docker-compose.phaseOne.yml

services:
  conductor:
    profiles: ['phaseOne', 'phaseTwo', 'phaseThree', 'platform', 'stageDev', 'data', 'clean']
    image: node:18-alpine
    container_name: conductor
    ports:
      - '9204:9204'
    volumes:
      - ./volumes/data-song-db:/song/db-folder-init
      - ./configs/elasticsearchConfigs/file_data_index_template.json:/usr/share/elasticsearch/config/file_data_index_template.json
      - ./configs/elasticsearchConfigs/tabular_data_index_template.json:/usr/share/elasticsearch/config/tabular_data_index_template.json
      - ./apps/csv-processor:/csv-processor
      - ./apps/stage:/stage
      - ./data:/data
      - ./scripts:/scripts
      - ./volumes/health:/health
    environment:
      PROFILE: ${PROFILE:-platform}
      ES_URL: http://elasticsearch:9200
      ES_USER: elastic
      ES_PASS: myelasticpassword
      ARRANGER_FILE_URL: http://arranger-file:5050/graphql
      ARRANGER_TABULAR_URL: http://arranger-tabular:5051/graphql
      FILE_INDEX_NAME: file-index
      FILE_ES_TEMPLATE_FILE: /usr/share/elasticsearch/config/file_data_index_template.json
      FILE_ES_TEMPLATE_NAME: file_template
      FILE_ES_ALIAS_NAME: file_centric
      TABULAR_INDEX_NAME: tabular-index
      TABULAR_ES_TEMPLATE_FILE: /usr/share/elasticsearch/config/tabular_data_index_template.json
      TABULAR_ES_TEMPLATE_NAME: tabular_template
      TABULAR_ES_ALIAS_NAME: tabular_centric
      STAGE_URL: http://stage:3000
      TABULAR_DATA_FILE: /data/tabularData.csv
    command: >
      sh -c '
        apk add --no-cache --quiet curl >/dev/null 2>&1
        set -e
          echo "Profile is set to: $PROFILE"
          case "$PROFILE" in
            phaseOne)
              echo "Running phaseOne deployment..."
              chmod +x scripts/deployments/phaseOne.sh
              scripts/deployments/phaseOne.sh
              ;;
            PhaseTwo)
              echo "Running phaseTwo deployment..."
              chmod +x scripts/deployments/phaseTwo.sh
              scripts/deployments/phaseTwo.sh
              ;;
            phaseThree)
              echo "Running phaseThree deployment ..."
              chmod +x scripts/deployments/phaseThree.sh
              scripts/deployments/phaseThree.sh
              ;;
            platform)
              echo "Running platform deployment..."
              chmod +x scripts/deployments/platform.sh
              scripts/deployments/platform.sh
              ;;
            stageDev)
              echo "Running Stage Dev deployment..."
              chmod +x scripts/deployments/stageDev.sh
              scripts/deployments/stageDev.sh
              ;;
            data)
              echo "Running mock data submission..."
              chmod +x scripts/services/phaseOne/submitMockData.sh
              scripts/services/phaseOne/submitMockData.sh
              ;;
            clean)
              echo "Removing mock data..."
              chmod +x scripts/services/phaseOne/clearElasticsearchData.sh
              scripts/services/phaseOne/clearElasticsearchData.sh
              ;;
            *)
              echo "Invalid profile: $PROFILE. Available options are [platform, songDev, scoreDev,
      maestroDev, arrangerDev, stageDev]."
              exit 1
              ;;
          esac
          exit 0
      '
    healthcheck:
      test: ['CMD', 'test', '-f', '/health/conductor_health']
      interval: 5s
      timeout: 40s
      retries: 100
      start_period: 30s
    networks:
      - conductor-network

  # ==================================================================================
  #  PhaseOne: Search & Discovery
  # ==================================================================================

  elasticsearch:
    profiles: ['phaseOne', 'phaseTwo', 'phaseThree', 'platform', 'stageDev']
    image: docker.elastic.co/elasticsearch/elasticsearch:7.17.1
    container_name: elasticsearch
    platform: linux/amd64
    ports:
      - '9200:9200'
    environment:
      discovery.type: single-node
      cluster.name: workflow.elasticsearch
      ES_JAVA_OPTS: -Xms512m -Xmx2048m
      ES_USER: elastic
      ELASTIC_PASSWORD: myelasticpassword
      xpack.security.enabled: 'true'
    logging:
      driver: 'json-file'
      options:
        max-size: '50m'
        max-file: '10'
    volumes:
      - elasticsearch-data:/usr/share/elasticsearch/data
    healthcheck:
      test:
        'curl --silent --fail localhost:9200/_cluster/health?wait_for_status=yellow&timeout=50s ||
        exit 1'
      interval: 10s
      timeout: 10s
      retries: 5
      start_period: 25s
    networks:
      - conductor-network

  # ======================================
  # Arranger-Server file data
  # ======================================
  # Search API generation with compatible search UI components
  # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#running-arranger
  # --------------------------------------
  arranger-file:
    profiles: ['phaseOne', 'phaseTwo', 'phaseThree', 'platform', 'stageDev']
    image: ghcr.io/overture-stack/arranger-server:3.0.0-beta.36
    container_name: arranger-file
    platform: linux/amd64
    depends_on:
      conductor:
        condition: service_healthy
    ports:
      - '5050:5050'
    volumes:
      - ./configs/arrangerConfigs/fileDataConfigs/base.json:/app/modules/server/configs/base.json
      - ./configs/arrangerConfigs/fileDataConfigs/extended.json:/app/modules/server/configs/extended.json
      - ./configs/arrangerConfigs/fileDataConfigs/facets.json:/app/modules/server/configs/facets.json
      - ./configs/arrangerConfigs/fileDataConfigs/matchbox.json:/app/modules/server/configs/matchbox.json
      - ./configs/arrangerConfigs/fileDataConfigs/table.json:/app/modules/server/configs/table.json
    environment:
      # Elasticsearch Variables
      ES_HOST: http://elasticsearch:9200
      ES_USER: elastic
      ES_PASS: myelasticpassword
      ES_ARRANGER_SET_INDEX: file_arranger_set
      # Arranger Variables
      DEBUG: false
      ENABLE_LOGS: false
    networks:
      - conductor-network

  # ======================================
  # Arranger-Server Tabular
  # ======================================
  # Search API generation with compatible search UI components
  # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#running-arranger
  # --------------------------------------
  arranger-tabular:
    profiles: ['phaseOne', 'phaseTwo', 'phaseThree', 'platform', 'stageDev']
    image: ghcr.io/overture-stack/arranger-server:3.0.0-beta.36
    container_name: arranger-tabular
    platform: linux/amd64
    depends_on:
      conductor:
        condition: service_healthy
    ports:
      - '5051:5051'
    volumes:
      - ./configs/arrangerConfigs/tabularDataConfigs/base.json:/app/modules/server/configs/base.json
      - ./configs/arrangerConfigs/tabularDataConfigs/extended.json:/app/modules/server/configs/extended.json
      - ./configs/arrangerConfigs/tabularDataConfigs/facets.json:/app/modules/server/configs/facets.json
      - ./configs/arrangerConfigs/tabularDataConfigs/matchbox.json:/app/modules/server/configs/matchbox.json
      - ./configs/arrangerConfigs/tabularDataConfigs/table.json:/app/modules/server/configs/table.json
    environment:
      # Elasticsearch Variables
      ES_HOST: http://elasticsearch:9200
      ES_USER: elastic
      ES_PASS: myelasticpassword
      ES_ARRANGER_SET_INDEX: tabular_arranger_set
      # Arranger Variables (Port required)
      PORT: 5051
      DEBUG: false
      ENABLE_LOGS: false
    networks:
      - conductor-network

  # ======================================
  # Stage Phase One
  # ======================================
  # The react-based, front end portal UI for Overture
  # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#setting-up-stage
  # --------------------------------------
  stage:
    profiles: ['phaseOne']
    image: localstageimage:1.0
    container_name: stage
    pull_policy: never
    platform: linux/arm64/v8
    depends_on:
      conductor:
        condition: service_healthy
    ports:
      - '3000:3000'
    environment:
      # Stage Variables
      NEXTAUTH_URL: http://localhost:3000/api/auth
      NEXT_PUBLIC_LAB_NAME: Prelude Portal
      NEXT_PUBLIC_ADMIN_EMAIL: example@example.com
      NEXT_PUBLIC_DEBUG: true
      NEXT_PUBLIC_SHOW_MOBILE_WARNING: true
      NEXT_PUBLIC_ENABLE_DOWNLOADS: true
      # File Arranger Variables
      NEXT_PUBLIC_ARRANGER_FILE_API: http://arranger-file:5050
      NEXT_PUBLIC_ARRANGER_FILE_DOCUMENT_TYPE: file
      NEXT_PUBLIC_ARRANGER_FILE_INDEX: file_centric
      NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS:
        repositories.code, analysis.analysis_id, object_id, study_id, file.name, file.size,
        file.md5sum, file_access, analysis.experiment.acknowledgements.strategy, file.data_type,
        analysis.experiment.data.sequence_length
      # Tabular Arranger Variables
      NEXT_PUBLIC_ARRANGER_TABULAR_API: http://arranger-tabular:5051
      NEXT_PUBLIC_ARRANGER_TABULAR_DOCUMENT_TYPE: file
      NEXT_PUBLIC_ARRANGER_TABULAR_INDEX: tabular_centric
      # Song Variables (For Swagger Pages)
      NEXT_PUBLIC_SONG_API: http://localhost:8080
      NEXTAUTH_SECRET: 'your-secure-secret-here'
    volumes:
      - stage-data:/usr/src/public/static/dms_user_assets
    networks:
      - conductor-network

volumes:
  elasticsearch-data:
  stage-data:
networks:
  conductor-network:
    driver: bridge