def testDatasetsSearch(self):
request = protocol.SearchDatasetsRequest()
datasets = self.backend.getDatasets()
path = '/datasets/search'
self.verifySearchMethod(
request, path, protocol.SearchDatasetsResponse, datasets,
self.verifyDatasetsEqual)
def getAllDatasets(self):
"""
Gets all datasets available
"""
path = 'datasets/search'
request = protocol.SearchDatasetsRequest()
responseData = self.sendSearchRequest(path, request,
protocol.SearchDatasetsResponse)
return responseData.datasets
def searchDatasets(self):
"""
Returns an iterator over the Datasets on the server.
:return: An iterator over the :class:`ga4gh.protocol.Dataset`
objects on the server.
"""
request = protocol.SearchDatasetsRequest()
request.pageSize = self._pageSize
return self._runSearchRequest(
request, "datasets", protocol.SearchDatasetsResponse)
def testPhenotypeAssociationSetSearch(self):
request = protocol.SearchDatasetsRequest()
response = self.sendSearchRequest("datasets/search", request,
protocol.SearchDatasetsResponse)
datasetId = response.datasets[0].id
request = protocol.SearchPhenotypeAssociationSetsRequest()
request.dataset_id = datasetId
response = self.sendSearchRequest(
"phenotypeassociationsets/search", request,
protocol.SearchPhenotypeAssociationSetsResponse)
# there should be an array
self.assertIsNotNone(response.phenotype_association_sets)
# there should be at least one entry
self.assertGreater(len(response.phenotype_association_sets), 0)
def getPhenotypeAssociationSetId(self):
"""
Gets the dataset phenotype association set ID
"""
request = protocol.SearchDatasetsRequest()
response = self.sendSearchRequest("datasets/search", request,
protocol.SearchDatasetsResponse)
datasetId = response.datasets[0].id
request = protocol.SearchPhenotypeAssociationSetsRequest()
request.dataset_id = datasetId
response = self.sendPostRequest("phenotypeassociationsets/search",
request)
response = protocol.fromJson(
response.data, protocol.SearchPhenotypeAssociationSetsResponse)
return response.phenotype_association_sets[0].id
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:
datasetsRequest = protocol.SearchDatasetsRequest()
datasetsResponse = self._httpClient.searchDatasets(
datasetsRequest)
datasetIds = [dataset.id for dataset in datasetsResponse]
variantSetIds = []
for datasetId in datasetIds:
variantSetsRequest = protocol.SearchVariantSetsRequest()
variantSetsRequest.datasetIds = [datasetId]
response = self._httpClient.searchVariantSets(
variantSetsRequest)
datasetVariantSetIds = [
variantSet.id for variantSet in response]
variantSetIds.extend(datasetVariantSetIds)
request.variantSetIds = variantSetIds
else:
setCommaSeparatedAttribute(request, args, 'variantSetIds')
self._setRequest(request, args)
def testSearchDatasets(self):
request = protocol.SearchDatasetsRequest()
request.pageSize = self.pageSize
self.httpClient.searchDatasets()
self.httpClient._runSearchRequest.assert_called_once_with(
request, "datasets", protocol.SearchDatasetsResponse)
def sendDatasetsSearch(self):
request = protocol.SearchDatasetsRequest()
return self.sendPostRequest('/datasets/search', request)
def createSearchDatasetsRequest(self):
request = protocol.SearchDatasetsRequest()
return request
