nwb file returned and viewed from class error

[ahabdallah27]

I am creating a class and calling the class from a Jupyter notebook. I am noticing an error when trying to read the nwb file. If I run the code in a .py file, no error is produced and if I run print(nwbFile) instead of nwbFile, no error is produced. I am running pynwb version 2.6.0. Interestingly, the contents of the file does still get printed out (as shown in the error message below), but I cannot interact with it by drilling down into the fields. Additionally, any call I make to the file causes the error. For example, nwbFile.units, would result in the same error, but it would still print out the contents of the units table. This form of printing isn't useful and removes the appeal of using the Jupyter Notebook to view the data. Any thoughts on what the cause of the error is and how to fix it? I'd like to be able to view the file by drilling into it.

file = NWBCreate() #my class
nwbFile = file.get_nwb(subject, date, run)
nwbFile

def get_nwb(self, subject, date, run, save=False):
        direc, identifier, zFileName, subjectName = self.__get_directory_details(subject, date, run)
        filePath = os.path.join(direc, zFileName)
        if os.path.isfile(filePath):
            io = NWBHDF5IO(filePath, "r")
            nwbFile = io.read()
            io.close()
        else:
            zDataFrame = self.__get_binaries_data_frame(direc)
            nwbFile = self.__create_nwb_file(direc, identifier, subjectName, zDataFrame)

            if save:
                with NWBHDF5IO(filePath, "w") as nwbFileIO:
                    nwbFileIO.write(nwbFile)
        
        return nwbFile

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File ~/opt/anaconda3/envs/bmi/lib/python3.9/site-packages/IPython/core/formatters.py:344, in BaseFormatter.__call__(self, obj)
    342     method = get_real_method(obj, self.print_method)
    343     if method is not None:
--> 344         return method()
    345     return None
    346 else:

File ~/opt/anaconda3/envs/bmi/lib/python3.9/site-packages/hdmf/container.py:618, in Container._repr_html_(self)
    616 html_repr += "<div class='container-wrap'>"
    617 html_repr += f"<div class='container-header'><div class='xr-obj-type'><h3>{header_text}</h3></div></div>"
--> 618 html_repr += self._generate_html_repr(self.fields, is_field=True)
    619 html_repr += "</div>"
    620 return html_repr

File ~/opt/anaconda3/envs/bmi/lib/python3.9/site-packages/hdmf/container.py:630, in Container._generate_html_repr(self, fields, level, access_code, is_field)
    628 current_access_code = f"{access_code}.{key}" if is_field else f"{access_code}['{key}']"
    629 if hasattr(value, '_generate_field_html'):
--> 630     html_repr += value._generate_field_html(key, value, level, current_access_code)
    631 else:
    632     html_repr += self._generate_field_html(key, value, level, current_access_code)

File ~/opt/anaconda3/envs/bmi/lib/python3.9/site-packages/hdmf/container.py:655, in Container._generate_field_html(self, key, value, level, access_code)
    651     return f'<div style="margin-left: {level * 20}px;" class="container-fields"><span class="field-key"' \
...
    760         pass  # Fall back to Python read pathway below

File h5py/_selector.pyx:376, in h5py._selector.Reader.read()

ValueError: Dset_id is not a dataset id (dset_id is not a dataset ID)

root pynwb.file.NWBFile at 0x140392828125296
Fields:
  acquisition: {
    Decode <class 'pynwb.base.TimeSeries'>,
    FingerAnglesTIMRL <class 'pynwb.base.TimeSeries'>,
    NeuralFeature <class 'pynwb.base.TimeSeries'>,
    ParasiteTime <class 'pynwb.base.TimeSeries'>,
    RawInputVals <class 'pynwb.base.TimeSeries'>,
    SampleWidth <class 'pynwb.base.TimeSeries'>
  }
  devices: {
    Utah Array <class 'pynwb.device.Device'>
  }
  electrode_groups: {
    BMI electrodes <class 'pynwb.ecephys.ElectrodeGroup'>
  }
...
  timestamps_reference_time: 2022-09-06 10:13:44-04:00
  trials: trials <class 'pynwb.epoch.TimeIntervals'>
  units: units <class 'pynwb.misc.Units'>

If I run these lines in the Jupyter Notebook directly instead of calling from the class, I do not get any error. Therefore I suspect there is an issue with loading the file from a class in a Jupyter Notebook.

if os.path.isfile(filePath):
    io = NWBHDF5IO(filePath, "r")
    nwbFile = io.read()

nwbFile

[CodyCBakerPhD]

The io needs to stay open when accessing data (which a printout command will do) in the nwbfile it was read from; so I'd try removing io.close()

[ahabdallah27]

Thanks, that does work. I thought I should close io after reading, but it sounds like garbage collection should handle this.