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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/
https://github.com/pykeen/pykeen/
MIT License
46 stars 4 forks source link

MSig is empty #23

Closed mali-git closed 5 years ago

mali-git commented 5 years ago

MSig is empty (see msig.keen.summary.json) after installing the corresponding package thrugh the CLI: biokeen start

pip freeze: requirements.txt

Therefore, msig.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'