qc.yml

# 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 ]
    paths:
      - 'src/**'
  pull_request:
    branches: [ master ]
    paths:
      - 'src/**'

  # 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
          ROBOT_JAVA_ARGS: -Xmx6G
        run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' GH_ACTION=true BRI=true MIR=false IMP=false test > TESTLOG.log

      - 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/uberon-edit-plus-tax-equivs.owl -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" > comment.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"
  
      - name: Last rows of QC report
        if: steps.check.outcome == 'failure'
        run: |
          tail -20 src/ontology/TESTLOG.log
          exit 1