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')