beacon2-pi-api/docker-compose.yml at main · BU-ISCIII/beacon2-pi-api · GitHub

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version: '3.1'

networks:
  idp-priv:
  pub:

services:
  beaconprod:
    restart: unless-stopped
    build:
      context: .
    container_name: beaconprod
    environment:
      - ISSUER=http://172.20.10.47:8082/realms/Beacon
      - JWKS_URL=http://idp:8082/realms/Beacon/protocol/openid-connect/certs
      - CLIENT_ID=beacon
      - CLIENT_SECRET=b26ca0f9-1137-4bee-b453-ee51eefbe7ba
    ports:
      - "5050:5050"
    volumes:
      - /var/log/local/apps/beacon/logs.log:/beacon/logs/logs.log:Z
      - /opt/beacon/beacon2-pi-api-isciii/beacon/conf/conf.py:/beacon/conf/conf.py:Z
      - /opt/beacon/beacon2-pi-api-isciii/beacon/connections/mongo/conf.py:/beacon/connections/mongo/conf.py:Z
      - /opt/beacon/beacon2-pi-api-isciii/beacon/permissions:/beacon/permissions:Z
      - /opt/beacon/beacon2-pi-api-isciii/beacon/auth/idp_providers:/beacon/auth/idp_providers:Z
      - /opt/beacon/beacon2-pi-api-isciii/beacon/models:/beacon/models:Z
      - /opt/beacon/beacon2-pi-api-isciii/beacon/conf/models:/beacon/conf/models:Z
      - /opt/beacon/beacon2-pi-api-isciii/certs/client.pem:/etc/beacon/certs/client.pem:ro,z
      - /opt/beacon/beacon2-pi-api-isciii/certs/ca.crt:/etc/beacon/certs/ca.crt:ro,z
      - /opt/beacon/beacon2-pi-api-isciii/certs/beacon_server.crt:/etc/beacon/certs/beacon_server.crt:ro,z
      - /opt/beacon/beacon2-pi-api-isciii/certs/beacon_server.key:/etc/beacon/certs/beacon_server.key:ro,z
    networks:
      - pub

#  admin-ui:
#    restart: always
#    build:
#      context: ./adminui
#    image: localhost/admin-ui:prod
#    container_name: admin-ui
#    ports:
#      - "3001:3001"
#    entrypoint: ['bash','/home/app/web/start.sh']
#    volumes:
#      - /opt/beacon/beacon2-pi-api-isciii/beacon:/home/app/web/beacon:Z
#      - /opt/beacon/beacon2-pi-api-isciii/adminui:/home/app/web:Z
#    networks:
#      - pub

  idp:
    image: quay.io/keycloak/keycloak:18.0.0
    hostname: idp
    container_name: idp
    command:
      - start-dev
      - --import-realm
    environment:
      - KEYCLOAK_ADMIN=admin
      - KEYCLOAK_ADMIN_PASSWORD=secret
      - KC_DB=postgres
      - KC_DB_URL=jdbc:postgresql://idp-db:5432/keycloak
      - KC_DB_USERNAME=admin
      - KC_DB_PASSWORD=secret
      - KC_HTTP_PORT=8082
      - KC_HOSTNAME_URL=http://172.20.10.47:8082
      - KC_HOSTNAME_ADMIN_URL=http://172.20.10.47:8082
    volumes:
      - /opt/beacon/beacon2-pi-api-isciii/beacon/auth/realms/beacon-realm.json:/opt/keycloak/data/import/beacon-realm.json:ro,Z
    ports:
      - "8082:8082"
      - "9991:8443"
    networks:
      - idp-priv
      - pub
    depends_on:
      - idp-db

  idp-db:
    image: postgres:15
    hostname: idp-db
    container_name: idp-db
    command: postgres -c logging_collector=on -c log_directory=/var/log/postgresql -c log_filename=postgresql.log
    environment:
      - POSTGRES_DB=keycloak
      - POSTGRES_USER=admin
      - POSTGRES_PASSWORD=secret
    volumes:
      - /opt/beacon/beacon2-pi-api-isciii/postgres/data:/var/lib/postgresql/data:Z
      - /var/log/local/apps/beacon/:/var/log/postgresql:Z
    networks:
      - idp-priv

  db:
    image: docker.io/library/mongo:5.0.32
    hostname: mongo
    container_name: mongoprod
    ports:
      - 27017:27017
    environment:
      MONGO_INITDB_ROOT_USERNAME: root
      MONGO_INITDB_ROOT_PASSWORD: example
      MONGO_INITDB_DATABASE: beacon
    volumes:
      - /opt/beacon/beacon2-pi-api-isciii/beacon/connections/mongo/mongo-init/:/docker-entrypoint-initdb.d/:ro,Z
      - /opt/beacon/beacon2-pi-api-isciii/beacon/connections/mongo/data/:/data:Z
      - /opt/beacon/beacon2-pi-api-isciii/beacon/connections/mongo/data/db:/data/db:Z
      - /opt/beacon/beacon2-pi-api-isciii/beacon/connections/mongo/data/configdb:/data/configdb:Z
      - /opt/beacon/beacon2-pi-api-isciii/beacon/connections/mongo/data/caseLevelData:/data/caseLevelData:Z
      - /opt/beacon/beacon2-pi-api-isciii/beacon/connections/mongo/mongod.conf:/data/mongod.conf:ro,Z
      - /var/log/local/apps/beacon/mongod.log:/var/log/mongodb/mongod.log:Z
      - /opt/beacon/beacon2-pi-api-isciii/certs/server.pem:/etc/mongo/certs/server.pem:ro,z
      - /opt/beacon/beacon2-pi-api-isciii/certs/ca.crt:/etc/mongo/certs/ca.crt:ro,z
    networks:
      - pub
    healthcheck:
      test: echo 'db.runCommand("ping").ok' | mongosh --tls --tlsCertificateKeyFile /etc/mongo/certs/server.pem --tlsCAFile /etc/mongo/certs/ca.crt --tlsAllowInvalidCertificates localhost:27017/test --quiet
      interval: 300s
      timeout: 10s
      retries: 3
      start_period: 30s

    command: ["--config", "/data/mongod.conf", "--tlsMode", "requireTLS", "--tlsCertificateKeyFile", "/etc/mongo/certs/server.pem", "--tlsCAFile", "/etc/mongo/certs/ca.crt", "--tlsAllowInvalidCertificates"]

  mongo-express:
    image: mongo-express
    restart: always
    ports:
      - 8081:8081
    environment:
      ME_CONFIG_MONGODB_ADMINUSERNAME: root
      ME_CONFIG_MONGODB_ADMINPASSWORD: example
      ME_CONFIG_MONGODB_URL: mongodb://root:example@mongo:27017/?tls=true&tlsCAFile=/etc/mongo/certs/ca.crt&tlsCertificateKeyFile=/etc/mongo/certs/client.pem&tlsAllowInvalidCertificates=true
      ME_CONFIG_MONGODB_SSL: "true"
      ME_CONFIG_MONGODB_SSLVALIDATE: "true"
      ME_CONFIG_MONGODB_CA_FILE: /etc/mongo/certs/ca.crt
      ME_CONFIG_MONGODB_TLS: "true"
      ME_CONFIG_MONGODB_TLS_CA_FILE: /etc/mongo/certs/ca.crt
      ME_CONFIG_MONGODB_TLS_CERT_KEY_FILE: /etc/mongo/certs/client.pem
      ME_CONFIG_MONGODB_ENABLE_ADMIN: "true"
    volumes:
      - /opt/beacon/beacon2-pi-api-isciii/certs:/etc/mongo/certs:ro,z
    depends_on:
      - db
    networks:
      - pub

  beacon-ri-tools:
    image: ghcr.io/ega-archive/beacon2-ri-tools-v2:2.0.6
    hostname: beacon-ri-tools
    container_name: ri-tools
    networks:
      - pub
    tty: true
    volumes:
      - /opt/beacon/beacon2-pi-api-isciii/ri-tools/output_docs:/usr/src/app/output_docs:Z
      - /opt/beacon/beacon2-pi-api-isciii/ri-tools/conf:/usr/src/app/conf:Z
      - /opt/beacon/beacon2-pi-api-isciii/ri-tools/files/vcf/files_to_read:/usr/src/app/files/vcf/files_to_read:Z
      - /opt/beacon/beacon2-pi-api-isciii/ri-tools/csv:/usr/src/app/csv:Z
      - /opt/beacon/beacon2-pi-api-isciii/ri-tools/pipelines:/usr/src/app/pipelines:Z
      - /opt/beacon/beacon2-pi-api-isciii/ri-tools/files/updated_json:/usr/src/app/files/updated_json:Z
      - /opt/beacon/beacon2-pi-api-isciii/ri-tools/patches/genomicVariations_vcf.py:/usr/src/app/genomicVariations_vcf.py:ro,z
      - /opt/beacon/beacon2-pi-api-isciii/certs/ca.crt:/etc/mongo/certs/ca.crt:ro,z
      - /opt/beacon/beacon2-pi-api-isciii/certs/client.pem:/etc/mongo/certs/client.pem:ro,z

  phenopackets-to-BFF:
    image: ghcr.io/ega-archive/phenopackets-to-bff:latest
    restart: always
    hostname: phenopackets-to-BFF
    container_name: phenopackets-to-BFF
    volumes:
      - /opt/beacon/beacon2-pi-api-isciii/ri-tools/phenopackets-to-BFF/:/usr/src/app/examples:Z
    networks:
      - pub

#  templateUI:
#    image: ghcr.io/ega-archive/beacon-template-ui:main
#    restart: always
#    hostname: template-ui
#    container_name: template-ui
#    command: node /opt/yarn-v1.22.22/bin/yarn.js start
#    ports:
#      - 3000:3000
#    volumes:
#      - /opt/beacon/beacon2-pi-api-isciii/template-ui/src/config/config.json:/client/src/config/config.json:Z
#      - /opt/beacon/beacon2-pi-api-isciii/template-ui/.env:/client/.env:Z
#    networks:
#      - pub
#    environment:
#      - CHOKIDAR_USEPOLLING=true
#      - WATCHPACK_POLLING=true

  template-ui:
    build: ./template-ui/client
    restart: always
    hostname: template-ui
    container_name: template-ui
    ports:
      - 3000:3000
    volumes:
      - /opt/beacon/beacon2-pi-api-isciii/template-ui/client/src/config/config.json:/client/src/config/config.json:ro,Z
    networks:
      - pub

  apache-beacon:
    image: registry.access.redhat.com/ubi9/httpd-24
    container_name: apache-beacon
    restart: unless-stopped
    depends_on:
      - beaconprod
      - template-ui
    ports:
      - "8443:8080"
    volumes:
      - /etc/localtime:/etc/localtime:ro
      - /usr/share/zoneinfo:/usr/share/zoneinfo
      - /opt/beacon/beacon2-pi-api-isciii/conf/beacon_apache_reverse_proxy.conf:/etc/httpd/conf.d/beacon.conf:ro,Z
      - /var/log/local/apps/beacon/apache:/var/log/httpd:Z
    networks:
      - pub