Validation as a Separate Step

Author: M-Jafarkhani

.github/workflows/run-benchmark.yml

@@ -99,6 +99,12 @@ jobs:
             activate-environment: postprocessing 
             use-mamba: true
             environment-file: benchmarks/linear-elastic-plate-with-hole/environment_postprocessing.yml
+      
+      - name: Validate Provenance
+        shell: bash -l {0}
+        run: |
+          python benchmarks/linear-elastic-plate-with-hole/validate_provenance.py \
+            --provenance_folderpath "./$SNAKEMAKE_PROVENANCE_FILE" 
 
       - name: Run plotting script
         shell: bash -l {0}

benchmarks/linear-elastic-plate-with-hole/plot_provenance.py

@@ -281,25 +281,23 @@ def run(args, parameters, metrics, tools):
 
     Performs the following steps:
     1. Initialize the ProvenanceAnalyzer
-    2. Validate the RO-Crate metadata structure
-    3. Load and query the provenance graph
-    4. Validate query results against summary.json ground truth data
-    5. Apply custom filters to the data
-    6. Generate visualization plot
+    2. Load and query the provenance graph
+    3. Validate query results against summary.json ground truth data
+    4. Apply custom filters to the data
+    5. Generate visualization plot
 
     Args:
         args (argparse.Namespace): Parsed command-line arguments.
         parameters (list): List of parameter names to extract.
         metrics (list): List of metric names to extract.
         tools (list): List of tool names to process.
     """
+    
     analyzer = ProvenanceAnalyzer(
         provenance_folderpath=args.provenance_folderpath,
         provenance_filename=args.provenance_filename,
     )
 
-    analyzer.validate_provevance()
-
     provenance_df = load_and_query_graph(analyzer, parameters, metrics, tools)
 
     validate_provenance_data(

benchmarks/linear-elastic-plate-with-hole/validate_provenance.py

@@ -0,0 +1,33 @@
+import argparse
+from provenance import ProvenanceAnalyzer
+
+
+def parse_args():
+    parser = argparse.ArgumentParser(
+        description="Process research object zip to validate against profile."
+    )
+    parser.add_argument(
+        "--provenance_folderpath",
+        type=str,
+        required=True,
+        help="Path to the folder containing provenance data",
+    )
+    return parser.parse_args()
+
+
+def run(args):
+    analyzer = ProvenanceAnalyzer(
+        provenance_folderpath=args.provenance_folderpath,
+        provenance_filename=args.provenance_filename,
+    )
+
+    analyzer.validate_provevance()
+
+
+def main():
+    args = parse_args()
+    run(args)
+
+
+if __name__ == "__main__":
+    main()