ontology/.github/workflows/diff.yml at dev · OpenEnergyPlatform/ontology · GitHub

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name: 'Create ROBOT diffs on Pull requests'

on:
  # Triggers the workflow on pull request events for the master branch
  pull_request:
    branches: [ dev ]
    paths:
      - 'src/ontology/**'

  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

jobs:
  create_diff_file:
    runs-on: ubuntu-latest
    container: obolibrary/odklite:latest
    continue-on-error: true
    steps:
      # Checks-out the branch being merged into master in the root directory
      # The ontology obo file path will be: src/ontology/fypo-edit.owl
      - uses: actions/checkout@v5
      # Checks-out the master branch in a subfolder called master
      # The ontology obo file path will be: master/src/ontology/fypo-edit.owl
      - uses: actions/checkout@v5
        with:
          ref: dev
          path: dev
      - name: Run robot diff
        # -Xmx6G extension is to set 6gb of memory for java virtual machine
        # See https://github.com/obophenotype/cell-ontology/blob/master/.github/workflows/diff.yml
        # Firstly, we remove all term tracker annotations since they only bloat the comment
        # The last line fetches all changed .omn and .owl files in src/ collects the changes in respective .changes.md files
        shell: bash
        run: |
          set -x
          robot --version
          export ROBOT_JAVA_ARGS=-Xmx6G
          git config --global --add safe.directory $PWD
          git fetch origin ${{ github.base_ref }}
          CHANGES=($(git diff --name-only origin/dev | grep -E "src/.*(omn|owl)"))
          for c in ${CHANGES[@]}; do
            # Drop term tracker annotations
            robot remove --select complement --drop-axiom-annotations https://openenergyplatform.org/ontology/oeo/OEO_00020426 --input $c \
                  remove --term https://openenergyplatform.org/ontology/oeo/OEO_00020426 --output $c && \
            robot remove --select complement --drop-axiom-annotations https://openenergyplatform.org/ontology/oeo/OEO_00020426 --input dev/$c \
                  remove --term https://openenergyplatform.org/ontology/oeo/OEO_00020426 --output dev/$c && \
            robot diff --labels True --left ./dev/$c --right $c -f markdown > $c.changes.md || true # Get diff and ignore error
          done
      - name: Format comment
        # Create a comment where the diffs can be folded, so it does not take so much space
        # Finds all previously created .changes.md files and embeds them in collapsible sections
        run: |
            printf "# Changed axioms per ontology\n\n _**Note**: Changes in term tracker annotations are not displayed_\n\n" > comment.md
            find . -name "*.changes.md"
            find . -name "*.changes.md" -exec bash -c \
              'printf "<details><summary>%s: %s changes</summary>\n\n%s\n</details>\n\n" $(basename $0 ".changes.md") $(grep -E "^- \[" $0 | wc -l) "$(cat $0)"' {} \; >> comment.md
            realpath comment.md
            cat comment.md
#            printf "# Errors reported\n\n" >> comment.md;
#            printf "\`\`\`\n" >> comment.md;
#            cat errors.tsv >> comment.md;
#            printf "\n\`\`\`\n" >> comment.md;
      - name: Post comment in the PR
        # Note how the path to comment.md needs ../../ in the path.
        # Because we provide an identifier, the comment will be overwritten every time the action
        # is run. I guess one could have an identifier that contains the commit_id so that a new
        # comment is posted every time a change is made in the branch that is being merged.
        env:
            GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
        uses: NejcZdovc/comment-pr@v1.1.1
        with:
          file: "../../comment.md"
          identifier: "DIFF_COMMENT"