[BUG] Zenodo api error response not saved nor displayed

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Assessment

Difficulty
2/5
Estimated time
1-3 hours
Newbie friendliness
68/100
Issue type
Bug
Clarity
Clearly specified
Activity status
Quiet
Tech stack
python
Domain
api

Research direction

Start in brainles_preprocessing/utils/zenodo.py, especially _get_metadata_and_archive_url(), where the 403 message is raised. Use the provided Podman reproduction or inspect the failing request path, then verify that the Zenodo error response is included in the logged failure alongside the status code.

Written by the indexing model from the issue text.

Description

bug

Describe the bug
When using AtlasCentricPreprocessing, the atlases are downloaded from zenodo on the first run. However, in the event of a non-200 status code, the error response returned along with the status code is neither displayed nor logged, resulting in an unhelpful "Cannot find record '15236131' on Zenodo (response.status_code=403)." We do not know from this message what caused the 403 forbidden error, and Zenodo reports in its documentation that the error response should contain further explanation/debugging steps. Given that using the browser to visit the same api url returns valid json, it is very hard to debug the problem without the error response.

To Reproduce
Steps to reproduce the behavior:
This 403 error might be hard to reproduce since it is intermittent for me in a debian bookworm container. I will try my best to help reproduce the error but I cannot guarantee.

  1. Create a Containerfile with this content
FROM python:3.12-bookworm

RUN pip install brats[preprocessing] pybids

WORKDIR /workspace

COPY . .

CMD ["python", "/workspace/main.py"]
  1. Create a minimal main.py in the same directory with this content:
from brainles_preprocessing.constants import Atlas
from brainles_preprocessing.modality import Modality, CenterModality
from brainles_preprocessing.preprocessor import (
    AtlasCentricPreprocessor,
)
from brainles_preprocessing.registration import ANTsRegistrator

preprocessor = AtlasCentricPreprocessor(
    center_modality=CenterModality(),  # Fill in info about your local data here
    moving_modalities=[
        Modality()  # Fill in info about your local data here
    ],
    registrator=ANTsRegistrator(),
    atlas_image_path=Atlas.BRATS_MNI152,
)
preprocessor.run()
  1. Build the container using podman -v /data/dir/on/your/machine:/mounted/data/dir -t zenodo-test:latest .
  2. Run the container using podman run zenodo-test
    I hope that this does it.

Expected behavior
The error response is logged along with the status code.

Screenshots

2026-01-23 00:53:26.460 | ERROR    | brainles_preprocessing.utils.zenodo:_get_metadata_and_archive_url:144 - Cannot find record '15236131' on Zenodo (response.status_code=403).
Traceback (most recent call last):
  File "/workspace/main.py", line 301, in <module>
    main()
  File "/workspace/main.py", line 297, in main
    register_to_atlas(temp, output, first_session)
  File "/workspace/main.py", line 225, in register_to_atlas
    preprocessor = AtlasCentricPreprocessor(
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/brainles_preprocessing/preprocessor/atlas_centric_preprocessor.py", line 61, in __init__
    atlas_folder = fetch_atlases()
                   ^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/brainles_preprocessing/utils/zenodo.py", line 32, in fetch_atlases
    return record.fetch()
           ^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/brainles_preprocessing/utils/zenodo.py", line 71, in fetch
    zenodo_response = self._get_metadata_and_archive_url()
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/brainles_preprocessing/utils/zenodo.py", line 145, in _get_metadata_and_archive_url
    raise ZenodoException(error_msg)
brainles_preprocessing.utils.zenodo.ZenodoException: Cannot find record '15236131' on Zenodo (response.status_code=403).

Environment

operating system and version?

Debian bookworm, no nvidia

Python environment and version?

e.g. Conda environment with Python 3.10. Check your Python version with:
Python 3.12

version of brainles_preprocessing ?

please specify your version of brainles_preprocessing (please make sure you run the latest version): 0.6.8

Additional context

Dominant language
C
Stars
39
Forks
11
PR merge metrics
No merged PRs in 30d

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