From b31e677b06d0cfb2502f6ce327a3833077263802 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 18 Jul 2023 15:11:59 -0400
Subject: [PATCH 1/6] add .nwb to known zarr suffixes

---
 dandi/consts.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dandi/consts.py b/dandi/consts.py
index 34391185a..59b422165 100644
--- a/dandi/consts.py
+++ b/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

From 50499999b89e4faff61f897bcf0339aaa8649da3 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 18 Jul 2023 15:32:30 -0400
Subject: [PATCH 2/6] add zarr backend to pynwb_utils

---
 dandi/pynwb_utils.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/dandi/pynwb_utils.py b/dandi/pynwb_utils.py
index b7cfaa6d4..076d4d54f 100644
--- a/dandi/pynwb_utils.py
+++ b/dandi/pynwb_utils.py
@@ -13,6 +13,7 @@
 from fscacher import PersistentCache
 import h5py
 import hdmf
+import hdmf_zarr
 from packaging.version import Version
 import pynwb
 from pynwb import NWBHDF5IO
@@ -482,14 +483,15 @@ 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
 

From 9bfb9ca0fca9b0d54db5771a3e6f7f59a44b841b Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 18 Jul 2023 15:36:49 -0400
Subject: [PATCH 3/6] add extra zarr file to existing directory fixture

---
 dandi/tests/fixtures.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/dandi/tests/fixtures.py b/dandi/tests/fixtures.py
index 2ad4505ab..5977d53d3 100644
--- a/dandi/tests/fixtures.py
+++ b/dandi/tests/fixtures.py
@@ -229,6 +229,17 @@ def organized_nwb_dir2(
         ),
         **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

From 5d48f40a59fcba470582f02c4566444839306c18 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 18 Jul 2023 15:37:56 -0400
Subject: [PATCH 4/6] add hdmf_zarr to requirements

---
 setup.cfg | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.cfg b/setup.cfg
index b9326e731..9a6e12b44 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -38,6 +38,7 @@ install_requires =
     fasteners
     fscacher >= 0.3.0
     hdmf != 3.5.0
+    hdmf_zarr
     humanize
     interleave ~= 0.1
     joblib

From 71e8c3d743dfa2c4fceea62c434463b825a1a8e8 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 18 Jul 2023 15:43:13 -0400
Subject: [PATCH 5/6] black and import

---
 dandi/pynwb_utils.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/dandi/pynwb_utils.py b/dandi/pynwb_utils.py
index 076d4d54f..b13d3ae53 100644
--- a/dandi/pynwb_utils.py
+++ b/dandi/pynwb_utils.py
@@ -6,7 +6,7 @@
 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
@@ -483,7 +483,11 @@ def get_object_id(path: str | Path | Readable) -> Any:
 
 
 def make_nwb_file(
-    filename: StrPath, *args: Any, cache_spec: bool = False, backend: Literal["hdf5", "zarr"] = "hdf5", **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
 

From 14c9c1e4a2f401223f0ee136962408c84376054a Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Thu, 4 Jan 2024 11:33:16 -0500
Subject: [PATCH 6/6] Update dandi/consts.py

---
 dandi/consts.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dandi/consts.py b/dandi/consts.py
index 59b422165..34391185a 100644
--- a/dandi/consts.py
+++ b/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", ".nwb"]
+ZARR_EXTENSIONS = [".ngff", ".zarr"]
 
 #: Maximum allowed depth of a Zarr directory tree
 MAX_ZARR_DEPTH = 7