Adding Environments in context

bids_prov/merge.py

@@ -33,7 +33,7 @@ def get_associated_sidecar(layout: BIDSLayout, data_file: BIDSFile) -> dict:
     return layout.get_file(sidecar_filename)
 
 def filter_provenance_group(files: list, group: str) -> list:
-    """ Filter a given BIDSFile list, returning the sub-list containig the BIDS
+    """ Filter a given BIDSFile list, returning the sub-list containing the BIDS
     `prov` entity equal to group
     """
     return [f for f in files if f'prov-{group}' in f.filename]
@@ -62,10 +62,15 @@ def get_described_datasets(layout: BIDSLayout) -> list:
     for file in files:
         metadata = file.get_dict()
         if 'GeneratedBy' in metadata:
-            for generated_by_obj in metadata['GeneratedBy']:
-                if 'Id' in generated_by_obj:
-                    out_files.append(file)
-                    break
+            # If GeneratedBy is either a list of objects or a list of activity ids
+            if isinstance(metadata['GeneratedBy'], list):
+                for generated_by_obj in metadata['GeneratedBy']:
+                    if 'Name' not in generated_by_obj:
+                        out_files.append(file)
+                        break
+            # If GeneratedBy is an activity id
+            else:
+                out_files.append(file)
 
     return out_files
 
@@ -98,9 +103,12 @@ def get_dataset_entity_record(description_file: BIDSJSONFile) -> dict:
     }
 
     # Get provenance-related metadata
-    for generated_by_obj in metadata['GeneratedBy']:
-        if 'Id' in generated_by_obj:
-            entity['GeneratedBy'].append(generated_by_obj['Id'])
+    if isinstance(metadata['GeneratedBy'], list):
+        for generated_by_obj in metadata['GeneratedBy']:
+            if 'Name' not in generated_by_obj:
+                entity['GeneratedBy'].append(generated_by_obj)
+    else:
+        entity['GeneratedBy'].append(metadata['GeneratedBy'])
 
     return entity
 

context.json

@@ -39,11 +39,16 @@
           "@id": "prov:used",
           "@type": "@id"
         },
+        "ActedOnBehalfOf" : {
+          "@id": "prov:actedOnBehalfOf",
+          "@type": "@id"
+        },
         "Entities": "prov:Entity",
         "Entity": "prov:Entity",
+        "Environments": "prov:Entity",
         "Activities": "prov:Activity",
         "Activity": "prov:Activity",
-        "Software": "prov:Agent",
+        "Software": "prov:SoftwareAgent",
         "Atlocation": "prov:atLocation"
     }
 }

dev-requirements.txt

@@ -12,4 +12,5 @@ pre-commit
 rdflib
 boutiques
 markdownify
-rfc3986
+rfc3986
+pybids

examples/from_parsers/context_2025_07_11_14h40m18s.txt → examples/from_parsers/context_2025_09_30_09h08m00s.txt

@@ -1,4 +1,4 @@
-Date : 2025_07_11_14h40m18s
+Date : 2025_09_30_09h08m00s
 Processing files...
     file= nidmresults-examples/afni_alt_onesided_proc.sub_001
     file= nidmresults-examples/afni_alt_onesided_proc.sub_001
@@ -69,4 +69,4 @@ Processing files...
     file= nidmresults-examples/spm_thr_voxelfdrp05_batch.m
     file= nidmresults-examples/spm_thr_voxelfwep05_batch.m
     file= nidmresults-examples/spm_thr_voxelunct4_batch.m
-End of processed files. Results in dir : 'examples/from_parsers'. Time required: 0:00:02.016392
+End of processed files. Results in dir : 'examples/from_parsers'. Time required: 0:00:02.101514

pyproject.toml

@@ -45,6 +45,7 @@ pydot = "^2.0.0"
 pyld = "^2.0.4"
 pyyaml = "^6.0.1"
 requests = "^2.32.3"
+pybids = "^0.18.1"
 
 [tool.poetry.group.dev.dependencies]
 black = "^24.4.2"