Allow Non-Compliant JSON (e.g. NaN values)

[garrettmflynn]

fix catalystneuro/neuroconv#515

This PR will prepare us to accept NaN values passed back as metadata from the Ophys interfaces.

[CodyCBakerPhD]

@garrettmflynn Should we try one ophys interface branched from this before merging? Or just take the dive

[garrettmflynn]

Yeah worth the test. I'll see if Bruker loads, since that was the interface noted in the related Bug.

[garrettmflynn]

@CodyCBakerPhD Any idea why this would happen?

[2023-09-18 11:18:15,008] ERROR in app: Exception on /neuroconv/metadata [POST]
Traceback (most recent call last):
  File "/opt/anaconda3/envs/nwb-guide/lib/python3.10/site-packages/flask/app.py", line 1484, in full_dispatch_request
    rv = self.dispatch_request()
  File "/opt/anaconda3/envs/nwb-guide/lib/python3.10/site-packages/flask/app.py", line 1469, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)
  File "/opt/anaconda3/envs/nwb-guide/lib/python3.10/site-packages/flask_restx/api.py", line 404, in wrapper
    resp = resource(*args, **kwargs)
  File "/opt/anaconda3/envs/nwb-guide/lib/python3.10/site-packages/flask/views.py", line 109, in view
    return current_app.ensure_sync(self.dispatch_request)(**kwargs)
  File "/opt/anaconda3/envs/nwb-guide/lib/python3.10/site-packages/flask_restx/resource.py", line 46, in dispatch_request
    resp = meth(*args, **kwargs)
  File "/Users/garrettflynn/Documents/Github/nwb-guide/pyflask/apis/neuroconv.py", line 70, in post
    return get_metadata_schema(neuroconv_api.payload.get("source_data"), neuroconv_api.payload.get("interfaces"))
  File "/Users/garrettflynn/Documents/Github/nwb-guide/pyflask/manageNeuroconv/manage_neuroconv.py", line 117, in get_metadata_schema
    converter = instantiate_custom_converter(source_data, interfaces)
  File "/Users/garrettflynn/Documents/Github/nwb-guide/pyflask/manageNeuroconv/manage_neuroconv.py", line 80, in instantiate_custom_converter
    return CustomNWBConverter(source_data)
  File "/opt/anaconda3/envs/nwb-guide/lib/python3.10/site-packages/neuroconv/nwbconverter.py", line 65, in __init__
    self.data_interface_objects = {
  File "/opt/anaconda3/envs/nwb-guide/lib/python3.10/site-packages/neuroconv/nwbconverter.py", line 66, in <dictcomp>
    name: data_interface(**source_data[name])
  File "/opt/anaconda3/envs/nwb-guide/lib/python3.10/site-packages/neuroconv/datainterfaces/ophys/brukertiff/brukertiffdatainterface.py", line 29, in __init__
    super().__init__(folder_path=folder_path, verbose=verbose)
  File "/opt/anaconda3/envs/nwb-guide/lib/python3.10/site-packages/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py", line 25, in __init__
    self.imaging_extractor = self.get_extractor()(**source_data)
  File "/opt/anaconda3/envs/nwb-guide/lib/python3.10/site-packages/neuroconv/baseextractorinterface.py", line 25, in get_extractor
    extractor = getattr(
AttributeError: module 'roiextractors' has no attribute 'BrukerTiffImagingExtractor'

[CodyCBakerPhD]

@garrettmflynn Fresh conda environment? Are you using latest pip install -U roiextractors?

[CodyCBakerPhD]

@garrettmflynn I'm guessing a version mismatch between neuroconv and roiextractors here, these names were changed somewhat recently

The interface should be BrukerTiffSinglePlaneImagingInterface which uses the BrukerTiffSinglePlaneImagingExtractor which should be available with latest of both packages

[garrettmflynn]

Okay sure. It prompted me to install roiextractors manually, so I likely have an outdated environment

[garrettmflynn]

Correcting for #376, this works great.

[garrettmflynn]

Replaced with #393