def testVariantsSearch(self):
referenceName = '1'
request = protocol.SearchVariantsRequest()
request.reference_name = referenceName
request.start = 0
request.end = 0
request.variant_set_id = self.variantSet.getId()
# Request windows is too small, no results
path = '/variants/search'
responseData = self.sendSearchRequest(
path, request, protocol.SearchVariantsResponse)
self.assertEqual("", responseData.next_page_token)
self.assertEqual(0, len(responseData.variants))
# Larger request window, expect results
request.end = 2 ** 16
responseData = self.sendSearchRequest(
path, request, protocol.SearchVariantsResponse)
self.assertTrue(protocol.validate(
protocol.toJson(responseData), protocol.SearchVariantsResponse))
self.assertGreater(len(responseData.variants), 0)
# Verify all results are in the correct range, set and reference
for variant in responseData.variants:
self.assertGreaterEqual(variant.start, 0)
self.assertLessEqual(variant.end, 2 ** 16)
self.assertEqual(variant.variant_set_id, self.variantSet.getId())
self.assertEqual(variant.reference_name, referenceName)
def validateRequest(self, jsonDict, requestClass):
"""
Ensures the jsonDict corresponds to a valid instance of requestClass
Throws an error if the data is invalid
"""
if self._requestValidation:
if not protocol.validate(jsonDict, requestClass):
raise exceptions.RequestValidationFailureException(
jsonDict, requestClass)
def assertObjectNotSupported(self, response):
"""
Checks that the specified response returns a not supported 501 status
"""
self.assertEqual(501, response.status_code)
error = protocol.fromJson(response.data, protocol.GAException)
self.assertTrue(protocol.validate(protocol.toJson(error), type(error)))
self.assertGreater(error.error_code, 0)
self.assertGreater(len(error.message), 0)
def assertObjectNotFound(self, response):
"""
Checks that the specified response contains a search failure.
"""
self.assertEqual(404, response.status_code)
error = protocol.fromJson(response.data, protocol.GAException)
self.assertTrue(protocol.validate(protocol.toJson(error), type(error)))
self.assertGreater(error.error_code, 0)
self.assertGreater(len(error.message), 0)
def validateRequest(self, jsonDict, requestClass):
"""
Ensures the jsonDict corresponds to a valid instance of requestClass
Throws an error if the data is invalid
"""
if self._requestValidation:
if not protocol.validate(jsonDict, requestClass):
raise exceptions.RequestValidationFailureException(
jsonDict, requestClass)
def sendSearchRequest(self, path, request, responseClass):
"""
Sends the specified protocol request instance as JSON, and
parses the result into an instance of the specified response.
"""
response = self.sendJsonPostRequest(path, protocol.toJson(request))
self.assertEqual(200, response.status_code)
responseData = protocol.fromJson(response.data, responseClass)
self.assertTrue(
protocol.validate(protocol.toJson(responseData), responseClass))
return responseData
def sendSearchRequest(self, path, request, responseClass):
"""
Sends the specified protocol request instance as JSON, and
parses the result into an instance of the specified response.
"""
response = self.sendJsonPostRequest(path, protocol.toJson(request))
self.assertEqual(200, response.status_code)
responseData = protocol.fromJson(response.data, responseClass)
self.assertTrue(
protocol.validate(protocol.toJson(responseData), responseClass))
return responseData
def testGoodMappings(self):
ontology = self._gaObject
for term in self._oboReader:
self.assertIn(term.id, ontology.getTermIds(term.name))
gaTerm = ontology.getGaTermByName(term.name)
self.assertTrue(protocol.validate(protocol.toJson(gaTerm),
OntologyTerm))
self.assertEqual(gaTerm.term, term.name)
self.assertIn(gaTerm.id, ontology.getTermIds(term.name))
self.assertEqual(
gaTerm.source_version, ontology.getSourceVersion())
self.assertEqual(gaTerm.source_name, ontology.getName())
def testVariantAnnotationSetsSearch(self):
self.assertIsNotNone(self.variantAnnotationSet)
request = protocol.SearchVariantAnnotationSetsRequest()
request.variant_set_id = "b4d=="
path = '/variantannotationsets/search'
response = self.sendJsonPostRequest(path, protocol.toJson(request))
responseData = protocol.fromJson(response.data, protocol.GAException)
self.assertTrue(protocol.validate(protocol.toJson(responseData),
protocol.GAException))
self.assertEqual(responseData.error_code, 758389611)
self.assertEqual(responseData.message,
'No object of this type exists with id \'b4d==\'')
request.variant_set_id = self.variantSet.getId()
response = self.sendJsonPostRequest(path, protocol.toJson(request))
responseData = protocol.fromJson(response.data, protocol.
SearchVariantAnnotationSetsResponse)
self.assertTrue(protocol.validate(
protocol.toJson(responseData),
protocol.SearchVariantAnnotationSetsResponse))
self.assertGreater(len(responseData.variant_annotation_sets), 0,
"Expect some results for a known good ID")
