get_class creates class which can not read text data back

[t-b]

pynwb: 1.4.0
hdfm: 2.1.0
python 3.7.4
h5py 2.10.0
Windows

Below is a MWE and the backtrace.

I'm a bit suprised I had to pass a list at

data = ["abcd"]

into UserCommentDevice.

I'd be glad to hear about workarounds.

MWE:

from pynwb.spec import NWBNamespaceBuilder, NWBGroupSpec, NWBAttributeSpec, NWBDatasetSpec
from pynwb import load_namespaces, get_class

name = 'test_multicontainerinterface'
ns_path = name + ".namespace.yaml"
ext_source = name + ".extensions.yaml"

ns_builder = NWBNamespaceBuilder(name + ' extensions', name, version='0.1.0')
ns_builder.include_type('NWBDataInterface', namespace='core')
ns_builder.include_type('NWBData', namespace='core')

user_comment_string = NWBDatasetSpec('device specific user text notes',
                                            neurodata_type_def='UserCommentString',
                                            neurodata_type_inc='NWBData',
                                            dtype="text")

potato_sack = NWBGroupSpec(neurodata_type_def='PotatoSack',
                           neurodata_type_inc='NWBDataInterface',
                           name='potato_sack',
                           doc='A sack of potatoes', quantity='?',
                           datasets=[user_comment_string])

ns_builder.add_spec(ext_source, potato_sack)
ns_builder.export(ns_path)

from pynwb import register_class, load_namespaces
from pynwb.file import MultiContainerInterface, NWBContainer

load_namespaces(ns_path)

UserCommentString = get_class("UserCommentString", name)

@register_class('PotatoSack', name)
class PotatoSack(MultiContainerInterface):

    __clsconf__ = {
        'attr': 'user_comment_string',
        'type': UserCommentString,
        'add': 'add_potato',
        'get': 'get_potato',
        'create': 'create_potato',
    }


####################
# Then use the objects (again, this would often be done in a different file).

from pynwb import NWBHDF5IO, NWBFile
from datetime import datetime
from dateutil.tz import tzlocal

# You can add potatoes to a potato sack in different ways
potato_sack = PotatoSack(user_comment_string=UserCommentString(name='potato1', data = ["abcd"]))

nwbfile = NWBFile("a file with metadata", "NB123A", datetime(2018, 6, 1, tzinfo=tzlocal()))

pmod = nwbfile.create_processing_module('module_name', 'desc')
pmod.add_container(potato_sack)

with NWBHDF5IO('test_multicontainerinterface.nwb', 'w') as io:
    io.write(nwbfile)

####################
# This is how you read the NWB file (again, this would often be done in a
# different file).

load_namespaces(ns_path)
io = NWBHDF5IO('test_multicontainerinterface.nwb', 'r')
nwb = io.read()

$ python extensions.py
Traceback (most recent call last):
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1137, in construct
    obj.__init__(**kwargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 560, in func_call
    pargs = _check_args(args, kwargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 553, in _check_args
    raise ExceptionType(msg)
TypeError: TypeMap.__get_cls_dict.<locals>.__init__: incorrect type for 'data' (got 'str', expected 'ndarray, list, tuple, Dataset, HDMFDataset, AbstractDataChunkIterator, DataIO or Data')

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "extensions.py", line 69, in <module>
    nwb = io.read()
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\backends\hdf5\h5tools.py", line 414, in read
    return call_docval_func(super().read, kwargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 405, in call_docval_func
    return func(*fargs, **fkwargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\backends\io.py", line 36, in read
    container = self.__manager.construct(f_builder)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\manager.py", line 238, in construct
    result = self.__type_map.construct(builder, self, None)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\manager.py", line 857, in construct
    return obj_mapper.construct(builder, build_manager, parent)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1105, in construct
    subspecs = self.__get_subspec_values(builder, self.spec, manager)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1035, in __get_subspec_values
    self.__get_sub_builders(groups, spec.groups, manager, ret)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1085, in __get_sub_builders
    ret.update(self.__get_subspec_values(sub_builder, subspec, manager))
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1035, in __get_subspec_values
    self.__get_sub_builders(groups, spec.groups, manager, ret)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1077, in __get_sub_builders
    sub_builder = self.__flatten(sub_builder, subspec, manager)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1090, in __flatten
    tmp = [manager.construct(b) for b in sub_builder]
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1090, in <listcomp>
    tmp = [manager.construct(b) for b in sub_builder]
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\manager.py", line 234, in construct
    result = self.__type_map.construct(builder, self, parent)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\manager.py", line 857, in construct
    return obj_mapper.construct(builder, build_manager, parent)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1105, in construct
    subspecs = self.__get_subspec_values(builder, self.spec, manager)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1035, in __get_subspec_values
    self.__get_sub_builders(groups, spec.groups, manager, ret)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1077, in __get_sub_builders
    sub_builder = self.__flatten(sub_builder, subspec, manager)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1090, in __flatten
    tmp = [manager.construct(b) for b in sub_builder]
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1090, in <listcomp>
    tmp = [manager.construct(b) for b in sub_builder]
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\manager.py", line 234, in construct
    result = self.__type_map.construct(builder, self, parent)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\manager.py", line 857, in construct
    return obj_mapper.construct(builder, build_manager, parent)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1105, in construct
    subspecs = self.__get_subspec_values(builder, self.spec, manager)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1036, in __get_subspec_values
    self.__get_sub_builders(datasets, spec.datasets, manager, ret)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1077, in __get_sub_builders
    sub_builder = self.__flatten(sub_builder, subspec, manager)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1090, in __flatten
    tmp = [manager.construct(b) for b in sub_builder]
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1090, in <listcomp>
    tmp = [manager.construct(b) for b in sub_builder]
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\manager.py", line 234, in construct
    result = self.__type_map.construct(builder, self, parent)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\manager.py", line 857, in construct
    return obj_mapper.construct(builder, build_manager, parent)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py", line 561, in func_call
    return func(args[0], **pargs)
  File "C:\users\thomas\Anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py", line 1140, in construct
    raise Exception(msg) from ex
Exception: Could not construct UserCommentString object due to: TypeMap.__get_cls_dict.<locals>.__init__: incorrect type for 'data' (got 'str', expected 'ndarray, list, tuple, Dataset, HDMFDataset, AbstractDataChunkIterator, DataIO or Data')

[oruebel]

@t-b sorry, I just noticed that we seemed to have missed this issue. Is this still a problem?

[t-b]

Thanks for pinging. Indeed this is fixed with pynwb
5fcd364 (Add environment-ros3.yml to MANIFEST.in (#1398), 2021-08-13), hdmf b3437314 (Remove regex test for setting an unsettable property (#664), 2021-08-16) and h5py 3.3.