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

@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_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

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::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
create_pipeline(pipeline_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
delete_pipeline(pipeline_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_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::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
get_pipeline(pipeline_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_pipeline_controller_config(operation_id: nil, validation_token: nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
list_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. 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
list_pipelines(name_prefix: nil, page_size: nil, page_token: nil, project_id: nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
run_pipeline(run_pipeline_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
set_pipeline_operation_status(set_operation_status_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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

apply_command_defaults(command) click to toggle source
# 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