Moving all provenance records to json sidecar / dcm2niix example

Author: bclenet

examples/dcm2niix_3/README.md

@@ -6,14 +6,13 @@ This example aims at showing provenance traces from a DICOM to Nifti conversion,
 
 This time, we describe the provenance records using BIDS Prov, but inside several *JSON* files.
 
+The example illustrates a case where only one file is generated, hence all provenance records are stored in the *JSON* sidecar file `sub-02_T1w.json`.s
+
 After conversion, and adding provenance traces, the resulting directory tree looks like this:
 
 ```
 prov/
-├── prov-dcm2niix_act.prov.json
-├── prov-dcm2niix_base.prov.json
-├── prov-dcm2niix_env.prov.json
-└── prov-dcm2niix_soft.prov.json
+└── prov-dcm2niix_base.prov.json
 sourcedata/
 sub-02/
 └── anat
@@ -61,16 +60,8 @@ We introduce the following BIDS entity that is currently not existing:
     * Format: `prov-<label>`
     * Definition: A grouping of provenance traces. Defining multiple provenance traces groups is appropriate when several processings have been performed on data.
 
-We introduce the following BIDS suffixes that are currently not existing:
-* `act`: the file describes BIDS Prov `Activities` for the group of provenance traces
-* `soft`: the file describes BIDS Prov `Software` for the group of provenance traces
-* `env`: the file describes BIDS Prov `Environments` for the group of provenance traces
-* `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.
 
-In this example, we rely on the fact that nodes defined in the `prov/*.prov.jsonld` files have `bids::prov/` as base IRIs.
-
 The `code/merge_prov.py` code is responsible for:
 * merging the JSON provenance traces into the base JSON-LD graph;
 * create an `Entity` and linking it to the `Activity` described by the `GeneratedBy` field in the case of JSON sidecars.

examples/dcm2niix_3/code/merge_prov.py

@@ -8,13 +8,10 @@
 
 # List of available prov files
 prov_soft_files = [
-  'prov/prov-dcm2niix_soft.prov.json'
 ]
 prov_env_files = [
-  'prov/prov-dcm2niix_env.prov.json'
 ]
 prov_act_files = [
-  'prov/prov-dcm2niix_act.prov.json'
 ]
 sidecar_files = [
   'sub-02/anat/sub-02_T1w.json'

examples/dcm2niix_3/prov/merged/prov-dcm2niix.prov.jsonld

@@ -1,37 +1,35 @@
 {
   "Records": {
-    "Software": [
-      {
-        "Label": "dcm2niix",
-        "Version": "v1.0.20220720",
-        "Id": "bids::prov/#dcm2niix-khhkm7u1"
-      }
-    ],
-    "Activities": [
-      {
-        "Label": "Conversion",
-        "Command": "dcm2niix -o . -f sub-%i/anat/sub-%i_T1w sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
-        "AssociatedWith": "bids::prov/#dcm2niix-khhkm7u1",
-        "Used": [
-          "bids::prov/#fedora-uldfv058",
-          {
-            "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
-            "Type": "Entity",
-            "Label": "dicoms"
-          }
-        ],
-        "Id": "bids::prov/#conversion-00f3a18f"
-      }
-    ],
+    "Software": [],
+    "Activities": [],
     "Entities": [
-      {
-        "Label": "Fedora release 36 (Thirty Six)",
-        "OperatingSystem": "GNU/Linux 6.2.15-100.fc36.x86_64",
-        "Id": "bids::prov/#fedora-uldfv058"
-      },
       {
         "Id": "bids::sub-02/anat/sub-02_T1w.nii",
-        "GeneratedBy": "bids::prov/#conversion-00f3a18f"
+        "GeneratedBy": {
+          "Id": "bids::sub-02/anat/#conversion-00f3a18f",
+          "Type": "Activity",
+          "Label": "Conversion",
+          "Command": "dcm2niix -o . -f sub-%i/anat/sub-%i_T1w sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
+          "AssociatedWith": {
+            "Id": "bids::sub-02/anat/#dcm2niix-khhkm7u1",
+            "Type": "Software",
+            "Label": "dcm2niix",
+            "Version": "v1.0.20220720"
+          },
+          "Used": [
+            {
+              "Id": "bids::sub-02/anat/#fedora-uldfv058",
+              "Type": "Entity",
+              "Label": "Fedora release 36 (Thirty Six)",
+              "OperatingSystem": "GNU/Linux 6.2.15-100.fc36.x86_64"
+            },
+            {
+              "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
+              "Type": "Entity",
+              "Label": "dicoms"
+            }
+          ]
+        }
       }
     ]
   },

examples/dcm2niix_3/prov/merged/prov-dcm2niix.prov.png

@@ -20,5 +20,29 @@
         -0.128044   ],
     "ConversionSoftware": "dcm2niix",
     "ConversionSoftwareVersion": "v1.0.20220720",
-    "GeneratedBy": "bids::prov/#conversion-00f3a18f"
+    "GeneratedBy": {
+        "Id": "bids::sub-02/anat/#conversion-00f3a18f",
+        "Type": "Activity",
+        "Label": "Conversion",
+        "Command": "dcm2niix -o . -f sub-%i/anat/sub-%i_T1w sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
+        "AssociatedWith": {
+            "Id": "bids::sub-02/anat/#dcm2niix-khhkm7u1",
+            "Type": "Software",
+            "Label": "dcm2niix",
+            "Version": "v1.0.20220720"
+        },
+        "Used": [
+          { 
+            "Id": "bids::sub-02/anat/#fedora-uldfv058",
+            "Type": "Entity",
+            "Label": "Fedora release 36 (Thirty Six)",
+            "OperatingSystem": "GNU/Linux 6.2.15-100.fc36.x86_64"
+          },
+          {
+            "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
+            "Type": "Entity",
+            "Label": "dicoms"
+          }
+        ]
+    }
 }