gene_to_uniprot_from_mygene (mapping of HGNC issue)

[lpalbou]

We got a message this morning on the alliance helpdesk that the ribbon wasn't working for a new HGNC id: https://agr-jira.atlassian.net/browse/AGRHELP-74 (may require jira account to access)

I checked the biolink log and essentially there is no uniprot results for that new HGNC id:
http://mygene.info/v3/query?q=HGNC:53833&fields=uniprot

As a counter example, we do have uniprot results for older HGNC:
http://mygene.info/v3/query?q=HGNC:11998&fields=uniprot

Error log of https://github.com/geneontology/biolink-api/blob/master/biolink/api/entityset/endpoints/slimmer.py#L149:

results:  {'took': 2, 'total': 1, 'max_score': 13.838859, 'hits': [{'_id': '114483833', '_score': 13.838859}]}
hit:  {'_id': '114483833', '_score': 13.838859}
2020-07-22 09:47:10,636 - root - ERROR - An exception occurred: 'uniprot'
[2020-07-22 09:47:10,636] ERROR in app: Exception on /api/ontology/ribbon/ [GET]
Traceback (most recent call last):
  File "/Users/albou/go-api/biolink-api/venv/lib/python3.7/site-packages/flask/app.py", line 1949, in full_dispatch_request
    rv = self.dispatch_request()
  File "/Users/albou/go-api/biolink-api/venv/lib/python3.7/site-packages/flask/app.py", line 1935, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/Users/albou/go-api/biolink-api/venv/lib/python3.7/site-packages/flask_restplus/api.py", line 325, in wrapper
    resp = resource(*args, **kwargs)
  File "/Users/albou/go-api/biolink-api/venv/lib/python3.7/site-packages/flask/views.py", line 89, in view
    return self.dispatch_request(*args, **kwargs)
  File "/Users/albou/go-api/biolink-api/venv/lib/python3.7/site-packages/flask_restplus/resource.py", line 44, in dispatch_request
    resp = meth(*args, **kwargs)
  File "/Users/albou/go-api/biolink-api/biolink/api/ontol/endpoints/ontology_endpoint.py", line 363, in get
    prots = gene_to_uniprot_from_mygene(s)
  File "/Users/albou/go-api/biolink-api/biolink/api/entityset/endpoints/slimmer.py", line 153, in gene_to_uniprot_from_mygene
    if 'Swiss-Prot' in hit['uniprot']:
KeyError: 'uniprot'
2020-07-22 09:47:10,636 - app - ERROR - Exception on /api/ontology/ribbon/ [GET]
Traceback (most recent call last):
  File "/Users/albou/go-api/biolink-api/venv/lib/python3.7/site-packages/flask/app.py", line 1949, in full_dispatch_request
    rv = self.dispatch_request()
  File "/Users/albou/go-api/biolink-api/venv/lib/python3.7/site-packages/flask/app.py", line 1935, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/Users/albou/go-api/biolink-api/venv/lib/python3.7/site-packages/flask_restplus/api.py", line 325, in wrapper
    resp = resource(*args, **kwargs)
  File "/Users/albou/go-api/biolink-api/venv/lib/python3.7/site-packages/flask/views.py", line 89, in view
    return self.dispatch_request(*args, **kwargs)
  File "/Users/albou/go-api/biolink-api/venv/lib/python3.7/site-packages/flask_restplus/resource.py", line 44, in dispatch_request
    resp = meth(*args, **kwargs)
  File "/Users/albou/go-api/biolink-api/biolink/api/ontol/endpoints/ontology_endpoint.py", line 363, in get
    prots = gene_to_uniprot_from_mygene(s)
  File "/Users/albou/go-api/biolink-api/biolink/api/entityset/endpoints/slimmer.py", line 153, in gene_to_uniprot_from_mygene
    if 'Swiss-Prot' in hit['uniprot']:
KeyError: 'uniprot'

Notes:

• unless putting more efforts into ID mapping, I don't think there is anything to do here except to wait that mygene.info gets updated
• worryingly, I don't see anymore that gene_to_uniprot_from_mygene() in the biolink repo (GO is using a fork of biolink). Has it been transferred to another file ?

@deepakunni3 @cmungall

[kshefchek]

the code is still there but was refactored in 34be1d7