def testVariantsSearch(self):
dataset = self.backend.getDatasets()[0]
variantSet = dataset.getVariantSets()[0]
referenceName = '1'
request = protocol.SearchVariantsRequest()
request.referenceName = referenceName
request.start = 0
request.end = 0
request.variantSetId = variantSet.getId()
# Request windows is too small, no results
path = '/variants/search'
responseData = self.sendSearchRequest(path, request,
protocol.SearchVariantsResponse)
self.assertIsNone(responseData.nextPageToken)
self.assertEqual([], responseData.variants)
# Larger request window, expect results
request.end = 2**16
responseData = self.sendSearchRequest(path, request,
protocol.SearchVariantsResponse)
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, variantSet.getId())
self.assertEqual(variant.referenceName, referenceName)
def searchVariants(self,
variantSetId,
start=None,
end=None,
referenceName=None,
callSetIds=None):
"""
Returns an iterator over the Variants fulfilling the specified
conditions from the specified VariantSet.
:param str variantSetId: The ID of the
:class:`ga4gh.protocol.VariantSet` of interest.
:param int start: TODO
:param int end: TODO
:param str referenceName: The name of the
:class:`ga4gh.protocol.Reference` we wish to return variants from.
:param list callSetIds: TODO
:return: An iterator over the :class:`ga4gh.protocol.Variant` objects
defined by the query parameters.
:rtype: iter
"""
request = protocol.SearchVariantsRequest()
request.referenceName = referenceName
request.start = start
request.end = end
request.variantSetId = variantSetId
request.callSetIds = callSetIds
request.pageSize = self._pageSize
return self._runSearchRequest(request, "variants",
protocol.SearchVariantsResponse)
def testSearchVariants(self):
variantSetIds = [
variantSet.id for variantSet in self.getVariantSets(pageSize=1)
]
request = protocol.SearchVariantsRequest()
request.variantSetId = variantSetIds[0]
responseStr = self._backend.runSearchVariants(request.toJsonString())
response = protocol.SearchVariantsResponse.fromJsonString(responseStr)
self.assertTrue(isinstance(response, protocol.SearchVariantsResponse))
def sendVariantsSearch(self):
response = self.sendVariantSetsSearch()
variantSets = protocol.SearchVariantSetsResponse().fromJsonString(
response.data).variantSets
request = protocol.SearchVariantsRequest()
request.variantSetId = variantSets[0].id
request.referenceName = "1"
request.start = 0
request.end = 1
return self.sendPostRequest('/variants/search', request)
def testSearchVariants(self):
request = protocol.SearchVariantsRequest()
request.referenceName = self.referenceName
request.start = self.start
request.end = self.end
request.variantSetId = self.variantSetId
request.callSetIds = self.callSetIds
request.pageSize = self.pageSize
self.httpClient.searchVariants(
self.variantSetId, start=self.start, end=self.end,
referenceName=self.referenceName, callSetIds=self.callSetIds)
self.httpClient._runSearchRequest.assert_called_once_with(
request, "variants", protocol.SearchVariantsResponse)
def _heavyQuery(variantSetId, callSetIds):
"""
Very heavy query: calls for the specified list of callSetIds
on chromosome 2 (11 pages, 90 seconds to fetch the entire thing
on a high-end desktop machine)
"""
request = protocol.SearchVariantsRequest()
request.reference_name = '2'
request.variant_set_id = variantSetId
for callSetId in callSetIds:
request.call_set_ids.add(callSetId)
request.page_size = 100
request.end = 100000
return request
def runDemo():
httpClient = client.HttpClient("http://server:80/current")
request = protocol.SearchVariantsRequest()
request.variantSetIds = ["1kg-phase1"]
request.referenceName = "2"
request.start = 33100
request.end = 34000
for variant in httpClient.searchVariants(request):
print(variant.referenceName,
variant.start,
variant.end,
variant.referenceBases,
variant.alternateBases,
sep="\t")
def getVariants(
self, variantSetIds, referenceName, start=0, end=2 ** 32,
pageSize=100, callSetIds=None):
"""
Returns an iterator over the specified list of variants,
abstracting out paging details.
"""
request = protocol.SearchVariantsRequest()
request.variantSetIds = variantSetIds
request.referenceName = referenceName
request.start = start
request.end = end
request.callSetIds = callSetIds
return self.resultIterator(
request, pageSize, self._backend.searchVariants,
protocol.SearchVariantsResponse, "variants")
def createSearchVariantsRequest(self):
request = protocol.SearchVariantsRequest()
request.referenceName = self.args.referenceName
request.variantName = self.args.variantName
request.start = self.args.start
request.end = self.args.end
if self.usingWorkaroundsFor(client.HttpClient.workaroundGoogle):
request.maxCalls = self.args.maxCalls
if self.args.callSetIds == []:
request.callSetIds = []
elif self.args.callSetIds == '*':
# For v0.5.1 the semantics are for the empty list to correspond
# to all calls. This should be set to None for v0.6
request.callSetIds = []
else:
request.callSetIds = self.args.callSetIds.split(",")
setCommaSeparatedAttribute(request, self.args, 'variantSetIds')
return request
def testGetVariant(self):
# get a variant from the search method
referenceName = '1'
start = 0
dataset = self.backend.getDatasets()[0]
variantSet = dataset.getVariantSets()[0]
request = protocol.SearchVariantsRequest()
request.variantSetId = variantSet.getId()
request.referenceName = referenceName
request.start = start
request.end = 2**16
path = '/variants/search'
responseData = self.sendSearchRequest(path, request,
protocol.SearchVariantsResponse)
variants = responseData.variants[:10]
# get 'the same' variant using the get method
for variant in variants:
path = '/variants'
responseObject = self.sendGetObject(path, variant.id,
protocol.Variant)
self.assertEqual(responseObject, variant)
def searchVariants(self,
variantSetId,
start=None,
end=None,
referenceName=None,
callSetIds=None):
"""
Returns an iterator over the Variants fulfilling the specified
conditions from the specified VariantSet.
:param str variantSetId: The ID of the
:class:`ga4gh.protocol.VariantSet` of interest.
:param int start: Required. The beginning of the window (0-based,
inclusive) for which overlapping variants should be returned.
Genomic positions are non-negative integers less than reference
length. Requests spanning the join of circular genomes are
represented as two requests one on each side of the join
(position 0).
:param int end: Required. The end of the window (0-based, exclusive)
for which overlapping variants should be returned.
:param str referenceName: The name of the
:class:`ga4gh.protocol.Reference` we wish to return variants from.
:param list callSetIds: Only return variant calls which belong to call
sets with these IDs. If an empty array, returns variants without
any call objects. If null, returns all variant calls.
:return: An iterator over the :class:`ga4gh.protocol.Variant` objects
defined by the query parameters.
:rtype: iter
"""
request = protocol.SearchVariantsRequest()
request.referenceName = referenceName
request.start = start
request.end = end
request.variantSetId = variantSetId
request.callSetIds = callSetIds
request.pageSize = self._pageSize
return self._runSearchRequest(request, "variants",
protocol.SearchVariantsResponse)
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):
self.request = protocol.SearchVariantsRequest()
self.backend = backend.SimulatedBackend()
self.dataset = self.backend.getDatasets()[0]
def setUp(self):
self.request = protocol.SearchVariantsRequest()
self.backend = backend.SimulatedBackend()
self.datasetId = self.backend.getDatasetIds()[0]
self.dataset = self.backend.getDataset(self.datasetId)
self.variantSetLocalId = 'variantSet'
def setUp(self):
self.request = protocol.SearchVariantsRequest()
self.backend = backend.SimulatedBackend()
self.datasetId = self.backend.getDatasetIds()[0]
self.variantSetId = "{}:variantSetId".format(self.datasetId)
def setUp(self):
self.request = protocol.SearchVariantsRequest()
self.backend = backend.Backend(datarepo.SimulatedDataRepository())
self.dataset = self.backend.getDataRepository().getDatasets()[0]
