Merge branch 'dev' into support_overwrite_file

CHANGELOG.md

@@ -13,6 +13,7 @@
 * Added test for opening file with consolidated metadata from DANDI. @mavaylon1 [#206](https://github.com/hdmf-dev/hdmf-zarr/pull/206)
 * Add dimension labels compatible with xarray. @mavaylon1 [#207](https://github.com/hdmf-dev/hdmf-zarr/pull/207)
 * Added link_data --> clear_cache relationship to support repacking zarr nwbfiles: [#215](https://github.com/hdmf-dev/hdmf-zarr/pull/215)
+* Added `NWBZarrIO.read_nwb` convenience method to simplify reading an NWB file. @oruebel [#226](https://github.com/hdmf-dev/hdmf-zarr/pull/226)
 
 ## 0.8.0 (June 4, 2024)
 ### Bug Fixes

src/hdmf_zarr/nwb.py

@@ -1,6 +1,7 @@
 """Module with Zarr backend for NWB for integration with PyNWB"""
 from warnings import warn
-from .backend import ZarrIO
+from pathlib import Path
+from .backend import ZarrIO, SUPPORTED_ZARR_STORES
 
 from hdmf.utils import (docval,
                         popargs,
@@ -63,5 +64,30 @@ def export(self, **kwargs):
             kwargs['container'] = nwbfile
             super().export(**kwargs)
 
+        @staticmethod
+        @docval({'name': 'path',
+                 'type': (str, Path, *SUPPORTED_ZARR_STORES),
+                 'doc': 'the path to the Zarr file or a supported Zarr store'},
+                is_method=False)
+        def read_nwb(**kwargs):
+            """
+            Helper factory method for reading an NWB file and return the NWBFile object
+            """
+            # Retrieve the filepath
+            path = popargs('path', kwargs)
+            if isinstance(path, Path):
+                path = str(path)
+            # determine default storage options to use when opening a file from S3
+            storage_options = {}
+            if isinstance(path, str) and path.startswith(("s3://")):
+                storage_options = dict(anon=True)
+
+            # open the file with NWBZarrIO and rad the file
+            io = NWBZarrIO(path=path, mode="r", load_namespaces=True, storage_options=storage_options)
+            nwbfile = io.read()
+
+            # return the NWBFile object
+            return nwbfile
+
 except ImportError:
     warn("PyNWB is not installed. Support for NWBZarrIO is disabled.")

tests/unit/test_fsspec_streaming.py

@@ -8,17 +8,21 @@
 
 
 class TestFSSpecStreaming(unittest.TestCase):
-    @unittest.skipIf(not HAVE_FSSPEC, "fsspec not installed")
-    def test_fsspec_streaming(self):
+
+    def setUp(self):
         # PLACEHOLDER test file from Allen Institute for Neural Dynamics
         # TODO: store a small test file and use it to speed up testing
-        remote_path = (
+        self.s3_aind_path = (
             "s3://aind-open-data/ecephys_625749_2022-08-03_15-15-06_nwb_2023-05-16_16-34-55/"
             "ecephys_625749_2022-08-03_15-15-06_nwb/"
             "ecephys_625749_2022-08-03_15-15-06_experiment1_recording1.nwb.zarr/"
         )
+        # DANDISET: 000719/icephys_9_27_2024
+        self.https_s3_path = "https://dandiarchive.s3.amazonaws.com/zarr/7515c603-9940-4598-aa1b-8bf32dc9b10c/"
 
-        with NWBZarrIO(remote_path, mode="r", storage_options=dict(anon=True)) as io:
+    @unittest.skipIf(not HAVE_FSSPEC, "fsspec not installed")
+    def test_fsspec_streaming(self):
+        with NWBZarrIO(self.s3_aind_path, mode="r", storage_options=dict(anon=True)) as io:
             nwbfile = io.read()
 
         self.assertEqual(nwbfile.identifier, "ecephys_625749_2022-08-03_15-15-06")
@@ -32,10 +36,20 @@ def test_s3_open_with_consolidated_(self):
         """
         The file is a Zarr file with consolidated metadata.
         """
-        s3_path = "https://dandiarchive.s3.amazonaws.com/zarr/ccefbc9f-30e7-4a4c-b044-5b59d300040b/"
-        with NWBZarrIO(s3_path, mode='r') as read_io:
+        with NWBZarrIO(self.https_s3_path, mode='r') as read_io:
             read_io.open()
             self.assertIsInstance(read_io.file.store, zarr.storage.ConsolidatedMetadataStore)
-        with NWBZarrIO(s3_path, mode='-r') as read_io:
+        with NWBZarrIO(self.https_s3_path, mode='-r') as read_io:
             read_io.open()
             self.assertIsInstance(read_io.file.store, zarr.storage.FSStore)
+
+
+    @unittest.skipIf(not HAVE_FSSPEC, "fsspec not installed")
+    def test_fsspec_streaming_via_read_nwb(self):
+        """
+        Test reading from s3 using the convenience function NWBZarrIO.read_nwb
+        """
+        # Test with a s3:// URL
+        nwbfile = NWBZarrIO.read_nwb(self.s3_aind_path)
+        self.assertEqual(nwbfile.identifier, "ecephys_625749_2022-08-03_15-15-06")
+        self.assertEqual(nwbfile.institution, "AIND")

tests/unit/test_nwbzarrio.py

@@ -0,0 +1,56 @@
+import unittest
+from hdmf_zarr import NWBZarrIO
+import os
+import shutil
+from datetime import datetime
+from dateutil.tz import tzlocal
+
+try:
+    from pynwb import NWBFile
+    PYNWB_AVAILABLE = True
+except ImportError:
+    PYNWB_AVAILABLE = False
+
+
+@unittest.skipIf(not PYNWB_AVAILABLE, "PyNWB not installed")
+class TestNWBZarrIO(unittest.TestCase):
+
+    def setUp(self):
+        self.filepath = "test_io.zarr"
+
+    def tearDown(self):
+        if os.path.exists(self.filepath):
+            shutil.rmtree(self.filepath)
+
+    def write_test_file(self):
+        # Create the NWBFile
+        nwbfile = NWBFile(
+            session_description="my first synthetic recording",
+            identifier="EXAMPLE_ID",
+            session_start_time=datetime.now(tzlocal()),
+            experimenter="Dr. Bilbo Baggins",
+            lab="Bag End Laboratory",
+            institution="University of Middle Earth at the Shire",
+            experiment_description="I went on an adventure with thirteen dwarves "
+                                   "to reclaim vast treasures.",
+            session_id="LONELYMTN",
+        )
+
+        # Create a device
+        _ = nwbfile.create_device(
+            name="array", description="the best array", manufacturer="Probe Company 9000"
+        )
+        with NWBZarrIO(path=self.filepath, mode="w") as io:
+            io.write(nwbfile)
+
+    def test_read_nwb(self):
+        """
+        Test reading a local file with NWBZarrIO.read_nwb.
+
+        NOTE: See TestFSSpecStreaming.test_fsspec_streaming_via_read_nwb for corresponding tests
+              for reading a remote file with NWBZarrIO.read_nwb
+        """
+        self.write_test_file()
+        nwbfile = NWBZarrIO.read_nwb(path=self.filepath)
+        self.assertEqual(len(nwbfile.devices), 1)
+        self.assertTupleEqual(nwbfile.experimenter, ('Dr. Bilbo Baggins',))