Class: Google::Apis::GenomicsV1alpha2::GenomicsService

Inherits:
Core::BaseService show all
Defined in:
generated/google/apis/genomics_v1alpha2/service.rb

Overview

Genomics API

Uploads, processes, queries, and searches Genomics data in the cloud.

Examples:

require 'google/apis/genomics_v1alpha2'

Genomics = Google::Apis::GenomicsV1alpha2 # Alias the module
service = Genomics::GenomicsService.new

See Also:

Instance Attribute Summary collapse

Attributes inherited from Core::BaseService

#authorization, #base_path, #batch_path, #client, #client_options, #request_options, #root_url, #upload_path

Instance Method Summary collapse

Methods inherited from Core::BaseService

#batch, #batch_upload, #fetch_all, #http

Methods included from Core::Logging

#logger

Constructor Details

#initialize ⇒ GenomicsService

Returns a new instance of GenomicsService



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 45

def initialize
  super('https://genomics.googleapis.com/', '')
  @batch_path = 'batch'
end

Instance Attribute Details

#key ⇒ String

Returns 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.

Returns:

  • (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.



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 38

def key
  @key
end

#quota_user ⇒ String

Returns 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.

Returns:

  • (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.



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 43

def quota_user
  @quota_user
end

Instance Method Details

#cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1alpha2::Empty

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 permission:

  • genomics.operations.cancel

Parameters:

  • name (String) —

    The name of the operation resource to be cancelled.

  • cancel_operation_request_object (Google::Apis::GenomicsV1alpha2::CancelOperationRequest) (defaults to: nil)
  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 79

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

#create_pipeline(pipeline_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1alpha2::Pipeline

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.

Parameters:

  • pipeline_object (Google::Apis::GenomicsV1alpha2::Pipeline) (defaults to: nil)
  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 217

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

#delete_pipeline(pipeline_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1alpha2::Empty

Deletes a pipeline based on ID. Caller must have WRITE permission to the project.

Parameters:

  • pipeline_id (String) —

    Caller must have WRITE access to the project in which this pipeline is defined.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 250

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

#get_operation(name, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1alpha2::Operation

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 permission:

  • genomics.operations.get

Parameters:

  • name (String) —

    The name of the operation resource.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 116

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

#get_pipeline(pipeline_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1alpha2::Pipeline

Retrieves a pipeline based on ID. Caller must have READ permission to the project.

Parameters:

  • pipeline_id (String) —

    Caller must have READ access to the project in which this pipeline is defined.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 282

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

#get_pipeline_controller_config(operation_id: nil, validation_token: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1alpha2::ControllerConfig

Gets controller configuration information. Should only be called by VMs created by the Pipelines Service and not by end users.

Parameters:

  • operation_id (String) —

    The operation to retrieve controller configuration for.

  • validation_token (Fixnum)
  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 314

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

#list_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1alpha2::ListOperationsResponse

Lists operations that match the specified filter in the request. Authorization requires the following Google IAM permission:

  • genomics.operations.list

Parameters:

  • name (String) —

    The name of the operation's parent resource.

  • filter (String) —

    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. 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
  • page_size (Fixnum) —

    The maximum number of results to return. If unspecified, defaults to

    1. The maximum value is 2048.
  • page_token (String) —

    The standard list page token.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 181

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

#list_pipelines(name_prefix: nil, page_size: nil, page_token: nil, project_id: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1alpha2::ListPipelinesResponse

Lists pipelines. Caller must have READ permission to the project.

Parameters:

  • name_prefix (String) —

    Pipelines with names that match this prefix should be returned. If unspecified, all pipelines in the project, up to pageSize, will be returned.

  • page_size (Fixnum) —

    Number of pipelines to return at once. Defaults to 256, and max is 2048.

  • page_token (String) —

    Token to use to indicate where to start getting results. If unspecified, returns the first page of results.

  • project_id (String) —

    Required. The name of the project to search for pipelines. Caller must have READ access to this project.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 357

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

#run_pipeline(run_pipeline_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1alpha2::Operation

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.

Parameters:

  • run_pipeline_request_object (Google::Apis::GenomicsV1alpha2::RunPipelineRequest) (defaults to: nil)
  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 395

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

#set_pipeline_operation_status(set_operation_status_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1alpha2::Empty

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.

Parameters:

  • set_operation_status_request_object (Google::Apis::GenomicsV1alpha2::SetOperationStatusRequest) (defaults to: nil)
  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



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# File 'generated/google/apis/genomics_v1alpha2/service.rb', line 427

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