Adding provenance record for the JSON sidecar

Author: bclenet

examples/dcm2niix_4/README.md

@@ -30,6 +30,8 @@ We use:
 * the `GeneratedBy` field of JSON sidecar, already existing in the BIDS specification
 * modality agnostic files inside the `prov/` directory
 
+Note that we assume that both `sub-02_T1w.nii` and its JSON sidecar `sub-02_T1w.json` were generated by the same Activity.
+
 ## Provenance merge
 
 The python script `code/merge_prov.py` aims at merging all provenance records into one JSON-LD graph.

examples/dcm2niix_4/code/merge_prov.py

@@ -70,12 +70,31 @@
   with open(sidecar_file, encoding = 'utf-8') as file:
     data = json.load(file)
     if 'GeneratedBy' in data:
-      activity_id = data['GeneratedBy']
+
+      # Get activity data and id
+      activity_data = data['GeneratedBy']
+      activity_id = ""
+      if "Id" in activity_data:
+        activity_id = activity_data['Id']
+      else:
+        activity_id = activity_data
+
+      # Provenance for the data file
       for data_file in data_files:
-        base_provenance['Records']['Entities'].append({
-          "Id": f"bids::{data_file}",
+        base_provenance['Records']['Entities'].append(
+          {
+            "Id": f"bids::{data_file}",
+            "GeneratedBy": activity_data
+          }
+        )
+
+      # Provenance for the sidecar
+      base_provenance['Records']['Entities'].append(
+        {
+          "Id": f"bids::{sidecar_filename}",
           "GeneratedBy": activity_id
-          })
+        }
+      )
 
 # Write jsonld
 with open('prov/merged/prov-dcm2niix.prov.jsonld', 'w', encoding = 'utf-8') as file:

examples/dcm2niix_4/prov/merged/prov-dcm2niix.prov.jsonld

@@ -32,6 +32,10 @@
       {
         "Id": "bids::sub-02/anat/sub-02_T1w.nii",
         "GeneratedBy": "bids::prov/#conversion-00f3a18f"
+      },
+      {
+        "Id": "bids::sub-02/anat/sub-02_T1w.json",
+        "GeneratedBy": "bids::prov/#conversion-00f3a18f"
       }
     ]
   },