docker-compose.yml

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# to you under the Apache License, Version 2.0 (the
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#
#   http://www.apache.org/licenses/LICENSE-2.0
#
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# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
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# specific language governing permissions and limitations
# under the License.
#

# Basic Airflow cluster configuration for CeleryExecutor with Redis and PostgreSQL.
#
# WARNING: This configuration is for local development. Do not use it in a production deployment.
#
# This configuration supports basic configuration using environment variables or an .env file
# The following variables are supported:
#
# AIRFLOW_IMAGE_NAME           - Docker image name used to run Airflow.
#                                Default: apache/airflow:2.2.3
# AIRFLOW_UID                  - User ID in Airflow containers
#                                Default: 50000
# Those configurations are useful mostly in case of standalone testing/running Airflow in test/try-out mode
#
# _AIRFLOW_WWW_USER_USERNAME   - Username for the administrator account (if requested).
#                                Default: airflow
# _AIRFLOW_WWW_USER_PASSWORD   - Password for the administrator account (if requested).
#                                Default: airflow
# _PIP_ADDITIONAL_REQUIREMENTS - Additional PIP requirements to add when starting all containers.
#                                Default: ''
#
# Feel free to modify this file to suit your needs.
---
version: '3'
x-airflow-common:
  &airflow-common
  # In order to add custom dependencies or upgrade provider packages you can use your extended image.
  # Comment the image line, place your Dockerfile in the directory where you placed the docker-compose.yaml
  # and uncomment the "build" line below, Then run `docker-compose build` to build the images.
  #image: ${AIRFLOW_IMAGE_NAME:-apache/airflow:2.2.3}
  build: 
    context: ./airflow
  env_file:
    - .env
  environment:
    &airflow-common-env
    AIRFLOW__CORE__EXECUTOR: CeleryExecutor
    AIRFLOW__CORE__SQL_ALCHEMY_CONN: postgresql+psycopg2://airflow:airflow@postgres/airflow
    AIRFLOW__CELERY__RESULT_BACKEND: db+postgresql://airflow:airflow@postgres/airflow
    AIRFLOW__CELERY__BROKER_URL: redis://:@redis:6379/0
    AIRFLOW__CORE__FERNET_KEY: ''
    AIRFLOW__CORE__DAGS_ARE_PAUSED_AT_CREATION: 'true'
    AIRFLOW__CORE__LOAD_EXAMPLES: 'false'
    AIRFLOW__API__AUTH_BACKEND: 'airflow.api.auth.backend.basic_auth'
    _PIP_ADDITIONAL_REQUIREMENTS: ${_PIP_ADDITIONAL_REQUIREMENTS:-}
    AIRFLOW_VAR_USER_DATA_DIR: /usr/local/airflow/user/data
    AIRFLOW_VAR_LC_UPLOAD_CONFIG: /usr/local/airflow/upload_config.yaml
    AIRFLOW_VAR_R2RML_CLI_DIR: /usr/local/airflow/r2rml
  volumes:
    - ./airflow/dags:/opt/airflow/dags
    - ./airflow/ontop-cli-4.1.0:/usr/local/airflow/r2rml
    - shared-data:/usr/local/airflow/user/data/input
    - ./upload_config.yaml:/usr/local/airflow/upload_config.yaml
    - airflow-logs-volume:/opt/airflow/logs
    # - ./plugins:/opt/airflow/plugins
    # !! READ ME!! 
    # There seems to be an file permission issue with RHEL 8.6.
    # File permissions between the host and container isn't automatically resolved during docker compose up.
    # To mitigate that, replace 50000 (uid) below with the uid of your host system which can be obtained with 'id -u' command.
  user: "${AIRFLOW_UID:-50000}:0"
  depends_on:
    &airflow-common-depends-on
    redis:
      condition: service_healthy
    postgres:
      condition: service_healthy

services:
  postgres:
    image: postgres:13
    # enable ports if pgadmin needs to access postgres
    #ports:
    #  - 5432:5432
    environment:
      POSTGRES_USER: airflow
      POSTGRES_PASSWORD: airflow
      # change the database name as per your need. If changes are made here,
      # changes need to be made here as https://gitlab.com/UM-CDS/protrait/fairifier2/-/blob/main/postgres/create_second_db.sql#L1
      # If database does not exists is an issue, change here to "data" or change in postgres sql.
      POSTGRES_DB: airflow
    volumes:
      - postgres-db-volume:/var/lib/postgresql/data
      - ./postgres/create_second_db.sql:/docker-entrypoint-initdb.d/create_second_db.sql

    healthcheck:
      test: ["CMD", "pg_isready", "-U", "airflow"]
      interval: 5s
      retries: 5
    restart: always

  redis:
    image: redis:latest
    expose:
      - 6379
    healthcheck:
      test: ["CMD", "redis-cli", "ping"]
      interval: 5s
      timeout: 30s
      retries: 50
    restart: always

  airflow-webserver:
    <<: *airflow-common
    command: webserver
    ports:
      - 8080:8080
    healthcheck:
      test: ["CMD", "curl", "--fail", "http://localhost:8080/health"]
      interval: 10s
      timeout: 10s
      retries: 5
    restart: always
    depends_on:
      <<: *airflow-common-depends-on
      airflow-init:
        condition: service_completed_successfully

  airflow-scheduler:
    <<: *airflow-common
    command: scheduler
    healthcheck:
      test: ["CMD-SHELL", 'airflow jobs check --job-type SchedulerJob --hostname "$${HOSTNAME}"']
      interval: 10s
      timeout: 10s
      retries: 5
    restart: always
    depends_on:
      <<: *airflow-common-depends-on
      airflow-init:
        condition: service_completed_successfully

  airflow-worker:
    <<: *airflow-common
    command: celery worker
    healthcheck:
      test:
        - "CMD-SHELL"
        - 'celery --app airflow.executors.celery_executor.app inspect ping -d "celery@$${HOSTNAME}"'
      interval: 10s
      timeout: 10s
      retries: 5
    environment:
      <<: *airflow-common-env
      # Required to handle warm shutdown of the celery workers properly
      # See https://airflow.apache.org/docs/docker-stack/entrypoint.html#signal-propagation
      DUMB_INIT_SETSID: "0"
    restart: always
    depends_on:
      <<: *airflow-common-depends-on
      airflow-init:
        condition: service_completed_successfully

  airflow-triggerer:
    <<: *airflow-common
    command: triggerer
    healthcheck:
      test: ["CMD-SHELL", 'airflow jobs check --job-type TriggererJob --hostname "$${HOSTNAME}"']
      interval: 10s
      timeout: 10s
      retries: 5
    restart: always
    depends_on:
      <<: *airflow-common-depends-on
      airflow-init:
        condition: service_completed_successfully

  graphdb:
    image: jvsoest/graphdb-free:fairstation
    ports: 
        - 7200:7200
    environment:
        - GDB_HEAP_SIZE=2g
        - GDB_MIN_MEM=1g
        - GDB_MAX_MEM=2g
    depends_on:
      <<: *airflow-common-depends-on
      airflow-init:
        condition: service_completed_successfully

  term-mapper:
    image: jvsoest/term-mapper
    ports:
        - 5001:5000
    environment:
        - ENDPOINT_URL=http://graphdb:7200/repositories/data

  dashapp:
    image: ghcr.io/maastrichtu-cds/fairifier2-app:latest
    ports:
      - 5005:5050
    links:
      - graphdb:graphdb
    volumes:
      - shared-data:/input
      - ./backup:/backup
    environment:
      - TRIPLE_STORE_ADDR=http://graphdb:7200
      - DATA_GRAPH_ADDR=http://localhost/GenericList2_stagingDB
      - ONTOLOGY_GRAPH_ADDR=http://localhost/ontology
      - ANNOTATIONS_GRAPH_ADDR=http://data.local/mapping
    depends_on:
      <<: *airflow-common-depends-on
      airflow-init:
        condition: service_completed_successfully

  airflow-init:
    <<: *airflow-common
    entrypoint: /bin/bash
    # yamllint disable rule:line-length
    command:
      - -c
      - |
        function ver() {
          printf "%04d%04d%04d%04d" $${1//./ }
        }
        airflow_version=$$(gosu airflow airflow version)
        airflow_version_comparable=$$(ver $${airflow_version})
        min_airflow_version=2.2.0
        min_airflow_version_comparable=$$(ver $${min_airflow_version})
        if (( airflow_version_comparable < min_airflow_version_comparable )); then
          echo
          echo -e "\033[1;31mERROR!!!: Too old Airflow version $${airflow_version}!\e[0m"
          echo "The minimum Airflow version supported: $${min_airflow_version}. Only use this or higher!"
          echo
          exit 1
        fi
        if [[ -z "${AIRFLOW_UID}" ]]; then
          echo
          echo -e "\033[1;33mWARNING!!!: AIRFLOW_UID not set!\e[0m"
          echo "If you are on Linux, you SHOULD follow the instructions below to set "
          echo "AIRFLOW_UID environment variable, otherwise files will be owned by root."
          echo "For other operating systems you can get rid of the warning with manually created .env file:"
          echo "    See: https://airflow.apache.org/docs/apache-airflow/stable/start/docker.html#setting-the-right-airflow-user"
          echo
        fi
        one_meg=1048576
        mem_available=$$(($$(getconf _PHYS_PAGES) * $$(getconf PAGE_SIZE) / one_meg))
        cpus_available=$$(grep -cE 'cpu[0-9]+' /proc/stat)
        disk_available=$$(df / | tail -1 | awk '{print $$4}')
        warning_resources="false"
        if (( mem_available < 4000 )) ; then
          echo
          echo -e "\033[1;33mWARNING!!!: Not enough memory available for Docker.\e[0m"
          echo "At least 4GB of memory required. You have $$(numfmt --to iec $$((mem_available * one_meg)))"
          echo
          warning_resources="true"
        fi
        if (( cpus_available < 2 )); then
          echo
          echo -e "\033[1;33mWARNING!!!: Not enough CPUS available for Docker.\e[0m"
          echo "At least 2 CPUs recommended. You have $${cpus_available}"
          echo
          warning_resources="true"
        fi
        if (( disk_available < one_meg * 10 )); then
          echo
          echo -e "\033[1;33mWARNING!!!: Not enough Disk space available for Docker.\e[0m"
          echo "At least 10 GBs recommended. You have $$(numfmt --to iec $$((disk_available * 1024 )))"
          echo
          warning_resources="true"
        fi
        if [[ $${warning_resources} == "true" ]]; then
          echo
          echo -e "\033[1;33mWARNING!!!: You have not enough resources to run Airflow (see above)!\e[0m"
          echo "Please follow the instructions to increase amount of resources available:"
          echo "   https://airflow.apache.org/docs/apache-airflow/stable/start/docker.html#before-you-begin"
          echo
        fi
        mkdir -p /sources/logs /sources/dags /sources/plugins
        chown -R "${AIRFLOW_UID}:0" /sources/{logs,dags,plugins}
        exec /entrypoint airflow version
    # yamllint enable rule:line-length
    environment:
      <<: *airflow-common-env
      _AIRFLOW_DB_UPGRADE: 'true'
      _AIRFLOW_WWW_USER_CREATE: 'true'
      _AIRFLOW_WWW_USER_USERNAME: ${_AIRFLOW_WWW_USER_USERNAME:-airflow}
      _AIRFLOW_WWW_USER_PASSWORD: ${_AIRFLOW_WWW_USER_PASSWORD:-airflow}
    user: "0:0"
    volumes:
      - .:/sources

  airflow-cli:
    <<: *airflow-common
    profiles:
      - debug
    environment:
      <<: *airflow-common-env
      CONNECTION_CHECK_MAX_COUNT: "0"
    # Workaround for entrypoint issue. See: https://github.com/apache/airflow/issues/16252
    command:
      - bash
      - -c
      - airflow

  flower:
    <<: *airflow-common
    command: celery flower
    ports:
      - 5555:5555
    healthcheck:
      test: ["CMD", "curl", "--fail", "http://localhost:5555/"]
      interval: 10s
      timeout: 10s
      retries: 5
    restart: always
    depends_on:
      <<: *airflow-common-depends-on
      airflow-init:
        condition: service_completed_successfully

volumes:
  postgres-db-volume:
  airflow-logs-volume:
  shared-data: