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
"""
prompt_message = (
'Deleting variant set {0} will delete all its contents '
'(variants, callsets, and calls). '
'The variant set object is not deleted.').format(
args.variant_set_id)
if not console_io.PromptContinue(message=prompt_message):
raise GenomicsError('Deletion aborted by user.')
apitools_client = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY]
genomics_messages = self.context[lib.GENOMICS_MESSAGES_MODULE_KEY]
req = genomics_messages.GenomicsVariantsetsDeleteRequest(
variantSetId=str(args.variant_set_id), )
ret = apitools_client.variantsets.Delete(req)
log.DeletedResource('{0}'.format(args.variant_set_id))
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
"""
# Look it up first so that we can display the name
existing_cs = genomics_util.GetCallSet(self.context, args.id)
prompt_message = (
'Deleting call set {0} ({1}) will delete all objects in the '
'call set.').format(existing_cs.id, existing_cs.name)
if not console_io.PromptContinue(message=prompt_message):
raise GenomicsError('Deletion aborted by user.')
apitools_client = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY]
genomics_messages = self.context[lib.GENOMICS_MESSAGES_MODULE_KEY]
call_set = genomics_messages.GenomicsCallsetsDeleteRequest(
callSetId=args.id, )
apitools_client.callsets.Delete(call_set)
log.DeletedResource('{0} ({1})'.format(existing_cs.id,
existing_cs.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 = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY]
genomics_messages = self.context[lib.GENOMICS_MESSAGES_MODULE_KEY]
# Look it up first so that we can display it
op = apitools_client.operations.Get(
genomics_messages.GenomicsOperationsGetRequest(name=args.name))
self.format(op)
if not console_io.PromptContinue(message='This operation will be canceled'):
raise GenomicsError('Cancel aborted by user.')
apitools_client.operations.Cancel(
genomics_messages.GenomicsOperationsCancelRequest(name=args.name))
log.status.write('Canceled [{0}].\n'.format(args.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
"""
prompt_message = (
'Deleting dataset {0} will delete all objects in the dataset. '
'Deleted datasets can be recovered with the "restore" command '
'up to one week after the deletion occurs.').format(args.id)
if not console_io.PromptContinue(message=prompt_message):
raise GenomicsError('Deletion aborted by user.')
apitools_client = self.context[commands.GENOMICS_APITOOLS_CLIENT_KEY]
genomics_messages = self.context[commands.GENOMICS_MESSAGES_MODULE_KEY]
dataset = genomics_messages.GenomicsDatasetsDeleteRequest(
datasetId=str(args.id), )
apitools_client.datasets.Delete(dataset)
log.Print('Deleted dataset {0}'.format(args.id))
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:
an Operation message which tracks the asynchronous import
"""
apitools_client = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY]
genomics_messages = self.context[lib.GENOMICS_MESSAGES_MODULE_KEY]
if not args.source_uris:
raise GenomicsError(
'at least one value is required for --source-uris')
partition_enum = (genomics_messages.ImportReadGroupSetsRequest.
PartitionStrategyValueValuesEnum)
partition_strat = None
if args.partition_strategy:
if args.partition_strategy not in partition_enum.to_dict():
raise GenomicsError(
'--partition-strategy must be one of {0}; received: {1}'.
format(sorted(partition_enum.names()),
args.partition_strategy))
partition_strat = partition_enum.lookup_by_name(
args.partition_strategy)
try:
return apitools_client.readgroupsets.Import(
genomics_messages.ImportReadGroupSetsRequest(
datasetId=args.dataset_id,
sourceUris=args.source_uris,
referenceSetId=args.reference_set_id,
partitionStrategy=partition_strat,
))
except apitools_base.HttpError as error:
# Map our error messages (JSON API camelCased) back into flag names.
msg = (genomics_util.GetErrorMessage(error).replace(
'datasetId', '--dataset-id').replace(
'partitionStrategy', '--partition-strategy').replace(
'sourceUris',
'--source-uris').replace('referenceSetId',
'--reference-set-id'))
unused_type, unused_value, traceback = sys.exc_info()
raise exceptions.HttpException, msg, traceback
def ValidateLimitFlag(limit):
"""Validates a limit flag value.
Args:
limit: the limit flag value to sanitize.
Raises:
GenomicsError: if the provided limit flag value is negative
"""
if limit is None:
return
if limit < 0:
raise GenomicsError(
'--limit must be a non-negative integer; received: {0}'
.format(limit))
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))