Documenting differences in ontology files (attempt 2) #1
Workflow file for this run
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| name: 'Create OAK diffs on Pull requests' | |
| on: | |
| # Triggers the workflow on pull request events for the master branch | |
| 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: | |
| edit_file: | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.5 | |
| steps: | |
| # Checks-out main branch under "main" directory | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: master | |
| path: master | |
| # - name: Install oaklib | |
| # run: pip install oaklib | |
| # - name: Diff classification | |
| # run: | | |
| # export ROBOT_JAVA_ARGS=-Xmx6G | |
| # runoak -i simpleobo:tmp/hp-edit-master.obo diff -X simpleobo:tmp/hp-edit-pr.obo -o reports/difference_main-branch_base.md --output-type md | |
| # - name: Upload diff | |
| # uses: actions/upload-artifact@v4 | |
| # with: | |
| # name: difference_main-branch_base.md | |
| # path: src/ontology/reports/difference_main-branch_base.md | |
| classify_branch: | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.5 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Classify ontology | |
| run: | | |
| cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE hp-edit.owl && make tmp/hp-edit.obo | |
| - name: Upload PR hp-edit.obo | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: hp-edit-pr.obo | |
| path: src/ontology/tmp/hp-edit.obo | |
| retention-days: 1 | |
| classify_main: | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.5 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| ref: master | |
| - name: Classify ontology | |
| run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE hp-edit.owl && make tmp/hp-edit.obo | |
| - name: Upload master hp-edit.obo | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: hp-edit-master.obo | |
| path: src/ontology/tmp/hp-edit.obo | |
| retention-days: 1 | |
| diff_classification: | |
| needs: | |
| - classify_branch | |
| - classify_main | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.5 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Download master classification | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: hp-edit-master.obo | |
| path: src/ontology/tmp/hp-edit-master.obo | |
| - name: Download PR classification | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: hp-edit-pr.obo | |
| path: src/ontology/tmp/hp-edit-pr.obo | |
| - name: Diff classification | |
| run: | | |
| export ROBOT_JAVA_ARGS=-Xmx6G; cd src/ontology; | |
| runoak -i simpleobo:tmp/hp-edit-master.obo diff -X simpleobo:tmp/hp-edit-pr.obo -o reports/difference_main-branch_base.md --output-type md | |
| - name: Upload diff | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: difference_main-branch_base.md | |
| path: src/ontology/reports/difference_main-branch_base.md | |
| post_comment: | |
| needs: [diff_classification, edit_file] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Download reasoned diff | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: difference_main-branch_base.md | |
| path: src/ontology/reports/difference_main-branch_base.md | |
| - name: Prepare reasoned comment | |
| run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology: </summary> \n\" >comment.md; cat difference_main-branch_base.md/difference_main-branch_base.md >>comment.md" | |
| - name: Post reasoned comment | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| uses: NejcZdovc/[email protected] | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: "../../comment.md" | |
| identifier: "REASONED" | |
| - uses: actions/checkout@v4 | |
| - name: Download edit diff | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: edit-diff.md | |
| path: edit-diff.md | |
| - name: Prepare edit file comment | |
| run: "echo \"<details>\n <summary> Here's a diff of your edit file (unreasoned) </summary> \n\" >edit-comment.md; cat edit-diff.md/edit-diff.md >>edit-comment.md" | |
| - name: Post comment | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| uses: NejcZdovc/[email protected] | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: "../../edit-comment.md" | |
| identifier: "UNREASONED" |