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sorgerlab / indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
http://indra.bio
BSD 2-Clause "Simplified" License
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Access Biopax #1444

Closed Siliegia closed 1 month ago

Siliegia commented 3 months ago

I suddenly can not retrieve biopax statements with INDRA. Just running the code from the documentation results in an error message:

from indra.tools.gene_network import GeneNetwork
gn = GeneNetwork(['H2AX'])
biopax_stmts = gn.get_biopax_stmts()

ConnectionError: ('Connection aborted.', BadStatusLine('\x00\x00\x12\x04\x00\x00\x00\x00\x00\x00\x03\x00\x00\x00\x80\x00\x04\x00\x01\x00\x00\x00\x05\x00ÿÿÿ\x00\x00\x04\x08\x00\x00\x00\x00\x00\x7fÿ\x00\x00\x00\x00\x08\x07\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01'))
bgyori commented 3 months ago

Hi @Siliegia, this is due to the fact that the Pathway Commons web service switched from http to https. This requires updating the client that calls Pathway Commons by doing

pip install -U pybiopax

to get its latest version. Please let me know if that works!

stephanmg commented 3 months ago

@bgyori thanks, this fixed it for me.