def testCallSetsSearch(self):
path = '/callsets/search'
for dataset in self.backend.getDatasets():
for variantSet in dataset.getVariantSets():
callSets = variantSet.getCallSets()
self.assertGreater(len(callSets), 0)
request = protocol.SearchCallSetsRequest()
request.variantSetId = variantSet.getId()
self.verifySearchMethod(request, path,
protocol.SearchCallSetsResponse,
callSets, self.verifyCallSetsEqual)
# Check if we can search for the callset with a good name.
for callSet in callSets:
request = protocol.SearchCallSetsRequest()
request.variantSetId = variantSet.getId()
request.name = callSet.getLocalId()
self.verifySearchMethod(request, path,
protocol.SearchCallSetsResponse,
[callSet],
self.verifyCallSetsEqual)
# Check if we can search for the callset with a bad name.
for badId in self.getBadIds():
request = protocol.SearchCallSetsRequest()
request.variantSetId = variantSet.getId()
request.name = badId
self.verifySearchResultsEmpty(
request, path, protocol.SearchCallSetsResponse)
# Check for searches within missing variantSets.
for badId in self.getBadIds():
request = protocol.SearchCallSetsRequest()
request.variantSetId = badId
self.verifySearchMethodFails(request, path)
def sendCallSetsSearch(self):
response = self.sendVariantSetsSearch()
variantSets = protocol.SearchVariantSetsResponse().fromJsonString(
response.data).variantSets
request = protocol.SearchCallSetsRequest()
request.variantSetId = variantSets[0].id
return self.sendPostRequest('/callsets/search', request)
def testSearchCallSets(self):
request = protocol.SearchCallSetsRequest()
request.variantSetId = self.variantSetId
request.name = self.objectName
request.pageSize = self.pageSize
self.httpClient.searchCallSets(self.variantSetId, name=self.objectName)
self.httpClient._runSearchRequest.assert_called_once_with(
request, "callsets", protocol.SearchCallSetsResponse)
def testSearchCallSets(self):
variantSetIds = [
variantSet.id for variantSet in self.getVariantSets(pageSize=1)
]
request = protocol.SearchCallSetsRequest()
request.variantSetId = variantSetIds[0]
responseStr = self._backend.runSearchCallSets(request.toJsonString())
response = protocol.SearchCallSetsResponse.fromJsonString(responseStr)
self.assertTrue(isinstance(response, protocol.SearchCallSetsResponse))
def getCallSets(self, variantSetId, pageSize=100):
"""
Returns an iterator over the callsets in a specified
variant set.
"""
request = protocol.SearchCallSetsRequest()
request.variantSetIds = [variantSetId]
return self.resultIterator(request, pageSize,
self._backend.runSearchCallSets,
protocol.SearchCallSetsResponse, "callSets")
def testSearchCallSets(self):
request = protocol.SearchCallSetsRequest()
request.variant_set_id = self.variantSetId
request.name = self.objectName
request.bio_sample_id = self.bioSampleId
request.page_size = self.pageSize
self.httpClient.search_call_sets(self.variantSetId,
name=self.objectName,
bio_sample_id=self.bioSampleId)
self.httpClient._run_search_request.assert_called_once_with(
request, "callsets", protocol.SearchCallSetsResponse)
def searchCallSets(self, variantSetId, name=None):
"""
Returns an iterator over the CallSets fulfilling the specified
conditions from the specified VariantSet.
:param str name: Only CallSets matching the specified name will
be returned.
:return: An iterator over the :class:`ga4gh.protocol.CallSet`
objects defined by the query parameters.
"""
request = protocol.SearchCallSetsRequest()
request.variantSetId = variantSetId
request.name = name
request.pageSize = self._pageSize
return self._runSearchRequest(
request, "callsets", protocol.SearchCallSetsResponse)
def searchCallSets(self, variantSetId, name=None, bioSampleId=None):
"""
Returns an iterator over the CallSets fulfilling the specified
conditions from the specified VariantSet.
:param str variantSetId: Find callsets belonging to the
provided variant set.
:param str name: Only CallSets matching the specified name will
be returned.
:param str bioSampleId: Only CallSets matching this id will
be returned.
:return: An iterator over the :class:`ga4gh.protocol.CallSet`
objects defined by the query parameters.
"""
request = protocol.SearchCallSetsRequest()
request.variant_set_id = variantSetId
request.name = pb.string(name)
request.bio_sample_id = pb.string(bioSampleId)
request.page_size = pb.int(self._pageSize)
return self._runSearchRequest(
request, "callsets", protocol.SearchCallSetsResponse)
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 createSearchCallSetsRequest(self):
request = protocol.SearchCallSetsRequest()
setCommaSeparatedAttribute(request, self.args, 'variantSetIds')
request.name = self.args.name
return request
def createSearchCallSetsRequest(self):
request = protocol.SearchCallSetsRequest()
request.variantSetId = self.args.variantSetId
request.name = self.args.name
return request
