docker-compose.yml

version: "3.8"

services:
  database:
    image: "${DOCKER_REPO}genepi-devdb:latest"
    profiles: [ "backend", "web", "gisaid", "all" ]
    platform: linux/amd64
    ports:
      - "5432:5432"
    environment:
      - POSTGRES_USER=postgres
      - POSTGRES_PASSWORD=password_postgres
      - POSTGRES_DB=aspen_db
      # The postgres image declares a mounted volume at /var/lib/postgresql/data
      # by default, which means that the data in that directory is difficult to
      # snapshot and export. Here, we're telling Postgres to use this (non-mounted)
      # directory as its storage location instead so it works with our db snapshot
      # workflow.
      - PGDATA=/var/lib/czge/data
    command: [ "postgres" ]
    networks:
      genepinet:
        aliases:
          - database.genepinet.localdev
  frontend:
    image: "${DOCKER_REPO}genepi-frontend"
    profiles: [ "frontend", "web", "all" ]
    platform: linux/amd64
    build:
      context: src/frontend
      cache_from:
        - "${DOCKER_REPO}genepi-frontend:branch-trunk"
      args:
        - BUILDKIT_INLINE_CACHE=1
        - HAPPY_COMMIT
        - HAPPY_BRANCH
    restart: always
    environment:
      HOST: 0.0.0.0
      PORT: 8000
      BUILD_PATH: build
      API_URL: http://backend.genepinet.localdev:3000
      SPLIT_FRONTEND_KEY: ${SPLIT_FRONTEND_KEY}
      CHOKIDAR_USEPOLLING: "true"
      ONETRUST_FRONTEND_KEY: ${ONETRUST_FRONTEND_KEY}
      PLAUSIBLE_FRONTEND_KEY: ${PLAUSIBLE_FRONTEND_KEY}
    ports:
      - "8000:8000"
    volumes:
      - ./src/frontend:/usr/src/app
      - /usr/src/app/node_modules # Use node_modules built in container, not from the mounted source dir
    networks:
      genepinet:
        aliases:
          - frontend.genepinet.localdev
  backend:
    image: "${DOCKER_REPO}genepi-backend"
    profiles: [ "backend", "web", "gisaid", "all" ]
    platform: linux/amd64
    build:
      context: src/backend
      cache_from:
        - "${DOCKER_REPO}genepi-backend:branch-trunk"
      args:
        - BUILDKIT_INLINE_CACHE=1
    restart: always
    stdin_open: true # Helps with pdb
    tty: true # Helps with pdb
    depends_on:
      - database
    ports:
      - "3000:3000"
    environment:
      - API_URL=http://backend.genepinet.localdev:3000
      - FLASK_ENV=development
      - PYTHONUNBUFFERED=1
      - WORKERS=2
      - RESTART_ON_FAILURE=yes
      - BOTO_ENDPOINT_URL=http://localstack.genepinet.localdev:4566
      - AWS_ACCESS_KEY_ID=dev_access_key_id
      - AWS_SECRET_ACCESS_KEY=dev_secret_access_key
      - FRONTEND_URL=http://frontend.genepinet.localdev:8000
      - AWS_REGION=us-west-2
      - DB=docker
      - ENV=local
      - FLASK_APP=aspen.main
      - FLASK_DEBUG=1
      - DEPLOYMENT_STAGE=local
      - NEXTSTRAIN_SFN_ARN=arn:aws:states:us-west-2:000000000000:stateMachine:nextstrain-sfn
      - PYTHONPATH=.
    volumes:
      - ./src/backend:/usr/src/app
    entrypoint: []
    # NOTE -- Using relative paths for entrypoints/commands breaks pycharm debugging
    command:
      [
        "/usr/local/bin/supervisord",
        "-c",
        "/usr/src/app/etc/supervisord.conf"
      ]
    networks:
      genepinet:
        aliases:
          - backend.genepinet.localdev
  localstack:
    platform: linux/amd64
    image: localstack/localstack:0.13.0
    profiles: [ "backend", "web", "gisaid", "all" ]
    ports:
      - "4566:4566"
      - "8083:8083"
    environment:
      - HOSTNAME_EXTERNAL=localstack
      - LEGACY_PERSISTENCE=1
      - EAGER_SERVICE_LOADING=1
      - SERVICES=s3,secretsmanager,stepfunctions,ssm,iam
      - DEBUG=1
      - DATA_DIR=/tmp/localstack/data
      - PORT_WEB_UI=${PORT_WEB_UI- }
      - HOST_TMP_FOLDER=${TMPDIR}
      - DEFAULT_REGION=us-west-2
    volumes:
      - localstack:/tmp/localstack
    networks:
      genepinet:
        aliases:
          - localstack.genepinet.localdev
  oidc:
    platform: linux/amd64
    image: ghcr.io/soluto/oidc-server-mock:latest
    profiles: [ "backend", "web", "gisaid", "all" ]
    ports:
      - "4011:80"
      - "8443:8443"
    environment:
      ASPNETCORE_ENVIRONMENT: Development
      SERVER_OPTIONS_INLINE: |
        {
          "AccessTokenJwtType": "JWT",
          "Discovery": {
            "ShowKeySet": true
          }
        }
      API_SCOPES_PATH: /tmp/config/api_scopes.json
      API_RESOURCES_PATH: /tmp/config/api_resources.json
      USERS_CONFIGURATION_PATH: /tmp/config/users.json
      CLIENTS_CONFIGURATION_PATH: /tmp/config/clients-config.json
      ASPNETCORE_URLS: https://+:8443;http://+:80
      # ASPNETCORE_Kestrel__Certificates__Default__Password: <password for pfx file>
      ASPNETCORE_Kestrel__Certificates__Default__Path: /tmp/pkcs12/certificate.pfx
    volumes:
      - ./oauth/pkcs12:/tmp/pkcs12:ro
      - ./oauth:/tmp/config:ro
    networks:
      genepinet:
        aliases:
          - oidc.genepinet.localdev
  gisaid:
    image: "${DOCKER_REPO}genepi-gisaid"
    profiles: [ "gisaid", "jobs", "all" ]
    platform: linux/amd64
    build:
      context: src/backend/
      dockerfile: Dockerfile.gisaid
      cache_from:
        - "${DOCKER_REPO}genepi-gisaid:branch-trunk"
      args:
        - BUILDKIT_INLINE_CACHE=1
        - HAPPY_COMMIT
        - HAPPY_BRANCH
    command: [ "true" ]
    volumes:
      - ./src/backend:/usr/src/app
    environment:
      - AWS_REGION=us-west-2
      - BOTO_ENDPOINT_URL=http://localstack.genepinet.localdev:4566
      - AWS_ACCESS_KEY_ID=dev_access_key_id
      - AWS_SECRET_ACCESS_KEY=dev_secret_access_key
    restart: "no"
    networks:
      genepinet:
        aliases:
          - gisaid.genepinet.localdev
  pangolin:
    image: "${DOCKER_REPO}genepi-pangolin"
    profiles: [ "pangolin", "jobs", "all" ]
    platform: linux/amd64
    build:
      context: src/backend
      dockerfile: Dockerfile.pangolin
      cache_from:
        - "${DOCKER_REPO}genepi-pangolin:branch-trunk"
      args:
        - BUILDKIT_INLINE_CACHE=1
    environment:
      - AWS_REGION=us-west-2
      - BOTO_ENDPOINT_URL=http://localstack.genepinet.localdev:4566
      - AWS_ACCESS_KEY_ID=dev_access_key_id
      - AWS_SECRET_ACCESS_KEY=dev_secret_access_key
      - FLASK_ENV=development
      - PYTHONUNBUFFERED=1
      - DB=docker
      - ENV=local
      - DEPLOYMENT_STAGE=local
      - PYTHONPATH=.
    command: [ "true" ]
    restart: "no"
    networks:
      genepinet:
        aliases:
          - pangolin.genepinet.localdev
    volumes:
      - ./src/backend:/usr/src/app
  lineage_qc:
    image: "${DOCKER_REPO}genepi-lineage-qc"
    profiles: [ "lineage_qc", "jobs", "all" ]
    platform: linux/amd64
    build:
      context: src/backend
      dockerfile: Dockerfile.lineage_qc
      cache_from:
        - "${DOCKER_REPO}genepi-lineage-qc:branch-trunk"
      args:
        - BUILDKIT_INLINE_CACHE=1
    environment:
      - AWS_REGION=us-west-2
      - BOTO_ENDPOINT_URL=http://localstack.genepinet.localdev:4566
      - AWS_ACCESS_KEY_ID=dev_access_key_id
      - AWS_SECRET_ACCESS_KEY=dev_secret_access_key
      - FLASK_ENV=development
      - PYTHONUNBUFFERED=1
      - DB=docker
      - ENV=local
      - DEPLOYMENT_STAGE=local
      - PYTHONPATH=.
    command: [ "true" ]
    restart: "no"
    networks:
      genepinet:
        aliases:
          - lineage-qc.genepinet.localdev
    volumes:
      - ./src/backend:/usr/src/app
  nextstrain:
    image: "${DOCKER_REPO}genepi-nextstrain"
    profiles: [ "nextstrain", "jobs", "all" ]
    platform: linux/amd64
    build:
      context: src/backend
      dockerfile: Dockerfile.nextstrain
      cache_from:
        - "${DOCKER_REPO}genepi-nextstrain:branch-trunk"
      args:
        - BUILDKIT_INLINE_CACHE=1
    environment:
      - AWS_REGION=us-west-2
      - AWS_ACCESS_KEY_ID=dev_access_key_id
      - AWS_SECRET_ACCESS_KEY=dev_secret_access_key
      - FLASK_ENV=development
      - PYTHONUNBUFFERED=1
      - GENEPI_CONFIG_SECRET_NAME=genepi-config
      - BOTO_ENDPOINT_URL=http://localstack.genepinet.localdev:4566
      - DB=docker
      - ENV=local
      - DEPLOYMENT_STAGE=local
      - PYTHONPATH=.
    command: [ "true" ]
    restart: "no"
    networks:
      genepinet:
        aliases:
          - nextstrain.genepinet.localdev
    volumes:
      - ./src/backend:/usr/src/app
networks:
  genepinet:
    name: genepinet
    driver: overlay
    attachable: true
volumes:
  localstack: