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Description
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.
- 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"]
- 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()
- Build the container using
podman -v /data/dir/on/your/machine:/mounted/data/dir -t zenodo-test:latest . - 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年01月23日 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