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SmartDataAnalytics / BioKEEN

A computational library for learning and evaluating biological knowledge graph embeddings - please see the main PyKEEN repo at https://github.com/pykeen/pykeen/

Home Page:https://github.com/pykeen/pykeen/

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KEGG is empty

mali-git opened this issue · comments

commented

After executing biokeen startand selecting KEGG as DB, I got following exception:

Traceback (most recent call last):
File "/Users/mehdi/virtual_envs/BioKEEN/bin/biokeen", line 11, in
load_entry_point('biokeen', 'console_scripts', 'biokeen')()
File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/Users/mehdi/virtual_envs/BioKEEN/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/BioKEEN/lib/python3.6/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/Users/mehdi/PycharmProjects/BioKEEN/src/biokeen/cli/cli.py", line 57, in start
do_prompt_bio2bel=(not no_prompt_bio2bel),
File "/Users/mehdi/PycharmProjects/BioKEEN/src/biokeen/cli/prompts.py", line 44, in prompt_biokeen_config
for name in select_bio2bel_repository()
File "/Users/mehdi/PycharmProjects/BioKEEN/src/biokeen/cli/prompts.py", line 44, in
for name in select_bio2bel_repository()
File "/Users/mehdi/PycharmProjects/BioKEEN/src/biokeen/content.py", line 47, in install_bio2bel_module
graph = from_json_path(json_path)
File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/pybel/io/nodelink.py", line 99, in from_json_path
return from_json_file(f, check_version=check_version)
File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/pybel/io/nodelink.py", line 110, in from_json_file
return from_json(graph_json_dict, check_version=check_version)
File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/pybel/io/nodelink.py", line 87, in from_json
graph = node_link_graph(graph_json_dict)
File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/pybel/io/nodelink.py", line 179, in node_link_graph
_dsl = parse_result_to_dsl(node_data)
File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/pybel/tokens.py", line 43, in parse_result_to_dsl
return _simple_po_to_dict(tokens)
File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/pybel/tokens.py", line 106, in _simple_po_to_dict
name=tokens[NAME],
KeyError: 'name'

kegg.keen.summary.json shows 0 entities and 0 relations

commented

this one looks like more of a problem...