Merge branch 'master' into issue-3471

.github/CODEOWNERS

@@ -1,10 +1,9 @@
 # Uberon code owners (Guardians of the main branch)
 # GitHub documentation about CODEOWNERS file - https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
 
-*       @anitacaron
 *.yaml @matentzn
 *Makefile @gouttegd
-*uberon.Makefile @gouttegd @matentzn @anitacaron
+*uberon.Makefile @gouttegd @matentzn
 
 
 #docs/*  [email protected] 

.github/workflows/auto-pr-ontobot.yml

@@ -6,7 +6,30 @@ on:
     types: [ opened, edited ]
 
 jobs:
+  check:
+    runs-on: ubuntu-latest
+    outputs:
+      phraseExists: ${{ steps.check-body.outputs.result }}
+    steps:
+      - name: Check if issue body contains 'Hey ontobot'
+        id: check-body
+        uses: actions/github-script@v6
+        with:
+          script: |
+            const issue = await github.rest.issues.get({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number
+            });
+            if (!issue.data.body) {
+              console.log('Issue body is empty or null');
+              return false;
+            }
+            return issue.data.body.toLowerCase().includes('hey ontobot');
+  
   build:
+    needs: check
+    if: needs.check.outputs.phraseExists == 'true'
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -24,7 +47,7 @@ jobs:
         id: gh-script-issue
         uses: actions/github-script@v6
         with:
-          # github-token: ${{ secrets.GH_TOKEN }}
+          github-token: ${{ secrets.ONTOBOT_TOKEN }}
           script: |
             const issue_number = context.issue.number
             const repo = context.repo.owner+"/"+context.repo.repo
@@ -34,7 +57,7 @@ jobs:
         id: gh-script-repo
         uses: actions/github-script@v6
         with:
-          # github-token: ${{ secrets.GH_TOKEN }}
+          github-token: ${{ secrets.ONTOBOT_TOKEN }}
           script: |
             const repo = context.repo.owner+"/"+context.repo.repo
             return repo
@@ -55,7 +78,7 @@ jobs:
           ochange process-issue ${{ env.resource }} \
           -r ${{ steps.gh-script-repo.outputs.result }} \
           -n ${{ steps.gh-script-issue.outputs.result }} \
-          -g ${{ secrets.GH_TOKEN }} \
+          -g ${{ secrets.ONTOBOT_TOKEN }} \
           -p UBERON
 
       - name: Create Pull Request
@@ -70,4 +93,4 @@ jobs:
           committer: ${{ env.ISSUE_CREATOR }} <${{ env.ISSUE_CREATOR }}@users.noreply.github.com>
           base: ${{ github.head_ref }}
           branch: ${{ env.branch-name }}
-          # token: ${{ secrets.GH_TOKEN }}
+          token: ${{ secrets.ONTOBOT_TOKEN }}

.github/workflows/diff.yml

@@ -4,12 +4,14 @@ 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:
-  diff-reports:
-    if: ${{ github.event.issue.pull_request }}
-    runs-on: macos-latest
+  branch_status:
+    if: ${{ github.event.issue.pull_request && github.event.issue.state == 'open' }}
+    runs-on: ubuntu-latest
     permissions:
       contents: read
       pull-requests: read
@@ -20,58 +22,164 @@ jobs:
           trigger: '#gogoeditdiff'
         env:
           GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
-      - uses: docker-practice/actions-setup-docker@master
+      # Checks-out current branch
+      - uses: xt0rted/pull-request-comment-branch@v2
+        id: comment-branch
+      - uses: actions/checkout@v4
         if: steps.check.outputs.triggered == 'true'
-      - run: |
-          set -x
-          docker version
+        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'
-      - name: Install ODK
-        run: docker pull obolibrary/odklite
+        with:
+          ref: ${{ steps.comment-branch.outputs.head_ref }}
+          fetch-depth: 0
+      - name: Check current branch status
         if: steps.check.outputs.triggered == 'true'
-      # Checks-out current branch
-      - uses: xt0rted/pull-request-comment-branch@v1
+        id: info
+        run: |
+          echo "status=$(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: ${{ github.event.issue.pull_request }}
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.5.3
+    steps:
+      - uses: khan/[email protected]
+        id: check
+        with:
+          trigger: '#gogoeditdiff'
+        env:
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
+      - uses: xt0rted/pull-request-comment-branch@v2
         id: comment-branch
-      - uses: actions/checkout@v3
+      - 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@v3
+          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: |
-          cd src/ontology
-          docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite robot diff --left ../../master/src/ontology/uberon-edit.obo --left-catalog ../../master/src/ontology/catalog-v001.xml --right uberon-edit.obo --right-catalog catalog-v001.xml -f markdown -o edit-diff.md
+        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@v3
+        uses: actions/upload-artifact@v4
         with:
           name: edit-diff.md
-          path: src/ontology/edit-diff.md
-      - name: Make step for branch
+          path: edit-diff.md
+  classify_branch:
+    needs: [branch_status]
+    if: ${{ github.event.issue.pull_request }}
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.5.3
+    steps:
+      - uses: khan/[email protected]
+        id: check
+        with:
+          trigger: '#gogoeditdiff'
+        env:
+          GITHUB_TOKEN: '${{ 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: cd src/ontology && mkdir -p tmp reports mirror && docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite make BRI=false MIR=false PAT=false IMP=false uberon-simple.owl > TESTLOG.log
-      - name: Make step for master
+        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'
-        run: cd master/src/ontology && mkdir -p tmp reports mirror && docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite make BRI=false MIR=false PAT=false IMP=false uberon-simple.owl > TESTLOG.log
-      - name: Diff report
+        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: ${{ github.event.issue.pull_request }}
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.5.3
+    steps:
+      - uses: khan/[email protected]
+        id: check
+        with:
+          trigger: '#gogoeditdiff'
+        env:
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
+      - uses: actions/checkout@v4
         if: steps.check.outputs.triggered == 'true'
-        run: |
-          cd src/ontology
-          docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite robot diff --left ../../master/src/ontology/uberon-simple.owl --left-catalog catalog-v001.xml --right uberon-simple.owl --right-catalog ../../master/src/ontology/catalog-v001.xml -f markdown -o simple-report.md
+        with:
+          ref: master
+      - name: Classify ontology main branch
+        if: steps.check.outputs.triggered == 'true'
+        run: export ROBOT_JAVA_ARGS='-Xmx9G'; cd src/ontology; make BRI=false MIR=false PAT=false IMP=false COMP=false uberon-base.owl > TESTLOG.log
+      - name: Upload classified ontology main branch
+        if: steps.check.outputs.triggered == 'true'
+        uses: actions/upload-artifact@v4
+        with:
+          name: uberon-base-main.owl
+          path: src/ontology/uberon-base.owl
+          retention-days: 1
+  diff_classification:
+    needs: [classify_branch, classify_main]
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.5.3
+    steps:
+      - uses: khan/[email protected]
+        id: check
+        with:
+          trigger: '#gogoeditdiff'
+        env:  
+          GITHUB_TOKEN: '${{ 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@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: simple-report.md
-          path: src/ontology/simple-report.md
+          name: classification-diff.md
+          path: src/ontology/classification-diff.md
   post_comment:
-    needs: [diff-reports]
+    needs: [edit_file, diff_classification]
     runs-on: ubuntu-latest
     steps:
       - uses: khan/[email protected]
@@ -80,42 +188,40 @@ jobs:
           trigger: '#gogoeditdiff'
         env:
           GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         if: steps.check.outputs.triggered == 'true'
       - name: Download reasoned diff
         if: steps.check.outputs.triggered == 'true'
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: simple-report.md
+          name: classification-diff.md
       - name: Prepare reasoned comment
-        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 simple-report.md >> comment.md"
         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'
-        env:
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
-        uses: NejcZdovc/[email protected]
+        uses: NejcZdovc/[email protected]
         with:
           file: "../../comment.md"
           identifier: "REASONED"
-      - uses: actions/checkout@v3
+          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@v2
+        uses: actions/download-artifact@v4
         with:
           name: 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-comment.md"
         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'
-        env:
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
-        uses: NejcZdovc/[email protected]
+        uses: NejcZdovc/[email protected]
         with:
           file: "../../edit-comment.md"
           identifier: "UNREASONED"
+          github_token: ${{secrets.GITHUB_TOKEN}}
 
 
 

.github/workflows/post-release-diff.yml

@@ -0,0 +1,30 @@
+name: Post release diff
+
+on:
+  # Triggers the workflow on pull request events for the master branch
+  pull_request:
+    branches: [ master ]
+    paths:
+      - 'src/ontology/diffs/uberon-diff.md'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+
+  post_diff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Prepare release diff comment
+        env:
+            GITHUB_SHA: ${{ github.sha }}
+        run: "echo \"[Here's a diff of how this release impacts uberon-base.owl](https://github.com/obophenotype/uberon/blob/${{ env.GITHUB_SHA }}/src/ontology/diffs/uberon-diff.md)\" >comment.md"
+      - name: Post comment
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: NejcZdovc/comment-pr@v2
+        with:
+          github_token: ${{ env.GITHUB_TOKEN }}
+          file: "../../comment.md"
+          identifier: "UBERON-DIFF"