def Run(self, args): """This is what gets called when the user runs this command. Args: args: an argparse namespace, All the arguments that were provided to this command invocation. Returns: A list of variants that meet the search criteria. """ genomics_util.ValidateLimitFlag(args.limit) genomics_util.ValidateLimitFlag(args.limit_calls, 'limit_calls') apitools_client = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY] req_class = (self.context[ lib.GENOMICS_MESSAGES_MODULE_KEY].SearchVariantsRequest) request = req_class(variantSetIds=[args.variant_set_id], callSetIds=args.call_set_ids, variantName=args.variant_name, referenceName=args.reference_name, start=args.start, end=args.end, maxCalls=args.limit_calls) return apitools_base.list_pager.YieldFromList( apitools_client.variants, request, limit=args.limit, method='Search', batch_size_attribute='pageSize', batch_size=args.limit, # Use limit if any, else server default. field='variants')
def Run(self, args): """Run 'callsets list'. Args: args: argparse.Namespace, The arguments that this command was invoked with. Returns: The list of callsets matching the given variant set ids. Raises: HttpException: An http error response was received while executing api request. """ genomics_util.ValidateLimitFlag(args.limit) apitools_client = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY] req_class = (self.context[ lib.GENOMICS_MESSAGES_MODULE_KEY].SearchCallSetsRequest) request = req_class(name=args.name, variantSetIds=args.variant_set_ids) res = apitools_base.list_pager.YieldFromList( apitools_client.callsets, request, method='Search', limit=args.limit, batch_size_attribute='pageSize', batch_size=None, # Use server default. field='callSets') return res
def Run(self, args): """Run 'datasets list'. Args: args: argparse.Namespace, The arguments that this command was invoked with. Returns: The list of datasets for this project. Raises: HttpException: An http error response was received while executing api request. """ genomics_util.ValidateLimitFlag(args.limit) apitools_client = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY] req_class = (self.context[ lib.GENOMICS_MESSAGES_MODULE_KEY].GenomicsDatasetsListRequest) request = req_class(projectId=genomics_util.GetProjectId()) return apitools_base.list_pager.YieldFromList( apitools_client.datasets, request, limit=args.limit, batch_size_attribute='pageSize', batch_size=args.limit, # Use limit if any, else server default. field='datasets')
def Run(self, args): """Run 'operations list'. Args: args: argparse.Namespace, The arguments that this command was invoked with. Returns: The list of operations for this project. Raises: HttpException: An http error response was received while executing api request. """ genomics_util.ValidateLimitFlag(args.limit) apitools_client = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY] genomics_messages = self.context[lib.GENOMICS_MESSAGES_MODULE_KEY] if args.where: args.where += ' AND ' args.where += 'projectId=%s' % genomics_util.GetProjectId() request = genomics_messages.GenomicsOperationsListRequest( name='operations', filter=args.where) return apitools_base.list_pager.YieldFromList( apitools_client.operations, request, limit=args.limit, batch_size_attribute='pageSize', batch_size=args.limit, # Use limit if any, else server default. field='operations')