Merge pull request #341 from CanDIG/daisieh/program #85
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| name: Github Actions Test | |
| on: [push] | |
| jobs: | |
| build: | |
| env: | |
| POSTGRES_USER: admin | |
| POSTGRES_PASSWORD: OG0pjmnQDWUTvLotYrxPrg | |
| POSTGRES_HOST: localhost | |
| POSTGRES_HOST_AUTH_METHOD: password | |
| POSTGRES_DB: metadata | |
| POSTGRES_PORT: 5432 | |
| HTSGET_TEST_KEY: thisisatest | |
| DB_PATH: localhost | |
| SERVER_LOCAL_DATA: ${{github.workspace}}/data | |
| PGPASSWORD: OG0pjmnQDWUTvLotYrxPrg | |
| INDEXING_PATH: ${{github.workspace}}/tmp | |
| INDEXING_SWITCH_FILE: ${{github.workspace}}/indexer_on | |
| TESTENV_URL: http://localhost:3000 | |
| AGGREGATE_COUNT_THRESHOLD: 5 | |
| POSTGRES_USERNAME: admin | |
| runs-on: ubuntu-latest | |
| # Add in environment variables for the entire "build" job | |
| services: | |
| postgres_main: | |
| image: postgres:latest | |
| env: | |
| POSTGRES_USER: ${{ env.POSTGRES_USER }} | |
| POSTGRES_PASSWORD: ${{ env.POSTGRES_PASSWORD }} | |
| POSTGRES_DB: ${{ env.POSTGRES_DB }} | |
| ports: | |
| - 5432:5432 | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| strategy: | |
| matrix: | |
| python-version: ['3.12'] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install requirements | |
| run: | | |
| pip install -r requirements.txt | |
| bash create_db.sh | |
| mkdir -p ${{ env.INDEXING_PATH }} | |
| touch ${{ env.INDEXING_SWITCH_FILE }} | |
| sed -i s@\<AGGREGATE_COUNT_THRESHOLD\>@${{env.AGGREGATE_COUNT_THRESHOLD}}@ config.ini | |
| sed -i s@\<POSTGRES_USERNAME\>@${{env.POSTGRES_USERNAME}}@ config.ini | |
| - name: Test | |
| run: | | |
| python htsget_server/server.py & | |
| python htsget_server/indexing.py & | |
| sleep 5 | |
| pytest tests/test_htsget_server.py |