URLError when loading ComPath

[mali-git]

Traceback (most recent call last):
File "/Users/mehdi/virtual_envs/iswc/bin/biokeen", line 10, in
sys.exit(main())
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/biokeen/cli/cli.py", line 52, in start
config = prompt_biokeen_config(connection=connection, rebuild=rebuild)
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/biokeen/cli/prompts.py", line 42, in prompt_biokeen_config
for name in select_bio2bel_repository()
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/biokeen/cli/prompts.py", line 42, in
for name in select_bio2bel_repository()
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/biokeen/content.py", line 73, in install_bio2bel_module
graph = manager.to_bel()
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/compath_resources/manager.py", line 28, in to_bel
return get_bel()
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/compath_resources/manager.py", line 38, in get_bel
df = get_df()
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/compath_resources/parser.py", line 24, in get_df
pd.read_csv(KEGG_WIKIPATHWAYS_URL),
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/pandas/io/parsers.py", line 702, in parser_f
return _read(filepath_or_buffer, kwds)
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/pandas/io/parsers.py", line 413, in _read
filepath_or_buffer, encoding, compression)
File "/Users/mehdi/virtual_envs/iswc/lib/python3.6/site-packages/pandas/io/common.py", line 202, in get_filepath_or_buffer
req = _urlopen(filepath_or_buffer)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
return opener.open(url, data, timeout)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 526, in open
response = self._open(req, data)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 544, in _open
'_open', req)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
result = func(*args)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
context=self._context, check_hostname=self._check_hostname)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:777)>

[cthoyt]

What's the code you have to run to get this error?

[mali-git]

What's the code you have to run to get this error?

I started BioKEEN through the CLI biokeen start and wanted to access ComPath.

[cthoyt]

it worked for me with a clean install. This error looks like its due to a network connection