Adding argument for metadata indexing by generate_inputs (#367)

Argument passed transparently on to pybids BIDSLayout

snakebids/core/input_generation.py

@@ -56,6 +56,7 @@ def generate_inputs(
     participant_label: Iterable[str] | str | None = ...,
     exclude_participant_label: Iterable[str] | str | None = ...,
     use_bids_inputs: Literal[True] | None = ...,
+    index_metadata: bool = ...,
     validate: bool = ...,
     pybids_database_dir: Path | str | None = ...,
     pybids_reset_database: bool = ...,
@@ -75,6 +76,7 @@ def generate_inputs(
     participant_label: Iterable[str] | str | None = ...,
     exclude_participant_label: Iterable[str] | str | None = ...,
     use_bids_inputs: Literal[False] = ...,
+    index_metadata: bool = ...,
     validate: bool = ...,
     pybids_database_dir: Path | str | None = ...,
     pybids_reset_database: bool = ...,
@@ -93,6 +95,7 @@ def generate_inputs(
     participant_label: Iterable[str] | str | None = None,
     exclude_participant_label: Iterable[str] | str | None = None,
     use_bids_inputs: bool | None = None,
+    index_metadata: bool = False,
     validate: bool = False,
     pybids_database_dir: Path | str | None = None,
     pybids_reset_database: bool | None = None,
@@ -163,6 +166,10 @@ def generate_inputs(
         :class`BidsDataset`. Setting to True is deprecated as of v0.8, as this is now
         the default behaviour
 
+    index_metadata
+        If True indexes metadata of BIDS directory using pybids, otherwise skips
+        indexing.
+
     validate
         If True performs validation of BIDS directory using pybids, otherwise
         skips validation.
@@ -277,6 +284,7 @@ def generate_inputs(
             pybids_config=pybids_config,
             pybidsdb_dir=pybidsdb_dir,
             pybidsdb_reset=pybidsdb_reset,
+            index_metadata=index_metadata,
             validate=validate,
         )
         if not _all_custom_paths(pybids_inputs)
@@ -392,6 +400,7 @@ def _gen_bids_layout(
     pybidsdb_dir: Path | str | None,
     pybidsdb_reset: bool,
     pybids_config: Path | str | None = None,
+    index_metadata: bool = False,
     validate: bool = False,
 ) -> BIDSLayout:
     """Create (or reindex) the BIDSLayout.
@@ -414,6 +423,9 @@ def _gen_bids_layout(
         A boolean that determines whether to reset / overwrite
         existing database.
 
+    index_metadata
+        A boolen that determines whether to parse and index metadata
+
     validate
         A boolean that determines whether to validate the bids dataset
 
@@ -438,7 +450,7 @@ def _gen_bids_layout(
         config=pybids_config,
         database_path=pybidsdb_dir,
         reset_database=pybidsdb_reset,
-        indexer=BIDSLayoutIndexer(validate=False, index_metadata=False),
+        indexer=BIDSLayoutIndexer(validate=False, index_metadata=index_metadata),
     )
 
 

snakebids/tests/test_generate_inputs.py

@@ -1227,6 +1227,27 @@ def test_nonstandard_custom_pybids_config(tmpdir: Path):
         )
 
 
+def test_index_metadata(mocker: MockerFixture):
+    from snakebids.core import input_generation
+
+    spy = mocker.spy(input_generation, "BIDSLayoutIndexer")
+    mocker.patch.object(input_generation, "BIDSLayout", side_effect=ValueError)
+
+    # Simplest case -- one input type, using pybids
+    with pytest.raises(ValueError):  # noqa
+        generate_inputs(
+            pybids_inputs={"foo": {}},
+            bids_dir=...,  # type: ignore
+            derivatives=...,  # type: ignore
+            index_metadata=True,
+        )
+
+    spy.assert_called_once_with(
+        validate=False,
+        index_metadata=True,
+    )
+
+
 def test_t1w():
     # create config
     real_bids_dir = "snakebids/tests/data/bids_t1w"