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