docker-compose.yaml

version: "3.9"

# Shared environment variable configuration between the app service profiles
x-env: &env
  ST_SECRET_KEY:
  ST_DATABASE_URI: "mysql+pymysql://${MYSQL_USER}:${MYSQL_PASSWORD}@mysql/${MYSQL_DATABASE}"
  MINIO_ENDPOINT: minio:9000
  MINIO_ACCESS_KEY:
  MINIO_SECRET_KEY:
  MINIO_REGION_NAME:
  SLURM_ENDPOINT:
  SLURM_USER:
  SLURM_JWT:

services:
  mysql:
    image: mysql:8.0
    restart: on-failure
    environment:
      TZ: America/Toronto
      MYSQL_DATABASE:
      MYSQL_USER:
      MYSQL_PASSWORD:
      MYSQL_ROOT_PASSWORD:
    ports:
      - "${MYSQL_HOST_PORT:-127.0.0.1:3306}:3306"
    volumes:
      - ${MYSQL_VOLUME}:/var/lib/mysql
  minio:
    image: minio/minio:RELEASE.2022-06-20T23-13-45Z
    restart: on-failure
    environment:
      TZ: America/Toronto
      MINIO_ROOT_USER: "${MINIO_ACCESS_KEY}"
      MINIO_ROOT_PASSWORD: "${MINIO_SECRET_KEY}"
      MINIO_REGION_NAME:
      MINIO_UPDATE: "off"
    ports:
      - "${MINIO_HOST_PORT:-127.0.0.1:9000}:9000"
      - "${CONSOLE_HOST_PORT:-127.0.0.1:9090}:9090"
    volumes:
      - ${MINIO_VOLUME}:/data
    command: server /data --console-address ":9090"
  app:
    build: flask
    image: ghcr.io/ccmbioinfo/stager:dev
    environment:
      <<: *env
    ports:
      - "${FLASK_HOST_PORT:-127.0.0.1:5000}:5000"
    depends_on:
      - mysql
      - minio
    volumes:
      - ./flask:/usr/src/stager
  app_debug:
    build: flask
    image: ghcr.io/ccmbioinfo/stager:dev
    profiles:
      - debug
    environment:
      <<: *env
      FLASK_DEBUG: 1
      PYTHONDONTWRITEBYTECODE: 1
      DEBUG_METRICS: 1
    ports:
      - "${FLASK_HOST_PORT:-127.0.0.1:5000}:5000"
      - "${DEBUG_HOST_PORT:-127.0.0.1:5678}:5678"
    depends_on:
      - mysql
      - minio
    volumes:
      - ./flask:/usr/src/stager
    entrypoint: ["python", "-m", "debugpy", "--listen", "0.0.0.0:5678", "-m", "flask", "run", "--host=0.0.0.0"]
  # Simulated production gunicorn configuration
  app_gunicorn:
    build:
      context: flask
      dockerfile: ../Dockerfile
      args:
        GIT_SHA:
    image: ghcr.io/ccmbioinfo/stager:latest
    user: www-data
    profiles:
      - gunicorn
    environment:
      <<: *env
      SQLALCHEMY_SIDECAR: /var/tmp/sqlalchemy.fifo
    tmpfs:
      - /tmp
    volumes:
      - log-fifo:/var/tmp
    ports:
      - "${FLASK_HOST_PORT:-127.0.0.1:5000}:5000"
      - "${METRICS_HOST_PORT:-127.0.0.1:8080}:8080"
    depends_on:
      - mysql
      - minio
  # See __init__.py::config_logger for an explainer
  sidecar-sqlalchemy:
    image: busybox
    user: www-data
    profiles:
      - gunicorn
    init: true
    command: tail -f -n +1 /var/log/stager/sqlalchemy.fifo
    volumes:
      - log-fifo:/var/log/stager:ro
    depends_on:
      - app_gunicorn
    restart: unless-stopped
volumes:
  log-fifo: