def ValidateLimitFlag(limit, flag_name='limit'):
"""Validates a limit flag value.
Args:
limit: the limit flag value to sanitize.
flag_name: the name of the limit flag - defaults to limit
Raises:
GenomicsError: if the provided limit flag value is negative
"""
if limit is None:
return
if limit < 0:
raise GenomicsError(
'--{0} must be a non-negative integer; received: {1}'.format(
flag_name, limit))
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
"""
op = None
apitools_client = genomics_util.GetGenomicsClient('v2alpha1')
genomics_messages = genomics_util.GetGenomicsMessages('v2alpha1')
name, v2 = genomics_util.CanonicalizeOperationName(args.name)
if v2:
op = apitools_client.projects_operations.Get(
genomics_messages.GenomicsProjectsOperationsGetRequest(
name=name))
else:
apitools_client = genomics_util.GetGenomicsClient()
genomics_messages = genomics_util.GetGenomicsMessages()
op = apitools_client.operations.Get(
genomics_messages.GenomicsOperationsGetRequest(name=name))
operation_string = io.StringIO()
print_format = display.Displayer(self, args).GetFormat()
resource_printer.Print(op, print_format, out=operation_string)
if not console_io.PromptContinue(
message='%s\n%s' %
(operation_string.getvalue(), 'This operation will be canceled')):
raise GenomicsError('Cancel aborted by user.')
if v2:
apitools_client.projects_operations.Cancel(
genomics_messages.GenomicsProjectsOperationsCancelRequest(
name=name))
else:
apitools_client.operations.Cancel(
genomics_messages.GenomicsOperationsCancelRequest(name=name))
log.status.write('Canceled [{0}].\n'.format(name))
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 = genomics_util.GetGenomicsClient()
genomics_messages = genomics_util.GetGenomicsMessages()
if not (args.name or args.reference_set_id):
raise GenomicsError(
'Must specify --name and/or --reference-set-id')
updated = genomics_messages.ReadGroupSet()
mask = []
# TODO(b/26871577): Consider using resource parser here
if args.name:
updated.name = args.name
mask.append('name')
if args.reference_set_id:
updated.referenceSetId = args.reference_set_id
mask.append('referenceSetId')
request = genomics_messages.GenomicsReadgroupsetsPatchRequest(
readGroupSet=updated,
readGroupSetId=str(args.id),
updateMask=','.join(mask))
result = apitools_client.readgroupsets.Patch(request)
name = str(result.id)
if result.name:
name += ', name: {0}'.format(result.name)
if result.referenceSetId:
name += ', referenceSetId: {0}'.format(result.referenceSetId)
log.UpdatedResource(name, kind='readgroupset')
return result
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.
GenomicsError: if canceled by the user.
Returns:
None
"""
apitools_client = genomics_util.GetGenomicsClient()
genomics_messages = genomics_util.GetGenomicsMessages()
get_request = genomics_messages.GenomicsVariantsetsGetRequest(
variantSetId=str(args.variant_set_id))
variant_set = apitools_client.variantsets.Get(get_request)
prompt_message = (
'Deleting variant set {0}: "{1}" will also delete all its contents '
'(variants, callsets, and calls).').format(args.variant_set_id,
variant_set.name)
if not console_io.PromptContinue(message=prompt_message):
raise GenomicsError('Deletion aborted by user.')
req = genomics_messages.GenomicsVariantsetsDeleteRequest(
variantSetId=args.variant_set_id, )
ret = apitools_client.variantsets.Delete(req)
log.DeletedResource('{0}: "{1}"'.format(args.variant_set_id,
variant_set.name))
return ret
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]
if not (args.name or args.reference_set_id):
raise GenomicsError(
'Must specify --name and/or --reference-set-id')
updated = genomics_messages.ReadGroupSet()
mask = []
# TODO(b/26871577): Consider using resource parser here
if args.name:
updated.name = args.name
mask.append('name')
if args.reference_set_id:
updated.referenceSetId = args.reference_set_id
mask.append('referenceSetId')
request = genomics_messages.GenomicsReadgroupsetsPatchRequest(
readGroupSet=updated,
readGroupSetId=str(args.id),
updateMask=','.join(mask))
return apitools_client.readgroupsets.Patch(request)