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Create ROBOT diffs on Pull requests

Make the Allen Ontologies more discoverable #1696

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Make the Allen Ontologies more discoverable

Make the Allen Ontologies more discoverable #1696

Workflow file for this run

.github/workflows/diff.yml at e22380d
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: ${{ github.event.issue.pull_request }}
runs-on: ubuntu-latest
permissions:
contents: read
pull-requests: read
steps:
- uses: khan/pull-request-comment-trigger@v1.1.0
id: check
with:
trigger: '#gogoeditdiff'
env:
GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
# 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: ${{ github.event.issue.pull_request }}
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5
steps:
- uses: khan/pull-request-comment-trigger@v1.1.0
id: check
with:
trigger: '#gogoeditdiff'
env:
GITHUB_TOKEN: '${{ 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: ${{ github.event.issue.pull_request }}
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5
steps:
- uses: khan/pull-request-comment-trigger@v1.1.0
id: check
with:
trigger: '#gogoeditdiff'
env:
GITHUB_TOKEN: '${{ 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: ${{ github.event.issue.pull_request }}
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5
steps:
- uses: khan/pull-request-comment-trigger@v1.1.0
id: check
with:
trigger: '#gogoeditdiff'
env:
GITHUB_TOKEN: '${{ 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
steps:
- uses: khan/pull-request-comment-trigger@v1.1.0
id: check
with:
trigger: '#gogoeditdiff'
env:
GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
- uses: actions/checkout@v4
if: steps.check.outputs.triggered == 'true'
- name: Download classified ontology main branch
if: steps.check.outputs.triggered == 'true'
uses: actions/download-artifact@v4
with:
name: uberon-base-main.owl
path: src/ontology/uberon-base-main.owl
- name: Download classified ontology in PR branch
if: steps.check.outputs.triggered == 'true'
uses: actions/download-artifact@v4
with:
name: uberon-base-pr.owl
path: src/ontology/uberon-base-pr.owl
- name: Diff classification
if: steps.check.outputs.triggered == 'true'
run: export ROBOT_JAVA_ARGS='-Xmx9G'; cd src/ontology; robot diff --labels True --left uberon-base-main.owl/uberon-base.owl --left-catalog catalog-v001.xml --right uberon-base-pr.owl/uberon-base.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md
- name: Upload diff
if: steps.check.outputs.triggered == 'true'
uses: actions/upload-artifact@v4
with:
name: classification-diff.md
path: src/ontology/classification-diff.md
post_comment:
needs: [edit_file, diff_classification]
runs-on: ubuntu-latest
steps:
- uses: khan/pull-request-comment-trigger@v1.1.0
id: check
with:
trigger: '#gogoeditdiff'
env:
GITHUB_TOKEN: '${{ 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/comment-pr@v2.0.0
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/comment-pr@v2.0.0
with:
file: "../../edit-comment.md"
identifier: "UNREASONED"
github_token: ${{secrets.GITHUB_TOKEN}}