closes #4549; closes #4441; closes #4621 #167
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| name: 'Create ROBOT 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: | |
| jobs: | |
| create_diff_file: | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odklite:v1.4 | |
| steps: | |
| # Checks-out the branch being merged into master in the root directory | |
| # The ontology obo file path will be: src/ontology/fypo-edit.owl | |
| - uses: actions/checkout@v2 | |
| # Checks-out the master branch in a subfolder called master | |
| # The ontology obo file path will be: master/src/ontology/fypo-edit.owl | |
| - uses: actions/checkout@v2 | |
| with: | |
| ref: master | |
| path: master | |
| - name: Run robot diff | |
| # -Xmx6G extension is to set 6gb of memory for java virtual machine | |
| # The second line produces the difference in the edit files only | |
| # The third line produces the difference after reasoner. I still have to figure what the best file for this is. | |
| # robot diff --labels True --left master/fypo.owl --right fypo.owl -f markdown -o reasoned-diff.md; | |
| # To edit the second and third line for another ontology, test the robot code locally, and edit accordingly. | |
| # For example, FYPO does not need an extra --right-catalog but other ontologies may need it | |
| # See https://github.com/obophenotype/cell-ontology/blob/master/.github/workflows/diff.yml | |
| run: > | |
| export ROBOT_JAVA_ARGS=-Xmx6G; | |
| robot diff --labels True --left master/src/ontology/fypo-edit.owl --right src/ontology/fypo-edit.owl -f markdown -o edit-diff.md; | |
| robot --catalog src/ontology/catalog-v001.xml report -i src/ontology/fypo-edit.owl -l true --fail-on None --base-iri http://purl.obolibrary.org/obo/FYPO_ --base-iri http://purl.obolibrary.org/obo/fypo --print 5 -o errors.tsv; | |
| - name: Format comment | |
| # Create a comment where the diffs can be folded, so it does not take so much space | |
| # add this eventually: cat reasoned-diff.md >> comment.md; | |
| run: > | |
| printf "# Changes added to the edit file this PR\n" > comment.md; | |
| printf "<details>\n<summary>Click to expand</summary>\n\n" >> comment.md; | |
| cat edit-diff.md >> comment.md; | |
| printf "\n</details\n\n>" >> comment.md; | |
| printf "# Changes to ontology after reasoner runs\n" >> comment.md; | |
| printf "<details>\n<summary>Click to expand</summary>\n\n" >> comment.md; | |
| printf "\nComing soon\n>" >> comment.md; | |
| printf "\n</details>\n\n" >> comment.md; | |
| printf "# Errors reported\n\n" >> comment.md; | |
| printf "\`\`\`\n" >> comment.md; | |
| cat errors.tsv >> comment.md; | |
| printf "\n\`\`\`\n" >> comment.md; | |
| - name: Post comment in the PR | |
| # Note how the path to comment.md needs ../../ in the path. | |
| # Because we provide an identifier, the comment will be overwritten every time the action | |
| # is run. I guess one could have an identifier that contains the commit_id so that a new | |
| # comment is posted every time a change is made in the branch that is being merged. | |
| env: | |
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} | |
| uses: NejcZdovc/[email protected] | |
| with: | |
| file: "../../comment.md" | |
| identifier: "DIFF_COMMENT" |