Class: Google::Apis::GenomicsV2alpha1::GenomicsService

Inherits:
Core::BaseService show all
Defined in:
generated/google/apis/genomics_v2alpha1/service.rb

Overview

Genomics API

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

Examples:

require 'google/apis/genomics_v2alpha1'

Genomics = Google::Apis::GenomicsV2alpha1 # 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_v2alpha1/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_v2alpha1/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_v2alpha1/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::GenomicsV2alpha1::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::GenomicsV2alpha1::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_v2alpha1/service.rb', line 119

def cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v2alpha1/{+name}:cancel', options)
  command.request_representation = Google::Apis::GenomicsV2alpha1::CancelOperationRequest::Representation
  command.request_object = cancel_operation_request_object
  command.response_representation = Google::Apis::GenomicsV2alpha1::Empty::Representation
  command.response_class = Google::Apis::GenomicsV2alpha1::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

#check_worker_in(id, check_in_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV2alpha1::CheckInResponse

The worker uses this method to retrieve the assigned operation and provide periodic status updates.

Parameters:

  • id (String) —

    The worker id, assigned when it was created.

  • check_in_request_object (Google::Apis::GenomicsV2alpha1::CheckInRequest) (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_v2alpha1/service.rb', line 256

def check_worker_in(id, check_in_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v2alpha1/workers/{id}:checkIn', options)
  command.request_representation = Google::Apis::GenomicsV2alpha1::CheckInRequest::Representation
  command.request_object = check_in_request_object
  command.response_representation = Google::Apis::GenomicsV2alpha1::CheckInResponse::Representation
  command.response_class = Google::Apis::GenomicsV2alpha1::CheckInResponse
  command.params['id'] = id unless 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_project_operation(name, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV2alpha1::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_v2alpha1/service.rb', line 156

def get_project_operation(name, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v2alpha1/{+name}', options)
  command.response_representation = Google::Apis::GenomicsV2alpha1::Operation::Representation
  command.response_class = Google::Apis::GenomicsV2alpha1::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

#list_project_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV2alpha1::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_v2alpha1/service.rb', line 221

def list_project_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v2alpha1/{+name}', options)
  command.response_representation = Google::Apis::GenomicsV2alpha1::ListOperationsResponse::Representation
  command.response_class = Google::Apis::GenomicsV2alpha1::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

#run_pipeline(run_pipeline_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV2alpha1::Operation

Runs a pipeline. Note: Before you can use this method, the Genomics Service Agent must have access to your project. This is done automatically when the Cloud Genomics API is first enabled, but if you delete this permission, or if you enabled the Cloud Genomics API before the v2alpha1 API launch, you must disable and re-enable the API to grant the Genomics Service Agent the required permissions. Authorization requires the following Google IAM permission:

  • genomics.operations.create

Parameters:

  • run_pipeline_request_object (Google::Apis::GenomicsV2alpha1::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_v2alpha1/service.rb', line 79

def run_pipeline(run_pipeline_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v2alpha1/pipelines:run', options)
  command.request_representation = Google::Apis::GenomicsV2alpha1::RunPipelineRequest::Representation
  command.request_object = run_pipeline_request_object
  command.response_representation = Google::Apis::GenomicsV2alpha1::Operation::Representation
  command.response_class = Google::Apis::GenomicsV2alpha1::Operation
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end