From 34cf9b3e4e8eccdd3590fc470f1ce45543011b39 Mon Sep 17 00:00:00 2001 From: Lingyun Zhao <33519183+lingyun1010@users.noreply.github.com> Date: Thu, 10 Aug 2023 10:55:18 +0100 Subject: [PATCH 1/2] Fix the props and func for marker gene heatmap tab (#351) * Fix the props and func for marker gene heatmap tab * Remove unused parameter --- .../experiment-page/src/TSnePlotViewRoute.js | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/app/src/main/javascript/bundles/experiment-page/src/TSnePlotViewRoute.js b/app/src/main/javascript/bundles/experiment-page/src/TSnePlotViewRoute.js index 54c930b3c..21f982fa1 100644 --- 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) } From f2d44d4f5d5bcc0bfbee6113475ebfb3a3b6a937 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alfonso=20Mu=C3=B1oz-Pomer=20Fuentes?= Date: Thu, 31 Aug 2023 11:15:22 +0100 Subject: [PATCH 2/2] Improve Docker Compose scripts to prepare the dev environment (#354) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Don’t use cached layers when building local images * Declare Postgres variables so that they’re set to the env file values * Prefix container names with project name * Correctly reference bioentity collection env vars in command script --- .../gradle-cache/docker-compose.yml | 4 +++- .../postgres/docker-compose.yml | 4 +++- .../prepare-dev-environment/solr/docker-compose.yml | 12 +++++++++--- docker/prepare-dev-environment/solr/run.sh | 10 +++++----- .../volumes/docker-compose.yml | 4 +++- 5 files changed, 23 insertions(+), 11 deletions(-) diff --git a/docker/prepare-dev-environment/gradle-cache/docker-compose.yml b/docker/prepare-dev-environment/gradle-cache/docker-compose.yml index e149850d1..734db87fc 100644 --- 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 index fe8e716e1..6b1d203c9 100644 --- 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 index cdba053af..a41221032 100644 --- 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 index 456dacaa2..ab23e6e9c 100755 --- 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 "πŸ“‘ 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 "πŸ“‘ 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 "πŸ“‘ 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 "πŸ“‘ 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 "πŸ” 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 "πŸŒ„ 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 index c3cb7a68a..842f58937 100644 --- 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