Revisit how the Allen ontologies are imported into composite-metazoan
#1552
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| name: 'Create ROBOT diffs on Pull requests' | |
| on: | |
| issue_comment: | |
| types: [created] | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| diff-reports: | |
| if: ${{ github.event.issue.pull_request }} | |
| runs-on: macos-latest | |
| permissions: | |
| contents: read | |
| pull-requests: read | |
| steps: | |
| - uses: khan/pull-request-comment-trigger@v1.1.0 | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| - uses: better0fdead/actions-setup-docker@better0fdead/increase-timeout | |
| if: steps.check.outputs.triggered == 'true' | |
| - run: | | |
| set -x | |
| docker version | |
| if: steps.check.outputs.triggered == 'true' | |
| - name: Install ODK | |
| run: docker pull obolibrary/odklite | |
| if: steps.check.outputs.triggered == 'true' | |
| # Checks-out current branch | |
| - uses: xt0rted/pull-request-comment-branch@v2.0.0 | |
| id: comment-branch | |
| - uses: actions/checkout@v3 | |
| if: steps.check.outputs.triggered == 'true' | |
| with: | |
| ref: ${{ steps.comment-branch.outputs.head_ref }} | |
| # Checks-out master branch under "master" directory | |
| - uses: actions/checkout@v3 | |
| if: steps.check.outputs.triggered == 'true' | |
| with: | |
| ref: master | |
| path: master | |
| - name: Diff classification | |
| if: steps.check.outputs.triggered == 'true' | |
| run: | | |
| cd src/ontology | |
| docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite robot diff --left ../../master/src/ontology/uberon-edit.obo --left-catalog ../../master/src/ontology/catalog-v001.xml --right uberon-edit.obo --right-catalog catalog-v001.xml -f markdown -o edit-diff.md | |
| - name: Upload diff | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: edit-diff.md | |
| path: src/ontology/edit-diff.md | |
| - name: Make step for branch | |
| if: steps.check.outputs.triggered == 'true' | |
| run: cd src/ontology && mkdir -p tmp reports mirror && docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite make BRI=false MIR=false PAT=false IMP=false uberon-simple.owl > TESTLOG.log | |
| - name: Make step for master | |
| if: steps.check.outputs.triggered == 'true' | |
| run: cd master/src/ontology && mkdir -p tmp reports mirror && docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite make BRI=false MIR=false PAT=false IMP=false uberon-simple.owl > TESTLOG.log | |
| - name: Diff report | |
| if: steps.check.outputs.triggered == 'true' | |
| run: | | |
| cd src/ontology | |
| docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite robot diff --left ../../master/src/ontology/uberon-simple.owl --left-catalog catalog-v001.xml --right uberon-simple.owl --right-catalog ../../master/src/ontology/catalog-v001.xml -f markdown -o simple-report.md | |
| - name: Upload diff | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: simple-report.md | |
| path: src/ontology/simple-report.md | |
| post_comment: | |
| needs: [diff-reports] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: khan/pull-request-comment-trigger@v1.1.0 | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| - uses: actions/checkout@v3 | |
| if: steps.check.outputs.triggered == 'true' | |
| - name: Download reasoned diff | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: simple-report.md | |
| - name: Prepare reasoned comment | |
| run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology (on -simple file): </summary> \n\" > comment.md; cat simple-report.md >> comment.md" | |
| if: steps.check.outputs.triggered == 'true' | |
| - name: Post reasoned comment | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: NejcZdovc/comment-pr@v2.0.0 | |
| with: | |
| file: "../../comment.md" | |
| identifier: "REASONED" | |
| github_token: ${{secrets.GITHUB_TOKEN}} | |
| - uses: actions/checkout@v3 | |
| if: steps.check.outputs.triggered == 'true' | |
| - name: Download edit diff | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: 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-comment.md" | |
| if: steps.check.outputs.triggered == 'true' | |
| - name: Post comment | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: NejcZdovc/comment-pr@v2.0.0 | |
| with: | |
| file: "../../edit-comment.md" | |
| identifier: "UNREASONED" | |
| github_token: ${{secrets.GITHUB_TOKEN}} | |