omopcat/docker-compose.yml at main · SAFEHR-data/omopcat · GitHub

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services:
  preprocess:
    build:
      context: .
      dockerfile: preprocessing/Dockerfile
      args:
        # Required for running on GAE
        HTTP_PROXY: ${HTTP_PROXY}
        HTTPS_PROXY: ${HTTPS_PROXY}
        CORES: ${BUILD_CORES_MAKE}
    image: omopcat_preprocessing:latest
    platform: linux/amd64
    environment:
      ENV: ${ENV}
      PREPROCESS_OUT_PATH: /mnt/preprocessing/data
      DB_NAME: ${PREPROCESS_DB_NAME}
      HOST: ${PREPROCESS_HOST}
      PORT: ${PREPROCESS_PORT}
      DB_USERNAME: ${PREPROCESS_DB_USERNAME}
      DB_PASSWORD: ${PREPROCESS_DB_PASSWORD}
      DB_CDM_SCHEMA: ${PREPROCESS_DB_CDM_SCHEMA}
      EUNOMIA_DATA_FOLDER: /mnt/preprocessing/data-raw/test_db
      LOW_FREQUENCY_THRESHOLD: ${LOW_FREQUENCY_THRESHOLD}
      LOW_FREQUENCY_REPLACEMENT: ${LOW_FREQUENCY_REPLACEMENT}
      SUMMARISE_LEVEL: ${PREPROCESS_SUMMARISE_LEVEL}
    command: ["R", "-e", "omopcat.preprocessing::preprocess()"]
    volumes:
      - ${DATA_VOLUME_PATH}:/mnt/preprocessing/data
      - ${TEST_DB_PATH}:/mnt/preprocessing/data-raw/test_db

  omopcat:
    build:
      # Use repo root as context so we can copy scripts directory to container
      context: .
      dockerfile: app/Dockerfile
      args:
        # Required for running on GAE
        HTTP_PROXY: ${HTTP_PROXY}
        HTTPS_PROXY: ${HTTPS_PROXY}
        CORES: ${BUILD_CORES_MAKE}
    image: omopcat:latest
    platform: linux/amd64
    restart: unless-stopped
    environment:
      ENV: ${ENV}
      HTTP_PROXY: ${HTTP_PROXY}
      HTTPS_PROXY: ${HTTPS_PROXY}
      GOLEM_CONFIG_ACTIVE: production
      OMOPCAT_DATA_PATH: /etc/omopcat/data
      LOW_FREQUENCY_THRESHOLD: ${LOW_FREQUENCY_THRESHOLD}
      LOW_FREQUENCY_REPLACEMENT: ${LOW_FREQUENCY_REPLACEMENT}
      SUMMARISE_LEVEL: ${PREPROCESS_SUMMARISE_LEVEL}
      CATALOGUE_NAME: ${CATALOGUE_NAME}
    volumes:
      - ${DATA_VOLUME_PATH}:/etc/omopcat/data
    # Port exposed internally only - nginx will proxy external requests
    expose:
      - "3838"

  nginx:
    build:
      context: .
      dockerfile: www/Dockerfile.nginx
    platform: linux/amd64
    restart: unless-stopped
    ports:
      - ${SHINY_PORT}:80
      - "443:443"
    environment:
      SERVER_NAME: ${SERVER_NAME:-localhost}
    depends_on:
      - omopcat
    volumes:
      - ./www/config:/etc/nginx/conf.d:rw
      - certbot_data:/etc/letsencrypt

volumes:
  certbot_data: