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.id = "http://ohsu.edu/cgd/5c895709"
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.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 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 testPhenotypeSearchQualifiersSensitivityPATO_0000396(self):
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
ontologyterm = protocol.OntologyTerm()
ontologyterm.id = "http://purl.obolibrary.org/obo/PATO_0000396"
request.qualifiers.extend([ontologyterm])
postUrl = '/phenotypes/search'
response = self.sendSearchRequest(postUrl, request,
protocol.SearchPhenotypesResponse)
self.assertGreater(len(response.phenotypes), 0)
def sendPhenotypesSearch(self):
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = self.phenotypeAssociationSetId
return self.sendPostRequest('/phenotypes/search', request)