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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

Reactome is empty #26

Closed mali-git closed 5 years ago

mali-git commented 5 years ago

Installation: pip install git+https://github.com/SmartDataAnalytics/BioKEEN.git Command: biokeen start pip freeze: requirements.txt

Exception: ... unhandled: p(hgnc:VPS29) partOf bp(reactome:"Signaling by WNT") unhandled: p(hgnc:VPS29) partOf bp(reactome:"WNT ligand biogenesis and trafficking") unhandled: p(hgnc:MOB1A) partOf bp(reactome:"Signal Transduction") unhandled: p(hgnc:MOB1A) partOf bp(reactome:"Signaling by Hippo") unhandled: p(hgnc:GREM2) partOf bp(reactome:"Signal Transduction") unhandled: p(hgnc:GREM2) partOf bp(reactome:"Signaling by BMP") unhandled: p(hgnc:GREM2) partOf bp(reactome:"Signaling by TGF-beta family members") unhandled: p(hgnc:BMPR2) partOf bp(reactome:"Signal Transduction") unhandled: p(hgnc:BMPR2) partOf bp(reactome:"Signaling by BMP") unhandled: p(hgnc:BMPR2) partOf bp(reactome:"Signaling by TGF-beta family members") unhandled: p(hgnc:RIT1) partOf bp(reactome:"Signal Transduction") unhandled: p(hgnc:RIT1) partOf bp(reactome:"Signaling by NTRK1 (TRKA)") unhandled: p(hgnc:RIT1) partOf bp(reactome:"Signaling by NTRKs") unhandled: p(hgnc:RIT1) partOf bp(reactome:"Signaling by Receptor Tyrosine Kinases") unhandled: p(hgnc:RIT1) partOf bp(reactome:"Signalling to ERKs") unhandled: p(hgnc:RIT1) partOf bp(reactome:"Signalling to p38 via RIT and RIN") unhandled: p(hgnc:MOB1B) partOf bp(reactome:"Signal Transduction") unhandled: p(hgnc:MOB1B) partOf bp(reactome:"Signaling by Hippo") unhandled: p(hgnc:THBS4) partOf bp(reactome:"Signal Transduction") unhandled: p(hgnc:THBS4) partOf bp(reactome:"Signaling by PDGF") unhandled: p(hgnc:THBS4) partOf bp(reactome:"Signaling by Receptor Tyrosine Kinases") unhandled: p(hgnc:GRAP) partOf bp(reactome:"Signal Transduction") unhandled: p(hgnc:GRAP) partOf bp(reactome:"Signaling by Receptor Tyrosine Kinases") unhandled: p(hgnc:GRAP) partOf bp(reactome:"Signaling by SCF-KIT") unhandled: p(hgnc:AMHR2) partOf bp(reactome:"Signal Transduction") unhandled: p(hgnc:AMHR2) partOf bp(reactome:"Signaling by BMP") unhandled: p(hgnc:AMHR2) partOf bp(reactome:"Signaling by TGF-beta family members") preparing TSV: 100%|██████████████████████████████████████████████████████████| 110618/110618 [00:06<00:00, 16751.05it/s] 🍩 no statements generated Traceback (most recent call last): File "/Users/mali/development/virtual_envs/test/bin/biokeen", line 10, in sys.exit(main()) File "/Users/mali/development/virtual_envs/test/lib/python3.7/site-packages/click/core.py", line 764, in call return self.main(args, kwargs) File "/Users/mali/development/virtual_envs/test/lib/python3.7/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/Users/mali/development/virtual_envs/test/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/test/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/test/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(args, **kwargs) File "/Users/mali/development/virtual_envs/test/lib/python3.7/site-packages/biokeen/cli/cli.py", line 57, in start do_prompt_bio2bel=(not no_prompt_bio2bel), File "/Users/mali/development/virtual_envs/test/lib/python3.7/site-packages/biokeen/cli/prompts.py", line 50, in prompt_biokeen_config if os.path.exists(path): File "/Users/mali/development/virtual_envs/test/bin/../lib/python3.7/genericpath.py", line 19, in exists os.stat(path) TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType