Fixes #2673 NTR CxG type IIx muscle cell #3858
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
| # Basic ODK workflow | |
| name: CI | |
| # Controls when the action will run. | |
| on: | |
| # Triggers the workflow on push or pull request events but only for the master branch | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| # This workflow contains a single job called "ontology_qc" | |
| ontology_qc: | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.5.2 | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v3 | |
| - name: Run ontology QC checks | |
| id: check | |
| continue-on-error: true | |
| env: | |
| DEFAULT_BRANCH: master | |
| run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false | |
| - name: Reason over taxon constraints | |
| id: explaintc | |
| continue-on-error: true | |
| if: steps.check.outcome == 'failure' | |
| run: | | |
| if [ -s src/ontology/reports/taxon-constraint-check.txt ]; then | |
| robot explain -i src/ontology/tmp/cl-plus-taxon-disjoints.ofn -M unsatisfiability -u all -r ELK -e taxon-unsats.md | |
| echo "<details>\n<summary>This PR violates some taxon constraints. Here is what the reasoner has to say:</summary>\n" > comments.md | |
| cat taxon-unsats.md >> comment.md | |
| echo "</details>" >> comment.md | |
| exit 1 | |
| fi | |
| - name: Post explanation for taxon constraint violations | |
| if: steps.explaintc.outcome == 'failure' | |
| uses: NejcZdovc/comment-pr@v2 | |
| with: | |
| github_token: ${{secrets.GITHUB_TOKEN}} | |
| file: "../../comment.md" | |
| identifier: "TAXON_CONSTRAINTS_REASONING" | |
| # If the check failed, then the entire job should fail, even if we | |
| # allowed it to continue so that we could post the message with | |
| # the explanations. | |
| - name: Fail on error | |
| if: steps.check.outcome == 'failure' | |
| run: exit 1 | |