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diff.yml
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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"