NWBHDF5IO ER and ER_Manager (#1684)

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## PyNWB 2.4.0 (Upcoming)
 
 ### Enhancements and minor changes
+- Add support for `ExternalResources`. @mavaylon1 [#1684](https://github.com/NeurodataWithoutBorders/pynwb/pull/1684)
 - Update links for making a release. @mavaylon1 [#1720](https://github.com/NeurodataWithoutBorders/pynwb/pull/1720)
 
 ## PyNWB 2.3.3 (June 26, 2023)

requirements-min.txt

@@ -1,7 +1,7 @@
 # minimum versions of package dependencies for installing PyNWB
 h5py==2.10  # support for selection of datasets with list of indices added in 2.10
-hdmf==3.5.4
-numpy==1.16
+hdmf==3.7.0
+numpy==1.18
 pandas==1.1.5
 python-dateutil==2.7.3
 setuptools

requirements.txt

@@ -1,6 +1,6 @@
 # pinned dependencies to reproduce an entire development environment to use PyNWB
 h5py==3.8.0
-hdmf==3.5.4
+hdmf==3.7.0
 numpy==1.24.2
 pandas==2.0.0
 python-dateutil==2.8.2

setup.py

@@ -20,7 +20,7 @@
 
 reqs = [
     'h5py>=2.10',
-    'hdmf>=3.5.4',
+    'hdmf>=3.7.0',
     'numpy>=1.16',
     'pandas>=1.1.5',
     'python-dateutil>=2.7.3',

src/pynwb/__init__.py

@@ -215,10 +215,13 @@ class NWBHDF5IO(_HDF5IO):
             {'name': 'file', 'type': [h5py.File, 'S3File'], 'doc': 'a pre-existing h5py.File object', 'default': None},
             {'name': 'comm', 'type': "Intracomm", 'doc': 'the MPI communicator to use for parallel I/O',
              'default': None},
-            {'name': 'driver', 'type': str, 'doc': 'driver for h5py to use when opening HDF5 file', 'default': None})
+            {'name': 'driver', 'type': str, 'doc': 'driver for h5py to use when opening HDF5 file', 'default': None},
+            {'name': 'external_resources_path', 'type': str, 'doc': 'The path to the ExternalResources',
+             'default': None},)
     def __init__(self, **kwargs):
-        path, mode, manager, extensions, load_namespaces, file_obj, comm, driver =\
-            popargs('path', 'mode', 'manager', 'extensions', 'load_namespaces', 'file', 'comm', 'driver', kwargs)
+        path, mode, manager, extensions, load_namespaces, file_obj, comm, driver, external_resources_path =\
+            popargs('path', 'mode', 'manager', 'extensions', 'load_namespaces',
+                    'file', 'comm', 'driver', 'external_resources_path', kwargs)
         # Define the BuildManager to use
         if load_namespaces:
             if manager is not None:
@@ -247,7 +250,8 @@ def __init__(self, **kwargs):
             elif manager is None:
                 manager = get_manager()
         # Open the file
-        super().__init__(path, manager=manager, mode=mode, file=file_obj, comm=comm, driver=driver)
+        super().__init__(path, manager=manager, mode=mode, file=file_obj, comm=comm,
+                         driver=driver, external_resources_path=external_resources_path)
 
     @property
     def nwb_version(self):
@@ -297,7 +301,8 @@ def read(self, **kwargs):
                 raise TypeError("NWB version %s not supported. PyNWB supports NWB files version 2 and above." %
                                 str(file_version_str))
         # read the file
-        return super().read(**kwargs)
+        file = super().read(**kwargs)
+        return file
 
     @docval({'name': 'src_io', 'type': HDMFIO,
              'doc': 'the HDMFIO object (such as NWBHDF5IO) that was used to read the data to export'},
@@ -349,7 +354,6 @@ def export(self, **kwargs):
 from .core import NWBContainer, NWBData  # noqa: F401,E402
 from .base import TimeSeries, ProcessingModule  # noqa: F401,E402
 from .file import NWBFile  # noqa: F401,E402
-
 from . import behavior  # noqa: F401,E402
 from . import device  # noqa: F401,E402
 from . import ecephys  # noqa: F401,E402

src/pynwb/file.py

@@ -8,6 +8,7 @@
 import pandas as pd
 
 from hdmf.common import DynamicTableRegion, DynamicTable
+from hdmf.container import ExternalResourcesManager
 from hdmf.utils import docval, getargs, get_docval, popargs, popargs_to_dict, AllowPositional
 
 from . import register_class, CORE_NAMESPACE
@@ -149,7 +150,7 @@ def __init__(self, **kwargs):
 
 
 @register_class('NWBFile', CORE_NAMESPACE)
-class NWBFile(MultiContainerInterface):
+class NWBFile(MultiContainerInterface, ExternalResourcesManager):
     """
     A representation of an NWB file.
     """

src/pynwb/resources.py

@@ -0,0 +1,10 @@
+from hdmf.common import ExternalResources as hdmf_ExternalResources
+from . import get_type_map as tm
+from hdmf.utils import docval, get_docval
+
+
+class ExternalResources(hdmf_ExternalResources):
+    @docval(*get_docval(hdmf_ExternalResources.__init__))
+    def __init__(self, **kwargs):
+        kwargs['type_map'] = tm()
+        super().__init__(**kwargs)

tests/unit/test_resources.py

@@ -0,0 +1,11 @@
+from pynwb.resources import ExternalResources
+from pynwb.testing import TestCase
+
+
+class TestNWBContainer(TestCase):
+    def test_constructor(self):
+        """
+        Test constructor
+        """
+        er = ExternalResources()
+        self.assertIsInstance(er, ExternalResources)