update-owl.yaml

name: "Update OWL"

on:
  push:
    branches: [master]

jobs:
  generate-owl:
    if: ${{ ! contains(github.event.head_commit.message, 'Update OWL file') }}
    runs-on: ubuntu-latest
    permissions:
      contents: write
      pull-requests: write
    steps:
      - name: Checkout Repository
        uses: actions/checkout@v3
      - name: Extract version from OBO
        run: |
          CV_VERSION=`grep data-version psi-ms.obo | grep -oP "(\d+.\d+.\d+)"`
          echo CV_VERSION=${CV_VERSION}
          echo "CV_VERSION=${CV_VERSION}" >> $GITHUB_ENV
      - name: Generate OWL
        run: |
          # Replace the imports of the UO and PATO ontology .obo files with the equivalent .owl files
          cp psi-ms.obo tmp.obo
          sed -e "s/pato.obo/pato.owl/g" -e "s/uo.obo/uo.owl/g" -i tmp.obo
          head -n 50 tmp.obo

          python -m pip install fastobo
          python scripts/prepare_template.py tmp.obo cv_template.tsv
          echo Generated template with `wc -l cv_template.tsv`

          wget -nv --no-check-certificate https://github.com/ontodev/robot/releases/download/v1.9.5/robot.jar
          export JAVA_TOOL_OPTIONS=-Xmx6G
          # java -jar robot.jar -vvv template -p "PEFF: http://purl.obolibrary.org/obo/PEFF_" -i psi-ms.obo -t cv_template.tsv convert -f ofn -o psi-ms.owl
          java -jar robot.jar convert -v -i tmp.obo -o psi-ms.owl --format owl
          rm *robot.jar*
          rm *tmp.obo* *cv_template.tsv*
      - name: Create pull request
        id: cpr
        uses: peter-evans/create-pull-request@v4
        with:
          token: ${{ secrets.PSI_MS_CV_GITHUB_TOKEN }}
          commit-message: Update OWL file
          committer: GitHub <noreply@github.com>
          author: GitHub <noreply@github.com>
          branch: update-owl-file
          delete-branch: true
          title: Update OWL file
          body: This automated PR updates the OWL file corresponding to the OBO file
      - name: Approve pull request
        if: (steps.cpr.outputs.pull-request-operation == 'created' ||	steps.cpr.outputs.pull-request-operation == 'updated')
        uses: juliangruber/approve-pull-request-action@v1
        with:
          github-token: ${{ secrets.GITHUB_TOKEN }}
          number: ${{ steps.cpr.outputs.pull-request-number }}
      - name: Merge pull request
        if: (steps.cpr.outputs.pull-request-operation == 'created' ||	steps.cpr.outputs.pull-request-operation == 'updated')
        uses: peter-evans/enable-pull-request-automerge@v3
        with:
          token: ${{ secrets.PSI_MS_CV_GITHUB_TOKEN }}
          pull-request-number: ${{ steps.cpr.outputs.pull-request-number }}
          merge-method: squash
      - name: GitHub Tag
        id: new_tag
        uses: mathieudutour/github-tag-action@v5.6
        with:
          github_token: ${{ secrets.PSI_MS_CV_GITHUB_TOKEN }}
          pre_release_branches: test-tag
          custom_tag: ${{ env.CV_VERSION }}