1677 lines
106 KiB
Ruby
1677 lines
106 KiB
Ruby
# Copyright 2015 Google Inc.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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require 'google/apis/core/base_service'
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require 'google/apis/core/json_representation'
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require 'google/apis/core/hashable'
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require 'google/apis/errors'
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module Google
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module Apis
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module GenomicsV1
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# Genomics API
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#
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# An API to store, process, explore, and share genomic data. It supports
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# reference-based alignments, genetic variants, and reference genomes. This API
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# provides an implementation of the Global Alliance for Genomics and Health (
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# GA4GH) v0.5.1 API as well as several extensions.
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#
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# @example
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# require 'google/apis/genomics_v1'
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#
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# Genomics = Google::Apis::GenomicsV1 # Alias the module
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# service = Genomics::GenomicsService.new
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#
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# @see
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class GenomicsService < Google::Apis::Core::BaseService
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# @return [String]
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# API key. Your API key identifies your project and provides you with API access,
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# quota, and reports. Required unless you provide an OAuth 2.0 token.
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attr_accessor :key
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# @return [String]
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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attr_accessor :quota_user
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def initialize
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super('https://genomics.googleapis.com/', '')
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end
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# Lists datasets within a project. For the definitions of datasets and other
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# genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.
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# com/genomics/fundamentals-of-google-genomics)
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# @param [String] project_id
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# Required. The project to list datasets for.
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# @param [Fixnum] page_size
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# The maximum number of results to return in a single page. If unspecified,
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# defaults to 50. The maximum value is 1024.
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# @param [String] page_token
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# The continuation token, which is used to page through large result sets. To
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# get the next page of results, set this parameter to the value of `
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# nextPageToken` from the previous response.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::ListDatasetsResponse] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::ListDatasetsResponse]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def list_datasets(project_id: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block)
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command = make_simple_command(:get, 'v1/datasets', options)
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command.response_representation = Google::Apis::GenomicsV1::ListDatasetsResponse::Representation
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command.response_class = Google::Apis::GenomicsV1::ListDatasetsResponse
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command.query['projectId'] = project_id unless project_id.nil?
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command.query['pageSize'] = page_size unless page_size.nil?
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command.query['pageToken'] = page_token unless page_token.nil?
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command.query['fields'] = fields unless fields.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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execute_or_queue_command(command, &block)
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end
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# Creates a new dataset. For the definitions of datasets and other genomics
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# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
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# genomics/fundamentals-of-google-genomics)
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# @param [Google::Apis::GenomicsV1::Dataset] dataset_object
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::Dataset]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil, &block)
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command = make_simple_command(:post, 'v1/datasets', options)
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command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation
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command.request_object = dataset_object
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command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
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command.response_class = Google::Apis::GenomicsV1::Dataset
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command.query['fields'] = fields unless fields.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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execute_or_queue_command(command, &block)
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end
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# Gets a dataset by ID. For the definitions of datasets and other genomics
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# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
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# genomics/fundamentals-of-google-genomics)
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# @param [String] dataset_id
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# The ID of the dataset.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::Dataset]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block)
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command = make_simple_command(:get, 'v1/datasets/{datasetId}', options)
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command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
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command.response_class = Google::Apis::GenomicsV1::Dataset
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command.params['datasetId'] = dataset_id unless dataset_id.nil?
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command.query['fields'] = fields unless fields.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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execute_or_queue_command(command, &block)
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end
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# Updates a dataset. For the definitions of datasets and other genomics
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# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
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# genomics/fundamentals-of-google-genomics) This method supports patch semantics.
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# @param [String] dataset_id
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# The ID of the dataset to be updated.
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# @param [Google::Apis::GenomicsV1::Dataset] dataset_object
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# @param [String] update_mask
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# An optional mask specifying which fields to update. At this time, the only
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# mutable field is name. The only acceptable value is "name". If unspecified,
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# all mutable fields will be updated.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::Dataset]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
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command = make_simple_command(:patch, 'v1/datasets/{datasetId}', options)
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command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation
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command.request_object = dataset_object
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command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
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command.response_class = Google::Apis::GenomicsV1::Dataset
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command.params['datasetId'] = dataset_id unless dataset_id.nil?
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command.query['updateMask'] = update_mask unless update_mask.nil?
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command.query['fields'] = fields unless fields.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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execute_or_queue_command(command, &block)
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end
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# Deletes a dataset. For the definitions of datasets and other genomics
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# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
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# genomics/fundamentals-of-google-genomics)
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# @param [String] dataset_id
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# The ID of the dataset to be deleted.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::Empty]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block)
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command = make_simple_command(:delete, 'v1/datasets/{datasetId}', options)
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command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
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command.response_class = Google::Apis::GenomicsV1::Empty
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command.params['datasetId'] = dataset_id unless dataset_id.nil?
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command.query['fields'] = fields unless fields.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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execute_or_queue_command(command, &block)
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end
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# Undeletes a dataset by restoring a dataset which was deleted via this API. For
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# the definitions of datasets and other genomics resources, see [Fundamentals of
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# Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-
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# genomics) This operation is only possible for a week after the deletion
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# occurred.
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# @param [String] dataset_id
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# The ID of the dataset to be undeleted.
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# @param [Google::Apis::GenomicsV1::UndeleteDatasetRequest] undelete_dataset_request_object
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::Dataset]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
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command = make_simple_command(:post, 'v1/datasets/{datasetId}:undelete', options)
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command.request_representation = Google::Apis::GenomicsV1::UndeleteDatasetRequest::Representation
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command.request_object = undelete_dataset_request_object
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command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
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command.response_class = Google::Apis::GenomicsV1::Dataset
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command.params['datasetId'] = dataset_id unless dataset_id.nil?
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command.query['fields'] = fields unless fields.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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execute_or_queue_command(command, &block)
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end
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# Sets the access control policy on the specified dataset. Replaces any existing
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# policy. For the definitions of datasets and other genomics resources, see [
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# Fundamentals of Google Genomics](https://cloud.google.com/genomics/
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# fundamentals-of-google-genomics) See Setting a Policy for more information.
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# @param [String] resource
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# REQUIRED: The resource for which policy is being specified. Format is `
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# datasets/`.
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# @param [Google::Apis::GenomicsV1::SetIamPolicyRequest] set_iam_policy_request_object
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::Policy]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
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command = make_simple_command(:post, 'v1/{+resource}:setIamPolicy', options)
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command.request_representation = Google::Apis::GenomicsV1::SetIamPolicyRequest::Representation
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command.request_object = set_iam_policy_request_object
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command.response_representation = Google::Apis::GenomicsV1::Policy::Representation
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command.response_class = Google::Apis::GenomicsV1::Policy
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command.params['resource'] = resource unless resource.nil?
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command.query['fields'] = fields unless fields.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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execute_or_queue_command(command, &block)
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end
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# Gets the access control policy for the dataset. This is empty if the policy or
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# resource does not exist. See Getting a Policy for more information. For the
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# definitions of datasets and other genomics resources, see [Fundamentals of
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# Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-
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# genomics)
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# @param [String] resource
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# REQUIRED: The resource for which policy is being specified. Format is `
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# datasets/`.
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# @param [Google::Apis::GenomicsV1::GetIamPolicyRequest] get_iam_policy_request_object
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::Policy]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
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command = make_simple_command(:post, 'v1/{+resource}:getIamPolicy', options)
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command.request_representation = Google::Apis::GenomicsV1::GetIamPolicyRequest::Representation
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command.request_object = get_iam_policy_request_object
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command.response_representation = Google::Apis::GenomicsV1::Policy::Representation
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command.response_class = Google::Apis::GenomicsV1::Policy
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command.params['resource'] = resource unless resource.nil?
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command.query['fields'] = fields unless fields.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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execute_or_queue_command(command, &block)
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end
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# Returns permissions that a caller has on the specified resource. See Testing
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# Permissions for more information. For the definitions of datasets and other
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# genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.
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# com/genomics/fundamentals-of-google-genomics)
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# @param [String] resource
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# REQUIRED: The resource for which policy is being specified. Format is `
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# datasets/`.
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# @param [Google::Apis::GenomicsV1::TestIamPermissionsRequest] test_iam_permissions_request_object
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::TestIamPermissionsResponse] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::TestIamPermissionsResponse]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
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command = make_simple_command(:post, 'v1/{+resource}:testIamPermissions', options)
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command.request_representation = Google::Apis::GenomicsV1::TestIamPermissionsRequest::Representation
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command.request_object = test_iam_permissions_request_object
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command.response_representation = Google::Apis::GenomicsV1::TestIamPermissionsResponse::Representation
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command.response_class = Google::Apis::GenomicsV1::TestIamPermissionsResponse
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command.params['resource'] = resource unless resource.nil?
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command.query['fields'] = fields unless fields.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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execute_or_queue_command(command, &block)
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end
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# Gets the latest state of a long-running operation. Clients can use this method
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# to poll the operation result at intervals as recommended by the API service.
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# @param [String] name
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# The name of the operation resource.
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# @param [String] fields
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# 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::GenomicsV1::Operation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::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
|
|
def get_operation(name, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:get, 'v1/{+name}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::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
|
|
|
|
# Lists operations that match the specified filter in the request.
|
|
# @param [String] name
|
|
# The name of the operation collection.
|
|
# @param [String] filter
|
|
# A string for filtering Operations. 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 `= 1432140000` * `projectId
|
|
# = my-project AND createTime >= 1432140000 AND createTime <= 1432150000 AND
|
|
# status = RUNNING`
|
|
# @param [Fixnum] page_size
|
|
# The maximum number of results to return. If unspecified, defaults to 256. The
|
|
# maximum value is 2048.
|
|
# @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::GenomicsV1::ListOperationsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::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
|
|
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, 'v1/{+name}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::ListOperationsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::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
|
|
|
|
# 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.
|
|
# @param [String] name
|
|
# The name of the operation resource to be cancelled.
|
|
# @param [Google::Apis::GenomicsV1::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::GenomicsV1::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::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
|
|
def cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/{+name}:cancel', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::CancelOperationRequest::Representation
|
|
command.request_object = cancel_operation_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::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 read group sets by asynchronously importing the provided information.
|
|
# For the definitions of read group sets and other genomics resources, see [
|
|
# Fundamentals of Google Genomics](https://cloud.google.com/genomics/
|
|
# fundamentals-of-google-genomics) The caller must have WRITE permissions to the
|
|
# dataset. ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf)
|
|
# import - Tags will be converted to strings - tag types are not preserved -
|
|
# Comments (`@CO`) in the input file header will not be preserved - Original
|
|
# header order of references (`@SQ`) will not be preserved - Any reverse
|
|
# stranded unmapped reads will be reverse complemented, and their qualities (
|
|
# also the "BQ" and "OQ" tags, if any) will be reversed - Unmapped reads will be
|
|
# stripped of positional information (reference name and position)
|
|
# @param [Google::Apis::GenomicsV1::ImportReadGroupSetsRequest] import_read_group_sets_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::GenomicsV1::Operation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::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
|
|
def import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/readgroupsets:import', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::ImportReadGroupSetsRequest::Representation
|
|
command.request_object = import_read_group_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Operation
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Exports a read group set to a BAM file in Google Cloud Storage. For the
|
|
# definitions of read group sets and other genomics resources, see [Fundamentals
|
|
# of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-
|
|
# genomics) Note that currently there may be some differences between exported
|
|
# BAM files and the original BAM file at the time of import. See [
|
|
# ImportReadGroupSets](google.genomics.v1.ReadServiceV1.ImportReadGroupSets) for
|
|
# caveats.
|
|
# @param [String] read_group_set_id
|
|
# Required. The ID of the read group set to export. The caller must have READ
|
|
# access to this read group set.
|
|
# @param [Google::Apis::GenomicsV1::ExportReadGroupSetRequest] export_read_group_set_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::GenomicsV1::Operation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::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
|
|
def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/readgroupsets/{readGroupSetId}:export', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::ExportReadGroupSetRequest::Representation
|
|
command.request_object = export_read_group_set_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Operation
|
|
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_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
|
|
|
|
# Searches for read group sets matching the criteria. For the definitions of
|
|
# read group sets and other genomics resources, see [Fundamentals of Google
|
|
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
# Implements [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/
|
|
# schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
|
|
# @param [Google::Apis::GenomicsV1::SearchReadGroupSetsRequest] search_read_group_sets_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::GenomicsV1::SearchReadGroupSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse]
|
|
#
|
|
# @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
|
|
def search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/readgroupsets/search', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsRequest::Representation
|
|
command.request_object = search_read_group_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates a read group set. For the definitions of read group sets and other
|
|
# genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.
|
|
# com/genomics/fundamentals-of-google-genomics) This method supports patch
|
|
# semantics.
|
|
# @param [String] read_group_set_id
|
|
# The ID of the read group set to be updated. The caller must have WRITE
|
|
# permissions to the dataset associated with this read group set.
|
|
# @param [Google::Apis::GenomicsV1::ReadGroupSet] read_group_set_object
|
|
# @param [String] update_mask
|
|
# An optional mask specifying which fields to update. Supported fields: * name. *
|
|
# referenceSetId. Leaving `updateMask` unset is equivalent to specifying all
|
|
# mutable fields.
|
|
# @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::GenomicsV1::ReadGroupSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::ReadGroupSet]
|
|
#
|
|
# @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
|
|
def patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:patch, 'v1/readgroupsets/{readGroupSetId}', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
|
|
command.request_object = read_group_set_object
|
|
command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
|
|
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
|
|
command.query['updateMask'] = update_mask unless update_mask.nil?
|
|
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 read group set. For the definitions of read group sets and other
|
|
# genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.
|
|
# com/genomics/fundamentals-of-google-genomics)
|
|
# @param [String] read_group_set_id
|
|
# The ID of the read group set to be deleted. The caller must have WRITE
|
|
# permissions to the dataset associated with this read group set.
|
|
# @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::GenomicsV1::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::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
|
|
def delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:delete, 'v1/readgroupsets/{readGroupSetId}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_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 a read group set by ID. For the definitions of read group sets and other
|
|
# genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.
|
|
# com/genomics/fundamentals-of-google-genomics)
|
|
# @param [String] read_group_set_id
|
|
# The ID of the read group set.
|
|
# @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::GenomicsV1::ReadGroupSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::ReadGroupSet]
|
|
#
|
|
# @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
|
|
def get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
|
|
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_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
|
|
|
|
# Lists fixed width coverage buckets for a read group set, each of which
|
|
# correspond to a range of a reference sequence. Each bucket summarizes coverage
|
|
# information across its corresponding genomic range. For the definitions of
|
|
# read group sets and other genomics resources, see [Fundamentals of Google
|
|
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
# Coverage is defined as the number of reads which are aligned to a given base
|
|
# in the reference sequence. Coverage buckets are available at several
|
|
# precomputed bucket widths, enabling retrieval of various coverage 'zoom levels'
|
|
# . The caller must have READ permissions for the target read group set.
|
|
# @param [String] read_group_set_id
|
|
# Required. The ID of the read group set over which coverage is requested.
|
|
# @param [String] reference_name
|
|
# The name of the reference to query, within the reference set associated with
|
|
# this query. Optional.
|
|
# @param [String] start
|
|
# The start position of the range on the reference, 0-based inclusive. If
|
|
# specified, `referenceName` must also be specified. Defaults to 0.
|
|
# @param [String] end_
|
|
# The end position of the range on the reference, 0-based exclusive. If
|
|
# specified, `referenceName` must also be specified. If unset or 0, defaults to
|
|
# the length of the reference.
|
|
# @param [String] target_bucket_width
|
|
# The desired width of each reported coverage bucket in base pairs. This will be
|
|
# rounded down to the nearest precomputed bucket width; the value of which is
|
|
# returned as `bucketWidth` in the response. Defaults to infinity (each bucket
|
|
# spans an entire reference sequence) or the length of the target range, if
|
|
# specified. The smallest precomputed `bucketWidth` is currently 2048 base pairs;
|
|
# this is subject to change.
|
|
# @param [String] page_token
|
|
# The continuation token, which is used to page through large result sets. To
|
|
# get the next page of results, set this parameter to the value of `
|
|
# nextPageToken` from the previous response.
|
|
# @param [Fixnum] page_size
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
# defaults to 1024. The maximum value is 2048.
|
|
# @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::GenomicsV1::ListCoverageBucketsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::ListCoverageBucketsResponse]
|
|
#
|
|
# @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
|
|
def list_coverage_buckets(read_group_set_id, reference_name: nil, start: nil, end_: nil, target_bucket_width: nil, page_token: nil, page_size: nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}/coveragebuckets', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::ListCoverageBucketsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::ListCoverageBucketsResponse
|
|
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
|
|
command.query['referenceName'] = reference_name unless reference_name.nil?
|
|
command.query['start'] = start unless start.nil?
|
|
command.query['end'] = end_ unless end_.nil?
|
|
command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil?
|
|
command.query['pageToken'] = page_token unless page_token.nil?
|
|
command.query['pageSize'] = page_size unless page_size.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 a list of reads for one or more read group sets. For the definitions of
|
|
# read group sets and other genomics resources, see [Fundamentals of Google
|
|
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
# Reads search operates over a genomic coordinate space of reference sequence &
|
|
# position defined over the reference sequences to which the requested read
|
|
# group sets are aligned. If a target positional range is specified, search
|
|
# returns all reads whose alignment to the reference genome overlap the range. A
|
|
# query which specifies only read group set IDs yields all reads in those read
|
|
# group sets, including unmapped reads. All reads returned (including reads on
|
|
# subsequent pages) are ordered by genomic coordinate (by reference sequence,
|
|
# then position). Reads with equivalent genomic coordinates are returned in an
|
|
# unspecified order. This order is consistent, such that two queries for the
|
|
# same content (regardless of page size) yield reads in the same order across
|
|
# their respective streams of paginated responses. Implements [GlobalAllianceApi.
|
|
# searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/
|
|
# avro/readmethods.avdl#L85).
|
|
# @param [Google::Apis::GenomicsV1::SearchReadsRequest] search_reads_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::GenomicsV1::SearchReadsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::SearchReadsResponse]
|
|
#
|
|
# @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
|
|
def search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/reads/search', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::SearchReadsRequest::Representation
|
|
command.request_object = search_reads_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::SearchReadsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::SearchReadsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Returns a stream of all the reads matching the search request, ordered by
|
|
# reference name, position, and ID.
|
|
# @param [Google::Apis::GenomicsV1::StreamReadsRequest] stream_reads_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::GenomicsV1::StreamReadsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::StreamReadsResponse]
|
|
#
|
|
# @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
|
|
def stream_reads(stream_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/reads:stream', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::StreamReadsRequest::Representation
|
|
command.request_object = stream_reads_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::StreamReadsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::StreamReadsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Searches for reference sets which match the given criteria. For the
|
|
# definitions of references and other genomics resources, see [Fundamentals of
|
|
# Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-
|
|
# genomics) Implements [GlobalAllianceApi.searchReferenceSets](https://github.
|
|
# com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#
|
|
# L71)
|
|
# @param [Google::Apis::GenomicsV1::SearchReferenceSetsRequest] search_reference_sets_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::GenomicsV1::SearchReferenceSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::SearchReferenceSetsResponse]
|
|
#
|
|
# @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
|
|
def search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/referencesets/search', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::SearchReferenceSetsRequest::Representation
|
|
command.request_object = search_reference_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::SearchReferenceSetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::SearchReferenceSetsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a reference set. For the definitions of references and other genomics
|
|
# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
|
|
# genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.
|
|
# getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/
|
|
# resources/avro/referencemethods.avdl#L83).
|
|
# @param [String] reference_set_id
|
|
# The ID of the reference set.
|
|
# @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::GenomicsV1::ReferenceSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::ReferenceSet]
|
|
#
|
|
# @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
|
|
def get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:get, 'v1/referencesets/{referenceSetId}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::ReferenceSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::ReferenceSet
|
|
command.params['referenceSetId'] = reference_set_id unless reference_set_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
|
|
|
|
# Searches for references which match the given criteria. For the definitions of
|
|
# references and other genomics resources, see [Fundamentals of Google Genomics](
|
|
# https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [
|
|
# GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.
|
|
# 1/src/main/resources/avro/referencemethods.avdl#L146).
|
|
# @param [Google::Apis::GenomicsV1::SearchReferencesRequest] search_references_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::GenomicsV1::SearchReferencesResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::SearchReferencesResponse]
|
|
#
|
|
# @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
|
|
def search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/references/search', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::SearchReferencesRequest::Representation
|
|
command.request_object = search_references_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::SearchReferencesResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::SearchReferencesResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a reference. For the definitions of references and other genomics
|
|
# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
|
|
# genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.
|
|
# getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/
|
|
# avro/referencemethods.avdl#L158).
|
|
# @param [String] reference_id
|
|
# The ID of the reference.
|
|
# @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::GenomicsV1::Reference] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::Reference]
|
|
#
|
|
# @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
|
|
def get_reference(reference_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:get, 'v1/references/{referenceId}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::Reference::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Reference
|
|
command.params['referenceId'] = reference_id unless reference_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
|
|
|
|
# Lists the bases in a reference, optionally restricted to a range. For the
|
|
# definitions of references and other genomics resources, see [Fundamentals of
|
|
# Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-
|
|
# genomics) Implements [GlobalAllianceApi.getReferenceBases](https://github.com/
|
|
# ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).
|
|
# @param [String] reference_id
|
|
# The ID of the reference.
|
|
# @param [String] start_position
|
|
# The start position (0-based) of this query. Defaults to 0.
|
|
# @param [String] end_position
|
|
# The end position (0-based, exclusive) of this query. Defaults to the length of
|
|
# this reference.
|
|
# @param [String] page_token
|
|
# The continuation token, which is used to page through large result sets. To
|
|
# get the next page of results, set this parameter to the value of `
|
|
# nextPageToken` from the previous response.
|
|
# @param [Fixnum] page_size
|
|
# The maximum number of bases to return in a single page. If unspecified,
|
|
# defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base
|
|
# pairs).
|
|
# @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::GenomicsV1::ListBasesResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::ListBasesResponse]
|
|
#
|
|
# @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
|
|
def list_reference_bases(reference_id, start_position: nil, end_position: nil, page_token: nil, page_size: nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:get, 'v1/references/{referenceId}/bases', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::ListBasesResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::ListBasesResponse
|
|
command.params['referenceId'] = reference_id unless reference_id.nil?
|
|
command.query['start'] = start_position unless start_position.nil?
|
|
command.query['end'] = end_position unless end_position.nil?
|
|
command.query['pageToken'] = page_token unless page_token.nil?
|
|
command.query['pageSize'] = page_size unless page_size.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 variant data by asynchronously importing the provided information. For
|
|
# the definitions of variant sets and other genomics resources, see [
|
|
# Fundamentals of Google Genomics](https://cloud.google.com/genomics/
|
|
# fundamentals-of-google-genomics) The variants for import will be merged with
|
|
# any existing variant that matches its reference sequence, start, end,
|
|
# reference bases, and alternative bases. If no such variant exists, a new one
|
|
# will be created. When variants are merged, the call information from the new
|
|
# variant is added to the existing variant, and other fields (such as key/value
|
|
# pairs) are discarded. In particular, this means for merged VCF variants that
|
|
# have conflicting INFO fields, some data will be arbitrarily discarded. As a
|
|
# special case, for single-sample VCF files, QUAL and FILTER fields will be
|
|
# moved to the call level; these are sometimes interpreted in a call-specific
|
|
# context. Imported VCF headers are appended to the metadata already in a
|
|
# variant set.
|
|
# @param [Google::Apis::GenomicsV1::ImportVariantsRequest] import_variants_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::GenomicsV1::Operation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::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
|
|
def import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/variants:import', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::ImportVariantsRequest::Representation
|
|
command.request_object = import_variants_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Operation
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a list of variants matching the criteria. For the definitions of variants
|
|
# and other genomics resources, see [Fundamentals of Google Genomics](https://
|
|
# cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [
|
|
# GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/
|
|
# src/main/resources/avro/variantmethods.avdl#L126).
|
|
# @param [Google::Apis::GenomicsV1::SearchVariantsRequest] search_variants_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::GenomicsV1::SearchVariantsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::SearchVariantsResponse]
|
|
#
|
|
# @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
|
|
def search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/variants/search', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::SearchVariantsRequest::Representation
|
|
command.request_object = search_variants_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::SearchVariantsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::SearchVariantsResponse
|
|
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 new variant. For the definitions of variants and other genomics
|
|
# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
|
|
# genomics/fundamentals-of-google-genomics)
|
|
# @param [Google::Apis::GenomicsV1::Variant] variant_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::GenomicsV1::Variant] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::Variant]
|
|
#
|
|
# @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
|
|
def create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/variants', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::Variant::Representation
|
|
command.request_object = variant_object
|
|
command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Variant
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates a variant. For the definitions of variants and other genomics
|
|
# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
|
|
# genomics/fundamentals-of-google-genomics) This method supports patch semantics.
|
|
# Returns the modified variant without its calls.
|
|
# @param [String] variant_id
|
|
# The ID of the variant to be updated.
|
|
# @param [Google::Apis::GenomicsV1::Variant] variant_object
|
|
# @param [String] update_mask
|
|
# An optional mask specifying which fields to update. At this time, mutable
|
|
# fields are names and info. Acceptable values are "names" and "info". If
|
|
# unspecified, all mutable fields will be updated.
|
|
# @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::GenomicsV1::Variant] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::Variant]
|
|
#
|
|
# @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
|
|
def patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:patch, 'v1/variants/{variantId}', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::Variant::Representation
|
|
command.request_object = variant_object
|
|
command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Variant
|
|
command.params['variantId'] = variant_id unless variant_id.nil?
|
|
command.query['updateMask'] = update_mask unless update_mask.nil?
|
|
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 variant. For the definitions of variants and other genomics
|
|
# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
|
|
# genomics/fundamentals-of-google-genomics)
|
|
# @param [String] variant_id
|
|
# The ID of the variant to be deleted.
|
|
# @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::GenomicsV1::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::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
|
|
def delete_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:delete, 'v1/variants/{variantId}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
command.params['variantId'] = variant_id unless variant_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 a variant by ID. For the definitions of variants and other genomics
|
|
# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
|
|
# genomics/fundamentals-of-google-genomics)
|
|
# @param [String] variant_id
|
|
# The ID of the variant.
|
|
# @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::GenomicsV1::Variant] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::Variant]
|
|
#
|
|
# @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
|
|
def get_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:get, 'v1/variants/{variantId}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Variant
|
|
command.params['variantId'] = variant_id unless variant_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
|
|
|
|
# Returns a stream of all the variants matching the search request, ordered by
|
|
# reference name, position, and ID.
|
|
# @param [Google::Apis::GenomicsV1::StreamVariantsRequest] stream_variants_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::GenomicsV1::StreamVariantsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::StreamVariantsResponse]
|
|
#
|
|
# @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
|
|
def stream_variants(stream_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/variants:stream', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::StreamVariantsRequest::Representation
|
|
command.request_object = stream_variants_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::StreamVariantsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::StreamVariantsResponse
|
|
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 new variant set. For the definitions of variant sets and other
|
|
# genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.
|
|
# com/genomics/fundamentals-of-google-genomics) The provided variant set must
|
|
# have a valid `datasetId` set - all other fields are optional. Note that the `
|
|
# id` field will be ignored, as this is assigned by the server.
|
|
# @param [Google::Apis::GenomicsV1::VariantSet] variant_set_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::GenomicsV1::VariantSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::VariantSet]
|
|
#
|
|
# @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
|
|
def create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/variantsets', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation
|
|
command.request_object = variant_set_object
|
|
command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::VariantSet
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Exports variant set data to an external destination. For the definitions of
|
|
# variant sets and other genomics resources, see [Fundamentals of Google
|
|
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
# @param [String] variant_set_id
|
|
# Required. The ID of the variant set that contains variant data which should be
|
|
# exported. The caller must have READ access to this variant set.
|
|
# @param [Google::Apis::GenomicsV1::ExportVariantSetRequest] export_variant_set_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::GenomicsV1::Operation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::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
|
|
def export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/variantsets/{variantSetId}:export', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::ExportVariantSetRequest::Representation
|
|
command.request_object = export_variant_set_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Operation
|
|
command.params['variantSetId'] = variant_set_id unless variant_set_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 a variant set by ID. For the definitions of variant sets and other
|
|
# genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.
|
|
# com/genomics/fundamentals-of-google-genomics)
|
|
# @param [String] variant_set_id
|
|
# Required. The ID of the variant set.
|
|
# @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::GenomicsV1::VariantSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::VariantSet]
|
|
#
|
|
# @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
|
|
def get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:get, 'v1/variantsets/{variantSetId}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::VariantSet
|
|
command.params['variantSetId'] = variant_set_id unless variant_set_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
|
|
|
|
# Returns a list of all variant sets matching search criteria. For the
|
|
# definitions of variant sets and other genomics resources, see [Fundamentals of
|
|
# Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-
|
|
# genomics) Implements [GlobalAllianceApi.searchVariantSets](https://github.com/
|
|
# ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).
|
|
# @param [Google::Apis::GenomicsV1::SearchVariantSetsRequest] search_variant_sets_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::GenomicsV1::SearchVariantSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::SearchVariantSetsResponse]
|
|
#
|
|
# @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
|
|
def search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/variantsets/search', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::SearchVariantSetsRequest::Representation
|
|
command.request_object = search_variant_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::SearchVariantSetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::SearchVariantSetsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Deletes the contents of a variant set. The variant set object is not deleted.
|
|
# For the definitions of variant sets and other genomics resources, see [
|
|
# Fundamentals of Google Genomics](https://cloud.google.com/genomics/
|
|
# fundamentals-of-google-genomics)
|
|
# @param [String] variant_set_id
|
|
# The ID of the variant set to be deleted.
|
|
# @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::GenomicsV1::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::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
|
|
def delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:delete, 'v1/variantsets/{variantSetId}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
command.params['variantSetId'] = variant_set_id unless variant_set_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
|
|
|
|
# Updates a variant set using patch semantics. For the definitions of variant
|
|
# sets and other genomics resources, see [Fundamentals of Google Genomics](https:
|
|
# //cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
# @param [String] variant_set_id
|
|
# The ID of the variant to be updated (must already exist).
|
|
# @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
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# @param [String] update_mask
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# An optional mask specifying which fields to update. Supported fields: *
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# metadata. Leaving `updateMask` unset is equivalent to specifying all mutable
|
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# fields.
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# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
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|
# @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.
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# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::VariantSet]
|
|
#
|
|
# @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
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def patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
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command = make_simple_command(:patch, 'v1/variantsets/{variantSetId}', options)
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command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation
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command.request_object = variant_set_object
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command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
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command.response_class = Google::Apis::GenomicsV1::VariantSet
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command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
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command.query['updateMask'] = update_mask unless update_mask.nil?
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command.query['fields'] = fields unless fields.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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execute_or_queue_command(command, &block)
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end
|
|
|
|
# Gets a list of call sets matching the criteria. For the definitions of call
|
|
# sets and other genomics resources, see [Fundamentals of Google Genomics](https:
|
|
# //cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [
|
|
# GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/
|
|
# src/main/resources/avro/variantmethods.avdl#L178).
|
|
# @param [Google::Apis::GenomicsV1::SearchCallSetsRequest] search_call_sets_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::GenomicsV1::SearchCallSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::SearchCallSetsResponse]
|
|
#
|
|
# @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
|
|
def search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/callsets/search', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::SearchCallSetsRequest::Representation
|
|
command.request_object = search_call_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::SearchCallSetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::SearchCallSetsResponse
|
|
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 new call set. For the definitions of call sets and other genomics
|
|
# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
|
|
# genomics/fundamentals-of-google-genomics)
|
|
# @param [Google::Apis::GenomicsV1::CallSet] call_set_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::GenomicsV1::CallSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::CallSet]
|
|
#
|
|
# @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
|
|
def create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:post, 'v1/callsets', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation
|
|
command.request_object = call_set_object
|
|
command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::CallSet
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates a call set. For the definitions of call sets and other genomics
|
|
# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
|
|
# genomics/fundamentals-of-google-genomics) This method supports patch semantics.
|
|
# @param [String] call_set_id
|
|
# The ID of the call set to be updated.
|
|
# @param [Google::Apis::GenomicsV1::CallSet] call_set_object
|
|
# @param [String] update_mask
|
|
# An optional mask specifying which fields to update. At this time, the only
|
|
# mutable field is name. The only acceptable value is "name". If unspecified,
|
|
# all mutable fields will be updated.
|
|
# @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::GenomicsV1::CallSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::CallSet]
|
|
#
|
|
# @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
|
|
def patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:patch, 'v1/callsets/{callSetId}', options)
|
|
command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation
|
|
command.request_object = call_set_object
|
|
command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::CallSet
|
|
command.params['callSetId'] = call_set_id unless call_set_id.nil?
|
|
command.query['updateMask'] = update_mask unless update_mask.nil?
|
|
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 call set. For the definitions of call sets and other genomics
|
|
# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
|
|
# genomics/fundamentals-of-google-genomics)
|
|
# @param [String] call_set_id
|
|
# The ID of the call set to be deleted.
|
|
# @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::GenomicsV1::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::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
|
|
def delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:delete, 'v1/callsets/{callSetId}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
command.params['callSetId'] = call_set_id unless call_set_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 a call set by ID. For the definitions of call sets and other genomics
|
|
# resources, see [Fundamentals of Google Genomics](https://cloud.google.com/
|
|
# genomics/fundamentals-of-google-genomics)
|
|
# @param [String] call_set_id
|
|
# The ID of the call set.
|
|
# @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::GenomicsV1::CallSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1::CallSet]
|
|
#
|
|
# @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
|
|
def get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
command = make_simple_command(:get, 'v1/callsets/{callSetId}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::CallSet
|
|
command.params['callSetId'] = call_set_id unless call_set_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
|
|
|
|
protected
|
|
|
|
def apply_command_defaults(command)
|
|
command.query['key'] = key unless key.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
end
|
|
end
|
|
end
|
|
end
|
|
end
|