Add tests for linked entities

Author: bclenet

bids_prov/merge.py

@@ -24,6 +24,7 @@ def get_associated_sidecar(layout: BIDSLayout, data_file: BIDSFile) -> dict:
         derivative datasets.
 
         Return the associated sidecar of a BIDSFile in a given BIDSLayout.
+        This returns None if no such sidecar exists.
     """
     filename = Path(data_file.path)
     extensions = ''.join(filename.suffixes)

bids_prov/tests/samples_test/provenance_ds00/README.md

@@ -0,0 +1,53 @@
+# BEP028 example dataset - SPM based fMRI statistical analysis with no provenance records
+
+This example aims at showing a functional MRI preprocessing performed with [`SPM`](https://www.fil.ion.ucl.ac.uk/spm/) before provenance records are added to it.
+
+## Source dataset
+
+This is a derivative dataset, based upon `sub-01` data from OpenfMRI DS000011 classification learning and tone counting experiment (cf. https://openfmri.org/dataset/ds000011/)
+
+## Code
+
+The Matlab batch file `code/spm_preprocessing.m` allows to perform the preprocessing.
+
+## Directory tree
+
+The directory tree is as follows:
+
+```
+.
+├── code
+│   ├── merge_prov.py
+│   └── spm_preprocessing.m
+├── dataset_description.json
+├── prov
+│   ├── prov-spm_act.json
+│   ├── prov-spm_ent.json
+│   ├── prov-spm.jsonld
+│   ├── prov-spm.png
+│   └── prov-spm_soft.json
+├── README.md
+└── SPM
+    └── PREPROCESSING
+        ├── ANATOMICAL
+        │   ├── c1sub-01_T1w.nii
+        │   ├── c2sub-01_T1w.nii
+        │   ├── c3sub-01_T1w.nii
+        │   ├── c4sub-01_T1w.nii
+        │   ├── c5sub-01_T1w.nii
+        │   ├── msub-01_T1w.nii
+        │   ├── sub-01_T1w.nii
+        │   ├── sub-01_T1w.nii.gz
+        │   ├── sub-01_T1w_seg8.mat
+        │   ├── wmsub-01_T1w.nii
+        │   └── y_sub-01_T1w.nii
+        └── FUNCTIONAL
+            ├── meansub-01_task-tonecounting_bold.nii
+            ├── rp_sub-01_task-tonecounting_bold.txt
+            ├── sub-01_task-tonecounting_bold.mat
+            ├── sub-01_task-tonecounting_bold.nii
+            ├── sub-01_task-tonecounting_bold.nii.gz
+            ├── swsub-01_task-tonecounting_bold.nii
+            └── wsub-01_task-tonecounting_bold.nii
+
+```

bids_prov/tests/samples_test/provenance_ds00/dataset_description.json

@@ -0,0 +1,29 @@
+{
+    "Name": "SPM-based fMRI statistical analysis",
+    "BIDSVersion": "1.10.0",
+    "DatasetType": "derivative",
+    "License": "CC0",
+    "Authors": [
+        "Boris Clénet",
+        "Thomas Betton",
+        "Hermann Courteille",
+        "Cyril Regan"
+    ],
+    "GeneratedBy": [
+        {
+            "Name": "SPM preprocessing"
+        }
+    ],
+    "SourceDatasets": [
+        {
+            "URL": "ds000011",
+            "Version": "1.0.0"
+        },
+        {
+            "URL": "https://github.com/incf-nidash/nidmresults-examples/"
+        }
+    ],
+    "DatasetLinks": {
+        "ds000011": "https://doi.org/10.18112/openneuro.ds000011.v1.0.0"
+    }
+}