fix(id_mapping): fix typo taxId -> taxid

[Rapsssito]

As described in title. This is the error I get directly from the request instance (without my change):

400 {"url":"http://rest.uniprot.org/idmapping/run","messages":["Invalid parameter 'taxId'"]}

Steps to reproduce the problem (P38398 comes from human BRCA1):

request = IdMappingClient.submit(
        taxon_id=9606, source="UniProtKB_AC-ID", dest="Ensembl_Protein", ids=['P38398']
)

[multimeric]

Okay that test failure isn't your fault. Can I have a test for this though please?

[Rapsssito]

I believe there is already a test for that:

Unipressed/test/test_id_mapping/test_id_mapping.py

Lines 163 to 174 in 4734fef

	def test_taxon_id_yeast():
	# Checks that setting a taxon_id filter returns results from only yeast
	request = IdMappingClient.submit(
	source="Gene_Name", dest="UniProtKB", ids={"STE2"}, taxon_id=4932
	)
	sleep(5)
	results = {result["to"] for result in request.each_result()}
	assert len(results) >= 5
	# Real yeast gene
	assert "P0CI39" in results
	# Mouse gene
	assert "P14719" not in results

[multimeric]

Ah I see. I'll have to test that this is broken on the master branch first then.

[multimeric]

Hmm, the tests are working on master (minus the flaky ID mapping one), so I think the current approach is correct

In the API docs here it is shown as taxId. Why do you think this change is needed?

[Rapsssito]

This is the code I am using:

request = IdMappingClient.submit(taxon_id=9606, source="UniProtKB_AC-ID", dest="Ensembl_Protein",ids=uniprot_accessions)

It was not working for me at first. However, after this change, it started working. I took inspiration from here, where it is described as "taxid" not "taxId".

[multimeric]

I took inspiration from here, where it is described as "taxid" not "taxId".

That's using a different (I presume older) API than Unipressed uses

It was not working for me at first. However, after this change, it started working

I wonder if that's because your taxon ID doesn't match your uniprot IDs, and therefore the change you proposed removes the taxon filter and gets you your expected results. I would double check your inputs. I'm pretty sure the current approach in Unipressed is correct.

[Rapsssito]

@multimeric, this is the error I get directly from the request (without my change):

400 {"url":"http://rest.uniprot.org/idmapping/run","messages":["Invalid parameter 'taxId'"]}

I don't think it is related to the taxon IDs not matching.

Try running this code. Let me know if it works for you (P38398 comes from human BRCA1).

request = IdMappingClient.submit(
        taxon_id=9606, source="UniProtKB_AC-ID", dest="Ensembl_Protein", ids=['P38398']
)

(BTW, I am using Python 3.12.7)

[multimeric]

Hmm true enough, something is going on here. My best guess is that it relates to how you're doing UniProtKB_AC-ID -> Ensembl_Protein whereas the current test is Gene_Name -> UniProtKB. I think in uniprot some of the databases are inconsistent with each other, so I could imagine one of these mappers expecting a non-standard parameter. If so, we can patch it here, but I (or you) should also submit it as a bug to Uniprot themselves.

Can you please add your example above as a new test case.

[multimeric]

I have sent this issue to UniProt support. Ticket #258772.

[ahmadshadab]

Hi @multimeric ,
I've replied to you support email. "taxId" is applicable only when from field is "Gene_Name" but Swagger documents it as an optional field which is confusing. We will update the code to make validation more lenient.
Thanks,
Shadab
UniProt

[multimeric]

Thanks @ahmadshadab. Looks like I'll have to tweak the interface and docs to make this clear to users. I think the current behaviour is okay in the meantime.