add NWBHDF5IO.read_nwb() method (#1979)

Co-authored-by: Ryan Ly <[email protected]>

Author: h-mayorquin

CHANGELOG.md

@@ -2,6 +2,9 @@
 
 ## PyNWB 2.8.3 (Upcoming)
 
+### Enhancements and minor changes
+* Added `NWBHDF5IO.read_nwb` convenience method to simplify reading an NWB file. @h-mayorquin [#1979](https://github.com/NeurodataWithoutBorders/pynwb/pull/1979)
+
 ### Documentation and tutorial enhancements
 - Added documentation example for `SpikeEventSeries`. @stephprince [#1983](https://github.com/NeurodataWithoutBorders/pynwb/pull/1983)
 

requirements-opt.txt

@@ -1,3 +1,8 @@
 linkml-runtime==1.7.4; python_version >= "3.9"
 schemasheets==0.2.1; python_version >= "3.9"
 oaklib==0.5.32; python_version >= "3.9"
+
+# for streaming tests
+fsspec==2024.10.0
+requests==2.32.3
+aiohttp==3.10.10

src/pynwb/__init__.py

@@ -506,6 +506,34 @@ def export(self, **kwargs):
         kwargs['container'] = nwbfile
         super().export(**kwargs)
 
+    @staticmethod
+    @docval({'name': 'path', 'type': (str, Path), 'doc': 'the path to the HDF5 file', 'default': None},
+            {'name': 'file', 'type': [h5py.File, 'S3File'], 'doc': 'a pre-existing h5py.File object', 'default': None},
+            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)
+        file = popargs('file', kwargs)
+        
+        path = str(path) if path is not None else None
+
+        # Streaming case
+        if path is not None and (path.startswith("s3://") or path.startswith("http")):
+            import fsspec
+            fsspec_file_system = fsspec.filesystem("http")
+            ffspec_file = fsspec_file_system.open(path, "rb")
+
+            open_file = h5py.File(ffspec_file, "r")
+            io = NWBHDF5IO(file=open_file)
+            nwbfile = io.read()
+        else:
+            io = NWBHDF5IO(path=path, file=file, mode="r", load_namespaces=True)
+            nwbfile = io.read()
+
+        return nwbfile
 
 from . import io as __io  # noqa: F401,E402
 from .core import NWBContainer, NWBData  # noqa: F401,E402

tests/integration/hdf5/test_io.py

@@ -18,6 +18,13 @@
 from pynwb.testing.mock.file import mock_NWBFile
 
 
+import unittest
+try:
+    import fsspec # noqa f401
+    HAVE_FSSPEC = True 
+except ImportError:
+    HAVE_FSSPEC = False
+
 class TestHDF5Writer(TestCase):
 
     _required_tests = ('test_nwbio', 'test_write_clobber', 'test_write_cache_spec', 'test_write_no_cache_spec')
@@ -586,3 +593,38 @@ def test_can_read_file_old_version(self):
     def test_can_read_file_invalid_hdf5_file(self):
         # current file is not an HDF5 file
         self.assertFalse(NWBHDF5IO.can_read(__file__))
+
+    def test_read_nwb_method_path(self):
+        
+        # write the example file
+        with NWBHDF5IO(self.path, 'w') as io:
+            io.write(self.nwbfile)
+            
+        # test that the read_nwb method works
+        read_nwbfile = NWBHDF5IO.read_nwb(path=self.path)
+        self.assertContainerEqual(read_nwbfile, self.nwbfile)
+
+        read_nwbfile.get_read_io().close()
+        
+    def test_read_nwb_method_file(self):
+        
+        # write the example file
+        with NWBHDF5IO(self.path, 'w') as io:
+            io.write(self.nwbfile)
+            
+        import h5py
+        
+        file = h5py.File(self.path, 'r')
+        
+        read_nwbfile = NWBHDF5IO.read_nwb(file=file)
+        self.assertContainerEqual(read_nwbfile, self.nwbfile)
+
+        read_nwbfile.get_read_io().close()
+    
+    @unittest.skipIf(not HAVE_FSSPEC, "fsspec library not available")
+    def test_read_nwb_method_s3_path(self):
+        s3_test_path = "https://dandiarchive.s3.amazonaws.com/blobs/11e/c89/11ec8933-1456-4942-922b-94e5878bb991"
+        read_nwbfile = NWBHDF5IO.read_nwb(path=s3_test_path)
+        assert read_nwbfile.identifier == "3f77c586-6139-4777-a05d-f603e90b1330"
+    
+        assert read_nwbfile.subject.subject_id == "1"