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Can't import the core module #289

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xiangpin opened this issue Mar 19, 2024 · 1 comment
Open

Can't import the core module #289

xiangpin opened this issue Mar 19, 2024 · 1 comment
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bug Problem in the code

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@xiangpin
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Describe the bug

error in from pypath.core import network

To Reproduce
Steps to reproduce the behavior:

>>> import pypath
>>> from pypath.core import network
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/core/network.py", line 44, in <module>
    import pypath.core.interaction as interaction_mod
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/core/interaction.py", line 41, in <module>
    import pypath.core.evidence as pypath_evidence
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/core/evidence.py", line 38, in <module>
    import pypath.core.entity as entity
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/core/entity.py", line 34, in <module>
    import pypath.utils.mapping as mapping
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/utils/__init__.py", line 20, in <module>
    from . import orthology as homology
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/utils/orthology.py", line 45, in <module>
    import pypath.utils.mapping as mapping
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/utils/mapping.py", line 65, in <module>
    import pypath.internals.maps as maps
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/internals/maps.py", line 24, in <module>
    import pypath.internals.input_formats as input_formats
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/internals/input_formats.py", line 27, in <module>
    import pypath.inputs.uniprot as uniprot_input
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/inputs/uniprot.py", line 41, in <module>
    import pypath.utils.taxonomy as taxonomy
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/utils/taxonomy.py", line 85, in <module>
    for t in ensembl_input.ensembl_organisms()
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/inputs/ensembl.py", line 46, in ensembl_organisms
    c = curl.Curl(url)
        ^^^^^^^^^^^^^^
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/share/curl.py", line 937, in __init__
    self.curl_setup()
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/share/curl.py", line 1272, in curl_setup
    self.curl_init(url = url)
  File "/biostack/tools/pyvenv/decoupler_1.6.0/lib/python3.11/site-packages/pypath/share/curl.py", line 1182, in curl_init
    self.curl.setopt(self.curl.SSL_ENABLE_ALPN, self.alpn)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: trying to obtain a non-existing attribute: SSL_ENABLE_ALPN

Expected behavior
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Traceback
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Log file
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This way we can see better exactly at which operation and at
processing of which dataset the error occured.

Desktop (please complete the following information):

  • OS: [e.g. Centos]
  • Python version: [e.g. 3.11]
  • Version or commit hash [e.g. v0.16.10]

Additional context
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@xiangpin xiangpin added the bug Problem in the code label Mar 19, 2024
@deeenes deeenes self-assigned this Mar 20, 2024
@deeenes
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deeenes commented Mar 20, 2024

Hello, can you please share the version of your PycURL and libcurl?

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