Joint BIDS-NWB metadata extraction.

dandi/files/bids.py

@@ -226,7 +226,7 @@ def get_metadata(
         digest: Optional[Digest] = None,
         ignore_errors: bool = True,
     ) -> BareAsset:
-        bids_metadata = BIDSAsset.get_metadata(self)
+        bids_metadata = BIDSAsset.get_metadata(self, digest, ignore_errors)
         nwb_metadata = NWBAsset.get_metadata(self, digest, ignore_errors)
         return BareAsset(
             **{**bids_metadata.dict(), **nwb_metadata.dict(exclude_none=True)}

dandi/metadata.py

@@ -88,12 +88,14 @@ def get_metadata(
     bids_dataset_description = find_bids_dataset_description(path)
     if bids_dataset_description:
         dandiset_path = find_parent_directory_containing("dandiset.yaml", path)
-        bids_dataset_description = find_bids_dataset_description(path)
         df = dandi_file(
             Path(path),
             dandiset_path,
             bids_dataset_description=bids_dataset_description,
         )
+        if not digest:
+            _digest = "0" * 32 + "-1"
+            digest = Digest.dandi_etag(_digest)
         path_metadata = df.get_metadata(digest=digest)
         assert isinstance(df, bids.BIDSAsset)
         meta["bids_version"] = df.get_validation_bids_version()
@@ -105,7 +107,7 @@ def get_metadata(
                 pass
             else:
                 meta[key] = value
-    elif path.endswith((".NWB", ".nwb")):
+    if path.endswith((".NWB", ".nwb")):
         if nwb_has_external_links(path):
             raise NotImplementedError(
                 f"NWB files with external links are not supported: {path}"
@@ -150,8 +152,10 @@ def get_metadata(
                 __import__(import_mod)
 
         meta["nd_types"] = get_neurodata_types(path)
-    else:
-        raise RuntimeError("Unable to get metadata from non-BIDS, non-NWB asset.")
+    if not meta:
+        raise RuntimeError(
+            "Unable to get metadata from non-BIDS, non-NWB asset: `%s`." % path
+        )
     return meta
 
 

dandi/tests/fixtures.py

@@ -41,6 +41,7 @@
 BIDS_TESTDATA_SELECTION = [
     "asl003",
     "eeg_cbm",
+    "ieeg_epilepsyNWB",
     # uncomment once upstream releases fixed spec:
     # https://github.com/bids-standard/bids-specification/pull/1346#event-7696972438
     # "hcp_example_bids",
@@ -537,6 +538,18 @@ def bids_dandiset(new_dandiset: SampleDandiset, bids_examples: str) -> SampleDan
     return new_dandiset
 
 
+@pytest.fixture()
+def bids_nwb_dandiset(
+    new_dandiset: SampleDandiset, bids_examples: str
+) -> SampleDandiset:
+    copytree(
+        os.path.join(bids_examples, "ieeg_epilepsyNWB"),
+        str(new_dandiset.dspath) + "/",
+    )
+    (new_dandiset.dspath / "CHANGES").write_text("0.1.0 2014-11-03\n")
+    return new_dandiset
+
+
 @pytest.fixture()
 def bids_dandiset_invalid(
     new_dandiset: SampleDandiset, bids_error_examples: str

dandi/tests/test_metadata.py

@@ -1,6 +1,8 @@
 from datetime import datetime, timedelta
 import json
+import os
 from pathlib import Path
+import shutil
 from typing import Any, Dict, Optional, Tuple, Union
 
 from dandischema.consts import DANDI_SCHEMA_VERSION
@@ -48,6 +50,32 @@ def test_get_metadata(simple1_nwb: str, simple1_nwb_metadata: Dict[str, Any]) ->
     assert target_metadata == metadata
 
 
+def test_bids_nwb_metadata_integration(bids_examples, tmp_path):
+    """
+    Notes
+    -----
+    * Generating data manually here, as fixture workflow calls `new_dandiset`,
+        which requires spinning up docker:
+        https://github.com/dandi/dandi-cli/pull/1183#discussion_r1061622910
+    """
+
+    source_dpath = os.path.join(bids_examples, "ieeg_epilepsyNWB")
+    dpath = os.path.join(tmp_path, "ieeg_epilepsyNWB")
+    shutil.copytree(source_dpath, dpath)
+
+    file_path = os.path.join(
+        dpath,
+        *"sub-01/ses-postimp/ieeg/sub-01_ses-postimp_task-seizure_run-01_ieeg.nwb".split(
+            "/"
+        )
+    )
+    metadata = get_metadata(file_path)
+    # This is a key sourced from both NWB and BIDS:
+    assert metadata["subject_id"] == "01"
+    # This is a key sourced from NWB only:
+    assert metadata["sex"] == "U"
+
+
 @pytest.mark.parametrize(
     "age,duration",
     [