Update PortalDataset.yaml #113
Workflow file for this run
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| name: main-ci | |
| on: | |
| pull_request: # default types: opened, synchronize, reopened | |
| branches: [main] | |
| paths: | |
| - 'modules/**' | |
| - '.github/workflows/main-ci.yml' | |
| workflow_dispatch: | |
| env: | |
| SCHEMATIC_VERSION: 24.7.2 # please update .devcontainer as well until this can be set globally somewhere... | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token. | |
| fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository | |
| - name: Get skip flags | |
| id: check_skip_flags | |
| run: echo "HEAD_COMMIT_MESSAGE=$(git show -s --format=%s)" >> "$GITHUB_OUTPUT" | |
| - name: Setup custom build tools and make jsonld | |
| shell: bash | |
| run: | | |
| bash < <(curl -s https://raw.githubusercontent.com/babashka/babashka/master/install) | |
| git clone --depth 1 https://github.com/anngvu/retold.git | |
| make | |
| - name: Install tools and regenerate registered jsons for Superdataset, PortalDataset, etc | |
| run: | | |
| pip install linkml==v1.8.1 | |
| npm install -g json-dereference-cli | |
| make PortalDataset | |
| make PortalStudy | |
| make Superdataset | |
| # Set up supported python. | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10.12' | |
| - name: Setup schematic and do another convert pass | |
| id: schematic-convert | |
| run: | | |
| pip install schematicpy==${{ env.SCHEMATIC_VERSION }} | |
| pip show schematicpy | |
| schematic schema convert NF.jsonld | |
| - name: Commit files if there are changes | |
| run: | | |
| if [[ $(git diff --exit-code) ]]; then | |
| echo "Changes in src modules affect final jsonld or json artifacts and will be committed" | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "nf-osi[bot]" | |
| git add . | |
| git commit -m "Rebuild NF.jsonld, json" | |
| else | |
| echo "Changes in src modules did not affect final jsonld or json artifacts" | |
| echo "Note that tests will still be run in the next job" | |
| fi | |
| - name: Push changes | |
| uses: ad-m/github-push-action@master | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| branch: ${{ github.event.pull_request.head.ref }} | |
| # Additionally test PRs | |
| test: | |
| name: Test with schematic current version | |
| needs: [build] | |
| runs-on: ubuntu-latest | |
| env: | |
| SCHEMATIC_SERVICE_ACCT_CREDS: ${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }} | |
| permissions: | |
| pull-requests: write | |
| if: ${{ !contains(github.event.pull_request.labels.*.name, 'skip tests') }} | |
| # strategy: | |
| # matrix: | |
| # cannot actually do parallel/concurrent testing because of API rate limits, | |
| # so we currently only test with one schematic version because it takes much too long with sequential | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10.12' | |
| - name: Setup schematic | |
| id: setup-schematic | |
| run: | | |
| pip install schematicpy==${{ env.SCHEMATIC_VERSION }} | |
| pip show schematicpy | |
| - name: Test generate | |
| working-directory: tests/generate | |
| continue-on-error: true | |
| run: ./basic_templates.sh | |
| - name: Test validate | |
| working-directory: tests/validate | |
| continue-on-error: true | |
| run: ./run_config.sh | |
| - name: Test submit | |
| working-directory: tests/submit | |
| continue-on-error: true | |
| # Only test submit needs SYNAPSE_AUTH_TOKEN | |
| env: | |
| SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }} | |
| # Need to set up csvtool for use in test environment | |
| run: | | |
| sudo apt install csvtool | |
| printf "[authentication]\nSYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN" > .synapseConfig | |
| ./test_submit.sh | |
| - name: Create test suite report | |
| working-directory: tests | |
| continue-on-error: true | |
| run: docker run -v $(pwd):/tests -e SCHEMATIC=${{ env.SCHEMATIC_VERSION }} rocker/tidyverse R -e "rmarkdown::render('tests/test-suite-report.Rmd')" | |
| - name: Report on test suite as PR comment | |
| uses: mshick/add-pr-comment@v2 | |
| with: | |
| message-id: test-suite-report-${{ env.SCHEMATIC_VERSION }} | |
| message-path: | | |
| tests/test-suite-report.md | |
| - name: Upload test artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: test-logs-${{ env.SCHEMATIC_VERSION }} | |
| path: tests/**/logs | |