def testReads(self):
# search read group sets
path = utils.applyVersion('/readgroupsets/search')
request = protocol.SearchReadGroupSetsRequest()
request.datasetId = 'simulatedDataset1'
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(response.status_code, 200)
responseData = protocol.SearchReadGroupSetsResponse.fromJsonString(
response.data)
readGroupSets = responseData.readGroupSets
self.assertEqual(len(readGroupSets), 1)
# search reads
path = utils.applyVersion('/reads/search')
request = protocol.SearchReadsRequest()
readGroupId = readGroupSets[0].readGroups[0].id
request.readGroupIds = [readGroupId]
request.referenceId = "chr1"
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(response.status_code, 200)
responseData = protocol.SearchReadsResponse.fromJsonString(
response.data)
alignments = responseData.alignments
self.assertEqual(len(alignments), self.numAlignmentsPerReadGroup)
for alignment in alignments:
self.assertEqual(alignment.readGroupId, readGroupId)
def testReferences(self):
# search for reference sets
path = utils.applyVersion('/referencesets/search')
request = protocol.SearchReferenceSetsRequest()
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(response.status_code, 200)
responseData = protocol.SearchReferenceSetsResponse.fromJsonString(
response.data)
referenceSets = responseData.referenceSets
self.assertEqual(self.numReferenceSets, len(referenceSets))
# search for references
path = utils.applyVersion('/references/search')
request = protocol.SearchReferencesRequest()
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(response.status_code, 200)
responseData = protocol.SearchReferencesResponse.fromJsonString(
response.data)
references = responseData.references
self.assertEqual(
self.numReferenceSets * self.numReferencesPerReferenceSet,
len(references))
for referenceSet in referenceSets:
# fetch the reference set
path = utils.applyVersion('/referencesets/{}'.format(
referenceSet.id))
response = self.app.get(path)
self.assertEqual(response.status_code, 200)
fetchedReferenceSet = protocol.ReferenceSet.fromJsonString(
response.data)
self.assertEqual(fetchedReferenceSet, referenceSet)
self.assertEqual(len(fetchedReferenceSet.referenceIds),
self.numReferencesPerReferenceSet)
for referenceId in referenceSet.referenceIds:
# fetch the reference
path = utils.applyVersion('/references/{}'.format(referenceId))
response = self.app.get(path)
self.assertEqual(response.status_code, 200)
fetchedReference = protocol.Reference.fromJsonString(
response.data)
self.assertEqual(fetchedReference.id, referenceId)
# fetch the bases
path = utils.applyVersion(
'/references/{}/bases'.format(referenceId))
args = protocol.ListReferenceBasesRequest().toJsonDict()
response = self.app.get(path, data=args)
self.assertEqual(response.status_code, 200)
bases = protocol.ListReferenceBasesResponse.fromJsonString(
response.data)
self.assertEqual(len(bases.sequence), 200)
self.assertEqual(set(bases.sequence), set(['A', 'C', 'T',
'G']))
calculatedDigest = hashlib.md5(bases.sequence).hexdigest()
self.assertEqual(calculatedDigest,
fetchedReference.md5checksum)
def testRouteReferences(self):
paths = ['/references/1', 'references/1/bases', 'referencesets/1']
for path in paths:
versionedPath = utils.applyVersion(path)
self.assertEqual(404, self.app.get(versionedPath).status_code)
paths = ['/references/search']
for path in paths:
versionedPath = utils.applyVersion(path)
self.assertEqual(404, self.app.get(versionedPath).status_code)
self.verifySearchRouting('/referencesets/search', True)
def testRouteReferences(self):
paths = ['/references/1', 'references/1/bases', 'referencesets/1']
for path in paths:
versionedPath = utils.applyVersion(path)
self.assertEqual(404, self.app.get(versionedPath).status_code)
paths = ['/references/search']
for path in paths:
versionedPath = utils.applyVersion(path)
self.assertEqual(404, self.app.get(versionedPath).status_code)
self.verifySearchRouting('/referencesets/search', True)
def test404sReturnJson(self):
paths = [
'/doesNotExist',
utils.applyVersion('/doesNotExist'),
utils.applyVersion('/reads/sea'),
utils.applyVersion('/variantsets/id/doesNotExist'),
]
for path in paths:
response = self.app.get(path)
protocol.GAException.fromJsonString(response.get_data())
self.assertEqual(404, response.status_code)
def testRouteReferences(self):
referenceId = "referenceSet0:srs0"
paths = ['/references/{}', '/references/{}/bases']
for path in paths:
path = path.format(referenceId)
versionedPath = utils.applyVersion(path)
self.assertEqual(200, self.app.get(versionedPath).status_code)
referenceSetId = "referenceSet0"
paths = ['/referencesets/{}']
for path in paths:
path = path.format(referenceSetId)
versionedPath = utils.applyVersion(path)
self.assertEqual(200, self.app.get(versionedPath).status_code)
self.verifySearchRouting('/referencesets/search', True)
self.verifySearchRouting('/references/search', True)
def verifySearchRouting(self, path, getDefined=False):
"""
Verifies that the specified path has the correct routing for a
search command. If getDefined is False we check to see if it
returns the correct status code.
"""
versionedPath = utils.applyVersion(path)
response = self.app.post(versionedPath)
protocol.GAException.fromJsonString(response.get_data())
self.assertEqual(415, response.status_code)
if not getDefined:
getResponse = self.app.get(versionedPath)
protocol.GAException.fromJsonString(getResponse.get_data())
self.assertEqual(405, getResponse.status_code)
# Malformed requests should return 400
for badJson in ["", None, "JSON", "<xml/>", "{]"]:
badResponse = self.app.post(
versionedPath,
data=badJson,
headers={'Content-type': 'application/json'})
self.assertEqual(400, badResponse.status_code)
# OPTIONS should return success
self.assertEqual(200, self.app.options(versionedPath).status_code)
def sendPostRequest(self, path, request):
"""
Sends the specified GA request object and returns the response.
"""
versionedPath = utils.applyVersion(path)
headers = {"Content-type": "application/json", "Origin": self.exampleUrl}
return self.app.post(versionedPath, headers=headers, data=request.toJsonString())
def sendListRequest(self, path, request):
versionedPath = utils.applyVersion(path)
headers = {
'Origin': self.exampleUrl,
}
data = request.toJsonDict()
response = self.app.get(versionedPath, data=data, headers=headers)
return response
def sendGetRequest(self, path):
"""
Sends a get request to the specified URL and returns the response.
"""
versionedPath = utils.applyVersion(path)
headers = {
'Origin': self.exampleUrl,
}
return self.app.get(versionedPath, headers=headers)
def testGetVariantSet(self):
path = utils.applyVersion("/variantsets")
for variantSetId in self.variantSetIds:
response = self.sendObjectGetRequest(path, variantSetId)
self.assertEqual(200, response.status_code)
responseObject = protocol.VariantSet.fromJsonString(response.data)
self.assertEqual(responseObject.id, variantSetId)
for badId in ["", "terribly bad ID value", "x" * 1000]:
response = self.sendObjectGetRequest(path, badId)
self.assertEqual(404, response.status_code)
def sendPostRequest(self, path, request):
"""
Sends the specified GA request object and returns the response.
"""
versionedPath = utils.applyVersion(path)
headers = {
'Content-type': 'application/json',
'Origin': self.exampleUrl,
}
return self.app.post(versionedPath,
headers=headers,
data=request.toJsonString())
def testVariantsSearch(self):
expectedIds = self.variantSetIds[:1]
referenceName = '1'
request = protocol.GASearchVariantsRequest()
request.referenceName = referenceName
request.start = 0
request.end = 0
request.variantSetIds = expectedIds
# Request windows is too small, no results
path = utils.applyVersion('/variants/search')
response = self.sendJsonPostRequest(
path, request.toJsonString())
self.assertEqual(200, response.status_code)
responseData = protocol.GASearchVariantsResponse.fromJsonString(
response.data)
self.assertIsNone(responseData.nextPageToken)
self.assertEqual([], responseData.variants)
# Larger request window, expect results
request.end = 2 ** 16
path = utils.applyVersion('/variants/search')
response = self.sendJsonPostRequest(
path, request.toJsonString())
self.assertEqual(200, response.status_code)
responseData = protocol.GASearchVariantsResponse.fromJsonString(
response.data)
self.assertTrue(protocol.GASearchVariantsResponse.validate(
responseData.toJsonDict()))
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.assertTrue(variant.variantSetId in expectedIds)
self.assertEqual(variant.referenceName, referenceName)
def testVariantsSearch(self):
expectedId = self.variantSetIds[0]
referenceName = '1'
request = protocol.SearchVariantsRequest()
request.referenceName = referenceName
request.start = 0
request.end = 0
request.variantSetId = expectedId
# Request windows is too small, no results
path = utils.applyVersion('/variants/search')
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(200, response.status_code)
responseData = protocol.SearchVariantsResponse.fromJsonString(
response.data)
self.assertIsNone(responseData.nextPageToken)
self.assertEqual([], responseData.variants)
# Larger request window, expect results
request.end = 2**16
path = utils.applyVersion('/variants/search')
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(200, response.status_code)
responseData = protocol.SearchVariantsResponse.fromJsonString(
response.data)
self.assertTrue(
protocol.SearchVariantsResponse.validate(
responseData.toJsonDict()))
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.variantSetId, expectedId)
self.assertEqual(variant.referenceName, referenceName)
def setUp(self):
# TODO replace this with ALL post methods once the rest of the
# end points have been implemented. This should also add an API
# to protocol.py to simplify and document the process of getting
# the correct API endpoints and classes. That is, we shouldn't
# use protocol.postMethods directly, but instead call a function.
supportedMethods = set([
protocol.SearchCallSetsRequest,
protocol.SearchVariantSetsRequest,
protocol.SearchVariantsRequest,
])
self.endPointMap = {}
for endPoint, requestClass, responseClass in protocol.postMethods:
if requestClass in supportedMethods:
path = utils.applyVersion(endPoint)
self.endPointMap[path] = requestClass
def setUp(self):
self.app = _app
# TODO replace this with ALL post methods once the rest of the
# end points have been implemented. This should also add an API
# to protocol.py to simplify and document the process of getting
# the correct API endpoints and classes. That is, we shouldn't
# use protocol.postMethods directly, but instead call a function.
supportedMethods = set([
protocol.GASearchCallSetsRequest,
protocol.GASearchVariantSetsRequest,
protocol.GASearchVariantsRequest,
])
self.endPointMap = {}
for endPoint, requestClass, responseClass in protocol.postMethods:
if requestClass in supportedMethods:
path = utils.applyVersion(endPoint)
self.endPointMap[path] = requestClass
def testVariantSetsSearch(self):
expectedIds = self.variantSetIds
request = protocol.GASearchVariantSetsRequest()
request.pageSize = len(expectedIds)
path = utils.applyVersion('/variantsets/search')
response = self.sendJsonPostRequest(
path, request.toJsonString())
self.assertEqual(200, response.status_code)
responseData = protocol.GASearchVariantSetsResponse.fromJsonString(
response.data)
self.assertTrue(protocol.GASearchVariantSetsResponse.validate(
responseData.toJsonDict()))
self.assertIsNone(responseData.nextPageToken)
self.assertEqual(len(expectedIds), len(responseData.variantSets))
for variantSet in responseData.variantSets:
self.assertTrue(variantSet.id in expectedIds)
def testVariantSetsSearch(self):
expectedIds = self.variantSetIds
request = protocol.SearchVariantSetsRequest()
request.pageSize = len(expectedIds)
path = utils.applyVersion('/variantsets/search')
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(200, response.status_code)
responseData = protocol.SearchVariantSetsResponse.fromJsonString(
response.data)
self.assertTrue(
protocol.SearchVariantSetsResponse.validate(
responseData.toJsonDict()))
self.assertIsNone(responseData.nextPageToken)
self.assertEqual(len(expectedIds), len(responseData.variantSets))
for variantSet in responseData.variantSets:
self.assertTrue(variantSet.id in expectedIds)
def testCallSetsSearch(self):
# TODO remove the @nottest decorator here once calls have been
# properly implemented in the simulator.
request = protocol.GASearchCallSetsRequest()
request.name = None
path = utils.applyVersion('/callsets/search')
# when variantSetIds are wrong, no results
request.variantSetIds = ["xxxx"]
response = self.sendJsonPostRequest(
path, request.toJsonString())
self.assertEqual(200, response.status_code)
responseData = protocol.GASearchCallSetsResponse.fromJsonString(
response.data)
self.assertIsNone(responseData.nextPageToken)
self.assertEqual([], responseData.callSets)
# if no callset name is given return all callsets
request.variantSetIds = self.variantSetIds[:1]
response = self.sendJsonPostRequest(
path, request.toJsonString())
self.assertEqual(200, response.status_code)
responseData = protocol.GASearchCallSetsResponse.fromJsonString(
response.data)
self.assertTrue(protocol.GASearchCallSetsResponse.validate(
responseData.toJsonDict()))
self.assertNotEqual([], responseData.callSets)
# TODO test the length of responseData.callSets equal to all callsets
# Verify all results are of the correct type and range
for callSet in responseData.callSets:
self.assertIs(type(callSet.info), dict)
self.assertIs(type(callSet.variantSetIds), list)
splits = callSet.id.split(".")
variantSetId = '.'.join(splits[:2])
callSetName = splits[-1]
self.assertIn(variantSetId, callSet.variantSetIds)
self.assertEqual(callSetName, callSet.name)
self.assertEqual(callSetName, callSet.sampleId)
def testCallSetsSearch(self):
# TODO remove the @skipIf decorator here once calls have been
# properly implemented in the simulator.
request = protocol.SearchCallSetsRequest()
request.name = None
path = utils.applyVersion('/callsets/search')
# when variantSetIds are wrong, no results
request.variantSetIds = ["xxxx"]
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(200, response.status_code)
responseData = protocol.SearchCallSetsResponse.fromJsonString(
response.data)
self.assertIsNone(responseData.nextPageToken)
self.assertEqual([], responseData.callSets)
# if no callset name is given return all callsets
request.variantSetIds = self.variantSetIds[:1]
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(200, response.status_code)
responseData = protocol.SearchCallSetsResponse.fromJsonString(
response.data)
self.assertTrue(
protocol.SearchCallSetsResponse.validate(
responseData.toJsonDict()))
self.assertNotEqual([], responseData.callSets)
# TODO test the length of responseData.callSets equal to all callsets
# Verify all results are of the correct type and range
for callSet in responseData.callSets:
self.assertIs(type(callSet.info), dict)
self.assertIs(type(callSet.variantSetIds), list)
splits = callSet.id.split(".")
variantSetId = '.'.join(splits[:2])
callSetName = splits[-1]
self.assertIn(variantSetId, callSet.variantSetIds)
self.assertEqual(callSetName, callSet.name)
self.assertEqual(callSetName, callSet.sampleId)
def verifySearchRouting(self, path, getDefined=False):
"""
Verifies that the specified path has the correct routing for a search
command. If getDefined is False we check to see if it returns the
correct status code.
"""
versionedPath = utils.applyVersion(path)
response = self.app.post(versionedPath)
protocol.GAException.fromJsonString(response.get_data())
self.assertEqual(415, response.status_code)
if not getDefined:
getResponse = self.app.get(versionedPath)
protocol.GAException.fromJsonString(getResponse.get_data())
self.assertEqual(405, getResponse.status_code)
# Malformed requests should return 400
for badJson in ["", None, "JSON", "<xml/>", "{]"]:
badResponse = self.app.post(
versionedPath, data=badJson,
headers={'Content-type': 'application/json'})
self.assertEqual(400, badResponse.status_code)
# OPTIONS should return success
self.assertEqual(200, self.app.options(versionedPath).status_code)
def runRequest(method, path):
requestPath = path.replace('<id>', 'someId')
versionedPath = utils.applyVersion(requestPath)
response = method(versionedPath)
protocol.GAException.fromJsonString(response.get_data())
self.assertEqual(response.status_code, 501)
def testRouteCallsets(self):
path = utils.applyVersion('/callsets/search')
self.assertEqual(415, self.app.post(path).status_code)
self.assertEqual(200, self.app.options(path).status_code)
self.assertEqual(405, self.app.get(path).status_code)
def test404sReturnJson(self):
path = utils.applyVersion('/doesNotExist')
response = self.app.get(path)
protocol.GAException.fromJsonString(response.get_data())
self.assertEqual(404, response.status_code)
def testRouteCallsets(self):
path = utils.applyVersion('/callsets/search')
self.assertEqual(415, self.app.post(path).status_code)
self.assertEqual(200, self.app.options(path).status_code)
self.assertEqual(405, self.app.get(path).status_code)
def test404sReturnJson(self):
path = utils.applyVersion('/doesNotExist')
response = self.app.get(path)
protocol.GAException.fromJsonString(response.get_data())
self.assertEqual(404, response.status_code)
