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scverse / squidpy

Spatial Single Cell Analysis in Python
https://squidpy.readthedocs.io/en/stable/
BSD 3-Clause "New" or "Revised" License
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Cannot load Visium_FFPE_Mouse_Brain,Visium_FFPE_Human_Normal_Prostate. Error: HTTP Error 403: Forbidden #782

Open Rayjrz opened 7 months ago

Rayjrz commented 7 months ago

Description

WARNING: Failed to open the url with default certificates, trying with certifi. Visium_FFPE_Mouse_Brain. Error: HTTP Error 403: Forbidden

WARNING: Failed to open the url with default certificates, trying with certifi. Failed to load dataset: Visium_FFPE_Human_Normal_Prostate. Error: HTTP Error 403: Forbidden

Minimal reproducible example

adata0 = sq.datasets.visium(sample_id='Visium_FFPE_Mouse_Brain', include_hires_tiff=True)
adata1 = sq.datasets.visium(sample_id='Visium_FFPE_Human_Normal_Prostate', include_hires_tiff=True)

Traceback

```pytb --------------------------------------------------------------------------- HTTPError Traceback (most recent call last) File ~/lib/python3.9/site-packages/scanpy/readwrite.py:952, in _download(url, path) 951 try: --> 952 open_url = urlopen(req) 953 except URLError: ```

Version

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wang-youzi commented 2 months ago

I encountered the same question when I use sq.datasets.slideseqv2(), have you solved question? I'll be appreciated if you give a reply.

Rayjrz commented 2 months ago

I encountered the same question when I use sq.datasets.slideseqv2(), have you solved question? I'll be appreciated if you give a reply.

Actually, I gave up on squidpy. I suggest you download and load the dataset with scanpy.

giovp commented 2 days ago

we should probably deprecate the datasets module, since it seems that the API requests have often issues, and also that there are many more datasets, that can't be directly read with squidpy functions, in the 10x portal