OMOP_Atlas_WebAPI_Docker/docker-compose.yml at master · sk4na/OMOP_Atlas_WebAPI_Docker · GitHub

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services:
  omop54:
    build: .
    container_name: omop54
    ports: ["5432:5432"]
    environment:
      - POSTGRES_PASSWORD=password
      - POSTGRES_USER=postgres
      - CONSTRAINTS=true
      - OMOP_DB=omop54
      - CDM_SCHEMA=cdm
      - RESULTS_SCHEMA=results
      - TEMP_SCHEMA=temp
      - OHDSI_DB_USER=ohdsi
      - OHDSI_DB_PASS=ohdsi
    volumes:
      - ./vocab:/VOCAB
    healthcheck:
      test: ["CMD-SHELL","pg_isready -h 127.0.0.1 -p 5432 -U postgres -d omop54 >/dev/null 2>&1"]
      interval: 30s
      timeout: 10s
      retries: 120
      start_period: 60s

  webapi:
    image: ohdsi/webapi:latest
    container_name: ohdsi-webapi
    depends_on:
      omop54:
        condition: service_healthy
    environment:
      DATASOURCE_DRIVERCLASSNAME: org.postgresql.Driver
      DATASOURCE_URL: jdbc:postgresql://omop54:5432/omop54
      DATASOURCE_USERNAME: ohdsi
      DATASOURCE_PASSWORD: ohdsi
      DATASOURCE_OHDSI_SCHEMA: webapi

      SPRING_JPA_PROPERTIES_HIBERNATE_DIALECT: org.hibernate.dialect.PostgreSQLDialect
      SPRING_JPA_PROPERTIES_HIBERNATE_DEFAULT_SCHEMA: webapi
      SPRING_BATCH_REPOSITORY_TABLEPREFIX: webapi.BATCH_

      FLYWAY_DATASOURCE_DRIVERCLASSNAME: org.postgresql.Driver
      FLYWAY_DATASOURCE_URL: jdbc:postgresql://omop54:5432/omop54
      FLYWAY_DATASOURCE_USERNAME: ohdsi
      FLYWAY_DATASOURCE_PASSWORD: ohdsi
      FLYWAY_LOCATIONS: classpath:db/migration/postgresql
      FLYWAY_PLACEHOLDERS_OHDSISCHEMA: webapi
      FLYWAY_SCHEMAS: webapi

      SECURITY_ORIGIN: "http://localhost:8081"
      SECURITY_CORS_ENABLED: "true"
      SECURITY_SSL_ENABLED: "false"

      # Just to be sure proxies don't mess with it
      JAVA_TOOL_OPTIONS: >-
        -Djava.net.preferIPv4Stack=true
        -Dhttp.proxyHost=
        -Dhttps.proxyHost=
        -DsocksProxyHost=

    ports:
      - "8080:8080"
    healthcheck:
      test: ["CMD", "wget", "--spider", "-q", "http://localhost:8080/WebAPI/info"]
      interval: 30s
      timeout: 10s
      retries: 10
      start_period: 60s

  atlas:
    image: ohdsi/atlas:latest
    container_name: ohdsi-atlas
    depends_on: ["webapi"]
    ports: ["8081:8080"]
    volumes:
      - ./config-local.js:/usr/share/nginx/html/assets/config-local.js:ro
      - ./default.conf:/etc/nginx/conf.d/default.conf:ro

  webapi-seeder:
    image: postgres:14
    container_name: ohdsi-webapi-seeder
    depends_on:
      omop54:
        condition: service_healthy
      webapi:
        condition: service_healthy
    volumes:
      - ./scripts/seed-webapi.sh:/seed-webapi.sh:ro
    environment:
      PGHOST: omop54
      PGPORT: 5432
      PGDATABASE: omop54
      PGUSER: postgres
      PGPASSWORD: password
      WEBAPI_SCHEMA: webapi
      CDM_SCHEMA: cdm
      RESULTS_SCHEMA: results
      OHDSI_DB_USER: ohdsi
      OHDSI_DB_PASS: ohdsi
    command: ["/bin/bash", "/seed-webapi.sh"]
    restart: "no"

  achilles:
    profiles: ["achilles"]
    build:
      context: .
      dockerfile: Achilles.Dockerfile
    container_name: ohdsi-achilles
    depends_on:
      omop54:
        condition: service_healthy
    environment:
      DBMS: postgresql
      DB_HOST: omop54
      DB_PORT: "5432"
      DB_NAME: omop54
      DB_USER: ohdsi
      DB_PASSWORD: ohdsi

      CDM_SCHEMA: cdm
      VOCAB_SCHEMA: cdm
      RESULTS_SCHEMA: results
      TEMP_SCHEMA: temp

      # Optional knobs
      CDM_VERSION: "5.4"
      NUM_THREADS: "4"
      SMALL_CELL_COUNT: "5"
      CREATE_TABLES: "true"     # let Achilles create its results tables if missing
      EXPORT_JSON: "true"       # also export JSON for Achilles Web, diagnostics, etc.
    volumes:
      - ./scripts/run_achilles.R:/run_achilles.R:ro
      - ./achilles-output:/output
    command: ["Rscript", "/run_achilles.R"]
    restart: "no"