Adding provenance record for the JSON sidecar

Author: bclenet

examples/heudiconv/README.md

@@ -144,6 +144,7 @@ We introduce the following BIDS suffixes that are currently not existing:
 * `base`: the file describes common BIDS Prov parameters for the group of provenance traces (version and context for BIDS Prov)
 
 We use the `GeneratedBy` field of JSON sidecars to link to Activities that created the file the sidecars refers to.
+We use the `SidecarGeneratedBy` field of JSON sidecars to link to Activities that created or modified the sidecars itself.
 
 In this example, we rely on the fact that nodes defined in the `prov/*.prov.jsonld` files have `bids::prov/` as base IRIs.
 

examples/heudiconv/code/merge_prov.py

@@ -20,7 +20,6 @@
 	'prov/prov-heudiconv_ent.prov.json'
 ]
 sidecar_files = [
-	'sub-001/sub-001_scans.json',
 	'sub-001/anat/sub-001_run-1_T1w.json'
 ]
 
@@ -88,6 +87,12 @@
 					"Id": f"bids::{data_file}",
 					"GeneratedBy": activity_id
 					})
+		if 'SidecarGeneratedBy' in data:
+			activity_id = data['SidecarGeneratedBy']
+			base_provenance['Records']['Entities'].append({
+				"Id": f"bids::{sidecar_filename}",
+				"GeneratedBy": activity_id
+				})
 
 # Write jsonld
 with open('prov/merged/prov-heudiconv.prov.jsonld', 'w', encoding = 'utf-8') as file:

examples/heudiconv/prov/merged/prov-heudiconv.prov.jsonld

@@ -99,13 +99,16 @@
         "GeneratedBy": "bids::prov/#preparation-conversion-1xkhm1ft",
         "Id": "bids::scans.json"
       },
-      {
-        "Id": "bids::sub-001/sub-001_scans.tsv",
-        "GeneratedBy": "bids::prov/#preparation-conversion-1xkhm1ft"
-      },
       {
         "Id": "bids::sub-001/anat/sub-001_run-1_T1w.nii.gz",
         "GeneratedBy": "bids::prov/#conversion-00f3a18f"
+      },
+      {
+        "Id": "bids::sub-001/anat/sub-001_run-1_T1w.json",
+        "GeneratedBy": [
+          "bids::prov/#preparation-conversion-1xkhm1ft",
+          "bids::prov/#conversion-00f3a18f"
+        ]
       }
     ]
   },

examples/heudiconv/prov/merged/prov-heudiconv.prov.png

@@ -18,5 +18,9 @@
   "SliceThickness": 0.666667,
   "SoftwareVersions": "0.4.11",
   "SpacingBetweenSlices": 0.666667,
-  "GeneratedBy": "bids::prov/#conversion-00f3a18f"
+  "GeneratedBy": "bids::prov/#conversion-00f3a18f",
+  "SidecarGeneratedBy": [
+    "bids::prov/#preparation-conversion-1xkhm1ft",
+    "bids::prov/#conversion-00f3a18f"
+  ]
 }