FIX: Match only within relative path when indexer is validating

bids/layout/index.py

@@ -26,16 +26,22 @@ def _extract_entities(bidsfile, entities):
     return match_vals
 
 
-def _check_path_matches_patterns(path, patterns):
+def _check_path_matches_patterns(path, patterns, root=None):
     """Check if the path matches at least one of the provided patterns. """
     if not patterns:
         return False
+
     path = path.absolute()
+    if root is not None:
+        path = Path("/") / path.relative_to(root)
+
+    # Path now can be downcast to str
+    path = str(path)
     for patt in patterns:
-        if isinstance(patt, Path):
-            if path == patt:
+        if isinstance(patt, (str, Path)):
+            if str(patt) in path:
                 return True
-        elif patt.search(str(path)):
+        elif patt.search(path):
             return True
     return False
 
@@ -115,17 +121,17 @@ def session(self):
         return self._layout.connection_manager.session
 
     def _validate_dir(self, d, default=None):
-        if _check_path_matches_patterns(d, self._include_patterns):
+        if _check_path_matches_patterns(d, self._include_patterns, root=self._layout._root):
             return True
-        if _check_path_matches_patterns(d, self._exclude_patterns):
+        if _check_path_matches_patterns(d, self._exclude_patterns, root=self._layout._root):
             return False
         return default
 
     def _validate_file(self, f, default=None):
         # Inclusion takes priority over exclusion
-        if _check_path_matches_patterns(f, self._include_patterns):
+        if _check_path_matches_patterns(f, self._include_patterns, root=self._layout._root):
             return True
-        if _check_path_matches_patterns(f, self._exclude_patterns):
+        if _check_path_matches_patterns(f, self._exclude_patterns, root=self._layout._root):
             return False
 
         # If inclusion/exclusion is inherited from a parent directory, that

bids/layout/tests/test_layout.py

@@ -13,7 +13,7 @@
 
 from bids.layout import BIDSLayout, Query
 from bids.layout.models import Config
-from bids.layout.index import BIDSLayoutIndexer
+from bids.layout.index import BIDSLayoutIndexer, _check_path_matches_patterns
 from bids.layout.utils import PaddedInt
 from bids.tests import get_test_data_path
 from bids.utils import natural_sort
@@ -835,3 +835,33 @@ def test_padded_run_roundtrip(layout_ds005):
     assert ents["run"] == 1
     newpath = layout_ds005.build_path(ents, absolute_paths=False)
     assert newpath == "sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz"
+
+@pytest.mark.parametrize(
+    "fname", [
+        "sub-01/anat/sub-01_T1w.nii.gz",
+        ".datalad",
+        "code",
+        "sub-01/.datalad",
+    ],
+)
+def test_indexer_patterns(fname):
+    root = Path("/home/user/.cache/data/")
+    path = root / fname
+
+    assert _check_path_matches_patterns(
+        path,
+        ["code"],
+        root=None,
+    ) is (fname == "code")
+
+    assert _check_path_matches_patterns(
+        path,
+        [re.compile(r"/\.")],
+        root=None,
+    ) is True
+
+    assert _check_path_matches_patterns(
+        path,
+        [re.compile(r"/\.")],
+        root=root,
+    ) is (".datalad" in fname)