Wikipathways is empty

[mali-git]

Wikipathways is empty (see wikipathways.keen.summary.json) after installing the corresponding package thrugh the CLI.
Therefore, wikipathways.keen.tsv will not be created and following exception will occur:

Traceback (most recent call last):
File "/Users/mali/development/virtual_envs/biokeen/bin/biokeen", line 10, in
sys.exit(main())
File "/Users/mali/development/virtual_envs/biokeen/lib/python3.7/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/Users/mali/development/virtual_envs/biokeen/lib/python3.7/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/Users/mali/development/virtual_envs/biokeen/lib/python3.7/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/mali/development/virtual_envs/biokeen/lib/python3.7/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/mali/development/virtual_envs/biokeen/lib/python3.7/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/Users/mali/development/virtual_envs/biokeen/lib/python3.7/site-packages/biokeen/cli/cli.py", line 62, in start
pykeen.run(config)
File "/Users/mali/development/virtual_envs/biokeen/lib/python3.7/site-packages/pykeen/run.py", line 136, in run
pipeline_results = pipeline.run()
File "/Users/mali/development/virtual_envs/biokeen/lib/python3.7/site-packages/pykeen/utilities/pipeline.py", line 78, in run
mapped_pos_train_triples = self._get_train_triples()
File "/Users/mali/development/virtual_envs/biokeen/lib/python3.7/site-packages/pykeen/utilities/pipeline.py", line 187, in _get_train_triples
train_pos = load_data(self.config[pkc.TRAINING_SET_PATH])
File "/Users/mali/development/virtual_envs/biokeen/lib/python3.7/site-packages/pykeen/utilities/pipeline.py", line 207, in load_data
for p in path
File "/Users/mali/development/virtual_envs/biokeen/lib/python3.7/site-packages/pykeen/utilities/pipeline.py", line 207, in
for p in path
File "/Users/mali/development/virtual_envs/biokeen/lib/python3.7/site-packages/pykeen/utilities/pipeline.py", line 213, in _load_data_helper
if path.startswith(f'{prefix}:'):
AttributeError: 'NoneType' object has no attribute 'startswith'

[cthoyt]

You have to give some information about your environment otherwise this won't be easy to address. Show me the output of pip freeze and the code that you ran that caused this message (do the same for all of the other issues)

[mali-git]

You have to give some information about your environment otherwise this won't be easy to address. Show me the output of pip freeze and the code that you ran that caused this message (do the same for all of the other issues)

Command: biokeen startand selected wikipathways from the CLI.

pip freeze: requirements.txt