Build the “composite“ life stages ontology directly in Uberon #1800
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| name: 'Create ROBOT diffs on Pull requests' | |
| on: | |
| issue_comment: | |
| types: [created] | |
| env: | |
| DEFAULT_BRANCH: ${{ github.event.repository.default_branch }} | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| branch_status: | |
| if: ${{ github.event.issue.pull_request && github.event.issue.state == 'open' }} | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| pull-requests: read | |
| steps: | |
| - uses: khan/[email protected] | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| # Checks-out current branch | |
| - uses: xt0rted/pull-request-comment-branch@v2 | |
| id: comment-branch | |
| - uses: actions/checkout@v4 | |
| if: steps.check.outputs.triggered == 'true' | |
| with: | |
| ref: ${{ steps.comment-branch.outputs.head_ref }} | |
| # Checks-out master branch under "master" directory | |
| - uses: actions/checkout@v4 | |
| if: steps.check.outputs.triggered == 'true' | |
| with: | |
| ref: ${{ steps.comment-branch.outputs.head_ref }} | |
| fetch-depth: 0 | |
| - name: Check current branch status | |
| if: steps.check.outputs.triggered == 'true' | |
| id: info | |
| run: | | |
| echo "status=$(git rev-list --left-right --count origin/$DEFAULT_BRANCH...origin/`git branch --show-current` | awk '{print $1}')" | |
| echo "status=$(git rev-list --left-right --count origin/$DEFAULT_BRANCH...origin/`git branch --show-current` | awk '{print $1}')" >> $GITHUB_OUTPUT | |
| - name: Warn users with a comment | |
| if: steps.info.outputs.status >= 1 | |
| run: echo "Your branch is ${{ steps.info.outputs.status }} commit/s behind, please update your branch." > warncomment.md | |
| - name: Post comment | |
| if: steps.info.outputs.status >= 1 && steps.check.outputs.triggered == 'true' | |
| env: | |
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} | |
| uses: NejcZdovc/comment-pr@v2 | |
| with: | |
| github_token: ${{secrets.GITHUB_TOKEN}} | |
| file: "../../warncomment.md" | |
| - name: Fail step if branch is behind | |
| if: steps.info.outputs.status >= 1 && steps.check.outputs.triggered == 'true' | |
| run: | | |
| echo "Your branch is ${{ steps.info.outputs.status }} commit/s behind, please update your branch." | |
| exit 1 | |
| edit_file: | |
| needs: [branch_status] | |
| if: ${{ github.event.issue.pull_request }} | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.5.3 | |
| steps: | |
| - uses: khan/[email protected] | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| - uses: xt0rted/pull-request-comment-branch@v2 | |
| id: comment-branch | |
| - uses: actions/checkout@v4 | |
| if: steps.check.outputs.triggered == 'true' | |
| with: | |
| ref: ${{ steps.comment-branch.outputs.head_ref }} | |
| path: branch | |
| - uses: actions/checkout@v4 | |
| if: steps.check.outputs.triggered == 'true' | |
| with: | |
| ref: master | |
| path: master | |
| - name: Diff classification | |
| if: steps.check.outputs.triggered == 'true' | |
| run: export ROBOT_JAVA_ARGS='-Xmx9G'; robot diff --labels True --left master/src/ontology/uberon-edit.obo --left-catalog master/src/ontology/catalog-v001.xml --right branch/src/ontology/uberon-edit.obo --right-catalog branch/src/ontology/catalog-v001.xml -f markdown -o edit-diff.md | |
| - name: Upload diff | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: edit-diff.md | |
| path: edit-diff.md | |
| classify_branch: | |
| needs: [branch_status] | |
| if: ${{ github.event.issue.pull_request }} | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.5.3 | |
| steps: | |
| - uses: khan/[email protected] | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| - uses: xt0rted/pull-request-comment-branch@v2 | |
| id: comment-branch | |
| - uses: actions/checkout@v4 | |
| if: steps.check.outputs.triggered == 'true' | |
| with: | |
| ref: ${{ steps.comment-branch.outputs.head_ref }} | |
| - name: Classify ontology PR branch | |
| if: steps.check.outputs.triggered == 'true' | |
| run: export ROBOT_JAVA_ARGS='-Xmx9G'; cd src/ontology; make BRI=false MIR=false PAT=false IMP=false COMP=false uberon-base.owl > TESTLOG.log | |
| - name: Upload classified ontology in PR branch | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: uberon-base-pr.owl | |
| path: src/ontology/uberon-base.owl | |
| retention-days: 1 | |
| classify_main: | |
| needs: [branch_status] | |
| if: ${{ github.event.issue.pull_request }} | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.5.3 | |
| steps: | |
| - uses: khan/[email protected] | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| - uses: actions/checkout@v4 | |
| if: steps.check.outputs.triggered == 'true' | |
| with: | |
| ref: master | |
| - name: Classify ontology main branch | |
| if: steps.check.outputs.triggered == 'true' | |
| run: export ROBOT_JAVA_ARGS='-Xmx9G'; cd src/ontology; make BRI=false MIR=false PAT=false IMP=false COMP=false uberon-base.owl > TESTLOG.log | |
| - name: Upload classified ontology main branch | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: uberon-base-main.owl | |
| path: src/ontology/uberon-base.owl | |
| retention-days: 1 | |
| diff_classification: | |
| needs: [classify_branch, classify_main] | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.5.3 | |
| steps: | |
| - uses: khan/[email protected] | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| - uses: actions/checkout@v4 | |
| if: steps.check.outputs.triggered == 'true' | |
| - name: Download classified ontology main branch | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: uberon-base-main.owl | |
| path: src/ontology/uberon-base-main.owl | |
| - name: Download classified ontology in PR branch | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: uberon-base-pr.owl | |
| path: src/ontology/uberon-base-pr.owl | |
| - name: Diff classification | |
| if: steps.check.outputs.triggered == 'true' | |
| run: export ROBOT_JAVA_ARGS='-Xmx9G'; cd src/ontology; robot diff --labels True --left uberon-base-main.owl/uberon-base.owl --left-catalog catalog-v001.xml --right uberon-base-pr.owl/uberon-base.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md | |
| - name: Upload diff | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: classification-diff.md | |
| path: src/ontology/classification-diff.md | |
| post_comment: | |
| needs: [edit_file, diff_classification] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: khan/[email protected] | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| - uses: actions/checkout@v4 | |
| if: steps.check.outputs.triggered == 'true' | |
| - name: Download reasoned diff | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: classification-diff.md | |
| - name: Prepare reasoned comment | |
| if: steps.check.outputs.triggered == 'true' | |
| run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology (on -base file): </summary> \n\" > comment.md; cat classification-diff.md >> comment.md" | |
| - name: Post reasoned comment | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: NejcZdovc/[email protected] | |
| with: | |
| file: "../../comment.md" | |
| identifier: "REASONED" | |
| github_token: ${{secrets.GITHUB_TOKEN}} | |
| - uses: actions/checkout@v4 | |
| if: steps.check.outputs.triggered == 'true' | |
| - name: Download edit diff | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: edit-diff.md | |
| - name: Prepare edit file comment | |
| if: steps.check.outputs.triggered == 'true' | |
| 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" | |
| - name: Post comment | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: NejcZdovc/[email protected] | |
| with: | |
| file: "../../edit-comment.md" | |
| identifier: "UNREASONED" | |
| github_token: ${{secrets.GITHUB_TOKEN}} | |