copy-pasted jinja and edited as per Nico

obophenotype · Mar 21, 2024 · c3ea1fa · c3ea1fa
1 parent 448b5d5
commit c3ea1fa
Show file tree

Hide file tree

Showing 2 changed files with 130 additions and 2 deletions.
diff --git a/.github/workflows/ontology_diff.yml b/.github/workflows/ontology_diff.yml
@@ -2,8 +2,8 @@ name: Post Markdown Comment on Pull Request
 
 on:
   workflow_dispatch:
-  pull_request:
-    types: [opened, synchronize]
+  # pull_request:
+  #   types: [opened, synchronize]
 
 jobs:
   post-comment:

diff --git a/.github/workflows/ontology_diff_2.yml b/.github/workflows/ontology_diff_2.yml
@@ -0,0 +1,128 @@
+name: 'Create OAK 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:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  edit_file:
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.5
+    steps:
+      # Checks-out main branch under "main" directory
+      - uses: actions/checkout@v4
+        with:
+          ref: master
+          path: master
+
+    #   - name: Install oaklib
+    #     run: pip install oaklib
+
+    #   - name: Diff classification
+    #     run: |
+    #         export ROBOT_JAVA_ARGS=-Xmx6G
+    #         runoak -i simpleobo:tmp/hp-edit-master.obo diff -X simpleobo:tmp/hp-edit-pr.obo -o reports/difference_main-branch_base.md --output-type md 
+
+    #   - name: Upload diff
+    #     uses: actions/upload-artifact@v4
+    #     with:
+    #       name: difference_main-branch_base.md
+    #       path: src/ontology/reports/difference_main-branch_base.md
+  classify_branch:
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.5
+    steps:
+      - uses: actions/checkout@v4
+      - name: Classify ontology
+        run: |
+            cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE hp-edit.owl && make tmp/hp-edit.obo
+            
+      - name: Upload PR hp-edit.obo
+        uses: actions/upload-artifact@v4
+        with:
+          name: hp-edit-pr.obo
+          path: src/ontology/tmp/hp-edit.obo
+          retention-days: 1
+  classify_main:
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.5
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: master
+      - name: Classify ontology
+        run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE hp-edit.owl && make tmp/hp-edit.obo
+      - name: Upload master hp-edit.obo
+        uses: actions/upload-artifact@v4
+        with:
+          name: hp-edit-master.obo
+          path: src/ontology/tmp/hp-edit.obo
+          retention-days: 1
+  diff_classification:
+    needs:
+      - classify_branch
+      - classify_main
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.5
+    steps:
+      - uses: actions/checkout@v4
+      - name: Download master classification
+        uses: actions/download-artifact@v4
+        with:
+          name: hp-edit-master.obo
+          path: src/ontology/tmp/hp-edit-master.obo
+      - name: Download PR classification
+        uses: actions/download-artifact@v4
+        with:
+          name: hp-edit-pr.obo
+          path: src/ontology/tmp/hp-edit-pr.obo
+      - name: Diff classification
+        run: | 
+            export ROBOT_JAVA_ARGS=-Xmx6G; cd src/ontology;
+            runoak -i simpleobo:tmp/hp-edit-master.obo diff -X simpleobo:tmp/hp-edit-pr.obo -o reports/difference_main-branch_base.md --output-type md 
+      - name: Upload diff
+        uses: actions/upload-artifact@v4
+        with:
+          name: difference_main-branch_base.md
+          path: src/ontology/reports/difference_main-branch_base.md
+  post_comment:
+    needs: [diff_classification, edit_file]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Download reasoned diff
+        uses: actions/download-artifact@v4
+        with:
+          name: difference_main-branch_base.md
+          path: src/ontology/reports/difference_main-branch_base.md
+      - name: Prepare reasoned comment
+        run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology: </summary> \n\" >comment.md; cat difference_main-branch_base.md/difference_main-branch_base.md >>comment.md"
+      - name: Post reasoned comment
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: NejcZdovc/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          file: "../../comment.md"
+          identifier: "REASONED"
+      - uses: actions/checkout@v4
+      - name: Download edit diff
+        uses: actions/download-artifact@v4
+        with:
+          name: edit-diff.md
+          path: edit-diff.md
+      - name: Prepare edit file comment
+        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
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: NejcZdovc/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          file: "../../edit-comment.md"
+          identifier: "UNREASONED"