def testGenotypeSearchFeaturePagingAll(self):
"""
Loop through all pages
"""
request = self._createPagingRequest()
request.page_size = 1
feature_set_id = request.feature_set_id
postUrl = "features/search"
response = self.sendSearchRequest(
postUrl,
request,
protocol.SearchFeaturesResponse)
self.assertEqual(1, len(response.features))
self.assertIsNotNone(response.next_page_token)
pageCount = 1
while response.next_page_token:
previous_id = response.features[0].id
request = protocol.SearchFeaturesRequest()
request.feature_set_id = feature_set_id
request.page_size = 1
request.page_token = response.next_page_token
request.name = "KIT *wild"
response = self.sendSearchRequest(
postUrl,
request,
protocol.SearchFeaturesResponse)
self.assertEqual(1, len(response.features))
self.assertNotEqual(previous_id, response.features[0].id)
pageCount += 1
self.assertEqual(3, pageCount)
def testGenotypesSearchByNameKIT(self):
request = protocol.SearchFeaturesRequest()
datasetName, featureSet = self.getCGDDataSetFeatureSet()
request.feature_set_id = featureSet.id
request.name = \
"KIT *wild"
postUrl = "features/search"
response = self.sendSearchRequest(postUrl, request,
protocol.SearchFeaturesResponse)
self.assertEqual(3, len(response.features))
def testGenotypesSearchByNameError(self):
"""
Search for feature by name with a malformed regular expression.
"""
# setup phenotype query
request = protocol.SearchFeaturesRequest()
datasetName, featureSet = self.getCGDDataSetFeatureSet()
request.feature_set_id = featureSet.id
request.name = "*" # invalid regular expression
postUrl = "features/search"
response = self.sendJsonPostRequest(postUrl, protocol.toJson(request))
self.assertEqual(400, response.status_code)
def testGenotypesSearchByName(self):
# setup phenotype query
request = protocol.SearchFeaturesRequest()
datasetName, featureSet = self.getCGDDataSetFeatureSet()
request.feature_set_id = featureSet.id
request.name = "RET M918T missense mutation"
postUrl = "features/search"
response = self.sendSearchRequest(postUrl, request,
protocol.SearchFeaturesResponse)
self.assertEqual(1, len(response.features))
self.assertEqual(
"http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=965",
datamodel.FeatureCompoundId.parse(
response.features[0].id).featureId)
self.assertEqual(request.name, response.features[0].name)
def _createPagingRequest(self):
request = protocol.SearchFeaturesRequest()
datasetName, featureSet = self.getCGDDataSetFeatureSet()
request.feature_set_id = featureSet.id
request.name = "KIT *wild"
return request