[BUG] Unable to reach cellxgene servers

[LysSanzMoreta]

Code:

import cellxgene_census
census = cellxgene_census.open_soma(census_version="2023-07-25")

Error: Unable to reach cellxgene servers: requests.exceptions.ConnectionError: HTTPSConnectionPool(host='census.cellxgene.cziscience.com', port=443): Max retries exceeded with url: /cellxgene-census/v1/mirrors.json (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x786c03698fa0>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))

Environment in python 3.10 (I have also tried with python 3.9 in case that helped):

name: base
channels:
  - conda-forge
  - pytorch
  - defaults
  - nvidia
  - bioconda
dependencies:
  - pyopenssl
  - python=3.9
  - requests
  - pip:
    - -r requirements.txt
  - numpy
  - pytorch::pytorch=2.1=py3.9_cuda12.1*
  - torchvision=>0.16
  - torchaudio
  - biopython
  - h5py
  - scipy
  - scikit-learn
  - pandas
  - matplotlib
  - hdf5plugin
  - pyro-ppl
  - scanpy
  - dill
  - umap-learn
  - seaborn
  - dataframe_image
  - xmltodict
  - nbconvert
  - bioconda::cellxgene
  - conda-forge::lightning
  - numba
  - conda-forge::scvi-tools==1.0.4
  - conda-forge::jax[cuda12_pip]
  - conda-forge::jaxlib
  - conda-forge::huggingface_hub
  - conda-forge::leidenalg

requirements.txt

gget
cellxgene-census
twine
build
imgkit

Perhaps you are doing some server maintenance at the moment? Everything was working until today :)

Thanks!

[MaximilianLombardo]

Hi @LysSanzMoreta

Can you confirm the cellxgene-census package version you are using? I tried replicating the error with version 1.9.1 and python 3.9 in a conda environment and didn't encounter the error.

[LysSanzMoreta]

Hi! I use micromamba as the package manager and it has installed version 1.10.2 for python 3.9 and 1.11.1 for python 10

Python 10:

cellxgene                 0.16.7
cellxgene-census          1.11.1

Python 9:

cellxgene                 0.16.7
cellxgene-census          1.10.2

Should I force a downgrade?

[ebezzi]

Hey @LysSanzMoreta,

this seems to be an issue with your DNS resolver. Normally those are temporary but I'm assuming the issue is persistent for you.

You should be able to isolate the issue from your Python environment by connecting to that file manually, e.g. via curl https://census.cellxgene.cziscience.com/cellxgene-census/v1/mirrors.json. If that also fails, I recommend contacting your IT administrator as they might have added some network restrictions.

[LysSanzMoreta]

@ebezzi Hmm, yeah, it might have been something with the VPN they make me use. I did thought it could be that yesterday, so I deactivated it, nonetheless the problem persisted.

I did not think about re-starting the computer though (basic IT tip hehhe)...

Today, it seems to be working again (I have not activated the VPN). So to sum up, if it helps anyone, do not use the VPN and in case of using the VPN, deactivate it and re-start the computer.

Thanks!

[MaximilianLombardo]

awesome thanks @ebezzi and @LysSanzMoreta !