fix: collect data interactions with sessions and bids filters

niworkflows/utils/bids.py

@@ -189,8 +189,9 @@ def collect_data(
         The BIDS directory
     participant_label : :obj:`str`
         The participant identifier
-    session_id : :obj:`str`, None, or :obj:`bids.layout.Query`
-        The session identifier. By default, all sessions will be used.
+    session_id : :obj:`str`, :obj:`list`, None, or :obj:`bids.layout.Query`
+        The session identifier(s). By default, all sessions will be used.
+        If specified, BIDS filters may only select sessions among these.
     task : :obj:`str` or None
         The task identifier (for BOLD queries)
     echo : :obj:`int` or None
@@ -273,29 +274,27 @@ def collect_data(
     for acq, entities in bids_filters.items():
         if acq not in queries:  # filter with no matching query
             continue
-        # BIDS filters will not be able to override subject / session entities
+        # BIDS filters may narrow down, but not override, subject / session entities
         for entity, param in reserved_entities:
             if param == Query.OPTIONAL:
                 continue
-            if entity in entities and listify(param) != listify(entities[entity]):
+            if entity in entities and not set(listify(entities[entity])) <= set(listify(param)):
                 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:
-                # avoid clobbering layout.get
-                del layout_get_kwargs[entity]
 
     if task:
         queries['bold']['task'] = queries['pet']['task'] = task
 
     if echo:
         queries['bold']['echo'] = echo
 
+    # Query entities take precedence over the defaults, for that query only
     subj_data = {
-        dtype: sorted(layout.get(**layout_get_kwargs, **query)) for dtype, query in queries.items()
+        dtype: sorted(layout.get(**{**layout_get_kwargs, **query}))
+        for dtype, query in queries.items()
     }
 
     # Special case: multi-echo BOLD, grouping echos

niworkflows/utils/tests/test_bids.py

@@ -1,5 +1,9 @@
 """Tests for :mod:`niworkflows.utils.bids`."""
 
+from pathlib import Path
+
+import pytest
+
 from ..bids import collect_data
 from ..testing import generate_bids_skeleton
 
@@ -8,6 +12,17 @@
     '01': [{'anat': [{'suffix': 'T1w', 'metadata': {'EchoTime': 1}}]}],
 }
 
+SESSIONS_SKELETON = {
+    '01': [
+        {
+            'session': session,
+            'anat': [{'suffix': 'T1w'}],
+            'func': [{'task': 'rest', 'suffix': 'bold', 'metadata': {'RepetitionTime': 2.0}}],
+        }
+        for session in ('anat', 'func1', 'func2')
+    ],
+}
+
 
 def test_collect_data_ignores_filter_without_query(tmp_path):
     """A filter naming a suffix absent from ``queries`` is dropped, not an error."""
@@ -22,3 +37,47 @@ def test_collect_data_ignores_filter_without_query(tmp_path):
         bids_filters={'pet': {'session': '15'}},
     )
     assert len(subj_data['t1w']) == 1
+
+
+@pytest.mark.parametrize(
+    ('session_id', 'bold_session', 't1w', 'bold'),
+    [
+        (None, 'func2', ['anat', 'func1', 'func2'], ['func2']),
+        (['anat', 'func1'], 'func1', ['anat', 'func1'], ['func1']),
+        ('func1', 'func1', ['func1'], ['func1']),
+    ],
+    ids=['no_session_id', 'narrow_sessions', 'clobber_session'],
+)
+def test_collect_data_session_filters(tmp_path, session_id, bold_session, t1w, bold):
+    """BIDS filters narrow down the requested sessions for their query only."""
+    root = tmp_path / 'bids'
+    generate_bids_skeleton(root, SESSIONS_SKELETON)
+
+    subj_data, _ = collect_data(
+        root,
+        '01',
+        session_id=session_id,
+        bids_validate=False,
+        bids_filters={'bold': {'session': bold_session}},
+    )
+
+    def _sessions(files):
+        return [Path(f).parts[-3].removeprefix('ses-') for f in files]
+
+    assert _sessions(subj_data['t1w']) == t1w
+    assert _sessions(subj_data['bold']) == bold
+
+
+def test_collect_data_session_filter_conflict(tmp_path):
+    """BIDS filters cannot select sessions outside of the requested ones."""
+    root = tmp_path / 'bids'
+    generate_bids_skeleton(root, SESSIONS_SKELETON)
+
+    with pytest.raises(ValueError, match='Conflicting entities for "session"'):
+        collect_data(
+            root,
+            '01',
+            session_id=['anat', 'func1'],
+            bids_validate=False,
+            bids_filters={'bold': {'session': 'func2'}},
+        )