class Google::Apis::GenomicsV2alpha1::GenomicsService

Genomics API

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

@example

require 'google/apis/genomics_v2alpha1'

Genomics = Google::Apis::GenomicsV2alpha1 # Alias the module
service = Genomics::GenomicsService.new

@see cloud.google.com/genomics

Attributes

key[RW]

@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.
quota_user[RW]

@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

new() click to toggle source
Calls superclass method
# File lib/google/apis/genomics_v2alpha1/service.rb, line 45
def initialize
  super('https://genomics.googleapis.com/', '',
        client_name: 'google-apis-genomics_v2alpha1',
        client_version: Google::Apis::GenomicsV2alpha1::GEM_VERSION)
  @batch_path = 'batch'
end

Public Instance Methods

cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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::GenomicsV2alpha1::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::GenomicsV2alpha1::Empty] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV2alpha1::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_v2alpha1/service.rb, line 118
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_project_worker_in(id, check_in_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

The worker uses this method to retrieve the assigned operation and provide periodic status updates. @param [String] id

The VM identity token for authenticating the VM instance. https://cloud.google.
com/compute/docs/instances/verifying-instance-identity

@param [Google::Apis::GenomicsV2alpha1::CheckInRequest] check_in_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::GenomicsV2alpha1::CheckInResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV2alpha1::CheckInResponse]

@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_v2alpha1/service.rb, line 238
def check_project_worker_in(id, check_in_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command = make_simple_command(:post, 'v2alpha1/{+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
check_worker_in(id, check_in_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

The worker uses this method to retrieve the assigned operation and provide periodic status updates. @param [String] id

The VM identity token for authenticating the VM instance. https://cloud.google.
com/compute/docs/instances/verifying-instance-identity

@param [Google::Apis::GenomicsV2alpha1::CheckInRequest] check_in_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::GenomicsV2alpha1::CheckInResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV2alpha1::CheckInResponse]

@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_v2alpha1/service.rb, line 273
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, &block) click to toggle source

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::GenomicsV2alpha1::Operation] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV2alpha1::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_v2alpha1/service.rb, line 153
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, &block) click to toggle source

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. 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::GenomicsV2alpha1::ListOperationsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV2alpha1::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_v2alpha1/service.rb, line 202
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, &block) click to toggle source

Runs a pipeline. The returned Operation's metadata field will contain a google. genomics.v2alpha1.Metadata object describing the status of the pipeline execution. The [response] field will contain a google.genomics.v2alpha1. RunPipelineResponse object if the pipeline completes successfully. 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](cloud.google.com/iam/ ) permission: * `genomics.operations.create` [1]: /genomics/gsa @param [Google::Apis::GenomicsV2alpha1::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::GenomicsV2alpha1::Operation] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV2alpha1::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_v2alpha1/service.rb, line 81
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

Protected Instance Methods

apply_command_defaults(command) click to toggle source
# File lib/google/apis/genomics_v2alpha1/service.rb, line 287
def apply_command_defaults(command)
  command.query['key'] = key unless key.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
end