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.
Raises:
HttpException: An http error response was received while executing api
request.
Returns:
an ExportVariantSetResponse
"""
apitools_client = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY]
genomics_messages = self.context[lib.GENOMICS_MESSAGES_MODULE_KEY]
enum = genomics_messages.ExportVariantSetRequest.FormatValueValuesEnum
call_set_ids = args.call_set_ids if args.call_set_ids else []
project_id = args.bigquery_project
if not project_id:
project_id = genomics_util.GetProjectId()
request = genomics_messages.GenomicsVariantsetsExportRequest(
variantSetId=args.id,
exportVariantSetRequest=genomics_messages.ExportVariantSetRequest(
callSetIds=call_set_ids,
projectId=project_id,
format=enum.FORMAT_BIGQUERY,
bigqueryDataset=args.bigquery_dataset,
bigqueryTable=args.table))
return apitools_client.variantsets.Export(request)
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')
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.
Raises:
HttpException: An http error response was received while executing api
request.
Returns:
None
"""
apitools_client = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY]
genomics_messages = self.context[lib.GENOMICS_MESSAGES_MODULE_KEY]
dataset = genomics_messages.Dataset(
name=args.name,
projectId=genomics_util.GetProjectId(),
)
return apitools_client.datasets.Create(dataset)