[23.1] Fix closed transaction error on galaxy startup/check jobs #19575
Workflow file for this run
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| name: Database indexes | |
| on: | |
| push: | |
| paths-ignore: | |
| - 'client/**' | |
| - 'doc/**' | |
| - 'lib/galaxy_test/selenium/**' | |
| pull_request: | |
| paths-ignore: | |
| - 'client/**' | |
| - 'doc/**' | |
| - 'lib/galaxy_test/selenium/**' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| working-directory: 'galaxy root' | |
| jobs: | |
| check: | |
| name: Check database indexes | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| db: ['postgresql', 'sqlite'] | |
| postgresql-version: ['13'] | |
| python-version: ['3.7'] | |
| include: | |
| - db: postgresql | |
| postgresql-version: '9.6' | |
| python-version: '3.7' | |
| services: | |
| postgres: | |
| image: postgres:${{ matrix.postgresql-version }} | |
| env: | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| POSTGRES_DB: postgres | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| path: 'galaxy root' | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Get full Python version | |
| id: full-python-version | |
| shell: bash | |
| run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT | |
| - name: Cache pip dir | |
| uses: actions/cache@v3 | |
| id: pip-cache | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }} | |
| - name: Cache tox env | |
| uses: actions/cache@v3 | |
| with: | |
| path: .tox | |
| key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-check-indexes | |
| - name: Install tox | |
| run: pip install tox | |
| - name: Set database connection on PostgreSQL | |
| if: matrix.db == 'postgresql' | |
| run: echo 'GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION=postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8' >> $GITHUB_ENV | |
| - name: Check indexes | |
| run: tox -e check_indexes |