def _heavyQuery():
"""
Very heavy query: all calls on chromosome 2
(11 pages, 90 seconds to fetch the entire thing
on a high-end desktop machine)
"""
request = protocol.GASearchVariantsRequest()
request.referenceName = '2'
request.variantSetIds = ['1000g_2013']
request.callSetIds = None
request.pageSize = 100
request.end = 100000
return request
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.GASearchVariantsRequest()
request.referenceName = '2'
request.variantSetIds = [variantSetId]
request.callSetIds = callSetIds
request.pageSize = 100
request.end = 100000
return request
def getVariants(
self, variantSetIds, referenceName, start=0, end=2 ** 32,
pageSize=100, callSetIds=[]):
"""
Returns an iterator over the specified list of variants, abstracting
out paging details.
"""
request = protocol.GASearchVariantsRequest()
request.variantSetIds = variantSetIds
request.referenceName = referenceName
request.start = start
request.end = end
request.callSetIds = callSetIds
return self.resultIterator(
request, pageSize, self._backend.searchVariants,
protocol.GASearchVariantsResponse, "variants")
def query():
variant_set_id = request.form['populationId']
variants_request = protocol.GASearchVariantsRequest()
variants_request.variantSetIds = [request.form['populationId']]
variants_request.referenceName = request.form['chrom']
variants_request.start = int(request.form['position']) - 1 # GA4GH API is zero-based
variants_request.end = int(request.form['position'])
response = variants_client.searchVariants(variants_request)
for variant in response:
for alt in variant.alternateBases:
if alt == request.form['allele']:
return "True"
return "False"
def __init__(self, args):
super(VariantSearchRunner, self).__init__(args)
request = protocol.GASearchVariantsRequest()
request.referenceName = args.referenceName
request.variantName = args.variantName
request.start = args.start
request.end = args.end
if self.usingWorkaroundsFor(client.HTTPClient.workaroundGoogle):
request.maxCalls = args.maxCalls
if args.callSetIds == []:
request.callSetIds = []
elif args.callSetIds == '*':
request.callSetIds = None
else:
request.callSetIds = args.callSetIds.split(",")
setCommaSeparatedAttribute(request, args, 'variantSetIds')
self.setHttpClient(request, args)
def __init__(self, args):
svr = protocol.GASearchVariantsRequest()
svr.referenceName = args.referenceName
svr.variantName = args.variantName
svr.start = args.start
svr.end = args.end
svr.pageSize = args.pageSize
if args.callSetIds == []:
svr.callSetIds = []
elif args.callSetIds == '*':
svr.callSetIds = None
else:
svr.callSetIds = args.callSetIds.split(",")
svr.variantSetIds = args.variantSetIds.split(",")
self._request = svr
self._verbosity = args.verbose
self._httpClient = client.HTTPClient(args.baseUrl, args.verbose)
def testVariantsSearch(self):
# TODO: As above, get these from the test backend API
expectedIds = ['example_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
response = self.sendJSONPostRequest('/variants/search',
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
response = self.sendJSONPostRequest('/variants/search',
request.toJSONString())
self.assertEqual(200, response.status_code)
responseData = protocol.GASearchVariantsResponse.fromJSONString(
response.data)
self.assertTrue(
protocol.GASearchVariantsResponse.validate(
responseData.toJSONDict()))
self.assertNotEqual([], responseData.variants)
# 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)