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Handle NWB files #38

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appukuttan-shailesh opened this issue Mar 29, 2021 · 4 comments
Open

Handle NWB files #38

appukuttan-shailesh opened this issue Mar 29, 2021 · 4 comments
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bug Something isn't working enhancement New feature or request

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@appukuttan-shailesh
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appukuttan-shailesh commented Mar 29, 2021

I am trying to load NWB files from the Allen Brain Atlas in the neo viewer.
I believe it doesn't currently support this file format.

I get an error when trying with:
https://object.cscs.ch/v1/AUTH_c0a333ecf7c045809321ce9d9ecdfdea/VF_paper_demo/live_paper/temp/525011725_ephys.nwb
(NWB file from here:
https://celltypes.brain-map.org/experiment/electrophysiology/525011903)

If and when implemented, it would also be nice if neo viewer can handle download URLs such as:
https://celltypes.brain-map.org/api/v2/well_known_file_download/618211597
(target URL on download button of above Allen Brain entry page) where the file name and extension is not visible in the URL directly.

If knowing the file format/extension is necessary for neo viewer to work, we can consider appending a query param at the end of the url e.g. ?format=NWB

@appukuttan-shailesh appukuttan-shailesh added bug Something isn't working enhancement New feature or request labels Jun 22, 2022
@apdavison
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try &type=NWBIO

@appukuttan-shailesh
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I have tried this, for the following file:
https://object.cscs.ch/v1/AUTH_c0a333ecf7c045809321ce9d9ecdfdea/VF_paper_demo/live_paper/temp/525011725_ephys.nwb
added &type=NWBIO to have URL:
https://object.cscs.ch/v1/AUTH_c0a333ecf7c045809321ce9d9ecdfdea/VF_paper_demo/live_paper/temp/525011725_ephys.nwb&type=NWBIO

But still get an error:

{"data":"HTTPError at /api/blockdata/\nHTTP Error 404: Not Found\n\nRequest Method: GET\nRequest URL: https://neo-viewer.brainsimulation.eu/api/blockdata/?format=json&url=https:%2F%2Fobject.cscs.ch%2Fv1%2FAUTH_c0a333ecf7c045809321ce9d9ecdfdea%2FVF_paper_demo%2Flive_paper%2Ftemp%2F525011725_ephys.nwb%26type%3DNWBIO\nDjango Version: 2.2.3\nPython Executable: /usr/local/bin/uwsgi\nPython Version: 3.7.3\nPython Path: ['.', '', '/home/docker', '/home/docker/site', '/usr/local/lib/python3.6/dist-packages', '/usr/lib/python3.6/dist-packages', '/usr/lib/python37.zip', '/usr/lib/py
.... (long error)

@apdavison
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apdavison commented Jun 22, 2022

sorry, I didn't explain where to add the "type" query parameter. It should be

https://neo-viewer.brainsimulation.eu/api/blockdata/?format=json&type=NWBIO&url=https:%2F%2Fobject.cscs.ch%2Fv1%2FAUTH_c0a333ecf7c045809321ce9d9ecdfdea%2FVF_paper_demo%2Flive_paper%2Ftemp%2F525011725_ephys.nwb

this produces a different error, which we'll need to fix in Neo.

@apdavison
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see NeuralEnsemble/python-neo#1131

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