Add .nwb to known Zarr suffixes; add tests for NWB Zarr backend

dandi/consts.py

@@ -167,7 +167,7 @@ def urls(self) -> Iterator[str]:
 VIDEO_FILE_EXTENSIONS = [".mp4", ".avi", ".wmv", ".mov", ".flv", ".mkv"]
 VIDEO_FILE_MODULES = ["processing", "acquisition"]
 
-ZARR_EXTENSIONS = [".ngff", ".zarr"]
+ZARR_EXTENSIONS = [".ngff", ".zarr", ".nwb"]
 
 #: Maximum allowed depth of a Zarr directory tree
 MAX_ZARR_DEPTH = 7

dandi/pynwb_utils.py

@@ -6,13 +6,14 @@
 import os.path as op
 from pathlib import Path
 import re
-from typing import IO, Any, Dict, List, Optional, Tuple, TypeVar, Union, cast
+from typing import IO, Any, Dict, List, Literal, Optional, Tuple, TypeVar, Union, cast
 import warnings
 
 import dandischema
 from fscacher import PersistentCache
 import h5py
 import hdmf
+import hdmf_zarr
 from packaging.version import Version
 import pynwb
 from pynwb import NWBHDF5IO
@@ -482,14 +483,19 @@ def get_object_id(path: str | Path | Readable) -> Any:
 
 
 def make_nwb_file(
-    filename: StrPath, *args: Any, cache_spec: bool = False, **kwargs: Any
+    filename: StrPath,
+    *args: Any,
+    cache_spec: bool = False,
+    backend: Literal["hdf5", "zarr"] = "hdf5",
+    **kwargs: Any,
 ) -> StrPath:
     """A little helper to produce an .nwb file in the path using NWBFile
 
     Note: it doesn't cache_spec by default
     """
+    backends = dict(hdf5=pynwb.NWBHDF5IO, zarr=hdmf_zarr.NWBZarrIO)
     nwbfile = pynwb.NWBFile(*args, **kwargs)
-    with pynwb.NWBHDF5IO(filename, "w") as io:
+    with backends[backend](filename, "w") as io:
         io.write(nwbfile, cache_spec=cache_spec)
     return filename
 

dandi/tests/fixtures.py

@@ -229,6 +229,17 @@
         ),
         **simple1_nwb_metadata,
     )
+    make_nwb_file(
+        tmp_path / "simple1_zarr.nwb",
+        backend="zarr",
+        subject=pynwb.file.Subject(
+            subject_id="lizard001",
+            date_of_birth=datetime(2016, 12, 1, tzinfo=tzutc()),
+            sex="F",
+            species="Gekko gecko",
+        ),
+        **simple1_nwb_metadata,
+    )
     (tmp_path / dandiset_metadata_file).write_text("{}\n")
     r = CliRunner().invoke(organize, ["-f", "move", "--dandiset-path", str(tmp_path)])
     assert r.exit_code == 0, r.stdout

setup.cfg

@@ -38,6 +38,7 @@ install_requires =
     fasteners
     fscacher >= 0.3.0
     hdmf != 3.5.0
+    hdmf_zarr
     humanize
     interleave ~= 0.1
     joblib