Fix modelSystemName enum limit with conditional filtering #331
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| name: main-ci | |
| on: | |
| pull_request: # default types: opened, synchronize, reopened | |
| branches: [main] | |
| paths: | |
| - 'modules/**' | |
| - '.github/workflows/main-ci.yml' | |
| - 'utils/gen-json-schema-class.py' | |
| 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)" >> "$GITHUB_OUTPUT" | |
| - name: Setup custom build tools and make jsonld | |
| shell: bash | |
| run: | | |
| bash < <(curl -s https://raw.githubusercontent.com/babashka/babashka/master/install) | |
| git clone --depth 1 https://github.com/anngvu/retold.git | |
| pip install linkml==v1.8.1 synapseclient jsonref | |
| npm install -g json-dereference-cli | |
| echo "$HOME/.local/bin" >> $GITHUB_PATH | |
| make -B | |
| - name: Generate and validate JSON schemas for all templates (classes) | |
| env: | |
| SYNAPSE_AUTH_TOKEN: ${{ secrets.DATA_MODEL_SERVICE }} | |
| run: | | |
| echo "Generating JSON schemas and validating them!" | |
| python utils/gen-json-schema-class.py | |
| make Superdataset | |
| - name: Report schema validation results as PR comment | |
| uses: mshick/add-pr-comment@v2 | |
| if: always() | |
| with: | |
| message-id: schema-validation-report | |
| message-path: | | |
| schema-validation-log.md | |
| # Set up supported python. | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10.12' | |
| - name: Setup schematic and do another convert pass | |
| id: schematic-convert | |
| run: | | |
| pip install schematicpy==${{ env.SCHEMATIC_VERSION }} | |
| pip show schematicpy | |
| schematic schema convert NF.jsonld | |
| python utils/fix_display_names.py retold_NF.jsonld NF.jsonld | |
| - name: Check if artifacts changed | |
| id: check_artifacts | |
| run: | | |
| if [[ $(git diff --exit-code) ]]; then | |
| echo "changed=true" >> "$GITHUB_OUTPUT" | |
| echo "✅ Artifacts built successfully and have changes" | |
| else | |
| echo "changed=false" >> "$GITHUB_OUTPUT" | |
| echo "✅ Artifacts built successfully with no changes" | |
| fi | |
| - name: Report artifact build status as PR comment | |
| uses: mshick/add-pr-comment@v2 | |
| with: | |
| message-id: artifact-build-report | |
| message: | | |
| ## ✅ Artifact Build Status | |
| All artifacts have been successfully built and validated from source modules. | |
| **Artifacts validated:** | |
| - `NF.jsonld` (schematic-compatible JSON-LD) | |
| - `dist/NF.yaml` (LinkML YAML) | |
| - `dist/NF.ttl` (Turtle RDF) | |
| - `registered-json-schemas/*.json` (Synapse JSON schemas) | |
| **Note:** Artifacts are not committed to this PR to avoid merge conflicts. All artifacts will be automatically rebuilt and committed to `main` after merge. | |
| - name: Upload artifacts for subsequent jobs | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts | |
| path: | | |
| NF.jsonld | |
| dist/NF.yaml | |
| dist/NF.ttl | |
| registered-json-schemas/*.json | |
| retention-days: 1 | |
| analyze: | |
| name: Analyze data model changes | |
| needs: [build] | |
| runs-on: ubuntu-latest | |
| permissions: | |
| pull-requests: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10.12' | |
| - name: Install dependencies | |
| run: | | |
| pip install rdflib | |
| - name: Get main branch pre-built NF.ttl for comparison | |
| run: | | |
| git fetch origin main:main | |
| git checkout main -- dist/NF.ttl | |
| mv dist/NF.ttl dist/NF_main.ttl | |
| git checkout ${{ github.event.pull_request.head.ref }} | |
| - name: Download built NF.ttl from build job | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts | |
| path: . | |
| - name: Run comparison analysis | |
| run: | | |
| python utils/compare.py > analysis_output.md | |
| - name: Post analysis as PR comment | |
| uses: mshick/add-pr-comment@v2 | |
| with: | |
| message-id: data-model-analysis | |
| message-path: analysis_output.md | |
| # Additionally test PRs | |
| test: | |
| name: Test with schematic current version | |
| needs: [build] | |
| runs-on: ubuntu-latest | |
| env: | |
| SCHEMATIC_VERSION: 24.7.2 | |
| 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: ${{ github.event.pull_request.head.ref }} | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10.12' | |
| - name: Download built artifacts from build job | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts | |
| path: . | |
| - name: Setup schematic | |
| id: setup-schematic | |
| run: | | |
| pip install schematicpy==${{ env.SCHEMATIC_VERSION }} | |
| pip show schematicpy | |
| - name: Test generate | |
| working-directory: tests/schematic/generate | |
| continue-on-error: true | |
| run: ./basic_templates.sh | |
| - name: Test validate | |
| working-directory: tests/schematic/validate | |
| continue-on-error: true | |
| run: ./run_config.sh | |
| - name: Create schematic test suite report | |
| working-directory: tests/schematic | |
| 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-${{ env.SCHEMATIC_VERSION }} | |
| message-path: | | |
| tests/schematic/test-suite-report.md | |
| - name: Upload test artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: test-logs-${{ env.SCHEMATIC_VERSION }} | |
| path: tests/**/logs | |