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snap-stanford / SATURN

MIT License
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Sapiens (~15gb) data not available #29

Closed dummyindex closed 9 months ago

dummyindex commented 9 months ago

Hi all,

I encountered the following error when running Vignettes/tabula_mammals/tabula_data_loader.ipynb. Then downloaded data is about 4kb. When I directly access the S3 resource via browser, it says the resource is not available any more.

~/scRNA_seq_analysis$ curl -o local.h5ad "https://corpora-data-prod.s3.amazonaws.com/fab1d235-d9fe-4028-81db-029983860486/local.h5ad?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=ASIATLYQ5N5XZNDJPEGL%2F20221114%2Fus-west-2%2Fs3%2Faws4_request&X-Amz-Date=20221114T221256Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Security-Token=IQoJb3JpZ2luX2VjEOb%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIGUYH1BwUeJ8qU9taeb2hCvi%2F0dTEHS37xMN6Q39Ta6sAiEA%2FMiR4YsqsRnYF2z%2FDAGKzWL%2B0bJSukfpgGStcLYjC%2FYq9AMI3%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARABGgwyMzE0MjY4NDY1NzUiDAwv4dxIReZ9v1Oo%2FyrIA6IjTpSaQQ4gDz%2B1C1Dj7lyFVvrL7utErmjWxPlBUsu4If7vNUilOFGbbV61JjfGL6jQ%2BzldF0no31GnuUTkaRu911YQQ4y0jA2shO8eNBIClJFAcI1pZkL0R9V%2FZ5YVfmC6mejtP3ypZr2XJbh%2Bhvt2j5K40woSB03kq4n5p7LYnog23xKu32FI%2FSYhk8ClLExlzdORK%2BWjruGOvdKaIhlKWzg0Z7NA2J0Luiny%2BmFyxdT9Htb%2Bf5PxoaQSl7sej9EX6B8SIRdyhzaDYPEqQpbJMFPyrdVm4JP0%2FH3RCvpOzfCYveFLGSp8TtWDU0dg6%2FqyAwgbgwsiEtD75hRtIINs%2ByRAby0M052UuP5G%2F2yNMo%2BbylpO7rpXckVOKNWS8MO9RLFow8gC5TjXx9MSAMcwL1ZBDfAScSSTWDZ6ED0LyjK10wWHHUlNXPR33u1GVkoJ7MLpfNyvh9nMsoqRGFXQ0KwcJQTjwJTubkyFwh0CILWms9szj10wZ3PUuReWjUTdRLdBX%2FP8WFo9uxPDTN7%2FxZlPqzx4NHTdRTSIBJWqPos7xVtNC2nenXBHWd4e6Aj3vVddtdqNMEo%2BKuhvamPafbX1zMErHTCo58qbBjqlAUS2BiVHW12a1oLKoIgB5xwQacskrdKuwjhcSy8i%2BjwOX%2FzfbvcrEmWkPeZ2eo%2FTu%2BmjaeM0r3CuqMYtz5%2BmV%2BuIK8OCcJd08WmwurdrEWUEyh1X4GePGo7XDouj7Kxd4GJJqznF9ZR%2BhJ3wncEcL2lEYoN84PpL2apBY8Gud4SHN2LLmN%2FPxTIQfN35OfI%2FxVllKULZ1Kqq7fuT792jivEp8DeQUA%3D%3D&X-Amz-Signature=ca0c9a3590f8a1a5826c01737ec1e8875ce0c107055fa6536102ae7787224dc8"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   370    0   370    0     0   1113      0 --:--:-- --:--:-- --:--:--  1111

S3 web output of the link above:

This XML file does not appear to have any style information associated with it. The document tree is shown below.
<Error>
<Code>AccessDenied</Code>
<Message>Request has expired</Message>
<X-Amz-Expires>604800</X-Amz-Expires>
<Expires>2022-11-21T22:12:56Z</Expires>
<ServerTime>2024-02-19T06:32:18Z</ServerTime>
<RequestId>AX41NPQQTAB8KC49</RequestId>
<HostId>V3dELcusesGBZpxTDp7kNhai88MrSCI7HAen7iZcymAAD7fjvP/EbwmmMp4FahfA76sEJnLLFUs=</HostId>
</Error>

System: Ubuntu Can you share the local.h5ad (Sapiens data)? Thanks!

Yanay1 commented 9 months ago

You can download tabula sapiens from here as well: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5 although they might have renamed some of the columns.