python-app.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Python application

# Note: The following events will trigger this workflow:
#       1. Someone pushes a commit to `main` that includes changes to any of the listed files.
#       2. Someone opens a pull request that includes changes to any of the listed files.
#       3. Someone clicks the "Run workflow" button on the "Actions" tab on GitHub.
#
#  References:
#  - https://docs.github.com/en/actions/writing-workflows/choosing-when-your-workflow-runs/triggering-a-workflow#example-including-paths
#  - https://docs.github.com/en/actions/writing-workflows/workflow-syntax-for-github-actions#filter-pattern-cheat-sheet
#
on:
  push:
    branches: [ main ]
    paths:
      - '.github/workflows/python-app.yml'
      - 'Makefile'
      - '**/Dockerfile'
      - '**.py'
      - 'requirements/main.txt'
      # Every file in the `data` directory or in any of its subdirectories:
      - 'metadata-translation/notebooks/data/**'
  pull_request:
    paths:
      - '.github/workflows/python-app.yml'
      - 'Makefile'
      - '**/Dockerfile'
      - '**.py'
      - 'requirements/main.txt'
      - 'metadata-translation/notebooks/data/**'
  # Allow developers to trigger this workflow manually via the "Actions" page on GitHub.
  # Reference: https://docs.github.com/en/actions/managing-workflow-runs-and-deployments/managing-workflow-runs/manually-running-a-workflow
  workflow_dispatch: { }


jobs:
  build:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4 # update version to maintain consistency across workflows
    # Prepare the MongoDB keyfile to be mounted by the `mongo` container.
    #
    # Note: This is to prevent MongoDB from reporting the error:
    #       > "permissions on /path/to/keyfile are too open"
    #
    # Note: In containers using the `mongo` image, UID 999 refers to a user named `mongodb`
    #       and GID 999 refers to a group named `mongodb`, which that user belongs to.
    #       You can verify this by looking at the Dockerfile layers on Docker Hub.
    #       Reference: https://hub.docker.com/layers/library/mongo/8.0.5/images/sha256-90bf5066fed8a3cd59345d963922bc5cb557d4b4b2a0e38dfd9ee299c405741b
    #
    # Note: Since, by default, the GHA Runner does not have a user whose UID is 999,
    #       we created one there first (otherwise, we couldn't `chown` to that UID).
    #       Note that the GHA Runner _does_, by default, have a group whose GID is 999.
    #       Reference: https://man7.org/linux/man-pages/man8/useradd.8.html
    #
    - name: Restrict access to MongoDB keyfile
      run: |
        useradd -g 999 -u 999 temp_mongodb_user
        chown 999:999 ./mongoKeyFile
        chmod 600     ./mongoKeyFile
    - name: Set up Python 3.10
      uses: actions/setup-python@v4
      with:
        python-version: '3.10'
# deprecated: Consider merging python.app.yml and lint.yml
#    - name: Lint with flake8
#      run: |
#        pip install flake8
#        make lint
    - name: Remove volumes left over from previous workflow runs
      run: |
        docker volume ls
        make down-test
        docker volume ls
    - name: Build and run containers upon which test runner depends
      run: make up-test

    # Use `mongosh` (available within the `mongo` container) to set up
    # a replicate set of which the MongoDB instance on the `mongo`
    # container is the only member.
    #
    # Note: We do this explicitly here since the "mongo-init" approach
    #       we use on our local computers does not seem to work on GHA.
    #
    # Note: We sleep for a few seconds to give the MongoDB server some
    #       time to boot to the point of being able to process commands.
    #       We run `docker compose ps` to show some information that can
    #       help us debug this step/workflow.
    #
    # References:
    # - File: `.docker/mongo_init/initialize_replica_set.sh`
    # - https://engineering.synatic.com/a-simple-way-to-run-a-mongodb-replica-set-in-github-actions
    #
    - name: Set up MongoDB replica set
      run: |
        docker volume ls
        docker compose --file docker-compose.test.yml ps -a
        echo 'Sleeping'
        sleep 15
        echo 'Waking up'
        echo 'Logs from mongo-init'
        docker compose --file docker-compose.test.yml logs mongo-init
        echo 'Logs from mongo'
        docker compose --file docker-compose.test.yml logs mongo
        echo '---'
        docker compose --file docker-compose.test.yml ps -a
        docker compose --file docker-compose.test.yml exec mongo \
          mongosh \
            --host localhost \
            --port 27017 \
            --username admin \
            --password root \
            --eval 'rs.initiate({_id: "rs0", members: [{_id: 0, host: "localhost"}]})'
    - name: Build test runner container image
      run: make test-build
    - name: Run tests
      run: make test-run