def testNoFind(self):
request = protocol.SearchGenotypePhenotypeRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
request.feature_ids.extend(["FOOBAR"])
response = self.sendSearchRequest(
'/featurephenotypeassociations/search', request,
protocol.SearchGenotypePhenotypeResponse)
self.assertEqual(0, len(response.associations))
def testGenotypePhenotypeSearchPhenotype(self):
"""
Search for associations given a phenotype
"""
request = protocol.SearchGenotypePhenotypeRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
request.phenotype_ids.extend(["http://ohsu.edu/cgd/25abbb09"])
response = self.sendSearchRequest(
'/featurephenotypeassociations/search', request,
protocol.SearchGenotypePhenotypeResponse)
self.assertEqual(1, len(response.associations[0].feature_ids))
def testGenotypePhenotypeSearchEvidence(self):
"""
Search for associations given an evidence
"""
request = protocol.SearchGenotypePhenotypeRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
eq = protocol.EvidenceQuery()
eq.description = "imatinib"
request.evidence.extend([eq])
response = self.sendSearchRequest(
'/featurephenotypeassociations/search', request,
protocol.SearchGenotypePhenotypeResponse)
self.assertEqual(1, len(response.associations[0].feature_ids))
def testSearchGenotypePhenotype(self):
request = protocol.SearchGenotypePhenotypeRequest()
request.phenotype_association_set_id = \
self.phenotype_association_set_id
request.feature_ids.extend(self.feature_ids)
request.phenotype_ids.extend(self.phenotype_ids)
request.evidence.extend([self.evidence])
request.page_size = self.pageSize
self.httpClient.search_genotype_phenotype(
phenotype_association_set_id=self.phenotype_association_set_id,
feature_ids=self.feature_ids,
phenotype_ids=self.phenotype_ids,
evidence=[self.evidence])
self.httpClient._run_search_request.assert_called_once_with(
request, "featurephenotypeassociations",
protocol.SearchGenotypePhenotypeResponse)
def testGenotypePhenotypeSearchFeature(self):
"""
Search for associations given a feature
"""
# simulate user interacting with sequenceAnnotations
request = protocol.SearchGenotypePhenotypeRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
datasetName, featureSet = self.getCGDDataSetFeatureSet()
featureId = \
"http://ohsu.edu/cgd/27d2169c"
obfuscated = self.getObfuscatedFeatureCompoundId(
datasetName, featureSet.name, featureId)
# use the feature to look up associations
request.feature_ids.extend([obfuscated])
response = self.sendSearchRequest(
'/featurephenotypeassociations/search', request,
protocol.SearchGenotypePhenotypeResponse)
self.assertEqual(1, len(response.associations[0].feature_ids))
def testGenotypePhenotypeSearchEnsureEnvironment(self):
request = protocol.SearchGenotypePhenotypeRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
datasetName, featureSet = self.getCGDDataSetFeatureSet()
featureId = \
"http://ohsu.edu/cgd/27d2169c"
obfuscated = self.getObfuscatedFeatureCompoundId(
datasetName, featureSet.name, featureId)
request.feature_ids.extend([obfuscated])
eq = protocol.EvidenceQuery()
eq.description = "imatinib"
request.evidence.extend([eq])
response = self.sendSearchRequest(
'/featurephenotypeassociations/search', request,
protocol.SearchGenotypePhenotypeResponse)
self.assertEqual(1,
len(response.associations[0].environmental_contexts))
environmentalContext = response.associations[0] \
.environmental_contexts[0]
self.assertEqual('imatinib', environmentalContext.description)
def testGenotypePhenotypeSearchEnsureEvidence(self):
"""
Ensure evidence level is serialized in responses
"""
request = protocol.SearchGenotypePhenotypeRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
datasetName, featureSet = self.getCGDDataSetFeatureSet()
featureId = \
"http://ohsu.edu/cgd/27d2169c"
obfuscated = self.getObfuscatedFeatureCompoundId(
datasetName, featureSet.name, featureId)
request.feature_ids.extend([obfuscated])
response = self.sendSearchRequest(
'/featurephenotypeassociations/search', request,
protocol.SearchGenotypePhenotypeResponse)
self.assertEqual(1, len(response.associations[0].evidence))
evidence = response.associations[0].evidence[0]
self.assertEqual('decreased_sensitivity', evidence.description)
def search_genotype_phenotype(self,
phenotype_association_set_id=None,
feature_ids=None,
phenotype_ids=None,
evidence=None):
"""
Returns an iterator over the GeneotypePhenotype associations from
the server
"""
request = protocol.SearchGenotypePhenotypeRequest()
request.phenotype_association_set_id = phenotype_association_set_id
if feature_ids:
request.feature_ids.extend(feature_ids)
if phenotype_ids:
request.phenotype_ids.extend(phenotype_ids)
if evidence:
request.evidence.extend(evidence)
request.page_size = pb.int(self._page_size)
self._logger.debug("search_genotype_phenotype {}".format(request))
return self._run_search_request(
request, "featurephenotypeassociations",
protocol.SearchGenotypePhenotypeResponse)
def testCompoundFeatureSearch(self):
datasetName, featureSet = self.getCGDDataSetFeatureSet()
featureId = \
"http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=736"
obfuscated = self.getObfuscatedFeatureCompoundId(
datasetName, featureSet.name, featureId)
request = protocol.GetFeatureRequest
request.feature_id = obfuscated
response = self.sendGetRequest('/features/{}'.format(obfuscated))
feature = protocol.fromJson(response.data, protocol.Feature)
self.assertIsNotNone(feature)
featureId = feature.id
request = protocol.SearchGenotypePhenotypeRequest()
request.phenotype_association_set_id = \
self.getPhenotypeAssociationSetId()
request.feature_ids.append(featureId)
response = self.sendSearchRequest(
'/featurephenotypeassociations/search', request,
protocol.SearchGenotypePhenotypeResponse)
self.assertEqual(1, len(response.associations))
self.assertEqual(1, len(response.associations[0].feature_ids))
def sendGenotypePhenotypesSearch(self):
request = protocol.SearchGenotypePhenotypeRequest()
request.phenotype_association_set_id = self.phenotypeAssociationSetId
return self.sendPostRequest('/featurephenotypeassociations/search',
request)
