Integration Tests #359
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ########################################################################### | |
| # 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 |