Merge branch 'main' into patch-read-indicator

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

@@ -22,11 +22,11 @@ jobs:
     if: always()
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-    - name: csvlinter
-      uses: kcheriyath/csvlinter@V0.6.0
-      with:
-        find_pattern: "*.csv"
+      - uses: actions/checkout@v4
+      - name: csvlinter
+        uses: kcheriyath/csvlinter@V0.6.0
+        with:
+          find_pattern: "*.csv"
 
   validate:
     name: Validate CSV
@@ -125,42 +125,47 @@ jobs:
           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)
+          from io import StringIO
           
-          df.to_csv('HTAN.dependencies.csv', index=False)
+          def fetch_and_save_attribute_table():
+              url = "https://schematic.api.sagebionetworks.org/v1/visualize/attributes"
+              jsonld_url = "https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld"
+              
+              params = {'schema_url': jsonld_url}
+              
+              print("Fetching attribute table...")
+              response = requests.get(url, params=params)
+              print(f"Status Code: {response.status_code}")
+              
+              if response.status_code == 200:
+                  content_type = response.headers.get('Content-Type', '')
+                  if 'text/html' in content_type:
+                      print("Response in text/html format, converting to CSV...")
+                      try:
+                          df = pd.read_csv(StringIO(response.text))
+                          print("Fetched attribute table.")
+                          
+                          df.to_csv('HTAN.dependencies.csv', index=False)
+                          print("Saved to HTAN.dependencies.csv.")
+                      except Exception as e:
+                          print(f"Error processing CSV: {e}")
+                  else:
+                      print("Unexpected content type. Expected text/html but got:", content_type)
+              else:
+                  print(f"Failed to fetch data. Status Code: {response.status_code}")
+                  
+          fetch_and_save_attribute_table()
           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 }}
-
+          git commit -m "Update HTAN.dependencies.csv with the latest attribute table" || echo "No changes to commit"
+  
       - name: Create Pull Request
-        if: github.event_name != 'pull_request'
-        uses: peter-evans/create-pull-request@v3
+        uses: peter-evans/create-pull-request@v5
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           commit-message: "Update HTAN.dependencies.csv"