63 benchmarking package development

.github/workflows/run-benchmark.yml

@@ -37,42 +37,19 @@ jobs:
       - name: Update environment
         run: mamba env update -n model-validation -f environment_benchmarks.yml
 
-      - name: generate-config-files
+      - name: Run Example linear-elastic-plate-with-hole_fenics using Benchmarking package
         shell: bash -l {0}
         run: |
-          cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
-          python generate_config.py
-
-      - name: run_linear-elastic-plate-with-hole-benchmarks_snakemake
-        shell: bash -l {0}
-        run: |
-          cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
-          snakemake --use-conda --force --cores 'all'
-          snakemake --use-conda --force --cores all \
-            --reporter metadata4ing \
-            --report-metadata4ing-paramscript ../common/parameter_extractor.py \
-            --report-metadata4ing-config metadata4ing.config \
-            --report-metadata4ing-filename $SNAKEMAKE_RESULT_FILE
-
-      - name: run_linear-elastic-plate-with-hole-benchmarks_nextflow
-        shell: bash -l {0}
-        run: |
-          cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
-          nextflow run main.nf -params-file workflow_config.json -c ../common/nextflow.config -plugins nf-prov@1.4.0
+          cd $GITHUB_WORKSPACE/examples/linear-elastic-plate-with-hole/fenics/
+          python run_benchmark.py
 
       - name: Archive Linear Elastic plate with a hole benchmark data for snakemake
         uses: actions/upload-artifact@v4
         with:
             name: snakemake_results_linear-elastic-plate-with-hole
             path: |
-              benchmarks/linear-elastic-plate-with-hole/${{ env.SNAKEMAKE_RESULT_FILE }}.zip
+              examples/linear-elastic-plate-with-hole/fenics/results/
 
-      - name: Archive Linear Elastic plate with a hole benchmark data for nextflow
-        uses: actions/upload-artifact@v4
-        with:
-            name: nextflow_results_linear-elastic-plate-with-hole
-            path: |
-              benchmarks/linear-elastic-plate-with-hole/nextflow_results/
 
   process-artifacts:
     runs-on: ubuntu-latest
@@ -129,34 +106,32 @@ 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

.gitignore

@@ -1,2 +1,4 @@
 .snakemake
-site
+site
+examples/linear-elastic-plate-with-hole/fenics/conda_envs
+examples/linear-elastic-plate-with-hole/linear-elastic-plate-with-hole

benchmarks/common/create_provenance.py

@@ -0,0 +1,25 @@
+import semantic_benchmark
+import utils
+
+def main():
+    benchmark_file = "/Users/mahdi/Documents/GitHub/NFDI4IngModelValidationPlatform/examples/linear-elastic-plate-with-hole/benchmark.json"
+    simulation_result_path = "/Users/mahdi/Documents/GitHub/NFDI4IngModelValidationPlatform/examples/linear-elastic-plate-with-hole/fenics/results"
+    benchmark_object = semantic_benchmark.BenchmarkLoader(benchmark_file).load()
+
+    for step in benchmark_object.processing_steps:
+        print(f"Processing Step: {step.label}")
+        for config in step.configurations:
+            print(f"  Configuration: {config.label}")
+            for part in config.parts:
+                if isinstance(part, semantic_benchmark.NumericalParameter):
+                    print(f"    Numerical Parameter: {part.label} = {part.numerical_value} {part.unit}")
+                elif isinstance(part, semantic_benchmark.TextParameter):
+                    print(f"    Text Parameter: {part.label} = {part.string_value}")
+
+        for tool in step.employed_tools:
+            print(f"  Employed Tool: {tool.label}")
+
+    utils.create_main_ro(simulation_result_path, benchmark_object)
+
+if __name__ == "__main__":
+    main()

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!")