Merge branch 'master' into bugfix/client-cache-#209

.github/workflows/ci-build.yml

@@ -50,6 +50,10 @@ jobs:
       run: |
         sed -i -e "s/^payara_user: \"glassfish\"/payara_user: \"runner\"/" icat-ansible/group_vars/all/vars.yml
 
+    # Force hostname to localhost - bug fix for previous ICAT Ansible issues on Actions
+    - name: Change hostname to localhost
+      run: sudo hostname -b localhost
+
     # Create local instance of ICAT
     - name: Run ICAT Ansible Playbook
       run: |

README.md

@@ -335,6 +335,13 @@ PowerShell:
 > flask run
 ```
 
+The Flask app can be configured so that code changes are monitored and the server will
+reload itself when a change is detected. This setting can be toggled using
+`flask_reloader` in `config.json`. This is useful for development purposes. It should be
+noted that when this setting is enabled, the API will go through the startup process
+twice. In the case of the ICAT backend, this could dramatically increase startup time if
+the API is configured with a large initial client pool size.
+
 
 ## Authentication
 Each request requires a valid session ID to be provided in the Authorization header.

datagateway_api/common/backends.py

@@ -24,7 +24,6 @@ def create_backend(backend_type):
     elif backend_type == "python_icat":
         backend = PythonICATBackend()
     else:
-        # Might turn to a warning so the abstract class can be tested?
         sys.exit(f"Invalid config value '{backend_type}' for config option backend")
 
     return backend

datagateway_api/common/config.py

@@ -58,6 +58,12 @@ def get_db_url(self):
         except KeyError:
             sys.exit("Missing config value, DB_URL")
 
+    def is_flask_reloader(self):
+        try:
+            return self.config["flask_reloader"]
+        except KeyError:
+            sys.exit("Missing config value, flask_reloader")
+
     def get_icat_url(self):
         try:
             return self.config["ICAT_URL"]

datagateway_api/common/icat/filters.py

@@ -117,22 +117,30 @@ def __init__(self, fields):
     def apply_filter(self, query):
         try:
             log.info("Adding ICAT distinct filter to ICAT query")
-            if (
-                query.aggregate == "COUNT"
-                or query.aggregate == "AVG"
-                or query.aggregate == "SUM"
-            ):
+            log.debug("Fields for distinct filter: %s", self.fields)
+
+            # These aggregate keywords not currently used in the API, but conditional
+            # present in case they're used in the future
+            if query.aggregate == "AVG" or query.aggregate == "SUM":
                 # Distinct can be combined with other aggregate functions
                 query.setAggregate(f"{query.aggregate}:DISTINCT")
+            elif query.aggregate == "COUNT":
+                # When count and distinct keywords are used together when selecting
+                # multiple attributes, Python ICAT will always throw an error on query
+                # execution (more info:
+                # https://github.com/icatproject/python-icat/issues/76). This appears to
+                # be a JPQL limitation, something that cannot be fixed in Python ICAT.
+                # As a result, the API will get the distinct results and manually
+                # perform `len()` on the list, using `manual_count` as a flag to
+                # recognise this situation
+                query.setAggregate("DISTINCT")
+                log.debug("Manual count flag enabled")
+                query.manual_count = True
             else:
                 query.setAggregate("DISTINCT")
 
-            # Using where filters to identify which fields to apply distinct too
-            for field in self.fields:
-                where_filter = PythonICATWhereFilter(field, "null", "ne")
-                where_filter.apply_filter(query)
+            query.setAttributes(self.fields)
 
-            log.debug("Fields for distinct filter: %s", self.fields)
         except ValueError as e:
             raise FilterError(e)
 

datagateway_api/common/icat/helpers.py

@@ -577,6 +577,7 @@ def get_facility_cycles_for_instrument(
 
     query_aggregate = "COUNT:DISTINCT" if count_query else "DISTINCT"
     query = ICATQuery(client, "FacilityCycle", aggregate=query_aggregate)
+    query.isis_endpoint = True
 
     instrument_id_check = PythonICATWhereFilter(
         "facility.instruments.id", instrument_id, "eq",
@@ -657,6 +658,7 @@ def get_investigations_for_instrument_in_facility_cycle(
 
     query_aggregate = "COUNT:DISTINCT" if count_query else "DISTINCT"
     query = ICATQuery(client, "Investigation", aggregate=query_aggregate)
+    query.isis_endpoint = True
 
     instrument_id_check = PythonICATWhereFilter(
         "facility.instruments.id", instrument_id, "eq",