You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Haven't been able to reproduce this consistently, but attempts to ground using the Translator endpoint (though OAK) will sometimes fail in an uncontrolled way.
Stack trace c/o @enockniyonkuru
Traceback (most recent call last):
File "/Users/niyone/Desktop/maxo/automaxo/main.py", line 54, in <module>
main()
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/Users/niyone/Desktop/maxo/automaxo/main.py", line 51, in main
runner.run()
File "/Users/niyone/Desktop/maxo/automaxo/main.py", line 27, in run
process_ontogpt_articles(self.no_replaced_tsv_file_path, self.ontogpt_yaml_files_dir, template='maxo')
File "/Users/niyone/Desktop/maxo/automaxo/src/automaxo/ontogpt_article_processor.py", line 106, in run_in_notebook
main.main(standalone_mode=False, args=[
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/Users/niyone/Desktop/maxo/automaxo/src/automaxo/ontogpt_article_processor.py", line 103, in main
process_tsv_file(input_file, ke, output_dir,existing_pmids, template )
File "/Users/niyone/Desktop/maxo/automaxo/src/automaxo/ontogpt_article_processor.py", line 73, in process_tsv_file
process_article(pubmed_id, text, ke, output_dir,template )
File "/Users/niyone/Desktop/maxo/automaxo/src/automaxo/ontogpt_article_processor.py", line 32, in process_article
results = ke.extract_from_text(text=text)
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/ontogpt/engines/spires_engine.py", line 95, in extract_from_text
extracted_object = self.parse_completion_payload(
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/ontogpt/engines/spires_engine.py", line 558, in parse_completion_payload
return self.ground_annotation_object(raw, cls)
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/ontogpt/engines/spires_engine.py", line 628, in ground_annotation_object
obj = self.ground_annotation_object(val, rng_cls)
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/ontogpt/engines/spires_engine.py", line 630, in ground_annotation_object
obj = self.normalize_named_entity(val, slot.range) # type: ignore
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/ontogpt/engines/knowledge_engine.py", line 348, in normalize_named_entity
for normalized_id in self.normalize_identifier(obj_id, cls):
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/ontogpt/engines/knowledge_engine.py", line 412, in normalize_identifier
for obj_id in self.map_identifier(input_id, cls):
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/ontogpt/engines/knowledge_engine.py", line 446, in map_identifier
for mapping in mapper.sssom_mappings([input_id]):
File "/Users/niyone/Desktop/maxo/automaxo/.venv/lib/python3.9/site-packages/oaklib/implementations/translator/translator_implementation.py", line 83, in sssom_mappings
equiv_identifiers = data.get("equivalent_identifiers", [])
AttributeError: 'str' object has no attribute 'get'
The text was updated successfully, but these errors were encountered:
Haven't been able to reproduce this consistently, but attempts to ground using the Translator endpoint (though OAK) will sometimes fail in an uncontrolled way.
Stack trace c/o @enockniyonkuru
The text was updated successfully, but these errors were encountered: