Fetch Rhea for 2,3-butanediol dehydrogenase fails

[danolson1]

I'm trying to get the RHEA:75423 reaction, 2,3-butanediol dehydrogenase.
https://www.rhea-db.org/rhea/75423

This code:
pe.fetch_rhea("RHEA:75423", vessel_id='v0')

Gives this error:

---------------------------------------------------------------------------
ValidationError                           Traceback (most recent call last)
File [~\AppData\Local\miniconda3\envs\pyenzyme\Lib\site-packages\pyenzyme\fetcher\chebi.py:146](http://localhost:8926/lab/tree/~/AppData/Local/miniconda3/envs/pyenzyme/Lib/site-packages/pyenzyme/fetcher/chebi.py#line=145), in ChEBIClient.get_entry_by_id(self, chebi_id)
    144     raise ChEBIError(f"No data found for ChEBI ID {chebi_id}")
--> 146 chebi_response = ChEBIApiResponse(raw_response_data)
    148 entry = list(chebi_response.root.values())[0]

File [~\AppData\Local\miniconda3\envs\pyenzyme\Lib\site-packages\pydantic\root_model.py:68](http://localhost:8926/lab/tree/~/AppData/Local/miniconda3/envs/pyenzyme/Lib/site-packages/pydantic/root_model.py#line=67), in RootModel.__init__(self, root, **data)
     67     root = data  # type: ignore
---> 68 self.__pydantic_validator__.validate_python(root, self_instance=self)

ValidationError: 1 validation error for ChEBIApiResponse
CHEBI:15686.data.definition
  Input should be a valid string [type=string_type, input_value=None, input_type=NoneType]
    For further information visit https://errors.pydantic.dev/2.12/v/string_type

During handling of the above exception, another exception occurred:

ChEBIError                                Traceback (most recent call last)
File [~\AppData\Local\miniconda3\envs\pyenzyme\Lib\site-packages\pyenzyme\fetcher\chebi.py:322](http://localhost:8926/lab/tree/~/AppData/Local/miniconda3/envs/pyenzyme/Lib/site-packages/pyenzyme/fetcher/chebi.py#line=321), in fetch_chebi(chebi_id, smallmol_id, vessel_id)
    321 client = ChEBIClient()
--> 322 chebi_entry = client.get_entry_by_id(chebi_id)
    324 small_molecule = process_chebi_entry(chebi_entry)

File [~\AppData\Local\miniconda3\envs\pyenzyme\Lib\site-packages\pyenzyme\fetcher\chebi.py:154](http://localhost:8926/lab/tree/~/AppData/Local/miniconda3/envs/pyenzyme/Lib/site-packages/pyenzyme/fetcher/chebi.py#line=153), in ChEBIClient.get_entry_by_id(self, chebi_id)
    153             raise e
--> 154         raise ChEBIError(f"Failed to parse ChEBI response: {str(e)}", e)
    155 else:

ChEBIError: Failed to parse ChEBI response: 1 validation error for ChEBIApiResponse
CHEBI:15686.data.definition
  Input should be a valid string [type=string_type, input_value=None, input_type=NoneType]
    For further information visit https://errors.pydantic.dev/2.12/v/string_type

The above exception was the direct cause of the following exception:

ValueError                                Traceback (most recent call last)
Cell In[61], line 1
----> 1 pe.fetch_rhea("RHEA:75423", vessel_id='v0')

File [~\AppData\Local\miniconda3\envs\pyenzyme\Lib\site-packages\pyenzyme\fetcher\rhea.py:184](http://localhost:8926/lab/tree/~/AppData/Local/miniconda3/envs/pyenzyme/Lib/site-packages/pyenzyme/fetcher/rhea.py#line=183), in fetch_rhea(rhea_id, vessel_id)
    182 # Process each chemical species in the reaction
    183 for i in range(n_reactants + n_products):
--> 184     small_molecule = fetch_chebi(
    185         client.chebi_ids[i],
    186         vessel_id=vessel_id,
    187     )
    188     small_molecules.append(small_molecule)
    190     if i < n_reactants:

File [~\AppData\Local\miniconda3\envs\pyenzyme\Lib\site-packages\pyenzyme\fetcher\chebi.py:336](http://localhost:8926/lab/tree/~/AppData/Local/miniconda3/envs/pyenzyme/Lib/site-packages/pyenzyme/fetcher/chebi.py#line=335), in fetch_chebi(chebi_id, smallmol_id, vessel_id)
    334     raise ConnectionError(str(e)) from e
    335 else:
--> 336     raise ValueError(str(e)) from e

ValueError: Failed to parse ChEBI response: 1 validation error for ChEBIApiResponse
CHEBI:15686.data.definition
  Input should be a valid string [type=string_type, input_value=None, input_type=NoneType]
    For further information visit https://errors.pydantic.dev/2.12/v/string_type

It looks like the problem is with the CHEBI import for CHEBI:15686 (R-acetoin)

[danolson1]

I'm getting a similar error for deuterated water
https://www.ebi.ac.uk/chebi/CHEBI:41981

[JR-1991]

@danolson1 thanks for sharing! The ChEBI API has been changed quite recently and I have assumed the definition property would always be present. However, it seems like this is not the case. I have fixed it locally and will push a PR to get the fix into the code base.