Merge pull request #441 from ncihtan/action-dependencies-table

Add action to build dependencies table

.github/workflows/build-dependencies-table.yml

@@ -0,0 +1,61 @@
+name: Build Dependencies Table
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  update-table:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install requests pandas
+
+    - name: Fetch attribute table
+      run: |
+        python - <<EOF
+        import requests
+        import pandas as pd
+
+        url = "https://schematic.api.sagebionetworks.org/v1/ui/"  # Endpoint URL
+        jsonld_url = "https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld"
+        
+        response = requests.get(jsonld_url)
+        response.raise_for_status()
+        model_jsonld = response.json()
+
+        response = requests.post(url, json=model_jsonld)
+        response.raise_for_status()
+        attribute_table = response.json()  # Adjust this line based on the actual response format
+
+        df = pd.DataFrame(attribute_table)
+        
+        df.to_csv('HTAN.dependencies.csv', index=False)
+        EOF
+
+    - name: Commit changes
+      run: |
+        git config --global user.name "github-actions[bot]"
+        git config --global user.email "github-actions[bot]@users.noreply.github.com"
+        git add HTAN.dependencies.csv
+        git commit -m "Update HTAN.dependencies.csv with the latest attribute table"
+
+    - name: Create Pull Request
+      uses: aditigopalan/create-pull-request@v3
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        commit-message: "Update HTAN.dependencies.csv"
+        branch: update-attribute-table
+        title: "Update HTAN.dependencies.csv"
+        body: "This PR updates HTAN.dependencies.csv with the latest attribute table."

.github/workflows/ci-lint-validate-convert.yml

@@ -1,20 +1,15 @@
-name: Make JSON-LD
+name: Make JSON-LD and Build Dependencies Table
 
 on:
   pull_request:
     branches: 'main'
     paths: 'HTAN.model.csv'
+  release:
+    types: [published]
   workflow_dispatch:
 
 concurrency:
-# cancel the current running workflow from the same branch, PR when a new workflow is triggered
-# when the trigger is not a PR but a push, it will use the commit sha to generate the concurrency group
-# {{ github.workflow }}: the workflow name is used to generate the concurrency group. This allows you to have more than one workflows
-# {{ github.ref_type }}: the type of Git ref object created in the repository. Can be either branch or tag
-# {{ github.sha }}: full commit sha
-# credit: https://github.com/Sage-Bionetworks-Workflows/sagetasks/blob/main/.github/workflows/ci.yml
-  group: >-
-    ${{ github.workflow }}-${{ github.ref_type }}-${{ github.sha }}
+  group: ${{ github.workflow }}-${{ github.ref_type }}-${{ github.sha }}
   cancel-in-progress: true
 
 env:
@@ -87,11 +82,79 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
       - name: Commit the changes
         run: |
-          # Specifying the full email allows the avatar to show up: https://github.com/orgs/community/discussions/26560
           git add HTAN.model.jsonld
           git commit -m "GitHub Action: convert *.model.csv to *.model.jsonld" || echo "No changes to commit"
       - name: Push changes back to PR
         if: github.event_name == 'pull_request'
         uses: r-lib/actions/pr-push@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  build-dependencies:
+    name: Build Dependencies Table
+    needs: convert
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Fetch latest changes
+        run: git pull origin main
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install requests pandas
+
+      - name: Fetch attribute table
+        run: |
+          python - <<EOF
+          import requests
+          import pandas as pd
+
+          url = "https://schematic.api.sagebionetworks.org/v1/ui/"  # Endpoint URL
+          if "${{ github.event_name }}" == "pull_request":
+              jsonld_url = "https://raw.githubusercontent.com/${{ github.repository }}/pull/${{ github.event.pull_request.number }}/head/HTAN.model.jsonld"
+          else:
+              jsonld_url = "https://raw.githubusercontent.com/${{ github.repository }}/main/HTAN.model.jsonld"
+          
+          response = requests.get(jsonld_url)
+          response.raise_for_status()
+          model_jsonld = response.json()
+
+          response = requests.post(url, json=model_jsonld)
+          response.raise_for_status()
+          attribute_table = response.json()  # Adjust this line based on the actual response format
+
+          df = pd.DataFrame(attribute_table)
+          
+          df.to_csv('HTAN.dependencies.csv', index=False)
+          EOF
+
+      - name: Commit changes
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git add HTAN.dependencies.csv
+          git commit -m "Update HTAN.dependencies.csv with the latest attribute table"
+
+      - name: Create Pull Request
+        if: github.event_name == 'pull_request'
+        uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Create Pull Request
+        if: github.event_name != 'pull_request'
+        uses: peter-evans/create-pull-request@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: "Update HTAN.dependencies.csv"
+          branch: update-attribute-table
+          title: "Update HTAN.dependencies.csv"
+          body: "This PR updates HTAN.dependencies.csv with the latest attribute table."