AttributeError: 'str' object has no attribute 'get'

[emanuelecavalleri]

Hello @caufieldjh! I have recently upgraded ontoGPT to its latest version. I've encountered an issue while executing commands such as “ontogpt extract -t gene_protein -i abstract_geneProtein.txt” which results in the following error message:

Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.11/bin/ontogpt", line 8, in
sys.exit(main())
^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ontogpt/cli.py", line 336, in extract
results = ke.extract_from_text(text=text, cls=target_class_def, show_prompt=show_prompt)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ontogpt/engines/spires_engine.py", line 97, in extract_from_text
extracted_object = self.parse_completion_payload(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ontogpt/engines/spires_engine.py", line 559, in parse_completion_payload
return self.ground_annotation_object(raw, cls)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ontogpt/engines/spires_engine.py", line 629, in ground_annotation_object
obj = self.ground_annotation_object(val, rng_cls)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ontogpt/engines/spires_engine.py", line 631, in ground_annotation_object
obj = self.normalize_named_entity(val, slot.range) # type: ignore
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ontogpt/engines/knowledge_engine.py", line 352, in normalize_named_entity
for normalized_id in self.normalize_identifier(obj_id, cls):
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ontogpt/engines/knowledge_engine.py", line 416, in normalize_identifier
for obj_id in self.map_identifier(input_id, cls):
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ontogpt/engines/knowledge_engine.py", line 449, in map_identifier
for mapping in mapper.sssom_mappings([input_id]):
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/oaklib/implementations/translator/translator_implementation.py", line 62, in sssom_mappings
equiv_identifiers = data.get("equivalent_identifiers", [])
^^^^^^^^
AttributeError: 'str' object has no attribute 'get'

---

Package Versions:
ontogpt: 0.3.3
oaklib: 0.5.20
sssom: 0.3.41

Thanks in advance!
Emanuele

[caufieldjh]

Hi @emanuelecavalleri - this is a bug in oaklib that got fixed here: INCATools/ontology-access-kit#663 , but hasn't made it into a released version of that package yet.
In the meantime, there's an easy fix:
Open oaklib's translator_implementation.py (so on your system, "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/oaklib/implementations/translator/translator_implementation.py") with your choice of editor and find the line beginning with NODE_NORMALIZER_ENDPOINT.
It should be around line 26.
In the URL in that line, change the "1.3" to "1.4" so the line then reads:

NODE_NORMALIZER_ENDPOINT = "https://nodenormalization-sri.renci.org/1.4/get_normalized_nodes"

This should clear up that error.