Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
>>> 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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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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Describe the bug
error in
from pypath.core import network
To Reproduce Steps to reproduce the behavior:
Expected behavior A clear and concise description of what you expected to happen.
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Log file Please attach the log file or at least the last few lines of it. 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):
Additional context Add any other context about the problem here.