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Can't read remote VCF files over https on Linux #216

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tomwhite opened this issue Jul 21, 2021 · 0 comments
Open

Can't read remote VCF files over https on Linux #216

tomwhite opened this issue Jul 21, 2021 · 0 comments

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@tomwhite
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This still happens with 0.30.9, and it was happening with 0.30.4 before too:

Python 3.8.11 (default, Jul  5 2021, 19:22:52) 
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from cyvcf2 import VCF
>>> VCF('test.vcf.gz')
<cyvcf2.cyvcf2.VCF object at 0x7fbfcb7f84a0>
>>> VCF('https://github.com/brentp/cyvcf2/raw/master/cyvcf2/tests/test.vcf.gz')
[E::hts_open_format] Failed to open file "https://github.com/brentp/cyvcf2/raw/master/cyvcf2/tests/test.vcf.gz" : Input/output error
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "cyvcf2/cyvcf2.pyx", line 257, in cyvcf2.cyvcf2.VCF.__init__
  File "cyvcf2/cyvcf2.pyx", line 189, in cyvcf2.cyvcf2.HTSFile._open_htsfile
OSError: Error opening https://github.com/brentp/cyvcf2/raw/master/cyvcf2/tests/test.vcf.gz

If the file is local it works OK.

As @ccwang002 commented here this is likely to be due to how ssl is linked.

Environment:

Current runner version: '2.278.0'
Operating System
  Ubuntu
  20.04.2
  LTS
Virtual Environment
  Environment: ubuntu-20.04
  Version: 20210718.1
  Included Software: https://github.com/actions/virtual-environments/blob/ubuntu20/20210718.1/images/linux/Ubuntu2004-README.md
 Image Release: https://github.com/actions/virtual-environments/releases/tag/ubuntu20%2F20210718.1
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