def testVariantSetsSearch(self):
path = '/variantsets/search'
for dataset in self.backend.getDatasets():
variantSets = dataset.getVariantSets()
request = protocol.SearchVariantSetsRequest()
request.datasetId = dataset.getId()
self.verifySearchMethod(request, path,
protocol.SearchVariantSetsResponse,
variantSets, self.verifyVariantSetsEqual)
for badId in self.getBadIds():
request = protocol.SearchVariantSetsRequest()
request.datasetId = badId
self.verifySearchMethodFails(request, path)
def testSearchVariantSets(self):
request = protocol.SearchVariantSetsRequest()
request.datasetId = self.datasetId
request.pageSize = self.pageSize
self.httpClient.searchVariantSets(self.datasetId)
self.httpClient._runSearchRequest.assert_called_once_with(
request, "variantsets", protocol.SearchVariantSetsResponse)
def testSearchVariantSets(self):
request = protocol.SearchVariantSetsRequest()
responseStr = self._backend.searchVariantSets(request.toJsonString())
response = protocol.SearchVariantSetsResponse.fromJsonString(
responseStr)
self.assertTrue(
isinstance(response, protocol.SearchVariantSetsResponse))
def testDatasetNotFound(self):
request = protocol.SearchVariantSetsRequest()
datasetId = 'doesNotExist'
request.datasetIds = [datasetId]
with self.assertRaises(exceptions.DatasetNotFoundException):
self._backend._getDatasetFromRequest(request)
with self.assertRaises(exceptions.DatasetNotFoundException):
self._backend._getDatasetFromCompoundId(datasetId + ':notUsed')
def getVariantSets(self, pageSize=100):
"""
Returns an iterator over the variantSets, abstracting away
the details of the pageSize.
"""
request = protocol.SearchVariantSetsRequest()
request.datasetIds = [self._backend.getDatasetIds()[0]]
return self.resultIterator(
request, pageSize, self._backend.searchVariantSets,
protocol.SearchVariantSetsResponse, "variantSets")
def testRunSearchRequest(self):
request = protocol.SearchVariantSetsRequest()
responseStr = self._backend.runSearchRequest(
request.toJsonString(), protocol.SearchVariantSetsRequest,
protocol.SearchVariantSetsResponse,
self._backend.variantSetsGenerator)
response = protocol.SearchVariantSetsResponse.fromJsonString(
responseStr)
self.assertTrue(
isinstance(response, protocol.SearchVariantSetsResponse))
def __init__(self, args):
super(SearchVariantsRunner, self).__init__(args)
request = RequestFactory(args).createSearchVariantsRequest()
# if no variantSets have been specified, send a request to
# the server to grab all variantSets and then continue
if args.variantSetIds is None:
variantSetsRequest = protocol.SearchVariantSetsRequest()
response = self._httpClient.searchVariantSets(variantSetsRequest)
variantSetIds = [variantSet.id for variantSet in response]
request.variantSetIds = variantSetIds
else:
setCommaSeparatedAttribute(request, args, 'variantSetIds')
self._setRequest(request, args)
def searchVariantSets(self, datasetId):
"""
Returns an iterator over the VariantSets fulfilling the specified
conditions from the specified Dataset.
:param str datasetId: The ID of the :class:`ga4gh.protocol.Dataset`
of interest.
:return: An iterator over the :class:`ga4gh.protocol.VariantSet`
objects defined by the query parameters.
"""
request = protocol.SearchVariantSetsRequest()
request.datasetId = datasetId
request.pageSize = self._pageSize
return self._runSearchRequest(
request, "variantsets", protocol.SearchVariantSetsResponse)
def testOneDatasetRestriction(self):
# no datasetIds attr
request = protocol.SearchReadsRequest()
with self.assertRaises(AssertionError):
self._backend._getDatasetFromRequest(request)
# datasetIds attr
request = protocol.SearchVariantSetsRequest()
with self.assertRaises(exceptions.NotExactlyOneDatasetException):
self._backend._getDatasetFromRequest(request)
datasetId = 'dataset1'
request.datasetIds = [datasetId]
dataset = self._backend._getDatasetFromRequest(request)
self.assertEquals(dataset.getId(), datasetId)
request.datasetIds = ['dataset1', 'dataset2']
with self.assertRaises(exceptions.NotExactlyOneDatasetException):
self._backend._getDatasetFromRequest(request)
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 testDatasetNotFound(self):
request = protocol.SearchVariantSetsRequest()
datasetId = 'doesNotExist'
request.datasetId = datasetId
with self.assertRaises(exceptions.DatasetNotFoundException):
self._backend.getDataset(request.datasetId)
def sendVariantSetsSearch(self):
request = protocol.SearchVariantSetsRequest()
request.datasetId = self.datasetId
return self.sendPostRequest('/variantsets/search', request)
def createSearchVariantSetsRequest(self):
request = protocol.SearchVariantSetsRequest()
setCommaSeparatedAttribute(request, self.args, 'datasetIds')
request.pageSize = self.args.pageSize
request.pageToken = None
return request
def sendVariantSetsSearch(self, datasetIds=[""]):
request = protocol.SearchVariantSetsRequest()
request.datasetIds = datasetIds
return self.sendRequest('/variantsets/search', request)
def createSearchVariantSetsRequest(self):
request = protocol.SearchVariantSetsRequest()
request.datasetId = self.args.datasetId
request.pageSize = self.args.pageSize
request.pageToken = None
return request
def sendVariantSetsSearch(self):
request = protocol.SearchVariantSetsRequest()
request.datasetIds = ["simulatedDataset1"]
return self.sendPostRequest('/variantsets/search', request)
