1228 lines
50 KiB
Ruby
1228 lines
50 KiB
Ruby
# Copyright 2015 Google Inc.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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require 'date'
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require 'google/apis/core/base_service'
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require 'google/apis/core/json_representation'
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require 'google/apis/core/hashable'
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require 'google/apis/errors'
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module Google
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module Apis
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module GenomicsV1alpha2
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# The request message for Operations.CancelOperation.
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class CancelOperationRequest
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include Google::Apis::Core::Hashable
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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end
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end
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# Describes a Compute Engine resource that is being managed by a running
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# pipeline.
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class ComputeEngine
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include Google::Apis::Core::Hashable
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# The names of the disks that were created for this pipeline.
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# Corresponds to the JSON property `diskNames`
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# @return [Array<String>]
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attr_accessor :disk_names
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# The instance on which the operation is running.
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# Corresponds to the JSON property `instanceName`
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# @return [String]
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attr_accessor :instance_name
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# The machine type of the instance.
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# Corresponds to the JSON property `machineType`
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# @return [String]
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attr_accessor :machine_type
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# The availability zone in which the instance resides.
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# Corresponds to the JSON property `zone`
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# @return [String]
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attr_accessor :zone
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@disk_names = args[:disk_names] if args.key?(:disk_names)
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@instance_name = args[:instance_name] if args.key?(:instance_name)
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@machine_type = args[:machine_type] if args.key?(:machine_type)
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@zone = args[:zone] if args.key?(:zone)
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end
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end
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# Stores the information that the controller will fetch from the
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# server in order to run. Should only be used by VMs created by the
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# Pipelines Service and not by end users.
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class ControllerConfig
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include Google::Apis::Core::Hashable
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#
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# Corresponds to the JSON property `cmd`
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# @return [String]
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attr_accessor :cmd
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#
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# Corresponds to the JSON property `disks`
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# @return [Hash<String,String>]
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attr_accessor :disks
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#
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# Corresponds to the JSON property `gcsLogPath`
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# @return [String]
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attr_accessor :gcs_log_path
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#
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# Corresponds to the JSON property `gcsSinks`
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# @return [Hash<String,Google::Apis::GenomicsV1alpha2::RepeatedString>]
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attr_accessor :gcs_sinks
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#
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# Corresponds to the JSON property `gcsSources`
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# @return [Hash<String,Google::Apis::GenomicsV1alpha2::RepeatedString>]
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attr_accessor :gcs_sources
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#
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# Corresponds to the JSON property `image`
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# @return [String]
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attr_accessor :image
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#
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# Corresponds to the JSON property `machineType`
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# @return [String]
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attr_accessor :machine_type
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#
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# Corresponds to the JSON property `vars`
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# @return [Hash<String,String>]
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attr_accessor :vars
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@cmd = args[:cmd] if args.key?(:cmd)
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@disks = args[:disks] if args.key?(:disks)
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@gcs_log_path = args[:gcs_log_path] if args.key?(:gcs_log_path)
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@gcs_sinks = args[:gcs_sinks] if args.key?(:gcs_sinks)
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@gcs_sources = args[:gcs_sources] if args.key?(:gcs_sources)
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@image = args[:image] if args.key?(:image)
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@machine_type = args[:machine_type] if args.key?(:machine_type)
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@vars = args[:vars] if args.key?(:vars)
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end
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end
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# A Google Compute Engine disk resource specification.
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class Disk
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include Google::Apis::Core::Hashable
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# Deprecated. Disks created by the Pipelines API will be deleted at the end
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# of the pipeline run, regardless of what this field is set to.
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# Corresponds to the JSON property `autoDelete`
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# @return [Boolean]
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attr_accessor :auto_delete
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alias_method :auto_delete?, :auto_delete
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# Required at create time and cannot be overridden at run time.
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# Specifies the path in the docker container where files on
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# this disk should be located. For example, if `mountPoint`
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# is `/mnt/disk`, and the parameter has `localPath`
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# `inputs/file.txt`, the docker container can access the data at
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# `/mnt/disk/inputs/file.txt`.
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# Corresponds to the JSON property `mountPoint`
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# @return [String]
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attr_accessor :mount_point
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# Required. The name of the disk that can be used in the pipeline
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# parameters. Must be 1 - 63 characters.
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# The name "boot" is reserved for system use.
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# Corresponds to the JSON property `name`
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# @return [String]
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attr_accessor :name
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# Specifies how a sourced-base persistent disk will be mounted. See
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# https://cloud.google.com/compute/docs/disks/persistent-disks#
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# use_multi_instances
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# for more details.
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# Can only be set at create time.
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# Corresponds to the JSON property `readOnly`
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# @return [Boolean]
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attr_accessor :read_only
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alias_method :read_only?, :read_only
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# The size of the disk. Defaults to 500 (GB).
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# This field is not applicable for local SSD.
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# Corresponds to the JSON property `sizeGb`
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# @return [Fixnum]
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attr_accessor :size_gb
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# The full or partial URL of the persistent disk to attach. See
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# https://cloud.google.com/compute/docs/reference/latest/instances#resource
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# and
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# https://cloud.google.com/compute/docs/disks/persistent-disks#snapshots
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# for more details.
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# Corresponds to the JSON property `source`
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# @return [String]
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attr_accessor :source
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# Required. The type of the disk to create.
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# Corresponds to the JSON property `type`
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# @return [String]
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attr_accessor :type
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@auto_delete = args[:auto_delete] if args.key?(:auto_delete)
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@mount_point = args[:mount_point] if args.key?(:mount_point)
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@name = args[:name] if args.key?(:name)
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@read_only = args[:read_only] if args.key?(:read_only)
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@size_gb = args[:size_gb] if args.key?(:size_gb)
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@source = args[:source] if args.key?(:source)
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@type = args[:type] if args.key?(:type)
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end
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end
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# The Docker execuctor specification.
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class DockerExecutor
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include Google::Apis::Core::Hashable
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# Required. The command or newline delimited script to run. The command
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# string will be executed within a bash shell.
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# If the command exits with a non-zero exit code, output parameter
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# de-localization will be skipped and the pipeline operation's
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# `error` field will be populated.
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# Maximum command string length is 16384.
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# Corresponds to the JSON property `cmd`
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# @return [String]
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attr_accessor :cmd
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# Required. Image name from either Docker Hub or Google Container Registry.
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# Users that run pipelines must have READ access to the image.
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# Corresponds to the JSON property `imageName`
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# @return [String]
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attr_accessor :image_name
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@cmd = args[:cmd] if args.key?(:cmd)
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@image_name = args[:image_name] if args.key?(:image_name)
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end
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end
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# A generic empty message that you can re-use to avoid defining duplicated
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# empty messages in your APIs. A typical example is to use it as the request
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# or the response type of an API method. For instance:
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# service Foo `
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# rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty);
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# `
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# The JSON representation for `Empty` is empty JSON object ````.
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class Empty
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include Google::Apis::Core::Hashable
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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end
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end
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# The read group set import response.
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class ImportReadGroupSetsResponse
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include Google::Apis::Core::Hashable
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# IDs of the read group sets that were created.
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# Corresponds to the JSON property `readGroupSetIds`
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# @return [Array<String>]
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attr_accessor :read_group_set_ids
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids)
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end
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end
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# The variant data import response.
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class ImportVariantsResponse
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include Google::Apis::Core::Hashable
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# IDs of the call sets created during the import.
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# Corresponds to the JSON property `callSetIds`
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# @return [Array<String>]
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attr_accessor :call_set_ids
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
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end
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end
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# The response message for Operations.ListOperations.
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class ListOperationsResponse
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include Google::Apis::Core::Hashable
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# The standard List next-page token.
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# Corresponds to the JSON property `nextPageToken`
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# @return [String]
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attr_accessor :next_page_token
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# A list of operations that matches the specified filter in the request.
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# Corresponds to the JSON property `operations`
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# @return [Array<Google::Apis::GenomicsV1alpha2::Operation>]
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attr_accessor :operations
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
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@operations = args[:operations] if args.key?(:operations)
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end
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end
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# The response of ListPipelines. Contains at most `pageSize`
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# pipelines. If it contains `pageSize` pipelines, and more pipelines
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# exist, then `nextPageToken` will be populated and should be
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# used as the `pageToken` argument to a subsequent ListPipelines
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# request.
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class ListPipelinesResponse
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include Google::Apis::Core::Hashable
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# The token to use to get the next page of results.
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# Corresponds to the JSON property `nextPageToken`
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# @return [String]
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attr_accessor :next_page_token
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# The matched pipelines.
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# Corresponds to the JSON property `pipelines`
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# @return [Array<Google::Apis::GenomicsV1alpha2::Pipeline>]
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attr_accessor :pipelines
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
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@pipelines = args[:pipelines] if args.key?(:pipelines)
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end
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end
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# LocalCopy defines how a remote file should be copied to and from the VM.
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class LocalCopy
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include Google::Apis::Core::Hashable
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# Required. The name of the disk where this parameter is
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# located. Can be the name of one of the disks specified in the
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# Resources field, or "boot", which represents the Docker
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# instance's boot disk and has a mount point of `/`.
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# Corresponds to the JSON property `disk`
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# @return [String]
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attr_accessor :disk
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# Required. The path within the user's docker container where
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# this input should be localized to and from, relative to the specified
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# disk's mount point. For example: file.txt,
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# Corresponds to the JSON property `path`
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# @return [String]
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attr_accessor :path
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@disk = args[:disk] if args.key?(:disk)
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@path = args[:path] if args.key?(:path)
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end
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end
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# The logging options for the pipeline run.
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class LoggingOptions
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include Google::Apis::Core::Hashable
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# The location in Google Cloud Storage to which the pipeline logs
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# will be copied. Can be specified as a fully qualified directory
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# path, in which case logs will be output with a unique identifier
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# as the filename in that directory, or as a fully specified path,
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# which must end in `.log`, in which case that path will be
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# used, and the user must ensure that logs are not
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# overwritten. Stdout and stderr logs from the run are also
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# generated and output as `-stdout.log` and `-stderr.log`.
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# Corresponds to the JSON property `gcsPath`
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# @return [String]
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attr_accessor :gcs_path
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@gcs_path = args[:gcs_path] if args.key?(:gcs_path)
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end
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end
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# This resource represents a long-running operation that is the result of a
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# network API call.
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class Operation
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include Google::Apis::Core::Hashable
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# If the value is `false`, it means the operation is still in progress.
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# If `true`, the operation is completed, and either `error` or `response` is
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# available.
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# Corresponds to the JSON property `done`
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# @return [Boolean]
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attr_accessor :done
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alias_method :done?, :done
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# The `Status` type defines a logical error model that is suitable for different
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# programming environments, including REST APIs and RPC APIs. It is used by
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# [gRPC](https://github.com/grpc). The error model is designed to be:
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# - Simple to use and understand for most users
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# - Flexible enough to meet unexpected needs
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# # Overview
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# The `Status` message contains three pieces of data: error code, error message,
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# and error details. The error code should be an enum value of
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# google.rpc.Code, but it may accept additional error codes if needed. The
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# error message should be a developer-facing English message that helps
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# developers *understand* and *resolve* the error. If a localized user-facing
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# error message is needed, put the localized message in the error details or
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# localize it in the client. The optional error details may contain arbitrary
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# information about the error. There is a predefined set of error detail types
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# in the package `google.rpc` that can be used for common error conditions.
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# # Language mapping
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# The `Status` message is the logical representation of the error model, but it
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# is not necessarily the actual wire format. When the `Status` message is
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# exposed in different client libraries and different wire protocols, it can be
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# mapped differently. For example, it will likely be mapped to some exceptions
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# in Java, but more likely mapped to some error codes in C.
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# # Other uses
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# The error model and the `Status` message can be used in a variety of
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# environments, either with or without APIs, to provide a
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# consistent developer experience across different environments.
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# Example uses of this error model include:
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# - Partial errors. If a service needs to return partial errors to the client,
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# it may embed the `Status` in the normal response to indicate the partial
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# errors.
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# - Workflow errors. A typical workflow has multiple steps. Each step may
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# have a `Status` message for error reporting.
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# - Batch operations. If a client uses batch request and batch response, the
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# `Status` message should be used directly inside batch response, one for
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# each error sub-response.
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# - Asynchronous operations. If an API call embeds asynchronous operation
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# results in its response, the status of those operations should be
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# represented directly using the `Status` message.
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# - Logging. If some API errors are stored in logs, the message `Status` could
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# be used directly after any stripping needed for security/privacy reasons.
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# Corresponds to the JSON property `error`
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# @return [Google::Apis::GenomicsV1alpha2::Status]
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attr_accessor :error
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# An OperationMetadata object. This will always be returned with the Operation.
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# Corresponds to the JSON property `metadata`
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# @return [Hash<String,Object>]
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attr_accessor :metadata
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# The server-assigned name, which is only unique within the same service that
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# originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-
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# qzoWAgEw`
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# Corresponds to the JSON property `name`
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# @return [String]
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attr_accessor :name
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# If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If
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# importing Variants, an ImportVariantsResponse is returned. For pipelines and
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# exports, an Empty response is returned.
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# Corresponds to the JSON property `response`
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# @return [Hash<String,Object>]
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attr_accessor :response
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@done = args[:done] if args.key?(:done)
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@error = args[:error] if args.key?(:error)
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@metadata = args[:metadata] if args.key?(:metadata)
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@name = args[:name] if args.key?(:name)
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@response = args[:response] if args.key?(:response)
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end
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end
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# An event that occurred during an Operation.
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class OperationEvent
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include Google::Apis::Core::Hashable
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# Required description of event.
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# Corresponds to the JSON property `description`
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# @return [String]
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attr_accessor :description
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# Optional time of when event finished. An event can have a start time and no
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# finish time. If an event has a finish time, there must be a start time.
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# Corresponds to the JSON property `endTime`
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# @return [String]
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attr_accessor :end_time
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# Optional time of when event started.
|
|
# Corresponds to the JSON property `startTime`
|
|
# @return [String]
|
|
attr_accessor :start_time
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@description = args[:description] if args.key?(:description)
|
|
@end_time = args[:end_time] if args.key?(:end_time)
|
|
@start_time = args[:start_time] if args.key?(:start_time)
|
|
end
|
|
end
|
|
|
|
# Metadata describing an Operation.
|
|
class OperationMetadata
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# This field is deprecated. Use `labels` instead. Optionally provided by the
|
|
# caller when submitting the request that creates the operation.
|
|
# Corresponds to the JSON property `clientId`
|
|
# @return [String]
|
|
attr_accessor :client_id
|
|
|
|
# The time at which the job was submitted to the Genomics service.
|
|
# Corresponds to the JSON property `createTime`
|
|
# @return [String]
|
|
attr_accessor :create_time
|
|
|
|
# The time at which the job stopped running.
|
|
# Corresponds to the JSON property `endTime`
|
|
# @return [String]
|
|
attr_accessor :end_time
|
|
|
|
# Optional event messages that were generated during the job's execution.
|
|
# This also contains any warnings that were generated during import
|
|
# or export.
|
|
# Corresponds to the JSON property `events`
|
|
# @return [Array<Google::Apis::GenomicsV1alpha2::OperationEvent>]
|
|
attr_accessor :events
|
|
|
|
# Optionally provided by the caller when submitting the request that creates
|
|
# the operation.
|
|
# Corresponds to the JSON property `labels`
|
|
# @return [Hash<String,String>]
|
|
attr_accessor :labels
|
|
|
|
# The Google Cloud Project in which the job is scoped.
|
|
# Corresponds to the JSON property `projectId`
|
|
# @return [String]
|
|
attr_accessor :project_id
|
|
|
|
# The original request that started the operation. Note that this will be in
|
|
# current version of the API. If the operation was started with v1beta2 API
|
|
# and a GetOperation is performed on v1 API, a v1 request will be returned.
|
|
# Corresponds to the JSON property `request`
|
|
# @return [Hash<String,Object>]
|
|
attr_accessor :request
|
|
|
|
# Runtime metadata on this Operation.
|
|
# Corresponds to the JSON property `runtimeMetadata`
|
|
# @return [Hash<String,Object>]
|
|
attr_accessor :runtime_metadata
|
|
|
|
# The time at which the job began to run.
|
|
# Corresponds to the JSON property `startTime`
|
|
# @return [String]
|
|
attr_accessor :start_time
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@client_id = args[:client_id] if args.key?(:client_id)
|
|
@create_time = args[:create_time] if args.key?(:create_time)
|
|
@end_time = args[:end_time] if args.key?(:end_time)
|
|
@events = args[:events] if args.key?(:events)
|
|
@labels = args[:labels] if args.key?(:labels)
|
|
@project_id = args[:project_id] if args.key?(:project_id)
|
|
@request = args[:request] if args.key?(:request)
|
|
@runtime_metadata = args[:runtime_metadata] if args.key?(:runtime_metadata)
|
|
@start_time = args[:start_time] if args.key?(:start_time)
|
|
end
|
|
end
|
|
|
|
# The pipeline object. Represents a transformation from a set of input
|
|
# parameters to a set of output parameters. The transformation is defined
|
|
# as a docker image and command to run within that image. Each pipeline
|
|
# is run on a Google Compute Engine VM. A pipeline can be created with the
|
|
# `create` method and then later run with the `run` method, or a pipeline can
|
|
# be defined and run all at once with the `run` method.
|
|
class Pipeline
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# User-specified description.
|
|
# Corresponds to the JSON property `description`
|
|
# @return [String]
|
|
attr_accessor :description
|
|
|
|
# The Docker execuctor specification.
|
|
# Corresponds to the JSON property `docker`
|
|
# @return [Google::Apis::GenomicsV1alpha2::DockerExecutor]
|
|
attr_accessor :docker
|
|
|
|
# Input parameters of the pipeline.
|
|
# Corresponds to the JSON property `inputParameters`
|
|
# @return [Array<Google::Apis::GenomicsV1alpha2::PipelineParameter>]
|
|
attr_accessor :input_parameters
|
|
|
|
# Required. A user specified pipeline name that does not have to be unique.
|
|
# This name can be used for filtering Pipelines in ListPipelines.
|
|
# Corresponds to the JSON property `name`
|
|
# @return [String]
|
|
attr_accessor :name
|
|
|
|
# Output parameters of the pipeline.
|
|
# Corresponds to the JSON property `outputParameters`
|
|
# @return [Array<Google::Apis::GenomicsV1alpha2::PipelineParameter>]
|
|
attr_accessor :output_parameters
|
|
|
|
# Unique pipeline id that is generated by the service when CreatePipeline
|
|
# is called. Cannot be specified in the Pipeline used in the
|
|
# CreatePipelineRequest, and will be populated in the response to
|
|
# CreatePipeline and all subsequent Get and List calls. Indicates that the
|
|
# service has registered this pipeline.
|
|
# Corresponds to the JSON property `pipelineId`
|
|
# @return [String]
|
|
attr_accessor :pipeline_id
|
|
|
|
# Required. The project in which to create the pipeline. The caller must have
|
|
# WRITE access.
|
|
# Corresponds to the JSON property `projectId`
|
|
# @return [String]
|
|
attr_accessor :project_id
|
|
|
|
# The system resources for the pipeline run.
|
|
# Corresponds to the JSON property `resources`
|
|
# @return [Google::Apis::GenomicsV1alpha2::PipelineResources]
|
|
attr_accessor :resources
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@description = args[:description] if args.key?(:description)
|
|
@docker = args[:docker] if args.key?(:docker)
|
|
@input_parameters = args[:input_parameters] if args.key?(:input_parameters)
|
|
@name = args[:name] if args.key?(:name)
|
|
@output_parameters = args[:output_parameters] if args.key?(:output_parameters)
|
|
@pipeline_id = args[:pipeline_id] if args.key?(:pipeline_id)
|
|
@project_id = args[:project_id] if args.key?(:project_id)
|
|
@resources = args[:resources] if args.key?(:resources)
|
|
end
|
|
end
|
|
|
|
# Parameters facilitate setting and delivering data into the
|
|
# pipeline's execution environment. They are defined at create time,
|
|
# with optional defaults, and can be overridden at run time.
|
|
# If `localCopy` is unset, then the parameter specifies a string that
|
|
# is passed as-is into the pipeline, as the value of the environment
|
|
# variable with the given name. A default value can be optionally
|
|
# specified at create time. The default can be overridden at run time
|
|
# using the inputs map. If no default is given, a value must be
|
|
# supplied at runtime.
|
|
# If `localCopy` is defined, then the parameter specifies a data
|
|
# source or sink, both in Google Cloud Storage and on the Docker container
|
|
# where the pipeline computation is run. The service account associated with
|
|
# the Pipeline (by
|
|
# default the project's Compute Engine service account) must have access to the
|
|
# Google Cloud Storage paths.
|
|
# At run time, the Google Cloud Storage paths can be overridden if a default
|
|
# was provided at create time, or must be set otherwise. The pipeline runner
|
|
# should add a key/value pair to either the inputs or outputs map. The
|
|
# indicated data copies will be carried out before/after pipeline execution,
|
|
# just as if the corresponding arguments were provided to `gsutil cp`.
|
|
# For example: Given the following `PipelineParameter`, specified
|
|
# in the `inputParameters` list:
|
|
# ```
|
|
# `name: "input_file", localCopy: `path: "file.txt", disk: "pd1"``
|
|
# ```
|
|
# where `disk` is defined in the `PipelineResources` object as:
|
|
# ```
|
|
# `name: "pd1", mountPoint: "/mnt/disk/"`
|
|
# ```
|
|
# We create a disk named `pd1`, mount it on the host VM, and map
|
|
# `/mnt/pd1` to `/mnt/disk` in the docker container. At
|
|
# runtime, an entry for `input_file` would be required in the inputs
|
|
# map, such as:
|
|
# ```
|
|
# inputs["input_file"] = "gs://my-bucket/bar.txt"
|
|
# ```
|
|
# This would generate the following gsutil call:
|
|
# ```
|
|
# gsutil cp gs://my-bucket/bar.txt /mnt/pd1/file.txt
|
|
# ```
|
|
# The file `/mnt/pd1/file.txt` maps to `/mnt/disk/file.txt` in the
|
|
# Docker container. Acceptable paths are:
|
|
# <table>
|
|
# <thead>
|
|
# <tr><th>Google Cloud storage path</th><th>Local path</th></tr>
|
|
# </thead>
|
|
# <tbody>
|
|
# <tr><td>file</td><td>file</td></tr>
|
|
# <tr><td>glob</td><td>directory</td></tr>
|
|
# </tbody>
|
|
# </table>
|
|
# For outputs, the direction of the copy is reversed:
|
|
# ```
|
|
# gsutil cp /mnt/disk/file.txt gs://my-bucket/bar.txt
|
|
# ```
|
|
# Acceptable paths are:
|
|
# <table>
|
|
# <thead>
|
|
# <tr><th>Local path</th><th>Google Cloud Storage path</th></tr>
|
|
# </thead>
|
|
# <tbody>
|
|
# <tr><td>file</td><td>file</td></tr>
|
|
# <tr>
|
|
# <td>file</td>
|
|
# <td>directory - directory must already exist</td>
|
|
# </tr>
|
|
# <tr>
|
|
# <td>glob</td>
|
|
# <td>directory - directory will be created if it doesn't exist</td></tr>
|
|
# </tbody>
|
|
# </table>
|
|
# One restriction due to docker limitations, is that for outputs that are found
|
|
# on the boot disk, the local path cannot be a glob and must be a file.
|
|
class PipelineParameter
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The default value for this parameter. Can be overridden at runtime.
|
|
# If `localCopy` is present, then this must be a Google Cloud Storage path
|
|
# beginning with `gs://`.
|
|
# Corresponds to the JSON property `defaultValue`
|
|
# @return [String]
|
|
attr_accessor :default_value
|
|
|
|
# Human-readable description.
|
|
# Corresponds to the JSON property `description`
|
|
# @return [String]
|
|
attr_accessor :description
|
|
|
|
# LocalCopy defines how a remote file should be copied to and from the VM.
|
|
# Corresponds to the JSON property `localCopy`
|
|
# @return [Google::Apis::GenomicsV1alpha2::LocalCopy]
|
|
attr_accessor :local_copy
|
|
|
|
# Required. Name of the parameter - the pipeline runner uses this string
|
|
# as the key to the input and output maps in RunPipeline.
|
|
# Corresponds to the JSON property `name`
|
|
# @return [String]
|
|
attr_accessor :name
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@default_value = args[:default_value] if args.key?(:default_value)
|
|
@description = args[:description] if args.key?(:description)
|
|
@local_copy = args[:local_copy] if args.key?(:local_copy)
|
|
@name = args[:name] if args.key?(:name)
|
|
end
|
|
end
|
|
|
|
# The system resources for the pipeline run.
|
|
class PipelineResources
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Optional. The number of accelerators of the specified type to attach.
|
|
# By specifying this parameter, you will download and install the following
|
|
# third-party software onto your managed Compute Engine instances:
|
|
# NVIDIA® Tesla® drivers and NVIDIA® CUDA toolkit.
|
|
# Corresponds to the JSON property `acceleratorCount`
|
|
# @return [Fixnum]
|
|
attr_accessor :accelerator_count
|
|
|
|
# Optional. The Compute Engine defined accelerator type.
|
|
# By specifying this parameter, you will download and install the following
|
|
# third-party software onto your managed Compute Engine instances: NVIDIA®
|
|
# Tesla® drivers and NVIDIA® CUDA toolkit.
|
|
# Please see https://cloud.google.com/compute/docs/gpus/ for a list of
|
|
# available accelerator types.
|
|
# Corresponds to the JSON property `acceleratorType`
|
|
# @return [String]
|
|
attr_accessor :accelerator_type
|
|
|
|
# The size of the boot disk. Defaults to 10 (GB).
|
|
# Corresponds to the JSON property `bootDiskSizeGb`
|
|
# @return [Fixnum]
|
|
attr_accessor :boot_disk_size_gb
|
|
|
|
# Disks to attach.
|
|
# Corresponds to the JSON property `disks`
|
|
# @return [Array<Google::Apis::GenomicsV1alpha2::Disk>]
|
|
attr_accessor :disks
|
|
|
|
# The minimum number of cores to use. Defaults to 1.
|
|
# Corresponds to the JSON property `minimumCpuCores`
|
|
# @return [Fixnum]
|
|
attr_accessor :minimum_cpu_cores
|
|
|
|
# The minimum amount of RAM to use. Defaults to 3.75 (GB)
|
|
# Corresponds to the JSON property `minimumRamGb`
|
|
# @return [Float]
|
|
attr_accessor :minimum_ram_gb
|
|
|
|
# Whether to assign an external IP to the instance. This is an experimental
|
|
# feature that may go away. Defaults to false.
|
|
# Corresponds to `--no_address` flag for [gcloud compute instances create]
|
|
# (https://cloud.google.com/sdk/gcloud/reference/compute/instances/create).
|
|
# In order to use this, must be true for both create time and run time.
|
|
# Cannot be true at run time if false at create time. If you need to ssh into
|
|
# a private IP VM for debugging, you can ssh to a public VM and then ssh into
|
|
# the private VM's Internal IP. If noAddress is set, this pipeline run may
|
|
# only load docker images from Google Container Registry and not Docker Hub.
|
|
# Before using this, you must
|
|
# [configure access to Google services from internal IPs](https://cloud.google.
|
|
# com/compute/docs/configure-private-google-access#
|
|
# configuring_access_to_google_services_from_internal_ips).
|
|
# Corresponds to the JSON property `noAddress`
|
|
# @return [Boolean]
|
|
attr_accessor :no_address
|
|
alias_method :no_address?, :no_address
|
|
|
|
# Whether to use preemptible VMs. Defaults to `false`. In order to use this,
|
|
# must be true for both create time and run time. Cannot be true at run time
|
|
# if false at create time.
|
|
# Corresponds to the JSON property `preemptible`
|
|
# @return [Boolean]
|
|
attr_accessor :preemptible
|
|
alias_method :preemptible?, :preemptible
|
|
|
|
# List of Google Compute Engine availability zones to which resource
|
|
# creation will restricted. If empty, any zone may be chosen.
|
|
# Corresponds to the JSON property `zones`
|
|
# @return [Array<String>]
|
|
attr_accessor :zones
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@accelerator_count = args[:accelerator_count] if args.key?(:accelerator_count)
|
|
@accelerator_type = args[:accelerator_type] if args.key?(:accelerator_type)
|
|
@boot_disk_size_gb = args[:boot_disk_size_gb] if args.key?(:boot_disk_size_gb)
|
|
@disks = args[:disks] if args.key?(:disks)
|
|
@minimum_cpu_cores = args[:minimum_cpu_cores] if args.key?(:minimum_cpu_cores)
|
|
@minimum_ram_gb = args[:minimum_ram_gb] if args.key?(:minimum_ram_gb)
|
|
@no_address = args[:no_address] if args.key?(:no_address)
|
|
@preemptible = args[:preemptible] if args.key?(:preemptible)
|
|
@zones = args[:zones] if args.key?(:zones)
|
|
end
|
|
end
|
|
|
|
#
|
|
class RepeatedString
|
|
include Google::Apis::Core::Hashable
|
|
|
|
#
|
|
# Corresponds to the JSON property `values`
|
|
# @return [Array<String>]
|
|
attr_accessor :values
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@values = args[:values] if args.key?(:values)
|
|
end
|
|
end
|
|
|
|
# The pipeline run arguments.
|
|
class RunPipelineArgs
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# This field is deprecated. Use `labels` instead. Client-specified pipeline
|
|
# operation identifier.
|
|
# Corresponds to the JSON property `clientId`
|
|
# @return [String]
|
|
attr_accessor :client_id
|
|
|
|
# Pipeline input arguments; keys are defined in the pipeline documentation.
|
|
# All input parameters that do not have default values must be specified.
|
|
# If parameters with defaults are specified here, the defaults will be
|
|
# overridden.
|
|
# Corresponds to the JSON property `inputs`
|
|
# @return [Hash<String,String>]
|
|
attr_accessor :inputs
|
|
|
|
# How long to keep the VM up after a failure (for example docker command
|
|
# failed, copying input or output files failed, etc). While the VM is up, one
|
|
# can ssh into the VM to debug. Default is 0; maximum allowed value is 1 day.
|
|
# Corresponds to the JSON property `keepVmAliveOnFailureDuration`
|
|
# @return [String]
|
|
attr_accessor :keep_vm_alive_on_failure_duration
|
|
|
|
# Labels to apply to this pipeline run. Labels will also be applied to
|
|
# compute resources (VM, disks) created by this pipeline run. When listing
|
|
# operations, operations can filtered by labels.
|
|
# Label keys may not be empty; label values may be empty. Non-empty labels
|
|
# must be 1-63 characters long, and comply with [RFC1035]
|
|
# (https://www.ietf.org/rfc/rfc1035.txt).
|
|
# Specifically, the name must be 1-63 characters long and match the regular
|
|
# expression `[a-z]([-a-z0-9]*[a-z0-9])?` which means the first
|
|
# character must be a lowercase letter, and all following characters must be
|
|
# a dash, lowercase letter, or digit, except the last character, which cannot
|
|
# be a dash.
|
|
# Corresponds to the JSON property `labels`
|
|
# @return [Hash<String,String>]
|
|
attr_accessor :labels
|
|
|
|
# The logging options for the pipeline run.
|
|
# Corresponds to the JSON property `logging`
|
|
# @return [Google::Apis::GenomicsV1alpha2::LoggingOptions]
|
|
attr_accessor :logging
|
|
|
|
# Pipeline output arguments; keys are defined in the pipeline
|
|
# documentation. All output parameters of without default values
|
|
# must be specified. If parameters with defaults are specified
|
|
# here, the defaults will be overridden.
|
|
# Corresponds to the JSON property `outputs`
|
|
# @return [Hash<String,String>]
|
|
attr_accessor :outputs
|
|
|
|
# Required. The project in which to run the pipeline. The caller must have
|
|
# WRITER access to all Google Cloud services and resources (e.g. Google
|
|
# Compute Engine) will be used.
|
|
# Corresponds to the JSON property `projectId`
|
|
# @return [String]
|
|
attr_accessor :project_id
|
|
|
|
# The system resources for the pipeline run.
|
|
# Corresponds to the JSON property `resources`
|
|
# @return [Google::Apis::GenomicsV1alpha2::PipelineResources]
|
|
attr_accessor :resources
|
|
|
|
# A Google Cloud Service Account.
|
|
# Corresponds to the JSON property `serviceAccount`
|
|
# @return [Google::Apis::GenomicsV1alpha2::ServiceAccount]
|
|
attr_accessor :service_account
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@client_id = args[:client_id] if args.key?(:client_id)
|
|
@inputs = args[:inputs] if args.key?(:inputs)
|
|
@keep_vm_alive_on_failure_duration = args[:keep_vm_alive_on_failure_duration] if args.key?(:keep_vm_alive_on_failure_duration)
|
|
@labels = args[:labels] if args.key?(:labels)
|
|
@logging = args[:logging] if args.key?(:logging)
|
|
@outputs = args[:outputs] if args.key?(:outputs)
|
|
@project_id = args[:project_id] if args.key?(:project_id)
|
|
@resources = args[:resources] if args.key?(:resources)
|
|
@service_account = args[:service_account] if args.key?(:service_account)
|
|
end
|
|
end
|
|
|
|
# The request to run a pipeline. If `pipelineId` is specified, it
|
|
# refers to a saved pipeline created with CreatePipeline and set as
|
|
# the `pipelineId` of the returned Pipeline object. If
|
|
# `ephemeralPipeline` is specified, that pipeline is run once
|
|
# with the given args and not saved. It is an error to specify both
|
|
# `pipelineId` and `ephemeralPipeline`. `pipelineArgs`
|
|
# must be specified.
|
|
class RunPipelineRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The pipeline object. Represents a transformation from a set of input
|
|
# parameters to a set of output parameters. The transformation is defined
|
|
# as a docker image and command to run within that image. Each pipeline
|
|
# is run on a Google Compute Engine VM. A pipeline can be created with the
|
|
# `create` method and then later run with the `run` method, or a pipeline can
|
|
# be defined and run all at once with the `run` method.
|
|
# Corresponds to the JSON property `ephemeralPipeline`
|
|
# @return [Google::Apis::GenomicsV1alpha2::Pipeline]
|
|
attr_accessor :ephemeral_pipeline
|
|
|
|
# The pipeline run arguments.
|
|
# Corresponds to the JSON property `pipelineArgs`
|
|
# @return [Google::Apis::GenomicsV1alpha2::RunPipelineArgs]
|
|
attr_accessor :pipeline_args
|
|
|
|
# The already created pipeline to run.
|
|
# Corresponds to the JSON property `pipelineId`
|
|
# @return [String]
|
|
attr_accessor :pipeline_id
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@ephemeral_pipeline = args[:ephemeral_pipeline] if args.key?(:ephemeral_pipeline)
|
|
@pipeline_args = args[:pipeline_args] if args.key?(:pipeline_args)
|
|
@pipeline_id = args[:pipeline_id] if args.key?(:pipeline_id)
|
|
end
|
|
end
|
|
|
|
# Runtime metadata that will be populated in the
|
|
# runtimeMetadata
|
|
# field of the Operation associated with a RunPipeline execution.
|
|
class RuntimeMetadata
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Describes a Compute Engine resource that is being managed by a running
|
|
# pipeline.
|
|
# Corresponds to the JSON property `computeEngine`
|
|
# @return [Google::Apis::GenomicsV1alpha2::ComputeEngine]
|
|
attr_accessor :compute_engine
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@compute_engine = args[:compute_engine] if args.key?(:compute_engine)
|
|
end
|
|
end
|
|
|
|
# A Google Cloud Service Account.
|
|
class ServiceAccount
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Email address of the service account. Defaults to `default`,
|
|
# which uses the compute service account associated with the project.
|
|
# Corresponds to the JSON property `email`
|
|
# @return [String]
|
|
attr_accessor :email
|
|
|
|
# List of scopes to be enabled for this service account on the VM.
|
|
# The following scopes are automatically included:
|
|
# * https://www.googleapis.com/auth/compute
|
|
# * https://www.googleapis.com/auth/devstorage.full_control
|
|
# * https://www.googleapis.com/auth/genomics
|
|
# * https://www.googleapis.com/auth/logging.write
|
|
# * https://www.googleapis.com/auth/monitoring.write
|
|
# Corresponds to the JSON property `scopes`
|
|
# @return [Array<String>]
|
|
attr_accessor :scopes
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@email = args[:email] if args.key?(:email)
|
|
@scopes = args[:scopes] if args.key?(:scopes)
|
|
end
|
|
end
|
|
|
|
# Request to set operation status. Should only be used by VMs
|
|
# created by the Pipelines Service and not by end users.
|
|
class SetOperationStatusRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
#
|
|
# Corresponds to the JSON property `errorCode`
|
|
# @return [String]
|
|
attr_accessor :error_code
|
|
|
|
#
|
|
# Corresponds to the JSON property `errorMessage`
|
|
# @return [String]
|
|
attr_accessor :error_message
|
|
|
|
#
|
|
# Corresponds to the JSON property `operationId`
|
|
# @return [String]
|
|
attr_accessor :operation_id
|
|
|
|
#
|
|
# Corresponds to the JSON property `timestampEvents`
|
|
# @return [Array<Google::Apis::GenomicsV1alpha2::TimestampEvent>]
|
|
attr_accessor :timestamp_events
|
|
|
|
#
|
|
# Corresponds to the JSON property `validationToken`
|
|
# @return [Fixnum]
|
|
attr_accessor :validation_token
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@error_code = args[:error_code] if args.key?(:error_code)
|
|
@error_message = args[:error_message] if args.key?(:error_message)
|
|
@operation_id = args[:operation_id] if args.key?(:operation_id)
|
|
@timestamp_events = args[:timestamp_events] if args.key?(:timestamp_events)
|
|
@validation_token = args[:validation_token] if args.key?(:validation_token)
|
|
end
|
|
end
|
|
|
|
# The `Status` type defines a logical error model that is suitable for different
|
|
# programming environments, including REST APIs and RPC APIs. It is used by
|
|
# [gRPC](https://github.com/grpc). The error model is designed to be:
|
|
# - Simple to use and understand for most users
|
|
# - Flexible enough to meet unexpected needs
|
|
# # Overview
|
|
# The `Status` message contains three pieces of data: error code, error message,
|
|
# and error details. The error code should be an enum value of
|
|
# google.rpc.Code, but it may accept additional error codes if needed. The
|
|
# error message should be a developer-facing English message that helps
|
|
# developers *understand* and *resolve* the error. If a localized user-facing
|
|
# error message is needed, put the localized message in the error details or
|
|
# localize it in the client. The optional error details may contain arbitrary
|
|
# information about the error. There is a predefined set of error detail types
|
|
# in the package `google.rpc` that can be used for common error conditions.
|
|
# # Language mapping
|
|
# The `Status` message is the logical representation of the error model, but it
|
|
# is not necessarily the actual wire format. When the `Status` message is
|
|
# exposed in different client libraries and different wire protocols, it can be
|
|
# mapped differently. For example, it will likely be mapped to some exceptions
|
|
# in Java, but more likely mapped to some error codes in C.
|
|
# # Other uses
|
|
# The error model and the `Status` message can be used in a variety of
|
|
# environments, either with or without APIs, to provide a
|
|
# consistent developer experience across different environments.
|
|
# Example uses of this error model include:
|
|
# - Partial errors. If a service needs to return partial errors to the client,
|
|
# it may embed the `Status` in the normal response to indicate the partial
|
|
# errors.
|
|
# - Workflow errors. A typical workflow has multiple steps. Each step may
|
|
# have a `Status` message for error reporting.
|
|
# - Batch operations. If a client uses batch request and batch response, the
|
|
# `Status` message should be used directly inside batch response, one for
|
|
# each error sub-response.
|
|
# - Asynchronous operations. If an API call embeds asynchronous operation
|
|
# results in its response, the status of those operations should be
|
|
# represented directly using the `Status` message.
|
|
# - Logging. If some API errors are stored in logs, the message `Status` could
|
|
# be used directly after any stripping needed for security/privacy reasons.
|
|
class Status
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The status code, which should be an enum value of google.rpc.Code.
|
|
# Corresponds to the JSON property `code`
|
|
# @return [Fixnum]
|
|
attr_accessor :code
|
|
|
|
# A list of messages that carry the error details. There is a common set of
|
|
# message types for APIs to use.
|
|
# Corresponds to the JSON property `details`
|
|
# @return [Array<Hash<String,Object>>]
|
|
attr_accessor :details
|
|
|
|
# A developer-facing error message, which should be in English. Any
|
|
# user-facing error message should be localized and sent in the
|
|
# google.rpc.Status.details field, or localized by the client.
|
|
# Corresponds to the JSON property `message`
|
|
# @return [String]
|
|
attr_accessor :message
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@code = args[:code] if args.key?(:code)
|
|
@details = args[:details] if args.key?(:details)
|
|
@message = args[:message] if args.key?(:message)
|
|
end
|
|
end
|
|
|
|
# Stores the list of events and times they occured for major events in job
|
|
# execution.
|
|
class TimestampEvent
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# String indicating the type of event
|
|
# Corresponds to the JSON property `description`
|
|
# @return [String]
|
|
attr_accessor :description
|
|
|
|
# The time this event occured.
|
|
# Corresponds to the JSON property `timestamp`
|
|
# @return [String]
|
|
attr_accessor :timestamp
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@description = args[:description] if args.key?(:description)
|
|
@timestamp = args[:timestamp] if args.key?(:timestamp)
|
|
end
|
|
end
|
|
end
|
|
end
|
|
end
|