class Google::Apis::GenomicsV1alpha2::GenomicsService
Genomics API
Uploads, processes, queries, and searches Genomics data in the cloud.
@example
require 'google/apis/genomics_v1alpha2' Genomics = Google::Apis::GenomicsV1alpha2 # Alias the module service = Genomics::GenomicsService.new
Attributes
@return [String]
API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
@return [String]
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.
Public Class Methods
# File lib/google/apis/genomics_v1alpha2/service.rb, line 45 def initialize super('https://genomics.googleapis.com/', '', client_name: 'google-apis-genomics_v1alpha2', client_version: Google::Apis::GenomicsV1alpha2::GEM_VERSION) @batch_path = 'batch' end
Public Instance Methods
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 the cancellation succeeded or the operation completed despite cancellation. Authorization requires the following [Google IAM](cloud.google.com/iam) permission: * `genomics.operations.cancel` @param [String] name
The name of the operation resource to be cancelled.
@param [Google::Apis::GenomicsV1alpha2::CancelOperationRequest] cancel_operation_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::GenomicsV1alpha2::Empty] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1alpha2::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
# File lib/google/apis/genomics_v1alpha2/service.rb, line 78 def cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1alpha2/{+name}:cancel', options) command.request_representation = Google::Apis::GenomicsV1alpha2::CancelOperationRequest::Representation command.request_object = cancel_operation_request_object command.response_representation = Google::Apis::GenomicsV1alpha2::Empty::Representation command.response_class = Google::Apis::GenomicsV1alpha2::Empty command.params['name'] = name unless name.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 pipeline that can be run later. Create takes a Pipeline
that has all fields other than `pipelineId` populated, and then returns the same pipeline with `pipelineId` populated. This id can be used to run the pipeline. Caller must have WRITE permission to the project. @param [Google::Apis::GenomicsV1alpha2::Pipeline] pipeline_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::GenomicsV1alpha2::Pipeline] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1alpha2::Pipeline]
@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
# File lib/google/apis/genomics_v1alpha2/service.rb, line 202 def create_pipeline(pipeline_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1alpha2/pipelines', options) command.request_representation = Google::Apis::GenomicsV1alpha2::Pipeline::Representation command.request_object = pipeline_object command.response_representation = Google::Apis::GenomicsV1alpha2::Pipeline::Representation command.response_class = Google::Apis::GenomicsV1alpha2::Pipeline 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 pipeline based on ID. Caller must have WRITE permission to the project. @param [String] pipeline_id
Caller must have WRITE access to the project in which this pipeline is defined.
@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::GenomicsV1alpha2::Empty] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1alpha2::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
# File lib/google/apis/genomics_v1alpha2/service.rb, line 234 def delete_pipeline(pipeline_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1alpha2/pipelines/{pipelineId}', options) command.response_representation = Google::Apis::GenomicsV1alpha2::Empty::Representation command.response_class = Google::Apis::GenomicsV1alpha2::Empty command.params['pipelineId'] = pipeline_id unless pipeline_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 latest state of a long-running operation. Clients can use this method to poll the operation result at intervals as recommended by the API service. Authorization requires the following [Google IAM](cloud.google.com/iam) permission: * `genomics.operations.get` @param [String] name
The name of the operation resource.
@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::GenomicsV1alpha2::Operation] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1alpha2::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
# File lib/google/apis/genomics_v1alpha2/service.rb, line 113 def get_operation(name, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1alpha2/{+name}', options) command.response_representation = Google::Apis::GenomicsV1alpha2::Operation::Representation command.response_class = Google::Apis::GenomicsV1alpha2::Operation command.params['name'] = name unless name.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Retrieves a pipeline based on ID. Caller must have READ permission to the project. @param [String] pipeline_id
Caller must have READ access to the project in which this pipeline is defined.
@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::GenomicsV1alpha2::Pipeline] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1alpha2::Pipeline]
@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
# File lib/google/apis/genomics_v1alpha2/service.rb, line 265 def get_pipeline(pipeline_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1alpha2/pipelines/{pipelineId}', options) command.response_representation = Google::Apis::GenomicsV1alpha2::Pipeline::Representation command.response_class = Google::Apis::GenomicsV1alpha2::Pipeline command.params['pipelineId'] = pipeline_id unless pipeline_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 controller configuration information. Should only be called by VMs created by the Pipelines Service and not by end users. @param [String] operation_id
The operation to retrieve controller configuration for.
@param [Fixnum] validation_token @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::GenomicsV1alpha2::ControllerConfig] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1alpha2::ControllerConfig]
@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
# File lib/google/apis/genomics_v1alpha2/service.rb, line 297 def get_pipeline_controller_config(operation_id: nil, validation_token: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1alpha2/pipelines:getControllerConfig', options) command.response_representation = Google::Apis::GenomicsV1alpha2::ControllerConfig::Representation command.response_class = Google::Apis::GenomicsV1alpha2::ControllerConfig command.query['operationId'] = operation_id unless operation_id.nil? command.query['validationToken'] = validation_token unless validation_token.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 operations that match the specified filter in the request. Authorization requires the following [Google IAM](cloud.google.com/iam) permission: * `genomics.operations.list` @param [String] name
The name of the operation's parent resource.
@param [String] filter
A string for filtering Operations. In v2alpha1, the following filter fields are supported: * createTime: The time this job was created * events: The set of event (names) that have occurred while running the pipeline. The : operator can be used to determine if a particular event has occurred. * error: If the pipeline is running, this value is NULL. Once the pipeline finishes, the value is the standard Google error code. * labels.key or labels."key with space" where key is a label key. * done: If the pipeline is running, this value is false. Once the pipeline finishes, the value is true. In v1 and v1alpha2, the following filter fields are supported: * projectId: Required. Corresponds to OperationMetadata.projectId. * createTime: The time this job was created, in seconds from the [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=` operators. * status: Can be `RUNNING`, `SUCCESS`, `FAILURE`, or ` CANCELED`. Only one status may be specified. * labels.key where key is a label key. Examples: * `projectId = my-project AND createTime >= 1432140000` * ` projectId = my-project AND createTime >= 1432140000 AND createTime <= 1432150000 AND status = RUNNING` * `projectId = my-project AND labels.color = * ` * `projectId = my-project AND labels.color = red`
@param [Fixnum] page_size
The maximum number of results to return. The maximum value is 256.
@param [String] page_token
The standard list page token.
@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::GenomicsV1alpha2::ListOperationsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1alpha2::ListOperationsResponse]
@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
# File lib/google/apis/genomics_v1alpha2/service.rb, line 167 def list_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1alpha2/{+name}', options) command.response_representation = Google::Apis::GenomicsV1alpha2::ListOperationsResponse::Representation command.response_class = Google::Apis::GenomicsV1alpha2::ListOperationsResponse command.params['name'] = name unless name.nil? command.query['filter'] = filter unless filter.nil? command.query['pageSize'] = page_size unless page_size.nil? command.query['pageToken'] = page_token unless page_token.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 pipelines. Caller must have READ permission to the project. @param [String] name_prefix
Pipelines with names that match this prefix should be returned. If unspecified, all pipelines in the project, up to `pageSize`, will be returned.
@param [Fixnum] page_size
Number of pipelines to return at once. Defaults to 256, and max is 2048.
@param [String] page_token
Token to use to indicate where to start getting results. If unspecified, returns the first page of results.
@param [String] project_id
Required. The name of the project to search for pipelines. Caller must have READ access to this project.
@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::GenomicsV1alpha2::ListPipelinesResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1alpha2::ListPipelinesResponse]
@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
# File lib/google/apis/genomics_v1alpha2/service.rb, line 337 def list_pipelines(name_prefix: nil, page_size: nil, page_token: nil, project_id: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1alpha2/pipelines', options) command.response_representation = Google::Apis::GenomicsV1alpha2::ListPipelinesResponse::Representation command.response_class = Google::Apis::GenomicsV1alpha2::ListPipelinesResponse command.query['namePrefix'] = name_prefix unless name_prefix.nil? 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
Runs a pipeline. If `pipelineId` is specified in the request, then run a saved pipeline. If `ephemeralPipeline` is specified, then run that pipeline once without saving a copy. The caller must have READ permission to the project where the pipeline is stored and WRITE permission to the project where the pipeline will be run, as VMs will be created and storage will be used. If a pipeline operation is still running after 6 days, it will be canceled. @param [Google::Apis::GenomicsV1alpha2::RunPipelineRequest] run_pipeline_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::GenomicsV1alpha2::Operation] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1alpha2::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
# File lib/google/apis/genomics_v1alpha2/service.rb, line 374 def run_pipeline(run_pipeline_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1alpha2/pipelines:run', options) command.request_representation = Google::Apis::GenomicsV1alpha2::RunPipelineRequest::Representation command.request_object = run_pipeline_request_object command.response_representation = Google::Apis::GenomicsV1alpha2::Operation::Representation command.response_class = Google::Apis::GenomicsV1alpha2::Operation command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Sets status of a given operation. Any new timestamps (as determined by description) are appended to TimestampEvents. Should only be called by VMs created by the Pipelines Service and not by end users. @param [Google::Apis::GenomicsV1alpha2::SetOperationStatusRequest] set_operation_status_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::GenomicsV1alpha2::Empty] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1alpha2::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
# File lib/google/apis/genomics_v1alpha2/service.rb, line 406 def set_pipeline_operation_status(set_operation_status_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:put, 'v1alpha2/pipelines:setOperationStatus', options) command.request_representation = Google::Apis::GenomicsV1alpha2::SetOperationStatusRequest::Representation command.request_object = set_operation_status_request_object command.response_representation = Google::Apis::GenomicsV1alpha2::Empty::Representation command.response_class = Google::Apis::GenomicsV1alpha2::Empty command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Protected Instance Methods
# File lib/google/apis/genomics_v1alpha2/service.rb, line 419 def apply_command_defaults(command) command.query['key'] = key unless key.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? end