStatic" v-model="modalShow" @ok="onOk" @hide="onHide">
         <template v-slot:modal-header>
             <h4 class="title m-0">
                 {{ modalTitle }}
diff --git a/client/galaxy/scripts/components/Toolshed/SearchList/Repositories.vue b/client/galaxy/scripts/components/Toolshed/SearchList/Repositories.vue
index 8325f7b5b46d..d224337b5bd3 100644
--- a/client/galaxy/scripts/components/Toolshed/SearchList/Repositories.vue
+++ b/client/galaxy/scripts/components/Toolshed/SearchList/Repositories.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <b-table striped :items="repositories" :fields="fields">
+        <b-table striped id="shed-search-results" :items="repositories" :fields="fields">
             <template v-slot:cell(name)="row">
                 <b-link href="javascript:void(0)" role="button" class="font-weight-bold" @click="row.toggleDetails">
                     {{ row.item.name }}
diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index aef773816718..d84922aa153c 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -50,6 +50,10 @@
     JOB_COMPLETION=WaitType("job_completion", 30),
     # Wait time for a GIE to spawn.
     GIE_SPAWN=WaitType("gie_spawn", 30),
+    # Wait time for toolshed search
+    SHED_SEARCH=WaitType('shed_search', 30),
+    # Wait time for repository installation
+    REPO_INSTALL=WaitType('repo_install', 60),
 )
 
 # Choose a moderate wait type for operations that don't specify a type.
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index f5619a118cb3..7b0afca6420a 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -353,6 +353,11 @@ tour:
 
 admin:
 
+  toolshed:
+    selectors:
+      repo_search: '#toolshed-repo-search'
+      search_results: '#shed-search-results'
+
   index:
     selectors:
       datatypes: '#admin-link-datatypes'
diff --git a/lib/galaxy_test/selenium/test_admin_app.py b/lib/galaxy_test/selenium/test_admin_app.py
index 746b4a4bc5bb..3c78f7687168 100644
--- a/lib/galaxy_test/selenium/test_admin_app.py
+++ b/lib/galaxy_test/selenium/test_admin_app.py
@@ -8,6 +8,41 @@ class AdminAppTestCase(SeleniumTestCase):
 
     requires_admin = True
 
+    @selenium_test
+    @flakey # This test relies on an external server that may or may not be available to the testing environment.
+    def test_admin_toolshed(self):
+        admin_component = self.components.admin
+        self.admin_login()
+        self.admin_open()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.screenshot("admin_landing")
+        admin_component.index.toolshed.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.screenshot("admin_toolshed_landing")
+        # admin_component.toolshed.selectors.repo_search.wait_for_visible()
+        repo_search_input = self.driver.find_element_by_id("toolshed-repo-search")
+        repo_search_input.clear()
+        repo_search_input.send_keys('all_fasta')
+        self.sleep_for(self.wait_types.SHED_SEARCH)
+        self.screenshot("admin_toolshed_search")
+        admin_component.toolshed.search_results.wait_for_visible()
+        repository_row = self.driver.find_element_by_link_text('data_manager_fetch_genome_dbkeys_all_fasta')
+        repository_row.click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.screenshot('admin_toolshed_repo_details')
+        install_button = self.driver.find_element_by_xpath("(//button[contains(., 'Install')])[1]")
+        install_button.click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.screenshot('admin_toolshed_repo_install_settings')
+        ok_button = self.driver.find_element_by_xpath("//*[@id='repo-install-settings___BV_modal_footer_']/button[contains(., 'OK')]")
+        ok_button.click()
+        self.sleep_for(self.wait_types.REPO_INSTALL)
+        self.screenshot('admin_toolshed_repo_installed')
+        uninstall_button = self.driver.find_element_by_xpath("(//button[contains(., 'Uninstall')])[1]")
+        uninstall_button.click()
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+        self.screenshot('admin_toolshed_repo_uninstalled')
+
     @selenium_test
     def test_admin_server_display(self):
         admin_component = self.components.admin

From 8858339bf074e0ba6145bee14f7ba92a3190f0c1 Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Fri, 17 Apr 2020 15:33:05 -0400
Subject: [PATCH 814/853] Remove commented out wait, add some information in
 comments.

---
 lib/galaxy_test/selenium/test_admin_app.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy_test/selenium/test_admin_app.py b/lib/galaxy_test/selenium/test_admin_app.py
index 3c78f7687168..4fc9a9a3e37f 100644
--- a/lib/galaxy_test/selenium/test_admin_app.py
+++ b/lib/galaxy_test/selenium/test_admin_app.py
@@ -19,10 +19,12 @@ def test_admin_toolshed(self):
         admin_component.index.toolshed.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
         self.screenshot("admin_toolshed_landing")
-        # admin_component.toolshed.selectors.repo_search.wait_for_visible()
         repo_search_input = self.driver.find_element_by_id("toolshed-repo-search")
         repo_search_input.clear()
         repo_search_input.send_keys('all_fasta')
+        # If this hasn't succeeded after 30 seconds, the @flakey context should
+        # allow the test to still pass, since there should definitely be results
+        # after 30 seconds.
         self.sleep_for(self.wait_types.SHED_SEARCH)
         self.screenshot("admin_toolshed_search")
         admin_component.toolshed.search_results.wait_for_visible()
@@ -38,6 +40,8 @@ def test_admin_toolshed(self):
         ok_button.click()
         self.sleep_for(self.wait_types.REPO_INSTALL)
         self.screenshot('admin_toolshed_repo_installed')
+        # Unfortunately reusing the element isn't feasible, since the div
+        # containing the button gets replaced with a new div and button.
         uninstall_button = self.driver.find_element_by_xpath("(//button[contains(., 'Uninstall')])[1]")
         uninstall_button.click()
         self.sleep_for(self.wait_types.UX_TRANSITION)

From 923e25826f99995d5b91c628b3ffd88101c41376 Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Fri, 17 Apr 2020 15:34:19 -0400
Subject: [PATCH 815/853] Also be consistent with type of quotes used.

---
 lib/galaxy_test/selenium/test_admin_app.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy_test/selenium/test_admin_app.py b/lib/galaxy_test/selenium/test_admin_app.py
index 4fc9a9a3e37f..6e6d386a49fb 100644
--- a/lib/galaxy_test/selenium/test_admin_app.py
+++ b/lib/galaxy_test/selenium/test_admin_app.py
@@ -15,19 +15,20 @@ def test_admin_toolshed(self):
         self.admin_login()
         self.admin_open()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot("admin_landing")
+        self.screenshot('admin_landing')
         admin_component.index.toolshed.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot("admin_toolshed_landing")
-        repo_search_input = self.driver.find_element_by_id("toolshed-repo-search")
+        self.screenshot('admin_toolshed_landing')
+        repo_search_input = self.driver.find_element_by_id('toolshed-repo-search')
         repo_search_input.clear()
         repo_search_input.send_keys('all_fasta')
         # If this hasn't succeeded after 30 seconds, the @flakey context should
         # allow the test to still pass, since there should definitely be results
         # after 30 seconds.
         self.sleep_for(self.wait_types.SHED_SEARCH)
-        self.screenshot("admin_toolshed_search")
+        self.screenshot('admin_toolshed_search')
         admin_component.toolshed.search_results.wait_for_visible()
+        # It's very unlikely that this data manager will ever stop existing.
         repository_row = self.driver.find_element_by_link_text('data_manager_fetch_genome_dbkeys_all_fasta')
         repository_row.click()
         self.sleep_for(self.wait_types.UX_RENDER)

From a91bd79316695924758eb05463ab5cf781e61b15 Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Fri, 17 Apr 2020 16:03:51 -0400
Subject: [PATCH 816/853] Missing import, E261.

---
 lib/galaxy_test/selenium/test_admin_app.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy_test/selenium/test_admin_app.py b/lib/galaxy_test/selenium/test_admin_app.py
index 6e6d386a49fb..0ab96f01e84a 100644
--- a/lib/galaxy_test/selenium/test_admin_app.py
+++ b/lib/galaxy_test/selenium/test_admin_app.py
@@ -1,3 +1,4 @@
+from galaxy_test.base.populators import flakey
 from .framework import (
     selenium_test,
     SeleniumTestCase,
@@ -9,7 +10,7 @@ class AdminAppTestCase(SeleniumTestCase):
     requires_admin = True
 
     @selenium_test
-    @flakey # This test relies on an external server that may or may not be available to the testing environment.
+    @flakey  # This test relies on an external server that may or may not be available to the testing environment.
     def test_admin_toolshed(self):
         admin_component = self.components.admin
         self.admin_login()

From c77efbf89bfdd22d7838c9ceca9bce1478f93efa Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 20 Apr 2020 12:57:10 +0200
Subject: [PATCH 817/853] fix links in Galaxy xsd docs

---
 lib/galaxy/tool_util/xsd/galaxy.xsd | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index a812c6dc04d2..eda3402fadd6 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -79,7 +79,7 @@ the tool menu immediately following the hyperlink for the tool (based on the
         <xs:element name="stdio" type="Stdio" minOccurs="0"/>
         <xs:element name="help" type="xs:string" minOccurs="0">
           <xs:annotation gxdocs:best_practices="help-tag">
-            <xs:documentation xml:lang="en"><![CDATA[This tag set includes all of the necessary details of how to use the tool. This tag set should be included as the next to the last tag set, before citations, in the tool config. Tool help is written in reStructuredText. Included here is only an overview of a subset of features. For more information see http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html .
+            <xs:documentation xml:lang="en"><![CDATA[This tag set includes all of the necessary details of how to use the tool. This tag set should be included as the next to the last tag set, before citations, in the tool config. Tool help is written in reStructuredText. Included here is only an overview of a subset of features. For more information see [here](http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html).
 
 tag | details
 --- | -------
@@ -217,7 +217,7 @@ fragments be repeated in a file (for instance similar conditional branches,
 repeated options, etc...) or among tools in the same repository. Galaxy tools
 have a macro system to address this problem.
 
-For more information, see https://planemo.readthedocs.io/en/latest/writing_advanced.html#macros-reusable-elements</xs:documentation>
+For more information, see [planemo documentation](https://planemo.readthedocs.io/en/latest/writing_advanced.html#macros-reusable-elements)</xs:documentation>
     </xs:annotation>
     <xs:sequence>
       <xs:element name="import" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
@@ -3820,7 +3820,7 @@ Style used for tool provided metadata file (i.e.
 - this can be either "legacy" or "default". The default of tools with a profile
 of 17.09 or newer are "default", and "legacy" for older and tools and tools
 without a specified profile. A discussion of the differences between the styles
-can be found at https://github.com/galaxyproject/galaxy/pull/4437 .
+can be found [here](https://github.com/galaxyproject/galaxy/pull/4437).
 ]]></xs:documentation>
       </xs:annotation>
     </xs:attribute>
@@ -4174,9 +4174,9 @@ Describe datasets to dynamically collect after the job complete.
 There are many simple tools with examples of this element distributed with
 Galaxy, including:
 
-* https://github.com/galaxyproject/galaxy/tree/master/test/functional/tools/multi_output.xml
-* https://github.com/galaxyproject/galaxy/tree/master/test/functional/tools/multi_output_assign_primary.xml
-* https://github.com/galaxyproject/galaxy/tree/master/test/functional/tools/multi_output_configured.xml
+* [multi_output.xml](https://github.com/galaxyproject/galaxy/tree/master/test/functional/tools/multi_output.xml)
+* [multi_output_assign_primary.xml](https://github.com/galaxyproject/galaxy/tree/master/test/functional/tools/multi_output_assign_primary.xml)
+* [multi_output_configured.xml](https://github.com/galaxyproject/galaxy/tree/master/test/functional/tools/multi_output_configured.xml)
 
 More information can be found on Planemo's documentation for
 [multiple output files](https://planemo.readthedocs.io/en/latest/writing_advanced.html#multiple-output-files).
@@ -4234,9 +4234,9 @@ expressions after the job is complete.
 There are many simple tools with examples of this element distributed with
 Galaxy, including:
 
-* https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/collection_split_on_column.xml
-* https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/collection_creates_dynamic_list_of_pairs.xml
-* https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/collection_creates_dynamic_nested.xml
+* [collection_split_on_column.xml](https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/collection_split_on_column.xml)
+* [collection_creates_dynamic_list_of_pairs.xml](https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/collection_creates_dynamic_list_of_pairs.xml)
+* [collection_creates_dynamic_nested.xml](https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/collection_creates_dynamic_nested.xml)
 
 ]]></xs:documentation>
     </xs:annotation>
@@ -5138,7 +5138,7 @@ Tools may use exit codes to indicate specific execution errors. Many programs us
 
 The exit code's range can be any consecutive group of integers. More advanced ranges, such as noncontiguous ranges, are currently not supported. Ranges can be specified in the form "m:n", where m is the start integer and n is the end integer. If ":n" is specified, then the exit code will be compared against all integers less than or equal to n. If "m:" is used, then the exit code will be compared against all integers greater than or equal to m. If the exit code matches, then the error level is applied and the error's description is added to stderr. If a tool's exit code does not match any of the supplied ``<exit_code>`` tags' ranges, then no errors are applied to the tool's execution.
 
-Note that most Unix and Linux variants only support positive integers 0 to 255 for exit codes. If an exit code falls out of the range 0 to 255, the usual convention is to only use the lower 8 bits for the exit code. The only known exception is if a job is broken into subtasks using the tasks runner and one of those tasks is stopped with a POSIX signal. (Note that signals should be used as a last resort for terminating processes.) In those cases, the task will receive -1 times the signal number. For example, suppose that a job uses the tasks runner and 8 tasks are created for the job. If one of the tasks hangs, then a sysadmin may choose to send the "kill" signal, SIGKILL, to the process. In that case, the task (and its job) will exit with an exit code of -9. More on POSIX signals can be found at https://en.wikipedia.org/wiki/Unix_signal as well as man pages on "signal".
+Note that most Unix and Linux variants only support positive integers 0 to 255 for exit codes. If an exit code falls out of the range 0 to 255, the usual convention is to only use the lower 8 bits for the exit code. The only known exception is if a job is broken into subtasks using the tasks runner and one of those tasks is stopped with a POSIX signal. (Note that signals should be used as a last resort for terminating processes.) In those cases, the task will receive -1 times the signal number. For example, suppose that a job uses the tasks runner and 8 tasks are created for the job. If one of the tasks hangs, then a sysadmin may choose to send the "kill" signal, SIGKILL, to the process. In that case, the task (and its job) will exit with an exit code of -9. More on POSIX signals can be found at [wikipedia](https://en.wikipedia.org/wiki/Unix_signal) as well as man pages on "signal".
 
 The ``<exit_code>`` tag's supported attributes are as follows:
 

From 2d021f6506c896871d8bb8555be7a23d59d19b71 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 20 Apr 2020 13:35:27 +0200
Subject: [PATCH 818/853] Apply suggestions from code review

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/tool_util/xsd/galaxy.xsd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index eda3402fadd6..f3a68c200f14 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -79,7 +79,7 @@ the tool menu immediately following the hyperlink for the tool (based on the
         <xs:element name="stdio" type="Stdio" minOccurs="0"/>
         <xs:element name="help" type="xs:string" minOccurs="0">
           <xs:annotation gxdocs:best_practices="help-tag">
-            <xs:documentation xml:lang="en"><![CDATA[This tag set includes all of the necessary details of how to use the tool. This tag set should be included as the next to the last tag set, before citations, in the tool config. Tool help is written in reStructuredText. Included here is only an overview of a subset of features. For more information see [here](http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html).
+            <xs:documentation xml:lang="en"><![CDATA[This tag set includes all of the necessary details of how to use the tool. This tag set should be included as the next to the last tag set, before citations, in the tool config. Tool help is written in reStructuredText. Included here is only an overview of a subset of features. For more information see [here](https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html).
 
 tag | details
 --- | -------
@@ -5138,7 +5138,7 @@ Tools may use exit codes to indicate specific execution errors. Many programs us
 
 The exit code's range can be any consecutive group of integers. More advanced ranges, such as noncontiguous ranges, are currently not supported. Ranges can be specified in the form "m:n", where m is the start integer and n is the end integer. If ":n" is specified, then the exit code will be compared against all integers less than or equal to n. If "m:" is used, then the exit code will be compared against all integers greater than or equal to m. If the exit code matches, then the error level is applied and the error's description is added to stderr. If a tool's exit code does not match any of the supplied ``<exit_code>`` tags' ranges, then no errors are applied to the tool's execution.
 
-Note that most Unix and Linux variants only support positive integers 0 to 255 for exit codes. If an exit code falls out of the range 0 to 255, the usual convention is to only use the lower 8 bits for the exit code. The only known exception is if a job is broken into subtasks using the tasks runner and one of those tasks is stopped with a POSIX signal. (Note that signals should be used as a last resort for terminating processes.) In those cases, the task will receive -1 times the signal number. For example, suppose that a job uses the tasks runner and 8 tasks are created for the job. If one of the tasks hangs, then a sysadmin may choose to send the "kill" signal, SIGKILL, to the process. In that case, the task (and its job) will exit with an exit code of -9. More on POSIX signals can be found at [wikipedia](https://en.wikipedia.org/wiki/Unix_signal) as well as man pages on "signal".
+Note that most Unix and Linux variants only support positive integers 0 to 255 for exit codes. If an exit code falls outside of this range, the usual convention is to only use the lower 8 bits for the exit code. The only known exception is if a job is broken into subtasks using the tasks runner and one of those tasks is stopped with a POSIX signal. (Note that signals should be used as a last resort for terminating processes.) In those cases, the task will receive -1 times the signal number. For example, suppose that a job uses the tasks runner and 8 tasks are created for the job. If one of the tasks hangs, then a sysadmin may choose to send the "kill" signal, SIGKILL, to the process. In that case, the task (and its job) will exit with an exit code of -9. More on POSIX signals can be found on [Wikipedia](https://en.wikipedia.org/wiki/Signal_(IPC)) as well as on the man page for "signal" (``man 7 signal``).
 
 The ``<exit_code>`` tag's supported attributes are as follows:
 

From e9c0ac1ebba57c8312f9c6efadf31640536e8d32 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 20 Apr 2020 00:12:28 -0400
Subject: [PATCH 819/853] Add unit test for config values

---
 test/unit/config/test_config_values.py | 211 +++++++++++++++++++++++++
 1 file changed, 211 insertions(+)
 create mode 100644 test/unit/config/test_config_values.py

diff --git a/test/unit/config/test_config_values.py b/test/unit/config/test_config_values.py
new file mode 100644
index 000000000000..cf82ab50c4b1
--- /dev/null
+++ b/test/unit/config/test_config_values.py
@@ -0,0 +1,211 @@
+import os
+from collections import namedtuple
+from datetime import timedelta
+
+import pytest
+
+from galaxy import config
+from galaxy.util import listify
+
+TestData = namedtuple('TestData', ('key', 'expected', 'loaded'))
+
+# TODO: all these will be fixed
+DO_NOT_TEST = [
+    'database_connection',
+    'pretty_datetime_format',
+    'heartbeat_log',
+    'ftp_upload_dir_template',
+    'workflow_resource_params_mapper',
+    'user_tool_filters',
+    'user_tool_label_filters',
+    'amqp_internal_connection',
+]
+
+
+class ExpectedValues:
+
+    RESOLVERS = {
+        'disable_library_comptypes': [''],  # TODO: we can do better
+        'mulled_channels': listify,
+        'object_store_store_by': 'uuid',
+        'password_expiration_period': timedelta,
+        'persistent_communication_rooms': listify,
+        'statsd_host': '',  # TODO: do we need '' as the default?
+        'tool_config_file': listify,
+        'tool_data_table_config_path': listify,
+        'tool_filters': listify,
+        'tool_label_filters': listify,
+        'tool_section_filters': listify,
+        'toolbox_filter_base_modules': listify,
+        'use_remote_user': None,  # TODO: should be False (config logic incorrect)
+        'user_library_import_symlink_whitelist': listify,
+        'user_tool_section_filters': listify,
+    }
+    # RESOLVERS provides expected values for config options.
+    # - key: config option
+    # - value: expected value or a callable. The callable will be called with a
+    #   single argument, which is the default value of the config option.
+
+    def __init__(self, config):
+        self._config = config
+        self._load_paths()
+
+    def _load_paths(self):
+        self._expected_paths = {
+            'admin_tool_recommendations_path': self._in_config_dir('tool_recommendations_overwrite.yml'),
+            'auth_config_file': self._in_config_dir('auth_conf.xml'),
+            'build_sites_config_file': self._in_sample_dir('build_sites.yml.sample'),
+            'builds_file_path': self._in_root_dir('tool-data/shared/ucsc/builds.txt'),
+            'citation_cache_data_dir': self._in_data_dir('citations/data'),
+            'citation_cache_lock_dir': self._in_data_dir('citations/locks'),
+            'cluster_files_directory': self._in_data_dir('pbs'),
+            'config_dir': self._in_config_dir(),
+            'data_dir': self._in_data_dir(),
+            'data_manager_config_file': self._in_config_dir('data_manager_conf.xml'),
+            'datatypes_config_file': self._in_sample_dir('datatypes_conf.xml.sample'),
+            'dependency_resolvers_config_file': self._in_config_dir('dependency_resolvers_conf.xml'),
+            'dynamic_proxy_session_map': self._in_data_dir('session_map.sqlite'),
+            'file_path': self._in_data_dir('objects'),
+            'galaxy_data_manager_data_path': self._in_root_dir('tool-data'),
+            'integrated_tool_panel_config': self._in_managed_config_dir('integrated_tool_panel.xml'),
+            'interactivetools_map': self._in_data_dir('interactivetools_map.sqlite'),
+            'involucro_path': self._in_root_dir('involucro'),
+            'job_config_file': self._in_config_dir('job_conf.xml'),
+            'job_metrics_config_file': self._in_sample_dir('job_metrics_conf.xml.sample'),
+            'job_resource_params_file': self._in_config_dir('job_resource_params_conf.xml'),
+            'len_file_path': self._in_root_dir('tool-data/shared/ucsc/chrom'),
+            'managed_config_dir': self._in_managed_config_dir(),
+            'markdown_export_css': self._in_config_dir('markdown_export.css'),
+            'markdown_export_css_invocation_reports': self._in_config_dir('markdown_export_invocation_reports.css'),
+            'markdown_export_css_pages': self._in_config_dir('markdown_export_pages.css'),
+            'migrated_tools_config': self._in_managed_config_dir('migrated_tools_conf.xml'),
+            'mulled_resolution_cache_data_dir': self._in_data_dir('mulled/data'),
+            'mulled_resolution_cache_lock_dir': self._in_data_dir('mulled/locks'),
+            'new_file_path': self._in_data_dir('tmp'),
+            'object_store_config_file': self._in_config_dir('object_store_conf.xml'),
+            'oidc_backends_config_file': self._in_config_dir('oidc_backends_config.xml'),
+            'oidc_config_file': self._in_config_dir('oidc_config.xml'),
+            'openid_consumer_cache_path': self._in_data_dir('openid_consumer_cache'),
+            'sanitize_whitelist_file': self._in_managed_config_dir('sanitize_whitelist.txt'),
+            'shed_data_manager_config_file': self._in_managed_config_dir('shed_data_manager_conf.xml'),
+            'shed_tool_config_file': self._in_managed_config_dir('shed_tool_conf.xml'),
+            'shed_tool_data_path': self._in_root_dir('tool-data'),
+            'shed_tool_data_table_config': self._in_managed_config_dir('shed_tool_data_table_conf.xml'),
+            'template_cache_path': self._in_data_dir('compiled_templates'),
+            'tool_config_file': self._in_sample_dir('tool_conf.xml.sample'),
+            'tool_data_path': self._in_root_dir('tool-data'),
+            'tool_data_table_config_path': self._in_sample_dir('tool_data_table_conf.xml.sample'),
+            'tool_path': self._in_root_dir('tools'),
+            'tool_sheds_config_file': self._in_config_dir('tool_sheds_conf.xml'),
+            'tool_test_data_directories': self._in_root_dir('test-data'),
+            'user_preferences_extra_conf_path': self._in_config_dir('user_preferences_extra_conf.yml'),
+            'whitelist_file': self._in_config_dir('disposable_email_whitelist.conf'),
+            'workflow_resource_params_file': self._in_config_dir('workflow_resource_params_conf.xml'),
+            'workflow_schedulers_config_file': self._in_config_dir('workflow_schedulers_conf.xml'),
+        }
+        # _expected_paths provides expected values for config options that are paths. Each value is
+        # wrapped in a function that ensures that the path (a) is resolved w.r.t. its parent as per
+        # schema and/or config module; and (b) is an absolute path. The base config paths used by
+        # each function are tested separately (see tests of base config properties in this module).
+        # The values are hardcoded intentionally for the sake of keeping the test readable and
+        # simple. They correspond to schema defaults, and should be adjusted if the schema is
+        # modified.
+
+    def _in_root_dir(self, path=None):
+        return self._in_dir(self._config.root, path)
+
+    def _in_config_dir(self, path=None):
+        return self._in_dir(self._config.config_dir, path)
+
+    def _in_data_dir(self, path=None):
+        return self._in_dir(self._config.data_dir, path)
+
+    def _in_managed_config_dir(self, path=None):
+        return self._in_dir(self._config.managed_config_dir, path)
+
+    def _in_sample_dir(self, path=None):
+        return self._in_dir(self._config.sample_config_dir, path)
+
+    def _in_dir(self, _dir, path):
+        return os.path.join(_dir, path) if path else _dir
+
+    def get_value(self, key, data):
+        value = data.get('default')
+        # 1. If this is a path, resolve it
+        if key in self._expected_paths:
+            value = self._expected_paths[key]
+        # 2. AFTER resolving paths, apply resolver, if one exists
+        if key in ExpectedValues.RESOLVERS:
+            resolver = ExpectedValues.RESOLVERS[key]
+            if callable(resolver):
+                value = resolver(value)
+            else:
+                value = resolver
+        return value
+
+
+@pytest.fixture
+def mock_config_file(monkeypatch):
+    # Set this to return None to force the creation of base config directories
+    # in _set_config_directories(). Used to test the values of these directories only.
+    monkeypatch.setattr(config, 'find_config_file', lambda x: None)
+
+
+@pytest.fixture
+def mock_config_running_from_source(monkeypatch, mock_config_file):
+    # Simulated condition: running from source, config_file is None.
+    monkeypatch.setattr(config, 'running_from_source', True)
+
+
+@pytest.fixture
+def mock_config_running_not_from_source(monkeypatch, mock_config_file):
+    # Simulated condition: running not from source, config_file is None.
+    monkeypatch.setattr(config, 'running_from_source', False)
+
+
+@pytest.fixture
+def appconfig(monkeypatch):
+    return config.Configuration()
+
+
+def test_root(appconfig):
+    assert appconfig.root == os.path.abspath('.')
+
+
+def test_base_config_if_running_from_source(mock_config_running_from_source, appconfig):
+    assert not appconfig.config_file
+    assert appconfig.config_dir == os.path.join(appconfig.root, 'config')
+    assert appconfig.data_dir == os.path.join(appconfig.root, 'database')
+    assert appconfig.managed_config_dir == appconfig.config_dir
+
+
+def test_base_config_if_running_not_from_source(mock_config_running_not_from_source, appconfig):
+    assert not appconfig.config_file
+    assert appconfig.config_dir == os.getcwd()
+    assert appconfig.data_dir == os.path.join(appconfig.config_dir, 'data')
+    assert appconfig.managed_config_dir == os.path.join(appconfig.data_dir, 'config')
+
+
+def test_common_base_config(appconfig):
+    assert appconfig.shed_tools_dir == os.path.join(appconfig.data_dir, 'shed_tools')
+    assert appconfig.sample_config_dir == os.path.join(appconfig.root, 'lib', 'galaxy', 'config', 'sample')
+
+
+def get_config_data():
+    configuration = config.Configuration()
+    ev = ExpectedValues(configuration)
+    items = ((k, v) for k, v in configuration.schema.app_schema.items() if k not in DO_NOT_TEST)
+    for key, data in items:
+        expected = ev.get_value(key, data)
+        loaded = getattr(configuration, key)
+        test_data = TestData(key=key, expected=expected, loaded=loaded)
+        yield pytest.param(test_data)
+
+
+def get_key(test_data):
+    return test_data.key
+
+
+@pytest.mark.parametrize('test_data', get_config_data(), ids=get_key)
+def test_config_defaults(test_data):
+    assert test_data.expected == test_data.loaded

From e0d7d597798f0fff149bec8cad83782077c53264 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 20 Apr 2020 01:26:35 -0400
Subject: [PATCH 820/853] Always call listify with do_strip=True

Fixes 2 broken tests
---
 test/unit/config/test_config_values.py | 28 +++++++++++++++-----------
 1 file changed, 16 insertions(+), 12 deletions(-)

diff --git a/test/unit/config/test_config_values.py b/test/unit/config/test_config_values.py
index cf82ab50c4b1..e2b154feb852 100644
--- a/test/unit/config/test_config_values.py
+++ b/test/unit/config/test_config_values.py
@@ -16,30 +16,34 @@
     'heartbeat_log',
     'ftp_upload_dir_template',
     'workflow_resource_params_mapper',
-    'user_tool_filters',
-    'user_tool_label_filters',
     'amqp_internal_connection',
 ]
 
 
+def listify_strip(value):
+    return listify(value, do_strip=True)
+
+
 class ExpectedValues:
 
     RESOLVERS = {
         'disable_library_comptypes': [''],  # TODO: we can do better
-        'mulled_channels': listify,
+        'mulled_channels': listify_strip,
         'object_store_store_by': 'uuid',
         'password_expiration_period': timedelta,
-        'persistent_communication_rooms': listify,
+        'persistent_communication_rooms': listify_strip,
         'statsd_host': '',  # TODO: do we need '' as the default?
-        'tool_config_file': listify,
-        'tool_data_table_config_path': listify,
-        'tool_filters': listify,
-        'tool_label_filters': listify,
-        'tool_section_filters': listify,
-        'toolbox_filter_base_modules': listify,
+        'tool_config_file': listify_strip,
+        'tool_data_table_config_path': listify_strip,
+        'tool_filters': listify_strip,
+        'tool_label_filters': listify_strip,
+        'tool_section_filters': listify_strip,
+        'toolbox_filter_base_modules': listify_strip,
         'use_remote_user': None,  # TODO: should be False (config logic incorrect)
-        'user_library_import_symlink_whitelist': listify,
-        'user_tool_section_filters': listify,
+        'user_library_import_symlink_whitelist': listify_strip,
+        'user_tool_section_filters': listify_strip,
+        'user_tool_filters': listify_strip,
+        'user_tool_label_filters': listify_strip,
     }
     # RESOLVERS provides expected values for config options.
     # - key: config option

From 13a6220f0c24f979ca226a3e7c81484efc659d67 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 20 Apr 2020 12:07:50 -0400
Subject: [PATCH 821/853] Correct usage of __getattr__

Should either return computer value or raise AttributeError
---
 test/unit/unittest_utils/galaxy_mock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unit/unittest_utils/galaxy_mock.py b/test/unit/unittest_utils/galaxy_mock.py
index 3cde0eaa3e3d..82ac950bdb4d 100644
--- a/test/unit/unittest_utils/galaxy_mock.py
+++ b/test/unit/unittest_utils/galaxy_mock.py
@@ -181,7 +181,7 @@ def __getattr__(self, name):
         # Handle the automatic config file _set options
         if name.endswith('_file_set'):
             return False
-        return super(MockAppConfig, self).__getattr__(name)
+        raise AttributeError(name)
 
     def __del__(self):
         if self._remove_root:

From a80f98741e3bc644b81f880cd64cb00c6c0a8c30 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 20 Apr 2020 19:16:45 +0200
Subject: [PATCH 822/853] update readme with python version

remove some details and link external page
---
 README.rst | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/README.rst b/README.rst
index ac5af154f943..60b0d5232cd6 100644
--- a/README.rst
+++ b/README.rst
@@ -24,12 +24,12 @@ Community support is available at `Galaxy Help <https://help.galaxyproject.org/>
 Galaxy Quickstart
 =================
 
-Galaxy requires Python 2.7 To check your python version, run:
+Galaxy requires Python 3.6 or 3.5 To check your python version, run:
 
 .. code:: console
 
     $ python -V
-    Python 2.7.3
+    Python 3.6.10
 
 Start Galaxy:
 
@@ -42,14 +42,13 @@ browser at:
 
 http://localhost:8080
 
-Configuration & Tools
-=====================
+For more installation details please see https://getgalaxy.org/.
 
-You may wish to make changes from the default configuration. This can be
-done in the ``config/galaxy.ini`` file.
+Tools
+=====================
 
 Tools can be either installed from the Tool Shed or added manually.
- For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
+For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
 Note that not all dependencies for the tools provided in the
 ``tool_conf.xml.sample`` are included. To install them please visit
 "Manage dependencies" in the admin interface.

From 19fb7c76ab15f0c026b7b84e985a3f37c21d9946 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 20 Apr 2020 19:17:46 +0200
Subject: [PATCH 823/853] drop empty line and newline

---
 README.rst | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/README.rst b/README.rst
index 60b0d5232cd6..be03167ec5c5 100644
--- a/README.rst
+++ b/README.rst
@@ -38,9 +38,7 @@ Start Galaxy:
     $ sh run.sh
 
 Once Galaxy completes startup, you should be able to view Galaxy in your
-browser at:
-
-http://localhost:8080
+browser at: http://localhost:8080
 
 For more installation details please see https://getgalaxy.org/.
 

From 68c398b97bc56cd76b469050eac1cf822bdac400 Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Mon, 20 Apr 2020 14:29:21 -0400
Subject: [PATCH 824/853] Remove unused import.

---
 lib/galaxy_test/selenium/test_history_multi_view.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/lib/galaxy_test/selenium/test_history_multi_view.py b/lib/galaxy_test/selenium/test_history_multi_view.py
index 14b59d137ee5..c5cc1c9a3a7a 100644
--- a/lib/galaxy_test/selenium/test_history_multi_view.py
+++ b/lib/galaxy_test/selenium/test_history_multi_view.py
@@ -1,5 +1,3 @@
-from selenium.common.exceptions import NoSuchElementException
-
 from .framework import (
     selenium_test,
     SeleniumTestCase

From eb2ef7d45dd911e80df95ec0fae99b8143f866c8 Mon Sep 17 00:00:00 2001
From: assuntad23 <assuntad@localhost.localdomain>
Date: Mon, 20 Apr 2020 17:52:17 -0400
Subject: [PATCH 825/853] removed v-bind semi-colon

---
 client/galaxy/scripts/components/RuleCollectionBuilder.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/RuleCollectionBuilder.vue b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
index f8bb6d6696d7..d27dd94ccad7 100644
--- a/client/galaxy/scripts/components/RuleCollectionBuilder.vue
+++ b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
@@ -446,7 +446,7 @@
                         :data="hotData.data"
                         :col-headers="colHeadersDisplay"
                         :read-only="true"
-                        :stretch-h="all"
+                        stretch-h="all"
                     >
                     </hot-table>
                 </div>

From 8433001d65ea236e7ab196149015e41d300565d0 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 20 Apr 2020 12:55:32 -0400
Subject: [PATCH 826/853] Factor out overriding tempdir into own method

---
 lib/galaxy/config/__init__.py             | 9 +++++----
 test/unit/config/test_config_values.py    | 6 ++++--
 test/unit/config/test_load_config.py      | 1 +
 test/unit/config/test_path_graph.py       | 2 ++
 test/unit/config/test_path_resolves_to.py | 2 ++
 test/unit/config/test_reload_config.py    | 1 +
 6 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index ccc1c4a08e4d..0ba1e29f6e70 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -348,11 +348,16 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
 
     def __init__(self, **kwargs):
         super(GalaxyAppConfiguration, self).__init__(**kwargs)
+        self._override_tempdir(kwargs)
         self._process_config(kwargs)
 
     def _load_schema(self):
         return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
 
+    def _override_tempdir(self, kwargs):
+        if string_as_bool(kwargs.get("override_tempdir", "True")):
+            tempfile.tempdir = self.new_file_path
+
     def _process_config(self, kwargs):
         # Resolve paths of other config files
         self.parse_config_file_options(kwargs)
@@ -377,10 +382,6 @@ def _process_config(self, kwargs):
             self.thread_local_log = threading.local()
         # Install database related configuration (if different)
         self.install_database_engine_options = get_database_engine_options(kwargs, model_prefix="install_")
-
-        override_tempdir = string_as_bool(kwargs.get("override_tempdir", "True"))
-        if override_tempdir:
-            tempfile.tempdir = self.new_file_path
         self.shared_home_dir = kwargs.get("shared_home_dir")
         self.cookie_path = kwargs.get("cookie_path")
         self.tool_path = self._in_root_dir(self.tool_path)
diff --git a/test/unit/config/test_config_values.py b/test/unit/config/test_config_values.py
index e2b154feb852..7cecd09d6d5b 100644
--- a/test/unit/config/test_config_values.py
+++ b/test/unit/config/test_config_values.py
@@ -169,7 +169,8 @@ def mock_config_running_not_from_source(monkeypatch, mock_config_file):
 
 @pytest.fixture
 def appconfig(monkeypatch):
-    return config.Configuration()
+    monkeypatch.setattr(config.GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
+    return config.GalaxyAppConfiguration()
 
 
 def test_root(appconfig):
@@ -196,7 +197,8 @@ def test_common_base_config(appconfig):
 
 
 def get_config_data():
-    configuration = config.Configuration()
+    config.GalaxyAppConfiguration._override_tempdir = lambda a, b: None  # method must be mocked
+    configuration = config.GalaxyAppConfiguration()
     ev = ExpectedValues(configuration)
     items = ((k, v) for k, v in configuration.schema.app_schema.items() if k not in DO_NOT_TEST)
     for key, data in items:
diff --git a/test/unit/config/test_load_config.py b/test/unit/config/test_load_config.py
index f7deb4a49cf8..4582a4744249 100644
--- a/test/unit/config/test_load_config.py
+++ b/test/unit/config/test_load_config.py
@@ -22,6 +22,7 @@ def get_schema(app_mapping):
 def mock_init(monkeypatch):
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
 
 
 def test_load_config_from_schema(mock_init):
diff --git a/test/unit/config/test_path_graph.py b/test/unit/config/test_path_graph.py
index 73c719594ea1..42543e2a64d7 100644
--- a/test/unit/config/test_path_graph.py
+++ b/test/unit/config/test_path_graph.py
@@ -49,6 +49,7 @@ def test_basecase(monkeypatch):
     }
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
     assert config.component1_path0 == 'value0'
@@ -159,6 +160,7 @@ def test_resolves_with_empty_component(monkeypatch):
     }
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
     assert config.path0 == 'value0'
diff --git a/test/unit/config/test_path_resolves_to.py b/test/unit/config/test_path_resolves_to.py
index 439d2c6c0017..4a7ce356ef20 100644
--- a/test/unit/config/test_path_resolves_to.py
+++ b/test/unit/config/test_path_resolves_to.py
@@ -44,6 +44,7 @@ def test_deprecated_prefixes_set_correctly(monkeypatch):
     # Before we mock them, check that correct values are assigned
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
     assert config.deprecated_dirs == {'config_dir': 'config', 'data_dir': 'database'}
@@ -53,6 +54,7 @@ def test_deprecated_prefixes_set_correctly(monkeypatch):
 def mock_init(monkeypatch):
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
     monkeypatch.setattr(GalaxyAppConfiguration, 'deprecated_dirs', MOCK_DEPRECATED_DIRS)
 
 
diff --git a/test/unit/config/test_reload_config.py b/test/unit/config/test_reload_config.py
index 3064b0475adf..de6dbdca2c7e 100644
--- a/test/unit/config/test_reload_config.py
+++ b/test/unit/config/test_reload_config.py
@@ -25,6 +25,7 @@ def mock_init(monkeypatch):
 
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
 
 
 def test_update_property(mock_init, monkeypatch):

From 3015b398868bd6bb66ffe60949e096372cbfb9c0 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 20 Apr 2020 19:24:12 +0200
Subject: [PATCH 827/853] split test outputs

---
 test/functional/tools/column_param.xml | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/test/functional/tools/column_param.xml b/test/functional/tools/column_param.xml
index dad77b65b6bd..5c39402bfdf9 100644
--- a/test/functional/tools/column_param.xml
+++ b/test/functional/tools/column_param.xml
@@ -1,8 +1,8 @@
 <tool id="column_param" name="Column Param">
   <command><![CDATA[
-    echo "col $col" >> '$output1' &&
-    echo "col_names $col_names" >> '$output1' &&
-	cut -f '$col' '$input1' >> '$output1'
+    cut -f '$col' '$input1' >> '$output1'
+    echo "col $col" >> '$output2' &&
+    echo "col_names $col_names" >> '$output2' &&
   ]]></command>
   <inputs>
     <param type="data" format="tabular" name="input1" label="Input 1" />
@@ -11,6 +11,7 @@
   </inputs>
   <outputs>
     <data name="output1" format="tabular" />
+    <data name="output2" format="tabular" />
   </outputs>
   <tests>
     <test>
@@ -18,10 +19,14 @@
       <param name="col" value="2" />
       <param name="col_names" value="2" />
       <output name="output1">
+        <assert_contents>
+          <has_line line="68" />
+        </assert_contents>
+      </output>
+      <output name="output2">
         <assert_contents>
           <has_line line="col 2" />
           <has_line line="col_names 2" />
-          <has_line line="68" />
         </assert_contents>
       </output>
     </test>

From 3c0f22d4511f4fe761be9fd92b2c74a6d3a7d468 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 21 Apr 2020 12:53:44 +0200
Subject: [PATCH 828/853] Use pygithub for issue creation

---
 scripts/bootstrap_history.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index ce753d653a7c..a5bc28231ad3 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -333,13 +333,10 @@ def release_issue(argv):
     )
     release_issue_contents = RELEASE_ISSUE_TEMPLATE.safe_substitute(**release_issue_template_params)
     github = _github_client()
-    github.issues.create(
-        data=dict(
-            title="Publication of Galaxy Release v %s" % release_name,
-            body=release_issue_contents,
-        ),
-        user=PROJECT_OWNER,
-        repo=PROJECT_NAME,
+    repo = github.get_repo("%s/%s" % (PROJECT_OWNER, PROJECT_NAME))
+    repo.create_issue(
+        title="Publication of Galaxy Release v %s" % release_name,
+        body=release_issue_contents,
     )
     return release_issue
 

From c5bfbf412f91aad24ed66e2eff2449da3fa2c0b9 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@gmail.com>
Date: Tue, 21 Apr 2020 12:05:05 +0100
Subject: [PATCH 829/853] More docs links

Remove roadmap
---
 README.rst | 23 +++++++++++------------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/README.rst b/README.rst
index be03167ec5c5..cc66ea4bcdb1 100644
--- a/README.rst
+++ b/README.rst
@@ -5,14 +5,14 @@ The latest information about Galaxy can be found on the `Galaxy Community Hub <h
 
 Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.
 
-.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
-    :target: https://webchat.freenode.net/?channels=galaxyproject
-    :alt: Chat on irc
-
 .. image:: https://img.shields.io/badge/chat-gitter-blue.svg
     :target: https://gitter.im/galaxyproject/Lobby
     :alt: Chat on gitter
 
+.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
+    :target: https://webchat.freenode.net/?channels=galaxyproject
+    :alt: Chat on irc
+
 .. image:: https://img.shields.io/badge/release-documentation-blue.svg
     :target: https://docs.galaxyproject.org/en/master/
     :alt: Release Documentation
@@ -24,7 +24,7 @@ Community support is available at `Galaxy Help <https://help.galaxyproject.org/>
 Galaxy Quickstart
 =================
 
-Galaxy requires Python 3.6 or 3.5 To check your python version, run:
+Galaxy requires Python 3.5 or 3.6 . To check your Python version, run:
 
 .. code:: console
 
@@ -40,10 +40,14 @@ Start Galaxy:
 Once Galaxy completes startup, you should be able to view Galaxy in your
 browser at: http://localhost:8080
 
-For more installation details please see https://getgalaxy.org/.
+For more installation details please see: https://getgalaxy.org/
+
+Documentation is available at: https://docs.galaxyproject.org/
+
+Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/
 
 Tools
-=====================
+=====
 
 Tools can be either installed from the Tool Shed or added manually.
 For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
@@ -55,8 +59,3 @@ Issues and Galaxy Development
 =============================
 
 Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .
-
-Roadmap
-=============================
-
-Interested in the next steps for Galaxy? Take a look at the `roadmap <https://github.com/galaxyproject/galaxy/projects/8>`__.

From 9cdc30f9e9882eafbcf09505b01abcde2cd8d53b Mon Sep 17 00:00:00 2001
From: nvk747 <nvk747@gmail.com>
Date: Thu, 5 Mar 2020 14:14:10 -0500
Subject: [PATCH 830/853] make isinstance check on map python2.7 compatible

---
 lib/galaxy/webapps/galaxy/api/tools.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index 360682a8afd9..1a8e117fb5b1 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -1,3 +1,4 @@
+import inspect
 import logging
 import os
 from collections import OrderedDict
@@ -206,7 +207,7 @@ def test_data(self, trans, id, **kwd):
         def json_encodeify(obj):
             if isinstance(obj, OrderedDict):
                 return dict(obj)
-            elif isinstance(obj, map):
+            elif inspect.isclass(map) and isinstance(obj, map):
                 return list(obj)
             else:
                 return obj

From 80bff95042f1d0f8037c7cdc8e82955ce4bd2c57 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 21 Apr 2020 13:23:52 +0200
Subject: [PATCH 831/853] Custom json encoding of test_data response is not
 neccessary anymore

Since we swapped out odict for OrderedDict (and OrderedDict can be
serialized to JSON), and there are no map objects in the tool test
response.
---
 lib/galaxy/webapps/galaxy/api/tools.py | 18 ++----------------
 1 file changed, 2 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index 1a8e117fb5b1..42ab7584400e 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -1,13 +1,10 @@
-import inspect
 import logging
 import os
-from collections import OrderedDict
 from json import dumps, loads
 
 from galaxy import exceptions, managers, util, web
 from galaxy.managers.collections_util import dictify_dataset_collection_instance
 from galaxy.tools import global_tool_errors
-from galaxy.util.json import safe_dumps
 from galaxy.web import (
     expose_api,
     expose_api_anonymous,
@@ -186,7 +183,7 @@ def tests_summary(self, trans, **kwd):
                     }
         return test_counts_by_tool
 
-    @expose_api_raw_anonymous_and_sessionless
+    @expose_api_anonymous_and_sessionless
     def test_data(self, trans, id, **kwd):
         """
         GET /api/tools/{tool_id}/test_data?tool_version={tool_version}
@@ -202,18 +199,7 @@ def test_data(self, trans, id, **kwd):
             kwd = kwd.get('payload')
         tool_version = kwd.get('tool_version', None)
         tool = self._get_tool(id, tool_version=tool_version, user=trans.user)
-
-        # Encode in this method to handle OrderedDict objects in tool representation.
-        def json_encodeify(obj):
-            if isinstance(obj, OrderedDict):
-                return dict(obj)
-            elif inspect.isclass(map) and isinstance(obj, map):
-                return list(obj)
-            else:
-                return obj
-
-        result = [t.to_dict() for t in tool.tests]
-        return safe_dumps(result, default=json_encodeify)
+        return [t.to_dict() for t in tool.tests]
 
     @web.require_admin
     @expose_api

From 4be1232a59761a17cf892ca6d21f145b9bd5ee75 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 21 Apr 2020 14:34:51 +0200
Subject: [PATCH 832/853] remove indentation

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 test/functional/tools/column_param.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/functional/tools/column_param.xml b/test/functional/tools/column_param.xml
index 5c39402bfdf9..66c9c66491df 100644
--- a/test/functional/tools/column_param.xml
+++ b/test/functional/tools/column_param.xml
@@ -1,8 +1,8 @@
 <tool id="column_param" name="Column Param">
   <command><![CDATA[
-    cut -f '$col' '$input1' >> '$output1'
-    echo "col $col" >> '$output2' &&
-    echo "col_names $col_names" >> '$output2' &&
+cut -f '$col' '$input1' > '$output1' &&
+echo "col $col" > '$output2' &&
+echo "col_names $col_names" >> '$output2'
   ]]></command>
   <inputs>
     <param type="data" format="tabular" name="input1" label="Input 1" />

From c6748d9e2fb14561fc66670a653a368615b7888e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 21 Apr 2020 09:37:16 -0400
Subject: [PATCH 833/853] Update lib/galaxy/tool_util/cwl/util.py

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
---
 lib/galaxy/tool_util/cwl/util.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/lib/galaxy/tool_util/cwl/util.py b/lib/galaxy/tool_util/cwl/util.py
index 3892b6aeebac..c480cdf3ead9 100644
--- a/lib/galaxy/tool_util/cwl/util.py
+++ b/lib/galaxy/tool_util/cwl/util.py
@@ -410,8 +410,6 @@ def element_to_cwl_json(element):
     if output_metadata is None:
         output_metadata = get_metadata(galaxy_output.history_content_type, galaxy_output.history_content_id)
 
-    print(output_metadata)
-
     def dataset_dict_to_json_content(dataset_dict):
         if "content" in dataset_dict:
             return json.loads(dataset_dict["content"])

From 43b9c152f7349311f2ed6b71b5a019ceb673dba2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 21 Apr 2020 16:05:44 +0200
Subject: [PATCH 834/853] Remove ToolDependency objects before removing
 ToolShedRepository

---
 test/integration/uses_shed.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/uses_shed.py b/test/integration/uses_shed.py
index d296ebf7565d..9b19f5bce5ce 100644
--- a/test/integration/uses_shed.py
+++ b/test/integration/uses_shed.py
@@ -72,8 +72,8 @@ def reset_shed_tools(self):
             model.RepositoryDependency,
             model.ToolVersion,
             model.ToolVersionAssociation,
+            model.ToolDependency,
             model.ToolShedRepository,
-            model.ToolDependency
         ]
         for item in models_to_delete:
             model.context.query(item).delete()

From 0e7e54f0ecc2c1dfeb7d9c7ef29879112c80c97e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 21 Apr 2020 16:06:08 +0200
Subject: [PATCH 835/853] Fix fastqc owner in test case

---
 test/integration/test_repository_operations.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/test_repository_operations.py b/test/integration/test_repository_operations.py
index 13a8c010372e..86329bd37619 100644
--- a/test/integration/test_repository_operations.py
+++ b/test/integration/test_repository_operations.py
@@ -52,7 +52,7 @@ def test_package_uninstall(self):
         self.uninstall_repository(*repo)
 
     def test_tool_with_package_dependency_uninstall(self):
-        repo = ('iuc', 'fastqc', 'e7b2202befea')
+        repo = ('devteam', 'fastqc', 'e7b2202befea')
         self.install_repository(*repo)
         self.uninstall_repository(*repo)
 

From 505b3b32a5c0aba3341d19506c3cebec8ad4e3cd Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 21 Apr 2020 16:13:53 +0200
Subject: [PATCH 836/853] Apply suggestions from code review

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/tool_util/xsd/galaxy.xsd    | 2 +-
 test/functional/tools/column_param.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index f994bc85272e..51450ab95fb1 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -2561,7 +2561,7 @@ Set to ``false`` to not force user to select an option in the list.</xs:document
         <xs:attribute name="use_header_names" type="PermissiveBoolean">
           <xs:annotation>
             <xs:documentation xml:lang="en">Used only if the ``type`` attribute
-value is ``data_column``, if ``true`` Galaxy assumes first row of ``data_ref``
+value is ``data_column``. If ``true``, Galaxy assumes the first row of ``data_ref``
 is a header and builds the select list with these values rather than the more
 generic ``c1`` ... ``cN`` (i.e. it will be ``c1: head1`` ... ``cN: headN``).
 Note that the content of the Cheetah variable is still
diff --git a/test/functional/tools/column_param.xml b/test/functional/tools/column_param.xml
index 66c9c66491df..b5933606e484 100644
--- a/test/functional/tools/column_param.xml
+++ b/test/functional/tools/column_param.xml
@@ -11,7 +11,7 @@ echo "col_names $col_names" >> '$output2'
   </inputs>
   <outputs>
     <data name="output1" format="tabular" />
-    <data name="output2" format="tabular" />
+    <data name="output2" format="txt" />
   </outputs>
   <tests>
     <test>

From fedaa108028404244811961f29a6ba6c325e34b8 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 20 Dec 2019 02:43:38 +0000
Subject: [PATCH 837/853] Add API to export a workflow invocation as a
 BioCompute Object

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 57 ++++++++++++++++++++
 lib/galaxy/webapps/galaxy/buildapp.py      |  1 +
 lib/galaxy_test/api/test_workflows.py      | 62 +++++++++++-----------
 3 files changed, 89 insertions(+), 31 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 13a59170d2a3..3509a06ae6c8 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -980,6 +980,63 @@ def _generate_report(self, trans, invocation_id, **kwd):
             target_format=target_format,
         )
 
+    @expose_api
+    def export_invocation_bco(self, trans, invocation_id, **kwd):
+        """
+        GET /api/invocations/{invocations_id}/export_bco
+        Return a BioCompute Object for the workflow invocation.
+        """
+        decoded_workflow_invocation_id = self.decode_id(invocation_id)
+        workflow_invocation = self.workflow_manager.get_invocation(trans, decoded_workflow_invocation_id)
+        history = workflow_invocation.history
+        workflow = workflow_invocation.workflow
+        stored_workflow = workflow.stored_workflow
+        contributing_users = {history.user, stored_workflow.user}
+
+        contributors = []
+        for contributing_user in contributing_users:
+            contributor = {
+                "orcid": "",
+                "affiliation": contributing_user.email.split('@')[-1],
+                "contribution": [],
+                "name": contributing_user.username,
+                "email": contributing_user.email,
+            }
+            contributors.append(contributor)
+
+        provenance_domain = {
+            'name': workflow.name,
+            'version': 'TODO',
+            'created': workflow_invocation.create_time.isoformat(),
+            'modified': workflow_invocation.update_time.isoformat(),
+            'contributors': contributors,
+            'license': 'TODO',
+        }
+
+        output_subdomain = []  # TODO
+
+        ret_dict = {
+            'bco_id': url_for('invocation_export_bco', invocation_id=invocation_id),
+            'bco_spec_version': 'https://w3id.org/biocompute/1.3.0/',
+            'checksum': 'TODO',
+            'provenance_domain': provenance_domain,
+            'usability_domain': history.annotations,
+            'extension_domain': {},
+            'description_domain': {
+                'keywords': stored_workflow.tags,
+                'platform': 'Galaxy',
+                'pipeline_steps': [],  # fill from the workflow steps
+            },
+            'execution_domain': {},
+            'parametric_domain': {},
+            'io_domain': {
+                'input_subdomain': [],
+                'output_subdomain': output_subdomain,
+            },
+            'error_domain': {},
+        }
+        return ret_dict
+
     @expose_api
     def invocation_step(self, trans, invocation_id, step_id, **kwd):
         """
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 9df4eb0ad505..96d15c93ab0b 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -604,6 +604,7 @@ def connect_invocation_endpoint(endpoint_name, endpoint_suffix, action, conditio
     connect_invocation_endpoint('show', '', action='show_invocation')
     connect_invocation_endpoint('show_report', '/report', action='show_invocation_report')
     connect_invocation_endpoint('show_report_pdf', '/report.pdf', action='show_invocation_report_pdf')
+    connect_invocation_endpoint('export_bco', '/export_bco', action='export_invocation_bco')
     connect_invocation_endpoint('jobs_summary', '/jobs_summary', action='invocation_jobs_summary')
     connect_invocation_endpoint('step_jobs_summary', '/step_jobs_summary', action='invocation_step_jobs_summary')
     connect_invocation_endpoint('cancel', '', action='cancel_invocation', conditions=dict(method=['DELETE']))
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index d4e2359c8de6..f7b94ffcf7d8 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -40,6 +40,21 @@
 from ._framework import ApiTestCase
 
 
+WORKFLOW_SIMPLE = """
+class: GalaxyWorkflow
+name: Simple Workflow
+inputs:
+  input1: data
+outputs:
+  wf_output_1:
+    outputSource: first_cat/out_file1
+steps:
+  first_cat:
+    tool_id: cat1
+    in:
+      input1: input1
+"""
+
 NESTED_WORKFLOW_AUTO_LABELS_MODERN_SYNTAX = """
 class: GalaxyWorkflow
 inputs:
@@ -1112,7 +1127,7 @@ def test_run_subworkflow_runtime_parameters(self):
             assert len([x for x in content.split("\n") if x]) == 2
 
     @skip_without_tool("cat")
-    def test_run_subworkflow_replacment_parameters(self):
+    def test_run_subworkflow_replacement_parameters(self):
         with self.dataset_populator.test_history() as history_id:
             test_data = """
 replacement_parameters:
@@ -1285,7 +1300,7 @@ def test_workflow_invocation_report_1(self):
   type: File
 """
         with self.dataset_populator.test_history() as history_id:
-            summary = self._run_jobs(r"""
+            summary = self._run_jobs("""
 class: GalaxyWorkflow
 inputs:
   input_1: data
@@ -1333,6 +1348,15 @@ def test_workflow_invocation_report_custom(self):
             assert "## Workflow Inputs" in markdown_content
             assert "## About This Report" in markdown_content
 
+    @skip_without_tool("cat1")
+    def test_export_invocation_bco(self):
+        with self.dataset_populator.test_history() as history_id:
+            summary = self._run_jobs(WORKFLOW_SIMPLE, test_data={"input1": "hello world"}, history_id=history_id)
+            invocation_id = summary.invocation_id
+            bco = self._get("invocations/%s/export_bco" % invocation_id).json()
+            self.assertEqual(bco['bco_spec_version'], 'https://w3id.org/biocompute/1.3.0/')
+            self.assertEqual(bco['provenance_domain']['name'], "Simple Workflow")
+
     @skip_without_tool("__APPLY_RULES__")
     def test_workflow_run_apply_rules(self):
         with self.dataset_populator.test_history() as history_id:
@@ -1399,19 +1423,7 @@ def test_workflow_request(self):
 
     def test_workflow_output_dataset(self):
         with self.dataset_populator.test_history() as history_id:
-            summary = self._run_jobs("""
-class: GalaxyWorkflow
-inputs:
-  input1: data
-outputs:
-  wf_output_1:
-    outputSource: first_cat/out_file1
-steps:
-  first_cat:
-    tool_id: cat1
-    in:
-      input1: input1
-""", test_data={"input1": "hello world"}, history_id=history_id)
+            summary = self._run_jobs(WORKFLOW_SIMPLE, test_data={"input1": "hello world"}, history_id=history_id)
             workflow_id = summary.workflow_id
             invocation_id = summary.invocation_id
             invocation_response = self._get("workflows/%s/invocations/%s" % (workflow_id, invocation_id))
@@ -2511,7 +2523,7 @@ def test_workflow_stability(self):
         for workflow_file in ["test_workflow_topoambigouity", "test_workflow_topoambigouity_auto_laidout"]:
             workflow = self.workflow_populator.load_workflow_from_resource(workflow_file)
             last_step_map = self._step_map(workflow)
-            for i in range(num_tests):
+            for _ in range(num_tests):
                 uploaded_workflow_id = self.workflow_populator.create_workflow(workflow)
                 downloaded_workflow = self._download_workflow(uploaded_workflow_id)
                 step_map = self._step_map(downloaded_workflow)
@@ -3399,19 +3411,7 @@ def test_validated_post_job_action_validated(self):
     @skip_without_tool("cat1")
     def test_validated_post_job_action_unvalidated_default(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
-class: GalaxyWorkflow
-inputs:
-  input1: data
-outputs:
-  wf_output_1:
-    outputSource: first_cat/out_file1
-steps:
-  first_cat:
-    tool_id: cat1
-    in:
-      input1: input1
-""", test_data={"input1": {"type": "File", "file_type": "fastqsanger", "value": "1.fastqsanger"}}, history_id=history_id)
+            self._run_jobs(WORKFLOW_SIMPLE, test_data={"input1": {"type": "File", "file_type": "fastqsanger", "value": "1.fastqsanger"}}, history_id=history_id)
             hda2 = self.dataset_populator.get_history_dataset_details(history_id, hid=2)
             assert hda2["validated_state"] == "unknown"
 
@@ -3876,7 +3876,7 @@ def _invoke_paused_workflow(self, history_id):
 
     def _wait_for_invocation_non_new(self, workflow_id, invocation_id):
         target_state_reached = False
-        for i in range(50):
+        for _ in range(50):
             invocation = self._invocation_details(workflow_id, invocation_id)
             if invocation['state'] != 'new':
                 target_state_reached = True
@@ -3892,7 +3892,7 @@ def _assert_invocation_non_terminal(self, workflow_id, invocation_id):
 
     def _wait_for_invocation_state(self, workflow_id, invocation_id, target_state):
         target_state_reached = False
-        for i in range(25):
+        for _ in range(25):
             invocation = self._invocation_details(workflow_id, invocation_id)
             if invocation['state'] == target_state:
                 target_state_reached = True

From 6604a1967a91de559edfe7e83ea9872d256bc7f9 Mon Sep 17 00:00:00 2001
From: HadleyKing <hadley_king@gwu.edu>
Date: Fri, 27 Dec 2019 16:05:43 -0500
Subject: [PATCH 838/853] More fields added in workflows.py for BCO

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 106 ++++++++++++++++++---
 1 file changed, 91 insertions(+), 15 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 3509a06ae6c8..c107c4bf371d 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -982,10 +982,12 @@ def _generate_report(self, trans, invocation_id, **kwd):
 
     @expose_api
     def export_invocation_bco(self, trans, invocation_id, **kwd):
-        """
+        '''
         GET /api/invocations/{invocations_id}/export_bco
         Return a BioCompute Object for the workflow invocation.
-        """
+        '''
+        # added a 'host' for testing purposes. This shoule be the actual host in production
+        host = 'galaxy.aws.biochemistry.gwu.edu'
         decoded_workflow_invocation_id = self.decode_id(invocation_id)
         workflow_invocation = self.workflow_manager.get_invocation(trans, decoded_workflow_invocation_id)
         history = workflow_invocation.history
@@ -993,44 +995,118 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
         stored_workflow = workflow.stored_workflow
         contributing_users = {history.user, stored_workflow.user}
 
+        # history_encoded_id = trans.security.encode_id(history.id)
+        workflow_encoded_id = trans.security.encode_id(stored_workflow.id)
+        # print('\n', history_encoded_id, '\n', workflow_encoded_id, '\n', invocation_id, '\n')
+
+        # list of Job IDs for invocation
+        invocation_dict = json.loads(self.show_invocation(trans, invocation_id))
+        jobs = []
+        for step in invocation_dict['steps']:
+            inv_step = str(step['id'])
+            job = self.invocation_step(trans, invocation_id, inv_step)
+            jobs.append(json.loads(job))
+
+        # listing the versions of the workflow for 'version' and 'derived_from'
+        versions = []
+        workflow_versions = self.workflow_manager.get_stored_accessible_workflow(trans, workflow_encoded_id, **kwd)
+        for i, w in enumerate(reversed(workflow_versions.workflows)):
+            version = {
+                'version': i,
+                'update_time': str(w.update_time),
+                'steps': len(w.steps),
+                'version_id': trans.security.encode_id(w.stored_workflow.id),
+            }
+            versions.append(version)
+        current_version = versions[-1]['version']
+
         contributors = []
         for contributing_user in contributing_users:
             contributor = {
-                "orcid": "",
-                "affiliation": contributing_user.email.split('@')[-1],
-                "contribution": [],
-                "name": contributing_user.username,
-                "email": contributing_user.email,
+                'orcid': '',
+                'affiliation': contributing_user.email.split('@')[-1],
+                'contribution': ['authoredBy'],
+                'name': contributing_user.username,
+                'email': contributing_user.email,
             }
             contributors.append(contributor)
 
+        reviewer = []
+        reviewer = {
+            'status': 'approved',
+            'reviewer_comment': '',
+            'date': workflow_invocation.update_time.isoformat(),
+            'reviewer': {
+                'name': contributing_user.username,
+                'affiliation': contributing_user.email.split('@')[-1],
+                'email': contributing_user.email,
+                # Would like to find a way to offer a choice on this value
+                'contribution': 'curatedBy'
+                # 'orcid': 'TO DO'
+            }
+        }
+
         provenance_domain = {
             'name': workflow.name,
-            'version': 'TODO',
+            'version': current_version,
+            'review': reviewer,
+            'derived_from': url_for('workflow', id=workflow_encoded_id, host=host),
             'created': workflow_invocation.create_time.isoformat(),
             'modified': workflow_invocation.update_time.isoformat(),
             'contributors': contributors,
-            'license': 'TODO',
+            'license': 'https://spdx.org/licenses/CC-BY-4.0.html',
         }
 
+        dict_workflow = json.loads(self.workflow_dict(trans, workflow_encoded_id))
+
+        pipeline_steps = []
+        for step in range(len(dict_workflow['steps'].keys())):
+            current_tool = dict_workflow['steps'][str(step)]
+            output_list = []
+            input_list = []
+            pipeline_step = {
+                'step_number': step,
+                'name': current_tool['name'],
+                'description': current_tool['annotation'],
+                'version': current_tool['tool_version'],
+                #  'prerequisite': prerequisite,
+                'input_list': input_list,
+                'output_list': output_list
+            }
+            prerequisite = []
+            try:
+                prerequisite = {
+                    'uri': {
+                        'name': current_tool['tool_shed_repository']['name'],
+                        'uri': current_tool['content_id'],
+                        #  'access_time': ''
+                    }
+                }
+                pipeline_step['prerequisite'] = prerequisite
+            except Exception:
+                continue
+            pipeline_steps.append(pipeline_step)
+
+        input_subdomain = []  # TODO
         output_subdomain = []  # TODO
 
         ret_dict = {
-            'bco_id': url_for('invocation_export_bco', invocation_id=invocation_id),
+            'bco_id': url_for('invocation_export_bco', invocation_id=invocation_id, host=host),
             'bco_spec_version': 'https://w3id.org/biocompute/1.3.0/',
             'checksum': 'TODO',
             'provenance_domain': provenance_domain,
-            'usability_domain': history.annotations,
+            'usability_domain': dict_workflow['annotation'],
             'extension_domain': {},
             'description_domain': {
-                'keywords': stored_workflow.tags,
-                'platform': 'Galaxy',
-                'pipeline_steps': [],  # fill from the workflow steps
+                'keywords': dict_workflow['tags'],
+                'xref': [],
+                'platform': ['Galaxy'],
+                'pipeline_steps': pipeline_steps,
             },
             'execution_domain': {},
             'parametric_domain': {},
             'io_domain': {
-                'input_subdomain': [],
+                'input_subdomain': input_subdomain,
                 'output_subdomain': output_subdomain,
             },
             'error_domain': {},

From 6309aa6a94fae9a8d8c8f97aacac290ce80c63df Mon Sep 17 00:00:00 2001
From: HadleyKing <hadley_king@gwu.edu>
Date: Mon, 6 Jan 2020 13:13:11 -0500
Subject: [PATCH 839/853] More changes to BCO

- Added `map_datasets` to access HDAs from HDCAs for BioCompute Object generaion.
- update to `contributors` and `reviewers` using `StoredWorkflowUserShareAssociation`
- update to `spec_version`
- update to `keywords` using `user_tname` feature
- `software_prerequisites` added and `execution_domain` started
- etags added using `uuid4().hex`
- added `parametric_domain`
---
 lib/galaxy/webapps/galaxy/api/workflows.py | 143 +++++++++++++++------
 lib/galaxy_test/api/test_workflows.py      |   2 +-
 2 files changed, 103 insertions(+), 42 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index c107c4bf371d..4274e6396f9a 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -980,6 +980,25 @@ def _generate_report(self, trans, invocation_id, **kwd):
             target_format=target_format,
         )
 
+    def map_datasets(self, content, *parents):
+        """
+        Iterate over the datasets of a given collection, recursing into collections, and
+        calling fn on each dataset.
+        Uses the same kwargs as `contents` above.
+        Added here to access HDAs from HDCAs for BioCompute Object generaion.
+        """
+        returned = []
+        # lots of nesting going on within the nesting
+        collection = content.collection if hasattr(content, 'collection') else content
+        this_parents = (content, ) + parents
+        for element in collection.elements:
+            next_parents = (element, ) + this_parents
+            if element.is_collection:
+                returned.extend(self.map_datasets(element.child_collection, *next_parents))
+            else:
+                returned.append(element.dataset_instance)
+        return returned
+
     @expose_api
     def export_invocation_bco(self, trans, invocation_id, **kwd):
         '''
@@ -993,19 +1012,28 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
         history = workflow_invocation.history
         workflow = workflow_invocation.workflow
         stored_workflow = workflow.stored_workflow
-        contributing_users = {history.user, stored_workflow.user}
 
-        # history_encoded_id = trans.security.encode_id(history.id)
+        # pull in the user info from those who the history and workflow has been shared with
+        contributing_users = [stored_workflow.user]
+        for association in trans.sa_session.query(model.StoredWorkflowUserShareAssociation):
+            if association.user not in contributing_users:
+                contributing_users.append(association.user)
+        for h_association in trans.sa_session.query(model.HistoryUserShareAssociation):
+            if h_association.user not in contributing_users:
+                contributing_users.append(h_association.user)
+
+        # may want to extend this to have more reviewers.
+        reviewing_users = [stored_workflow.user]
         workflow_encoded_id = trans.security.encode_id(stored_workflow.id)
-        # print('\n', history_encoded_id, '\n', workflow_encoded_id, '\n', invocation_id, '\n')
+        dict_workflow = json.loads(self.workflow_dict(trans, workflow_encoded_id))
+
+        h_contents = []
+        for content in history.contents_iter(types=["dataset", "dataset_collection"]):
+            h_contents.extend(self.map_datasets(content)) if hasattr(content, 'collection') else h_contents.append(content)
+        h_contents = list(set(h_contents))
 
-        # list of Job IDs for invocation
-        invocation_dict = json.loads(self.show_invocation(trans, invocation_id))
-        jobs = []
-        for step in invocation_dict['steps']:
-            inv_step = str(step['id'])
-            job = self.invocation_step(trans, invocation_id, inv_step)
-            jobs.append(json.loads(job))
+        # TODO add a keyword option/function to determine the spec_version used in BCO creation, and populate it accordingly
+        spec_version = 'https://w3id.org/biocompute/1.4.0/',
 
         # listing the versions of the workflow for 'version' and 'derived_from'
         versions = []
@@ -1023,33 +1051,35 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
         contributors = []
         for contributing_user in contributing_users:
             contributor = {
-                'orcid': '',
+                # 'orcid': '', TODO
+                'name': contributing_user.username,
                 'affiliation': contributing_user.email.split('@')[-1],
                 'contribution': ['authoredBy'],
-                'name': contributing_user.username,
                 'email': contributing_user.email,
             }
             contributors.append(contributor)
 
-        reviewer = []
-        reviewer = {
-            'status': 'approved',
-            'reviewer_comment': '',
-            'date': workflow_invocation.update_time.isoformat(),
-            'reviewer': {
-                'name': contributing_user.username,
-                'affiliation': contributing_user.email.split('@')[-1],
-                'email': contributing_user.email,
-                # Would like to find a way to offer a choice on this value
-                'contribution': 'curatedBy'
-                # 'orcid': 'TO DO'
+        reviewers = []
+        for reviewer in reviewing_users:
+            reviewer = {
+                'status': 'approved',
+                'reviewer_comment': '',
+                'date': workflow_invocation.update_time.isoformat(),
+                'reviewer': {
+                    # 'orcid': '',  TODO
+                    'name': contributing_user.username,
+                    'affiliation': contributing_user.email.split('@')[-1],
+                    # Would like to find a way to offer a choice on this value
+                    'contribution': 'curatedBy',
+                    'email': contributing_user.email
+                }
             }
-        }
+            reviewers.append(reviewer)
 
         provenance_domain = {
             'name': workflow.name,
             'version': current_version,
-            'review': reviewer,
+            'review': reviewers,
             'derived_from': url_for('workflow', id=workflow_encoded_id, host=host),
             'created': workflow_invocation.create_time.isoformat(),
             'modified': workflow_invocation.update_time.isoformat(),
@@ -1057,9 +1087,14 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
             'license': 'https://spdx.org/licenses/CC-BY-4.0.html',
         }
 
-        dict_workflow = json.loads(self.workflow_dict(trans, workflow_encoded_id))
+        keywords = []
+        for tag in stored_workflow.tags:
+            keywords.append(tag.user_tname)
+        for tag in history.tags:
+            if tag.user_tname not in keywords:
+                keywords.append(tag.user_tname)
 
-        pipeline_steps = []
+        pipeline_steps, software_prerequisites = [], []
         for step in range(len(dict_workflow['steps'].keys())):
             current_tool = dict_workflow['steps'][str(step)]
             output_list = []
@@ -1073,38 +1108,64 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
                 'input_list': input_list,
                 'output_list': output_list
             }
-            prerequisite = []
+            pipeline_steps.append(pipeline_step)
+            software_prerequisite = []
             try:
-                prerequisite = {
+                software_prerequisite = {
+                    'name': current_tool['tool_shed_repository']['name'],
+                    'version': current_tool['tool_version'],
                     'uri': {
-                        'name': current_tool['tool_shed_repository']['name'],
                         'uri': current_tool['content_id'],
-                        #  'access_time': ''
+                        'access_time': current_tool['uuid']
                     }
                 }
-                pipeline_step['prerequisite'] = prerequisite
             except Exception:
                 continue
-            pipeline_steps.append(pipeline_step)
+            software_prerequisites.append(software_prerequisite)
+
+        usability_domain = []
+        for a in stored_workflow.annotations:
+            usability_domain.append(a.annotation)
+        for h in history.annotations:
+            usability_domain.append(h.annotation)
+
+        parametric_domain = []
+        for inv_step in workflow_invocation.steps:
+            try:
+                for k, v in inv_step.workflow_step.tool_inputs.iteritems():
+                    param, value, step = k, v, inv_step.workflow_step.order_index
+                    parametric_domain.append({'param': param, 'value': value, 'step': step})
+            except Exception:
+                continue
+
+        execution_domain = {
+            'script_access_type': 'a_galaxy_workflow',
+            'script': [url_for('workflows', encoded_workflow_id=workflow_encoded_id)],
+            'script_driver': 'Galaxy',
+            'software_prerequisites': software_prerequisites,
+            'external_data_endpoints': [],
+            'environment_variables': {}
+        }
 
+        galaxy_extension = []  # TODO
         input_subdomain = []  # TODO
         output_subdomain = []  # TODO
 
         ret_dict = {
             'bco_id': url_for('invocation_export_bco', invocation_id=invocation_id, host=host),
-            'bco_spec_version': 'https://w3id.org/biocompute/1.3.0/',
-            'checksum': 'TODO',
+            'bco_spec_version': spec_version,
+            'etag': str(model.uuid4().hex),
             'provenance_domain': provenance_domain,
-            'usability_domain': dict_workflow['annotation'],
-            'extension_domain': {},
+            'usability_domain': usability_domain,
+            'extension_domain': galaxy_extension,
             'description_domain': {
-                'keywords': dict_workflow['tags'],
+                'keywords': keywords,
                 'xref': [],
                 'platform': ['Galaxy'],
                 'pipeline_steps': pipeline_steps,
             },
-            'execution_domain': {},
-            'parametric_domain': {},
+            'execution_domain': execution_domain,
+            'parametric_domain': parametric_domain,
             'io_domain': {
                 'input_subdomain': input_subdomain,
                 'output_subdomain': output_subdomain,
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index f7b94ffcf7d8..e63b4cd2cb46 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -1354,7 +1354,7 @@ def test_export_invocation_bco(self):
             summary = self._run_jobs(WORKFLOW_SIMPLE, test_data={"input1": "hello world"}, history_id=history_id)
             invocation_id = summary.invocation_id
             bco = self._get("invocations/%s/export_bco" % invocation_id).json()
-            self.assertEqual(bco['bco_spec_version'], 'https://w3id.org/biocompute/1.3.0/')
+            self.assertEqual(bco['spec_version'], 'https://w3id.org/biocompute/1.4.0/')
             self.assertEqual(bco['provenance_domain']['name'], "Simple Workflow")
 
     @skip_without_tool("__APPLY_RULES__")

From ae9d3d28adc72ba3b44a80784f47b6d7e4e2154b Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 7 Jan 2020 11:58:59 +0000
Subject: [PATCH 840/853] Use `HistoryContentsManager` and other fixes

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 38 +++++-----------------
 1 file changed, 8 insertions(+), 30 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 4274e6396f9a..636a7e9b96d4 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -21,6 +21,7 @@
 )
 from galaxy.managers import (
     histories,
+    history_contents,
     workflows
 )
 from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter
@@ -56,6 +57,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
     def __init__(self, app):
         super(WorkflowsAPIController, self).__init__(app)
         self.history_manager = histories.HistoryManager(app)
+        self.history_contents_manager = history_contents.HistoryContentsManager(app)
         self.workflow_manager = workflows.WorkflowsManager(app)
         self.workflow_contents_manager = workflows.WorkflowContentsManager(app)
         self.tool_recommendations = recommendations.ToolRecommendations()
@@ -980,33 +982,12 @@ def _generate_report(self, trans, invocation_id, **kwd):
             target_format=target_format,
         )
 
-    def map_datasets(self, content, *parents):
-        """
-        Iterate over the datasets of a given collection, recursing into collections, and
-        calling fn on each dataset.
-        Uses the same kwargs as `contents` above.
-        Added here to access HDAs from HDCAs for BioCompute Object generaion.
-        """
-        returned = []
-        # lots of nesting going on within the nesting
-        collection = content.collection if hasattr(content, 'collection') else content
-        this_parents = (content, ) + parents
-        for element in collection.elements:
-            next_parents = (element, ) + this_parents
-            if element.is_collection:
-                returned.extend(self.map_datasets(element.child_collection, *next_parents))
-            else:
-                returned.append(element.dataset_instance)
-        return returned
-
     @expose_api
     def export_invocation_bco(self, trans, invocation_id, **kwd):
         '''
         GET /api/invocations/{invocations_id}/export_bco
         Return a BioCompute Object for the workflow invocation.
         '''
-        # added a 'host' for testing purposes. This shoule be the actual host in production
-        host = 'galaxy.aws.biochemistry.gwu.edu'
         decoded_workflow_invocation_id = self.decode_id(invocation_id)
         workflow_invocation = self.workflow_manager.get_invocation(trans, decoded_workflow_invocation_id)
         history = workflow_invocation.history
@@ -1027,17 +1008,14 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
         workflow_encoded_id = trans.security.encode_id(stored_workflow.id)
         dict_workflow = json.loads(self.workflow_dict(trans, workflow_encoded_id))
 
-        h_contents = []
-        for content in history.contents_iter(types=["dataset", "dataset_collection"]):
-            h_contents.extend(self.map_datasets(content)) if hasattr(content, 'collection') else h_contents.append(content)
-        h_contents = list(set(h_contents))
+        # h_contents = self.history_contents_manager.contained(history)
 
         # TODO add a keyword option/function to determine the spec_version used in BCO creation, and populate it accordingly
-        spec_version = 'https://w3id.org/biocompute/1.4.0/',
+        spec_version = 'https://w3id.org/biocompute/1.4.0/'
 
         # listing the versions of the workflow for 'version' and 'derived_from'
         versions = []
-        workflow_versions = self.workflow_manager.get_stored_accessible_workflow(trans, workflow_encoded_id, **kwd)
+        workflow_versions = self.workflow_manager.get_stored_accessible_workflow(trans, workflow_encoded_id)
         for i, w in enumerate(reversed(workflow_versions.workflows)):
             version = {
                 'version': i,
@@ -1080,7 +1058,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
             'name': workflow.name,
             'version': current_version,
             'review': reviewers,
-            'derived_from': url_for('workflow', id=workflow_encoded_id, host=host),
+            'derived_from': url_for('workflow', id=workflow_encoded_id, qualified=True),
             'created': workflow_invocation.create_time.isoformat(),
             'modified': workflow_invocation.update_time.isoformat(),
             'contributors': contributors,
@@ -1152,8 +1130,8 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
         output_subdomain = []  # TODO
 
         ret_dict = {
-            'bco_id': url_for('invocation_export_bco', invocation_id=invocation_id, host=host),
-            'bco_spec_version': spec_version,
+            'bco_id': url_for('invocation_export_bco', invocation_id=invocation_id, qualified=True),
+            'spec_version': spec_version,
             'etag': str(model.uuid4().hex),
             'provenance_domain': provenance_domain,
             'usability_domain': usability_domain,

From 5218bd9514beda4f5eea07074710d643cc687d2a Mon Sep 17 00:00:00 2001
From: HadleyKing <HadleyKing@users.noreply.github.com>
Date: Tue, 7 Jan 2020 17:57:49 -0500
Subject: [PATCH 841/853] Addition of method for `output_subdomain` for BCO

- added method for populating the `pipeline_step.input_list` and `pipeline_step.output_list`
- added method for populating the `output_subdomain`
- [WIP] method for populating the `input_subdomain`
---
 lib/galaxy/webapps/galaxy/api/workflows.py | 92 ++++++++++++++++------
 1 file changed, 66 insertions(+), 26 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 636a7e9b96d4..db4384ddac44 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1006,6 +1006,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
         # may want to extend this to have more reviewers.
         reviewing_users = [stored_workflow.user]
         workflow_encoded_id = trans.security.encode_id(stored_workflow.id)
+        history_encoded_id = trans.security.encode_id(history.id)
         dict_workflow = json.loads(self.workflow_dict(trans, workflow_encoded_id))
 
         # h_contents = self.history_contents_manager.contained(history)
@@ -1072,34 +1073,73 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
             if tag.user_tname not in keywords:
                 keywords.append(tag.user_tname)
 
-        pipeline_steps, software_prerequisites = [], []
-        for step in range(len(dict_workflow['steps'].keys())):
-            current_tool = dict_workflow['steps'][str(step)]
-            output_list = []
-            input_list = []
-            pipeline_step = {
-                'step_number': step,
-                'name': current_tool['name'],
-                'description': current_tool['annotation'],
-                'version': current_tool['tool_version'],
-                #  'prerequisite': prerequisite,
-                'input_list': input_list,
-                'output_list': output_list
-            }
-            pipeline_steps.append(pipeline_step)
-            software_prerequisite = []
-            try:
-                software_prerequisite = {
-                    'name': current_tool['tool_shed_repository']['name'],
+        host = 'https://localhost:8080'
+        input_subdomain, output_subdomain, pipeline_steps, software_prerequisites = [], [], [], []
+        # Which `url_for` function option would generate this format below?
+        url_format = '{}/api/histories/{}/contents/{}'
+        for i, step in enumerate(workflow_invocation.steps):
+            current_tool = dict_workflow['steps'][str(i)]
+            if step.workflow_step.type == 'tool':
+                workflow_outputs_list , output_list, input_list = [], [], []
+                for wo in step.workflow_step.workflow_outputs:
+                    workflow_outputs_list.append(wo.output_name)
+                for job in step.jobs:
+                    for job_input in job.input_datasets:
+                        if hasattr(job_input.dataset, 'dataset_id'):
+                            inputobj = trans.security.encode_id(job_input.dataset.dataset_id)
+                            input_obj = {
+                                'filename': job_input.dataset.name,
+                                'uri': url_format.format(host, history_encoded_id, inputobj),
+                                'access_time': job_input.dataset.create_time.isoformat(),
+                            }
+                            input_list.append(input_obj)
+
+                    for job_output in job.output_datasets:
+                        if hasattr(job_output.dataset, 'dataset_id'):
+                            outobj = trans.security.encode_id(job_output.dataset.dataset_id)
+                            output_obj = {
+                                'filename': job_output.dataset.name,
+                                'uri': url_format.format(host, history_encoded_id, outobj),
+                                'access_time': job_output.dataset.create_time.isoformat(),
+                            }
+                            output_list.append(output_obj)
+
+                        if job_output.name in workflow_outputs_list:
+                            output = {
+                                'mediatype': job_output.dataset.extension,
+                                'uri': {
+                                    'filename': job_output.dataset.name,
+                                    'uri': url_format.format(host, history_encoded_id, outobj) ,
+                                    'access_time': job_output.dataset.create_time.isoformat(),
+                                }
+                            }
+                            output_subdomain.append(output)
+                pipeline_step = {
+                    'step_number': i,
+                    'name': current_tool['name'],
+                    'description': current_tool['annotation'],
                     'version': current_tool['tool_version'],
-                    'uri': {
-                        'uri': current_tool['content_id'],
-                        'access_time': current_tool['uuid']
-                    }
+                    #  'prerequisite': prerequisite,
+                    'input_list': input_list,
+                    'output_list': output_list
                 }
-            except Exception:
-                continue
-            software_prerequisites.append(software_prerequisite)
+                pipeline_steps.append(pipeline_step)
+                software_prerequisite = []
+                try:
+                    software_prerequisite = {
+                        'name': current_tool['tool_shed_repository']['name'],
+                        'version': current_tool['tool_version'],
+                        'uri': {
+                            'uri': current_tool['content_id'],
+                            'access_time': current_tool['uuid']
+                        }
+                    }
+                except Exception:
+                    continue
+                software_prerequisites.append(software_prerequisite)
+            # method to grab the workflow inputs? [WIP] TODO
+            if step.workflow_step.type != 'tool':
+                input_subdomain.append(step.workflow_step)
 
         usability_domain = []
         for a in stored_workflow.annotations:

From d2957507d44dbdf77e9fd3faada5625787f8efee Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 9 Jan 2020 19:13:22 +0000
Subject: [PATCH 842/853] Use `url_for()` to generate dataset URLs

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 25 ++++++++++------------
 1 file changed, 11 insertions(+), 14 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index db4384ddac44..dd28c0af0c68 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1005,9 +1005,9 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
 
         # may want to extend this to have more reviewers.
         reviewing_users = [stored_workflow.user]
-        workflow_encoded_id = trans.security.encode_id(stored_workflow.id)
-        history_encoded_id = trans.security.encode_id(history.id)
-        dict_workflow = json.loads(self.workflow_dict(trans, workflow_encoded_id))
+        encoded_workflow_id = trans.security.encode_id(stored_workflow.id)
+        encoded_history_id = trans.security.encode_id(history.id)
+        dict_workflow = json.loads(self.workflow_dict(trans, encoded_workflow_id))
 
         # h_contents = self.history_contents_manager.contained(history)
 
@@ -1016,7 +1016,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
 
         # listing the versions of the workflow for 'version' and 'derived_from'
         versions = []
-        workflow_versions = self.workflow_manager.get_stored_accessible_workflow(trans, workflow_encoded_id)
+        workflow_versions = self.workflow_manager.get_stored_accessible_workflow(trans, encoded_workflow_id)
         for i, w in enumerate(reversed(workflow_versions.workflows)):
             version = {
                 'version': i,
@@ -1059,7 +1059,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
             'name': workflow.name,
             'version': current_version,
             'review': reviewers,
-            'derived_from': url_for('workflow', id=workflow_encoded_id, qualified=True),
+            'derived_from': url_for('workflow', id=encoded_workflow_id, qualified=True),
             'created': workflow_invocation.create_time.isoformat(),
             'modified': workflow_invocation.update_time.isoformat(),
             'contributors': contributors,
@@ -1073,10 +1073,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
             if tag.user_tname not in keywords:
                 keywords.append(tag.user_tname)
 
-        host = 'https://localhost:8080'
         input_subdomain, output_subdomain, pipeline_steps, software_prerequisites = [], [], [], []
-        # Which `url_for` function option would generate this format below?
-        url_format = '{}/api/histories/{}/contents/{}'
         for i, step in enumerate(workflow_invocation.steps):
             current_tool = dict_workflow['steps'][str(i)]
             if step.workflow_step.type == 'tool':
@@ -1086,20 +1083,20 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
                 for job in step.jobs:
                     for job_input in job.input_datasets:
                         if hasattr(job_input.dataset, 'dataset_id'):
-                            inputobj = trans.security.encode_id(job_input.dataset.dataset_id)
+                            encoded_dataset_id = trans.security.encode_id(job_input.dataset.dataset_id)
                             input_obj = {
                                 'filename': job_input.dataset.name,
-                                'uri': url_format.format(host, history_encoded_id, inputobj),
+                                'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True),
                                 'access_time': job_input.dataset.create_time.isoformat(),
                             }
                             input_list.append(input_obj)
 
                     for job_output in job.output_datasets:
                         if hasattr(job_output.dataset, 'dataset_id'):
-                            outobj = trans.security.encode_id(job_output.dataset.dataset_id)
+                            encoded_dataset_id = trans.security.encode_id(job_output.dataset.dataset_id)
                             output_obj = {
                                 'filename': job_output.dataset.name,
-                                'uri': url_format.format(host, history_encoded_id, outobj),
+                                'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True),
                                 'access_time': job_output.dataset.create_time.isoformat(),
                             }
                             output_list.append(output_obj)
@@ -1109,7 +1106,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
                                 'mediatype': job_output.dataset.extension,
                                 'uri': {
                                     'filename': job_output.dataset.name,
-                                    'uri': url_format.format(host, history_encoded_id, outobj) ,
+                                    'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True),
                                     'access_time': job_output.dataset.create_time.isoformat(),
                                 }
                             }
@@ -1158,7 +1155,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
 
         execution_domain = {
             'script_access_type': 'a_galaxy_workflow',
-            'script': [url_for('workflows', encoded_workflow_id=workflow_encoded_id)],
+            'script': [url_for('workflows', encoded_workflow_id=encoded_workflow_id)],
             'script_driver': 'Galaxy',
             'software_prerequisites': software_prerequisites,
             'external_data_endpoints': [],

From 3464f2cd8b05d394142e2cecea637a7191347d2d Mon Sep 17 00:00:00 2001
From: HadleyKing <hadley_king@gwu.edu>
Date: Fri, 17 Jan 2020 05:55:16 -0500
Subject: [PATCH 843/853] Add output_subdomain. Fix #19

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index dd28c0af0c68..ac6a05d15852 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1164,7 +1164,6 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
 
         galaxy_extension = []  # TODO
         input_subdomain = []  # TODO
-        output_subdomain = []  # TODO
 
         ret_dict = {
             'bco_id': url_for('invocation_export_bco', invocation_id=invocation_id, qualified=True),

From 1df83a3844ed08a44bd73299c8bc3d4403c4b7c1 Mon Sep 17 00:00:00 2001
From: HadleyKing <hadley_king@gwu.edu>
Date: Sun, 26 Jan 2020 11:46:52 -0500
Subject: [PATCH 844/853] Remove dups in software_prerequisites

Add code to check for duplicate entries in execution_domain::software_prerequisites. Also add code for user suplied xref as suggested by @nsoranzo in #22
---
 lib/galaxy/webapps/galaxy/api/workflows.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index ac6a05d15852..d284e062e8ef 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1073,7 +1073,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
             if tag.user_tname not in keywords:
                 keywords.append(tag.user_tname)
 
-        input_subdomain, output_subdomain, pipeline_steps, software_prerequisites = [], [], [], []
+        tools, input_subdomain, output_subdomain, pipeline_steps, software_prerequisites = [], [], [], [], []
         for i, step in enumerate(workflow_invocation.steps):
             current_tool = dict_workflow['steps'][str(i)]
             if step.workflow_step.type == 'tool':
@@ -1133,11 +1133,15 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
                     }
                 except Exception:
                     continue
-                software_prerequisites.append(software_prerequisite)
+                if software_prerequisite['uri']['uri'] in tools:
+                    continue
+                else:
+                    software_prerequisites.append(software_prerequisite)
+                tools.append(software_prerequisite['uri']['uri'])
             # method to grab the workflow inputs? [WIP] TODO
             if step.workflow_step.type != 'tool':
                 input_subdomain.append(step.workflow_step)
-
+        print tools
         usability_domain = []
         for a in stored_workflow.annotations:
             usability_domain.append(a.annotation)
@@ -1174,7 +1178,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
             'extension_domain': galaxy_extension,
             'description_domain': {
                 'keywords': keywords,
-                'xref': [],
+                'xref': kwd.get('xref', []),
                 'platform': ['Galaxy'],
                 'pipeline_steps': pipeline_steps,
             },

From c0d96ce7f72a3d741952913e84cba3d8f01aeee5 Mon Sep 17 00:00:00 2001
From: Hadley King <HadleyKing@users.noreply.github.com>
Date: Mon, 27 Jan 2020 12:11:52 -0500
Subject: [PATCH 845/853] Update lib/galaxy/webapps/galaxy/api/workflows.py

Remove debugging line

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/webapps/galaxy/api/workflows.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index d284e062e8ef..fe9c038e5507 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1141,7 +1141,6 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
             # method to grab the workflow inputs? [WIP] TODO
             if step.workflow_step.type != 'tool':
                 input_subdomain.append(step.workflow_step)
-        print tools
         usability_domain = []
         for a in stored_workflow.annotations:
             usability_domain.append(a.annotation)

From 07dedab18455956f7d7b278de6a05557138a1bf8 Mon Sep 17 00:00:00 2001
From: Hadley King <HadleyKing@users.noreply.github.com>
Date: Mon, 27 Jan 2020 12:13:01 -0500
Subject: [PATCH 846/853] Update lib/galaxy/webapps/galaxy/api/workflows.py

Fix typo

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/webapps/galaxy/api/workflows.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index fe9c038e5507..d3e115b3a54c 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1121,7 +1121,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
                     'output_list': output_list
                 }
                 pipeline_steps.append(pipeline_step)
-                software_prerequisite = []
+                software_prerequisite = {}
                 try:
                     software_prerequisite = {
                         'name': current_tool['tool_shed_repository']['name'],

From 208cc042c847ccf1c3e761f45cae34994f58e492 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 27 Jan 2020 17:28:50 +0000
Subject: [PATCH 847/853] Prevent possible KeyError

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index d3e115b3a54c..faa6a2e86ac8 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1075,7 +1075,6 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
 
         tools, input_subdomain, output_subdomain, pipeline_steps, software_prerequisites = [], [], [], [], []
         for i, step in enumerate(workflow_invocation.steps):
-            current_tool = dict_workflow['steps'][str(i)]
             if step.workflow_step.type == 'tool':
                 workflow_outputs_list , output_list, input_list = [], [], []
                 for wo in step.workflow_step.workflow_outputs:
@@ -1111,6 +1110,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
                                 }
                             }
                             output_subdomain.append(output)
+                current_tool = dict_workflow['steps'][str(i)]
                 pipeline_step = {
                     'step_number': i,
                     'name': current_tool['name'],
@@ -1121,7 +1121,6 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
                     'output_list': output_list
                 }
                 pipeline_steps.append(pipeline_step)
-                software_prerequisite = {}
                 try:
                     software_prerequisite = {
                         'name': current_tool['tool_shed_repository']['name'],
@@ -1131,13 +1130,11 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
                             'access_time': current_tool['uuid']
                         }
                     }
+                    if software_prerequisite['uri']['uri'] not in tools:
+                        software_prerequisites.append(software_prerequisite)
+                        tools.append(software_prerequisite['uri']['uri'])
                 except Exception:
                     continue
-                if software_prerequisite['uri']['uri'] in tools:
-                    continue
-                else:
-                    software_prerequisites.append(software_prerequisite)
-                tools.append(software_prerequisite['uri']['uri'])
             # method to grab the workflow inputs? [WIP] TODO
             if step.workflow_step.type != 'tool':
                 input_subdomain.append(step.workflow_step)

From e7d382bcb87230c74a5539b8e89b64ee85121c66 Mon Sep 17 00:00:00 2001
From: HadleyKing <hadley_king@gwu.edu>
Date: Mon, 3 Feb 2020 16:07:06 -0500
Subject: [PATCH 848/853] Add to test_export_invocation_bco

- add lines to test for all top level and domain specific fields
- add method to check for parametric doamin
- add line to check for execution domain
---
 lib/galaxy_test/api/test_workflows.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index e63b4cd2cb46..ec3d11a2f8a6 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -1354,8 +1354,16 @@ def test_export_invocation_bco(self):
             summary = self._run_jobs(WORKFLOW_SIMPLE, test_data={"input1": "hello world"}, history_id=history_id)
             invocation_id = summary.invocation_id
             bco = self._get("invocations/%s/export_bco" % invocation_id).json()
+            print(self)
+            self._assert_has_keys(bco, "bco_id", "spec_version", "etag", "provenance_domain", "usability_domain", "description_domain", "execution_domain", "parametric_domain", "io_domain", "error_domain")
             self.assertEqual(bco['spec_version'], 'https://w3id.org/biocompute/1.4.0/')
             self.assertEqual(bco['provenance_domain']['name'], "Simple Workflow")
+            self._assert_has_keys(bco['description_domain'], "keywords", "xref", "platform", "pipeline_steps")
+#            if 'extension_domain' in bco: self._assert_has_keys(bco['extension_domain'], "extension_schema")
+            self._assert_has_keys(bco['execution_domain'], "script_access_type", "script", "script_driver", "software_prerequisites", "external_data_endpoints", "environment_variables")
+            for p in bco['parametric_domain']:
+                self._assert_has_keys(p, "param", "value", "step")
+            self._assert_has_keys(bco['io_domain'], "input_subdomain", "output_subdomain")
 
     @skip_without_tool("__APPLY_RULES__")
     def test_workflow_run_apply_rules(self):

From ce71d0f1af37c055cf44dd5b349087c90813d6a0 Mon Sep 17 00:00:00 2001
From: HadleyKing <hadley_king@gwu.edu>
Date: Mon, 3 Feb 2020 16:20:21 -0500
Subject: [PATCH 849/853] Add to test_export_invocation_bco

- add lines to test for all top level and domain specific fields
- add method to check for parametric doamin
- add line to check for execution domain
---
 lib/galaxy_test/api/test_workflows.py | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index ec3d11a2f8a6..e63b4cd2cb46 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -1354,16 +1354,8 @@ def test_export_invocation_bco(self):
             summary = self._run_jobs(WORKFLOW_SIMPLE, test_data={"input1": "hello world"}, history_id=history_id)
             invocation_id = summary.invocation_id
             bco = self._get("invocations/%s/export_bco" % invocation_id).json()
-            print(self)
-            self._assert_has_keys(bco, "bco_id", "spec_version", "etag", "provenance_domain", "usability_domain", "description_domain", "execution_domain", "parametric_domain", "io_domain", "error_domain")
             self.assertEqual(bco['spec_version'], 'https://w3id.org/biocompute/1.4.0/')
             self.assertEqual(bco['provenance_domain']['name'], "Simple Workflow")
-            self._assert_has_keys(bco['description_domain'], "keywords", "xref", "platform", "pipeline_steps")
-#            if 'extension_domain' in bco: self._assert_has_keys(bco['extension_domain'], "extension_schema")
-            self._assert_has_keys(bco['execution_domain'], "script_access_type", "script", "script_driver", "software_prerequisites", "external_data_endpoints", "environment_variables")
-            for p in bco['parametric_domain']:
-                self._assert_has_keys(p, "param", "value", "step")
-            self._assert_has_keys(bco['io_domain'], "input_subdomain", "output_subdomain")
 
     @skip_without_tool("__APPLY_RULES__")
     def test_workflow_run_apply_rules(self):

From 15fb84a3253378bc465be1d1eb74c018992f4029 Mon Sep 17 00:00:00 2001
From: HadleyKing <hadley_king@gwu.edu>
Date: Mon, 3 Feb 2020 16:23:05 -0500
Subject: [PATCH 850/853] Add to test_export_invocation_bco

- add lines to test for all top level and domain specific fields
- add method to check for parametric doamin
- add line to check for execution domain
---
 lib/galaxy_test/api/test_workflows.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index e63b4cd2cb46..a0c63f4f8960 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -1354,8 +1354,15 @@ def test_export_invocation_bco(self):
             summary = self._run_jobs(WORKFLOW_SIMPLE, test_data={"input1": "hello world"}, history_id=history_id)
             invocation_id = summary.invocation_id
             bco = self._get("invocations/%s/export_bco" % invocation_id).json()
+            self._assert_has_keys(bco, "bco_id", "spec_version", "etag", "provenance_domain", "usability_domain", "description_domain", "execution_domain", "parametric_domain", "io_domain", "error_domain")
             self.assertEqual(bco['spec_version'], 'https://w3id.org/biocompute/1.4.0/')
             self.assertEqual(bco['provenance_domain']['name'], "Simple Workflow")
+            self._assert_has_keys(bco['description_domain'], "keywords", "xref", "platform", "pipeline_steps")
+#            if 'extension_domain' in bco: self._assert_has_keys(bco['extension_domain'], "extension_schema")
+            self._assert_has_keys(bco['execution_domain'], "script_access_type", "script", "script_driver", "software_prerequisites", "external_data_endpoints", "environment_variables")
+            for p in bco['parametric_domain']:
+                self._assert_has_keys(p, "param", "value", "step")
+            self._assert_has_keys(bco['io_domain'], "input_subdomain", "output_subdomain")
 
     @skip_without_tool("__APPLY_RULES__")
     def test_workflow_run_apply_rules(self):

From bee175384a1aefd063be96b7a987ae1231f5b076 Mon Sep 17 00:00:00 2001
From: HadleyKing <hadley_king@gwu.edu>
Date: Wed, 19 Feb 2020 15:32:30 -0500
Subject: [PATCH 851/853] Add code to extract input_subdomain

fix #17
add code to parse data_collection_input and data_input objects from the workflow invocation for the input_subdomaiRremove debugging text
---
 lib/galaxy/webapps/galaxy/api/workflows.py | 26 ++++++++++++++++++----
 1 file changed, 22 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index faa6a2e86ac8..d81529211fa4 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1135,9 +1135,27 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
                         tools.append(software_prerequisite['uri']['uri'])
                 except Exception:
                     continue
-            # method to grab the workflow inputs? [WIP] TODO
-            if step.workflow_step.type != 'tool':
-                input_subdomain.append(step.workflow_step)
+
+            if step.workflow_step.type == 'data_input':
+                for output_assoc in step.output_datasets:
+                    encoded_dataset_id = trans.security.encode_id(output_assoc.dataset.id)
+                input_obj = {
+                    'filename': step.workflow_step.label,
+                    'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True),
+                    'access_time': step.workflow_step.update_time.isoformat(),
+                }
+                input_subdomain.append(input_obj)
+
+            if step.workflow_step.type == 'data_collection_input':
+                encoded_dataset_id = trans.security.encode_id(step.workflow_step.id)
+                input_obj = []
+                input_obj = {
+                    'filename': step.workflow_step.label,
+                    'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True),
+                    'access_time': step.workflow_step.update_time.isoformat(),
+                }
+                input_subdomain.append(input_obj)
+
         usability_domain = []
         for a in stored_workflow.annotations:
             usability_domain.append(a.annotation)
@@ -1163,7 +1181,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
         }
 
         galaxy_extension = []  # TODO
-        input_subdomain = []  # TODO
+        input_subdomain = input_subdomain  # TODO
 
         ret_dict = {
             'bco_id': url_for('invocation_export_bco', invocation_id=invocation_id, qualified=True),

From c055e54c1f79423df8a8ce769572c86d7e550ef3 Mon Sep 17 00:00:00 2001
From: HadleyKing <hadley_king@gwu.edu>
Date: Thu, 20 Feb 2020 18:34:37 -0500
Subject: [PATCH 852/853] Update to BCO Test

---
 lib/galaxy/webapps/galaxy/api/workflows.py | 3 +--
 lib/galaxy_test/api/test_workflows.py      | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index d81529211fa4..1c336c3859d8 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1012,7 +1012,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
         # h_contents = self.history_contents_manager.contained(history)
 
         # TODO add a keyword option/function to determine the spec_version used in BCO creation, and populate it accordingly
-        spec_version = 'https://w3id.org/biocompute/1.4.0/'
+        spec_version = kwd.get('spec_version', 'https://w3id.org/biocompute/1.4.0/')
 
         # listing the versions of the workflow for 'version' and 'derived_from'
         versions = []
@@ -1148,7 +1148,6 @@ def export_invocation_bco(self, trans, invocation_id, **kwd):
 
             if step.workflow_step.type == 'data_collection_input':
                 encoded_dataset_id = trans.security.encode_id(step.workflow_step.id)
-                input_obj = []
                 input_obj = {
                     'filename': step.workflow_step.label,
                     'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True),
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index a0c63f4f8960..cb80ff5af193 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -1358,7 +1358,7 @@ def test_export_invocation_bco(self):
             self.assertEqual(bco['spec_version'], 'https://w3id.org/biocompute/1.4.0/')
             self.assertEqual(bco['provenance_domain']['name'], "Simple Workflow")
             self._assert_has_keys(bco['description_domain'], "keywords", "xref", "platform", "pipeline_steps")
-#            if 'extension_domain' in bco: self._assert_has_keys(bco['extension_domain'], "extension_schema")
+            # if 'extension_domain' in bco: self._assert_has_keys(bco['extension_domain'], "extension_schema")
             self._assert_has_keys(bco['execution_domain'], "script_access_type", "script", "script_driver", "software_prerequisites", "external_data_endpoints", "environment_variables")
             for p in bco['parametric_domain']:
                 self._assert_has_keys(p, "param", "value", "step")

From 567006493758a5de595ee915952260c493107fb2 Mon Sep 17 00:00:00 2001
From: HadleyKing <hadley_king@gwu.edu>
Date: Thu, 20 Feb 2020 18:40:28 -0500
Subject: [PATCH 853/853] Add entry point for BCO UI

---
 .../WorkflowInvocationState.vue                      | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/WorkflowInvocationState/WorkflowInvocationState.vue b/client/galaxy/scripts/components/WorkflowInvocationState/WorkflowInvocationState.vue
index 17542e426e01..12bde25c3132 100644
--- a/client/galaxy/scripts/components/WorkflowInvocationState/WorkflowInvocationState.vue
+++ b/client/galaxy/scripts/components/WorkflowInvocationState/WorkflowInvocationState.vue
@@ -56,8 +56,13 @@
                 </div>
             </div>
             <span v-if="invocationSchedulingTerminal && jobStatesTerminal">
-                <a :href="invocationLink">View Invocation Report</a>
-                <a class="fa fa-print" :href="invocationPdfLink"></a>
+                <div>
+                    <a :href="invocationLink">View Invocation Report</a>
+                    <a class="fa fa-print" :href="invocationPdfLink"></a>
+                </div>
+                <div>
+                    <a :href="bcoLink">Create BioCompute Object</a>
+                </div>
             </span>
         </div>
     </div>
@@ -141,6 +146,9 @@ export default {
         invocationLink: function () {
             return getUrl(`workflows/invocations/report?id=${this.invocationId}`);
         },
+        bcoLink: function () {
+            return getUrl(`workflows/invocations/report?id=${this.invocationId}`);
+        },
         invocationPdfLink: function () {
             return getUrl(`api/invocations/${this.invocationId}/report.pdf`);
         },