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Novartis / cellxgene-gateway

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
Apache License 2.0
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ImportError: cannot import name 'url_decode_stream' from 'werkzeug.urls' #87

Closed ahrweber closed 8 months ago

ahrweber commented 9 months ago

I installed cellxgene-gateway using anaconda Python 3.11.5.

cellxgene-gateway does not start with error:

ImportError: cannot import name 'url_decode_stream' from 'werkzeug.urls' (/home/user/.cellxgene-gateway/lib/python3.11/site-packages/werkzeug/urls.py)

After search I got aware of some changes in flask version >= 3.0.

And the standard installation installed conda list | grep werkzeug

werkzeug 3.0.1 pypi_0 pypi

conda list | grep flask

flask 3.0.1 pypi_0 pypi

Solved the error by installing fix versions: pip install werkzeug==2.3.0 flask==2.2.2

After that cellxgene-gateway starts and works fine.

alokito commented 8 months ago

I'll pin the versions for now. cellxgene-gateway is due for a cycle of dependency updates.

alokito commented 8 months ago

@ahrweber this issue should be addressed in cellxgene-gateway 0.4.0, please confirm if you have time.