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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,23 @@ | ||
| FROM ubuntu:jammy | ||
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| # Update package list and install necessary tools | ||
| # Python 3 is required by index-bioentities but comes as part of Ubuntu | ||
| RUN apt-get update && \ | ||
| apt-get install -y --no-install-recommends \ | ||
| git openjdk-11-jdk jq rsync curl | ||
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| # Clean up APT cache and temporary files | ||
| RUN apt-get clean && \ | ||
| rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* | ||
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| # Create the necessary directory | ||
| RUN mkdir -p /root/bioentity-properties-jsonl | ||
| RUN mkdir -p /root/experiments-jsonl | ||
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| # Clone the necessary repositories | ||
| WORKDIR /root | ||
| RUN git clone --depth 1 --recurse-submodules https://github.com/ebi-gene-expression-group/index-bioentities.git | ||
| RUN git clone --depth 1 --recurse-submodules https://github.com/ebi-gene-expression-group/atlas-web-bulk.git | ||
| RUN git clone --depth 1 --recurse-submodules https://github.com/ebi-gene-expression-group/solr-bulk.git | ||
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| ENTRYPOINT ["/bin/bash", "-c"] |
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docker/prepare-dev-environment/solr-analytics/docker-compose.yml
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,92 @@ | ||
| version: "3.6" | ||
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| services: | ||
| solr-populator: | ||
| build: | ||
| context: ${DOCKERFILE_PATH} | ||
| no_cache: true | ||
| networks: | ||
| - atlas-test-net | ||
| ports: | ||
| - "8089:8089" | ||
| depends_on: | ||
| - gxa-postgres | ||
| - gxa-solrcloud-0 | ||
| - gxa-solrcloud-1 | ||
| volumes: | ||
| - gradle-wrapper-dists:/root/.gradle/wrapper/dists | ||
| - gradle-ro-dep-cache:/gradle-ro-dep-cache:ro | ||
| - atlas-data-bioentity-properties:/atlas-data/bioentity_properties | ||
| - atlas-data-exp:/atlas-data/exp | ||
| - atlas-data-expdesign:/atlas-data/expdesign | ||
| secrets: | ||
| - solrcloud.pem | ||
| environment: | ||
| JAVA_TOOL_OPTIONS: "-Dfile.encoding=UTF8" | ||
| JAVA_OPTS: "-Dsolr.httpclient.builder.factory=org.apache.solr.client.solrj.impl.PreemptiveBasicAuthClientBuilderFactory -Dbasicauth=${SOLR_USER}:${SOLR_PASSWORD}" | ||
| GRADLE_RO_DEP_CACHE: /gradle-ro-dep-cache | ||
| ZK_HOSTS: "${PROJECT_NAME}-${SOLR_CLOUD_ZK_CONTAINER_1_NAME}:2181,${PROJECT_NAME}-${SOLR_CLOUD_ZK_CONTAINER_2_NAME}:2181,${PROJECT_NAME}-${SOLR_CLOUD_ZK_CONTAINER_3_NAME}:2181" | ||
| SOLR_HOST: "http://${PROJECT_NAME}-${SOLR_CLOUD_CONTAINER_1_NAME}:8983/solr" | ||
| SOLR_NUM_SHARDS: 2 | ||
| NUM_DOCS_PER_BATCH: 20000 | ||
| SOLR_COLLECTION_BIOENTITIES: bioentities | ||
| SOLR_COLLECTION_BIOENTITIES_SCHEMA_VERSION: 1 | ||
| SOLR_COLLECTION_BULK_ANALYTICS: bulk-analytics | ||
| SOLR_COLLECTION_BULK_ANALYTICS_SCHEMA_VERSION: 1 | ||
| working_dir: /root | ||
| command: | ||
| - | | ||
| cd /root/atlas-web-bulk | ||
| ./gradlew -PdataFilesLocation=/root \ | ||
| -PexperimentFilesLocation=/atlas-data/exp \ | ||
| -PexperimentDesignLocation=/atlas-data/expdesign \ | ||
| -PjdbcUrl=jdbc:postgresql://${POSTGRES_HOST}:5432/${POSTGRES_DB} \ | ||
| -PjdbcUsername=${POSTGRES_USER} \ | ||
| -PjdbcPassword=${POSTGRES_PASSWORD} \ | ||
| -PzkHosts=$${ZK_HOSTS} \ | ||
| -PsolrHosts=$${SOLR_HOST} \ | ||
| -PsolrUser=${SOLR_USER} \ | ||
| -PsolrPassword=${SOLR_PASSWORD} \ | ||
| :cli:bootRun --args="bulk-analytics-json --output=/root/experiments-jsonl -e $(echo ${EXP_IDS} ${PRIVATE_EXP_IDS} | sed -e "s/ /,/g")" | ||
| cd /root/solr-bulk/bin | ||
| export SOLR_HOST="${PROJECT_NAME}-${SOLR_CLOUD_CONTAINER_1_NAME}:8983" | ||
| ./create-bulk-analytics-collection.sh | ||
| echo "bulk-analytics collection has been created" | ||
| ./create-bulk-analytics-schema.sh | ||
| echo "bulk-analytics schema has been created" | ||
| cd /root/index-bioentities/bin | ||
| export SOLR_COLLECTION=$${SOLR_COLLECTION_BULK_ANALYTICS} | ||
| export SCHEMA_VERSION=$${SOLR_COLLECTION_BULK_ANALYTICS_SCHEMA_VERSION} | ||
| export SOLR_HOSTS="${PROJECT_NAME}-${SOLR_CLOUD_CONTAINER_1_NAME}:8983" | ||
| export SOLR_PROCESSORS=dedupe | ||
| for FILE in `ls /root/experiments-jsonl/*.jsonl` | ||
| do | ||
| INPUT_JSONL=$${FILE} ./solr-jsonl-chunk-loader.sh >> /dev/stdout 2>&1 | ||
| done | ||
| secrets: | ||
| solrcloud.pem: | ||
| file: ${SOLR_PRIVATE_KEY:-/dev/null} | ||
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||
| volumes: | ||
| gradle-wrapper-dists: | ||
| external: true | ||
| name: ${PROJECT_NAME}_${GRADLE_WRAPPER_DISTS_VOL_NAME} | ||
| gradle-ro-dep-cache: | ||
| external: true | ||
| name: ${PROJECT_NAME}_${GRADLE_RO_DEP_CACHE_VOL_NAME} | ||
| atlas-data-bioentity-properties: | ||
| external: true | ||
| name: ${PROJECT_NAME}_${ATLAS_DATA_BIOENTITY_PROPERTIES_VOL_NAME} | ||
| atlas-data-exp: | ||
| external: true | ||
| name: ${PROJECT_NAME}_${ATLAS_DATA_EXP_VOL_NAME} | ||
| atlas-data-expdesign: | ||
| external: true | ||
| name: ${PROJECT_NAME}_${ATLAS_DATA_EXPDESIGN_VOL_NAME} | ||
|
|
||
| networks: | ||
| atlas-test-net: | ||
| name: atlas-test-net |
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