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 = genomics_util.GetGenomicsClient()
genomics_messages = genomics_util.GetGenomicsMessages()
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_exceptions.HttpError as error:
# Map our error messages (JSON API camelCased) back into flag names.
msg = (
exceptions.HttpException(error).payload.status_message.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 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()
name = args.name
if not name.startswith(_OPERATIONS_PREFIX):
name = _OPERATIONS_PREFIX + name
# Look up the operation so we can display it in the confirmation prompt
op = apitools_client.operations.Get(
genomics_messages.GenomicsOperationsGetRequest(name=name))
operation_string = 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.')
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
"""
# 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 = genomics_util.GetGenomicsClient()
genomics_messages = genomics_util.GetGenomicsMessages()
# Look it up first so that we can display the name
existing_rgs = apitools_client.readgroupsets.Get(
genomics_messages.GenomicsReadgroupsetsGetRequest(readGroupSetId=args.id))
prompt_message = (
'Deleting read group set {0} ({1}) will delete all objects in the read '
'group set.').format(args.id, existing_rgs.name)
if not console_io.PromptContinue(message=prompt_message):
raise GenomicsError('Deletion aborted by user.')
apitools_client.readgroupsets.Delete(
genomics_messages.GenomicsReadgroupsetsDeleteRequest(
readGroupSetId=str(args.id)))
log.DeletedResource('{0} ({1})'.format(args.id,
existing_rgs.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 = ('Restoring dataset {0} will restore all objects in '
'the dataset.').format(args.id)
if not console_io.PromptContinue(message=prompt_message):
raise GenomicsError('Restore aborted by user.')
apitools_client = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY]
genomics_messages = self.context[lib.GENOMICS_MESSAGES_MODULE_KEY]
dataset = genomics_messages.GenomicsDatasetsUndeleteRequest(
datasetId=str(args.id), )
return apitools_client.datasets.Undelete(dataset)
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_ds = genomics_util.GetDataset(args.id)
prompt_message = (
'Deleting dataset {0} ({1}) 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(
existing_ds.id, existing_ds.name)
if not console_io.PromptContinue(message=prompt_message):
raise GenomicsError('Deletion aborted by user.')
apitools_client = genomics_util.GetGenomicsClient()
genomics_messages = genomics_util.GetGenomicsMessages()
dataset = genomics_messages.GenomicsDatasetsDeleteRequest(
datasetId=str(args.id), )
apitools_client.datasets.Delete(dataset)
log.DeletedResource('{0} ({1})'.format(existing_ds.id,
existing_ds.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]
name = args.name
if not name.startswith(_OPERATIONS_PREFIX):
name = _OPERATIONS_PREFIX + name
# Look it up first so that we can display it
op = apitools_client.operations.Get(
genomics_messages.GenomicsOperationsGetRequest(name=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=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
"""
prompt_message = ('Restoring dataset {0} will restore all objects in '
'the dataset.').format(args.id)
if not console_io.PromptContinue(message=prompt_message):
raise GenomicsError('Restore aborted by user.')
apitools_client = genomics_util.GetGenomicsClient()
genomics_messages = genomics_util.GetGenomicsMessages()
dataset = genomics_messages.GenomicsDatasetsUndeleteRequest(
datasetId=args.id)
result = apitools_client.datasets.Undelete(dataset)
log.RestoredResource('{0}, id: {1}'.format(result.name, result.id),
kind='dataset')
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
"""
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
"""
client, resource = genomics_client.CreateFromName(args.name)
op = client.GetOperation(resource)
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.')
client.CancelOperation(resource)
log.status.write('Canceled [{0}].\n'.format(resource.RelativeName()))
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)