NWBHDF5IO ER and ER_Manager

CHANGELOG.md

@@ -1,5 +1,10 @@
 # PyNWB Changelog
 
+## PyNWB 2.3.4 (Upcoming)
+
+### Enhancements and minor changes
+- Add support for `ExternalResources`. @mavaylon1 [#1684](https://github.com/NeurodataWithoutBorders/pynwb/pull/1684)
+
 ## PyNWB 2.3.3 (June 26, 2023)
 
 ### Enhancements and minor changes

requirements-min.txt

@@ -1,6 +1,6 @@
 # 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
+hdmf==3.6.0
 numpy==1.16
 pandas==1.1.5
 python-dateutil==2.7.3

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==3.6.0
 numpy==1.24.2; python_version >= "3.8"
 numpy==1.21.5; python_version < "3.8"  # note that numpy 1.22 dropped python 3.7 support
 pandas==2.0.0; python_version >= "3.8"

setup.py

@@ -20,7 +20,7 @@
 
 reqs = [
     'h5py>=2.10',
-    'hdmf>=3.5.4',
+    'hdmf>=3.6.0',
     'numpy>=1.16',
     'pandas>=1.1.5',
     'python-dateutil>=2.7.3',

src/pynwb/__init__.py

@@ -13,6 +13,7 @@
 from hdmf.backends.hdf5 import HDF5IO as _HDF5IO
 from hdmf.build import BuildManager, TypeMap
 import hdmf.common
+from hdmf.common.resources import ExternalResources
 
 CORE_NAMESPACE = 'core'
 
@@ -215,10 +216,15 @@ 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', '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 =\
+            popargs('path', 'mode', 'manager', 'extensions', 'load_namespaces',
+                    'file', 'comm', 'driver', 'external_resources', kwargs)
+        self.external_resources = external_resources
         # Define the BuildManager to use
         if load_namespaces:
             if manager is not None:
@@ -297,7 +303,11 @@ 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)
+        if self.external_resources is not None:
+            er_read = ExternalResources.from_flat_tsv(path=self.external_resources)
+            file.link_resources(er_read)
+        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 +359,6 @@ 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)