Adding MetaCyc def xrefs as db xrefs. #28523 #6981
Workflow file for this run
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| name: Inference diff | |
| 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: | |
| classify_pr: | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:${{ vars.ODK_VERSION }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Classify ontology | |
| run: cd src/ontology; make -j 4 ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' reasoned.owl | |
| - name: Upload PR reasoned.owl | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: reasoned-pr.owl | |
| path: src/ontology/reasoned.owl | |
| retention-days: 1 | |
| classify_master: | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:${{ vars.ODK_VERSION }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: master | |
| - name: Classify ontology | |
| run: cd src/ontology; make -j 4 ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' reasoned.owl | |
| - name: Upload master reasoned.owl | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: reasoned-master.owl | |
| path: src/ontology/reasoned.owl | |
| retention-days: 1 | |
| diff_classification: | |
| needs: | |
| - classify_pr | |
| - classify_master | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:${{ vars.ODK_VERSION }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Download master classification | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: reasoned-master.owl | |
| path: reasoned-master.owl | |
| - name: Download PR classification | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: reasoned-pr.owl | |
| path: reasoned-pr.owl | |
| - name: Diff classification | |
| run: export ROBOT_JAVA_ARGS=-Xmx6G; cd src/ontology; robot diff --left ../../reasoned-master.owl/reasoned.owl --left-catalog catalog-v001.xml --right ../../reasoned-pr.owl/reasoned.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md | |
| - name: Upload diff | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: classification-diff.md | |
| path: src/ontology/classification-diff.md | |
| post_comment: | |
| needs: diff_classification | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Download diff | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: classification-diff.md | |
| path: classification-diff.md | |
| - name: Prepare comment | |
| run: "echo \"Here's a diff of how these changes impact the classified ontology: \n\" >comment.md; cat classification-diff.md/classification-diff.md >>comment.md" | |
| - name: Post comment | |
| uses: NejcZdovc/comment-pr@v1.1.1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| file: "../../comment.md" | |