Update registered exports #141
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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)" >> "$GITHUB_OUTPUT" | |
| - name: Setup custom build tools and make jsonld | |
| shell: bash | |
| run: | | |
| bash < <(curl -s https://raw.githubusercontent.com/babashka/babashka/master/install) | |
| git clone --depth 1 https://github.com/anngvu/retold.git | |
| make | |
| - name: Install tools and regenerate registered jsons for Superdataset, PortalDataset, etc | |
| run: | | |
| pip install linkml==v1.8.1 | |
| npm install -g json-dereference-cli | |
| make PortalDataset | |
| make PortalStudy | |
| make Superdataset | |
| make PortalPublication | |
| make Protocol | |
| # Set up supported python. | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10.12' | |
| - name: Setup schematic and do another convert pass | |
| id: schematic-convert | |
| run: | | |
| pip install schematicpy==${{ 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 | |