harmonising respiratory tract and MCC names #3987
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| # 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:v1.5.3 | |
| # 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 | |