docker-compose.yml

version: '3'

services:
  cbioportal:
    restart: unless-stopped
    image: ${DOCKER_IMAGE_CBIOPORTAL}
    container_name: cbioportal-container
    environment:
      SHOW_DEBUG_INFO: "true"
      PORTAL_HOME: "/cbioportal-webapp"
    ports:
      - "8080:8080"
    volumes:
     - ./study:/study/
     - ./config/application.properties:/cbioportal-webapp/application.properties:ro
    depends_on:
     - cbioportal-database
     - cbioportal-session
    networks:
     - cbio-net
    # TODO: servlet-api should be excluded from deps in mvn, the removal below is just a quick fix
    # This might be helpful: https://stackoverflow.com/questions/36233626
    command: /bin/sh -c "rm -rf /cbioportal-webapp/lib/servlet-api-2.5.jar && java -Xms2g -Xmx4g -cp '/cbioportal-webapp:/cbioportal-webapp/lib/*' org.cbioportal.PortalApplication --spring.config.location=cbioportal-webapp/application.properties --authenticate=false --session.service.url=http://cbioportal-session:5001/api/sessions/my_portal/"
  cbioportal-database:
    restart: unless-stopped
    image: ${DOCKER_IMAGE_MYSQL}
    container_name: cbioportal-database-container
    environment:
      MYSQL_DATABASE: cbioportal
      MYSQL_USER: cbio_user
      MYSQL_PASSWORD: somepassword
      MYSQL_ROOT_PASSWORD: somepassword
    volumes:
     - ./data/cgds.sql:/docker-entrypoint-initdb.d/cgds.sql:ro
     - ./data/seed.sql.gz:/docker-entrypoint-initdb.d/seed.sql.gz:ro
     - cbioportal_mysql_data:/var/lib/mysql
    networks:
     - cbio-net
    command: --local-infile=1
  cbioportal-session:
    restart: unless-stopped
    image: ${DOCKER_IMAGE_SESSION_SERVICE}
    container_name: cbioportal-session-container
    environment:
      SERVER_PORT: 5001
      JAVA_OPTS: -Dspring.data.mongodb.uri=mongodb://cbioportal-session-database:27017/session-service
    depends_on:
      - cbioportal-session-database
    networks:
      - cbio-net
  cbioportal-session-database:
    restart: unless-stopped
    image: mongo:4.2
    container_name: cbioportal-session-database-container
    environment:
      MONGO_INITDB_DATABASE: session_service
    volumes:
      - cbioportal_mongo_data:/data/db
    networks:
      - cbio-net

networks:
  cbio-net: 
  
volumes:
  cbioportal_mysql_data:
  cbioportal_mongo_data: