Merge branch 'main' into 48-add-rotating-cylinders-benchmark-using-dumux

Author: Sarbani-Roy

.github/workflows/run-benchmark.yml

@@ -129,34 +129,32 @@ jobs:
         shell: bash -l {0}
         continue-on-error: true
         run: |
-          LOG_FILE=rohub_upload_error.log
-
-          # Run Python and capture all stdout+stderr
-          python benchmarks/common/upload_provenance.py \
-            --provenance_folderpath "./${SNAKEMAKE_RESULT_FILE}.zip" \
-            --benchmark_name "linear-elastic-plate-with-hole" \
-            --username "${{ secrets.ROHUB_USERNAME }}" \
-            --password "${{ secrets.ROHUB_PASSWORD }}" \
-            2>&1 | tee "$LOG_FILE"
-
-          PYTHON_EXIT_CODE=${PIPESTATUS[0]}
-
-          # Check exit code: 0 = failure, 1 = success (per your convention)
-          if [ $PYTHON_EXIT_CODE -eq 0 ]; then
-            echo "=== RoHub upload failed — see log below ==="
-            cat "$LOG_FILE"
+          LOG_FILE="${GITHUB_WORKSPACE}/rohub_upload_error.log"
+
+          # Run Python and capture stdout+stderr
+          OUTPUT="$(
+            python benchmarks/common/upload_provenance.py \
+              --provenance_folderpath "./${SNAKEMAKE_RESULT_FILE}.zip" \
+              --benchmark_name "linear-elastic-plate-with-hole" \
+              --username "${{ secrets.ROHUB_USERNAME }}" \
+              --password "${{ secrets.ROHUB_PASSWORD }}" \
+            2>&1
+          )"
+          PYTHON_EXIT_CODE=$?
+
+          # Standard convention: 0 = success, non-zero = failure
+          if [ "$PYTHON_EXIT_CODE" -eq 0 ]; then
+            echo "RoHub upload succeeded"
+            rm -f "$LOG_FILE" || true
           else
-            echo "✅ RoHub upload succeeded"
-            rm -f "$LOG_FILE"
+            echo "=== RoHub upload failed — writing log to $LOG_FILE ==="
+            printf '%s\n' "$OUTPUT" | tee "$LOG_FILE"
           fi
 
-          # Export exit code for subsequent steps if needed
-          echo "python_exit_code=$PYTHON_EXIT_CODE" >> $GITHUB_ENV
-      
       - name: Upload RoHub error log
-        if: ${{ env.python_exit_code == '0' }}
+        if: always()
         uses: actions/upload-artifact@v4
         with:
           name: rohub-upload-error-log
-          path: rohub_upload_error.log
-
+          path: ${{ github.workspace }}/rohub_upload_error.log
+          if-no-files-found: ignore

benchmarks/common/provenance.py

@@ -124,7 +124,8 @@ def build_dynamic_query(self, parameters, metrics, tools=None, named_graph=None)
         )
 
         # Tool block with optional filter
-        tool_block = "?method m4i:implementedByTool ?tool .\n?tool a schema:SoftwareApplication ;\n rdfs:label ?tool_name .\n"
+        tool_predicate = "ssn:implementedBy" if named_graph else "m4i:implementedByTool"
+        tool_block = f"?method {tool_predicate} ?tool .\n?tool a schema:SoftwareApplication ;\n rdfs:label ?tool_name .\n"
         if tools:
             filter_cond = " || ".join(
                 f'CONTAINS(LCASE(?tool_name), "{t.lower()}")' for t in tools
@@ -152,7 +153,7 @@ def build_dynamic_query(self, parameters, metrics, tools=None, named_graph=None)
         PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
         PREFIX m4i: <http://w3id.org/nfdi4ing/metadata4ing#>
         PREFIX ssn: <http://www.w3.org/ns/ssn/>
-    
+        
         SELECT {select_vars} ?tool_name
         WHERE {{
             {where_block}
@@ -273,4 +274,4 @@ def validate_provenance(self):
             for issue in result.get_issues()
         )
 
-        print("RO-Crate is valid!")
+        print("RO-Crate is valid!")

benchmarks/common/upload_provenance.py

@@ -199,11 +199,11 @@ def main():
     args = parse_args()
     try:
         run(args)
-        sys.exit(1)
+        sys.exit(0)
     except Exception as error:
-        print("⚠️ RoHub upload failed:")
+        print("RoHub upload failed:")
         print(error)
-        sys.exit(0)
+        sys.exit(1)
 
 
 if __name__ == "__main__":

benchmarks/notebooks/RoCrate.ipynb

@@ -11,4 +11,4 @@ dependencies:
   - conda
   - pip
   - pip:
-      - "git+https://github.com/izus-fokus/snakemake-report-plugin-metadata4ing@v1.2.3#egg=snakemake-report-plugin-metadata4ing"
+      - "git+https://github.com/izus-fokus/snakemake-report-plugin-metadata4ing@v1.2.5#egg=snakemake-report-plugin-metadata4ing"