Compatibility fixes for IRIDA version 23.10.1 #354
Workflow file for this run
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| ########################################################################### | |
| # 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/[email protected] | |
| 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 |