Merge pull request #952 from nipreps/fix/collect-data-sessions

FIX: Do not allow filters to overwrite participant / session

Author: mgxd

niworkflows/utils/bids.py

@@ -22,13 +22,15 @@
 #
 """Helpers for handling BIDS-like neuroimaging structures."""
 
+import copy
 import json
 import re
 import warnings
 from pathlib import Path
 
 from bids import BIDSLayout
 from bids.layout import Query
+from bids.utils import listify
 from packaging.version import Version
 
 DEFAULT_BIDS_QUERIES = {
@@ -226,22 +228,43 @@ def collect_data(
     >>> bids_root['t1w']  # doctest: +ELLIPSIS
     ['.../ds051/sub-01/anat/sub-01_run-01_T1w.nii.gz']
 
+    >>> bids_root, _ = collect_data(
+    ...     str(datadir / 'ds114'),
+    ...     '01',
+    ...     bids_validate=False,
+    ...     session_id='retest',
+    ...     bids_filters={'bold': {'session': 'madeup'}})  # doctest: +ELLIPSIS
+    Traceback (most recent call last):
+      ...
+    ValueError: Conflicting entities for "session" found: madeup // retest
+
     """
     if isinstance(bids_dir, BIDSLayout):
         layout = bids_dir
     else:
         layout = BIDSLayout(str(bids_dir), validate=bids_validate)
 
+    if not queries:
+        queries = copy.deepcopy(DEFAULT_BIDS_QUERIES)
+
     layout_get_kwargs = {
         'return_type': 'file',
         'subject': participant_label,
         'extension': ['.nii', '.nii.gz'],
         'session': session_id or Query.OPTIONAL,
     }
 
-    queries = queries or DEFAULT_BIDS_QUERIES
+    reserved_entities = [('subject', participant_label), ('session', session_id)]
+
     bids_filters = bids_filters or {}
     for acq, entities in bids_filters.items():
+        # BIDS filters will not be able to override subject / session entities
+        for entity, param in reserved_entities:
+            if entity in entities and listify(param) != listify(entities[entity]):
+                raise ValueError(
+                    f'Conflicting entities for "{entity}" found: {entities[entity]} // {param}'
+                )
+
         queries[acq].update(entities)
         for entity in list(layout_get_kwargs.keys()):
             if entity in entities: