1521 lines
92 KiB
Ruby
1521 lines
92 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 DNA sequence reads, reference-
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# based alignments, and variant calls.
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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.
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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 returned by this request. 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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path = 'v1/datasets'
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command = make_simple_command(:get, path, 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.
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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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path = 'v1/datasets'
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command = make_simple_command(:post, path, 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.
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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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path = 'v1/datasets/{datasetId}'
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command = make_simple_command(:get, path, 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. 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][google.genomics.v1.Dataset.name]. The only acceptable
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# value is "name". If unspecified, 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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path = 'v1/datasets/{datasetId}'
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command = make_simple_command(:patch, path, 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.
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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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path = 'v1/datasets/{datasetId}'
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command = make_simple_command(:delete, path, 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.
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# This operation is only possible for a week after the deletion 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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path = 'v1/datasets/{datasetId}:undelete'
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command = make_simple_command(:post, path, 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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# 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.
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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::Operation] 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::Operation]
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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_operation(name, fields: nil, quota_user: nil, options: nil, &block)
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path = 'v1/{+name}'
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command = make_simple_command(:get, path, options)
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command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
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command.response_class = Google::Apis::GenomicsV1::Operation
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command.params['name'] = name unless name.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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# Lists operations that match the specified filter in the request.
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# @param [String] name
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# The name of the operation collection.
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# @param [String] filter
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# A string for filtering [Operations][google.longrunning.Operation]. The
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# following filter fields are supported: * projectId: Required. Corresponds to [
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# OperationMetadata.projectId][google.genomics.v1.OperationMetadata.project_id].
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# * createTime: The time this job was created, in seconds from the [epoch](http:/
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# /en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `= 1432140000` * `
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# projectId = my-project AND createTime >= 1432140000 AND createTime <=
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# 1432150000 AND status = RUNNING`
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# @param [Fixnum] page_size
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# The maximum number of results to return. If unspecified, defaults to 256. The
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# maximum value is 2048.
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# @param [String] page_token
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# The standard list page token.
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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::ListOperationsResponse] 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::ListOperationsResponse]
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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_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block)
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path = 'v1/{+name}'
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command = make_simple_command(:get, path, options)
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command.response_representation = Google::Apis::GenomicsV1::ListOperationsResponse::Representation
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command.response_class = Google::Apis::GenomicsV1::ListOperationsResponse
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command.params['name'] = name unless name.nil?
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command.query['filter'] = filter unless filter.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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# Starts asynchronous cancellation on a long-running operation. The server makes
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# a best effort to cancel the operation, but success is not guaranteed. Clients
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# may use [Operations.GetOperation][google.longrunning.Operations.GetOperation]
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# or [Operations.ListOperations][google.longrunning.Operations.ListOperations]
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# to check whether the cancellation succeeded or the operation completed despite
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# cancellation.
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# @param [String] name
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# The name of the operation resource to be cancelled.
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# @param [Google::Apis::GenomicsV1::CancelOperationRequest] cancel_operation_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::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 cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
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path = 'v1/{+name}:cancel'
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command = make_simple_command(:post, path, options)
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command.request_representation = Google::Apis::GenomicsV1::CancelOperationRequest::Representation
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command.request_object = cancel_operation_request_object
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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['name'] = name unless name.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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# This method is not implemented. To cancel an operation, please use [Operations.
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# CancelOperation][google.longrunning.Operations.CancelOperation].
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# @param [String] name
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# The name of the operation resource 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
|
|
def delete_operation(name, fields: nil, quota_user: nil, options: nil, &block)
|
|
path = 'v1/{+name}'
|
|
command = make_simple_command(:delete, path, options)
|
|
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.
|
|
# Note that currently comments in the input file header are **not** imported and
|
|
# some custom tags will be converted to strings, rather than preserving tag
|
|
# types. The caller must have WRITE permissions to the dataset.
|
|
# @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)
|
|
path = 'v1/readgroupsets:import'
|
|
command = make_simple_command(:post, path, 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. Note that
|
|
# currently there may be some differences between exported BAM files and the
|
|
# original BAM file at the time of import. In particular, comments in the input
|
|
# file header will not be preserved, some custom tags will be converted to
|
|
# strings, and original reference sequence order is not necessarily preserved.
|
|
# @param [String] read_group_set_id
|
|
# Required. The ID of the read group set to export.
|
|
# @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)
|
|
path = 'v1/readgroupsets/{readGroupSetId}:export'
|
|
command = make_simple_command(:post, path, 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. 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)
|
|
path = 'v1/readgroupsets/search'
|
|
command = make_simple_command(:post, path, 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. 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. At this time, mutable
|
|
# fields are [referenceSetId][google.genomics.v1.ReadGroupSet.reference_set_id]
|
|
# and [name][google.genomics.v1.ReadGroupSet.name]. Acceptable values are "
|
|
# referenceSetId" and "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::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)
|
|
path = 'v1/readgroupsets/{readGroupSetId}'
|
|
command = make_simple_command(:patch, path, 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.
|
|
# @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)
|
|
path = 'v1/readgroupsets/{readGroupSetId}'
|
|
command = make_simple_command(:delete, path, 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.
|
|
# @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)
|
|
path = 'v1/readgroupsets/{readGroupSetId}'
|
|
command = make_simple_command(:get, path, 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. 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)
|
|
path = 'v1/readgroupsets/{readGroupSetId}/coveragebuckets'
|
|
command = make_simple_command(:get, path, 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. 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 (reference sequence & position). Reads with
|
|
# equivalent genomic coordinates are returned in a deterministic order.
|
|
# 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)
|
|
path = 'v1/reads/search'
|
|
command = make_simple_command(:post, path, 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
|
|
|
|
# Searches for reference sets which match the given criteria. Implements [
|
|
# GlobalAllianceApi.searchReferenceSets](http://ga4gh.org/documentation/api/v0.5.
|
|
# 1/ga4gh_api.html#/schema/org.ga4gh.searchReferenceSets).
|
|
# @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)
|
|
path = 'v1/referencesets/search'
|
|
command = make_simple_command(:post, path, 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. 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)
|
|
path = 'v1/referencesets/{referenceSetId}'
|
|
command = make_simple_command(:get, path, 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. 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)
|
|
path = 'v1/references/search'
|
|
command = make_simple_command(:post, path, 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. 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)
|
|
path = 'v1/references/{referenceId}'
|
|
command = make_simple_command(:get, path, 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. 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
|
|
# Specifies the maximum number of bases to return in a single page.
|
|
# @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)
|
|
path = 'v1/references/{referenceId}/bases'
|
|
command = make_simple_command(:get, path, 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. The
|
|
# variants for import will be merged with any existing data and each other
|
|
# according to the behavior of mergeVariants. 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)
|
|
path = 'v1/variants:import'
|
|
command = make_simple_command(:post, path, 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. 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)
|
|
path = 'v1/variants/search'
|
|
command = make_simple_command(:post, path, 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.
|
|
# @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)
|
|
path = 'v1/variants'
|
|
command = make_simple_command(:post, path, 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. 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][google.genomics.v1.Variant.names] and [info][google.
|
|
# genomics.v1.Variant.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)
|
|
path = 'v1/variants/{variantId}'
|
|
command = make_simple_command(:patch, path, 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.
|
|
# @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)
|
|
path = 'v1/variants/{variantId}'
|
|
command = make_simple_command(:delete, path, 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.
|
|
# @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)
|
|
path = 'v1/variants/{variantId}'
|
|
command = make_simple_command(:get, path, 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
|
|
|
|
# Merges the given variants with existing variants. Each variant will be merged
|
|
# with an 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.
|
|
# @param [Google::Apis::GenomicsV1::MergeVariantsRequest] merge_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::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 merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
path = 'v1/variants:merge'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1::MergeVariantsRequest::Representation
|
|
command.request_object = merge_variants_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
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.
|
|
# @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)
|
|
path = 'v1/variantsets'
|
|
command = make_simple_command(:post, path, 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.
|
|
# @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)
|
|
path = 'v1/variantsets/{variantSetId}:export'
|
|
command = make_simple_command(:post, path, 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.
|
|
# @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)
|
|
path = 'v1/variantsets/{variantSetId}'
|
|
command = make_simple_command(:get, path, 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. 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)
|
|
path = 'v1/variantsets/search'
|
|
command = make_simple_command(:post, path, 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.
|
|
# @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)
|
|
path = 'v1/variantsets/{variantSetId}'
|
|
command = make_simple_command(:delete, path, 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. This method supports patch semantics.
|
|
# @param [String] variant_set_id
|
|
# The ID of the variant to be updated (must already exist).
|
|
# @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
|
|
# @param [String] update_mask
|
|
# An optional mask specifying which fields to update. At this time, the only
|
|
# mutable field is [metadata][google.genomics.v1.VariantSet.metadata]. The only
|
|
# acceptable value is "metadata". 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::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 patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
path = 'v1/variantsets/{variantSetId}'
|
|
command = make_simple_command(:patch, path, 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.params['variantSetId'] = variant_set_id unless variant_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
|
|
|
|
# Gets a list of call sets matching the criteria. 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)
|
|
path = 'v1/callsets/search'
|
|
command = make_simple_command(:post, path, 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.
|
|
# @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)
|
|
path = 'v1/callsets'
|
|
command = make_simple_command(:post, path, 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. 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][google.genomics.v1.CallSet.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)
|
|
path = 'v1/callsets/{callSetId}'
|
|
command = make_simple_command(:patch, path, 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.
|
|
# @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)
|
|
path = 'v1/callsets/{callSetId}'
|
|
command = make_simple_command(:delete, path, 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.
|
|
# @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)
|
|
path = 'v1/callsets/{callSetId}'
|
|
command = make_simple_command(:get, path, 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
|