display genotype data missing warning #1263
Workflow file for this run
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| on: | |
| pull_request: | |
| paths-ignore: | |
| - 'docs/**' | |
| - '**.md' | |
| jobs: | |
| test_breedbase: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: breedbase/breedbase:latest | |
| env: | |
| HOME: /root | |
| MODE: 'TESTING' | |
| SYSTEM: 'GITACTION' | |
| PGPASSWORD: postgres | |
| SGN_TEST_SERVER: http://test_breedbase:3010 | |
| SGN_REMOTE_SERVER_ADDR: selenium | |
| volumes: | |
| - ${{ github.workspace }}:/home/production/cxgn/sgn | |
| - ${{ github.workspace }}:/home/vagrant/cxgn/sgn | |
| options: --network-alias test_breedbase | |
| services: | |
| breedbase_db: | |
| image: postgres:12.9 | |
| env: | |
| 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 | |
| selenium: | |
| image: selenium/standalone-firefox:3.141.59 | |
| volumes: | |
| - ${{ github.workspace }}:/home/production/cxgn/sgn | |
| - ${{ github.workspace }}:/home/vagrant/cxgn/sgn | |
| options: --health-cmd="curl --silent --head http://localhost:4444 || exit 1" | |
| steps: | |
| - name: Checkout sgn | |
| uses: actions/checkout@v4 | |
| - name: Run unit tests | |
| run: prove --recurse t/unit 2>/dev/null | |
| - name: Load/dump fixture database and build node modules | |
| run: | | |
| echo "--version" > ~/.proverc | |
| perl t/test_fixture.pl --dumpupdatedfixture | |
| rm ~/.proverc | |
| # work around run_all_patches.pl "what the heck - no TTY??" error | |
| # https://github.com/actions/runner/issues/241#issuecomment-842566950 | |
| shell: 'script --flush --quiet --return --command "bash --noprofile --norc -eo pipefail {0}"' | |
| - name: Run unit_fixture tests | |
| # need entrypoint.sh to start slurm | |
| # --nopatch to skip running fixture and db patches (already done in previous step) | |
| run: /entrypoint.sh --nopatch t/unit_fixture 2>/dev/null | |
| - name: Run unit_mech tests | |
| run: /entrypoint.sh --nopatch t/unit_mech | |
| # selenium tests for a moment as separate folders - will change once full solgs are ready | |
| # but anyway, it will is still fully functional for tests purpose | |
| - name: Run selenium tests 01_list | |
| run: /entrypoint.sh --nopatch t/selenium2/01_list 2>/dev/null | |
| - name: Run selenium tests 02_trial | |
| run: /entrypoint.sh --nopatch t/selenium2/02_trial 2>/dev/null | |
| - name: Run selenium tests dataset | |
| run: /entrypoint.sh --nopatch t/selenium2/03_dataset 2>/dev/null | |
| - name: Run selenium tests breeders | |
| run: /entrypoint.sh --nopatch t/selenium2/breeders 2>/dev/null | |
| - name: Run selenium tests onto | |
| run: /entrypoint.sh --nopatch t/selenium2/onto 2>/dev/null | |
| - name: Run selenium tests search | |
| run: /entrypoint.sh --nopatch t/selenium2/search 2>/dev/null | |
| - name: Run selenium tests stock | |
| run: /entrypoint.sh --nopatch t/selenium2/stock 2>/dev/null | |
| - name: Run selenium tests tools | |
| run: /entrypoint.sh --nopatch t/selenium2/tools 2>/dev/null |