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[Bug]: nwbinspector CLI fails when url is provided #558

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stephprince opened this issue Jan 29, 2025 · 1 comment · May be fixed by #559
Open
3 tasks done

[Bug]: nwbinspector CLI fails when url is provided #558

stephprince opened this issue Jan 29, 2025 · 1 comment · May be fixed by #559
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@stephprince
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category: bug errors in the code or code behavior

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@stephprince
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What happened?

When running NWBInspector from the command line, providing a URL fails because the inspector attempts to inspect it as a dandi file path

nwbinspector "https://dandiarchive.s3.amazonaws.com/blobs/3d7/39a/3d739ac0-10fb-41ef-80be-f1479cec44c0"

Traceback:

A newer version (0.66.4) of dandi/dandi-cli is available. You are using 0.64.0
Error 404 while sending GET request to https://api.dandiarchive.org/api/dandisets/https/: 
<!doctype html>
<html lang="en">
<head>
  <title>Not Found</title>
</head>
<body>
  <h1>Not Found</h1><p>The requested resource was not found on this server.</p>
</body>
</html>

Traceback (most recent call last):
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/dandi/dandiapi.py", line 822, in _get_data
    self.client.get(f"/dandisets/{self.identifier}/")
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/dandi/dandiapi.py", line 303, in get
    return self.request("GET", path, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/dandi/dandiapi.py", line 277, in request
    raise HTTP404Error(msg, response=result)
dandi.exceptions.HTTP404Error: Error 404 while sending GET request to https://api.dandiarchive.org/api/dandisets/https/: 
<!doctype html>
<html lang="en">
<head>
  <title>Not Found</title>
</head>
<body>
  <h1>Not Found</h1><p>The requested resource was not found on this server.</p>
</body>
</html>


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/smprince/anaconda3/envs/nwbinspector/bin/nwbinspector", line 8, in <module>
    sys.exit(_nwbinspector_cli())
             ^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/src/nwbinspector/_nwbinspector_cli.py", line 201, in _nwbinspector_cli
    messages = list(messages_iterator)
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/src/nwbinspector/_dandi_inspection.py", line 162, in inspect_dandi_file_path
    asset = dandiset.get_asset_by_path(path=dandi_file_path)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/dandi/dandiapi.py", line 1238, in get_asset_by_path
    (asset,) = (
    ^^^^^^^^
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/dandi/dandiapi.py", line 1238, in <genexpr>
    (asset,) = (
               ^
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/dandi/dandiapi.py", line 1191, in get_assets_with_path_prefix
    f"{self.version_api_path}assets/",
       ^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/dandi/dandiapi.py", line 912, in version_api_path
    return f"/dandisets/{self.identifier}/versions/{self.version_id}/"
                                                    ^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/dandi/dandiapi.py", line 832, in version_id
    self._version_id = self.version.identifier
                       ^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/dandi/dandiapi.py", line 840, in version
    self._get_data()
  File "/Users/smprince/anaconda3/envs/nwbinspector/lib/python3.12/site-packages/dandi/dandiapi.py", line 825, in _get_data
    raise NotFoundError(f"No such Dandiset: {self.identifier}")
dandi.exceptions.NotFoundError: No such Dandiset: https

Operating System

M1 macOS

Python Version

3.12

Were you streaming with ROS3?

No

Package Versions

Copy and paste your output here

Code of Conduct

  • I agree to follow this project's Code of Conduct
  • Have you ensured this bug was not already reported?
  • To the best of your ability, have you ensured this is a bug within the code that checks the NWBFile, rather than a bug in the NWBFile reader (e.g., PyNWB or MatNWB)?
@stephprince stephprince added the category: bug errors in the code or code behavior label Jan 29, 2025
@stephprince stephprince self-assigned this Jan 29, 2025
@stephprince
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stephprince commented Jan 29, 2025 •
edited
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I think this should be resolved by updating these lines:

nwbinspector/src/nwbinspector/_nwbinspector_cli.py

Lines 162 to 163 in 33ca373

# Scan a single NWB file in a Dandiset
elif stream and ":" in path:

to:

elif stream and ":" in path and not path_is_url:

I can make the related PR and tests.

@stephprince stephprince linked a pull request Jan 30, 2025 that will close this issue
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Allow nwbinspector CLI to accept URLs NeurodataWithoutBorders/nwbinspector
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