docker-compose.yml

version: '3.9'

volumes:
  atlasdb-postgres-data:
    name: atlasdb-postgres-data
  rstudio-home-data:
    name: rstudio-home-data
  rstudio-tmp-data:
    name: rstudio-tmp-data

services:
  
  traefik:
    image: docker.io/library/traefik:v2.9.4@sha256:4c388f477f5b7aa48420694d90db0ecb96b4ecede60b9b7589c87858abf87b60
    container_name: traefik
    restart: unless-stopped
    ipc: none
    read_only: true
    environment:
      BROADSEA_HOST: ${BROADSEA_HOST}
    labels:
     - "traefik.enable=true"
    ports:
      - "80:80"
      - "443:443"
    volumes:
      - ./traefik/traefik-${HTTP_TYPE}.yml:/etc/traefik/traefik.yml:ro
      - ./traefik/config.yml:/etc/traefik/config.yml:ro
      - ${BROADSEA_CERTS_FOLDER}:/etc/certs:ro
      - /var/run/docker.sock:/var/run/docker.sock:ro

  broadsea-content:
    profiles: [ "default", "content" ]
    container_name: broadsea-content
    image: nginx
    restart: unless-stopped
    environment:
      CONTENT_ARES_DISPLAY: ${CONTENT_ARES_DISPLAY}
      CONTENT_ATLAS_DISPLAY: ${CONTENT_ATLAS_DISPLAY}
      CONTENT_HADES_DISPLAY: ${CONTENT_HADES_DISPLAY}
    volumes:
      - ./broadsea-content/images:/usr/share/nginx/html/images
      - ./broadsea-content/style.css:/usr/share/nginx/html/style.css
      - ./broadsea-content/index.html:/tmp/index.html
      - ./broadsea-content/envsubst.sh:/tmp/envsubst.sh:ro
    entrypoint: ["sh", "/tmp/envsubst.sh" ]
    labels:
      - "traefik.enable=true"

  broadsea-hades:
    profiles: [ "default", "hades" ]
    container_name: broadsea-hades
    image: ohdsi/broadsea-hades:4.2.1
    platform: "linux/amd64"
    environment:
      - USER=${HADES_USER}
      - PASSWORD=${HADES_PASSWORD}
    volumes:
      - rstudio-home-data:/home
      - rstudio-tmp-data:/tmp
    labels:
      - "traefik.enable=true"
    ports:
      - "8787:8787"
      - "6311:6311"

  # WebAPI and Atlas services based on the standard Docker Hub images -------------
  ohdsi-webapi-from-image:
    profiles: [ "default", "webapi-from-image" ]
    image: docker.io/ohdsi/webapi:latest
    extends: 
      file: "ohdsi-webapi.yml"
      service: ohdsi-webapi

  ohdsi-atlas-from-image:
    profiles: [ "default", "atlas-from-image" ]
    image: docker.io/ohdsi/atlas:latest
    extends: 
      file: "ohdsi-atlas.yml"
      service: ohdsi-atlas

  # WebAPI and Atlas services based on git repo (for developers) -------------
  ohdsi-webapi-from-git:
    profiles: [ "webapi-from-git" ]
    build: 
      context: ${WEBAPI_GITHUB_URL}
      args:
        MAVEN_PARAMS: "-DskipTests=true -DskipUnitTests=true"
    extends: 
      file: "ohdsi-webapi.yml"
      service: ohdsi-webapi

  ohdsi-atlas-from-git:
    profiles: [ "atlas-from-git" ]
    build: ${ATLAS_GITHUB_URL}
    extends: 
      file: "ohdsi-atlas.yml"
      service: ohdsi-atlas

  # -----------------------------------------------------------------

  broadsea-atlasdb:
    profiles: [ "default", "atlasdb" ]
    image: ohdsi/broadsea-atlasdb:2.0.0
    container_name: broadsea-atlasdb
    platform: "linux/amd64"
    cpus: 2
    mem_limit: "2G"
    environment:
      - POSTGRES_PASSWORD=mypass
    ports:
      - "5432:5432"
    volumes:
     - atlasdb-postgres-data:/var/lib/postgresql/data
     - ./100_populate_source_source_daimon.sql:/docker-entrypoint-initdb.d/100_populate_source_source_daimon.sql:ro
    healthcheck:
      test: ["CMD-SHELL", "pg_isready -U postgres"]
      interval: 5s
      timeout: 5s
      retries: 10

  broadsea-solr-vocab:
    profiles: [ "solr-vocab-no-import", "solr-vocab-with-import" ]
    container_name: solr-vocab
    restart: unless-stopped
    image: solr:8.11.1
    environment: 
      SOLR_OPTS: 
        -DVOCAB_VERSION=${VOCAB_VERSION}
        -DVOCAB_JDBC_DRIVER_PATH=${VOCAB_JDBC_DRIVER_PATH}
        -DVOCAB_JDBC_URL=${VOCAB_JDBC_URL}
        -DVOCAB_JDBC_USER=${VOCAB_JDBC_USER}
        -DVOCAB_JDBC_PASSWORD=${VOCAB_JDBC_PASSWORD}
    volumes:
      - ./${VOCAB_JDBC_FILE_NAME}:/opt/solr-8.11.1/server/lib/${VOCAB_JDBC_FILE_NAME}:ro
      - ./solr:/tmp/solr_config:ro
    ports:
      - "8983:8983"
    labels:
      - "traefik.enable=true"
    command:
      - solr-precreate
      - ${VOCAB_VERSION}
      - /tmp/solr_config
    healthcheck:
      test: curl --fail ${SOLR_VOCAB_ENDPOINT} || exit 1
      interval: 10s
      timeout: 5s
      retries: 5

  broadsea-solr-vocab-run-import:
    profiles: [ "solr-vocab-with-import" ]
    container_name: solr-vocab-run-import
    image: curlimages/curl
    depends_on:
      broadsea-solr-vocab:
        condition: service_healthy
    command: curl -d "vocab_database_schema=${VOCAB_DATABASE_SCHEMA}" \ 
             -X POST ${SOLR_VOCAB_ENDPOINT}/${VOCAB_VERSION}/dataimport?command=full-import&entity=concept

  broadsea-ares:
    profiles: [ "ares" ]
    container_name: broadsea-ares
    restart: unless-stopped
    build:
      context: https://github.com/alondhe/Ares.git#docker  # hack until Dockerfile is added to OHDSI/Ares
    volumes:
      - ${ARES_DATA_FOLDER}:/usr/share/nginx/html/ares/data:ro
    labels:
      - "traefik.enable=true"


  broadsea-omop-vocab-load:
    profiles: [ "omop-vocab-pg-load" ]
    container_name: omop-vocab-load
    extends:
      file: "postgres-load.yml"
      service: broadsea-postgres-load
    environment:
      VOCAB_PG_HOST: ${VOCAB_PG_HOST}
      VOCAB_PG_DATABASE: ${VOCAB_PG_DATABASE}
      VOCAB_PG_SCHEMA: ${VOCAB_PG_SCHEMA}
      VOCAB_PG_USER: ${VOCAB_PG_USER}
      VOCAB_PG_PASSWORD: ${VOCAB_PG_PASSWORD}
      UMLS_API_KEY: ${UMLS_API_KEY}
    volumes:
      - ./omop_vocab:/tmp
    entrypoint: ["sh", "/tmp/scripts/load_omop_vocab.sh" ]


  broadsea-phoebe-load:
    profiles: [ "phoebe-pg-load" ]
    container_name: broadsea-phoebe-load
    extends:
      file: "postgres-load.yml"
      service: broadsea-postgres-load
    environment:
      PHOEBE_PG_HOST: ${PHOEBE_PG_HOST}
      PHOEBE_PG_DATABASE: ${PHOEBE_PG_DATABASE}
      PHOEBE_PG_SCHEMA: ${PHOEBE_PG_SCHEMA}
      PHOEBE_PG_USER: ${PHOEBE_PG_USER}
      PHOEBE_PG_PASSWORD: ${PHOEBE_PG_PASSWORD}
    volumes:
      - ./phoebe:/tmp
    entrypoint: ["sh", "/tmp/load_phoebe.sh" ]