Merge pull request #788 from nipreps/fix/786-read-bids-meta

ENH: Allow passing a ``database_path`` to create a ``BIDSLayout``

Author: effigies

niworkflows/interfaces/bids.py

@@ -84,6 +84,7 @@ class _BIDSBaseInputSpec(BaseInterfaceInputSpec):
         (None, Directory(exists=True)), usedefault=True, desc="optional bids directory"
     )
     bids_validate = traits.Bool(True, usedefault=True, desc="enable BIDS validator")
+    index_db = Directory(exists=True, desc="a PyBIDS layout cache directory")
 
 
 class _BIDSInfoInputSpec(_BIDSBaseInputSpec):
@@ -832,7 +833,13 @@ def _outputs(self):
     def _run_interface(self, runtime):
         self.layout = self.inputs.bids_dir or self.layout
         self.layout = _init_layout(
-            self.inputs.in_file, self.layout, self.inputs.bids_validate
+            self.inputs.in_file,
+            self.layout,
+            self.inputs.bids_validate,
+            database_path=(
+                self.inputs.index_db if isdefined(self.inputs.index_db)
+                else None
+            )
         )
 
         # Fill in BIDS entities of the output ("*_id")

niworkflows/utils/bids.py

@@ -280,7 +280,7 @@ def get_metadata_for_nifti(in_file, bids_dir=None, validate=True):
     return _init_layout(in_file, bids_dir, validate).get_metadata(str(in_file))
 
 
-def _init_layout(in_file=None, bids_dir=None, validate=True):
+def _init_layout(in_file=None, bids_dir=None, validate=True, database_path=None):
     if isinstance(bids_dir, BIDSLayout):
         return bids_dir
 
@@ -294,7 +294,11 @@ def _init_layout(in_file=None, bids_dir=None, validate=True):
         if bids_dir is None:
             raise RuntimeError("Could not infer BIDS root")
 
-    layout = BIDSLayout(str(bids_dir), validate=validate)
+    layout = BIDSLayout(
+        str(bids_dir),
+        validate=validate,
+        database_path=database_path,
+    )
     return layout