[Bug]: DANDI Upload with session ID that contains "/" fails

[rly]

What happened?

See dandi/helpdesk#169 (comment)

The user has an NWB file with session_id = "BLA-projecting NBM/SI neuron from animal M24 on 26/07/2023". It looks like NeuroConv or dandi-cli is replacing the "/" in the session ID with "\" when renaming the file before upload, and therefore the file cannot be found.

DANDI uses the following format for file names: {dandiset_id}/sub-{subject_id}/sub-{subject_id}_ses-{session_id}.nwb so a "/" in the session ID (or subject ID) would cause problems unless handled in a special way.

The error is reported in NWB GUIDE, but from what I can trace, the error comes from calling neuroconv. See traceback below. The inputs to automatic_dandi_upload is a folder /Users/rly/NWB_GUIDE/.temp/upload/temp_20241211-150938 with contents:

ls -al ~/NWB_GUIDE/.temp/upload/temp_20241211-150938 
total 0
drwxr-xr-x  3 rly  staff   96 Dec 11 15:09 .
drwxr-xr-x  6 rly  staff  192 Dec 11 15:09 ..
lrwxr-xr-x  1 rly  staff   60 Dec 11 15:09 MACAQUE_CHOL_NBM_FL_20230726T173713.nwb -> /Users/rly/Downloads/MACAQUE_CHOL_NBM_FL_20230726T173713.nwb

So the file is renamed with the session ID by neuroconv or dandi organize.

Related:

• Forbid slashes in names of Groups and Datasets hdmf-dev/hdmf#1219
• [Feature]: Add check to make sure "/" characters are not in the session_id or subject_id NeurodataWithoutBorders/nwbinspector#543

Steps to Reproduce

See linked issue

Traceback

[2024-12-11 15:09:41,427] ERROR in app: Exception on /neuroconv/upload [POST]
Traceback (most recent call last):
  File "/Users/rly/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/flask/app.py", line 1484, in full_dispatch_request
    rv = self.dispatch_request()
  File "/Users/rly/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/flask/app.py", line 1469, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)
  File "/Users/rly/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/flask_restx/api.py", line 404, in wrapper
    resp = resource(*args, **kwargs)
  File "/Users/rly/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/flask/views.py", line 109, in view
    return current_app.ensure_sync(self.dispatch_request)(**kwargs)
  File "/Users/rly/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/flask_restx/resource.py", line 46, in dispatch_request
    resp = meth(*args, **kwargs)
  File "/Users/rly/Documents/NWB/nwb-guide/src/pyflask/namespaces/neuroconv.py", line 162, in post
    return upload_multiple_filesystem_objects_to_dandi(**neuroconv_namespace.payload)
  File "/Users/rly/Documents/NWB/nwb-guide/src/pyflask/manageNeuroconv/manage_neuroconv.py", line 1338, in upload_multiple_filesystem_objects_to_dandi
    results = upload_folder_to_dandi(**innerKwargs)
  File "/Users/rly/Documents/NWB/nwb-guide/src/pyflask/manageNeuroconv/manage_neuroconv.py", line 1366, in upload_folder_to_dandi
    return automatic_dandi_upload(
  File "/Users/rly/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/neuroconv/tools/data_transfers/_dandi.py", line 98, in automatic_dandi_upload
    organized_nwbfile.rename(organized_nwbfile.parent / corrected_name)
  File "/Users/rly/miniconda3/envs/nwb-guide/lib/python3.9/pathlib.py", line 1382, in rename
    self._accessor.rename(self, target)
FileNotFoundError: [Errno 2] No such file or directory: '/Users/rly/NWB_GUIDE/.temp/upload/tmpabsrwlgc/215860/sub-M24/sub-M24_icephys.nwb' -> '/Users/rly/NWB_GUIDE/.temp/upload/tmpabsrwlgc/215860/sub-M24/sub-M24_ses-BLA-projecting NBM/SI neuron from animal M24 on 26/07/2023_icephys.nwb'

Operating System

macOS

Python Executable

Python

Python Version

3.12

Package Versions

No response

Code of Conduct

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[h-mayorquin]

My suspicion is that this is on the dandi organize but we would need to confirm this. I will take a look at this.

@alessandratrapani
I have the vague memory that I discussed with you some modifications that you did to avoid this. Or was it subject that also messed with the dandi organize?