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[Bug report] - Unable to upload histology to Alyx #301

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khanalanup opened this issue Apr 7, 2022 · 0 comments
Open

[Bug report] - Unable to upload histology to Alyx #301

khanalanup opened this issue Apr 7, 2022 · 0 comments
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@khanalanup
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Unable to upload histology files to Alyx. Encounter the following error message: Failed to load the remote cache file

To Reproduce
"""
Register on Alyx the set of tracked traces (after histology) for a given mouse.
All your tracks should be in a single folder, and the files names should follow the nomenclature
{yyyy-mm-dd}{SubjectName}{SessionNumber}_{ProbeLabel}_pts.csv
Edit the variable 'path_tracks'(set it either to your local directory [example given here],
either to the Google folder if synched to your machine).
To check if the registration worked, go to the admin interface

experiments > trajectory estimates > search for the subject
If you want to test first, use ALYX_URL = "https://dev.alyx.internationalbrainlab.org"
And check the data appears on:
https://dev.alyx.internationalbrainlab.org/admin/experiments/trajectoryestimate/?
When you feel confident you can upload without error,
set EXAMPLE_OVERWRITE = False ,
change to the ALYX_URL = "https://alyx.internationalbrainlab.org"
and re-run.
With EXAMPLE_OVERWRITE = True, the script downloads an example dataset and runs
the registration (used for automatic testing of the example).
"""

Author: Olivier, Gaelle

from pathlib import Path

from one.api import ONE

from ibllib.pipes import histology

======== EDIT FOR USERS ====

Edit so as to reflect the directory containing your electrode tracks

path_tracks = "C:/Users/ibl-neuropix/Documents/UCLA Histology/00_to_add"

EXAMPLE_OVERWRITE = False # Put to False when wanting to run the script on your data

ALYX_URL = "https://dev.alyx.internationalbrainlab.org" # FOR TESTING

ALYX_URL = "https://alyx.internationalbrainlab.org" # UNCOMMENT WHEN READY

======== DO NOT EDIT BELOW ====

one = ONE(base_url=ALYX_URL)

if EXAMPLE_OVERWRITE:
# TODO Olivier : Function to download examples folder
cachepath = Path(one.alyx.cache_dir)
path_tracks = cachepath.joinpath('examples', 'histology', 'tracks_to_add')

histology.register_track_files(path_tracks=path_tracks, one=one, overwrite=True)
histology.detect_missing_histology_tracks(path_tracks=path_tracks, one=one)

Expected behavior
Failed to load the remote cache file

Screenshots
image

Desktop (please complete the following information):

  • OS: Windows 10
  • Browser: Firefox

Additional context
Encountering the same error message when loading the alignment gui

@khanalanup khanalanup added the bug Something isn't working label Apr 7, 2022
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