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Duplicate blob when uploading via CLI

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#1,650 3 commenti 0 reazioni 0 assegnatari Vedi su GitHub

I maintainer di solito rispondono entro 1 giorno

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Valutazione

Difficoltà
3/5
Tempo stimato
1-2 giorni
Idoneità per principianti
45/100
Tipo di issue
Bug
Chiarezza
Abbastanza chiara
Stato di attività
Ferma
Stack tecnologico
python
Ambito
cli

Direzione di ricerca

Riproduci con dandi organize . seguito da dandi upload ., utilizzando le versioni e l’endpoint API locale indicati. Inizia da dandi/upload.py, dandi/files/bases.py e dalla gestione dei symlink del comando organize; verifica che un symlink creato da organize non venga caricato due volte e che il caricamento venga completato senza il POST duplicato né il traceback.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

UX

I'm running a local instance of dandi-archive (master) using dandi-schema (master).

I've installed dandi cli via pip install dandi in a separate venv

pip freeze | grep dandi  
dandi==0.69.3
dandischema==0.11.1

$ dandi organize .
$ dandi upload .
Output and traceback 
2025-06-05 13:11:07,679 [    INFO] Found 3 files to consider
PATH                                                                     SIZE    ERRORS PROGRESS STATUS           MESSAGE                  
dandiset.yaml                                                            2.3 kB                  skipped          should be edited online  
...-unsorted-nac/sub-Temp-pref-F30-B30-5dpf-01-unsorted-nac_behavior.nwb 9.3 MB                  pre-validating                            
...mp-pref-F30-B30-5dpf-01-unsorted-nac_ses-20230808T111800_behavior.nwb 9.3 MB                  pre-validating                            
Summary:                                                                 18.7 MB                 1 skipped        1 should be edited online
                                                                                                 2 pre-validating                          
/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/hdmf/spec/namespace.py:583: UserWarning: Ignoring the following cached namespace(s) because another version is already loaded:
core - cached version: 2.4.0, loaded version: 2.8.0
The loaded extension(s) may not be compatible with the cached extension(s) in the file. Please check the extension documentation and ignore this warning if these versions are compatible.
  self.warn_for_ignored_namespaces(ignored_namespaces)
PATH                                                    SIZE    ERRORS PROGRESS STATUS                MESSAGE                              dandiset.yaml                                           2.3 kB                  skipped               should be edited online              
...-Temp-pref-F30-B30-5dpf-01-unsorted-nac_behavior.nwb 9.3 MB    0             ERROR                 Error 404 while sending POST reque...
...dpf-01-unsorted-nac_ses-20230808T111800_behavior.nwb 9.3 MB    0             ERROR                 Error 404 while sending POST reque...
Summary:                                                18.7 MB                 1 skipped             1 should be edited online            
                                                                                2 ERROR               2 Error some while sending POST re...
2025-06-05 13:11:08,841 [    INFO] Logs saved in /home/austin/.local/state/dandi-cli/log/2025.06.05-18.11.07Z-553648.log
Traceback (most recent call last):
  File "/home/austin/.pyenv/versions/tmp-dandi-cli/bin/dandi", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/click/core.py", line 1082, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/click/core.py", line 1697, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/click/decorators.py", line 45, in new_func
    return f(get_current_context().obj, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/dandi/cli/base.py", line 126, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/dandi/cli/cmd_upload.py", line 103, in upload
    upload(
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/dandi/upload.py", line 461, in upload
    raise upload_err
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/dandi/upload.py", line 359, in process_path
    for r in dfile.iter_upload(
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/dandi/files/bases.py", line 363, in iter_upload
    resp = client.post(
           ^^^^^^^^^^^^
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/dandi/dandiapi.py", line 317, in post
    return self.request("POST", path, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/austin/.pyenv/versions/3.11.12/envs/tmp-dandi-cli/lib/python3.11/site-packages/dandi/dandiapi.py", line 285, in request
    raise HTTP404Error(msg, response=result)
dandi.exceptions.HTTP404Error: Error 404 while sending POST request to http://localhost:8000/api/uploads/initialize/: {"detail":"Not found."}

The upload has made it into my dandiset locally, but we do have that traceback. Looking closer, I think this happens because dandi organize created a symlink, and dandi upload essentially tries to upload the same file twice.

Lingua principale
Python
Stelle
29
Fork
37
Merge medio
1g 5h
PR unite (30g)
20

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