Merge branch 'develop' of https://github.com/ebi-gene-expression-grou…

…p/atlas-web-single-cell into develop
ebi-gene-expression-group · Sep 7, 2023 · 06964f6 · 06964f6
2 parents 81b6102 + f2d44d4
commit 06964f6
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diff --git a/app/src/main/javascript/bundles/experiment-page/src/TSnePlotViewRoute.js b/app/src/main/javascript/bundles/experiment-page/src/TSnePlotViewRoute.js
@@ -107,7 +107,6 @@ class TSnePlotViewRoute extends React.Component {
           selectedPlotOptionLabel={this.state.selectedPlotOptionLabel}
           onChangePlotTypes={
             (plotOption) => {
-              console.log(plotOption)
               this.setState({
                 selectedPlotType: plotOption.value,
                 selectedPlotOption: defaultPlotMethodAndParameterisation[plotOption.value],
@@ -166,16 +165,14 @@ class TSnePlotViewRoute extends React.Component {
           wrapperClassName={`row expanded`}
           ks={ks}
           selectedClusterByCategory={search.cellGroupType || search.k || preferredK}
-          selectedClusterId={this.state.selectedClusterId}
-          onChangeClusterId={(colourByCategory, colourByValue) => {
+          selectedK={this.state.selectedClusterId}
+          onSelectK={(colourByValue) => {
+              this.setState({
+                selectedClusterId : colourByValue
+              })
               const query = new URLSearchParams(history.location.search)
               // If tsne plot is coloured by k
-              if (!query.has(`metadata`)) {
-                query.set(`k`, colourByValue)
-              } else {
-                query.set(`cellGroupType`, colourByValue)
-              }
-              query.set(`colourBy`, colourByCategory)
+              query.set(`k`, colourByValue)
               resetHighlightClusters(query)
               updateUrlWithParams(query)
             }

diff --git a/docker/prepare-dev-environment/gradle-cache/docker-compose.yml b/docker/prepare-dev-environment/gradle-cache/docker-compose.yml
@@ -2,7 +2,9 @@ version: "3.6"
 
 services:
   gradle-cache-populator:
-    build: ${DOCKERFILE_PATH}
+    build:
+      context: ${DOCKERFILE_PATH}
+      no_cache: true
     volumes:
       - gradle-wrapper-dists:/gradle-wrapper-dists
       - gradle-ro-dep-cache:/gradle-ro-dep-cache

diff --git a/docker/prepare-dev-environment/postgres/docker-compose.yml b/docker/prepare-dev-environment/postgres/docker-compose.yml
@@ -2,7 +2,9 @@ version: "3.6"
 
 services:
   postgres-populator:
-    build: ${DOCKERFILE_PATH}
+    build:
+      context: ${DOCKERFILE_PATH}
+      no_cache: true
     networks:
       - atlas-test-net
     depends_on:

diff --git a/docker/prepare-dev-environment/solr/docker-compose.yml b/docker/prepare-dev-environment/solr/docker-compose.yml
@@ -8,9 +8,15 @@ services:
       - atlas-test-net
     ports:
       - "5432:5432"
+    environment:
+      - POSTGRES_PASSWORD
+      - POSTGRES_USER
+      - POSTGRES_DB
 
   solr-populator:
-    build: ${DOCKERFILE_PATH}
+    build:
+      context: ${DOCKERFILE_PATH}
+      no_cache: true
     networks:
       - atlas-test-net
     depends_on:
@@ -58,8 +64,8 @@ services:
         ./create-bioentities-schema.sh
         ./create-bioentities-suggesters.sh
 
-        export SOLR_COLLECTION=${SOLR_COLLECTION_BIOENTITIES}
-        export SCHEMA_VERSION=${SOLR_COLLECTION_BIOENTITIES_SCHEMA_VERSION}
+        export SOLR_COLLECTION=$${SOLR_COLLECTION_BIOENTITIES}
+        export SCHEMA_VERSION=$${SOLR_COLLECTION_BIOENTITIES_SCHEMA_VERSION}
         for FILE in `ls /root/bioentity-properties-jsonl/*.jsonl`
         do
           INPUT_JSONL=$${FILE} ./solr-jsonl-chunk-loader.sh >> /dev/stdout 2>&1

diff --git a/docker/prepare-dev-environment/solr/run.sh b/docker/prepare-dev-environment/solr/run.sh
@@ -108,15 +108,15 @@ then
   print_done
 fi
 
-print_stage_name "📑 Copy ${SC_ATLAS_ONTOLOGY_FILE} to ${SOLR_CLOUD_CONTAINER_1_NAME}:${SOLR_USERFILES_PATH}"
-docker cp ${SC_ATLAS_ONTOLOGY_FILE} ${SOLR_CLOUD_CONTAINER_1_NAME}:${SOLR_USERFILES_PATH} >> ${LOG_FILE} 2>&1
+print_stage_name "📑 Copy ${SC_ATLAS_ONTOLOGY_FILE} to ${PROJECT_NAME}-${SOLR_CLOUD_CONTAINER_1_NAME}:${SOLR_USERFILES_PATH}"
+docker cp ${SC_ATLAS_ONTOLOGY_FILE} ${PROJECT_NAME}-${SOLR_CLOUD_CONTAINER_1_NAME}:${SOLR_USERFILES_PATH} >> ${LOG_FILE} 2>&1
 print_done
-print_stage_name "📑 Copy ${SC_ATLAS_ONTOLOGY_FILE} to ${SOLR_CLOUD_CONTAINER_2_NAME}:${SOLR_USERFILES_PATH}"
-docker cp ${SC_ATLAS_ONTOLOGY_FILE} ${SOLR_CLOUD_CONTAINER_2_NAME}:${SOLR_USERFILES_PATH} >> ${LOG_FILE} 2>&1
+print_stage_name "📑 Copy ${SC_ATLAS_ONTOLOGY_FILE} to ${PROJECT_NAME}-${SOLR_CLOUD_CONTAINER_2_NAME}:${SOLR_USERFILES_PATH}"
+docker cp ${SC_ATLAS_ONTOLOGY_FILE} ${PROJECT_NAME}-${SOLR_CLOUD_CONTAINER_2_NAME}:${SOLR_USERFILES_PATH} >> ${LOG_FILE} 2>&1
 print_done
 
 print_stage_name "🔏 Register ${SOLR_PUBLIC_KEY} in SolrCloud"
-docker exec ${SOLR_CLOUD_CONTAINER_1_NAME} ./bin/solr package add-key /run/secrets/solrcloud.der >> ${LOG_FILE} 2>&1
+docker exec ${PROJECT_NAME}-${SOLR_CLOUD_CONTAINER_1_NAME} ./bin/solr package add-key /run/secrets/solrcloud.der >> ${LOG_FILE} 2>&1
 print_done
 
 print_stage_name "🌄 Stop Solr 8 cluster in Docker Compose"

diff --git a/docker/prepare-dev-environment/volumes/docker-compose.yml b/docker/prepare-dev-environment/volumes/docker-compose.yml
@@ -2,7 +2,9 @@ version: "3.6"
 
 services:
   volumes-populator:
-    build: ${DOCKERFILE_PATH}
+    build:
+      context: ${DOCKERFILE_PATH}
+      no_cache: true
     volumes:
       - atlas-data-bioentity-properties:/atlas-data/bioentity_properties
       - atlas-data-exp:/atlas-data/exp