Update nucleiEnrichmentProtocol.csv with new entry WIP #299
Workflow file for this run
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| name: build | |
| on: | |
| pull_request: | |
| types: | |
| - opened | |
| - synchronize | |
| - labeled | |
| branches: | |
| - 'main' | |
| paths: | |
| - 'modules/**' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref_name }}-${{ github.triggering_actor }} | |
| cancel-in-progress: true | |
| jobs: | |
| schema-convert: | |
| runs-on: ubuntu-latest | |
| if: github.triggering_actor != 'commit-to-main-bot-adkp[bot]' | |
| outputs: | |
| CHANGED_MANIFESTS: ${{ steps.identify-changed-manifests.outputs.changed_manifests }} | |
| steps: | |
| - uses: actions/create-github-app-token@v2 | |
| id: app-token | |
| with: | |
| app-id: ${{ vars.COMMIT_BOT_ID }} | |
| private-key: ${{ secrets.COMMIT_BOT_KEY }} | |
| - uses: actions/checkout@v5 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ steps.app-token.outputs.token }} | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| cache: 'pip' | |
| - name: install libraries | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| - name: list changed attributes for manifest testing | |
| run: git diff --name-only origin/main HEAD > ./tests/changed-files.txt | |
| - name: assemble csv data model | |
| run: python scripts/assemble_csv_data_model.py modules AD.model.csv | |
| - name: commit csv changes | |
| uses: EndBug/add-and-commit@v9 | |
| with: | |
| default_author: github_actions | |
| add: 'AD.model.csv' | |
| message: "assemble *.model.csv from modules directory" | |
| push: true | |
| - name: convert .csv to .jsonld | |
| shell: bash | |
| run: schematic schema convert AD.model.csv | |
| - name: Commit JSON-LD changes | |
| uses: EndBug/add-and-commit@v9 | |
| with: | |
| default_author: github_actions | |
| add: "AD.model.jsonld" | |
| message: "convert *.model.csv to *.model.jsonld" | |
| push: true | |
| - name: Identify changed manifests | |
| working-directory: tests | |
| run: ./changed_manifest_selection.sh | |
| - name: Save changed manifests | |
| id: identify-changed-manifests | |
| working-directory: tests | |
| shell: bash | |
| run: | | |
| changed_manifests=$( jq -r '.[] | .schema_name' changed-templates.json ) | |
| echo "CHANGED_MANIFESTS="$changed_manifests"" >> "$GITHUB_OUTPUT" | |
| - name: Delay start of subsequent jobs | |
| shell: bash | |
| run: | | |
| echo "Delaying start of subsequent jobs" | |
| for i in $(seq 1 60); do | |
| sleep 1 | |
| printf "$i of 60 seconds\r" | |
| done | |
| test: | |
| if: github.event.action != 'labeled' | |
| runs-on: ubuntu-latest | |
| needs: [schema-convert] | |
| env: | |
| SCHEMATIC_SERVICE_ACCOUNT_CREDS: ${{ secrets.SCHEMATIC_SERVICE_ACCOUNT_CREDS }} | |
| steps: | |
| - env: | |
| CHANGED_MANIFESTS: ${{ needs.schema-convert.outputs.CHANGED_MANIFESTS }} | |
| run: | |
| echo "$CHANGED_MANIFESTS" | |
| - uses: actions/create-github-app-token@v2 | |
| id: app-token | |
| with: | |
| app-id: ${{ vars.COMMIT_BOT_ID }} | |
| private-key: ${{ secrets.COMMIT_BOT_KEY }} | |
| - uses: actions/checkout@v5 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ steps.app-token.outputs.token }} | |
| clean: false | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| cache: 'pip' | |
| - name: Install libraries | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| - name: Generate test manifests | |
| working-directory: tests | |
| run: bash ./generate_test_manifests.sh "${{ needs.schema-convert.outputs.CHANGED_MANIFESTS }}" | |
| - name: Create Test Suite Report | |
| working-directory: tests | |
| run: docker run -v $(pwd):/tests 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 | |
| message-path: | | |
| tests/test-suite-report.md | |
| - name: Upload test artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: test-logs | |
| path: tests | |
| merge: | |
| needs: [schema-convert] | |
| if: contains(github.event.pull_request.labels.*.name, 'automerge') && github.event.action != 'opened' && github.event.action != 'synchronize' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/create-github-app-token@v2 | |
| id: app-token | |
| with: | |
| app-id: ${{ vars.COMMIT_BOT_ID }} | |
| private-key: ${{ secrets.COMMIT_BOT_KEY }} | |
| - id: merge-and-delete | |
| uses: "pascalgn/automerge-action@v0.16.4" | |
| env: | |
| GITHUB_TOKEN: ${{ steps.app-token.outputs.token }} | |
| MERGE_LABELS: "automerge" | |
| MERGE_DELETE_BRANCH: "true" | |
| MERGE_METHOD: "squash" | |
| BASE_BRANCHES: "main" | |
| MERGE_ERROR_FAIL: "true" | |
| generate-and-upload-manifests: | |
| needs: [schema-convert, merge] | |
| if: contains(github.event.pull_request.labels.*.name, 'automerge') | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| SCHEMATIC_SERVICE_ACCOUNT_CREDS: ${{ secrets.SCHEMATIC_SERVICE_ACCOUNT_CREDS }} | |
| SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_TOKEN_DPE }} | |
| SYNAPSE_UPLOAD_FOLDER_ID: syn25878249 | |
| steps: | |
| - env: | |
| CHANGED_MANIFESTS: ${{ needs.schema-convert.outputs.CHANGED_MANIFESTS }} | |
| run: | |
| echo "$CHANGED_MANIFESTS" | |
| - uses: actions/create-github-app-token@v2 | |
| id: app-token | |
| with: | |
| app-id: ${{ vars.COMMIT_BOT_ID }} | |
| private-key: ${{ secrets.COMMIT_BOT_KEY }} | |
| - uses: actions/checkout@v5 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ steps.app-token.outputs.token }} | |
| clean: false | |
| ref: 'refs/heads/main' | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| cache: 'pip' | |
| - name: Install libraries | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| - name: Generate changed manifests | |
| working-directory: tests | |
| run: ./generate_changed_templates.sh "${{ needs.schema-convert.outputs.CHANGED_MANIFESTS }}" | |
| - name: Commit manifests to main | |
| uses: EndBug/add-and-commit@v9 | |
| with: | |
| default_author: github_actions | |
| add: "current-excel-manifests" | |
| message: "add changed manifests" | |
| push: true | |
| - name: Generate JSONSchema | |
| shell: bash | |
| run: schematic schema generate-jsonschema -dms AD.model.jsonld -od current-manifest-schemas -dml display_label | |
| - name: Commit schemas to main | |
| uses: EndBug/add-and-commit@v9 | |
| with: | |
| default_author: github_actions | |
| add: "current-manifest-schemas" | |
| message: "add schemas" | |
| push: true | |
| - name: Upload manifests to Synapse | |
| working-directory: current-excel-manifests | |
| run: ../tests/upload_templates.sh "${{ needs.schema-convert.outputs.CHANGED_MANIFESTS }}" | |