def testPhenotypesSearchDescriptionWildcard(self):
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
request.description = ".*sensitivity.*"
postUrl = '/phenotypes/search'
response = self.sendSearchRequest(
postUrl,
request,
protocol.SearchPhenotypesResponse)
self.assertEquals(7, len(response.phenotypes))
def testPhenotypesSearchOntologyTerm(self):
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
request.type.term_id = "http://ohsu.edu/cgd/5c895709"
postUrl = '/phenotypes/search'
response = self.sendSearchRequest(
postUrl,
request,
protocol.SearchPhenotypesResponse)
self.assertGreater(len(response.phenotypes), 0)
def testPhenotypesSearchDescription(self):
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
request.description = \
"Papillary thyroid carcinoma with sensitivity to therapy" # noqa
postUrl = '/phenotypes/search'
response = self.sendSearchRequest(
postUrl,
request,
protocol.SearchPhenotypesResponse)
self.assertGreater(len(response.phenotypes), 0)
def testPhenotypesSearchById(self):
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
# setup phenotype query
request.id = "http://ohsu.edu/cgd/30ebfd1a"
postUrl = '/phenotypes/search'
response = self.sendSearchRequest(
postUrl,
request,
protocol.SearchPhenotypesResponse)
self.assertEqual(request.id, response.phenotypes[0].id)
def testPhenotypeSearchMultipleQualifiers(self):
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
ontologyterm = protocol.OntologyTerm()
ontologyterm.term_id = "http://purl.obolibrary.org/obo/PATO_0000396"
ontologyterm2 = protocol.OntologyTerm()
ontologyterm2.term_id = "http://purl.obolibrary.org/obo/PATO_0000460"
request.qualifiers.extend([ontologyterm, ontologyterm2])
postUrl = '/phenotypes/search'
response = self.sendSearchRequest(postUrl, request,
protocol.SearchPhenotypesResponse)
self.assertGreater(len(response.phenotypes), 0)
def testPhenotypesSearchMultipleTerms(self):
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
request.description = "Melanoma, NOS with response to therapy"
request.age_of_onset.term_id = \
"http://purl.obolibrary.org/obo/HP_0003581"
postUrl = '/phenotypes/search'
response = self.sendSearchRequest(
postUrl,
request,
protocol.SearchPhenotypesResponse)
self.assertGreater(len(response.phenotypes), 0)
def testPhenotypeSearchQualifiersSensitivity(self):
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
ontologyterm = protocol.OntologyTerm()
ontologyterm.term_id = "http://ohsu.edu/cgd/sensitivity"
request.qualifiers.extend([ontologyterm])
postUrl = '/phenotypes/search'
response = self.sendSearchRequest(
postUrl,
request,
protocol.SearchPhenotypesResponse)
self.assertGreater(len(response.phenotypes), 0)
def search_phenotype(self,
phenotype_association_set_id=None,
phenotype_id=None,
description=None,
type_=None,
age_of_onset=None):
"""
Returns an iterator over the Phenotypes from the server
"""
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = phenotype_association_set_id
if phenotype_id:
request.id = phenotype_id
if description:
request.description = description
if type_:
request.type.mergeFrom(type_)
if age_of_onset:
request.age_of_onset = age_of_onset
request.page_size = pb.int(self._page_size)
return self._run_search_request(request, "phenotypes",
protocol.SearchPhenotypesResponse)
def sendPhenotypesSearch(self):
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = self.phenotypeAssociationSetId
return self.sendPostRequest('/phenotypes/search', request)