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monarch-initiative / curate-gpt

LLM-driven curation assist tool (pre-alpha)
https://monarch-initiative.github.io/curate-gpt/
BSD 3-Clause "New" or "Revised" License
49 stars 11 forks source link

Format code using `tox` #12

Closed hrshdhgd closed 7 months ago

hrshdhgd commented 7 months ago
hrshdhgd commented 7 months ago

74 errors as of now

FAILED tests/agents/test_chat.py::test_chat[100] - ValueError: Collection test does not exist.
FAILED tests/agents/test_chat.py::test_chat[10] - ValueError: Collection test does not exist.
FAILED tests/agents/test_concept_recognizer.py::test_concept_recognizer[concept_list0-A metabolic process that results in the breakdown of chemicals in vacuolar structures.-categories0-prefixes0-expected0] - ValueError: Collection terms_go does not exist.
FAILED tests/agents/test_concept_recognizer.py::test_concept_recognizer[concept_list0-A metabolic process that results in the breakdown of chemicals in vacuolar structures.-categories1-prefixes1-expected1] - ValueError: Collection terms_go does not exist.
FAILED tests/agents/test_concept_recognizer.py::test_concept_recognizer[concept_list0-Protoplasm-None-None-expected2] - ValueError: Collection terms_go does not exist.
FAILED tests/agents/test_concept_recognizer.py::test_concept_recognizer[concept_list0-The photosynthetic membrane of plants and algae-categories3-None-expected3] - ValueError: Collection terms_go does not exist.
FAILED tests/agents/test_concept_recognizer.py::test_concept_recognizer[concept_list1-A metabolic process that results in the breakdown of chemicals in vacuolar structures.-categories0-prefixes0-expected0] - ValueError: Collection terms_go does not exist.
FAILED tests/agents/test_concept_recognizer.py::test_concept_recognizer[concept_list1-A metabolic process that results in the breakdown of chemicals in vacuolar structures.-categories1-prefixes1-expected1] - ValueError: Collection terms_go does not exist.
FAILED tests/agents/test_concept_recognizer.py::test_concept_recognizer[concept_list1-Protoplasm-None-None-expected2] - ValueError: Collection terms_go does not exist.
FAILED tests/agents/test_concept_recognizer.py::test_concept_recognizer[concept_list1-The photosynthetic membrane of plants and algae-categories3-None-expected3] - ValueError: Collection terms_go does not exist.
FAILED tests/agents/test_concept_recognizer.py::test_concept_recognizer[two_pass-A metabolic process that results in the breakdown of chemicals in vacuolar structures.-categories0-prefixes0-expected0] - ValueError: Collection terms_go does not exist.
FAILED tests/agents/test_concept_recognizer.py::test_concept_recognizer[two_pass-A metabolic process that results in the breakdown of chemicals in vacuolar structures.-categories1-prefixes1-expected1] - ValueError: Collection terms_go does not exist.
FAILED tests/agents/test_concept_recognizer.py::test_concept_recognizer[two_pass-Protoplasm-None-None-expected2] - ValueError: Collection terms_go does not exist.
FAILED tests/agents/test_concept_recognizer.py::test_concept_recognizer[two_pass-The photosynthetic membrane of plants and algae-categories3-None-expected3] - ValueError: Collection terms_go does not exist.
FAILED tests/agents/test_dase.py::test_object_completion[A metabolic process that results in the breakdown of cysteine] - ValueError: Collection test does not exist.
FAILED tests/agents/test_dase.py::test_predict_missing - ValueError: Collection test does not exist.
FAILED tests/agents/test_dase.py::test_de_novo - ValueError: Collection test does not exist.
FAILED tests/agents/test_dragon.py::test_object_completion[vacuole envelope-label] - ValueError: Collection test does not exist.
FAILED tests/agents/test_dragon.py::test_object_completion[thylakoid membrane-label] - ValueError: Collection test does not exist.
FAILED tests/agents/test_dragon.py::test_object_completion[A metabolic process that results in the breakdown of cysteine-definition] - ValueError: Collection test does not exist.
FAILED tests/agents/test_dragon.py::test_predict_missing - ValueError: Collection test does not exist.
FAILED tests/agents/test_dragon.py::test_de_novo - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-True-nuclear membrane-NuclearMembrane] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-True-membrane of the nucleus-NuclearMembrane] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-True-metabolism-MetabolicProcess] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-True-upregulation of metabolism-PositiveRegulationOfMetabolicProcess] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-True-UpregulationOfMetabolism-PositiveRegulationOfMetabolicProcess] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-True-bacterium-Bacteria] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-True-taxon: bacteria-Bacteria] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-True-kinase-KinaseActivity] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-True-kinase inhibitor-KinaseInhibitorActivity] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-True-the membrane surrounding cell-PlasmaMembrane] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-False-nuclear membrane-NuclearMembrane] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-False-membrane of the nucleus-NuclearMembrane] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-False-metabolism-MetabolicProcess] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-False-upregulation of metabolism-PositiveRegulationOfMetabolicProcess] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-False-UpregulationOfMetabolism-PositiveRegulationOfMetabolicProcess] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-False-bacterium-Bacteria] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-False-taxon: bacteria-Bacteria] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-False-kinase-KinaseActivity] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-False-kinase inhibitor-KinaseInhibitorActivity] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields0-False-10-False-the membrane surrounding cell-PlasmaMembrane] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-True-nuclear membrane-NuclearMembrane] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-True-membrane of the nucleus-NuclearMembrane] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-True-metabolism-MetabolicProcess] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-True-upregulation of metabolism-PositiveRegulationOfMetabolicProcess] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-True-UpregulationOfMetabolism-PositiveRegulationOfMetabolicProcess] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-True-bacterium-Bacteria] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-True-taxon: bacteria-Bacteria] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-True-kinase-KinaseActivity] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-True-kinase inhibitor-KinaseInhibitorActivity] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-True-the membrane surrounding cell-PlasmaMembrane] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-False-nuclear membrane-NuclearMembrane] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-False-membrane of the nucleus-NuclearMembrane] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-False-metabolism-MetabolicProcess] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-False-upregulation of metabolism-PositiveRegulationOfMetabolicProcess] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-False-UpregulationOfMetabolism-PositiveRegulationOfMetabolicProcess] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-False-bacterium-Bacteria] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-False-taxon: bacteria-Bacteria] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-False-kinase-KinaseActivity] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-False-kinase inhibitor-KinaseInhibitorActivity] - ValueError: Collection test does not exist.
FAILED tests/agents/test_mapper.py::test_mapper[fields1-False-10-False-the membrane surrounding cell-PlasmaMembrane] - ValueError: Collection test does not exist.
FAILED tests/extract/test_extractor.py::test_extract[RecursiveExtractor-kwargs1-99] - openai.error.Timeout: Request timed out: HTTPSConnectionPool(host='api.openai.com', port=443): Read timed out. (read timeout=600)
FAILED tests/wrappers/test_clinvar.py::test_clinvar_transform - FileNotFoundError: [Errno 2] No such file or directory: '../curate-gpt/tests/input/clinvar-esummary-example.yaml'
FAILED tests/wrappers/test_evidence_agent.py::test_evidence_inference[WikipediaWrapper] - sqlite3.OperationalError: attempt to write a readonly database
FAILED tests/wrappers/test_gocam.py::test_gocam_object - FileNotFoundError: [Errno 2] No such file or directory: '../curate-gpt/tests/input/gocam-613aae0000000813.json'
FAILED tests/wrappers/test_hpoa.py::test_hpoa[True] - FileNotFoundError: [Errno 2] No such file or directory: '../curate-gpt/tests/input/example-phenotype-hpoa.tsv'
FAILED tests/wrappers/test_hpoa.py::test_hpoa[False] - FileNotFoundError: [Errno 2] No such file or directory: '../curate-gpt/tests/input/example-phenotype-hpoa.tsv'
FAILED tests/wrappers/test_json.py::test_json_objects - FileNotFoundError: [Errno 2] No such file or directory: '../curate-gpt/tests/input/biolink-model.yaml'
FAILED tests/wrappers/test_linkml_schema.py::test_linkml_schema_objects - FileNotFoundError: [Errno 2] No such file or directory: '../curate-gpt/tests/input/biolink-model.yaml'
FAILED tests/wrappers/test_ncbi_biosample.py::test_biosample_chat - sqlite3.OperationalError: attempt to write a readonly database
FAILED tests/wrappers/test_ontology.py::test_oak_objects - AttributeError: 'GraphDocument' object has no attribute 'nodes'
FAILED tests/wrappers/test_pubmed.py::test_pubmed_search - sqlite3.OperationalError: attempt to write a readonly database
FAILED tests/wrappers/test_pubmed.py::test_pubmed_chat - sqlite3.OperationalError: attempt to write a readonly database
ERROR tests/wrappers/test_clinvar.py::test_clinvar_chat - sqlite3.OperationalError: attempt to write a readonly database
ERROR tests/wrappers/test_ontology.py::test_oak_index - sqlite3.OperationalError: attempt to write a readonly database
ERROR tests/wrappers/test_ontology.py::test_oak_search - sqlite3.OperationalError: attempt to write a readonly database