google-api-client 0.9.pre1 → 0.9.pre2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/CHANGELOG.md +5 -0
- data/README.md +4 -3
- data/api_names.yaml +42 -0
- data/api_names_out.yaml +977 -651
- data/generated/google/apis/adexchangebuyer_v1_3.rb +1 -1
- data/generated/google/apis/adexchangeseller_v2_0.rb +1 -1
- data/generated/google/apis/adsense_v1_4.rb +1 -1
- data/generated/google/apis/adsensehost_v4_1.rb +1 -1
- data/generated/google/apis/androidenterprise_v1/classes.rb +31 -24
- data/generated/google/apis/androidenterprise_v1/service.rb +11 -6
- data/generated/google/apis/androidenterprise_v1.rb +2 -1
- data/generated/google/apis/appstate_v1.rb +1 -1
- data/generated/google/apis/autoscaler_v1beta2.rb +1 -1
- data/generated/google/apis/bigquery_v2/classes.rb +34 -0
- data/generated/google/apis/bigquery_v2/representations.rb +14 -0
- data/generated/google/apis/bigquery_v2/service.rb +2 -2
- data/generated/google/apis/bigquery_v2.rb +1 -1
- data/generated/google/apis/calendar_v3/classes.rb +8 -0
- data/generated/google/apis/calendar_v3/representations.rb +1 -0
- data/generated/google/apis/calendar_v3.rb +1 -1
- data/generated/google/apis/civicinfo_v2/classes.rb +61 -0
- data/generated/google/apis/civicinfo_v2/representations.rb +8 -0
- data/generated/google/apis/civicinfo_v2.rb +1 -1
- data/generated/google/apis/classroom_v1beta1/classes.rb +447 -0
- data/generated/google/apis/classroom_v1beta1/representations.rb +190 -0
- data/generated/google/apis/classroom_v1beta1/service.rb +791 -0
- data/generated/google/apis/classroom_v1beta1.rb +49 -0
- data/generated/google/apis/cloudmonitoring_v2beta2.rb +4 -1
- data/generated/google/apis/cloudresourcemanager_v1beta1/classes.rb +20 -19
- data/generated/google/apis/cloudresourcemanager_v1beta1/service.rb +34 -34
- data/generated/google/apis/cloudresourcemanager_v1beta1.rb +2 -5
- data/generated/google/apis/compute_v1/classes.rb +2638 -1136
- data/generated/google/apis/compute_v1/representations.rb +580 -0
- data/generated/google/apis/compute_v1/service.rb +2448 -305
- data/generated/google/apis/compute_v1.rb +1 -1
- data/generated/google/apis/container_v1/classes.rb +438 -0
- data/generated/google/apis/container_v1/representations.rb +163 -0
- data/generated/google/apis/container_v1/service.rb +346 -0
- data/generated/google/apis/container_v1.rb +35 -0
- data/generated/google/apis/container_v1beta1.rb +1 -1
- data/generated/google/apis/content_v2/service.rb +48 -12
- data/generated/google/apis/content_v2.rb +1 -1
- data/generated/google/apis/deploymentmanager_v2beta2/classes.rb +13 -9
- data/generated/google/apis/deploymentmanager_v2beta2/service.rb +110 -15
- data/generated/google/apis/deploymentmanager_v2beta2.rb +1 -1
- data/generated/google/apis/discovery_v1/classes.rb +7 -0
- data/generated/google/apis/discovery_v1/representations.rb +1 -0
- data/generated/google/apis/dns_v1/service.rb +4 -1
- data/generated/google/apis/dns_v1.rb +1 -1
- data/generated/google/apis/doubleclicksearch_v2.rb +1 -1
- data/generated/google/apis/drive_v2.rb +1 -1
- data/generated/google/apis/fitness_v1/classes.rb +65 -2
- data/generated/google/apis/fitness_v1/representations.rb +27 -0
- data/generated/google/apis/fitness_v1.rb +1 -1
- data/generated/google/apis/games_configuration_v1configuration.rb +1 -1
- data/generated/google/apis/games_v1.rb +1 -1
- data/generated/google/apis/genomics_v1/classes.rb +2287 -0
- data/generated/google/apis/genomics_v1/representations.rb +796 -0
- data/generated/google/apis/genomics_v1/service.rb +1520 -0
- data/generated/google/apis/genomics_v1.rb +47 -0
- data/generated/google/apis/genomics_v1beta2/service.rb +36 -0
- data/generated/google/apis/genomics_v1beta2.rb +1 -1
- data/generated/google/apis/identitytoolkit_v3.rb +1 -1
- data/generated/google/apis/mapsengine_v1.rb +1 -1
- data/generated/google/apis/oauth2_v2.rb +1 -1
- data/generated/google/apis/plus_domains_v1.rb +1 -1
- data/generated/google/apis/plus_v1.rb +1 -1
- data/generated/google/apis/prediction_v1_6/classes.rb +1 -1
- data/generated/google/apis/pubsub_v1beta2/classes.rb +42 -42
- data/generated/google/apis/pubsub_v1beta2/service.rb +26 -22
- data/generated/google/apis/pubsub_v1beta2.rb +1 -1
- data/generated/google/apis/replicapool_v1beta2/classes.rb +10 -0
- data/generated/google/apis/replicapool_v1beta2/representations.rb +1 -0
- data/generated/google/apis/replicapool_v1beta2.rb +1 -1
- data/generated/google/apis/resourceviews_v1beta2.rb +1 -1
- data/generated/google/apis/storage_v1/classes.rb +4 -2
- data/generated/google/apis/storage_v1.rb +1 -1
- data/generated/google/apis/youtube_analytics_v1.rb +1 -1
- data/generated/google/apis/youtube_v3/classes.rb +3 -3
- data/generated/google/apis/youtube_v3/representations.rb +1 -1
- data/generated/google/apis/youtube_v3/service.rb +78 -0
- data/generated/google/apis/youtube_v3.rb +1 -1
- data/google-api-client.gemspec +0 -1
- data/lib/google/api_client/auth/installed_app.rb +6 -4
- data/lib/google/api_client/auth/key_utils.rb +93 -0
- data/lib/google/apis/core/api_command.rb +12 -5
- data/lib/google/apis/core/http_command.rb +17 -7
- data/lib/google/apis/core/json_representation.rb +6 -2
- data/lib/google/apis/errors.rb +9 -2
- data/lib/google/apis/version.rb +1 -1
- data/script/generate +4 -3
- data/spec/google/apis/core/http_command_spec.rb +20 -0
- data/spec/google/apis/core/json_representation_spec.rb +1 -1
- metadata +15 -16
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# 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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# @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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# 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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|
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command.request_object = undelete_dataset_request_object
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|
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command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
|
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|
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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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|
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|
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# Gets the latest state of a long-running operation. Clients can use this method
|
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|
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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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|
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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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#
|
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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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#
|
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|
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# @return [Google::Apis::GenomicsV1::Operation]
|
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|
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#
|
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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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|
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
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|
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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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|
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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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|
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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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|
+
|
|
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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
|
|
294
|
+
# following filter fields are supported: * projectId: Required. Corresponds to [
|
|
295
|
+
# OperationMetadata.projectId][google.genomics.v1.OperationMetadata.project_id].
|
|
296
|
+
# * createTime: The time this job was created, in seconds from the [epoch](http:/
|
|
297
|
+
# /en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `= 1432140000` * `
|
|
298
|
+
# projectId = my-project AND createTime >= 1432140000 AND createTime <=
|
|
299
|
+
# 1432150000 AND status = RUNNING`
|
|
300
|
+
# @param [Fixnum] page_size
|
|
301
|
+
# The maximum number of results to return. If unspecified, defaults to 256. The
|
|
302
|
+
# maximum value is 2048.
|
|
303
|
+
# @param [String] page_token
|
|
304
|
+
# The standard List page token.
|
|
305
|
+
# @param [String] fields
|
|
306
|
+
# Selector specifying which fields to include in a partial response.
|
|
307
|
+
# @param [String] quota_user
|
|
308
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
309
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
310
|
+
# @param [Google::Apis::RequestOptions] options
|
|
311
|
+
# Request-specific options
|
|
312
|
+
#
|
|
313
|
+
# @yield [result, err] Result & error if block supplied
|
|
314
|
+
# @yieldparam result [Google::Apis::GenomicsV1::ListOperationsResponse] parsed result object
|
|
315
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
316
|
+
#
|
|
317
|
+
# @return [Google::Apis::GenomicsV1::ListOperationsResponse]
|
|
318
|
+
#
|
|
319
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
320
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
321
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
322
|
+
def list_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
323
|
+
path = 'v1/{+name}'
|
|
324
|
+
command = make_simple_command(:get, path, options)
|
|
325
|
+
command.response_representation = Google::Apis::GenomicsV1::ListOperationsResponse::Representation
|
|
326
|
+
command.response_class = Google::Apis::GenomicsV1::ListOperationsResponse
|
|
327
|
+
command.params['name'] = name unless name.nil?
|
|
328
|
+
command.query['filter'] = filter unless filter.nil?
|
|
329
|
+
command.query['pageSize'] = page_size unless page_size.nil?
|
|
330
|
+
command.query['pageToken'] = page_token unless page_token.nil?
|
|
331
|
+
command.query['fields'] = fields unless fields.nil?
|
|
332
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
333
|
+
execute_or_queue_command(command, &block)
|
|
334
|
+
end
|
|
335
|
+
|
|
336
|
+
# Starts asynchronous cancellation on a long-running operation. The server makes
|
|
337
|
+
# a best effort to cancel the operation, but success is not guaranteed. Clients
|
|
338
|
+
# may use [Operations.GetOperation][google.longrunning.Operations.GetOperation]
|
|
339
|
+
# or [Operations.ListOperations][google.longrunning.Operations.ListOperations]
|
|
340
|
+
# to check whether the cancellation succeeded or the operation completed despite
|
|
341
|
+
# cancellation.
|
|
342
|
+
# @param [String] name
|
|
343
|
+
# The name of the operation resource to be cancelled.
|
|
344
|
+
# @param [Google::Apis::GenomicsV1::CancelOperationRequest] cancel_operation_request_object
|
|
345
|
+
# @param [String] fields
|
|
346
|
+
# Selector specifying which fields to include in a partial response.
|
|
347
|
+
# @param [String] quota_user
|
|
348
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
349
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
350
|
+
# @param [Google::Apis::RequestOptions] options
|
|
351
|
+
# Request-specific options
|
|
352
|
+
#
|
|
353
|
+
# @yield [result, err] Result & error if block supplied
|
|
354
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
|
|
355
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
356
|
+
#
|
|
357
|
+
# @return [Google::Apis::GenomicsV1::Empty]
|
|
358
|
+
#
|
|
359
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
360
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
361
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
362
|
+
def cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
363
|
+
path = 'v1/{+name}:cancel'
|
|
364
|
+
command = make_simple_command(:post, path, options)
|
|
365
|
+
command.request_representation = Google::Apis::GenomicsV1::CancelOperationRequest::Representation
|
|
366
|
+
command.request_object = cancel_operation_request_object
|
|
367
|
+
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
368
|
+
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
369
|
+
command.params['name'] = name unless name.nil?
|
|
370
|
+
command.query['fields'] = fields unless fields.nil?
|
|
371
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
372
|
+
execute_or_queue_command(command, &block)
|
|
373
|
+
end
|
|
374
|
+
|
|
375
|
+
# This method is not implemented. To cancel an operation, please use [Operations.
|
|
376
|
+
# CancelOperation][google.longrunning.Operations.CancelOperation].
|
|
377
|
+
# @param [String] name
|
|
378
|
+
# The name of the operation resource to be deleted.
|
|
379
|
+
# @param [String] fields
|
|
380
|
+
# Selector specifying which fields to include in a partial response.
|
|
381
|
+
# @param [String] quota_user
|
|
382
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
383
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
384
|
+
# @param [Google::Apis::RequestOptions] options
|
|
385
|
+
# Request-specific options
|
|
386
|
+
#
|
|
387
|
+
# @yield [result, err] Result & error if block supplied
|
|
388
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
|
|
389
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
390
|
+
#
|
|
391
|
+
# @return [Google::Apis::GenomicsV1::Empty]
|
|
392
|
+
#
|
|
393
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
394
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
395
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
396
|
+
def delete_operation(name, fields: nil, quota_user: nil, options: nil, &block)
|
|
397
|
+
path = 'v1/{+name}'
|
|
398
|
+
command = make_simple_command(:delete, path, options)
|
|
399
|
+
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
400
|
+
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
401
|
+
command.params['name'] = name unless name.nil?
|
|
402
|
+
command.query['fields'] = fields unless fields.nil?
|
|
403
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
404
|
+
execute_or_queue_command(command, &block)
|
|
405
|
+
end
|
|
406
|
+
|
|
407
|
+
# Creates read group sets by asynchronously importing the provided information.
|
|
408
|
+
# Note that currently comments in the input file header are **not** imported and
|
|
409
|
+
# some custom tags will be converted to strings, rather than preserving tag
|
|
410
|
+
# types. The caller must have WRITE permissions to the dataset.
|
|
411
|
+
# @param [Google::Apis::GenomicsV1::ImportReadGroupSetsRequest] import_read_group_sets_request_object
|
|
412
|
+
# @param [String] fields
|
|
413
|
+
# Selector specifying which fields to include in a partial response.
|
|
414
|
+
# @param [String] quota_user
|
|
415
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
416
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
417
|
+
# @param [Google::Apis::RequestOptions] options
|
|
418
|
+
# Request-specific options
|
|
419
|
+
#
|
|
420
|
+
# @yield [result, err] Result & error if block supplied
|
|
421
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
|
|
422
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
423
|
+
#
|
|
424
|
+
# @return [Google::Apis::GenomicsV1::Operation]
|
|
425
|
+
#
|
|
426
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
427
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
428
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
429
|
+
def import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
430
|
+
path = 'v1/readgroupsets:import'
|
|
431
|
+
command = make_simple_command(:post, path, options)
|
|
432
|
+
command.request_representation = Google::Apis::GenomicsV1::ImportReadGroupSetsRequest::Representation
|
|
433
|
+
command.request_object = import_read_group_sets_request_object
|
|
434
|
+
command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
|
|
435
|
+
command.response_class = Google::Apis::GenomicsV1::Operation
|
|
436
|
+
command.query['fields'] = fields unless fields.nil?
|
|
437
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
438
|
+
execute_or_queue_command(command, &block)
|
|
439
|
+
end
|
|
440
|
+
|
|
441
|
+
# Exports a read group set to a BAM file in Google Cloud Storage. Note that
|
|
442
|
+
# currently there may be some differences between exported BAM files and the
|
|
443
|
+
# original BAM file at the time of import. In particular, comments in the input
|
|
444
|
+
# file header will not be preserved, some custom tags will be converted to
|
|
445
|
+
# strings, and original reference sequence order is not necessarily preserved.
|
|
446
|
+
# @param [String] read_group_set_id
|
|
447
|
+
# Required. The ID of the read group set to export.
|
|
448
|
+
# @param [Google::Apis::GenomicsV1::ExportReadGroupSetRequest] export_read_group_set_request_object
|
|
449
|
+
# @param [String] fields
|
|
450
|
+
# Selector specifying which fields to include in a partial response.
|
|
451
|
+
# @param [String] quota_user
|
|
452
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
453
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
454
|
+
# @param [Google::Apis::RequestOptions] options
|
|
455
|
+
# Request-specific options
|
|
456
|
+
#
|
|
457
|
+
# @yield [result, err] Result & error if block supplied
|
|
458
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
|
|
459
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
460
|
+
#
|
|
461
|
+
# @return [Google::Apis::GenomicsV1::Operation]
|
|
462
|
+
#
|
|
463
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
464
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
465
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
466
|
+
def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
467
|
+
path = 'v1/readgroupsets/{readGroupSetId}:export'
|
|
468
|
+
command = make_simple_command(:post, path, options)
|
|
469
|
+
command.request_representation = Google::Apis::GenomicsV1::ExportReadGroupSetRequest::Representation
|
|
470
|
+
command.request_object = export_read_group_set_request_object
|
|
471
|
+
command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
|
|
472
|
+
command.response_class = Google::Apis::GenomicsV1::Operation
|
|
473
|
+
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
|
|
474
|
+
command.query['fields'] = fields unless fields.nil?
|
|
475
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
476
|
+
execute_or_queue_command(command, &block)
|
|
477
|
+
end
|
|
478
|
+
|
|
479
|
+
# Searches for read group sets matching the criteria. Implements [
|
|
480
|
+
# GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/
|
|
481
|
+
# v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
|
|
482
|
+
# @param [Google::Apis::GenomicsV1::SearchReadGroupSetsRequest] search_read_group_sets_request_object
|
|
483
|
+
# @param [String] fields
|
|
484
|
+
# Selector specifying which fields to include in a partial response.
|
|
485
|
+
# @param [String] quota_user
|
|
486
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
487
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
488
|
+
# @param [Google::Apis::RequestOptions] options
|
|
489
|
+
# Request-specific options
|
|
490
|
+
#
|
|
491
|
+
# @yield [result, err] Result & error if block supplied
|
|
492
|
+
# @yieldparam result [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] parsed result object
|
|
493
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
494
|
+
#
|
|
495
|
+
# @return [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse]
|
|
496
|
+
#
|
|
497
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
498
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
499
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
500
|
+
def search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
501
|
+
path = 'v1/readgroupsets/search'
|
|
502
|
+
command = make_simple_command(:post, path, options)
|
|
503
|
+
command.request_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsRequest::Representation
|
|
504
|
+
command.request_object = search_read_group_sets_request_object
|
|
505
|
+
command.response_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse::Representation
|
|
506
|
+
command.response_class = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse
|
|
507
|
+
command.query['fields'] = fields unless fields.nil?
|
|
508
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
509
|
+
execute_or_queue_command(command, &block)
|
|
510
|
+
end
|
|
511
|
+
|
|
512
|
+
# Updates a read group set. This method supports patch semantics.
|
|
513
|
+
# @param [String] read_group_set_id
|
|
514
|
+
# The ID of the read group set to be updated. The caller must have WRITE
|
|
515
|
+
# permissions to the dataset associated with this read group set.
|
|
516
|
+
# @param [Google::Apis::GenomicsV1::ReadGroupSet] read_group_set_object
|
|
517
|
+
# @param [String] update_mask
|
|
518
|
+
# An optional mask specifying which fields to update. At this time, mutable
|
|
519
|
+
# fields are [referenceSetId][google.genomics.v1.ReadGroupSet.reference_set_id]
|
|
520
|
+
# and [name][google.genomics.v1.ReadGroupSet.name]. Acceptable values are "
|
|
521
|
+
# referenceSetId" and "name". If unspecified, all mutable fields will be updated.
|
|
522
|
+
# @param [String] fields
|
|
523
|
+
# Selector specifying which fields to include in a partial response.
|
|
524
|
+
# @param [String] quota_user
|
|
525
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
526
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
527
|
+
# @param [Google::Apis::RequestOptions] options
|
|
528
|
+
# Request-specific options
|
|
529
|
+
#
|
|
530
|
+
# @yield [result, err] Result & error if block supplied
|
|
531
|
+
# @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
|
|
532
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
533
|
+
#
|
|
534
|
+
# @return [Google::Apis::GenomicsV1::ReadGroupSet]
|
|
535
|
+
#
|
|
536
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
537
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
538
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
539
|
+
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)
|
|
540
|
+
path = 'v1/readgroupsets/{readGroupSetId}'
|
|
541
|
+
command = make_simple_command(:patch, path, options)
|
|
542
|
+
command.request_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
|
|
543
|
+
command.request_object = read_group_set_object
|
|
544
|
+
command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
|
|
545
|
+
command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
|
|
546
|
+
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
|
|
547
|
+
command.query['updateMask'] = update_mask unless update_mask.nil?
|
|
548
|
+
command.query['fields'] = fields unless fields.nil?
|
|
549
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
550
|
+
execute_or_queue_command(command, &block)
|
|
551
|
+
end
|
|
552
|
+
|
|
553
|
+
# Deletes a read group set.
|
|
554
|
+
# @param [String] read_group_set_id
|
|
555
|
+
# The ID of the read group set to be deleted. The caller must have WRITE
|
|
556
|
+
# permissions to the dataset associated with this read group set.
|
|
557
|
+
# @param [String] fields
|
|
558
|
+
# Selector specifying which fields to include in a partial response.
|
|
559
|
+
# @param [String] quota_user
|
|
560
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
561
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
562
|
+
# @param [Google::Apis::RequestOptions] options
|
|
563
|
+
# Request-specific options
|
|
564
|
+
#
|
|
565
|
+
# @yield [result, err] Result & error if block supplied
|
|
566
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
|
|
567
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
568
|
+
#
|
|
569
|
+
# @return [Google::Apis::GenomicsV1::Empty]
|
|
570
|
+
#
|
|
571
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
572
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
573
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
574
|
+
def delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
575
|
+
path = 'v1/readgroupsets/{readGroupSetId}'
|
|
576
|
+
command = make_simple_command(:delete, path, options)
|
|
577
|
+
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
578
|
+
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
579
|
+
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
|
|
580
|
+
command.query['fields'] = fields unless fields.nil?
|
|
581
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
582
|
+
execute_or_queue_command(command, &block)
|
|
583
|
+
end
|
|
584
|
+
|
|
585
|
+
# Gets a read group set by ID.
|
|
586
|
+
# @param [String] read_group_set_id
|
|
587
|
+
# The ID of the read group set.
|
|
588
|
+
# @param [String] fields
|
|
589
|
+
# Selector specifying which fields to include in a partial response.
|
|
590
|
+
# @param [String] quota_user
|
|
591
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
592
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
593
|
+
# @param [Google::Apis::RequestOptions] options
|
|
594
|
+
# Request-specific options
|
|
595
|
+
#
|
|
596
|
+
# @yield [result, err] Result & error if block supplied
|
|
597
|
+
# @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
|
|
598
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
599
|
+
#
|
|
600
|
+
# @return [Google::Apis::GenomicsV1::ReadGroupSet]
|
|
601
|
+
#
|
|
602
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
603
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
604
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
605
|
+
def get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
606
|
+
path = 'v1/readgroupsets/{readGroupSetId}'
|
|
607
|
+
command = make_simple_command(:get, path, options)
|
|
608
|
+
command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
|
|
609
|
+
command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
|
|
610
|
+
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
|
|
611
|
+
command.query['fields'] = fields unless fields.nil?
|
|
612
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
613
|
+
execute_or_queue_command(command, &block)
|
|
614
|
+
end
|
|
615
|
+
|
|
616
|
+
# Lists fixed width coverage buckets for a read group set, each of which
|
|
617
|
+
# correspond to a range of a reference sequence. Each bucket summarizes coverage
|
|
618
|
+
# information across its corresponding genomic range. Coverage is defined as the
|
|
619
|
+
# number of reads which are aligned to a given base in the reference sequence.
|
|
620
|
+
# Coverage buckets are available at several precomputed bucket widths, enabling
|
|
621
|
+
# retrieval of various coverage 'zoom levels'. The caller must have READ
|
|
622
|
+
# permissions for the target read group set.
|
|
623
|
+
# @param [String] read_group_set_id
|
|
624
|
+
# Required. The ID of the read group set over which coverage is requested.
|
|
625
|
+
# @param [String] reference_name
|
|
626
|
+
# The name of the reference to query, within the reference set associated with
|
|
627
|
+
# this query. Optional.
|
|
628
|
+
# @param [String] start
|
|
629
|
+
# The start position of the range on the reference, 0-based inclusive. If
|
|
630
|
+
# specified, `referenceName` must also be specified. Defaults to 0.
|
|
631
|
+
# @param [String] end_
|
|
632
|
+
# The end position of the range on the reference, 0-based exclusive. If
|
|
633
|
+
# specified, `referenceName` must also be specified. If unset or 0, defaults to
|
|
634
|
+
# the length of the reference.
|
|
635
|
+
# @param [String] target_bucket_width
|
|
636
|
+
# The desired width of each reported coverage bucket in base pairs. This will be
|
|
637
|
+
# rounded down to the nearest precomputed bucket width; the value of which is
|
|
638
|
+
# returned as `bucketWidth` in the response. Defaults to infinity (each bucket
|
|
639
|
+
# spans an entire reference sequence) or the length of the target range, if
|
|
640
|
+
# specified. The smallest precomputed `bucketWidth` is currently 2048 base pairs;
|
|
641
|
+
# this is subject to change.
|
|
642
|
+
# @param [String] page_token
|
|
643
|
+
# The continuation token, which is used to page through large result sets. To
|
|
644
|
+
# get the next page of results, set this parameter to the value of `
|
|
645
|
+
# nextPageToken` from the previous response.
|
|
646
|
+
# @param [Fixnum] page_size
|
|
647
|
+
# The maximum number of results to return in a single page. If unspecified,
|
|
648
|
+
# defaults to 1024. The maximum value is 2048.
|
|
649
|
+
# @param [String] fields
|
|
650
|
+
# Selector specifying which fields to include in a partial response.
|
|
651
|
+
# @param [String] quota_user
|
|
652
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
653
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
654
|
+
# @param [Google::Apis::RequestOptions] options
|
|
655
|
+
# Request-specific options
|
|
656
|
+
#
|
|
657
|
+
# @yield [result, err] Result & error if block supplied
|
|
658
|
+
# @yieldparam result [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] parsed result object
|
|
659
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
660
|
+
#
|
|
661
|
+
# @return [Google::Apis::GenomicsV1::ListCoverageBucketsResponse]
|
|
662
|
+
#
|
|
663
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
664
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
665
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
666
|
+
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)
|
|
667
|
+
path = 'v1/readgroupsets/{readGroupSetId}/coveragebuckets'
|
|
668
|
+
command = make_simple_command(:get, path, options)
|
|
669
|
+
command.response_representation = Google::Apis::GenomicsV1::ListCoverageBucketsResponse::Representation
|
|
670
|
+
command.response_class = Google::Apis::GenomicsV1::ListCoverageBucketsResponse
|
|
671
|
+
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
|
|
672
|
+
command.query['referenceName'] = reference_name unless reference_name.nil?
|
|
673
|
+
command.query['start'] = start unless start.nil?
|
|
674
|
+
command.query['end'] = end_ unless end_.nil?
|
|
675
|
+
command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil?
|
|
676
|
+
command.query['pageToken'] = page_token unless page_token.nil?
|
|
677
|
+
command.query['pageSize'] = page_size unless page_size.nil?
|
|
678
|
+
command.query['fields'] = fields unless fields.nil?
|
|
679
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
680
|
+
execute_or_queue_command(command, &block)
|
|
681
|
+
end
|
|
682
|
+
|
|
683
|
+
# Gets a list of reads for one or more read group sets. Reads search operates
|
|
684
|
+
# over a genomic coordinate space of reference sequence & position defined over
|
|
685
|
+
# the reference sequences to which the requested read group sets are aligned. If
|
|
686
|
+
# a target positional range is specified, search returns all reads whose
|
|
687
|
+
# alignment to the reference genome overlap the range. A query which specifies
|
|
688
|
+
# only read group set IDs yields all reads in those read group sets, including
|
|
689
|
+
# unmapped reads. All reads returned (including reads on subsequent pages) are
|
|
690
|
+
# ordered by genomic coordinate (reference sequence & position). Reads with
|
|
691
|
+
# equivalent genomic coordinates are returned in a deterministic order.
|
|
692
|
+
# Implements [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/
|
|
693
|
+
# blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).
|
|
694
|
+
# @param [Google::Apis::GenomicsV1::SearchReadsRequest] search_reads_request_object
|
|
695
|
+
# @param [String] fields
|
|
696
|
+
# Selector specifying which fields to include in a partial response.
|
|
697
|
+
# @param [String] quota_user
|
|
698
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
699
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
700
|
+
# @param [Google::Apis::RequestOptions] options
|
|
701
|
+
# Request-specific options
|
|
702
|
+
#
|
|
703
|
+
# @yield [result, err] Result & error if block supplied
|
|
704
|
+
# @yieldparam result [Google::Apis::GenomicsV1::SearchReadsResponse] parsed result object
|
|
705
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
706
|
+
#
|
|
707
|
+
# @return [Google::Apis::GenomicsV1::SearchReadsResponse]
|
|
708
|
+
#
|
|
709
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
710
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
711
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
712
|
+
def search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
713
|
+
path = 'v1/reads/search'
|
|
714
|
+
command = make_simple_command(:post, path, options)
|
|
715
|
+
command.request_representation = Google::Apis::GenomicsV1::SearchReadsRequest::Representation
|
|
716
|
+
command.request_object = search_reads_request_object
|
|
717
|
+
command.response_representation = Google::Apis::GenomicsV1::SearchReadsResponse::Representation
|
|
718
|
+
command.response_class = Google::Apis::GenomicsV1::SearchReadsResponse
|
|
719
|
+
command.query['fields'] = fields unless fields.nil?
|
|
720
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
721
|
+
execute_or_queue_command(command, &block)
|
|
722
|
+
end
|
|
723
|
+
|
|
724
|
+
# Searches for reference sets which match the given criteria. Implements [
|
|
725
|
+
# GlobalAllianceApi.searchReferenceSets](http://ga4gh.org/documentation/api/v0.5.
|
|
726
|
+
# 1/ga4gh_api.html#/schema/org.ga4gh.searchReferenceSets).
|
|
727
|
+
# @param [Google::Apis::GenomicsV1::SearchReferenceSetsRequest] search_reference_sets_request_object
|
|
728
|
+
# @param [String] fields
|
|
729
|
+
# Selector specifying which fields to include in a partial response.
|
|
730
|
+
# @param [String] quota_user
|
|
731
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
732
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
733
|
+
# @param [Google::Apis::RequestOptions] options
|
|
734
|
+
# Request-specific options
|
|
735
|
+
#
|
|
736
|
+
# @yield [result, err] Result & error if block supplied
|
|
737
|
+
# @yieldparam result [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] parsed result object
|
|
738
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
739
|
+
#
|
|
740
|
+
# @return [Google::Apis::GenomicsV1::SearchReferenceSetsResponse]
|
|
741
|
+
#
|
|
742
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
743
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
744
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
745
|
+
def search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
746
|
+
path = 'v1/referencesets/search'
|
|
747
|
+
command = make_simple_command(:post, path, options)
|
|
748
|
+
command.request_representation = Google::Apis::GenomicsV1::SearchReferenceSetsRequest::Representation
|
|
749
|
+
command.request_object = search_reference_sets_request_object
|
|
750
|
+
command.response_representation = Google::Apis::GenomicsV1::SearchReferenceSetsResponse::Representation
|
|
751
|
+
command.response_class = Google::Apis::GenomicsV1::SearchReferenceSetsResponse
|
|
752
|
+
command.query['fields'] = fields unless fields.nil?
|
|
753
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
754
|
+
execute_or_queue_command(command, &block)
|
|
755
|
+
end
|
|
756
|
+
|
|
757
|
+
# Gets a reference set. Implements [GlobalAllianceApi.getReferenceSet](https://
|
|
758
|
+
# github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.
|
|
759
|
+
# avdl#L83).
|
|
760
|
+
# @param [String] reference_set_id
|
|
761
|
+
# The ID of the reference set.
|
|
762
|
+
# @param [String] fields
|
|
763
|
+
# Selector specifying which fields to include in a partial response.
|
|
764
|
+
# @param [String] quota_user
|
|
765
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
766
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
767
|
+
# @param [Google::Apis::RequestOptions] options
|
|
768
|
+
# Request-specific options
|
|
769
|
+
#
|
|
770
|
+
# @yield [result, err] Result & error if block supplied
|
|
771
|
+
# @yieldparam result [Google::Apis::GenomicsV1::ReferenceSet] parsed result object
|
|
772
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
773
|
+
#
|
|
774
|
+
# @return [Google::Apis::GenomicsV1::ReferenceSet]
|
|
775
|
+
#
|
|
776
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
777
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
778
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
779
|
+
def get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
780
|
+
path = 'v1/referencesets/{referenceSetId}'
|
|
781
|
+
command = make_simple_command(:get, path, options)
|
|
782
|
+
command.response_representation = Google::Apis::GenomicsV1::ReferenceSet::Representation
|
|
783
|
+
command.response_class = Google::Apis::GenomicsV1::ReferenceSet
|
|
784
|
+
command.params['referenceSetId'] = reference_set_id unless reference_set_id.nil?
|
|
785
|
+
command.query['fields'] = fields unless fields.nil?
|
|
786
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
787
|
+
execute_or_queue_command(command, &block)
|
|
788
|
+
end
|
|
789
|
+
|
|
790
|
+
# Searches for references which match the given criteria. Implements [
|
|
791
|
+
# GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.
|
|
792
|
+
# 1/src/main/resources/avro/referencemethods.avdl#L146).
|
|
793
|
+
# @param [Google::Apis::GenomicsV1::SearchReferencesRequest] search_references_request_object
|
|
794
|
+
# @param [String] fields
|
|
795
|
+
# Selector specifying which fields to include in a partial response.
|
|
796
|
+
# @param [String] quota_user
|
|
797
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
798
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
799
|
+
# @param [Google::Apis::RequestOptions] options
|
|
800
|
+
# Request-specific options
|
|
801
|
+
#
|
|
802
|
+
# @yield [result, err] Result & error if block supplied
|
|
803
|
+
# @yieldparam result [Google::Apis::GenomicsV1::SearchReferencesResponse] parsed result object
|
|
804
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
805
|
+
#
|
|
806
|
+
# @return [Google::Apis::GenomicsV1::SearchReferencesResponse]
|
|
807
|
+
#
|
|
808
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
809
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
810
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
811
|
+
def search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
812
|
+
path = 'v1/references/search'
|
|
813
|
+
command = make_simple_command(:post, path, options)
|
|
814
|
+
command.request_representation = Google::Apis::GenomicsV1::SearchReferencesRequest::Representation
|
|
815
|
+
command.request_object = search_references_request_object
|
|
816
|
+
command.response_representation = Google::Apis::GenomicsV1::SearchReferencesResponse::Representation
|
|
817
|
+
command.response_class = Google::Apis::GenomicsV1::SearchReferencesResponse
|
|
818
|
+
command.query['fields'] = fields unless fields.nil?
|
|
819
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
820
|
+
execute_or_queue_command(command, &block)
|
|
821
|
+
end
|
|
822
|
+
|
|
823
|
+
# Gets a reference. Implements [GlobalAllianceApi.getReference](https://github.
|
|
824
|
+
# com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#
|
|
825
|
+
# L158).
|
|
826
|
+
# @param [String] reference_id
|
|
827
|
+
# The ID of the reference.
|
|
828
|
+
# @param [String] fields
|
|
829
|
+
# Selector specifying which fields to include in a partial response.
|
|
830
|
+
# @param [String] quota_user
|
|
831
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
832
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
833
|
+
# @param [Google::Apis::RequestOptions] options
|
|
834
|
+
# Request-specific options
|
|
835
|
+
#
|
|
836
|
+
# @yield [result, err] Result & error if block supplied
|
|
837
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Reference] parsed result object
|
|
838
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
839
|
+
#
|
|
840
|
+
# @return [Google::Apis::GenomicsV1::Reference]
|
|
841
|
+
#
|
|
842
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
843
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
844
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
845
|
+
def get_reference(reference_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
846
|
+
path = 'v1/references/{referenceId}'
|
|
847
|
+
command = make_simple_command(:get, path, options)
|
|
848
|
+
command.response_representation = Google::Apis::GenomicsV1::Reference::Representation
|
|
849
|
+
command.response_class = Google::Apis::GenomicsV1::Reference
|
|
850
|
+
command.params['referenceId'] = reference_id unless reference_id.nil?
|
|
851
|
+
command.query['fields'] = fields unless fields.nil?
|
|
852
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
853
|
+
execute_or_queue_command(command, &block)
|
|
854
|
+
end
|
|
855
|
+
|
|
856
|
+
# Lists the bases in a reference, optionally restricted to a range. Implements [
|
|
857
|
+
# GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.
|
|
858
|
+
# 5.1/src/main/resources/avro/referencemethods.avdl#L221).
|
|
859
|
+
# @param [String] reference_id
|
|
860
|
+
# The ID of the reference.
|
|
861
|
+
# @param [String] start_position
|
|
862
|
+
# The start position (0-based) of this query. Defaults to 0.
|
|
863
|
+
# @param [String] end_position
|
|
864
|
+
# The end position (0-based, exclusive) of this query. Defaults to the length of
|
|
865
|
+
# this reference.
|
|
866
|
+
# @param [String] page_token
|
|
867
|
+
# The continuation token, which is used to page through large result sets. To
|
|
868
|
+
# get the next page of results, set this parameter to the value of `
|
|
869
|
+
# nextPageToken` from the previous response.
|
|
870
|
+
# @param [Fixnum] page_size
|
|
871
|
+
# Specifies the maximum number of bases to return in a single page.
|
|
872
|
+
# @param [String] fields
|
|
873
|
+
# Selector specifying which fields to include in a partial response.
|
|
874
|
+
# @param [String] quota_user
|
|
875
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
876
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
877
|
+
# @param [Google::Apis::RequestOptions] options
|
|
878
|
+
# Request-specific options
|
|
879
|
+
#
|
|
880
|
+
# @yield [result, err] Result & error if block supplied
|
|
881
|
+
# @yieldparam result [Google::Apis::GenomicsV1::ListBasesResponse] parsed result object
|
|
882
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
883
|
+
#
|
|
884
|
+
# @return [Google::Apis::GenomicsV1::ListBasesResponse]
|
|
885
|
+
#
|
|
886
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
887
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
888
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
889
|
+
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)
|
|
890
|
+
path = 'v1/references/{referenceId}/bases'
|
|
891
|
+
command = make_simple_command(:get, path, options)
|
|
892
|
+
command.response_representation = Google::Apis::GenomicsV1::ListBasesResponse::Representation
|
|
893
|
+
command.response_class = Google::Apis::GenomicsV1::ListBasesResponse
|
|
894
|
+
command.params['referenceId'] = reference_id unless reference_id.nil?
|
|
895
|
+
command.query['start'] = start_position unless start_position.nil?
|
|
896
|
+
command.query['end'] = end_position unless end_position.nil?
|
|
897
|
+
command.query['pageToken'] = page_token unless page_token.nil?
|
|
898
|
+
command.query['pageSize'] = page_size unless page_size.nil?
|
|
899
|
+
command.query['fields'] = fields unless fields.nil?
|
|
900
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
901
|
+
execute_or_queue_command(command, &block)
|
|
902
|
+
end
|
|
903
|
+
|
|
904
|
+
# Creates variant data by asynchronously importing the provided information. The
|
|
905
|
+
# variants for import will be merged with any existing data and each other
|
|
906
|
+
# according to the behavior of mergeVariants. In particular, this means for
|
|
907
|
+
# merged VCF variants that have conflicting INFO fields, some data will be
|
|
908
|
+
# arbitrarily discarded. As a special case, for single-sample VCF files, QUAL
|
|
909
|
+
# and FILTER fields will be moved to the call level; these are sometimes
|
|
910
|
+
# interpreted in a call-specific context. Imported VCF headers are appended to
|
|
911
|
+
# the metadata already in a variant set.
|
|
912
|
+
# @param [Google::Apis::GenomicsV1::ImportVariantsRequest] import_variants_request_object
|
|
913
|
+
# @param [String] fields
|
|
914
|
+
# Selector specifying which fields to include in a partial response.
|
|
915
|
+
# @param [String] quota_user
|
|
916
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
917
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
918
|
+
# @param [Google::Apis::RequestOptions] options
|
|
919
|
+
# Request-specific options
|
|
920
|
+
#
|
|
921
|
+
# @yield [result, err] Result & error if block supplied
|
|
922
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
|
|
923
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
924
|
+
#
|
|
925
|
+
# @return [Google::Apis::GenomicsV1::Operation]
|
|
926
|
+
#
|
|
927
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
928
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
929
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
930
|
+
def import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
931
|
+
path = 'v1/variants:import'
|
|
932
|
+
command = make_simple_command(:post, path, options)
|
|
933
|
+
command.request_representation = Google::Apis::GenomicsV1::ImportVariantsRequest::Representation
|
|
934
|
+
command.request_object = import_variants_request_object
|
|
935
|
+
command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
|
|
936
|
+
command.response_class = Google::Apis::GenomicsV1::Operation
|
|
937
|
+
command.query['fields'] = fields unless fields.nil?
|
|
938
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
939
|
+
execute_or_queue_command(command, &block)
|
|
940
|
+
end
|
|
941
|
+
|
|
942
|
+
# Gets a list of variants matching the criteria. Implements [GlobalAllianceApi.
|
|
943
|
+
# searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/
|
|
944
|
+
# resources/avro/variantmethods.avdl#L126).
|
|
945
|
+
# @param [Google::Apis::GenomicsV1::SearchVariantsRequest] search_variants_request_object
|
|
946
|
+
# @param [String] fields
|
|
947
|
+
# Selector specifying which fields to include in a partial response.
|
|
948
|
+
# @param [String] quota_user
|
|
949
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
950
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
951
|
+
# @param [Google::Apis::RequestOptions] options
|
|
952
|
+
# Request-specific options
|
|
953
|
+
#
|
|
954
|
+
# @yield [result, err] Result & error if block supplied
|
|
955
|
+
# @yieldparam result [Google::Apis::GenomicsV1::SearchVariantsResponse] parsed result object
|
|
956
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
957
|
+
#
|
|
958
|
+
# @return [Google::Apis::GenomicsV1::SearchVariantsResponse]
|
|
959
|
+
#
|
|
960
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
961
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
962
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
963
|
+
def search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
964
|
+
path = 'v1/variants/search'
|
|
965
|
+
command = make_simple_command(:post, path, options)
|
|
966
|
+
command.request_representation = Google::Apis::GenomicsV1::SearchVariantsRequest::Representation
|
|
967
|
+
command.request_object = search_variants_request_object
|
|
968
|
+
command.response_representation = Google::Apis::GenomicsV1::SearchVariantsResponse::Representation
|
|
969
|
+
command.response_class = Google::Apis::GenomicsV1::SearchVariantsResponse
|
|
970
|
+
command.query['fields'] = fields unless fields.nil?
|
|
971
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
972
|
+
execute_or_queue_command(command, &block)
|
|
973
|
+
end
|
|
974
|
+
|
|
975
|
+
# Creates a new variant.
|
|
976
|
+
# @param [Google::Apis::GenomicsV1::Variant] variant_object
|
|
977
|
+
# @param [String] fields
|
|
978
|
+
# Selector specifying which fields to include in a partial response.
|
|
979
|
+
# @param [String] quota_user
|
|
980
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
981
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
982
|
+
# @param [Google::Apis::RequestOptions] options
|
|
983
|
+
# Request-specific options
|
|
984
|
+
#
|
|
985
|
+
# @yield [result, err] Result & error if block supplied
|
|
986
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
|
|
987
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
988
|
+
#
|
|
989
|
+
# @return [Google::Apis::GenomicsV1::Variant]
|
|
990
|
+
#
|
|
991
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
992
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
993
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
994
|
+
def create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
995
|
+
path = 'v1/variants'
|
|
996
|
+
command = make_simple_command(:post, path, options)
|
|
997
|
+
command.request_representation = Google::Apis::GenomicsV1::Variant::Representation
|
|
998
|
+
command.request_object = variant_object
|
|
999
|
+
command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
|
|
1000
|
+
command.response_class = Google::Apis::GenomicsV1::Variant
|
|
1001
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1002
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1003
|
+
execute_or_queue_command(command, &block)
|
|
1004
|
+
end
|
|
1005
|
+
|
|
1006
|
+
# Updates a variant. This method supports patch semantics. Returns the modified
|
|
1007
|
+
# variant without its calls.
|
|
1008
|
+
# @param [String] variant_id
|
|
1009
|
+
# The ID of the variant to be updated.
|
|
1010
|
+
# @param [Google::Apis::GenomicsV1::Variant] variant_object
|
|
1011
|
+
# @param [String] update_mask
|
|
1012
|
+
# An optional mask specifying which fields to update. At this time, mutable
|
|
1013
|
+
# fields are [names][google.genomics.v1.Variant.names] and [info][google.
|
|
1014
|
+
# genomics.v1.Variant.info]. Acceptable values are "names" and "info". If
|
|
1015
|
+
# unspecified, all mutable fields will be updated.
|
|
1016
|
+
# @param [String] fields
|
|
1017
|
+
# Selector specifying which fields to include in a partial response.
|
|
1018
|
+
# @param [String] quota_user
|
|
1019
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1020
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1021
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1022
|
+
# Request-specific options
|
|
1023
|
+
#
|
|
1024
|
+
# @yield [result, err] Result & error if block supplied
|
|
1025
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
|
|
1026
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1027
|
+
#
|
|
1028
|
+
# @return [Google::Apis::GenomicsV1::Variant]
|
|
1029
|
+
#
|
|
1030
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1031
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1032
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1033
|
+
def patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
1034
|
+
path = 'v1/variants/{variantId}'
|
|
1035
|
+
command = make_simple_command(:patch, path, options)
|
|
1036
|
+
command.request_representation = Google::Apis::GenomicsV1::Variant::Representation
|
|
1037
|
+
command.request_object = variant_object
|
|
1038
|
+
command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
|
|
1039
|
+
command.response_class = Google::Apis::GenomicsV1::Variant
|
|
1040
|
+
command.params['variantId'] = variant_id unless variant_id.nil?
|
|
1041
|
+
command.query['updateMask'] = update_mask unless update_mask.nil?
|
|
1042
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1043
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1044
|
+
execute_or_queue_command(command, &block)
|
|
1045
|
+
end
|
|
1046
|
+
|
|
1047
|
+
# Deletes a variant.
|
|
1048
|
+
# @param [String] variant_id
|
|
1049
|
+
# The ID of the variant to be deleted.
|
|
1050
|
+
# @param [String] fields
|
|
1051
|
+
# Selector specifying which fields to include in a partial response.
|
|
1052
|
+
# @param [String] quota_user
|
|
1053
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1054
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1055
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1056
|
+
# Request-specific options
|
|
1057
|
+
#
|
|
1058
|
+
# @yield [result, err] Result & error if block supplied
|
|
1059
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
|
|
1060
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1061
|
+
#
|
|
1062
|
+
# @return [Google::Apis::GenomicsV1::Empty]
|
|
1063
|
+
#
|
|
1064
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1065
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1066
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1067
|
+
def delete_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
1068
|
+
path = 'v1/variants/{variantId}'
|
|
1069
|
+
command = make_simple_command(:delete, path, options)
|
|
1070
|
+
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
1071
|
+
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
1072
|
+
command.params['variantId'] = variant_id unless variant_id.nil?
|
|
1073
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1074
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1075
|
+
execute_or_queue_command(command, &block)
|
|
1076
|
+
end
|
|
1077
|
+
|
|
1078
|
+
# Gets a variant by ID.
|
|
1079
|
+
# @param [String] variant_id
|
|
1080
|
+
# The ID of the variant.
|
|
1081
|
+
# @param [String] fields
|
|
1082
|
+
# Selector specifying which fields to include in a partial response.
|
|
1083
|
+
# @param [String] quota_user
|
|
1084
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1085
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1086
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1087
|
+
# Request-specific options
|
|
1088
|
+
#
|
|
1089
|
+
# @yield [result, err] Result & error if block supplied
|
|
1090
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
|
|
1091
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1092
|
+
#
|
|
1093
|
+
# @return [Google::Apis::GenomicsV1::Variant]
|
|
1094
|
+
#
|
|
1095
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1096
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1097
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1098
|
+
def get_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
1099
|
+
path = 'v1/variants/{variantId}'
|
|
1100
|
+
command = make_simple_command(:get, path, options)
|
|
1101
|
+
command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
|
|
1102
|
+
command.response_class = Google::Apis::GenomicsV1::Variant
|
|
1103
|
+
command.params['variantId'] = variant_id unless variant_id.nil?
|
|
1104
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1105
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1106
|
+
execute_or_queue_command(command, &block)
|
|
1107
|
+
end
|
|
1108
|
+
|
|
1109
|
+
# Merges the given variants with existing variants. Each variant will be merged
|
|
1110
|
+
# with an existing variant that matches its reference sequence, start, end,
|
|
1111
|
+
# reference bases, and alternative bases. If no such variant exists, a new one
|
|
1112
|
+
# will be created. When variants are merged, the call information from the new
|
|
1113
|
+
# variant is added to the existing variant, and other fields (such as key/value
|
|
1114
|
+
# pairs) are discarded.
|
|
1115
|
+
# @param [Google::Apis::GenomicsV1::MergeVariantsRequest] merge_variants_request_object
|
|
1116
|
+
# @param [String] fields
|
|
1117
|
+
# Selector specifying which fields to include in a partial response.
|
|
1118
|
+
# @param [String] quota_user
|
|
1119
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1120
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1121
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1122
|
+
# Request-specific options
|
|
1123
|
+
#
|
|
1124
|
+
# @yield [result, err] Result & error if block supplied
|
|
1125
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
|
|
1126
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1127
|
+
#
|
|
1128
|
+
# @return [Google::Apis::GenomicsV1::Empty]
|
|
1129
|
+
#
|
|
1130
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1131
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1132
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1133
|
+
def merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
1134
|
+
path = 'v1/variants:merge'
|
|
1135
|
+
command = make_simple_command(:post, path, options)
|
|
1136
|
+
command.request_representation = Google::Apis::GenomicsV1::MergeVariantsRequest::Representation
|
|
1137
|
+
command.request_object = merge_variants_request_object
|
|
1138
|
+
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
1139
|
+
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
1140
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1141
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1142
|
+
execute_or_queue_command(command, &block)
|
|
1143
|
+
end
|
|
1144
|
+
|
|
1145
|
+
# Creates a new variant set.
|
|
1146
|
+
# @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
|
|
1147
|
+
# @param [String] fields
|
|
1148
|
+
# Selector specifying which fields to include in a partial response.
|
|
1149
|
+
# @param [String] quota_user
|
|
1150
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1151
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1152
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1153
|
+
# Request-specific options
|
|
1154
|
+
#
|
|
1155
|
+
# @yield [result, err] Result & error if block supplied
|
|
1156
|
+
# @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
|
|
1157
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1158
|
+
#
|
|
1159
|
+
# @return [Google::Apis::GenomicsV1::VariantSet]
|
|
1160
|
+
#
|
|
1161
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1162
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1163
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1164
|
+
def create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
1165
|
+
path = 'v1/variantsets'
|
|
1166
|
+
command = make_simple_command(:post, path, options)
|
|
1167
|
+
command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation
|
|
1168
|
+
command.request_object = variant_set_object
|
|
1169
|
+
command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
|
|
1170
|
+
command.response_class = Google::Apis::GenomicsV1::VariantSet
|
|
1171
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1172
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1173
|
+
execute_or_queue_command(command, &block)
|
|
1174
|
+
end
|
|
1175
|
+
|
|
1176
|
+
# Exports variant set data to an external destination.
|
|
1177
|
+
# @param [String] variant_set_id
|
|
1178
|
+
# Required. The ID of the variant set that contains variant data which should be
|
|
1179
|
+
# exported. The caller must have READ access to this variant set.
|
|
1180
|
+
# @param [Google::Apis::GenomicsV1::ExportVariantSetRequest] export_variant_set_request_object
|
|
1181
|
+
# @param [String] fields
|
|
1182
|
+
# Selector specifying which fields to include in a partial response.
|
|
1183
|
+
# @param [String] quota_user
|
|
1184
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1185
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1186
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1187
|
+
# Request-specific options
|
|
1188
|
+
#
|
|
1189
|
+
# @yield [result, err] Result & error if block supplied
|
|
1190
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
|
|
1191
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1192
|
+
#
|
|
1193
|
+
# @return [Google::Apis::GenomicsV1::Operation]
|
|
1194
|
+
#
|
|
1195
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1196
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1197
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1198
|
+
def export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
1199
|
+
path = 'v1/variantsets/{variantSetId}:export'
|
|
1200
|
+
command = make_simple_command(:post, path, options)
|
|
1201
|
+
command.request_representation = Google::Apis::GenomicsV1::ExportVariantSetRequest::Representation
|
|
1202
|
+
command.request_object = export_variant_set_request_object
|
|
1203
|
+
command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
|
|
1204
|
+
command.response_class = Google::Apis::GenomicsV1::Operation
|
|
1205
|
+
command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
|
|
1206
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1207
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1208
|
+
execute_or_queue_command(command, &block)
|
|
1209
|
+
end
|
|
1210
|
+
|
|
1211
|
+
# Gets a variant set by ID.
|
|
1212
|
+
# @param [String] variant_set_id
|
|
1213
|
+
# Required. The ID of the variant set.
|
|
1214
|
+
# @param [String] fields
|
|
1215
|
+
# Selector specifying which fields to include in a partial response.
|
|
1216
|
+
# @param [String] quota_user
|
|
1217
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1218
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1219
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1220
|
+
# Request-specific options
|
|
1221
|
+
#
|
|
1222
|
+
# @yield [result, err] Result & error if block supplied
|
|
1223
|
+
# @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
|
|
1224
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1225
|
+
#
|
|
1226
|
+
# @return [Google::Apis::GenomicsV1::VariantSet]
|
|
1227
|
+
#
|
|
1228
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1229
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1230
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1231
|
+
def get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
1232
|
+
path = 'v1/variantsets/{variantSetId}'
|
|
1233
|
+
command = make_simple_command(:get, path, options)
|
|
1234
|
+
command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
|
|
1235
|
+
command.response_class = Google::Apis::GenomicsV1::VariantSet
|
|
1236
|
+
command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
|
|
1237
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1238
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1239
|
+
execute_or_queue_command(command, &block)
|
|
1240
|
+
end
|
|
1241
|
+
|
|
1242
|
+
# Returns a list of all variant sets matching search criteria. Implements [
|
|
1243
|
+
# GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.
|
|
1244
|
+
# 5.1/src/main/resources/avro/variantmethods.avdl#L49).
|
|
1245
|
+
# @param [Google::Apis::GenomicsV1::SearchVariantSetsRequest] search_variant_sets_request_object
|
|
1246
|
+
# @param [String] fields
|
|
1247
|
+
# Selector specifying which fields to include in a partial response.
|
|
1248
|
+
# @param [String] quota_user
|
|
1249
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1250
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1251
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1252
|
+
# Request-specific options
|
|
1253
|
+
#
|
|
1254
|
+
# @yield [result, err] Result & error if block supplied
|
|
1255
|
+
# @yieldparam result [Google::Apis::GenomicsV1::SearchVariantSetsResponse] parsed result object
|
|
1256
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1257
|
+
#
|
|
1258
|
+
# @return [Google::Apis::GenomicsV1::SearchVariantSetsResponse]
|
|
1259
|
+
#
|
|
1260
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1261
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1262
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1263
|
+
def search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
1264
|
+
path = 'v1/variantsets/search'
|
|
1265
|
+
command = make_simple_command(:post, path, options)
|
|
1266
|
+
command.request_representation = Google::Apis::GenomicsV1::SearchVariantSetsRequest::Representation
|
|
1267
|
+
command.request_object = search_variant_sets_request_object
|
|
1268
|
+
command.response_representation = Google::Apis::GenomicsV1::SearchVariantSetsResponse::Representation
|
|
1269
|
+
command.response_class = Google::Apis::GenomicsV1::SearchVariantSetsResponse
|
|
1270
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1271
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1272
|
+
execute_or_queue_command(command, &block)
|
|
1273
|
+
end
|
|
1274
|
+
|
|
1275
|
+
# Deletes the contents of a variant set. The variant set object is not deleted.
|
|
1276
|
+
# @param [String] variant_set_id
|
|
1277
|
+
# The ID of the variant set to be deleted.
|
|
1278
|
+
# @param [String] fields
|
|
1279
|
+
# Selector specifying which fields to include in a partial response.
|
|
1280
|
+
# @param [String] quota_user
|
|
1281
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1282
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1283
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1284
|
+
# Request-specific options
|
|
1285
|
+
#
|
|
1286
|
+
# @yield [result, err] Result & error if block supplied
|
|
1287
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
|
|
1288
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1289
|
+
#
|
|
1290
|
+
# @return [Google::Apis::GenomicsV1::Empty]
|
|
1291
|
+
#
|
|
1292
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1293
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1294
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1295
|
+
def delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
1296
|
+
path = 'v1/variantsets/{variantSetId}'
|
|
1297
|
+
command = make_simple_command(:delete, path, options)
|
|
1298
|
+
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
1299
|
+
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
1300
|
+
command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
|
|
1301
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1302
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1303
|
+
execute_or_queue_command(command, &block)
|
|
1304
|
+
end
|
|
1305
|
+
|
|
1306
|
+
# Updates a variant set. This method supports patch semantics.
|
|
1307
|
+
# @param [String] variant_set_id
|
|
1308
|
+
# The ID of the variant to be updated (must already exist).
|
|
1309
|
+
# @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
|
|
1310
|
+
# @param [String] update_mask
|
|
1311
|
+
# An optional mask specifying which fields to update. At this time, the only
|
|
1312
|
+
# mutable field is [metadata][google.genomics.v1.VariantSet.metadata]. The only
|
|
1313
|
+
# acceptable value is "metadata". If unspecified, all mutable fields will be
|
|
1314
|
+
# updated.
|
|
1315
|
+
# @param [String] fields
|
|
1316
|
+
# Selector specifying which fields to include in a partial response.
|
|
1317
|
+
# @param [String] quota_user
|
|
1318
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1319
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1320
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1321
|
+
# Request-specific options
|
|
1322
|
+
#
|
|
1323
|
+
# @yield [result, err] Result & error if block supplied
|
|
1324
|
+
# @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
|
|
1325
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1326
|
+
#
|
|
1327
|
+
# @return [Google::Apis::GenomicsV1::VariantSet]
|
|
1328
|
+
#
|
|
1329
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1330
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1331
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1332
|
+
def patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
1333
|
+
path = 'v1/variantsets/{variantSetId}'
|
|
1334
|
+
command = make_simple_command(:patch, path, options)
|
|
1335
|
+
command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation
|
|
1336
|
+
command.request_object = variant_set_object
|
|
1337
|
+
command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
|
|
1338
|
+
command.response_class = Google::Apis::GenomicsV1::VariantSet
|
|
1339
|
+
command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
|
|
1340
|
+
command.query['updateMask'] = update_mask unless update_mask.nil?
|
|
1341
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1342
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1343
|
+
execute_or_queue_command(command, &block)
|
|
1344
|
+
end
|
|
1345
|
+
|
|
1346
|
+
# Gets a list of call sets matching the criteria. Implements [GlobalAllianceApi.
|
|
1347
|
+
# searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/
|
|
1348
|
+
# resources/avro/variantmethods.avdl#L178).
|
|
1349
|
+
# @param [Google::Apis::GenomicsV1::SearchCallSetsRequest] search_call_sets_request_object
|
|
1350
|
+
# @param [String] fields
|
|
1351
|
+
# Selector specifying which fields to include in a partial response.
|
|
1352
|
+
# @param [String] quota_user
|
|
1353
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1354
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1355
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1356
|
+
# Request-specific options
|
|
1357
|
+
#
|
|
1358
|
+
# @yield [result, err] Result & error if block supplied
|
|
1359
|
+
# @yieldparam result [Google::Apis::GenomicsV1::SearchCallSetsResponse] parsed result object
|
|
1360
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1361
|
+
#
|
|
1362
|
+
# @return [Google::Apis::GenomicsV1::SearchCallSetsResponse]
|
|
1363
|
+
#
|
|
1364
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1365
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1366
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1367
|
+
def search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
1368
|
+
path = 'v1/callsets/search'
|
|
1369
|
+
command = make_simple_command(:post, path, options)
|
|
1370
|
+
command.request_representation = Google::Apis::GenomicsV1::SearchCallSetsRequest::Representation
|
|
1371
|
+
command.request_object = search_call_sets_request_object
|
|
1372
|
+
command.response_representation = Google::Apis::GenomicsV1::SearchCallSetsResponse::Representation
|
|
1373
|
+
command.response_class = Google::Apis::GenomicsV1::SearchCallSetsResponse
|
|
1374
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1375
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1376
|
+
execute_or_queue_command(command, &block)
|
|
1377
|
+
end
|
|
1378
|
+
|
|
1379
|
+
# Creates a new call set.
|
|
1380
|
+
# @param [Google::Apis::GenomicsV1::CallSet] call_set_object
|
|
1381
|
+
# @param [String] fields
|
|
1382
|
+
# Selector specifying which fields to include in a partial response.
|
|
1383
|
+
# @param [String] quota_user
|
|
1384
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1385
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1386
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1387
|
+
# Request-specific options
|
|
1388
|
+
#
|
|
1389
|
+
# @yield [result, err] Result & error if block supplied
|
|
1390
|
+
# @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
|
|
1391
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1392
|
+
#
|
|
1393
|
+
# @return [Google::Apis::GenomicsV1::CallSet]
|
|
1394
|
+
#
|
|
1395
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1396
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1397
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1398
|
+
def create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
1399
|
+
path = 'v1/callsets'
|
|
1400
|
+
command = make_simple_command(:post, path, options)
|
|
1401
|
+
command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation
|
|
1402
|
+
command.request_object = call_set_object
|
|
1403
|
+
command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
|
|
1404
|
+
command.response_class = Google::Apis::GenomicsV1::CallSet
|
|
1405
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1406
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1407
|
+
execute_or_queue_command(command, &block)
|
|
1408
|
+
end
|
|
1409
|
+
|
|
1410
|
+
# Updates a call set. This method supports patch semantics.
|
|
1411
|
+
# @param [String] call_set_id
|
|
1412
|
+
# The ID of the call set to be updated.
|
|
1413
|
+
# @param [Google::Apis::GenomicsV1::CallSet] call_set_object
|
|
1414
|
+
# @param [String] update_mask
|
|
1415
|
+
# An optional mask specifying which fields to update. At this time, the only
|
|
1416
|
+
# mutable field is [name][google.genomics.v1.CallSet.name]. The only acceptable
|
|
1417
|
+
# value is "name". If unspecified, all mutable fields will be updated.
|
|
1418
|
+
# @param [String] fields
|
|
1419
|
+
# Selector specifying which fields to include in a partial response.
|
|
1420
|
+
# @param [String] quota_user
|
|
1421
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1422
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1423
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1424
|
+
# Request-specific options
|
|
1425
|
+
#
|
|
1426
|
+
# @yield [result, err] Result & error if block supplied
|
|
1427
|
+
# @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
|
|
1428
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1429
|
+
#
|
|
1430
|
+
# @return [Google::Apis::GenomicsV1::CallSet]
|
|
1431
|
+
#
|
|
1432
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1433
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1434
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1435
|
+
def patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
|
|
1436
|
+
path = 'v1/callsets/{callSetId}'
|
|
1437
|
+
command = make_simple_command(:patch, path, options)
|
|
1438
|
+
command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation
|
|
1439
|
+
command.request_object = call_set_object
|
|
1440
|
+
command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
|
|
1441
|
+
command.response_class = Google::Apis::GenomicsV1::CallSet
|
|
1442
|
+
command.params['callSetId'] = call_set_id unless call_set_id.nil?
|
|
1443
|
+
command.query['updateMask'] = update_mask unless update_mask.nil?
|
|
1444
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1445
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1446
|
+
execute_or_queue_command(command, &block)
|
|
1447
|
+
end
|
|
1448
|
+
|
|
1449
|
+
# Deletes a call set.
|
|
1450
|
+
# @param [String] call_set_id
|
|
1451
|
+
# The ID of the call set to be deleted.
|
|
1452
|
+
# @param [String] fields
|
|
1453
|
+
# Selector specifying which fields to include in a partial response.
|
|
1454
|
+
# @param [String] quota_user
|
|
1455
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1456
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1457
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1458
|
+
# Request-specific options
|
|
1459
|
+
#
|
|
1460
|
+
# @yield [result, err] Result & error if block supplied
|
|
1461
|
+
# @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
|
|
1462
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1463
|
+
#
|
|
1464
|
+
# @return [Google::Apis::GenomicsV1::Empty]
|
|
1465
|
+
#
|
|
1466
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1467
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1468
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1469
|
+
def delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
1470
|
+
path = 'v1/callsets/{callSetId}'
|
|
1471
|
+
command = make_simple_command(:delete, path, options)
|
|
1472
|
+
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
1473
|
+
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
1474
|
+
command.params['callSetId'] = call_set_id unless call_set_id.nil?
|
|
1475
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1476
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1477
|
+
execute_or_queue_command(command, &block)
|
|
1478
|
+
end
|
|
1479
|
+
|
|
1480
|
+
# Gets a call set by ID.
|
|
1481
|
+
# @param [String] call_set_id
|
|
1482
|
+
# The ID of the call set.
|
|
1483
|
+
# @param [String] fields
|
|
1484
|
+
# Selector specifying which fields to include in a partial response.
|
|
1485
|
+
# @param [String] quota_user
|
|
1486
|
+
# Available to use for quota purposes for server-side applications. Can be any
|
|
1487
|
+
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
1488
|
+
# @param [Google::Apis::RequestOptions] options
|
|
1489
|
+
# Request-specific options
|
|
1490
|
+
#
|
|
1491
|
+
# @yield [result, err] Result & error if block supplied
|
|
1492
|
+
# @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
|
|
1493
|
+
# @yieldparam err [StandardError] error object if request failed
|
|
1494
|
+
#
|
|
1495
|
+
# @return [Google::Apis::GenomicsV1::CallSet]
|
|
1496
|
+
#
|
|
1497
|
+
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
1498
|
+
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
1499
|
+
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
1500
|
+
def get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block)
|
|
1501
|
+
path = 'v1/callsets/{callSetId}'
|
|
1502
|
+
command = make_simple_command(:get, path, options)
|
|
1503
|
+
command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
|
|
1504
|
+
command.response_class = Google::Apis::GenomicsV1::CallSet
|
|
1505
|
+
command.params['callSetId'] = call_set_id unless call_set_id.nil?
|
|
1506
|
+
command.query['fields'] = fields unless fields.nil?
|
|
1507
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1508
|
+
execute_or_queue_command(command, &block)
|
|
1509
|
+
end
|
|
1510
|
+
|
|
1511
|
+
protected
|
|
1512
|
+
|
|
1513
|
+
def apply_command_defaults(command)
|
|
1514
|
+
command.query['key'] = key unless key.nil?
|
|
1515
|
+
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
1516
|
+
end
|
|
1517
|
+
end
|
|
1518
|
+
end
|
|
1519
|
+
end
|
|
1520
|
+
end
|