allow users to claim received samples #1490
Workflow file for this run
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| name: microsetta-private-api CI | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| jobs: | |
| # derived from https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml | |
| postgres-runner-job: | |
| runs-on: ubuntu-latest | |
| # Service containers to run with `runner-job` | |
| services: | |
| # Label used to access the service container | |
| postgres: | |
| # Docker Hub image | |
| image: postgres:13.4 | |
| env: | |
| POSTGRES_DB: ag_test | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| # based on https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml#L44-L72 | |
| - 5432/tcp | |
| steps: | |
| # Downloads a copy of the code in your repository before running CI tests | |
| - name: Check out repository code | |
| uses: actions/checkout@v2 | |
| - name: Setup for conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: 3.7 | |
| - name: Install | |
| shell: bash -l {0} | |
| env: | |
| MFR_URL: "${{ secrets.MFR_URL }}" | |
| MFR_TEST_APIKEY: "${{ secrets.MFR_TEST_APIKEY }}" | |
| MFR_STUDY: "${{ secrets.MFR_STUDY }}" | |
| FUNDRAZR_TEST_APIKEY: "${{ secrets.FUNDRAZR_TEST_APIKEY }}" | |
| FUNDRAZR_TEST_URL: "${{ secrets.FUNDRAZR_TEST_URL }}" | |
| FUNDRAZR_TEST_ORG: "${{ secrets.FUNDRAZR_TEST_ORG }}" | |
| VS_ENDPOINT: "${{ secrets.VS_ENDPOINT }}" | |
| VS_USER: "${{ secrets.VS_USER }}" | |
| VS_PASSWORD: "${{ secrets.VS_PASSWORD }}" | |
| VS_CRYPTOKEY: "${{ secrets.VS_CRYPTOKEY }}" | |
| VS_REGCODE: "${{ secrets.VS_REGCODE }}" | |
| GOOGLE_GEOCODING_KEY: "${{ secrets.GOOGLE_GEOCODING_KEY }}" | |
| run: | | |
| # pull out the port so we can modify the configuration file easily | |
| pgport=${{ job.services.postgres.ports[5432] }} | |
| sed -i "s/self.port = 5432/self.port = $pgport/" microsetta_private_api/config_manager.py | |
| # use hashes to avoid delimiter overlap with a URL | |
| python set_github_secrets.py | |
| # PGPASSWORD is read by pg_restore, which is called by the build_db process. | |
| export PGPASSWORD=postgres | |
| conda create --yes -n test-microsetta-private python=3.9 | |
| conda activate test-microsetta-private | |
| conda install --yes --file ci/conda_requirements.txt | |
| pip install -r ci/pip_requirements.txt | |
| pip install -e . --no-deps | |
| # establish database state | |
| python microsetta_private_api/LEGACY/build_db.py | |
| - name: Test | |
| shell: bash -l {0} | |
| run: | | |
| conda activate test-microsetta-private | |
| # workaround for Python bpo-44413 | |
| # https://bugs.python.org/issue44413 | |
| # discussed further in Debian 1001774 | |
| # https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1001774 | |
| sudo timedatectl set-timezone America/Los_Angeles | |
| make test | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: flake8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.7 | |
| - name: install dependencies | |
| run: python -m pip install --upgrade pip | |
| - name: lint | |
| run: | | |
| pip install -q flake8 | |
| make lint | |