From e31f3fc20f610e5fafabefbe0f9f23578a24a120 Mon Sep 17 00:00:00 2001 From: Google APIs Date: Tue, 16 Jan 2018 00:35:13 +0000 Subject: [PATCH] Autogenerated update (2018-01-16) Update: - androiddeviceprovisioning_v1 - androidenterprise_v1 - androidpublisher_v2 - genomics_v1 - genomics_v1alpha2 --- api_names_out.yaml | 1 + .../apis/androiddeviceprovisioning_v1.rb | 2 +- .../androiddeviceprovisioning_v1/service.rb | 4 +- generated/google/apis/androidenterprise_v1.rb | 2 +- .../apis/androidenterprise_v1/classes.rb | 108 +- .../androidenterprise_v1/representations.rb | 47 +- .../apis/androidenterprise_v1/service.rb | 229 -- generated/google/apis/androidpublisher_v2.rb | 2 +- .../apis/androidpublisher_v2/classes.rb | 2 +- .../apis/androidpublisher_v2/service.rb | 15 +- generated/google/apis/genomics_v1.rb | 11 +- generated/google/apis/genomics_v1/classes.rb | 3068 ----------------- .../apis/genomics_v1/representations.rb | 1119 ------ generated/google/apis/genomics_v1/service.rb | 2026 ----------- generated/google/apis/genomics_v1alpha2.rb | 2 +- .../google/apis/genomics_v1alpha2/classes.rb | 38 - .../apis/genomics_v1alpha2/representations.rb | 26 - 17 files changed, 32 insertions(+), 6670 deletions(-) diff --git a/api_names_out.yaml b/api_names_out.yaml index 90222a463..84a2701f0 100644 --- a/api_names_out.yaml +++ b/api_names_out.yaml @@ -5574,6 +5574,7 @@ "/androidenterprise:v1/ManagedPropertyBundle/managedProperty/managed_property": managed_property "/androidenterprise:v1/NewDeviceEvent": new_device_event "/androidenterprise:v1/NewDeviceEvent/deviceId": device_id +"/androidenterprise:v1/NewDeviceEvent/dpcPackageName": dpc_package_name "/androidenterprise:v1/NewDeviceEvent/managementType": management_type "/androidenterprise:v1/NewDeviceEvent/userId": user_id "/androidenterprise:v1/NewPermissionsEvent": new_permissions_event diff --git a/generated/google/apis/androiddeviceprovisioning_v1.rb b/generated/google/apis/androiddeviceprovisioning_v1.rb index 85ba4293f..5e24bd945 100644 --- a/generated/google/apis/androiddeviceprovisioning_v1.rb +++ b/generated/google/apis/androiddeviceprovisioning_v1.rb @@ -26,7 +26,7 @@ module Google # @see https://developers.google.com/zero-touch/ module AndroiddeviceprovisioningV1 VERSION = 'V1' - REVISION = '20171216' + REVISION = '20180114' end end end diff --git a/generated/google/apis/androiddeviceprovisioning_v1/service.rb b/generated/google/apis/androiddeviceprovisioning_v1/service.rb index 929037853..0a41dc2fa 100644 --- a/generated/google/apis/androiddeviceprovisioning_v1/service.rb +++ b/generated/google/apis/androiddeviceprovisioning_v1/service.rb @@ -324,8 +324,8 @@ module Google # Required. The customer managing the devices. An API resource name in the # format `customers/[CUSTOMER_ID]`. # @param [Fixnum] page_size - # The maximum number of devices to show in a page of results. The default - # value returns all the devices in a single page. + # The maximum number of devices to show in a page of results. + # Must be between 1 and 100 inclusive. # @param [String] page_token # A token specifying which result page to return. # @param [String] fields diff --git a/generated/google/apis/androidenterprise_v1.rb b/generated/google/apis/androidenterprise_v1.rb index b2ea06f80..83511b250 100644 --- a/generated/google/apis/androidenterprise_v1.rb +++ b/generated/google/apis/androidenterprise_v1.rb @@ -25,7 +25,7 @@ module Google # @see https://developers.google.com/android/work/play/emm-api module AndroidenterpriseV1 VERSION = 'V1' - REVISION = '20180103' + REVISION = '20180111' # Manage corporate Android devices AUTH_ANDROIDENTERPRISE = 'https://www.googleapis.com/auth/androidenterprise' diff --git a/generated/google/apis/androidenterprise_v1/classes.rb b/generated/google/apis/androidenterprise_v1/classes.rb index 620f997a5..5bd09c99b 100644 --- a/generated/google/apis/androidenterprise_v1/classes.rb +++ b/generated/google/apis/androidenterprise_v1/classes.rb @@ -1321,6 +1321,11 @@ module Google # @return [String] attr_accessor :device_id + # Policy app on the device. + # Corresponds to the JSON property `dpcPackageName` + # @return [String] + attr_accessor :dpc_package_name + # Identifies the extent to which the device is controlled by an Android EMM in # various deployment configurations. # Possible values include: @@ -1342,6 +1347,7 @@ module Google # Update properties of this object def update!(**args) @device_id = args[:device_id] if args.key?(:device_id) + @dpc_package_name = args[:dpc_package_name] if args.key?(:dpc_package_name) @management_type = args[:management_type] if args.key?(:management_type) @user_id = args[:user_id] if args.key?(:user_id) end @@ -1647,7 +1653,7 @@ module Google # @return [String] attr_accessor :content_rating - # A localized promotional description, if available. + # The localized promotional description, if available. # Corresponds to the JSON property `description` # @return [String] attr_accessor :description @@ -1679,8 +1685,8 @@ module Google # @return [String] attr_accessor :kind - # The time (in milliseconds since epoch) when application was last published. ( - # Timestamp is approximate within 7 days of actual publish time.) + # The approximate time (within 7 days) the app was last published, expressed in + # milliseconds since epoch. # Corresponds to the JSON property `lastUpdatedTimestampMillis` # @return [Fixnum] attr_accessor :last_updated_timestamp_millis @@ -1690,7 +1696,7 @@ module Google # @return [Fixnum] attr_accessor :min_android_sdk_version - # The permissions required for this app. + # A list of permissions required by the app. # Corresponds to the JSON property `permissions` # @return [Array] attr_accessor :permissions @@ -2666,100 +2672,6 @@ module Google @user_value = args[:user_value] if args.key?(:user_value) end end - - # WebApp resource info. - class WebApp - include Google::Apis::Core::Hashable - - # A list of icons representing this website. Must have at least one element. - # Corresponds to the JSON property `icons` - # @return [Array] - attr_accessor :icons - - # The name of the web application as it is usually displayed to the user (e.g., - # amongst a list of other applications, or as a label for an icon). Required. - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # String that represents the start URL, i.e. the URL that should load when the - # user opens the application. Required. - # Corresponds to the JSON property `startUrl` - # @return [String] - attr_accessor :start_url - - # The ID of the application. - # Corresponds to the JSON property `webAppId` - # @return [String] - attr_accessor :web_app_id - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @icons = args[:icons] if args.key?(:icons) - @name = args[:name] if args.key?(:name) - @start_url = args[:start_url] if args.key?(:start_url) - @web_app_id = args[:web_app_id] if args.key?(:web_app_id) - end - end - - # Each image object represents an image that is used as part of a web - # application, suitable to use in various contexts depending on the semantics of - # the member that is using the object (e.g., an icon that is part of an - # application menu, etc.). - class WebAppImage - include Google::Apis::Core::Hashable - - # The actual bytes of the image. - # Corresponds to the JSON property `imageData` - # NOTE: Values are automatically base64 encoded/decoded in the client library. - # @return [String] - attr_accessor :image_data - - # The purposes this image may be used for. Optional. - # Corresponds to the JSON property `purposes` - # @return [Array] - attr_accessor :purposes - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @image_data = args[:image_data] if args.key?(:image_data) - @purposes = args[:purposes] if args.key?(:purposes) - end - end - - # The web app details for an enterprise. - class WebAppsListResponse - include Google::Apis::Core::Hashable - - # Identifies what kind of resource this is. Value: the fixed string " - # androidenterprise#webAppsListResponse". - # Corresponds to the JSON property `kind` - # @return [String] - attr_accessor :kind - - # The manifest describing a web app. - # Corresponds to the JSON property `webApp` - # @return [Array] - attr_accessor :web_app - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @kind = args[:kind] if args.key?(:kind) - @web_app = args[:web_app] if args.key?(:web_app) - end - end end end end diff --git a/generated/google/apis/androidenterprise_v1/representations.rb b/generated/google/apis/androidenterprise_v1/representations.rb index 8f86f01f6..d1af60237 100644 --- a/generated/google/apis/androidenterprise_v1/representations.rb +++ b/generated/google/apis/androidenterprise_v1/representations.rb @@ -436,24 +436,6 @@ module Google include Google::Apis::Core::JsonObjectSupport end - class WebApp - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class WebAppImage - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class WebAppsListResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - class Administrator # @private class Representation < Google::Apis::Core::JsonRepresentation @@ -800,6 +782,7 @@ module Google # @private class Representation < Google::Apis::Core::JsonRepresentation property :device_id, as: 'deviceId' + property :dpc_package_name, as: 'dpcPackageName' property :management_type, as: 'managementType' property :user_id, as: 'userId' end @@ -1140,34 +1123,6 @@ module Google property :user_value, as: 'userValue' end end - - class WebApp - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :icons, as: 'icons', class: Google::Apis::AndroidenterpriseV1::WebAppImage, decorator: Google::Apis::AndroidenterpriseV1::WebAppImage::Representation - - property :name, as: 'name' - property :start_url, as: 'startUrl' - property :web_app_id, as: 'webAppId' - end - end - - class WebAppImage - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :image_data, :base64 => true, as: 'imageData' - collection :purposes, as: 'purposes' - end - end - - class WebAppsListResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :kind, as: 'kind' - collection :web_app, as: 'webApp', class: Google::Apis::AndroidenterpriseV1::WebApp, decorator: Google::Apis::AndroidenterpriseV1::WebApp::Representation - - end - end end end end diff --git a/generated/google/apis/androidenterprise_v1/service.rb b/generated/google/apis/androidenterprise_v1/service.rb index d05e30f34..8154afde7 100644 --- a/generated/google/apis/androidenterprise_v1/service.rb +++ b/generated/google/apis/androidenterprise_v1/service.rb @@ -3518,235 +3518,6 @@ module Google command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end - - # Deletes an existing web app. - # @param [String] enterprise_id - # The ID of the enterprise. - # @param [String] web_app_id - # The ID of the web app. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # Overrides userIp if both are provided. - # @param [String] user_ip - # IP address of the site where the request originates. Use this if you want to - # enforce per-user limits. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [NilClass] No result returned for this method - # @yieldparam err [StandardError] error object if request failed - # - # @return [void] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_webapp(enterprise_id, web_app_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) - command = make_simple_command(:delete, 'enterprises/{enterpriseId}/webapps/{webAppId}', options) - command.params['enterpriseId'] = enterprise_id unless enterprise_id.nil? - command.params['webAppId'] = web_app_id unless web_app_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - command.query['userIp'] = user_ip unless user_ip.nil? - execute_or_queue_command(command, &block) - end - - # Gets an existing web app. - # @param [String] enterprise_id - # The ID of the enterprise. - # @param [String] web_app_id - # The ID of the web app. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # Overrides userIp if both are provided. - # @param [String] user_ip - # IP address of the site where the request originates. Use this if you want to - # enforce per-user limits. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::AndroidenterpriseV1::WebApp] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::AndroidenterpriseV1::WebApp] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_webapp(enterprise_id, web_app_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) - command = make_simple_command(:get, 'enterprises/{enterpriseId}/webapps/{webAppId}', options) - command.response_representation = Google::Apis::AndroidenterpriseV1::WebApp::Representation - command.response_class = Google::Apis::AndroidenterpriseV1::WebApp - command.params['enterpriseId'] = enterprise_id unless enterprise_id.nil? - command.params['webAppId'] = web_app_id unless web_app_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - command.query['userIp'] = user_ip unless user_ip.nil? - execute_or_queue_command(command, &block) - end - - # Creates a new web app for the enterprise. - # @param [String] enterprise_id - # The ID of the enterprise. - # @param [Google::Apis::AndroidenterpriseV1::WebApp] web_app_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # Overrides userIp if both are provided. - # @param [String] user_ip - # IP address of the site where the request originates. Use this if you want to - # enforce per-user limits. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::AndroidenterpriseV1::WebApp] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::AndroidenterpriseV1::WebApp] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def insert_webapp(enterprise_id, web_app_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) - command = make_simple_command(:post, 'enterprises/{enterpriseId}/webapps', options) - command.request_representation = Google::Apis::AndroidenterpriseV1::WebApp::Representation - command.request_object = web_app_object - command.response_representation = Google::Apis::AndroidenterpriseV1::WebApp::Representation - command.response_class = Google::Apis::AndroidenterpriseV1::WebApp - command.params['enterpriseId'] = enterprise_id unless enterprise_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - command.query['userIp'] = user_ip unless user_ip.nil? - execute_or_queue_command(command, &block) - end - - # Retrieves the details of all web apps for a given enterprise. - # @param [String] enterprise_id - # The ID of the enterprise. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # Overrides userIp if both are provided. - # @param [String] user_ip - # IP address of the site where the request originates. Use this if you want to - # enforce per-user limits. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::AndroidenterpriseV1::WebAppsListResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::AndroidenterpriseV1::WebAppsListResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def list_webapps(enterprise_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) - command = make_simple_command(:get, 'enterprises/{enterpriseId}/webapps', options) - command.response_representation = Google::Apis::AndroidenterpriseV1::WebAppsListResponse::Representation - command.response_class = Google::Apis::AndroidenterpriseV1::WebAppsListResponse - command.params['enterpriseId'] = enterprise_id unless enterprise_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - command.query['userIp'] = user_ip unless user_ip.nil? - execute_or_queue_command(command, &block) - end - - # Updates an existing web app. This method supports patch semantics. - # @param [String] enterprise_id - # The ID of the enterprise. - # @param [String] web_app_id - # The ID of the web app. - # @param [Google::Apis::AndroidenterpriseV1::WebApp] web_app_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # Overrides userIp if both are provided. - # @param [String] user_ip - # IP address of the site where the request originates. Use this if you want to - # enforce per-user limits. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::AndroidenterpriseV1::WebApp] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::AndroidenterpriseV1::WebApp] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def patch_webapp(enterprise_id, web_app_id, web_app_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) - command = make_simple_command(:patch, 'enterprises/{enterpriseId}/webapps/{webAppId}', options) - command.request_representation = Google::Apis::AndroidenterpriseV1::WebApp::Representation - command.request_object = web_app_object - command.response_representation = Google::Apis::AndroidenterpriseV1::WebApp::Representation - command.response_class = Google::Apis::AndroidenterpriseV1::WebApp - command.params['enterpriseId'] = enterprise_id unless enterprise_id.nil? - command.params['webAppId'] = web_app_id unless web_app_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - command.query['userIp'] = user_ip unless user_ip.nil? - execute_or_queue_command(command, &block) - end - - # Updates an existing web app. - # @param [String] enterprise_id - # The ID of the enterprise. - # @param [String] web_app_id - # The ID of the web app. - # @param [Google::Apis::AndroidenterpriseV1::WebApp] web_app_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # Overrides userIp if both are provided. - # @param [String] user_ip - # IP address of the site where the request originates. Use this if you want to - # enforce per-user limits. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::AndroidenterpriseV1::WebApp] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::AndroidenterpriseV1::WebApp] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def update_webapp(enterprise_id, web_app_id, web_app_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) - command = make_simple_command(:put, 'enterprises/{enterpriseId}/webapps/{webAppId}', options) - command.request_representation = Google::Apis::AndroidenterpriseV1::WebApp::Representation - command.request_object = web_app_object - command.response_representation = Google::Apis::AndroidenterpriseV1::WebApp::Representation - command.response_class = Google::Apis::AndroidenterpriseV1::WebApp - command.params['enterpriseId'] = enterprise_id unless enterprise_id.nil? - command.params['webAppId'] = web_app_id unless web_app_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - command.query['userIp'] = user_ip unless user_ip.nil? - execute_or_queue_command(command, &block) - end protected diff --git a/generated/google/apis/androidpublisher_v2.rb b/generated/google/apis/androidpublisher_v2.rb index f35270b79..34ea9a46f 100644 --- a/generated/google/apis/androidpublisher_v2.rb +++ b/generated/google/apis/androidpublisher_v2.rb @@ -25,7 +25,7 @@ module Google # @see https://developers.google.com/android-publisher module AndroidpublisherV2 VERSION = 'V2' - REVISION = '20171214' + REVISION = '20180114' # View and manage your Google Play Developer account AUTH_ANDROIDPUBLISHER = 'https://www.googleapis.com/auth/androidpublisher' diff --git a/generated/google/apis/androidpublisher_v2/classes.rb b/generated/google/apis/androidpublisher_v2/classes.rb index f5f9de4e1..fa1ab5f25 100644 --- a/generated/google/apis/androidpublisher_v2/classes.rb +++ b/generated/google/apis/androidpublisher_v2/classes.rb @@ -1595,7 +1595,7 @@ module Google class Track include Google::Apis::Core::Hashable - # + # Identifier for this track. One of "alpha", "beta", "production" or "rollout". # Corresponds to the JSON property `track` # @return [String] attr_accessor :track diff --git a/generated/google/apis/androidpublisher_v2/service.rb b/generated/google/apis/androidpublisher_v2/service.rb index c02ddc373..8d5c8ee03 100644 --- a/generated/google/apis/androidpublisher_v2/service.rb +++ b/generated/google/apis/androidpublisher_v2/service.rb @@ -1495,6 +1495,8 @@ module Google # @param [String] edit_id # Unique identifier for this edit. # @param [String] track + # The track to read or modify. Acceptable values are: "alpha", "beta", " + # production" or "rollout". # @param [String] fields # Selector specifying which fields to include in a partial response. # @param [String] quota_user @@ -1536,6 +1538,8 @@ module Google # @param [String] edit_id # Unique identifier for this edit. # @param [String] track + # The track to read or modify. Acceptable values are: "alpha", "beta", " + # production" or "rollout". # @param [Google::Apis::AndroidpublisherV2::Testers] testers_object # @param [String] fields # Selector specifying which fields to include in a partial response. @@ -1580,6 +1584,8 @@ module Google # @param [String] edit_id # Unique identifier for this edit. # @param [String] track + # The track to read or modify. Acceptable values are: "alpha", "beta", " + # production" or "rollout". # @param [Google::Apis::AndroidpublisherV2::Testers] testers_object # @param [String] fields # Selector specifying which fields to include in a partial response. @@ -1625,7 +1631,8 @@ module Google # @param [String] edit_id # Unique identifier for this edit. # @param [String] track - # The track type to read or modify. + # The track to read or modify. Acceptable values are: "alpha", "beta", " + # production" or "rollout". # @param [String] fields # Selector specifying which fields to include in a partial response. # @param [String] quota_user @@ -1708,7 +1715,8 @@ module Google # @param [String] edit_id # Unique identifier for this edit. # @param [String] track - # The track type to read or modify. + # The track to read or modify. Acceptable values are: "alpha", "beta", " + # production" or "rollout". # @param [Google::Apis::AndroidpublisherV2::Track] track_object # @param [String] fields # Selector specifying which fields to include in a partial response. @@ -1755,7 +1763,8 @@ module Google # @param [String] edit_id # Unique identifier for this edit. # @param [String] track - # The track type to read or modify. + # The track to read or modify. Acceptable values are: "alpha", "beta", " + # production" or "rollout". # @param [Google::Apis::AndroidpublisherV2::Track] track_object # @param [String] fields # Selector specifying which fields to include in a partial response. diff --git a/generated/google/apis/genomics_v1.rb b/generated/google/apis/genomics_v1.rb index a2e025b17..16cab7c9f 100644 --- a/generated/google/apis/genomics_v1.rb +++ b/generated/google/apis/genomics_v1.rb @@ -25,22 +25,13 @@ module Google # @see https://cloud.google.com/genomics module GenomicsV1 VERSION = 'V1' - REVISION = '20170916' - - # View and manage your data in Google BigQuery - AUTH_BIGQUERY = 'https://www.googleapis.com/auth/bigquery' + REVISION = '20180114' # View and manage your data across Google Cloud Platform services AUTH_CLOUD_PLATFORM = 'https://www.googleapis.com/auth/cloud-platform' - # Manage your data in Google Cloud Storage - AUTH_DEVSTORAGE_READ_WRITE = 'https://www.googleapis.com/auth/devstorage.read_write' - # View and manage Genomics data AUTH_GENOMICS = 'https://www.googleapis.com/auth/genomics' - - # View Genomics data - AUTH_GENOMICS_READONLY = 'https://www.googleapis.com/auth/genomics.readonly' end end end diff --git a/generated/google/apis/genomics_v1/classes.rb b/generated/google/apis/genomics_v1/classes.rb index 32bb07a9e..f93a6c184 100644 --- a/generated/google/apis/genomics_v1/classes.rb +++ b/generated/google/apis/genomics_v1/classes.rb @@ -22,316 +22,6 @@ module Google module Apis module GenomicsV1 - # An annotation describes a region of reference genome. The value of an - # annotation may be one of several canonical types, supplemented by arbitrary - # info tags. An annotation is not inherently associated with a specific - # sample or individual (though a client could choose to use annotations in - # this way). Example canonical annotation types are `GENE` and - # `VARIANT`. - class Annotation - include Google::Apis::Core::Hashable - - # The annotation set to which this annotation belongs. - # Corresponds to the JSON property `annotationSetId` - # @return [String] - attr_accessor :annotation_set_id - - # The end position of the range on the reference, 0-based exclusive. - # Corresponds to the JSON property `end` - # @return [Fixnum] - attr_accessor :end - - # The server-generated annotation ID, unique across all annotations. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # A map of additional read alignment information. This must be of the form - # map (string key mapping to a list of string values). - # Corresponds to the JSON property `info` - # @return [Hash>] - attr_accessor :info - - # The display name of this annotation. - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # The ID of the Google Genomics reference associated with this range. - # Corresponds to the JSON property `referenceId` - # @return [String] - attr_accessor :reference_id - - # The display name corresponding to the reference specified by - # `referenceId`, for example `chr1`, `1`, or `chrX`. - # Corresponds to the JSON property `referenceName` - # @return [String] - attr_accessor :reference_name - - # Whether this range refers to the reverse strand, as opposed to the forward - # strand. Note that regardless of this field, the start/end position of the - # range always refer to the forward strand. - # Corresponds to the JSON property `reverseStrand` - # @return [Boolean] - attr_accessor :reverse_strand - alias_method :reverse_strand?, :reverse_strand - - # The start position of the range on the reference, 0-based inclusive. - # Corresponds to the JSON property `start` - # @return [Fixnum] - attr_accessor :start - - # A transcript represents the assertion that a particular region of the - # reference genome may be transcribed as RNA. - # Corresponds to the JSON property `transcript` - # @return [Google::Apis::GenomicsV1::Transcript] - attr_accessor :transcript - - # The data type for this annotation. Must match the containing annotation - # set's type. - # Corresponds to the JSON property `type` - # @return [String] - attr_accessor :type - - # A variant annotation, which describes the effect of a variant on the - # genome, the coding sequence, and/or higher level consequences at the - # organism level e.g. pathogenicity. This field is only set for annotations - # of type `VARIANT`. - # Corresponds to the JSON property `variant` - # @return [Google::Apis::GenomicsV1::VariantAnnotation] - attr_accessor :variant - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @annotation_set_id = args[:annotation_set_id] if args.key?(:annotation_set_id) - @end = args[:end] if args.key?(:end) - @id = args[:id] if args.key?(:id) - @info = args[:info] if args.key?(:info) - @name = args[:name] if args.key?(:name) - @reference_id = args[:reference_id] if args.key?(:reference_id) - @reference_name = args[:reference_name] if args.key?(:reference_name) - @reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand) - @start = args[:start] if args.key?(:start) - @transcript = args[:transcript] if args.key?(:transcript) - @type = args[:type] if args.key?(:type) - @variant = args[:variant] if args.key?(:variant) - end - end - - # An annotation set is a logical grouping of annotations that share consistent - # type information and provenance. Examples of annotation sets include 'all - # genes from refseq', and 'all variant annotations from ClinVar'. - class AnnotationSet - include Google::Apis::Core::Hashable - - # The dataset to which this annotation set belongs. - # Corresponds to the JSON property `datasetId` - # @return [String] - attr_accessor :dataset_id - - # The server-generated annotation set ID, unique across all annotation sets. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # A map of additional read alignment information. This must be of the form - # map (string key mapping to a list of string values). - # Corresponds to the JSON property `info` - # @return [Hash>] - attr_accessor :info - - # The display name for this annotation set. - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # The ID of the reference set that defines the coordinate space for this - # set's annotations. - # Corresponds to the JSON property `referenceSetId` - # @return [String] - attr_accessor :reference_set_id - - # The source URI describing the file from which this annotation set was - # generated, if any. - # Corresponds to the JSON property `sourceUri` - # @return [String] - attr_accessor :source_uri - - # The type of annotations contained within this set. - # Corresponds to the JSON property `type` - # @return [String] - attr_accessor :type - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @dataset_id = args[:dataset_id] if args.key?(:dataset_id) - @id = args[:id] if args.key?(:id) - @info = args[:info] if args.key?(:info) - @name = args[:name] if args.key?(:name) - @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id) - @source_uri = args[:source_uri] if args.key?(:source_uri) - @type = args[:type] if args.key?(:type) - end - end - - # - class BatchCreateAnnotationsRequest - include Google::Apis::Core::Hashable - - # The annotations to be created. At most 4096 can be specified in a single - # request. - # Corresponds to the JSON property `annotations` - # @return [Array] - attr_accessor :annotations - - # A unique request ID which enables the server to detect duplicated requests. - # If provided, duplicated requests will result in the same response; if not - # provided, duplicated requests may result in duplicated data. For a given - # annotation set, callers should not reuse `request_id`s when writing - # different batches of annotations - behavior in this case is undefined. - # A common approach is to use a UUID. For batch jobs where worker crashes are - # a possibility, consider using some unique variant of a worker or run ID. - # Corresponds to the JSON property `requestId` - # @return [String] - attr_accessor :request_id - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @annotations = args[:annotations] if args.key?(:annotations) - @request_id = args[:request_id] if args.key?(:request_id) - end - end - - # - class BatchCreateAnnotationsResponse - include Google::Apis::Core::Hashable - - # The resulting per-annotation entries, ordered consistently with the - # original request. - # Corresponds to the JSON property `entries` - # @return [Array] - attr_accessor :entries - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @entries = args[:entries] if args.key?(:entries) - end - end - - # Associates `members` with a `role`. - class Binding - include Google::Apis::Core::Hashable - - # Specifies the identities requesting access for a Cloud Platform resource. - # `members` can have the following values: - # * `allUsers`: A special identifier that represents anyone who is - # on the internet; with or without a Google account. - # * `allAuthenticatedUsers`: A special identifier that represents anyone - # who is authenticated with a Google account or a service account. - # * `user:`emailid``: An email address that represents a specific Google - # account. For example, `alice@gmail.com` or `joe@example.com`. - # * `serviceAccount:`emailid``: An email address that represents a service - # account. For example, `my-other-app@appspot.gserviceaccount.com`. - # * `group:`emailid``: An email address that represents a Google group. - # For example, `admins@example.com`. - # * `domain:`domain``: A Google Apps domain name that represents all the - # users of that domain. For example, `google.com` or `example.com`. - # Corresponds to the JSON property `members` - # @return [Array] - attr_accessor :members - - # Role that is assigned to `members`. - # For example, `roles/viewer`, `roles/editor`, or `roles/owner`. - # Required - # Corresponds to the JSON property `role` - # @return [String] - attr_accessor :role - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @members = args[:members] if args.key?(:members) - @role = args[:role] if args.key?(:role) - end - end - - # A call set is a collection of variant calls, typically for one sample. It - # belongs to a variant set. - # For more genomics resource definitions, see [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - class CallSet - include Google::Apis::Core::Hashable - - # The date this call set was created in milliseconds from the epoch. - # Corresponds to the JSON property `created` - # @return [Fixnum] - attr_accessor :created - - # The server-generated call set ID, unique across all call sets. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # A map of additional call set information. This must be of the form - # map (string key mapping to a list of string values). - # Corresponds to the JSON property `info` - # @return [Hash>] - attr_accessor :info - - # The call set name. - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # The sample ID this call set corresponds to. - # Corresponds to the JSON property `sampleId` - # @return [String] - attr_accessor :sample_id - - # The IDs of the variant sets this call set belongs to. This field must - # have exactly length one, as a call set belongs to a single variant set. - # This field is repeated for compatibility with the - # [GA4GH 0.5.1 - # API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/ - # variants.avdl#L76). - # Corresponds to the JSON property `variantSetIds` - # @return [Array] - attr_accessor :variant_set_ids - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @created = args[:created] if args.key?(:created) - @id = args[:id] if args.key?(:id) - @info = args[:info] if args.key?(:info) - @name = args[:name] if args.key?(:name) - @sample_id = args[:sample_id] if args.key?(:sample_id) - @variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids) - end - end - # The request message for Operations.CancelOperation. class CancelOperationRequest include Google::Apis::Core::Hashable @@ -345,108 +35,6 @@ module Google end end - # A single CIGAR operation. - class CigarUnit - include Google::Apis::Core::Hashable - - # - # Corresponds to the JSON property `operation` - # @return [String] - attr_accessor :operation - - # The number of genomic bases that the operation runs for. Required. - # Corresponds to the JSON property `operationLength` - # @return [Fixnum] - attr_accessor :operation_length - - # `referenceSequence` is only used at mismatches - # (`SEQUENCE_MISMATCH`) and deletions (`DELETE`). - # Filling this field replaces SAM's MD tag. If the relevant information is - # not available, this field is unset. - # Corresponds to the JSON property `referenceSequence` - # @return [String] - attr_accessor :reference_sequence - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @operation = args[:operation] if args.key?(:operation) - @operation_length = args[:operation_length] if args.key?(:operation_length) - @reference_sequence = args[:reference_sequence] if args.key?(:reference_sequence) - end - end - - # - class ClinicalCondition - include Google::Apis::Core::Hashable - - # The MedGen concept id associated with this gene. - # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ - # Corresponds to the JSON property `conceptId` - # @return [String] - attr_accessor :concept_id - - # The set of external IDs for this condition. - # Corresponds to the JSON property `externalIds` - # @return [Array] - attr_accessor :external_ids - - # A set of names for the condition. - # Corresponds to the JSON property `names` - # @return [Array] - attr_accessor :names - - # The OMIM id for this condition. - # Search for these IDs at http://omim.org/ - # Corresponds to the JSON property `omimId` - # @return [String] - attr_accessor :omim_id - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @concept_id = args[:concept_id] if args.key?(:concept_id) - @external_ids = args[:external_ids] if args.key?(:external_ids) - @names = args[:names] if args.key?(:names) - @omim_id = args[:omim_id] if args.key?(:omim_id) - end - end - - # - class CodingSequence - include Google::Apis::Core::Hashable - - # The end of the coding sequence on this annotation's reference sequence, - # 0-based exclusive. Note that this position is relative to the reference - # start, and *not* the containing annotation start. - # Corresponds to the JSON property `end` - # @return [Fixnum] - attr_accessor :end - - # The start of the coding sequence on this annotation's reference sequence, - # 0-based inclusive. Note that this position is relative to the reference - # start, and *not* the containing annotation start. - # Corresponds to the JSON property `start` - # @return [Fixnum] - attr_accessor :start - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @end = args[:end] if args.key?(:end) - @start = args[:start] if args.key?(:start) - end - end - # Describes a Compute Engine resource that is being managed by a running # pipeline. class ComputeEngine @@ -485,72 +73,6 @@ module Google end end - # A bucket over which read coverage has been precomputed. A bucket corresponds - # to a specific range of the reference sequence. - class CoverageBucket - include Google::Apis::Core::Hashable - - # The average number of reads which are aligned to each individual - # reference base in this bucket. - # Corresponds to the JSON property `meanCoverage` - # @return [Float] - attr_accessor :mean_coverage - - # A 0-based half-open genomic coordinate range for search requests. - # Corresponds to the JSON property `range` - # @return [Google::Apis::GenomicsV1::Range] - attr_accessor :range - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @mean_coverage = args[:mean_coverage] if args.key?(:mean_coverage) - @range = args[:range] if args.key?(:range) - end - end - - # A Dataset is a collection of genomic data. - # For more genomics resource definitions, see [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - class Dataset - include Google::Apis::Core::Hashable - - # The time this dataset was created, in seconds from the epoch. - # Corresponds to the JSON property `createTime` - # @return [String] - attr_accessor :create_time - - # The server-generated dataset ID, unique across all datasets. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # The dataset name. - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # The Google Cloud project ID that this dataset belongs to. - # Corresponds to the JSON property `projectId` - # @return [String] - attr_accessor :project_id - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @create_time = args[:create_time] if args.key?(:create_time) - @id = args[:id] if args.key?(:id) - @name = args[:name] if args.key?(:name) - @project_id = args[:project_id] if args.key?(:project_id) - end - end - # A generic empty message that you can re-use to avoid defining duplicated # empty messages in your APIs. A typical example is to use it as the request # or the response type of an API method. For instance: @@ -570,571 +92,6 @@ module Google end end - # - class Entry - include Google::Apis::Core::Hashable - - # An annotation describes a region of reference genome. The value of an - # annotation may be one of several canonical types, supplemented by arbitrary - # info tags. An annotation is not inherently associated with a specific - # sample or individual (though a client could choose to use annotations in - # this way). Example canonical annotation types are `GENE` and - # `VARIANT`. - # Corresponds to the JSON property `annotation` - # @return [Google::Apis::GenomicsV1::Annotation] - attr_accessor :annotation - - # 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. - # Corresponds to the JSON property `status` - # @return [Google::Apis::GenomicsV1::Status] - attr_accessor :status - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @annotation = args[:annotation] if args.key?(:annotation) - @status = args[:status] if args.key?(:status) - end - end - - # - class Exon - include Google::Apis::Core::Hashable - - # The end position of the exon on this annotation's reference sequence, - # 0-based exclusive. Note that this is relative to the reference start, and - # *not* the containing annotation start. - # Corresponds to the JSON property `end` - # @return [Fixnum] - attr_accessor :end - - # The frame of this exon. Contains a value of 0, 1, or 2, which indicates - # the offset of the first coding base of the exon within the reading frame - # of the coding DNA sequence, if any. This field is dependent on the - # strandedness of this annotation (see - # Annotation.reverse_strand). - # For forward stranded annotations, this offset is relative to the - # exon.start. For reverse - # strand annotations, this offset is relative to the - # exon.end `- 1`. - # Unset if this exon does not intersect the coding sequence. Upon creation - # of a transcript, the frame must be populated for all or none of the - # coding exons. - # Corresponds to the JSON property `frame` - # @return [Fixnum] - attr_accessor :frame - - # The start position of the exon on this annotation's reference sequence, - # 0-based inclusive. Note that this is relative to the reference start, and - # **not** the containing annotation start. - # Corresponds to the JSON property `start` - # @return [Fixnum] - attr_accessor :start - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @end = args[:end] if args.key?(:end) - @frame = args[:frame] if args.key?(:frame) - @start = args[:start] if args.key?(:start) - end - end - - # - class Experiment - include Google::Apis::Core::Hashable - - # The instrument model used as part of this experiment. This maps to - # sequencing technology in the SAM spec. - # Corresponds to the JSON property `instrumentModel` - # @return [String] - attr_accessor :instrument_model - - # A client-supplied library identifier; a library is a collection of DNA - # fragments which have been prepared for sequencing from a sample. This - # field is important for quality control as error or bias can be introduced - # during sample preparation. - # Corresponds to the JSON property `libraryId` - # @return [String] - attr_accessor :library_id - - # The platform unit used as part of this experiment, for example - # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the - # @RG PU field in the SAM spec. - # Corresponds to the JSON property `platformUnit` - # @return [String] - attr_accessor :platform_unit - - # The sequencing center used as part of this experiment. - # Corresponds to the JSON property `sequencingCenter` - # @return [String] - attr_accessor :sequencing_center - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @instrument_model = args[:instrument_model] if args.key?(:instrument_model) - @library_id = args[:library_id] if args.key?(:library_id) - @platform_unit = args[:platform_unit] if args.key?(:platform_unit) - @sequencing_center = args[:sequencing_center] if args.key?(:sequencing_center) - end - end - - # The read group set export request. - class ExportReadGroupSetRequest - include Google::Apis::Core::Hashable - - # Required. A Google Cloud Storage URI for the exported BAM file. - # The currently authenticated user must have write access to the new file. - # An error will be returned if the URI already contains data. - # Corresponds to the JSON property `exportUri` - # @return [String] - attr_accessor :export_uri - - # Required. The Google Cloud project ID that owns this - # export. The caller must have WRITE access to this project. - # Corresponds to the JSON property `projectId` - # @return [String] - attr_accessor :project_id - - # The reference names to export. If this is not specified, all reference - # sequences, including unmapped reads, are exported. - # Use `*` to export only unmapped reads. - # Corresponds to the JSON property `referenceNames` - # @return [Array] - attr_accessor :reference_names - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @export_uri = args[:export_uri] if args.key?(:export_uri) - @project_id = args[:project_id] if args.key?(:project_id) - @reference_names = args[:reference_names] if args.key?(:reference_names) - end - end - - # The variant data export request. - class ExportVariantSetRequest - include Google::Apis::Core::Hashable - - # Required. The BigQuery dataset to export data to. This dataset must already - # exist. Note that this is distinct from the Genomics concept of "dataset". - # Corresponds to the JSON property `bigqueryDataset` - # @return [String] - attr_accessor :bigquery_dataset - - # Required. The BigQuery table to export data to. - # If the table doesn't exist, it will be created. If it already exists, it - # will be overwritten. - # Corresponds to the JSON property `bigqueryTable` - # @return [String] - attr_accessor :bigquery_table - - # If provided, only variant call information from the specified call sets - # will be exported. By default all variant calls are exported. - # Corresponds to the JSON property `callSetIds` - # @return [Array] - attr_accessor :call_set_ids - - # The format for the exported data. - # Corresponds to the JSON property `format` - # @return [String] - attr_accessor :format - - # Required. The Google Cloud project ID that owns the destination - # BigQuery dataset. The caller must have WRITE access to this project. This - # project will also own the resulting export job. - # Corresponds to the JSON property `projectId` - # @return [String] - attr_accessor :project_id - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @bigquery_dataset = args[:bigquery_dataset] if args.key?(:bigquery_dataset) - @bigquery_table = args[:bigquery_table] if args.key?(:bigquery_table) - @call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids) - @format = args[:format] if args.key?(:format) - @project_id = args[:project_id] if args.key?(:project_id) - end - end - - # - class ExternalId - include Google::Apis::Core::Hashable - - # The id used by the source of this data. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # The name of the source of this data. - # Corresponds to the JSON property `sourceName` - # @return [String] - attr_accessor :source_name - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @id = args[:id] if args.key?(:id) - @source_name = args[:source_name] if args.key?(:source_name) - end - end - - # Request message for `GetIamPolicy` method. - class GetIamPolicyRequest - include Google::Apis::Core::Hashable - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - end - end - - # The read group set import request. - class ImportReadGroupSetsRequest - include Google::Apis::Core::Hashable - - # Required. The ID of the dataset these read group sets will belong to. The - # caller must have WRITE permissions to this dataset. - # Corresponds to the JSON property `datasetId` - # @return [String] - attr_accessor :dataset_id - - # The partition strategy describes how read groups are partitioned into read - # group sets. - # Corresponds to the JSON property `partitionStrategy` - # @return [String] - attr_accessor :partition_strategy - - # The reference set to which the imported read group sets are aligned to, if - # any. The reference names of this reference set must be a superset of those - # found in the imported file headers. If no reference set id is provided, a - # best effort is made to associate with a matching reference set. - # Corresponds to the JSON property `referenceSetId` - # @return [String] - attr_accessor :reference_set_id - - # A list of URIs pointing at [BAM - # files](https://samtools.github.io/hts-specs/SAMv1.pdf) - # in Google Cloud Storage. - # Those URIs can include wildcards (*), but do not add or remove - # matching files before import has completed. - # Note that Google Cloud Storage object listing is only eventually - # consistent: files added may be not be immediately visible to - # everyone. Thus, if using a wildcard it is preferable not to start - # the import immediately after the files are created. - # Corresponds to the JSON property `sourceUris` - # @return [Array] - attr_accessor :source_uris - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @dataset_id = args[:dataset_id] if args.key?(:dataset_id) - @partition_strategy = args[:partition_strategy] if args.key?(:partition_strategy) - @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id) - @source_uris = args[:source_uris] if args.key?(:source_uris) - end - end - - # The read group set import response. - class ImportReadGroupSetsResponse - include Google::Apis::Core::Hashable - - # IDs of the read group sets that were created. - # Corresponds to the JSON property `readGroupSetIds` - # @return [Array] - attr_accessor :read_group_set_ids - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids) - end - end - - # The variant data import request. - class ImportVariantsRequest - include Google::Apis::Core::Hashable - - # The format of the variant data being imported. If unspecified, defaults to - # to `VCF`. - # Corresponds to the JSON property `format` - # @return [String] - attr_accessor :format - - # A mapping between info field keys and the InfoMergeOperations to - # be performed on them. This is plumbed down to the MergeVariantRequests - # generated by the resulting import job. - # Corresponds to the JSON property `infoMergeConfig` - # @return [Hash] - attr_accessor :info_merge_config - - # Convert reference names to the canonical representation. - # hg19 haploytypes (those reference names containing "_hap") - # are not modified in any way. - # All other reference names are modified according to the following rules: - # The reference name is capitalized. - # The "chr" prefix is dropped for all autosomes and sex chromsomes. - # For example "chr17" becomes "17" and "chrX" becomes "X". - # All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT". - # Corresponds to the JSON property `normalizeReferenceNames` - # @return [Boolean] - attr_accessor :normalize_reference_names - alias_method :normalize_reference_names?, :normalize_reference_names - - # A list of URIs referencing variant files in Google Cloud Storage. URIs can - # include wildcards [as described - # here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames). - # Note that recursive wildcards ('**') are not supported. - # Corresponds to the JSON property `sourceUris` - # @return [Array] - attr_accessor :source_uris - - # Required. The variant set to which variant data should be imported. - # Corresponds to the JSON property `variantSetId` - # @return [String] - attr_accessor :variant_set_id - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @format = args[:format] if args.key?(:format) - @info_merge_config = args[:info_merge_config] if args.key?(:info_merge_config) - @normalize_reference_names = args[:normalize_reference_names] if args.key?(:normalize_reference_names) - @source_uris = args[:source_uris] if args.key?(:source_uris) - @variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id) - end - end - - # The variant data import response. - class ImportVariantsResponse - include Google::Apis::Core::Hashable - - # IDs of the call sets created during the import. - # Corresponds to the JSON property `callSetIds` - # @return [Array] - attr_accessor :call_set_ids - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids) - end - end - - # A linear alignment can be represented by one CIGAR string. Describes the - # mapped position and local alignment of the read to the reference. - class LinearAlignment - include Google::Apis::Core::Hashable - - # Represents the local alignment of this sequence (alignment matches, indels, - # etc) against the reference. - # Corresponds to the JSON property `cigar` - # @return [Array] - attr_accessor :cigar - - # The mapping quality of this alignment. Represents how likely - # the read maps to this position as opposed to other locations. - # Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to - # the nearest integer. - # Corresponds to the JSON property `mappingQuality` - # @return [Fixnum] - attr_accessor :mapping_quality - - # An abstraction for referring to a genomic position, in relation to some - # already known reference. For now, represents a genomic position as a - # reference name, a base number on that reference (0-based), and a - # determination of forward or reverse strand. - # Corresponds to the JSON property `position` - # @return [Google::Apis::GenomicsV1::Position] - attr_accessor :position - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @cigar = args[:cigar] if args.key?(:cigar) - @mapping_quality = args[:mapping_quality] if args.key?(:mapping_quality) - @position = args[:position] if args.key?(:position) - end - end - - # - class ListBasesResponse - include Google::Apis::Core::Hashable - - # The continuation token, which is used to page through large result sets. - # Provide this value in a subsequent request to return the next page of - # results. This field will be empty if there aren't any additional results. - # Corresponds to the JSON property `nextPageToken` - # @return [String] - attr_accessor :next_page_token - - # The offset position (0-based) of the given `sequence` from the - # start of this `Reference`. This value will differ for each page - # in a paginated request. - # Corresponds to the JSON property `offset` - # @return [Fixnum] - attr_accessor :offset - - # A substring of the bases that make up this reference. - # Corresponds to the JSON property `sequence` - # @return [String] - attr_accessor :sequence - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @next_page_token = args[:next_page_token] if args.key?(:next_page_token) - @offset = args[:offset] if args.key?(:offset) - @sequence = args[:sequence] if args.key?(:sequence) - end - end - - # - class ListCoverageBucketsResponse - include Google::Apis::Core::Hashable - - # The length of each coverage bucket in base pairs. Note that buckets at the - # end of a reference sequence may be shorter. This value is omitted if the - # bucket width is infinity (the default behaviour, with no range or - # `targetBucketWidth`). - # Corresponds to the JSON property `bucketWidth` - # @return [Fixnum] - attr_accessor :bucket_width - - # The coverage buckets. The list of buckets is sparse; a bucket with 0 - # overlapping reads is not returned. A bucket never crosses more than one - # reference sequence. Each bucket has width `bucketWidth`, unless - # its end is the end of the reference sequence. - # Corresponds to the JSON property `coverageBuckets` - # @return [Array] - attr_accessor :coverage_buckets - - # The continuation token, which is used to page through large result sets. - # Provide this value in a subsequent request to return the next page of - # results. This field will be empty if there aren't any additional results. - # Corresponds to the JSON property `nextPageToken` - # @return [String] - attr_accessor :next_page_token - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @bucket_width = args[:bucket_width] if args.key?(:bucket_width) - @coverage_buckets = args[:coverage_buckets] if args.key?(:coverage_buckets) - @next_page_token = args[:next_page_token] if args.key?(:next_page_token) - end - end - - # The dataset list response. - class ListDatasetsResponse - include Google::Apis::Core::Hashable - - # The list of matching Datasets. - # Corresponds to the JSON property `datasets` - # @return [Array] - attr_accessor :datasets - - # The continuation token, which is used to page through large result sets. - # Provide this value in a subsequent request to return the next page of - # results. This field will be empty if there aren't any additional results. - # Corresponds to the JSON property `nextPageToken` - # @return [String] - attr_accessor :next_page_token - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @datasets = args[:datasets] if args.key?(:datasets) - @next_page_token = args[:next_page_token] if args.key?(:next_page_token) - end - end - # The response message for Operations.ListOperations. class ListOperationsResponse include Google::Apis::Core::Hashable @@ -1160,38 +117,6 @@ module Google end end - # - class MergeVariantsRequest - include Google::Apis::Core::Hashable - - # A mapping between info field keys and the InfoMergeOperations to - # be performed on them. - # Corresponds to the JSON property `infoMergeConfig` - # @return [Hash] - attr_accessor :info_merge_config - - # The destination variant set. - # Corresponds to the JSON property `variantSetId` - # @return [String] - attr_accessor :variant_set_id - - # The variants to be merged with existing variants. - # Corresponds to the JSON property `variants` - # @return [Array] - attr_accessor :variants - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @info_merge_config = args[:info_merge_config] if args.key?(:info_merge_config) - @variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id) - @variants = args[:variants] if args.key?(:variants) - end - end - # This resource represents a long-running operation that is the result of a # network API call. class Operation @@ -1386,729 +311,6 @@ module Google end end - # Defines an Identity and Access Management (IAM) policy. It is used to - # specify access control policies for Cloud Platform resources. - # A `Policy` consists of a list of `bindings`. A `Binding` binds a list of - # `members` to a `role`, where the members can be user accounts, Google groups, - # Google domains, and service accounts. A `role` is a named list of permissions - # defined by IAM. - # **Example** - # ` - # "bindings": [ - # ` - # "role": "roles/owner", - # "members": [ - # "user:mike@example.com", - # "group:admins@example.com", - # "domain:google.com", - # "serviceAccount:my-other-app@appspot.gserviceaccount.com", - # ] - # `, - # ` - # "role": "roles/viewer", - # "members": ["user:sean@example.com"] - # ` - # ] - # ` - # For a description of IAM and its features, see the - # [IAM developer's guide](https://cloud.google.com/iam). - class Policy - include Google::Apis::Core::Hashable - - # Associates a list of `members` to a `role`. - # `bindings` with no members will result in an error. - # Corresponds to the JSON property `bindings` - # @return [Array] - attr_accessor :bindings - - # `etag` is used for optimistic concurrency control as a way to help - # prevent simultaneous updates of a policy from overwriting each other. - # It is strongly suggested that systems make use of the `etag` in the - # read-modify-write cycle to perform policy updates in order to avoid race - # conditions: An `etag` is returned in the response to `getIamPolicy`, and - # systems are expected to put that etag in the request to `setIamPolicy` to - # ensure that their change will be applied to the same version of the policy. - # If no `etag` is provided in the call to `setIamPolicy`, then the existing - # policy is overwritten blindly. - # Corresponds to the JSON property `etag` - # NOTE: Values are automatically base64 encoded/decoded in the client library. - # @return [String] - attr_accessor :etag - - # Version of the `Policy`. The default version is 0. - # Corresponds to the JSON property `version` - # @return [Fixnum] - attr_accessor :version - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @bindings = args[:bindings] if args.key?(:bindings) - @etag = args[:etag] if args.key?(:etag) - @version = args[:version] if args.key?(:version) - end - end - - # An abstraction for referring to a genomic position, in relation to some - # already known reference. For now, represents a genomic position as a - # reference name, a base number on that reference (0-based), and a - # determination of forward or reverse strand. - class Position - include Google::Apis::Core::Hashable - - # The 0-based offset from the start of the forward strand for that reference. - # Corresponds to the JSON property `position` - # @return [Fixnum] - attr_accessor :position - - # The name of the reference in whatever reference set is being used. - # Corresponds to the JSON property `referenceName` - # @return [String] - attr_accessor :reference_name - - # Whether this position is on the reverse strand, as opposed to the forward - # strand. - # Corresponds to the JSON property `reverseStrand` - # @return [Boolean] - attr_accessor :reverse_strand - alias_method :reverse_strand?, :reverse_strand - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @position = args[:position] if args.key?(:position) - @reference_name = args[:reference_name] if args.key?(:reference_name) - @reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand) - end - end - - # - class Program - include Google::Apis::Core::Hashable - - # The command line used to run this program. - # Corresponds to the JSON property `commandLine` - # @return [String] - attr_accessor :command_line - - # The user specified locally unique ID of the program. Used along with - # `prevProgramId` to define an ordering between programs. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # The display name of the program. This is typically the colloquial name of - # the tool used, for example 'bwa' or 'picard'. - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # The ID of the program run before this one. - # Corresponds to the JSON property `prevProgramId` - # @return [String] - attr_accessor :prev_program_id - - # The version of the program run. - # Corresponds to the JSON property `version` - # @return [String] - attr_accessor :version - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @command_line = args[:command_line] if args.key?(:command_line) - @id = args[:id] if args.key?(:id) - @name = args[:name] if args.key?(:name) - @prev_program_id = args[:prev_program_id] if args.key?(:prev_program_id) - @version = args[:version] if args.key?(:version) - end - end - - # A 0-based half-open genomic coordinate range for search requests. - class Range - include Google::Apis::Core::Hashable - - # The end position of the range on the reference, 0-based exclusive. - # Corresponds to the JSON property `end` - # @return [Fixnum] - attr_accessor :end - - # The reference sequence name, for example `chr1`, - # `1`, or `chrX`. - # Corresponds to the JSON property `referenceName` - # @return [String] - attr_accessor :reference_name - - # The start position of the range on the reference, 0-based inclusive. - # Corresponds to the JSON property `start` - # @return [Fixnum] - attr_accessor :start - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @end = args[:end] if args.key?(:end) - @reference_name = args[:reference_name] if args.key?(:reference_name) - @start = args[:start] if args.key?(:start) - end - end - - # A read alignment describes a linear alignment of a string of DNA to a - # reference sequence, in addition to metadata - # about the fragment (the molecule of DNA sequenced) and the read (the bases - # which were read by the sequencer). A read is equivalent to a line in a SAM - # file. A read belongs to exactly one read group and exactly one - # read group set. - # For more genomics resource definitions, see [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # ### Reverse-stranded reads - # Mapped reads (reads having a non-null `alignment`) can be aligned to either - # the forward or the reverse strand of their associated reference. Strandedness - # of a mapped read is encoded by `alignment.position.reverseStrand`. - # If we consider the reference to be a forward-stranded coordinate space of - # `[0, reference.length)` with `0` as the left-most position and - # `reference.length` as the right-most position, reads are always aligned left - # to right. That is, `alignment.position.position` always refers to the - # left-most reference coordinate and `alignment.cigar` describes the alignment - # of this read to the reference from left to right. All per-base fields such as - # `alignedSequence` and `alignedQuality` share this same left-to-right - # orientation; this is true of reads which are aligned to either strand. For - # reverse-stranded reads, this means that `alignedSequence` is the reverse - # complement of the bases that were originally reported by the sequencing - # machine. - # ### Generating a reference-aligned sequence string - # When interacting with mapped reads, it's often useful to produce a string - # representing the local alignment of the read to reference. The following - # pseudocode demonstrates one way of doing this: - # out = "" - # offset = 0 - # for c in read.alignment.cigar ` - # switch c.operation ` - # case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": - # out += read.alignedSequence[offset:offset+c.operationLength] - # offset += c.operationLength - # break - # case "CLIP_SOFT", "INSERT": - # offset += c.operationLength - # break - # case "PAD": - # out += repeat("*", c.operationLength) - # break - # case "DELETE": - # out += repeat("-", c.operationLength) - # break - # case "SKIP": - # out += repeat(" ", c.operationLength) - # break - # case "CLIP_HARD": - # break - # ` - # ` - # return out - # ### Converting to SAM's CIGAR string - # The following pseudocode generates a SAM CIGAR string from the - # `cigar` field. Note that this is a lossy conversion - # (`cigar.referenceSequence` is lost). - # cigarMap = ` - # "ALIGNMENT_MATCH": "M", - # "INSERT": "I", - # "DELETE": "D", - # "SKIP": "N", - # "CLIP_SOFT": "S", - # "CLIP_HARD": "H", - # "PAD": "P", - # "SEQUENCE_MATCH": "=", - # "SEQUENCE_MISMATCH": "X", - # ` - # cigarStr = "" - # for c in read.alignment.cigar ` - # cigarStr += c.operationLength + cigarMap[c.operation] - # ` - # return cigarStr - class Read - include Google::Apis::Core::Hashable - - # The quality of the read sequence contained in this alignment record - # (equivalent to QUAL in SAM). - # `alignedSequence` and `alignedQuality` may be shorter than the full read - # sequence and quality. This will occur if the alignment is part of a - # chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR - # for this read will begin/end with a hard clip operator that will indicate - # the length of the excised sequence. - # Corresponds to the JSON property `alignedQuality` - # @return [Array] - attr_accessor :aligned_quality - - # The bases of the read sequence contained in this alignment record, - # **without CIGAR operations applied** (equivalent to SEQ in SAM). - # `alignedSequence` and `alignedQuality` may be - # shorter than the full read sequence and quality. This will occur if the - # alignment is part of a chimeric alignment, or if the read was trimmed. When - # this occurs, the CIGAR for this read will begin/end with a hard clip - # operator that will indicate the length of the excised sequence. - # Corresponds to the JSON property `alignedSequence` - # @return [String] - attr_accessor :aligned_sequence - - # A linear alignment can be represented by one CIGAR string. Describes the - # mapped position and local alignment of the read to the reference. - # Corresponds to the JSON property `alignment` - # @return [Google::Apis::GenomicsV1::LinearAlignment] - attr_accessor :alignment - - # The fragment is a PCR or optical duplicate (SAM flag 0x400). - # Corresponds to the JSON property `duplicateFragment` - # @return [Boolean] - attr_accessor :duplicate_fragment - alias_method :duplicate_fragment?, :duplicate_fragment - - # Whether this read did not pass filters, such as platform or vendor quality - # controls (SAM flag 0x200). - # Corresponds to the JSON property `failedVendorQualityChecks` - # @return [Boolean] - attr_accessor :failed_vendor_quality_checks - alias_method :failed_vendor_quality_checks?, :failed_vendor_quality_checks - - # The observed length of the fragment, equivalent to TLEN in SAM. - # Corresponds to the JSON property `fragmentLength` - # @return [Fixnum] - attr_accessor :fragment_length - - # The fragment name. Equivalent to QNAME (query template name) in SAM. - # Corresponds to the JSON property `fragmentName` - # @return [String] - attr_accessor :fragment_name - - # The server-generated read ID, unique across all reads. This is different - # from the `fragmentName`. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # A map of additional read alignment information. This must be of the form - # map (string key mapping to a list of string values). - # Corresponds to the JSON property `info` - # @return [Hash>] - attr_accessor :info - - # An abstraction for referring to a genomic position, in relation to some - # already known reference. For now, represents a genomic position as a - # reference name, a base number on that reference (0-based), and a - # determination of forward or reverse strand. - # Corresponds to the JSON property `nextMatePosition` - # @return [Google::Apis::GenomicsV1::Position] - attr_accessor :next_mate_position - - # The number of reads in the fragment (extension to SAM flag 0x1). - # Corresponds to the JSON property `numberReads` - # @return [Fixnum] - attr_accessor :number_reads - - # The orientation and the distance between reads from the fragment are - # consistent with the sequencing protocol (SAM flag 0x2). - # Corresponds to the JSON property `properPlacement` - # @return [Boolean] - attr_accessor :proper_placement - alias_method :proper_placement?, :proper_placement - - # The ID of the read group this read belongs to. A read belongs to exactly - # one read group. This is a server-generated ID which is distinct from SAM's - # RG tag (for that value, see - # ReadGroup.name). - # Corresponds to the JSON property `readGroupId` - # @return [String] - attr_accessor :read_group_id - - # The ID of the read group set this read belongs to. A read belongs to - # exactly one read group set. - # Corresponds to the JSON property `readGroupSetId` - # @return [String] - attr_accessor :read_group_set_id - - # The read number in sequencing. 0-based and less than numberReads. This - # field replaces SAM flag 0x40 and 0x80. - # Corresponds to the JSON property `readNumber` - # @return [Fixnum] - attr_accessor :read_number - - # Whether this alignment is secondary. Equivalent to SAM flag 0x100. - # A secondary alignment represents an alternative to the primary alignment - # for this read. Aligners may return secondary alignments if a read can map - # ambiguously to multiple coordinates in the genome. By convention, each read - # has one and only one alignment where both `secondaryAlignment` - # and `supplementaryAlignment` are false. - # Corresponds to the JSON property `secondaryAlignment` - # @return [Boolean] - attr_accessor :secondary_alignment - alias_method :secondary_alignment?, :secondary_alignment - - # Whether this alignment is supplementary. Equivalent to SAM flag 0x800. - # Supplementary alignments are used in the representation of a chimeric - # alignment. In a chimeric alignment, a read is split into multiple - # linear alignments that map to different reference contigs. The first - # linear alignment in the read will be designated as the representative - # alignment; the remaining linear alignments will be designated as - # supplementary alignments. These alignments may have different mapping - # quality scores. In each linear alignment in a chimeric alignment, the read - # will be hard clipped. The `alignedSequence` and - # `alignedQuality` fields in the alignment record will only - # represent the bases for its respective linear alignment. - # Corresponds to the JSON property `supplementaryAlignment` - # @return [Boolean] - attr_accessor :supplementary_alignment - alias_method :supplementary_alignment?, :supplementary_alignment - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @aligned_quality = args[:aligned_quality] if args.key?(:aligned_quality) - @aligned_sequence = args[:aligned_sequence] if args.key?(:aligned_sequence) - @alignment = args[:alignment] if args.key?(:alignment) - @duplicate_fragment = args[:duplicate_fragment] if args.key?(:duplicate_fragment) - @failed_vendor_quality_checks = args[:failed_vendor_quality_checks] if args.key?(:failed_vendor_quality_checks) - @fragment_length = args[:fragment_length] if args.key?(:fragment_length) - @fragment_name = args[:fragment_name] if args.key?(:fragment_name) - @id = args[:id] if args.key?(:id) - @info = args[:info] if args.key?(:info) - @next_mate_position = args[:next_mate_position] if args.key?(:next_mate_position) - @number_reads = args[:number_reads] if args.key?(:number_reads) - @proper_placement = args[:proper_placement] if args.key?(:proper_placement) - @read_group_id = args[:read_group_id] if args.key?(:read_group_id) - @read_group_set_id = args[:read_group_set_id] if args.key?(:read_group_set_id) - @read_number = args[:read_number] if args.key?(:read_number) - @secondary_alignment = args[:secondary_alignment] if args.key?(:secondary_alignment) - @supplementary_alignment = args[:supplementary_alignment] if args.key?(:supplementary_alignment) - end - end - - # A read group is all the data that's processed the same way by the sequencer. - class ReadGroup - include Google::Apis::Core::Hashable - - # The dataset to which this read group belongs. - # Corresponds to the JSON property `datasetId` - # @return [String] - attr_accessor :dataset_id - - # A free-form text description of this read group. - # Corresponds to the JSON property `description` - # @return [String] - attr_accessor :description - - # The experiment used to generate this read group. - # Corresponds to the JSON property `experiment` - # @return [Google::Apis::GenomicsV1::Experiment] - attr_accessor :experiment - - # The server-generated read group ID, unique for all read groups. - # Note: This is different than the @RG ID field in the SAM spec. For that - # value, see name. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # A map of additional read group information. This must be of the form - # map (string key mapping to a list of string values). - # Corresponds to the JSON property `info` - # @return [Hash>] - attr_accessor :info - - # The read group name. This corresponds to the @RG ID field in the SAM spec. - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # The predicted insert size of this read group. The insert size is the length - # the sequenced DNA fragment from end-to-end, not including the adapters. - # Corresponds to the JSON property `predictedInsertSize` - # @return [Fixnum] - attr_accessor :predicted_insert_size - - # The programs used to generate this read group. Programs are always - # identical for all read groups within a read group set. For this reason, - # only the first read group in a returned set will have this field - # populated. - # Corresponds to the JSON property `programs` - # @return [Array] - attr_accessor :programs - - # The reference set the reads in this read group are aligned to. - # Corresponds to the JSON property `referenceSetId` - # @return [String] - attr_accessor :reference_set_id - - # A client-supplied sample identifier for the reads in this read group. - # Corresponds to the JSON property `sampleId` - # @return [String] - attr_accessor :sample_id - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @dataset_id = args[:dataset_id] if args.key?(:dataset_id) - @description = args[:description] if args.key?(:description) - @experiment = args[:experiment] if args.key?(:experiment) - @id = args[:id] if args.key?(:id) - @info = args[:info] if args.key?(:info) - @name = args[:name] if args.key?(:name) - @predicted_insert_size = args[:predicted_insert_size] if args.key?(:predicted_insert_size) - @programs = args[:programs] if args.key?(:programs) - @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id) - @sample_id = args[:sample_id] if args.key?(:sample_id) - end - end - - # A read group set is a logical collection of read groups, which are - # collections of reads produced by a sequencer. A read group set typically - # models reads corresponding to one sample, sequenced one way, and aligned one - # way. - # * A read group set belongs to one dataset. - # * A read group belongs to one read group set. - # * A read belongs to one read group. - # For more genomics resource definitions, see [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - class ReadGroupSet - include Google::Apis::Core::Hashable - - # The dataset to which this read group set belongs. - # Corresponds to the JSON property `datasetId` - # @return [String] - attr_accessor :dataset_id - - # The filename of the original source file for this read group set, if any. - # Corresponds to the JSON property `filename` - # @return [String] - attr_accessor :filename - - # The server-generated read group set ID, unique for all read group sets. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # A map of additional read group set information. - # Corresponds to the JSON property `info` - # @return [Hash>] - attr_accessor :info - - # The read group set name. By default this will be initialized to the sample - # name of the sequenced data contained in this set. - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # The read groups in this set. There are typically 1-10 read groups in a read - # group set. - # Corresponds to the JSON property `readGroups` - # @return [Array] - attr_accessor :read_groups - - # The reference set to which the reads in this read group set are aligned. - # Corresponds to the JSON property `referenceSetId` - # @return [String] - attr_accessor :reference_set_id - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @dataset_id = args[:dataset_id] if args.key?(:dataset_id) - @filename = args[:filename] if args.key?(:filename) - @id = args[:id] if args.key?(:id) - @info = args[:info] if args.key?(:info) - @name = args[:name] if args.key?(:name) - @read_groups = args[:read_groups] if args.key?(:read_groups) - @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id) - end - end - - # A reference is a canonical assembled DNA sequence, intended to act as a - # reference coordinate space for other genomic annotations. A single reference - # might represent the human chromosome 1 or mitochandrial DNA, for instance. A - # reference belongs to one or more reference sets. - # For more genomics resource definitions, see [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - class Reference - include Google::Apis::Core::Hashable - - # The server-generated reference ID, unique across all references. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # The length of this reference's sequence. - # Corresponds to the JSON property `length` - # @return [Fixnum] - attr_accessor :length - - # MD5 of the upper-case sequence excluding all whitespace characters (this - # is equivalent to SQ:M5 in SAM). This value is represented in lower case - # hexadecimal format. - # Corresponds to the JSON property `md5checksum` - # @return [String] - attr_accessor :md5checksum - - # The name of this reference, for example `22`. - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human. - # Corresponds to the JSON property `ncbiTaxonId` - # @return [Fixnum] - attr_accessor :ncbi_taxon_id - - # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally - # with a version number, for example `GCF_000001405.26`. - # Corresponds to the JSON property `sourceAccessions` - # @return [Array] - attr_accessor :source_accessions - - # The URI from which the sequence was obtained. Typically specifies a FASTA - # format file. - # Corresponds to the JSON property `sourceUri` - # @return [String] - attr_accessor :source_uri - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @id = args[:id] if args.key?(:id) - @length = args[:length] if args.key?(:length) - @md5checksum = args[:md5checksum] if args.key?(:md5checksum) - @name = args[:name] if args.key?(:name) - @ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id) - @source_accessions = args[:source_accessions] if args.key?(:source_accessions) - @source_uri = args[:source_uri] if args.key?(:source_uri) - end - end - - # ReferenceBound records an upper bound for the starting coordinate of - # variants in a particular reference. - class ReferenceBound - include Google::Apis::Core::Hashable - - # The name of the reference associated with this reference bound. - # Corresponds to the JSON property `referenceName` - # @return [String] - attr_accessor :reference_name - - # An upper bound (inclusive) on the starting coordinate of any - # variant in the reference sequence. - # Corresponds to the JSON property `upperBound` - # @return [Fixnum] - attr_accessor :upper_bound - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @reference_name = args[:reference_name] if args.key?(:reference_name) - @upper_bound = args[:upper_bound] if args.key?(:upper_bound) - end - end - - # A reference set is a set of references which typically comprise a reference - # assembly for a species, such as `GRCh38` which is representative - # of the human genome. A reference set defines a common coordinate space for - # comparing reference-aligned experimental data. A reference set contains 1 or - # more references. - # For more genomics resource definitions, see [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - class ReferenceSet - include Google::Apis::Core::Hashable - - # Public id of this reference set, such as `GRCh37`. - # Corresponds to the JSON property `assemblyId` - # @return [String] - attr_accessor :assembly_id - - # Free text description of this reference set. - # Corresponds to the JSON property `description` - # @return [String] - attr_accessor :description - - # The server-generated reference set ID, unique across all reference sets. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # Order-independent MD5 checksum which identifies this reference set. The - # checksum is computed by sorting all lower case hexidecimal string - # `reference.md5checksum` (for all reference in this set) in - # ascending lexicographic order, concatenating, and taking the MD5 of that - # value. The resulting value is represented in lower case hexadecimal format. - # Corresponds to the JSON property `md5checksum` - # @return [String] - attr_accessor :md5checksum - - # ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human) - # indicating the species which this reference set is intended to model. Note - # that contained references may specify a different `ncbiTaxonId`, as - # assemblies may contain reference sequences which do not belong to the - # modeled species, for example EBV in a human reference genome. - # Corresponds to the JSON property `ncbiTaxonId` - # @return [Fixnum] - attr_accessor :ncbi_taxon_id - - # The IDs of the reference objects that are part of this set. - # `Reference.md5checksum` must be unique within this set. - # Corresponds to the JSON property `referenceIds` - # @return [Array] - attr_accessor :reference_ids - - # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally - # with a version number, for example `NC_000001.11`. - # Corresponds to the JSON property `sourceAccessions` - # @return [Array] - attr_accessor :source_accessions - - # The URI from which the references were obtained. - # Corresponds to the JSON property `sourceUri` - # @return [String] - attr_accessor :source_uri - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @assembly_id = args[:assembly_id] if args.key?(:assembly_id) - @description = args[:description] if args.key?(:description) - @id = args[:id] if args.key?(:id) - @md5checksum = args[:md5checksum] if args.key?(:md5checksum) - @ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id) - @reference_ids = args[:reference_ids] if args.key?(:reference_ids) - @source_accessions = args[:source_accessions] if args.key?(:source_accessions) - @source_uri = args[:source_uri] if args.key?(:source_uri) - end - end - # Runtime metadata that will be populated in the # runtimeMetadata # field of the Operation associated with a RunPipeline execution. @@ -2131,786 +333,6 @@ module Google end end - # - class SearchAnnotationSetsRequest - include Google::Apis::Core::Hashable - - # Required. The dataset IDs to search within. Caller must have `READ` access - # to these datasets. - # Corresponds to the JSON property `datasetIds` - # @return [Array] - attr_accessor :dataset_ids - - # Only return annotations sets for which a substring of the name matches this - # string (case insensitive). - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # The maximum number of results to return in a single page. If unspecified, - # defaults to 128. The maximum value is 1024. - # Corresponds to the JSON property `pageSize` - # @return [Fixnum] - attr_accessor :page_size - - # The continuation token, which is used to page through large result sets. - # To get the next page of results, set this parameter to the value of - # `nextPageToken` from the previous response. - # Corresponds to the JSON property `pageToken` - # @return [String] - attr_accessor :page_token - - # If specified, only annotation sets associated with the given reference set - # are returned. - # Corresponds to the JSON property `referenceSetId` - # @return [String] - attr_accessor :reference_set_id - - # If specified, only annotation sets that have any of these types are - # returned. - # Corresponds to the JSON property `types` - # @return [Array] - attr_accessor :types - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids) - @name = args[:name] if args.key?(:name) - @page_size = args[:page_size] if args.key?(:page_size) - @page_token = args[:page_token] if args.key?(:page_token) - @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id) - @types = args[:types] if args.key?(:types) - end - end - - # - class SearchAnnotationSetsResponse - include Google::Apis::Core::Hashable - - # The matching annotation sets. - # Corresponds to the JSON property `annotationSets` - # @return [Array] - attr_accessor :annotation_sets - - # The continuation token, which is used to page through large result sets. - # Provide this value in a subsequent request to return the next page of - # results. This field will be empty if there aren't any additional results. - # Corresponds to the JSON property `nextPageToken` - # @return [String] - attr_accessor :next_page_token - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @annotation_sets = args[:annotation_sets] if args.key?(:annotation_sets) - @next_page_token = args[:next_page_token] if args.key?(:next_page_token) - end - end - - # - class SearchAnnotationsRequest - include Google::Apis::Core::Hashable - - # Required. The annotation sets to search within. The caller must have - # `READ` access to these annotation sets. - # All queried annotation sets must have the same type. - # Corresponds to the JSON property `annotationSetIds` - # @return [Array] - attr_accessor :annotation_set_ids - - # The end position of the range on the reference, 0-based exclusive. If - # referenceId or - # referenceName - # must be specified, Defaults to the length of the reference. - # Corresponds to the JSON property `end` - # @return [Fixnum] - attr_accessor :end - - # The maximum number of results to return in a single page. If unspecified, - # defaults to 256. The maximum value is 2048. - # Corresponds to the JSON property `pageSize` - # @return [Fixnum] - attr_accessor :page_size - - # The continuation token, which is used to page through large result sets. - # To get the next page of results, set this parameter to the value of - # `nextPageToken` from the previous response. - # Corresponds to the JSON property `pageToken` - # @return [String] - attr_accessor :page_token - - # The ID of the reference to query. - # Corresponds to the JSON property `referenceId` - # @return [String] - attr_accessor :reference_id - - # The name of the reference to query, within the reference set associated - # with this query. - # Corresponds to the JSON property `referenceName` - # @return [String] - attr_accessor :reference_name - - # The start position of the range on the reference, 0-based inclusive. If - # specified, - # referenceId or - # referenceName - # must be specified. Defaults to 0. - # Corresponds to the JSON property `start` - # @return [Fixnum] - attr_accessor :start - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @annotation_set_ids = args[:annotation_set_ids] if args.key?(:annotation_set_ids) - @end = args[:end] if args.key?(:end) - @page_size = args[:page_size] if args.key?(:page_size) - @page_token = args[:page_token] if args.key?(:page_token) - @reference_id = args[:reference_id] if args.key?(:reference_id) - @reference_name = args[:reference_name] if args.key?(:reference_name) - @start = args[:start] if args.key?(:start) - end - end - - # - class SearchAnnotationsResponse - include Google::Apis::Core::Hashable - - # The matching annotations. - # Corresponds to the JSON property `annotations` - # @return [Array] - attr_accessor :annotations - - # The continuation token, which is used to page through large result sets. - # Provide this value in a subsequent request to return the next page of - # results. This field will be empty if there aren't any additional results. - # Corresponds to the JSON property `nextPageToken` - # @return [String] - attr_accessor :next_page_token - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @annotations = args[:annotations] if args.key?(:annotations) - @next_page_token = args[:next_page_token] if args.key?(:next_page_token) - end - end - - # The call set search request. - class SearchCallSetsRequest - include Google::Apis::Core::Hashable - - # Only return call sets for which a substring of the name matches this - # string. - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # The maximum number of results to return in a single page. If unspecified, - # defaults to 1024. - # Corresponds to the JSON property `pageSize` - # @return [Fixnum] - attr_accessor :page_size - - # The continuation token, which is used to page through large result sets. - # To get the next page of results, set this parameter to the value of - # `nextPageToken` from the previous response. - # Corresponds to the JSON property `pageToken` - # @return [String] - attr_accessor :page_token - - # Restrict the query to call sets within the given variant sets. At least one - # ID must be provided. - # Corresponds to the JSON property `variantSetIds` - # @return [Array] - attr_accessor :variant_set_ids - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @name = args[:name] if args.key?(:name) - @page_size = args[:page_size] if args.key?(:page_size) - @page_token = args[:page_token] if args.key?(:page_token) - @variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids) - end - end - - # The call set search response. - class SearchCallSetsResponse - include Google::Apis::Core::Hashable - - # The list of matching call sets. - # Corresponds to the JSON property `callSets` - # @return [Array] - attr_accessor :call_sets - - # The continuation token, which is used to page through large result sets. - # Provide this value in a subsequent request to return the next page of - # results. This field will be empty if there aren't any additional results. - # Corresponds to the JSON property `nextPageToken` - # @return [String] - attr_accessor :next_page_token - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @call_sets = args[:call_sets] if args.key?(:call_sets) - @next_page_token = args[:next_page_token] if args.key?(:next_page_token) - end - end - - # The read group set search request. - class SearchReadGroupSetsRequest - include Google::Apis::Core::Hashable - - # Restricts this query to read group sets within the given datasets. At least - # one ID must be provided. - # Corresponds to the JSON property `datasetIds` - # @return [Array] - attr_accessor :dataset_ids - - # Only return read group sets for which a substring of the name matches this - # string. - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # The maximum number of results to return in a single page. If unspecified, - # defaults to 256. The maximum value is 1024. - # Corresponds to the JSON property `pageSize` - # @return [Fixnum] - attr_accessor :page_size - - # The continuation token, which is used to page through large result sets. - # To get the next page of results, set this parameter to the value of - # `nextPageToken` from the previous response. - # Corresponds to the JSON property `pageToken` - # @return [String] - attr_accessor :page_token - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids) - @name = args[:name] if args.key?(:name) - @page_size = args[:page_size] if args.key?(:page_size) - @page_token = args[:page_token] if args.key?(:page_token) - end - end - - # The read group set search response. - class SearchReadGroupSetsResponse - include Google::Apis::Core::Hashable - - # The continuation token, which is used to page through large result sets. - # Provide this value in a subsequent request to return the next page of - # results. This field will be empty if there aren't any additional results. - # Corresponds to the JSON property `nextPageToken` - # @return [String] - attr_accessor :next_page_token - - # The list of matching read group sets. - # Corresponds to the JSON property `readGroupSets` - # @return [Array] - attr_accessor :read_group_sets - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @next_page_token = args[:next_page_token] if args.key?(:next_page_token) - @read_group_sets = args[:read_group_sets] if args.key?(:read_group_sets) - end - end - - # The read search request. - class SearchReadsRequest - include Google::Apis::Core::Hashable - - # The end position of the range on the reference, 0-based exclusive. If - # specified, `referenceName` must also be specified. - # Corresponds to the JSON property `end` - # @return [Fixnum] - attr_accessor :end - - # The maximum number of results to return in a single page. If unspecified, - # defaults to 256. The maximum value is 2048. - # Corresponds to the JSON property `pageSize` - # @return [Fixnum] - attr_accessor :page_size - - # The continuation token, which is used to page through large result sets. - # To get the next page of results, set this parameter to the value of - # `nextPageToken` from the previous response. - # Corresponds to the JSON property `pageToken` - # @return [String] - attr_accessor :page_token - - # The IDs of the read groups within which to search for reads. All specified - # read groups must belong to the same read group sets. Must specify one of - # `readGroupSetIds` or `readGroupIds`. - # Corresponds to the JSON property `readGroupIds` - # @return [Array] - attr_accessor :read_group_ids - - # The IDs of the read groups sets within which to search for reads. All - # specified read group sets must be aligned against a common set of reference - # sequences; this defines the genomic coordinates for the query. Must specify - # one of `readGroupSetIds` or `readGroupIds`. - # Corresponds to the JSON property `readGroupSetIds` - # @return [Array] - attr_accessor :read_group_set_ids - - # The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to - # `*`, only unmapped reads are returned. If unspecified, all reads (mapped - # and unmapped) are returned. - # Corresponds to the JSON property `referenceName` - # @return [String] - attr_accessor :reference_name - - # The start position of the range on the reference, 0-based inclusive. If - # specified, `referenceName` must also be specified. - # Corresponds to the JSON property `start` - # @return [Fixnum] - attr_accessor :start - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @end = args[:end] if args.key?(:end) - @page_size = args[:page_size] if args.key?(:page_size) - @page_token = args[:page_token] if args.key?(:page_token) - @read_group_ids = args[:read_group_ids] if args.key?(:read_group_ids) - @read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids) - @reference_name = args[:reference_name] if args.key?(:reference_name) - @start = args[:start] if args.key?(:start) - end - end - - # The read search response. - class SearchReadsResponse - include Google::Apis::Core::Hashable - - # The list of matching alignments sorted by mapped genomic coordinate, - # if any, ascending in position within the same reference. Unmapped reads, - # which have no position, are returned contiguously and are sorted in - # ascending lexicographic order by fragment name. - # Corresponds to the JSON property `alignments` - # @return [Array] - attr_accessor :alignments - - # The continuation token, which is used to page through large result sets. - # Provide this value in a subsequent request to return the next page of - # results. This field will be empty if there aren't any additional results. - # Corresponds to the JSON property `nextPageToken` - # @return [String] - attr_accessor :next_page_token - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @alignments = args[:alignments] if args.key?(:alignments) - @next_page_token = args[:next_page_token] if args.key?(:next_page_token) - end - end - - # - class SearchReferenceSetsRequest - include Google::Apis::Core::Hashable - - # If present, return reference sets for which a prefix of any of - # sourceAccessions - # match any of these strings. Accession numbers typically have a main number - # and a version, for example `NC_000001.11`. - # Corresponds to the JSON property `accessions` - # @return [Array] - attr_accessor :accessions - - # If present, return reference sets for which a substring of their - # `assemblyId` matches this string (case insensitive). - # Corresponds to the JSON property `assemblyId` - # @return [String] - attr_accessor :assembly_id - - # If present, return reference sets for which the - # md5checksum matches exactly. - # Corresponds to the JSON property `md5checksums` - # @return [Array] - attr_accessor :md5checksums - - # The maximum number of results to return in a single page. If unspecified, - # defaults to 1024. The maximum value is 4096. - # Corresponds to the JSON property `pageSize` - # @return [Fixnum] - attr_accessor :page_size - - # The continuation token, which is used to page through large result sets. - # To get the next page of results, set this parameter to the value of - # `nextPageToken` from the previous response. - # Corresponds to the JSON property `pageToken` - # @return [String] - attr_accessor :page_token - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @accessions = args[:accessions] if args.key?(:accessions) - @assembly_id = args[:assembly_id] if args.key?(:assembly_id) - @md5checksums = args[:md5checksums] if args.key?(:md5checksums) - @page_size = args[:page_size] if args.key?(:page_size) - @page_token = args[:page_token] if args.key?(:page_token) - end - end - - # - class SearchReferenceSetsResponse - include Google::Apis::Core::Hashable - - # The continuation token, which is used to page through large result sets. - # Provide this value in a subsequent request to return the next page of - # results. This field will be empty if there aren't any additional results. - # Corresponds to the JSON property `nextPageToken` - # @return [String] - attr_accessor :next_page_token - - # The matching references sets. - # Corresponds to the JSON property `referenceSets` - # @return [Array] - attr_accessor :reference_sets - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @next_page_token = args[:next_page_token] if args.key?(:next_page_token) - @reference_sets = args[:reference_sets] if args.key?(:reference_sets) - end - end - - # - class SearchReferencesRequest - include Google::Apis::Core::Hashable - - # If present, return references for which a prefix of any of - # sourceAccessions match - # any of these strings. Accession numbers typically have a main number and a - # version, for example `GCF_000001405.26`. - # Corresponds to the JSON property `accessions` - # @return [Array] - attr_accessor :accessions - - # If present, return references for which the - # md5checksum matches exactly. - # Corresponds to the JSON property `md5checksums` - # @return [Array] - attr_accessor :md5checksums - - # The maximum number of results to return in a single page. If unspecified, - # defaults to 1024. The maximum value is 4096. - # Corresponds to the JSON property `pageSize` - # @return [Fixnum] - attr_accessor :page_size - - # The continuation token, which is used to page through large result sets. - # To get the next page of results, set this parameter to the value of - # `nextPageToken` from the previous response. - # Corresponds to the JSON property `pageToken` - # @return [String] - attr_accessor :page_token - - # If present, return only references which belong to this reference set. - # Corresponds to the JSON property `referenceSetId` - # @return [String] - attr_accessor :reference_set_id - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @accessions = args[:accessions] if args.key?(:accessions) - @md5checksums = args[:md5checksums] if args.key?(:md5checksums) - @page_size = args[:page_size] if args.key?(:page_size) - @page_token = args[:page_token] if args.key?(:page_token) - @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id) - end - end - - # - class SearchReferencesResponse - include Google::Apis::Core::Hashable - - # The continuation token, which is used to page through large result sets. - # Provide this value in a subsequent request to return the next page of - # results. This field will be empty if there aren't any additional results. - # Corresponds to the JSON property `nextPageToken` - # @return [String] - attr_accessor :next_page_token - - # The matching references. - # Corresponds to the JSON property `references` - # @return [Array] - attr_accessor :references - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @next_page_token = args[:next_page_token] if args.key?(:next_page_token) - @references = args[:references] if args.key?(:references) - end - end - - # The search variant sets request. - class SearchVariantSetsRequest - include Google::Apis::Core::Hashable - - # Exactly one dataset ID must be provided here. Only variant sets which - # belong to this dataset will be returned. - # Corresponds to the JSON property `datasetIds` - # @return [Array] - attr_accessor :dataset_ids - - # The maximum number of results to return in a single page. If unspecified, - # defaults to 1024. - # Corresponds to the JSON property `pageSize` - # @return [Fixnum] - attr_accessor :page_size - - # The continuation token, which is used to page through large result sets. - # To get the next page of results, set this parameter to the value of - # `nextPageToken` from the previous response. - # Corresponds to the JSON property `pageToken` - # @return [String] - attr_accessor :page_token - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids) - @page_size = args[:page_size] if args.key?(:page_size) - @page_token = args[:page_token] if args.key?(:page_token) - end - end - - # The search variant sets response. - class SearchVariantSetsResponse - include Google::Apis::Core::Hashable - - # The continuation token, which is used to page through large result sets. - # Provide this value in a subsequent request to return the next page of - # results. This field will be empty if there aren't any additional results. - # Corresponds to the JSON property `nextPageToken` - # @return [String] - attr_accessor :next_page_token - - # The variant sets belonging to the requested dataset. - # Corresponds to the JSON property `variantSets` - # @return [Array] - attr_accessor :variant_sets - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @next_page_token = args[:next_page_token] if args.key?(:next_page_token) - @variant_sets = args[:variant_sets] if args.key?(:variant_sets) - end - end - - # The variant search request. - class SearchVariantsRequest - include Google::Apis::Core::Hashable - - # Only return variant calls which belong to call sets with these ids. - # Leaving this blank returns all variant calls. If a variant has no - # calls belonging to any of these call sets, it won't be returned at all. - # Corresponds to the JSON property `callSetIds` - # @return [Array] - attr_accessor :call_set_ids - - # The end of the window, 0-based exclusive. If unspecified or 0, defaults to - # the length of the reference. - # Corresponds to the JSON property `end` - # @return [Fixnum] - attr_accessor :end - - # The maximum number of calls to return in a single page. Note that this - # limit may be exceeded in the event that a matching variant contains more - # calls than the requested maximum. If unspecified, defaults to 5000. The - # maximum value is 10000. - # Corresponds to the JSON property `maxCalls` - # @return [Fixnum] - attr_accessor :max_calls - - # The maximum number of variants to return in a single page. If unspecified, - # defaults to 5000. The maximum value is 10000. - # Corresponds to the JSON property `pageSize` - # @return [Fixnum] - attr_accessor :page_size - - # The continuation token, which is used to page through large result sets. - # To get the next page of results, set this parameter to the value of - # `nextPageToken` from the previous response. - # Corresponds to the JSON property `pageToken` - # @return [String] - attr_accessor :page_token - - # Required. Only return variants in this reference sequence. - # Corresponds to the JSON property `referenceName` - # @return [String] - attr_accessor :reference_name - - # The beginning of the window (0-based, inclusive) for which - # overlapping variants should be returned. If unspecified, defaults to 0. - # Corresponds to the JSON property `start` - # @return [Fixnum] - attr_accessor :start - - # Only return variants which have exactly this name. - # Corresponds to the JSON property `variantName` - # @return [String] - attr_accessor :variant_name - - # At most one variant set ID must be provided. Only variants from this - # variant set will be returned. If omitted, a call set id must be included in - # the request. - # Corresponds to the JSON property `variantSetIds` - # @return [Array] - attr_accessor :variant_set_ids - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids) - @end = args[:end] if args.key?(:end) - @max_calls = args[:max_calls] if args.key?(:max_calls) - @page_size = args[:page_size] if args.key?(:page_size) - @page_token = args[:page_token] if args.key?(:page_token) - @reference_name = args[:reference_name] if args.key?(:reference_name) - @start = args[:start] if args.key?(:start) - @variant_name = args[:variant_name] if args.key?(:variant_name) - @variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids) - end - end - - # The variant search response. - class SearchVariantsResponse - include Google::Apis::Core::Hashable - - # The continuation token, which is used to page through large result sets. - # Provide this value in a subsequent request to return the next page of - # results. This field will be empty if there aren't any additional results. - # Corresponds to the JSON property `nextPageToken` - # @return [String] - attr_accessor :next_page_token - - # The list of matching Variants. - # Corresponds to the JSON property `variants` - # @return [Array] - attr_accessor :variants - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @next_page_token = args[:next_page_token] if args.key?(:next_page_token) - @variants = args[:variants] if args.key?(:variants) - end - end - - # Request message for `SetIamPolicy` method. - class SetIamPolicyRequest - include Google::Apis::Core::Hashable - - # Defines an Identity and Access Management (IAM) policy. It is used to - # specify access control policies for Cloud Platform resources. - # A `Policy` consists of a list of `bindings`. A `Binding` binds a list of - # `members` to a `role`, where the members can be user accounts, Google groups, - # Google domains, and service accounts. A `role` is a named list of permissions - # defined by IAM. - # **Example** - # ` - # "bindings": [ - # ` - # "role": "roles/owner", - # "members": [ - # "user:mike@example.com", - # "group:admins@example.com", - # "domain:google.com", - # "serviceAccount:my-other-app@appspot.gserviceaccount.com", - # ] - # `, - # ` - # "role": "roles/viewer", - # "members": ["user:sean@example.com"] - # ` - # ] - # ` - # For a description of IAM and its features, see the - # [IAM developer's guide](https://cloud.google.com/iam). - # Corresponds to the JSON property `policy` - # @return [Google::Apis::GenomicsV1::Policy] - attr_accessor :policy - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @policy = args[:policy] if args.key?(:policy) - 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: @@ -2982,496 +404,6 @@ module Google @message = args[:message] if args.key?(:message) end end - - # Request message for `TestIamPermissions` method. - class TestIamPermissionsRequest - include Google::Apis::Core::Hashable - - # REQUIRED: The set of permissions to check for the 'resource'. - # Permissions with wildcards (such as '*' or 'storage.*') are not allowed. - # Allowed permissions are: - # * `genomics.datasets.create` - # * `genomics.datasets.delete` - # * `genomics.datasets.get` - # * `genomics.datasets.list` - # * `genomics.datasets.update` - # * `genomics.datasets.getIamPolicy` - # * `genomics.datasets.setIamPolicy` - # Corresponds to the JSON property `permissions` - # @return [Array] - attr_accessor :permissions - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @permissions = args[:permissions] if args.key?(:permissions) - end - end - - # Response message for `TestIamPermissions` method. - class TestIamPermissionsResponse - include Google::Apis::Core::Hashable - - # A subset of `TestPermissionsRequest.permissions` that the caller is - # allowed. - # Corresponds to the JSON property `permissions` - # @return [Array] - attr_accessor :permissions - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @permissions = args[:permissions] if args.key?(:permissions) - end - end - - # A transcript represents the assertion that a particular region of the - # reference genome may be transcribed as RNA. - class Transcript - include Google::Apis::Core::Hashable - - # The range of the coding sequence for this transcript, if any. To determine - # the exact ranges of coding sequence, intersect this range with those of the - # exons, if any. If there are any - # exons, the - # codingSequence must start - # and end within them. - # Note that in some cases, the reference genome will not exactly match the - # observed mRNA transcript e.g. due to variance in the source genome from - # reference. In these cases, - # exon.frame will not necessarily - # match the expected reference reading frame and coding exon reference bases - # cannot necessarily be concatenated to produce the original transcript mRNA. - # Corresponds to the JSON property `codingSequence` - # @return [Google::Apis::GenomicsV1::CodingSequence] - attr_accessor :coding_sequence - - # The exons that compose - # this transcript. This field should be unset for genomes where transcript - # splicing does not occur, for example prokaryotes. - # Introns are regions of the transcript that are not included in the - # spliced RNA product. Though not explicitly modeled here, intron ranges can - # be deduced; all regions of this transcript that are not exons are introns. - # Exonic sequences do not necessarily code for a translational product - # (amino acids). Only the regions of exons bounded by the - # codingSequence correspond - # to coding DNA sequence. - # Exons are ordered by start position and may not overlap. - # Corresponds to the JSON property `exons` - # @return [Array] - attr_accessor :exons - - # The annotation ID of the gene from which this transcript is transcribed. - # Corresponds to the JSON property `geneId` - # @return [String] - attr_accessor :gene_id - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @coding_sequence = args[:coding_sequence] if args.key?(:coding_sequence) - @exons = args[:exons] if args.key?(:exons) - @gene_id = args[:gene_id] if args.key?(:gene_id) - end - end - - # - class UndeleteDatasetRequest - include Google::Apis::Core::Hashable - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - end - end - - # A variant represents a change in DNA sequence relative to a reference - # sequence. For example, a variant could represent a SNP or an insertion. - # Variants belong to a variant set. - # For more genomics resource definitions, see [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Each of the calls on a variant represent a determination of genotype with - # respect to that variant. For example, a call might assign probability of 0.32 - # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call - # belongs to a call set, which contains related calls typically from one - # sample. - class Variant - include Google::Apis::Core::Hashable - - # The bases that appear instead of the reference bases. - # Corresponds to the JSON property `alternateBases` - # @return [Array] - attr_accessor :alternate_bases - - # The variant calls for this particular variant. Each one represents the - # determination of genotype with respect to this variant. - # Corresponds to the JSON property `calls` - # @return [Array] - attr_accessor :calls - - # The date this variant was created, in milliseconds from the epoch. - # Corresponds to the JSON property `created` - # @return [Fixnum] - attr_accessor :created - - # The end position (0-based) of this variant. This corresponds to the first - # base after the last base in the reference allele. So, the length of - # the reference allele is (end - start). This is useful for variants - # that don't explicitly give alternate bases, for example large deletions. - # Corresponds to the JSON property `end` - # @return [Fixnum] - attr_accessor :end - - # A list of filters (normally quality filters) this variant has failed. - # `PASS` indicates this variant has passed all filters. - # Corresponds to the JSON property `filter` - # @return [Array] - attr_accessor :filter - - # The server-generated variant ID, unique across all variants. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # A map of additional variant information. This must be of the form - # map (string key mapping to a list of string values). - # Corresponds to the JSON property `info` - # @return [Hash>] - attr_accessor :info - - # Names for the variant, for example a RefSNP ID. - # Corresponds to the JSON property `names` - # @return [Array] - attr_accessor :names - - # A measure of how likely this variant is to be real. - # A higher value is better. - # Corresponds to the JSON property `quality` - # @return [Float] - attr_accessor :quality - - # The reference bases for this variant. They start at the given - # position. - # Corresponds to the JSON property `referenceBases` - # @return [String] - attr_accessor :reference_bases - - # The reference on which this variant occurs. - # (such as `chr20` or `X`) - # Corresponds to the JSON property `referenceName` - # @return [String] - attr_accessor :reference_name - - # The position at which this variant occurs (0-based). - # This corresponds to the first base of the string of reference bases. - # Corresponds to the JSON property `start` - # @return [Fixnum] - attr_accessor :start - - # The ID of the variant set this variant belongs to. - # Corresponds to the JSON property `variantSetId` - # @return [String] - attr_accessor :variant_set_id - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @alternate_bases = args[:alternate_bases] if args.key?(:alternate_bases) - @calls = args[:calls] if args.key?(:calls) - @created = args[:created] if args.key?(:created) - @end = args[:end] if args.key?(:end) - @filter = args[:filter] if args.key?(:filter) - @id = args[:id] if args.key?(:id) - @info = args[:info] if args.key?(:info) - @names = args[:names] if args.key?(:names) - @quality = args[:quality] if args.key?(:quality) - @reference_bases = args[:reference_bases] if args.key?(:reference_bases) - @reference_name = args[:reference_name] if args.key?(:reference_name) - @start = args[:start] if args.key?(:start) - @variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id) - end - end - - # - class VariantAnnotation - include Google::Apis::Core::Hashable - - # The alternate allele for this variant. If multiple alternate alleles - # exist at this location, create a separate variant for each one, as they - # may represent distinct conditions. - # Corresponds to the JSON property `alternateBases` - # @return [String] - attr_accessor :alternate_bases - - # Describes the clinical significance of a variant. - # It is adapted from the ClinVar controlled vocabulary for clinical - # significance described at: - # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ - # Corresponds to the JSON property `clinicalSignificance` - # @return [String] - attr_accessor :clinical_significance - - # The set of conditions associated with this variant. - # A condition describes the way a variant influences human health. - # Corresponds to the JSON property `conditions` - # @return [Array] - attr_accessor :conditions - - # Effect of the variant on the coding sequence. - # Corresponds to the JSON property `effect` - # @return [String] - attr_accessor :effect - - # Google annotation ID of the gene affected by this variant. This should - # be provided when the variant is created. - # Corresponds to the JSON property `geneId` - # @return [String] - attr_accessor :gene_id - - # Google annotation IDs of the transcripts affected by this variant. These - # should be provided when the variant is created. - # Corresponds to the JSON property `transcriptIds` - # @return [Array] - attr_accessor :transcript_ids - - # Type has been adapted from ClinVar's list of variant types. - # Corresponds to the JSON property `type` - # @return [String] - attr_accessor :type - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @alternate_bases = args[:alternate_bases] if args.key?(:alternate_bases) - @clinical_significance = args[:clinical_significance] if args.key?(:clinical_significance) - @conditions = args[:conditions] if args.key?(:conditions) - @effect = args[:effect] if args.key?(:effect) - @gene_id = args[:gene_id] if args.key?(:gene_id) - @transcript_ids = args[:transcript_ids] if args.key?(:transcript_ids) - @type = args[:type] if args.key?(:type) - end - end - - # A call represents the determination of genotype with respect to a particular - # variant. It may include associated information such as quality and phasing. - # For example, a call might assign a probability of 0.32 to the occurrence of - # a SNP named rs1234 in a call set with the name NA12345. - class VariantCall - include Google::Apis::Core::Hashable - - # The ID of the call set this variant call belongs to. - # Corresponds to the JSON property `callSetId` - # @return [String] - attr_accessor :call_set_id - - # The name of the call set this variant call belongs to. - # Corresponds to the JSON property `callSetName` - # @return [String] - attr_accessor :call_set_name - - # The genotype of this variant call. Each value represents either the value - # of the `referenceBases` field or a 1-based index into - # `alternateBases`. If a variant had a `referenceBases` - # value of `T` and an `alternateBases` - # value of `["A", "C"]`, and the `genotype` was - # `[2, 1]`, that would mean the call - # represented the heterozygous value `CA` for this variant. - # If the `genotype` was instead `[0, 1]`, the - # represented value would be `TA`. Ordering of the - # genotype values is important if the `phaseset` is present. - # If a genotype is not called (that is, a `.` is present in the - # GT string) -1 is returned. - # Corresponds to the JSON property `genotype` - # @return [Array] - attr_accessor :genotype - - # The genotype likelihoods for this variant call. Each array entry - # represents how likely a specific genotype is for this call. The value - # ordering is defined by the GL tag in the VCF spec. - # If Phred-scaled genotype likelihood scores (PL) are available and - # log10(P) genotype likelihood scores (GL) are not, PL scores are converted - # to GL scores. If both are available, PL scores are stored in `info`. - # Corresponds to the JSON property `genotypeLikelihood` - # @return [Array] - attr_accessor :genotype_likelihood - - # A map of additional variant call information. This must be of the form - # map (string key mapping to a list of string values). - # Corresponds to the JSON property `info` - # @return [Hash>] - attr_accessor :info - - # If this field is present, this variant call's genotype ordering implies - # the phase of the bases and is consistent with any other variant calls in - # the same reference sequence which have the same phaseset value. - # When importing data from VCF, if the genotype data was phased but no - # phase set was specified this field will be set to `*`. - # Corresponds to the JSON property `phaseset` - # @return [String] - attr_accessor :phaseset - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @call_set_id = args[:call_set_id] if args.key?(:call_set_id) - @call_set_name = args[:call_set_name] if args.key?(:call_set_name) - @genotype = args[:genotype] if args.key?(:genotype) - @genotype_likelihood = args[:genotype_likelihood] if args.key?(:genotype_likelihood) - @info = args[:info] if args.key?(:info) - @phaseset = args[:phaseset] if args.key?(:phaseset) - end - end - - # A variant set is a collection of call sets and variants. It contains summary - # statistics of those contents. A variant set belongs to a dataset. - # For more genomics resource definitions, see [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - class VariantSet - include Google::Apis::Core::Hashable - - # The dataset to which this variant set belongs. - # Corresponds to the JSON property `datasetId` - # @return [String] - attr_accessor :dataset_id - - # A textual description of this variant set. - # Corresponds to the JSON property `description` - # @return [String] - attr_accessor :description - - # The server-generated variant set ID, unique across all variant sets. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # The metadata associated with this variant set. - # Corresponds to the JSON property `metadata` - # @return [Array] - attr_accessor :metadata - - # User-specified, mutable name. - # Corresponds to the JSON property `name` - # @return [String] - attr_accessor :name - - # A list of all references used by the variants in a variant set - # with associated coordinate upper bounds for each one. - # Corresponds to the JSON property `referenceBounds` - # @return [Array] - attr_accessor :reference_bounds - - # The reference set to which the variant set is mapped. The reference set - # describes the alignment provenance of the variant set, while the - # `referenceBounds` describe the shape of the actual variant data. The - # reference set's reference names are a superset of those found in the - # `referenceBounds`. - # For example, given a variant set that is mapped to the GRCh38 reference set - # and contains a single variant on reference 'X', `referenceBounds` would - # contain only an entry for 'X', while the associated reference set - # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc. - # Corresponds to the JSON property `referenceSetId` - # @return [String] - attr_accessor :reference_set_id - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @dataset_id = args[:dataset_id] if args.key?(:dataset_id) - @description = args[:description] if args.key?(:description) - @id = args[:id] if args.key?(:id) - @metadata = args[:metadata] if args.key?(:metadata) - @name = args[:name] if args.key?(:name) - @reference_bounds = args[:reference_bounds] if args.key?(:reference_bounds) - @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id) - end - end - - # Metadata describes a single piece of variant call metadata. - # These data include a top level key and either a single value string (value) - # or a list of key-value pairs (info.) - # Value and info are mutually exclusive. - class VariantSetMetadata - include Google::Apis::Core::Hashable - - # A textual description of this metadata. - # Corresponds to the JSON property `description` - # @return [String] - attr_accessor :description - - # User-provided ID field, not enforced by this API. - # Two or more pieces of structured metadata with identical - # id and key fields are considered equivalent. - # Corresponds to the JSON property `id` - # @return [String] - attr_accessor :id - - # Remaining structured metadata key-value pairs. This must be of the form - # map (string key mapping to a list of string values). - # Corresponds to the JSON property `info` - # @return [Hash>] - attr_accessor :info - - # The top-level key. - # Corresponds to the JSON property `key` - # @return [String] - attr_accessor :key - - # The number of values that can be included in a field described by this - # metadata. - # Corresponds to the JSON property `number` - # @return [String] - attr_accessor :number - - # The type of data. Possible types include: Integer, Float, - # Flag, Character, and String. - # Corresponds to the JSON property `type` - # @return [String] - attr_accessor :type - - # The value field for simple metadata - # Corresponds to the JSON property `value` - # @return [String] - attr_accessor :value - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @description = args[:description] if args.key?(:description) - @id = args[:id] if args.key?(:id) - @info = args[:info] if args.key?(:info) - @key = args[:key] if args.key?(:key) - @number = args[:number] if args.key?(:number) - @type = args[:type] if args.key?(:type) - @value = args[:value] if args.key?(:value) - end - end end end end diff --git a/generated/google/apis/genomics_v1/representations.rb b/generated/google/apis/genomics_v1/representations.rb index 49663d14b..92544f967 100644 --- a/generated/google/apis/genomics_v1/representations.rb +++ b/generated/google/apis/genomics_v1/representations.rb @@ -22,192 +22,30 @@ module Google module Apis module GenomicsV1 - class Annotation - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class AnnotationSet - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class BatchCreateAnnotationsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class BatchCreateAnnotationsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class Binding - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class CallSet - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - class CancelOperationRequest class Representation < Google::Apis::Core::JsonRepresentation; end include Google::Apis::Core::JsonObjectSupport end - class CigarUnit - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ClinicalCondition - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class CodingSequence - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - class ComputeEngine class Representation < Google::Apis::Core::JsonRepresentation; end include Google::Apis::Core::JsonObjectSupport end - class CoverageBucket - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class Dataset - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - class Empty class Representation < Google::Apis::Core::JsonRepresentation; end include Google::Apis::Core::JsonObjectSupport end - class Entry - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class Exon - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class Experiment - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ExportReadGroupSetRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ExportVariantSetRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ExternalId - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class GetIamPolicyRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ImportReadGroupSetsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ImportReadGroupSetsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ImportVariantsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ImportVariantsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class LinearAlignment - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ListBasesResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ListCoverageBucketsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ListDatasetsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - class ListOperationsResponse class Representation < Google::Apis::Core::JsonRepresentation; end include Google::Apis::Core::JsonObjectSupport end - class MergeVariantsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - class Operation class Representation < Google::Apis::Core::JsonRepresentation; end @@ -226,362 +64,24 @@ module Google include Google::Apis::Core::JsonObjectSupport end - class Policy - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class Position - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class Program - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class Range - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class Read - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ReadGroup - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ReadGroupSet - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class Reference - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ReferenceBound - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ReferenceSet - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - class RuntimeMetadata class Representation < Google::Apis::Core::JsonRepresentation; end include Google::Apis::Core::JsonObjectSupport end - class SearchAnnotationSetsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchAnnotationSetsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchAnnotationsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchAnnotationsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchCallSetsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchCallSetsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchReadGroupSetsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchReadGroupSetsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchReadsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchReadsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchReferenceSetsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchReferenceSetsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchReferencesRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchReferencesResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchVariantSetsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchVariantSetsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchVariantsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SearchVariantsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class SetIamPolicyRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - class Status class Representation < Google::Apis::Core::JsonRepresentation; end include Google::Apis::Core::JsonObjectSupport end - class TestIamPermissionsRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class TestIamPermissionsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class Transcript - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class UndeleteDatasetRequest - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class Variant - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class VariantAnnotation - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class VariantCall - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class VariantSet - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class VariantSetMetadata - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class Annotation - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :annotation_set_id, as: 'annotationSetId' - property :end, :numeric_string => true, as: 'end' - property :id, as: 'id' - hash :info, as: 'info', :class => Array do - include Representable::JSON::Collection - items - end - - property :name, as: 'name' - property :reference_id, as: 'referenceId' - property :reference_name, as: 'referenceName' - property :reverse_strand, as: 'reverseStrand' - property :start, :numeric_string => true, as: 'start' - property :transcript, as: 'transcript', class: Google::Apis::GenomicsV1::Transcript, decorator: Google::Apis::GenomicsV1::Transcript::Representation - - property :type, as: 'type' - property :variant, as: 'variant', class: Google::Apis::GenomicsV1::VariantAnnotation, decorator: Google::Apis::GenomicsV1::VariantAnnotation::Representation - - end - end - - class AnnotationSet - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :dataset_id, as: 'datasetId' - property :id, as: 'id' - hash :info, as: 'info', :class => Array do - include Representable::JSON::Collection - items - end - - property :name, as: 'name' - property :reference_set_id, as: 'referenceSetId' - property :source_uri, as: 'sourceUri' - property :type, as: 'type' - end - end - - class BatchCreateAnnotationsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :annotations, as: 'annotations', class: Google::Apis::GenomicsV1::Annotation, decorator: Google::Apis::GenomicsV1::Annotation::Representation - - property :request_id, as: 'requestId' - end - end - - class BatchCreateAnnotationsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :entries, as: 'entries', class: Google::Apis::GenomicsV1::Entry, decorator: Google::Apis::GenomicsV1::Entry::Representation - - end - end - - class Binding - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :members, as: 'members' - property :role, as: 'role' - end - end - - class CallSet - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :created, :numeric_string => true, as: 'created' - property :id, as: 'id' - hash :info, as: 'info', :class => Array do - include Representable::JSON::Collection - items - end - - property :name, as: 'name' - property :sample_id, as: 'sampleId' - collection :variant_set_ids, as: 'variantSetIds' - end - end - class CancelOperationRequest # @private class Representation < Google::Apis::Core::JsonRepresentation end end - class CigarUnit - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :operation, as: 'operation' - property :operation_length, :numeric_string => true, as: 'operationLength' - property :reference_sequence, as: 'referenceSequence' - end - end - - class ClinicalCondition - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :concept_id, as: 'conceptId' - collection :external_ids, as: 'externalIds', class: Google::Apis::GenomicsV1::ExternalId, decorator: Google::Apis::GenomicsV1::ExternalId::Representation - - collection :names, as: 'names' - property :omim_id, as: 'omimId' - end - end - - class CodingSequence - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :end, :numeric_string => true, as: 'end' - property :start, :numeric_string => true, as: 'start' - end - end - class ComputeEngine # @private class Representation < Google::Apis::Core::JsonRepresentation @@ -592,168 +92,12 @@ module Google end end - class CoverageBucket - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :mean_coverage, as: 'meanCoverage' - property :range, as: 'range', class: Google::Apis::GenomicsV1::Range, decorator: Google::Apis::GenomicsV1::Range::Representation - - end - end - - class Dataset - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :create_time, as: 'createTime' - property :id, as: 'id' - property :name, as: 'name' - property :project_id, as: 'projectId' - end - end - class Empty # @private class Representation < Google::Apis::Core::JsonRepresentation end end - class Entry - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :annotation, as: 'annotation', class: Google::Apis::GenomicsV1::Annotation, decorator: Google::Apis::GenomicsV1::Annotation::Representation - - property :status, as: 'status', class: Google::Apis::GenomicsV1::Status, decorator: Google::Apis::GenomicsV1::Status::Representation - - end - end - - class Exon - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :end, :numeric_string => true, as: 'end' - property :frame, as: 'frame' - property :start, :numeric_string => true, as: 'start' - end - end - - class Experiment - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :instrument_model, as: 'instrumentModel' - property :library_id, as: 'libraryId' - property :platform_unit, as: 'platformUnit' - property :sequencing_center, as: 'sequencingCenter' - end - end - - class ExportReadGroupSetRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :export_uri, as: 'exportUri' - property :project_id, as: 'projectId' - collection :reference_names, as: 'referenceNames' - end - end - - class ExportVariantSetRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :bigquery_dataset, as: 'bigqueryDataset' - property :bigquery_table, as: 'bigqueryTable' - collection :call_set_ids, as: 'callSetIds' - property :format, as: 'format' - property :project_id, as: 'projectId' - end - end - - class ExternalId - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :id, as: 'id' - property :source_name, as: 'sourceName' - end - end - - class GetIamPolicyRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - end - end - - class ImportReadGroupSetsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :dataset_id, as: 'datasetId' - property :partition_strategy, as: 'partitionStrategy' - property :reference_set_id, as: 'referenceSetId' - collection :source_uris, as: 'sourceUris' - end - end - - class ImportReadGroupSetsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :read_group_set_ids, as: 'readGroupSetIds' - end - end - - class ImportVariantsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :format, as: 'format' - hash :info_merge_config, as: 'infoMergeConfig' - property :normalize_reference_names, as: 'normalizeReferenceNames' - collection :source_uris, as: 'sourceUris' - property :variant_set_id, as: 'variantSetId' - end - end - - class ImportVariantsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :call_set_ids, as: 'callSetIds' - end - end - - class LinearAlignment - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :cigar, as: 'cigar', class: Google::Apis::GenomicsV1::CigarUnit, decorator: Google::Apis::GenomicsV1::CigarUnit::Representation - - property :mapping_quality, as: 'mappingQuality' - property :position, as: 'position', class: Google::Apis::GenomicsV1::Position, decorator: Google::Apis::GenomicsV1::Position::Representation - - end - end - - class ListBasesResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :next_page_token, as: 'nextPageToken' - property :offset, :numeric_string => true, as: 'offset' - property :sequence, as: 'sequence' - end - end - - class ListCoverageBucketsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :bucket_width, :numeric_string => true, as: 'bucketWidth' - collection :coverage_buckets, as: 'coverageBuckets', class: Google::Apis::GenomicsV1::CoverageBucket, decorator: Google::Apis::GenomicsV1::CoverageBucket::Representation - - property :next_page_token, as: 'nextPageToken' - end - end - - class ListDatasetsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :datasets, as: 'datasets', class: Google::Apis::GenomicsV1::Dataset, decorator: Google::Apis::GenomicsV1::Dataset::Representation - - property :next_page_token, as: 'nextPageToken' - end - end - class ListOperationsResponse # @private class Representation < Google::Apis::Core::JsonRepresentation @@ -763,16 +107,6 @@ module Google end end - class MergeVariantsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - hash :info_merge_config, as: 'infoMergeConfig' - property :variant_set_id, as: 'variantSetId' - collection :variants, as: 'variants', class: Google::Apis::GenomicsV1::Variant, decorator: Google::Apis::GenomicsV1::Variant::Representation - - end - end - class Operation # @private class Representation < Google::Apis::Core::JsonRepresentation @@ -810,149 +144,6 @@ module Google end end - class Policy - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :bindings, as: 'bindings', class: Google::Apis::GenomicsV1::Binding, decorator: Google::Apis::GenomicsV1::Binding::Representation - - property :etag, :base64 => true, as: 'etag' - property :version, as: 'version' - end - end - - class Position - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :position, :numeric_string => true, as: 'position' - property :reference_name, as: 'referenceName' - property :reverse_strand, as: 'reverseStrand' - end - end - - class Program - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :command_line, as: 'commandLine' - property :id, as: 'id' - property :name, as: 'name' - property :prev_program_id, as: 'prevProgramId' - property :version, as: 'version' - end - end - - class Range - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :end, :numeric_string => true, as: 'end' - property :reference_name, as: 'referenceName' - property :start, :numeric_string => true, as: 'start' - end - end - - class Read - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :aligned_quality, as: 'alignedQuality' - property :aligned_sequence, as: 'alignedSequence' - property :alignment, as: 'alignment', class: Google::Apis::GenomicsV1::LinearAlignment, decorator: Google::Apis::GenomicsV1::LinearAlignment::Representation - - property :duplicate_fragment, as: 'duplicateFragment' - property :failed_vendor_quality_checks, as: 'failedVendorQualityChecks' - property :fragment_length, as: 'fragmentLength' - property :fragment_name, as: 'fragmentName' - property :id, as: 'id' - hash :info, as: 'info', :class => Array do - include Representable::JSON::Collection - items - end - - property :next_mate_position, as: 'nextMatePosition', class: Google::Apis::GenomicsV1::Position, decorator: Google::Apis::GenomicsV1::Position::Representation - - property :number_reads, as: 'numberReads' - property :proper_placement, as: 'properPlacement' - property :read_group_id, as: 'readGroupId' - property :read_group_set_id, as: 'readGroupSetId' - property :read_number, as: 'readNumber' - property :secondary_alignment, as: 'secondaryAlignment' - property :supplementary_alignment, as: 'supplementaryAlignment' - end - end - - class ReadGroup - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :dataset_id, as: 'datasetId' - property :description, as: 'description' - property :experiment, as: 'experiment', class: Google::Apis::GenomicsV1::Experiment, decorator: Google::Apis::GenomicsV1::Experiment::Representation - - property :id, as: 'id' - hash :info, as: 'info', :class => Array do - include Representable::JSON::Collection - items - end - - property :name, as: 'name' - property :predicted_insert_size, as: 'predictedInsertSize' - collection :programs, as: 'programs', class: Google::Apis::GenomicsV1::Program, decorator: Google::Apis::GenomicsV1::Program::Representation - - property :reference_set_id, as: 'referenceSetId' - property :sample_id, as: 'sampleId' - end - end - - class ReadGroupSet - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :dataset_id, as: 'datasetId' - property :filename, as: 'filename' - property :id, as: 'id' - hash :info, as: 'info', :class => Array do - include Representable::JSON::Collection - items - end - - property :name, as: 'name' - collection :read_groups, as: 'readGroups', class: Google::Apis::GenomicsV1::ReadGroup, decorator: Google::Apis::GenomicsV1::ReadGroup::Representation - - property :reference_set_id, as: 'referenceSetId' - end - end - - class Reference - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :id, as: 'id' - property :length, :numeric_string => true, as: 'length' - property :md5checksum, as: 'md5checksum' - property :name, as: 'name' - property :ncbi_taxon_id, as: 'ncbiTaxonId' - collection :source_accessions, as: 'sourceAccessions' - property :source_uri, as: 'sourceUri' - end - end - - class ReferenceBound - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :reference_name, as: 'referenceName' - property :upper_bound, :numeric_string => true, as: 'upperBound' - end - end - - class ReferenceSet - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :assembly_id, as: 'assemblyId' - property :description, as: 'description' - property :id, as: 'id' - property :md5checksum, as: 'md5checksum' - property :ncbi_taxon_id, as: 'ncbiTaxonId' - collection :reference_ids, as: 'referenceIds' - collection :source_accessions, as: 'sourceAccessions' - property :source_uri, as: 'sourceUri' - end - end - class RuntimeMetadata # @private class Representation < Google::Apis::Core::JsonRepresentation @@ -961,199 +152,6 @@ module Google end end - class SearchAnnotationSetsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :dataset_ids, as: 'datasetIds' - property :name, as: 'name' - property :page_size, as: 'pageSize' - property :page_token, as: 'pageToken' - property :reference_set_id, as: 'referenceSetId' - collection :types, as: 'types' - end - end - - class SearchAnnotationSetsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :annotation_sets, as: 'annotationSets', class: Google::Apis::GenomicsV1::AnnotationSet, decorator: Google::Apis::GenomicsV1::AnnotationSet::Representation - - property :next_page_token, as: 'nextPageToken' - end - end - - class SearchAnnotationsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :annotation_set_ids, as: 'annotationSetIds' - property :end, :numeric_string => true, as: 'end' - property :page_size, as: 'pageSize' - property :page_token, as: 'pageToken' - property :reference_id, as: 'referenceId' - property :reference_name, as: 'referenceName' - property :start, :numeric_string => true, as: 'start' - end - end - - class SearchAnnotationsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :annotations, as: 'annotations', class: Google::Apis::GenomicsV1::Annotation, decorator: Google::Apis::GenomicsV1::Annotation::Representation - - property :next_page_token, as: 'nextPageToken' - end - end - - class SearchCallSetsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :name, as: 'name' - property :page_size, as: 'pageSize' - property :page_token, as: 'pageToken' - collection :variant_set_ids, as: 'variantSetIds' - end - end - - class SearchCallSetsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :call_sets, as: 'callSets', class: Google::Apis::GenomicsV1::CallSet, decorator: Google::Apis::GenomicsV1::CallSet::Representation - - property :next_page_token, as: 'nextPageToken' - end - end - - class SearchReadGroupSetsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :dataset_ids, as: 'datasetIds' - property :name, as: 'name' - property :page_size, as: 'pageSize' - property :page_token, as: 'pageToken' - end - end - - class SearchReadGroupSetsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :next_page_token, as: 'nextPageToken' - collection :read_group_sets, as: 'readGroupSets', class: Google::Apis::GenomicsV1::ReadGroupSet, decorator: Google::Apis::GenomicsV1::ReadGroupSet::Representation - - end - end - - class SearchReadsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :end, :numeric_string => true, as: 'end' - property :page_size, as: 'pageSize' - property :page_token, as: 'pageToken' - collection :read_group_ids, as: 'readGroupIds' - collection :read_group_set_ids, as: 'readGroupSetIds' - property :reference_name, as: 'referenceName' - property :start, :numeric_string => true, as: 'start' - end - end - - class SearchReadsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :alignments, as: 'alignments', class: Google::Apis::GenomicsV1::Read, decorator: Google::Apis::GenomicsV1::Read::Representation - - property :next_page_token, as: 'nextPageToken' - end - end - - class SearchReferenceSetsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :accessions, as: 'accessions' - property :assembly_id, as: 'assemblyId' - collection :md5checksums, as: 'md5checksums' - property :page_size, as: 'pageSize' - property :page_token, as: 'pageToken' - end - end - - class SearchReferenceSetsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :next_page_token, as: 'nextPageToken' - collection :reference_sets, as: 'referenceSets', class: Google::Apis::GenomicsV1::ReferenceSet, decorator: Google::Apis::GenomicsV1::ReferenceSet::Representation - - end - end - - class SearchReferencesRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :accessions, as: 'accessions' - collection :md5checksums, as: 'md5checksums' - property :page_size, as: 'pageSize' - property :page_token, as: 'pageToken' - property :reference_set_id, as: 'referenceSetId' - end - end - - class SearchReferencesResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :next_page_token, as: 'nextPageToken' - collection :references, as: 'references', class: Google::Apis::GenomicsV1::Reference, decorator: Google::Apis::GenomicsV1::Reference::Representation - - end - end - - class SearchVariantSetsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :dataset_ids, as: 'datasetIds' - property :page_size, as: 'pageSize' - property :page_token, as: 'pageToken' - end - end - - class SearchVariantSetsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :next_page_token, as: 'nextPageToken' - collection :variant_sets, as: 'variantSets', class: Google::Apis::GenomicsV1::VariantSet, decorator: Google::Apis::GenomicsV1::VariantSet::Representation - - end - end - - class SearchVariantsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :call_set_ids, as: 'callSetIds' - property :end, :numeric_string => true, as: 'end' - property :max_calls, as: 'maxCalls' - property :page_size, as: 'pageSize' - property :page_token, as: 'pageToken' - property :reference_name, as: 'referenceName' - property :start, :numeric_string => true, as: 'start' - property :variant_name, as: 'variantName' - collection :variant_set_ids, as: 'variantSetIds' - end - end - - class SearchVariantsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :next_page_token, as: 'nextPageToken' - collection :variants, as: 'variants', class: Google::Apis::GenomicsV1::Variant, decorator: Google::Apis::GenomicsV1::Variant::Representation - - end - end - - class SetIamPolicyRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :policy, as: 'policy', class: Google::Apis::GenomicsV1::Policy, decorator: Google::Apis::GenomicsV1::Policy::Representation - - end - end - class Status # @private class Representation < Google::Apis::Core::JsonRepresentation @@ -1162,123 +160,6 @@ module Google property :message, as: 'message' end end - - class TestIamPermissionsRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :permissions, as: 'permissions' - end - end - - class TestIamPermissionsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :permissions, as: 'permissions' - end - end - - class Transcript - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :coding_sequence, as: 'codingSequence', class: Google::Apis::GenomicsV1::CodingSequence, decorator: Google::Apis::GenomicsV1::CodingSequence::Representation - - collection :exons, as: 'exons', class: Google::Apis::GenomicsV1::Exon, decorator: Google::Apis::GenomicsV1::Exon::Representation - - property :gene_id, as: 'geneId' - end - end - - class UndeleteDatasetRequest - # @private - class Representation < Google::Apis::Core::JsonRepresentation - end - end - - class Variant - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :alternate_bases, as: 'alternateBases' - collection :calls, as: 'calls', class: Google::Apis::GenomicsV1::VariantCall, decorator: Google::Apis::GenomicsV1::VariantCall::Representation - - property :created, :numeric_string => true, as: 'created' - property :end, :numeric_string => true, as: 'end' - collection :filter, as: 'filter' - property :id, as: 'id' - hash :info, as: 'info', :class => Array do - include Representable::JSON::Collection - items - end - - collection :names, as: 'names' - property :quality, as: 'quality' - property :reference_bases, as: 'referenceBases' - property :reference_name, as: 'referenceName' - property :start, :numeric_string => true, as: 'start' - property :variant_set_id, as: 'variantSetId' - end - end - - class VariantAnnotation - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :alternate_bases, as: 'alternateBases' - property :clinical_significance, as: 'clinicalSignificance' - collection :conditions, as: 'conditions', class: Google::Apis::GenomicsV1::ClinicalCondition, decorator: Google::Apis::GenomicsV1::ClinicalCondition::Representation - - property :effect, as: 'effect' - property :gene_id, as: 'geneId' - collection :transcript_ids, as: 'transcriptIds' - property :type, as: 'type' - end - end - - class VariantCall - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :call_set_id, as: 'callSetId' - property :call_set_name, as: 'callSetName' - collection :genotype, as: 'genotype' - collection :genotype_likelihood, as: 'genotypeLikelihood' - hash :info, as: 'info', :class => Array do - include Representable::JSON::Collection - items - end - - property :phaseset, as: 'phaseset' - end - end - - class VariantSet - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :dataset_id, as: 'datasetId' - property :description, as: 'description' - property :id, as: 'id' - collection :metadata, as: 'metadata', class: Google::Apis::GenomicsV1::VariantSetMetadata, decorator: Google::Apis::GenomicsV1::VariantSetMetadata::Representation - - property :name, as: 'name' - collection :reference_bounds, as: 'referenceBounds', class: Google::Apis::GenomicsV1::ReferenceBound, decorator: Google::Apis::GenomicsV1::ReferenceBound::Representation - - property :reference_set_id, as: 'referenceSetId' - end - end - - class VariantSetMetadata - # @private - class Representation < Google::Apis::Core::JsonRepresentation - property :description, as: 'description' - property :id, as: 'id' - hash :info, as: 'info', :class => Array do - include Representable::JSON::Collection - items - end - - property :key, as: 'key' - property :number, as: 'number' - property :type, as: 'type' - property :value, as: 'value' - end - end end end end diff --git a/generated/google/apis/genomics_v1/service.rb b/generated/google/apis/genomics_v1/service.rb index 4eca1629b..52aadd95c 100644 --- a/generated/google/apis/genomics_v1/service.rb +++ b/generated/google/apis/genomics_v1/service.rb @@ -47,929 +47,6 @@ module Google @batch_path = 'batch' end - # Creates one or more new annotations atomically. All annotations must - # belong to the same annotation set. Caller must have WRITE - # permission for this annotation set. For optimal performance, batch - # positionally adjacent annotations together. - # If the request has a systemic issue, such as an attempt to write to - # an inaccessible annotation set, the entire RPC will fail accordingly. For - # lesser data issues, when possible an error will be isolated to the - # corresponding batch entry in the response; the remaining well formed - # annotations will be created normally. - # For details on the requirements for each individual annotation resource, - # see - # CreateAnnotation. - # @param [Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest] batch_create_annotations_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/annotations:batchCreate', options) - command.request_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest::Representation - command.request_object = batch_create_annotations_request_object - command.response_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Creates a new annotation. Caller must have WRITE permission - # for the associated annotation set. - # The following fields are required: - # * annotationSetId - # * referenceName or - # referenceId - # ### Transcripts - # For annotations of type TRANSCRIPT, the following fields of - # transcript must be provided: - # * exons.start - # * exons.end - # All other fields may be optionally specified, unless documented as being - # server-generated (for example, the `id` field). The annotated - # range must be no longer than 100Mbp (mega base pairs). See the - # Annotation resource - # for additional restrictions on each field. - # @param [Google::Apis::GenomicsV1::Annotation] annotation_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Annotation] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def create_annotation(annotation_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/annotations', options) - command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation - command.request_object = annotation_object - command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation - command.response_class = Google::Apis::GenomicsV1::Annotation - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Deletes an annotation. Caller must have WRITE permission for - # the associated annotation set. - # @param [String] annotation_id - # The ID of the annotation to be deleted. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Empty] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/annotations/{annotationId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['annotationId'] = annotation_id unless annotation_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets an annotation. Caller must have READ permission - # for the associated annotation set. - # @param [String] annotation_id - # The ID of the annotation to be retrieved. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Annotation] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/annotations/{annotationId}', options) - command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation - command.response_class = Google::Apis::GenomicsV1::Annotation - command.params['annotationId'] = annotation_id unless annotation_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Searches for annotations that match the given criteria. Results are - # ordered by genomic coordinate (by reference sequence, then position). - # Annotations with equivalent genomic coordinates are returned in an - # unspecified order. This order is consistent, such that two queries for the - # same content (regardless of page size) yield annotations in the same order - # across their respective streams of paginated responses. Caller must have - # READ permission for the queried annotation sets. - # @param [Google::Apis::GenomicsV1::SearchAnnotationsRequest] search_annotations_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationsResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::SearchAnnotationsResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/annotations/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationsRequest::Representation - command.request_object = search_annotations_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchAnnotationsResponse - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Updates an annotation. Caller must have - # WRITE permission for the associated dataset. - # @param [String] annotation_id - # The ID of the annotation to be updated. - # @param [Google::Apis::GenomicsV1::Annotation] annotation_object - # @param [String] update_mask - # An optional mask specifying which fields to update. Mutable fields are - # name, - # variant, - # transcript, and - # info. If unspecified, all mutable - # fields will be updated. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Annotation] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def update_annotation(annotation_id, annotation_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:put, 'v1/annotations/{annotationId}', options) - command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation - command.request_object = annotation_object - command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation - command.response_class = Google::Apis::GenomicsV1::Annotation - command.params['annotationId'] = annotation_id unless annotation_id.nil? - command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Creates a new annotation set. Caller must have WRITE permission for the - # associated dataset. - # The following fields are required: - # * datasetId - # * referenceSetId - # All other fields may be optionally specified, unless documented as being - # server-generated (for example, the `id` field). - # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::AnnotationSet] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/annotationsets', options) - command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation - command.request_object = annotation_set_object - command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation - command.response_class = Google::Apis::GenomicsV1::AnnotationSet - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Deletes an annotation set. Caller must have WRITE permission - # for the associated annotation set. - # @param [String] annotation_set_id - # The ID of the annotation set to be deleted. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Empty] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_annotationset(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/annotationsets/{annotationSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets an annotation set. Caller must have READ permission for - # the associated dataset. - # @param [String] annotation_set_id - # The ID of the annotation set to be retrieved. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::AnnotationSet] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/annotationsets/{annotationSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation - command.response_class = Google::Apis::GenomicsV1::AnnotationSet - command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Searches for annotation sets that match the given criteria. Annotation sets - # are returned in an unspecified order. This order is consistent, such that - # two queries for the same content (regardless of page size) yield annotation - # sets in the same order across their respective streams of paginated - # responses. Caller must have READ permission for the queried datasets. - # @param [Google::Apis::GenomicsV1::SearchAnnotationSetsRequest] search_annotation_sets_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/annotationsets/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsRequest::Representation - command.request_object = search_annotation_sets_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Updates an annotation set. The update must respect all mutability - # restrictions and other invariants described on the annotation set resource. - # Caller must have WRITE permission for the associated dataset. - # @param [String] annotation_set_id - # The ID of the annotation set to be updated. - # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object - # @param [String] update_mask - # An optional mask specifying which fields to update. Mutable fields are - # name, - # source_uri, and - # info. If unspecified, all - # mutable fields will be updated. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::AnnotationSet] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:put, 'v1/annotationsets/{annotationSetId}', options) - command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation - command.request_object = annotation_set_object - command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation - command.response_class = Google::Apis::GenomicsV1::AnnotationSet - command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? - command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Creates a new call set. - # For the definitions of call sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [Google::Apis::GenomicsV1::CallSet] call_set_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::CallSet] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/callsets', options) - command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation - command.request_object = call_set_object - command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation - command.response_class = Google::Apis::GenomicsV1::CallSet - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Deletes a call set. - # For the definitions of call sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] call_set_id - # The ID of the call set to be deleted. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Empty] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/callsets/{callSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['callSetId'] = call_set_id unless call_set_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets a call set by ID. - # For the definitions of call sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] call_set_id - # The ID of the call set. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::CallSet] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/callsets/{callSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation - command.response_class = Google::Apis::GenomicsV1::CallSet - command.params['callSetId'] = call_set_id unless call_set_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Updates a call set. - # For the definitions of call sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # This method supports patch semantics. - # @param [String] call_set_id - # The ID of the call set to be updated. - # @param [Google::Apis::GenomicsV1::CallSet] call_set_object - # @param [String] update_mask - # An optional mask specifying which fields to update. At this time, the only - # mutable field is name. The only - # acceptable value is "name". If unspecified, all mutable fields will be - # updated. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::CallSet] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:patch, 'v1/callsets/{callSetId}', options) - command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation - command.request_object = call_set_object - command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation - command.response_class = Google::Apis::GenomicsV1::CallSet - command.params['callSetId'] = call_set_id unless call_set_id.nil? - command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets a list of call sets matching the criteria. - # For the definitions of call sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5. - # 1/src/main/resources/avro/variantmethods.avdl#L178). - # @param [Google::Apis::GenomicsV1::SearchCallSetsRequest] search_call_sets_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchCallSetsResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::SearchCallSetsResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/callsets/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchCallSetsRequest::Representation - command.request_object = search_call_sets_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchCallSetsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchCallSetsResponse - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Creates a new dataset. - # For the definitions of datasets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [Google::Apis::GenomicsV1::Dataset] dataset_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Dataset] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/datasets', options) - command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation - command.request_object = dataset_object - command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation - command.response_class = Google::Apis::GenomicsV1::Dataset - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Deletes a dataset and all of its contents (all read group sets, - # reference sets, variant sets, call sets, annotation sets, etc.) - # This is reversible (up to one week after the deletion) via - # the - # datasets.undelete - # operation. - # For the definitions of datasets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] dataset_id - # The ID of the dataset to be deleted. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Empty] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/datasets/{datasetId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['datasetId'] = dataset_id unless dataset_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets a dataset by ID. - # For the definitions of datasets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] dataset_id - # The ID of the dataset. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Dataset] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/datasets/{datasetId}', options) - command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation - command.response_class = Google::Apis::GenomicsV1::Dataset - command.params['datasetId'] = dataset_id unless dataset_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets the access control policy for the dataset. This is empty if the - # policy or resource does not exist. - # See Getting a - # Policy for more information. - # For the definitions of datasets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] resource - # REQUIRED: The resource for which policy is being specified. Format is - # `datasets/`. - # @param [Google::Apis::GenomicsV1::GetIamPolicyRequest] get_iam_policy_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Policy] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/{+resource}:getIamPolicy', options) - command.request_representation = Google::Apis::GenomicsV1::GetIamPolicyRequest::Representation - command.request_object = get_iam_policy_request_object - command.response_representation = Google::Apis::GenomicsV1::Policy::Representation - command.response_class = Google::Apis::GenomicsV1::Policy - command.params['resource'] = resource unless resource.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Lists datasets within a project. - # For the definitions of datasets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [Fixnum] page_size - # The maximum number of results to return in a single page. If unspecified, - # defaults to 50. The maximum value is 1024. - # @param [String] page_token - # The continuation token, which is used to page through large result sets. - # To get the next page of results, set this parameter to the value of - # `nextPageToken` from the previous response. - # @param [String] project_id - # Required. The Google Cloud project ID to list datasets for. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ListDatasetsResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::ListDatasetsResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def list_datasets(page_size: nil, page_token: nil, project_id: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/datasets', options) - command.response_representation = Google::Apis::GenomicsV1::ListDatasetsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::ListDatasetsResponse - command.query['pageSize'] = page_size unless page_size.nil? - command.query['pageToken'] = page_token unless page_token.nil? - command.query['projectId'] = project_id unless project_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Updates a dataset. - # For the definitions of datasets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # This method supports patch semantics. - # @param [String] dataset_id - # The ID of the dataset to be updated. - # @param [Google::Apis::GenomicsV1::Dataset] dataset_object - # @param [String] update_mask - # An optional mask specifying which fields to update. At this time, the only - # mutable field is name. The only - # acceptable value is "name". If unspecified, all mutable fields will be - # updated. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Dataset] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:patch, 'v1/datasets/{datasetId}', options) - command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation - command.request_object = dataset_object - command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation - command.response_class = Google::Apis::GenomicsV1::Dataset - command.params['datasetId'] = dataset_id unless dataset_id.nil? - command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Sets the access control policy on the specified dataset. Replaces any - # existing policy. - # For the definitions of datasets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # See Setting a - # Policy for more information. - # @param [String] resource - # REQUIRED: The resource for which policy is being specified. Format is - # `datasets/`. - # @param [Google::Apis::GenomicsV1::SetIamPolicyRequest] set_iam_policy_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Policy] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/{+resource}:setIamPolicy', options) - command.request_representation = Google::Apis::GenomicsV1::SetIamPolicyRequest::Representation - command.request_object = set_iam_policy_request_object - command.response_representation = Google::Apis::GenomicsV1::Policy::Representation - command.response_class = Google::Apis::GenomicsV1::Policy - command.params['resource'] = resource unless resource.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Returns permissions that a caller has on the specified resource. - # See Testing - # Permissions for more information. - # For the definitions of datasets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] resource - # REQUIRED: The resource for which policy is being specified. Format is - # `datasets/`. - # @param [Google::Apis::GenomicsV1::TestIamPermissionsRequest] test_iam_permissions_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::TestIamPermissionsResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::TestIamPermissionsResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/{+resource}:testIamPermissions', options) - command.request_representation = Google::Apis::GenomicsV1::TestIamPermissionsRequest::Representation - command.request_object = test_iam_permissions_request_object - command.response_representation = Google::Apis::GenomicsV1::TestIamPermissionsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::TestIamPermissionsResponse - command.params['resource'] = resource unless resource.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Undeletes a dataset by restoring a dataset which was deleted via this API. - # For the definitions of datasets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # This operation is only possible for a week after the deletion occurred. - # @param [String] dataset_id - # The ID of the dataset to be undeleted. - # @param [Google::Apis::GenomicsV1::UndeleteDatasetRequest] undelete_dataset_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Dataset] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/datasets/{datasetId}:undelete', options) - command.request_representation = Google::Apis::GenomicsV1::UndeleteDatasetRequest::Representation - command.request_object = undelete_dataset_request_object - command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation - command.response_class = Google::Apis::GenomicsV1::Dataset - command.params['datasetId'] = dataset_id unless dataset_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - # Starts asynchronous cancellation on a long-running operation. The server makes # a best effort to cancel the operation, but success is not guaranteed. Clients # may use Operations.GetOperation or Operations.ListOperations to check whether @@ -1092,1109 +169,6 @@ module Google command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end - - # Deletes a read group set. - # For the definitions of read group sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] read_group_set_id - # The ID of the read group set to be deleted. The caller must have WRITE - # permissions to the dataset associated with this read group set. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Empty] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/readgroupsets/{readGroupSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Exports a read group set to a BAM file in Google Cloud Storage. - # For the definitions of read group sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Note that currently there may be some differences between exported BAM - # files and the original BAM file at the time of import. See - # ImportReadGroupSets - # for caveats. - # @param [String] read_group_set_id - # Required. The ID of the read group set to export. The caller must have - # READ access to this read group set. - # @param [Google::Apis::GenomicsV1::ExportReadGroupSetRequest] export_read_group_set_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Operation] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/readgroupsets/{readGroupSetId}:export', options) - command.request_representation = Google::Apis::GenomicsV1::ExportReadGroupSetRequest::Representation - command.request_object = export_read_group_set_request_object - command.response_representation = Google::Apis::GenomicsV1::Operation::Representation - command.response_class = Google::Apis::GenomicsV1::Operation - command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets a read group set by ID. - # For the definitions of read group sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] read_group_set_id - # The ID of the read group set. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::ReadGroupSet] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation - command.response_class = Google::Apis::GenomicsV1::ReadGroupSet - command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Creates read group sets by asynchronously importing the provided - # information. - # For the definitions of read group sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # The caller must have WRITE permissions to the dataset. - # ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import - # - Tags will be converted to strings - tag types are not preserved - # - Comments (`@CO`) in the input file header will not be preserved - # - Original header order of references (`@SQ`) will not be preserved - # - Any reverse stranded unmapped reads will be reverse complemented, and - # their qualities (also the "BQ" and "OQ" tags, if any) will be reversed - # - Unmapped reads will be stripped of positional information (reference name - # and position) - # @param [Google::Apis::GenomicsV1::ImportReadGroupSetsRequest] import_read_group_sets_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Operation] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/readgroupsets:import', options) - command.request_representation = Google::Apis::GenomicsV1::ImportReadGroupSetsRequest::Representation - command.request_object = import_read_group_sets_request_object - command.response_representation = Google::Apis::GenomicsV1::Operation::Representation - command.response_class = Google::Apis::GenomicsV1::Operation - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Updates a read group set. - # For the definitions of read group sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # This method supports patch semantics. - # @param [String] read_group_set_id - # The ID of the read group set to be updated. The caller must have WRITE - # permissions to the dataset associated with this read group set. - # @param [Google::Apis::GenomicsV1::ReadGroupSet] read_group_set_object - # @param [String] update_mask - # An optional mask specifying which fields to update. Supported fields: - # * name. - # * referenceSetId. - # Leaving `updateMask` unset is equivalent to specifying all mutable - # fields. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::ReadGroupSet] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:patch, 'v1/readgroupsets/{readGroupSetId}', options) - command.request_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation - command.request_object = read_group_set_object - command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation - command.response_class = Google::Apis::GenomicsV1::ReadGroupSet - command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? - command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Searches for read group sets matching the criteria. - # For the definitions of read group sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/ - # v0.5.1/src/main/resources/avro/readmethods.avdl#L135). - # @param [Google::Apis::GenomicsV1::SearchReadGroupSetsRequest] search_read_group_sets_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/readgroupsets/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsRequest::Representation - command.request_object = search_read_group_sets_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Lists fixed width coverage buckets for a read group set, each of which - # correspond to a range of a reference sequence. Each bucket summarizes - # coverage information across its corresponding genomic range. - # For the definitions of read group sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Coverage is defined as the number of reads which are aligned to a given - # base in the reference sequence. Coverage buckets are available at several - # precomputed bucket widths, enabling retrieval of various coverage 'zoom - # levels'. The caller must have READ permissions for the target read group - # set. - # @param [String] read_group_set_id - # Required. The ID of the read group set over which coverage is requested. - # @param [Fixnum] end_ - # The end position of the range on the reference, 0-based exclusive. If - # specified, `referenceName` must also be specified. If unset or 0, defaults - # to the length of the reference. - # @param [Fixnum] page_size - # The maximum number of results to return in a single page. If unspecified, - # defaults to 1024. The maximum value is 2048. - # @param [String] page_token - # The continuation token, which is used to page through large result sets. - # To get the next page of results, set this parameter to the value of - # `nextPageToken` from the previous response. - # @param [String] reference_name - # The name of the reference to query, within the reference set associated - # with this query. Optional. - # @param [Fixnum] start - # The start position of the range on the reference, 0-based inclusive. If - # specified, `referenceName` must also be specified. Defaults to 0. - # @param [Fixnum] target_bucket_width - # The desired width of each reported coverage bucket in base pairs. This - # will be rounded down to the nearest precomputed bucket width; the value - # of which is returned as `bucketWidth` in the response. Defaults - # to infinity (each bucket spans an entire reference sequence) or the length - # of the target range, if specified. The smallest precomputed - # `bucketWidth` is currently 2048 base pairs; this is subject to - # change. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def list_coverage_buckets(read_group_set_id, end_: nil, page_size: nil, page_token: nil, reference_name: nil, start: nil, target_bucket_width: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}/coveragebuckets', options) - command.response_representation = Google::Apis::GenomicsV1::ListCoverageBucketsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::ListCoverageBucketsResponse - command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? - command.query['end'] = end_ unless end_.nil? - command.query['pageSize'] = page_size unless page_size.nil? - command.query['pageToken'] = page_token unless page_token.nil? - command.query['referenceName'] = reference_name unless reference_name.nil? - command.query['start'] = start unless start.nil? - command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets a list of reads for one or more read group sets. - # For the definitions of read group sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Reads search operates over a genomic coordinate space of reference sequence - # & position defined over the reference sequences to which the requested - # read group sets are aligned. - # If a target positional range is specified, search returns all reads whose - # alignment to the reference genome overlap the range. A query which - # specifies only read group set IDs yields all reads in those read group - # sets, including unmapped reads. - # All reads returned (including reads on subsequent pages) are ordered by - # genomic coordinate (by reference sequence, then position). Reads with - # equivalent genomic coordinates are returned in an unspecified order. This - # order is consistent, such that two queries for the same content (regardless - # of page size) yield reads in the same order across their respective streams - # of paginated responses. - # Implements - # [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/ - # src/main/resources/avro/readmethods.avdl#L85). - # @param [Google::Apis::GenomicsV1::SearchReadsRequest] search_reads_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchReadsResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::SearchReadsResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/reads/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchReadsRequest::Representation - command.request_object = search_reads_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchReadsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchReadsResponse - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets a reference. - # For the definitions of references and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/ - # src/main/resources/avro/referencemethods.avdl#L158). - # @param [String] reference_id - # The ID of the reference. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Reference] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Reference] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_reference(reference_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/references/{referenceId}', options) - command.response_representation = Google::Apis::GenomicsV1::Reference::Representation - command.response_class = Google::Apis::GenomicsV1::Reference - command.params['referenceId'] = reference_id unless reference_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Searches for references which match the given criteria. - # For the definitions of references and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0. - # 5.1/src/main/resources/avro/referencemethods.avdl#L146). - # @param [Google::Apis::GenomicsV1::SearchReferencesRequest] search_references_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchReferencesResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::SearchReferencesResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/references/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchReferencesRequest::Representation - command.request_object = search_references_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchReferencesResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchReferencesResponse - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Lists the bases in a reference, optionally restricted to a range. - # For the definitions of references and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0. - # 5.1/src/main/resources/avro/referencemethods.avdl#L221). - # @param [String] reference_id - # The ID of the reference. - # @param [Fixnum] end_position - # The end position (0-based, exclusive) of this query. Defaults to the length - # of this reference. - # @param [Fixnum] page_size - # The maximum number of bases to return in a single page. If unspecified, - # defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base - # pairs). - # @param [String] page_token - # The continuation token, which is used to page through large result sets. - # To get the next page of results, set this parameter to the value of - # `nextPageToken` from the previous response. - # @param [Fixnum] start_position - # The start position (0-based) of this query. Defaults to 0. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ListBasesResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::ListBasesResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def list_reference_bases(reference_id, end_position: nil, page_size: nil, page_token: nil, start_position: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/references/{referenceId}/bases', options) - command.response_representation = Google::Apis::GenomicsV1::ListBasesResponse::Representation - command.response_class = Google::Apis::GenomicsV1::ListBasesResponse - command.params['referenceId'] = reference_id unless reference_id.nil? - command.query['end'] = end_position unless end_position.nil? - command.query['pageSize'] = page_size unless page_size.nil? - command.query['pageToken'] = page_token unless page_token.nil? - command.query['start'] = start_position unless start_position.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets a reference set. - # For the definitions of references and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5. - # 1/src/main/resources/avro/referencemethods.avdl#L83). - # @param [String] reference_set_id - # The ID of the reference set. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ReferenceSet] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::ReferenceSet] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/referencesets/{referenceSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::ReferenceSet::Representation - command.response_class = Google::Apis::GenomicsV1::ReferenceSet - command.params['referenceSetId'] = reference_set_id unless reference_set_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Searches for reference sets which match the given criteria. - # For the definitions of references and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/ - # v0.5.1/src/main/resources/avro/referencemethods.avdl#L71) - # @param [Google::Apis::GenomicsV1::SearchReferenceSetsRequest] search_reference_sets_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/referencesets/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchReferenceSetsRequest::Representation - command.request_object = search_reference_sets_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchReferenceSetsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchReferenceSetsResponse - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Creates a new variant. - # For the definitions of variants and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [Google::Apis::GenomicsV1::Variant] variant_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Variant] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variants', options) - command.request_representation = Google::Apis::GenomicsV1::Variant::Representation - command.request_object = variant_object - command.response_representation = Google::Apis::GenomicsV1::Variant::Representation - command.response_class = Google::Apis::GenomicsV1::Variant - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Deletes a variant. - # For the definitions of variants and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] variant_id - # The ID of the variant to be deleted. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Empty] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/variants/{variantId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['variantId'] = variant_id unless variant_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets a variant by ID. - # For the definitions of variants and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] variant_id - # The ID of the variant. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Variant] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/variants/{variantId}', options) - command.response_representation = Google::Apis::GenomicsV1::Variant::Representation - command.response_class = Google::Apis::GenomicsV1::Variant - command.params['variantId'] = variant_id unless variant_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Creates variant data by asynchronously importing the provided information. - # For the definitions of variant sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # The variants for import will be merged with any existing variant that - # matches its reference sequence, start, end, reference bases, and - # alternative bases. If no such variant exists, a new one will be created. - # When variants are merged, the call information from the new variant - # is added to the existing variant, and Variant info fields are merged - # as specified in - # infoMergeConfig. - # As a special case, for single-sample VCF files, QUAL and FILTER fields will - # be moved to the call level; these are sometimes interpreted in a - # call-specific context. - # Imported VCF headers are appended to the metadata already in a variant set. - # @param [Google::Apis::GenomicsV1::ImportVariantsRequest] import_variants_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Operation] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variants:import', options) - command.request_representation = Google::Apis::GenomicsV1::ImportVariantsRequest::Representation - command.request_object = import_variants_request_object - command.response_representation = Google::Apis::GenomicsV1::Operation::Representation - command.response_class = Google::Apis::GenomicsV1::Operation - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Merges the given variants with existing variants. - # For the definitions of variants and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Each variant will be - # merged with an existing variant that matches its reference sequence, - # start, end, reference bases, and alternative bases. If no such variant - # exists, a new one will be created. - # When variants are merged, the call information from the new variant - # is added to the existing variant. Variant info fields are merged as - # specified in the - # infoMergeConfig - # field of the MergeVariantsRequest. - # Please exercise caution when using this method! It is easy to introduce - # mistakes in existing variants and difficult to back out of them. For - # example, - # suppose you were trying to merge a new variant with an existing one and - # both - # variants contain calls that belong to callsets with the same callset ID. - # // Existing variant - irrelevant fields trimmed for clarity - # ` - # "variantSetId": "10473108253681171589", - # "referenceName": "1", - # "start": "10582", - # "referenceBases": "G", - # "alternateBases": [ - # "A" - # ], - # "calls": [ - # ` - # "callSetId": "10473108253681171589-0", - # "callSetName": "CALLSET0", - # "genotype": [ - # 0, - # 1 - # ], - # ` - # ] - # ` - # // New variant with conflicting call information - # ` - # "variantSetId": "10473108253681171589", - # "referenceName": "1", - # "start": "10582", - # "referenceBases": "G", - # "alternateBases": [ - # "A" - # ], - # "calls": [ - # ` - # "callSetId": "10473108253681171589-0", - # "callSetName": "CALLSET0", - # "genotype": [ - # 1, - # 1 - # ], - # ` - # ] - # ` - # The resulting merged variant would overwrite the existing calls with those - # from the new variant: - # ` - # "variantSetId": "10473108253681171589", - # "referenceName": "1", - # "start": "10582", - # "referenceBases": "G", - # "alternateBases": [ - # "A" - # ], - # "calls": [ - # ` - # "callSetId": "10473108253681171589-0", - # "callSetName": "CALLSET0", - # "genotype": [ - # 1, - # 1 - # ], - # ` - # ] - # ` - # This may be the desired outcome, but it is up to the user to determine if - # if that is indeed the case. - # @param [Google::Apis::GenomicsV1::MergeVariantsRequest] merge_variants_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Empty] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variants:merge', options) - command.request_representation = Google::Apis::GenomicsV1::MergeVariantsRequest::Representation - command.request_object = merge_variants_request_object - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Updates a variant. - # For the definitions of variants and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # This method supports patch semantics. Returns the modified variant without - # its calls. - # @param [String] variant_id - # The ID of the variant to be updated. - # @param [Google::Apis::GenomicsV1::Variant] variant_object - # @param [String] update_mask - # An optional mask specifying which fields to update. At this time, mutable - # fields are names and - # info. Acceptable values are "names" and - # "info". If unspecified, all mutable fields will be updated. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Variant] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:patch, 'v1/variants/{variantId}', options) - command.request_representation = Google::Apis::GenomicsV1::Variant::Representation - command.request_object = variant_object - command.response_representation = Google::Apis::GenomicsV1::Variant::Representation - command.response_class = Google::Apis::GenomicsV1::Variant - command.params['variantId'] = variant_id unless variant_id.nil? - command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets a list of variants matching the criteria. - # For the definitions of variants and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5. - # 1/src/main/resources/avro/variantmethods.avdl#L126). - # @param [Google::Apis::GenomicsV1::SearchVariantsRequest] search_variants_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantsResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::SearchVariantsResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variants/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchVariantsRequest::Representation - command.request_object = search_variants_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchVariantsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchVariantsResponse - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Creates a new variant set. - # For the definitions of variant sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # The provided variant set must have a valid `datasetId` set - all other - # fields are optional. Note that the `id` field will be ignored, as this is - # assigned by the server. - # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::VariantSet] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variantsets', options) - command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation - command.request_object = variant_set_object - command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation - command.response_class = Google::Apis::GenomicsV1::VariantSet - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Deletes a variant set including all variants, call sets, and calls within. - # This is not reversible. - # For the definitions of variant sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] variant_set_id - # The ID of the variant set to be deleted. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Empty] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/variantsets/{variantSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Exports variant set data to an external destination. - # For the definitions of variant sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] variant_set_id - # Required. The ID of the variant set that contains variant data which - # should be exported. The caller must have READ access to this variant set. - # @param [Google::Apis::GenomicsV1::ExportVariantSetRequest] export_variant_set_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::Operation] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variantsets/{variantSetId}:export', options) - command.request_representation = Google::Apis::GenomicsV1::ExportVariantSetRequest::Representation - command.request_object = export_variant_set_request_object - command.response_representation = Google::Apis::GenomicsV1::Operation::Representation - command.response_class = Google::Apis::GenomicsV1::Operation - command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Gets a variant set by ID. - # For the definitions of variant sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] variant_set_id - # Required. The ID of the variant set. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::VariantSet] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/variantsets/{variantSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation - command.response_class = Google::Apis::GenomicsV1::VariantSet - command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Updates a variant set using patch semantics. - # For the definitions of variant sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] variant_set_id - # The ID of the variant to be updated (must already exist). - # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object - # @param [String] update_mask - # An optional mask specifying which fields to update. Supported fields: - # * metadata. - # * name. - # * description. - # Leaving `updateMask` unset is equivalent to specifying all mutable - # fields. - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::VariantSet] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:patch, 'v1/variantsets/{variantSetId}', options) - command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation - command.request_object = variant_set_object - command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation - command.response_class = Google::Apis::GenomicsV1::VariantSet - command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? - command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end - - # Returns a list of all variant sets matching search criteria. - # For the definitions of variant sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0. - # 5.1/src/main/resources/avro/variantmethods.avdl#L49). - # @param [Google::Apis::GenomicsV1::SearchVariantSetsRequest] search_variant_sets_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. - # @param [String] quota_user - # Available to use for quota purposes for server-side applications. Can be any - # arbitrary string assigned to a user, but should not exceed 40 characters. - # @param [Google::Apis::RequestOptions] options - # Request-specific options - # - # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantSetsResponse] parsed result object - # @yieldparam err [StandardError] error object if request failed - # - # @return [Google::Apis::GenomicsV1::SearchVariantSetsResponse] - # - # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried - # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification - # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variantsets/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchVariantSetsRequest::Representation - command.request_object = search_variant_sets_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchVariantSetsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchVariantSetsResponse - command.query['fields'] = fields unless fields.nil? - command.query['quotaUser'] = quota_user unless quota_user.nil? - execute_or_queue_command(command, &block) - end protected diff --git a/generated/google/apis/genomics_v1alpha2.rb b/generated/google/apis/genomics_v1alpha2.rb index ddcdb42f7..476e58993 100644 --- a/generated/google/apis/genomics_v1alpha2.rb +++ b/generated/google/apis/genomics_v1alpha2.rb @@ -25,7 +25,7 @@ module Google # @see https://cloud.google.com/genomics module GenomicsV1alpha2 VERSION = 'V1alpha2' - REVISION = '20171113' + REVISION = '20180114' # View and manage your data across Google Cloud Platform services AUTH_CLOUD_PLATFORM = 'https://www.googleapis.com/auth/cloud-platform' diff --git a/generated/google/apis/genomics_v1alpha2/classes.rb b/generated/google/apis/genomics_v1alpha2/classes.rb index e1323fe05..3c76bc3ec 100644 --- a/generated/google/apis/genomics_v1alpha2/classes.rb +++ b/generated/google/apis/genomics_v1alpha2/classes.rb @@ -260,44 +260,6 @@ module Google end end - # The read group set import response. - class ImportReadGroupSetsResponse - include Google::Apis::Core::Hashable - - # IDs of the read group sets that were created. - # Corresponds to the JSON property `readGroupSetIds` - # @return [Array] - attr_accessor :read_group_set_ids - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids) - end - end - - # The variant data import response. - class ImportVariantsResponse - include Google::Apis::Core::Hashable - - # IDs of the call sets created during the import. - # Corresponds to the JSON property `callSetIds` - # @return [Array] - attr_accessor :call_set_ids - - def initialize(**args) - update!(**args) - end - - # Update properties of this object - def update!(**args) - @call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids) - end - end - # The response message for Operations.ListOperations. class ListOperationsResponse include Google::Apis::Core::Hashable diff --git a/generated/google/apis/genomics_v1alpha2/representations.rb b/generated/google/apis/genomics_v1alpha2/representations.rb index f47a8697f..bb4d7cd13 100644 --- a/generated/google/apis/genomics_v1alpha2/representations.rb +++ b/generated/google/apis/genomics_v1alpha2/representations.rb @@ -58,18 +58,6 @@ module Google include Google::Apis::Core::JsonObjectSupport end - class ImportReadGroupSetsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - - class ImportVariantsResponse - class Representation < Google::Apis::Core::JsonRepresentation; end - - include Google::Apis::Core::JsonObjectSupport - end - class ListOperationsResponse class Representation < Google::Apis::Core::JsonRepresentation; end @@ -237,20 +225,6 @@ module Google end end - class ImportReadGroupSetsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :read_group_set_ids, as: 'readGroupSetIds' - end - end - - class ImportVariantsResponse - # @private - class Representation < Google::Apis::Core::JsonRepresentation - collection :call_set_ids, as: 'callSetIds' - end - end - class ListOperationsResponse # @private class Representation < Google::Apis::Core::JsonRepresentation