Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Transient errors with Translator endpoint #370

Open
caufieldjh opened this issue May 7, 2024 · 1 comment
Open

Transient errors with Translator endpoint #370

caufieldjh opened this issue May 7, 2024 · 1 comment

Comments

@caufieldjh
Copy link
Member

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'
@caufieldjh
Copy link
Member Author

Looks similar to #224 so perhaps the NodeNormalizer service changed locations again

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant