ci-test.yml

###########################################################################
# Integration test suite definition for IRIDA Uploader using GitHub Actions
###########################################################################

name: Integration Tests

on:
  pull_request: # Run on all pull requests
  push:
    branches:   # Run on any push to development or main
      - development
      - main
  schedule:     # Run weekly on development and main
    - cron: 0 2 * * 1
      branches: development
    - cron: 0 2 * * 1
      branches: main


jobs:
  build-unittests:
    runs-on: ubuntu-20.04 #See pre-installed software at https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md
    strategy:
      fail-fast: False #Setting so that if one of the test suites fail, the other will continue
      matrix:
        python-version: [3.7, 3.8, 3.9, "3.10", 3.11]

    steps:
    - uses: actions/checkout@v3 #Checkout the project from git
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}
    - name: Run Unit Tests
      run: make unittests
      env:
        COVERAGE_FILE: ".coverage.unit${{ matrix.python-version }}"
    - name: Store coverage file
      uses: actions/upload-artifact@v3
      with:
        name: coverage
        path: .coverage.unit${{ matrix.python-version }}

  build-pep8:
    runs-on: ubuntu-20.04 #See pre-installed software at https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md

    steps:
      - uses: actions/checkout@v3 #Checkout the project from git
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: 3.8
      - name: Run pep8
        run: make pep8

  build-docs:
    runs-on: ubuntu-20.04 #See pre-installed software at https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md

    steps:
      - uses: actions/checkout@v3 #Checkout the project from git
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: 3.7
      - name: Run mkdocs
        run: make docs

  build-irida-integration:
    runs-on: ubuntu-20.04 #See pre-installed software at https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md

    env:
      MYSQL_PORT: 3306
      MYSQL_USER: test
      MYSQL_PASSWORD: test
      MYSQL_DATABASE: irida_uploader_test
      MYSQL_HOST: 127.0.0.1
      MYSQL_ROOT_PASSWORD: password
      NODE_OPTIONS: "--max-old-space-size=4096"

    strategy:
      fail-fast: False #Setting so that if one of the test suites fail, the other will continue
      matrix:
        branch: ['main','development'] # IRIDA Branches to test against

    steps:
      - uses: actions/checkout@v3 #Checkout the project from git
      - name: Setup MySQL
        uses: mirromutth/mysql-action@v1.1
        with:
          host port: ${{ env.MYSQL_PORT }}
          character set server: 'utf8'
          collation server: 'utf8_general_ci'
          mysql version: '5.7'
          mysql database: ${{ env.MYSQL_DATABASE }}
          mysql user: ${{ env.MYSQL_USER }}
          mysql password: ${{ env.MYSQL_PASSWORD }}
          mysql root password: ${{ env.MYSQL_ROOT_PASSWORD }} #The root superuser password
      - name: Verify MySQL connection
        timeout-minutes: 10
        run: |
          while ! mysqladmin ping -h"${{ env.MYSQL_HOST }}" -P"${{ env.MYSQL_PORT }}" --silent; do
            sleep 1
          done
      - name: Set up JDK 17 # Installs java 17
        uses: actions/setup-java@v1
        with:
          java-version: 17
      - name: MySQL Setup (SUDO) # Sets ONLY_FULL_GROUP_BY flag and gives runner privileges over database
        run: |
          sudo mysql -e "SET GLOBAL sql_mode=(SELECT REPLACE(@@sql_mode,'ONLY_FULL_GROUP_BY',''));" -h ${{ env.MYSQL_HOST }} -P ${{ env.MYSQL_PORT }} -p${{ env.MYSQL_ROOT_PASSWORD }};
          sudo mysql -e "CREATE USER '${{ env.MYSQL_USER }}'@'%' IDENTIFIED BY '${{ env.MYSQL_PASSWORD }}'; GRANT ALL ON ${{ env.MYSQL_DATABASE }}.* to '${{ env.MYSQL_USER }}'@'%';" -h ${{ env.MYSQL_HOST }} -P ${{ env.MYSQL_PORT }} -p${{ env.MYSQL_ROOT_PASSWORD }};
      - name: Run Integration Tests ${{ matrix.branch }}
        timeout-minutes: 60
        run: make integrationtests branch=${{ matrix.branch }} db_host=${{ env.MYSQL_HOST }} db_port=${{ env.MYSQL_PORT }}
        env:
          COVERAGE_FILE: ".coverage.integration${{ matrix.branch }}"
      - name: Store coverage file
        uses: actions/upload-artifact@v3
        with:
          name: coverage
          path: .coverage.integration${{ matrix.branch }}

  coverage:
    if: github.event_name != 'schedule'
    name: Coverage
    runs-on: ubuntu-latest
    needs: [build-unittests, build-irida-integration]
    permissions:
      pull-requests: write
      contents: write
    steps:
      - uses: actions/checkout@v3
      - uses: actions/download-artifact@v3
        id: download
        with:
          name: 'coverage'
      - name: Coverage comment
        id: coverage_comment
        uses: py-cov-action/python-coverage-comment-action@v3
        with:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          MERGE_COVERAGE_FILES: true
      - name: Store Pull Request comment to be posted
        uses: actions/upload-artifact@v3
        if: steps.coverage_comment.outputs.COMMENT_FILE_WRITTEN == 'true'
        with:
          name: python-coverage-comment-action
          path: python-coverage-comment-action.txt