Error in writing the Preprocessed data

[jessierliu]

Was trying to re-preprocess the data (on a new file with only the raw in it), and got the following error when it was trying to write the processed data:

TypeError                                 Traceback (most recent call last)
~/ChangLab/projects/ecogVIS/ecogvis/functions/subDialogs.py in run(self)
    433                         mode=self.mode,
    434                         config=self.config,
--> 435                         new_file=self.new_fname)
    436 
    437 

~/ChangLab/projects/ecogVIS/ecogvis/signal_processing/processing_data.py in processing_data(path, subject, blocks, mode, config, new_file)
     26 
     27         if mode=='preprocess':
---> 28             preprocess_raw_data(block_path, config=config)
     29         elif mode=='decomposition':
     30             spectral_decomposition(block_path, bands_vals=config)

~/ChangLab/projects/ecogVIS/ecogvis/signal_processing/processing_data.py in preprocess_raw_data(block_path, config)
    294 
    295             # Write LFP to NWB file
--> 296             io.write(nwb)
    297             print('LFP saved in '+block_path)
    298 

/anaconda3/envs/ecog_vis/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    412                         raise_from(ExceptionType(msg), None)
    413 
--> 414                 return func(self, **parsed['args'])
    415         else:
    416             def func_call(*args, **kwargs):

/anaconda3/envs/ecog_vis/lib/python3.7/site-packages/hdmf/backends/hdf5/h5tools.py in write(self, **kwargs)
    217 
    218         cache_spec = popargs('cache_spec', kwargs)
--> 219         call_docval_func(super(HDF5IO, self).write, kwargs)
    220         if cache_spec:
    221             ref = self.__file.attrs.get(SPEC_LOC_ATTR)

/anaconda3/envs/ecog_vis/lib/python3.7/site-packages/hdmf/utils.py in call_docval_func(func, kwargs)
    305 def call_docval_func(func, kwargs):
    306     fargs, fkwargs = fmt_docval_args(func, kwargs)
--> 307     return func(*fargs, **fkwargs)
    308 
    309 

/anaconda3/envs/ecog_vis/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    412                         raise_from(ExceptionType(msg), None)
    413 
--> 414                 return func(self, **parsed['args'])
    415         else:
    416             def func_call(*args, **kwargs):

/anaconda3/envs/ecog_vis/lib/python3.7/site-packages/hdmf/backends/io.py in write(self, **kwargs)
     39     def write(self, **kwargs):
     40         container = popargs('container', kwargs)
---> 41         f_builder = self.__manager.build(container, source=self.__source)
     42         self.write_builder(f_builder, **kwargs)
     43 

/anaconda3/envs/ecog_vis/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    412                         raise_from(ExceptionType(msg), None)
    413 
--> 414                 return func(self, **parsed['args'])
    415         else:
    416             def func_call(*args, **kwargs):

/anaconda3/envs/ecog_vis/lib/python3.7/site-packages/hdmf/build/map.py in build(self, **kwargs)
    168                 # TODO: if Datasets attributes are allowed to be modified, we need to
    169                 # figure out how to handle that starting here.
--> 170                 result = self.__type_map.build(container, self, builder=result, source=source, spec_ext=spec_ext)
    171         return result
    172 

/anaconda3/envs/ecog_vis/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    412                         raise_from(ExceptionType(msg), None)
    413 
--> 414                 return func(self, **parsed['args'])
    415         else:
    416             def func_call(*args, **kwargs):

/anaconda3/envs/ecog_vis/lib/python3.7/site-packages/hdmf/build/map.py in build(self, **kwargs)
   1658         builder.set_attribute('namespace', namespace)
   1659         builder.set_attribute(attr_map.spec.type_key(), data_type)
-> 1660         builder.set_attribute(attr_map.spec.id_key(), container.object_id)
   1661         return builder
   1662 

/anaconda3/envs/ecog_vis/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    410                     if parse_err:
    411                         msg = ', '.join(parse_err)
--> 412                         raise_from(ExceptionType(msg), None)
    413 
    414                 return func(self, **parsed['args'])

/anaconda3/envs/ecog_vis/lib/python3.7/site-packages/six.py in raise_from(value, from_value)

TypeError: incorrect type for 'value' (got 'NoneType', expected 'NoneType')

[luiztauffer]

This is a problem on hdmf that just got solved these days. It hasn't been merged yet, so for now you should use the specific PR, just install it like this:

pip install git+https://github.com/hdmf-dev/hdmf.git@refs/pull/115/head 

[jessierliu]

Gotcha, thanks! It's working now.