Addition of marker genes to 52 cell types matched from the Human Lung Cell Atlas #1772
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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: ${{ github.event.issue.pull_request }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: khan/[email protected] | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| - uses: xt0rted/pull-request-comment-branch@v1 | |
| id: comment-branch | |
| # Checks-out current branch | |
| - uses: actions/checkout@v3 | |
| 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/[email protected] | |
| with: | |
| file: "../../warncomment.md" | |
| - name: fail | |
| 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: ${{ github.event.issue.pull_request }} | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odklite:v1.3.0 | |
| steps: | |
| - uses: khan/[email protected] | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| - uses: xt0rted/pull-request-comment-branch@v1 | |
| id: comment-branch | |
| - uses: actions/checkout@v3 | |
| if: steps.check.outputs.triggered == 'true' | |
| with: | |
| ref: ${{ steps.comment-branch.outputs.head_ref }} | |
| path: branch | |
| # Checks-out main branch under "main" 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: export ROBOT_JAVA_ARGS=-Xmx6G; robot diff --labels True --left master/src/ontology/cl-edit.owl --left-catalog master/src/ontology/catalog-v001.xml --right branch/src/ontology/cl-edit.owl --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@v2 | |
| with: | |
| name: edit-diff.md | |
| path: edit-diff.md | |
| classify_branch: | |
| needs: [branch_status] | |
| if: ${{ github.event.issue.pull_request }} | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odklite:v1.3.0 | |
| steps: | |
| - uses: khan/[email protected] | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| - uses: xt0rted/pull-request-comment-branch@v1 | |
| id: comment-branch | |
| - uses: actions/checkout@v3 | |
| if: steps.check.outputs.triggered == 'true' | |
| with: | |
| ref: ${{ steps.comment-branch.outputs.head_ref }} | |
| - name: Classify ontology | |
| if: steps.check.outputs.triggered == 'true' | |
| run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE cl-simple.owl | |
| - name: Upload PR cl-simple.owl | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: cl-simple-pr.owl | |
| path: src/ontology/cl-simple.owl | |
| retention-days: 1 | |
| classify_main: | |
| needs: [branch_status] | |
| if: ${{ github.event.issue.pull_request }} | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odklite:v1.3.0 | |
| steps: | |
| - uses: khan/[email protected] | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| - uses: actions/checkout@v3 | |
| if: steps.check.outputs.triggered == 'true' | |
| with: | |
| ref: master | |
| - name: Classify ontology | |
| if: steps.check.outputs.triggered == 'true' | |
| run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE cl-simple.owl | |
| - name: Upload master cl-simple.owl | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: cl-simple-master.owl | |
| path: src/ontology/cl-simple.owl | |
| retention-days: 1 | |
| diff_classification: | |
| needs: [classify_branch, classify_main] | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odklite:v1.3.0 | |
| steps: | |
| - uses: khan/[email protected] | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| - uses: actions/checkout@v3 | |
| if: steps.check.outputs.triggered == 'true' | |
| - name: Download master classification | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: cl-simple-master.owl | |
| path: src/ontology/cl-simple-master.owl | |
| - name: Download PR classification | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: cl-simple-pr.owl | |
| path: src/ontology/cl-simple-pr.owl | |
| - name: Diff classification | |
| if: steps.check.outputs.triggered == 'true' | |
| run: export ROBOT_JAVA_ARGS=-Xmx6G; cd src/ontology; robot diff --labels True --left cl-simple-master.owl/cl-simple.owl --left-catalog catalog-v001.xml --right cl-simple-pr.owl/cl-simple.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md | |
| - name: Upload diff | |
| if: steps.check.outputs.triggered == 'true' | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: classification-diff.md | |
| path: src/ontology/classification-diff.md | |
| post_comment: | |
| needs: [diff_classification, edit_file] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: khan/[email protected] | |
| id: check | |
| with: | |
| trigger: '#gogoeditdiff' | |
| env: | |
| GITHUB_TOKEN: '${{ 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@v2 | |
| with: | |
| name: classification-diff.md | |
| path: 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 -simple file): </summary> \n\" >comment.md; cat classification-diff.md/classification-diff.md >>comment.md" | |
| - name: Post reasoned comment | |
| if: steps.check.outputs.triggered == 'true' | |
| env: | |
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} | |
| uses: NejcZdovc/[email protected] | |
| with: | |
| file: "../../comment.md" | |
| identifier: "REASONED" | |
| - 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 | |
| path: 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-diff.md >>edit-comment.md" | |
| - name: Post comment | |
| if: steps.check.outputs.triggered == 'true' | |
| env: | |
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} | |
| uses: NejcZdovc/[email protected] | |
| with: | |
| file: "../../edit-comment.md" | |
| identifier: "UNREASONED" |