Nipype example : subject-level provenance inside prov/ dir

Author: bclenet

examples/nipype/README.md

@@ -17,7 +17,7 @@ In order to describe provenance records using BIDS Prov, we use:
 
 * the `GeneratedBy` field of JSON sidecar files, already existing in the BIDS specification;
 * modality agnostic files inside the `derivatives/flirt/prov/` directory
-* a modality agnostic file inside the `derivatives/flirt/sub-001/anat/` directory
+* a modality agnostic file inside the `derivatives/flirt/sub-001/anat/prov/` directory
 
 After running the workflow and adding provenance traces, the resulting directory tree looks like this:
 
@@ -35,7 +35,8 @@ After running the workflow and adding provenance traces, the resulting directory
 │       │   └── prov-flirt_soft.prov.json
 │       └── sub-001
 │           └── anat
-│               ├── sub-001_prov-flirt_act.prov.json
+│               ├── prov
+│               │   └── sub-001_prov-flirt_act.prov.json
 │               ├── sub-001_space-mni152nlin2009casym_T1w_brain.json
 │               ├── sub-001_space-mni152nlin2009casym_T1w_brain.nii.gz
 │               ├── sub-001_T1w_brain.json

examples/nipype/code/merge_prov.py

@@ -14,7 +14,7 @@
 	'derivatives/flirt/prov/prov-flirt_env.prov.json'
 ]
 prov_act_files = [
-	'derivatives/flirt/sub-001/anat/sub-001_prov-flirt_act.prov.json'
+	'derivatives/flirt/sub-001/anat/prov/sub-001_prov-flirt_act.prov.json'
 ]
 prov_ent_files = [
 	'derivatives/flirt/prov/prov-flirt_ent.prov.json'

examples/nipype/derivatives/flirt/prov/merged/prov-flirt.prov.jsonld

@@ -28,7 +28,7 @@
           },
           "bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
         ],
-        "Id": "bids::prov/#bet-ys913vx4"
+        "Id": "bids::sub-001/anat/prov/#bet-ys913vx4"
       },
       {
         "Label": "flirt",
@@ -39,12 +39,12 @@
             "Id": "bids::derivatives/bids_prov_workflow/brain_extraction/sub-001_T1w_brain.nii.gz",
             "Type": "Entity",
             "Label": "sub-001_T1w_brain.nii.gz",
-            "GeneratedBy": "bids::prov/#bet-ys913vx4"
+            "GeneratedBy": "bids::sub-001/anat/prov/#bet-ys913vx4"
           },
           "/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz",
           "bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
         ],
-        "Id": "bids::prov/#flirt-xzje9hjh"
+        "Id": "bids::sub-001/anat/prov/#flirt-xzje9hjh"
       },
       {
         "Label": "export_brain",
@@ -54,7 +54,7 @@
           "bids::derivatives/bids_prov_workflow/brain_extraction/sub-001_T1w_brain.nii.gz",
           "bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
         ],
-        "Id": "bids::prov/#export_file-i1cblvll"
+        "Id": "bids::sub-001/anat/prov/#export_file-i1cblvll"
       },
       {
         "Label": "export_brain_MNI_space",
@@ -65,11 +65,11 @@
             "Id": "bids::derivatives/bids_prov_workflow/flirt/sub-001_T1w_brain_flirt.nii.gz",
             "Type": "Entity",
             "Label": "sub-001_T1w_brain_flirt.nii.gz",
-            "GeneratedBy": "bids::prov/#flirt-xzje9hjh"
+            "GeneratedBy": "bids::sub-001/anat/prov/#flirt-xzje9hjh"
           },
           "bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
         ],
-        "Id": "bids::prov/#export_file-fpw3jrwy"
+        "Id": "bids::sub-001/anat/prov/#export_file-fpw3jrwy"
       }
     ],
     "Entities": [
@@ -84,11 +84,11 @@
       },
       {
         "Id": "bids::derivatives/flirt/sub-001/anat/sub-001_T1w_brain.nii.gz",
-        "GeneratedBy": "bids::prov/#export_file-i1cblvll"
+        "GeneratedBy": "bids::sub-001/anat/prov/#export_file-i1cblvll"
       },
       {
         "Id": "bids::derivatives/flirt/sub-001/anat/sub-001_space-mni152nlin2009casym_T1w_brain.nii.gz",
-        "GeneratedBy": "bids::prov/#export_file-fpw3jrwy"
+        "GeneratedBy": "bids::sub-001/anat/prov/#export_file-fpw3jrwy"
       }
     ]
   },

examples/nipype/derivatives/flirt/prov/merged/prov-flirt.prov.png

@@ -1,3 +1,3 @@
 {
-	"GeneratedBy": "bids::prov/#export_file-i1cblvll"
+	"GeneratedBy": "bids::sub-001/anat/prov/#export_file-i1cblvll"
 }

examples/nipype/derivatives/flirt/sub-001/anat/sub-001_T1w_brain.json

@@ -1,3 +1,3 @@
 {
-	"GeneratedBy": "bids::prov/#export_file-fpw3jrwy"
+	"GeneratedBy": "bids::sub-001/anat/prov/#export_file-fpw3jrwy"
 }