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.assertEqual(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 testSearchPhenotype(self):
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = \
self.phenotype_association_set_id
request.id = self.phenotype_ids[0]
request.page_size = self.pageSize
self.httpClient.search_phenotype(
phenotype_association_set_id=self.phenotype_association_set_id,
phenotype_id=self.phenotype_ids[0])
self.httpClient._run_search_request.assert_called_once_with(
request, "phenotypes", protocol.SearchPhenotypesResponse)
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 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 testPhenotypeSearchQualifiersSensitivityPATO_0000396(self):
request = protocol.SearchPhenotypesRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
ontologyterm = protocol.OntologyTerm()
ontologyterm.term_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)