Using lists for Used entities

Author: bclenet

examples/dcm2niix/README.md

@@ -56,6 +56,16 @@ tree sub-02/
 
 See the `dcm2niix.prov.jsonld` file.
 
-Some limitations :
-* for now, the values of Activities `Used` keys only refer to the first dicom file of a series, although each activity should be linked to all the data it actually used (i.e.: all dicom files in a directory in our case).
-* as there is a high number of dicom files (384 in `acq1/` and 5460 in `acq2/`), we did not create an entity for each of these. Only the first three files of each directory were represented.
+## Limitations
+
+### `Used` key for activities
+
+Although the BIDS-Prov spec mentions:
+
+> Used : OPTIONAL. UUID. Identifier of an entity used by this activity (the corresponding Entity must be defined with its own Entity record).
+
+We added entities as a list in to link all the dicom files of a directory to the corresponding conversion activity.
+
+### High number of dicom files
+
+As there is a high number of dicom files (384 in `acq1/` and 5460 in `acq2/`), we did not create an entity for each of these. Only the first three files of each directory were represented.

examples/dcm2niix/dcm2niix.prov.jsonld

@@ -11,7 +11,7 @@
     ],
     "Software": [
       {
-        "Id": "urn:dcm2niix",
+        "Id": "urn:dcm2niix-4a586b50",
         "Label": "dcm2niix",
         "Version": "v1.0.20220720"
       }
@@ -22,14 +22,22 @@
         "Label": "Conversion",
         "Command": "dcm2niix -o . -f sub-%i/ses-%t/anat/sub-%i_ses-%t_T1w sourcedata/acq1/dicoms/example-dicom-structural-master/dicoms/",
         "AssociatedWith": "urn:dcm2niix-4a586b50",
-        "Used": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm"
+        "Used": [
+          "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm",
+          "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm",
+          "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm"
+        ]
       },
       {
         "Id": "urn:conversion-5a66f5be",
         "Label": "Conversion",
         "Command": "dcm2niix -o . -f sub-%i/ses-%t/func/sub-%i_ses-%t_task-oneback_run-1_bold sourcedata/acq1/dicoms/example-dicom-structural-master/dicoms/",
         "AssociatedWith": "urn:dcm2niix-4a586b50",
-        "Used": "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586"
+        "Used": [
+          "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586",
+          "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588",
+          "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590"
+        ]
       }
     ],
     "Entities": [