2393 lines
144 KiB
Ruby
2393 lines
144 KiB
Ruby
# Copyright 2015 Google Inc.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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require 'google/apis/core/base_service'
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require 'google/apis/core/json_representation'
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require 'google/apis/core/hashable'
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require 'google/apis/errors'
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module Google
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module Apis
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module GenomicsV1beta2
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# Genomics API
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#
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# Provides access to Genomics data.
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#
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# @example
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# require 'google/apis/genomics_v1beta2'
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#
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# Genomics = Google::Apis::GenomicsV1beta2 # Alias the module
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# service = Genomics::GenomicsService.new
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#
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# @see https://developers.google.com/genomics/v1beta2/reference
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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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# Overrides userIp if both are provided.
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attr_accessor :quota_user
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# @return [String]
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# IP address of the site where the request originates. Use this if you want to
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# enforce per-user limits.
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attr_accessor :user_ip
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def initialize
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super('https://www.googleapis.com/', 'genomics/v1beta2/')
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end
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# Creates a new annotation set. Caller must have WRITE permission for the
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# associated dataset.
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# @param [Google::Apis::GenomicsV1beta2::AnnotationSet] annotation_set_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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# Overrides userIp if both are provided.
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# @param [String] user_ip
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# IP address of the site where the request originates. Use this if you want to
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# enforce per-user limits.
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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::GenomicsV1beta2::AnnotationSet] 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::GenomicsV1beta2::AnnotationSet]
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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_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
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path = 'annotationSets'
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command = make_simple_command(:post, path, options)
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command.request_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
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command.request_object = annotation_set_object
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command.response_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
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command.response_class = Google::Apis::GenomicsV1beta2::AnnotationSet
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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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command.query['userIp'] = user_ip unless user_ip.nil?
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execute_or_queue_command(command, &block)
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end
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# Deletes an annotation set. Caller must have WRITE permission for the
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# associated annotation set.
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# @param [String] annotation_set_id
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# The ID of the annotation set to be deleted.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# Overrides userIp if both are provided.
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# @param [String] user_ip
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# IP address of the site where the request originates. Use this if you want to
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# enforce per-user limits.
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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 [NilClass] No result returned for this method
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [void]
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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_annotation_set(annotation_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
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path = 'annotationSets/{annotationSetId}'
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command = make_simple_command(:delete, path, options)
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command.params['annotationSetId'] = annotation_set_id unless annotation_set_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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command.query['userIp'] = user_ip unless user_ip.nil?
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execute_or_queue_command(command, &block)
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end
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# Gets an annotation set. Caller must have READ permission for the associated
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# dataset.
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# @param [String] annotation_set_id
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# The ID of the annotation set to be retrieved.
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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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# Overrides userIp if both are provided.
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# @param [String] user_ip
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# IP address of the site where the request originates. Use this if you want to
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# enforce per-user limits.
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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::GenomicsV1beta2::AnnotationSet] 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::GenomicsV1beta2::AnnotationSet]
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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_annotation_set(annotation_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
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path = 'annotationSets/{annotationSetId}'
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command = make_simple_command(:get, path, options)
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command.response_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
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command.response_class = Google::Apis::GenomicsV1beta2::AnnotationSet
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command.params['annotationSetId'] = annotation_set_id unless annotation_set_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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command.query['userIp'] = user_ip unless user_ip.nil?
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execute_or_queue_command(command, &block)
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end
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# Updates an annotation set. The update must respect all mutability restrictions
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# and other invariants described on the annotation set resource. Caller must
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# have WRITE permission for the associated dataset. This method supports patch
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# semantics.
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# @param [String] annotation_set_id
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# The ID of the annotation set to be updated.
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# @param [Google::Apis::GenomicsV1beta2::AnnotationSet] annotation_set_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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# Overrides userIp if both are provided.
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# @param [String] user_ip
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# IP address of the site where the request originates. Use this if you want to
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# enforce per-user limits.
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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::GenomicsV1beta2::AnnotationSet] 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::GenomicsV1beta2::AnnotationSet]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def patch_annotation_set(annotation_set_id, annotation_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
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path = 'annotationSets/{annotationSetId}'
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command = make_simple_command(:patch, path, options)
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command.request_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
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command.request_object = annotation_set_object
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command.response_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
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command.response_class = Google::Apis::GenomicsV1beta2::AnnotationSet
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command.params['annotationSetId'] = annotation_set_id unless annotation_set_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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command.query['userIp'] = user_ip unless user_ip.nil?
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execute_or_queue_command(command, &block)
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end
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# Searches for annotation sets that match the given criteria. Results are
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# returned in a deterministic order. Caller must have READ permission for the
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# queried datasets.
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# @param [Google::Apis::GenomicsV1beta2::SearchAnnotationSetsRequest] search_annotation_sets_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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# Overrides userIp if both are provided.
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# @param [String] user_ip
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# IP address of the site where the request originates. Use this if you want to
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# enforce per-user limits.
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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::GenomicsV1beta2::SearchAnnotationSetsResponse] 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::GenomicsV1beta2::SearchAnnotationSetsResponse]
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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 search_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
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path = 'annotationSets/search'
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command = make_simple_command(:post, path, options)
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command.request_representation = Google::Apis::GenomicsV1beta2::SearchAnnotationSetsRequest::Representation
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command.request_object = search_annotation_sets_request_object
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command.response_representation = Google::Apis::GenomicsV1beta2::SearchAnnotationSetsResponse::Representation
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command.response_class = Google::Apis::GenomicsV1beta2::SearchAnnotationSetsResponse
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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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command.query['userIp'] = user_ip unless user_ip.nil?
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execute_or_queue_command(command, &block)
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end
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# Updates an annotation set. The update must respect all mutability restrictions
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# and other invariants described on the annotation set resource. Caller must
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# have WRITE permission for the associated dataset.
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# @param [String] annotation_set_id
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# The ID of the annotation set to be updated.
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# @param [Google::Apis::GenomicsV1beta2::AnnotationSet] annotation_set_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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# Overrides userIp if both are provided.
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# @param [String] user_ip
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# IP address of the site where the request originates. Use this if you want to
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# enforce per-user limits.
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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::GenomicsV1beta2::AnnotationSet] 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::GenomicsV1beta2::AnnotationSet]
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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 update_annotation_set(annotation_set_id, annotation_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
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path = 'annotationSets/{annotationSetId}'
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command = make_simple_command(:put, path, options)
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command.request_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
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command.request_object = annotation_set_object
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command.response_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
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command.response_class = Google::Apis::GenomicsV1beta2::AnnotationSet
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command.params['annotationSetId'] = annotation_set_id unless annotation_set_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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command.query['userIp'] = user_ip unless user_ip.nil?
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execute_or_queue_command(command, &block)
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end
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# Creates one or more new annotations atomically. All annotations must belong to
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# the same annotation set. Caller must have WRITE permission for this annotation
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# set. For optimal performance, batch positionally adjacent annotations together.
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# If the request has a systemic issue, such as an attempt to write to an
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# inaccessible annotation set, the entire RPC will fail accordingly. For lesser
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# data issues, when possible an error will be isolated to the corresponding
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# batch entry in the response; the remaining well formed annotations will be
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# created normally.
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# @param [Google::Apis::GenomicsV1beta2::BatchCreateAnnotationsRequest] batch_create_annotations_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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# Overrides userIp if both are provided.
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# @param [String] user_ip
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# IP address of the site where the request originates. Use this if you want to
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# enforce per-user limits.
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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::GenomicsV1beta2::BatchAnnotationsResponse] 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::GenomicsV1beta2::BatchAnnotationsResponse]
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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 batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
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path = 'annotations:batchCreate'
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command = make_simple_command(:post, path, options)
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command.request_representation = Google::Apis::GenomicsV1beta2::BatchCreateAnnotationsRequest::Representation
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command.request_object = batch_create_annotations_request_object
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command.response_representation = Google::Apis::GenomicsV1beta2::BatchAnnotationsResponse::Representation
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command.response_class = Google::Apis::GenomicsV1beta2::BatchAnnotationsResponse
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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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command.query['userIp'] = user_ip unless user_ip.nil?
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execute_or_queue_command(command, &block)
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end
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# Creates a new annotation. Caller must have WRITE permission for the associated
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# annotation set.
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# @param [Google::Apis::GenomicsV1beta2::Annotation] annotation_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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# Overrides userIp if both are provided.
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# @param [String] user_ip
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# IP address of the site where the request originates. Use this if you want to
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# enforce per-user limits.
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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::GenomicsV1beta2::Annotation] 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::GenomicsV1beta2::Annotation]
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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_annotation(annotation_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
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path = 'annotations'
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command = make_simple_command(:post, path, options)
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command.request_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
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command.request_object = annotation_object
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command.response_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
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command.response_class = Google::Apis::GenomicsV1beta2::Annotation
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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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command.query['userIp'] = user_ip unless user_ip.nil?
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execute_or_queue_command(command, &block)
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end
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# Deletes an annotation. Caller must have WRITE permission for the associated
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# annotation set.
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# @param [String] annotation_id
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# The ID of the annotation set to be deleted.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# Overrides userIp if both are provided.
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# @param [String] user_ip
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# IP address of the site where the request originates. Use this if you want to
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# enforce per-user limits.
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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 [NilClass] No result returned for this method
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [void]
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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_annotation(annotation_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
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path = 'annotations/{annotationId}'
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command = make_simple_command(:delete, path, options)
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command.params['annotationId'] = annotation_id unless annotation_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets an annotation. Caller must have READ permission for the associated
|
|
# annotation set.
|
|
# @param [String] annotation_id
|
|
# The ID of the annotation set to be retrieved.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Annotation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Annotation]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def get_annotation(annotation_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'annotations/{annotationId}'
|
|
command = make_simple_command(:get, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Annotation
|
|
command.params['annotationId'] = annotation_id unless annotation_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates an annotation. The update must respect all mutability restrictions and
|
|
# other invariants described on the annotation resource. Caller must have WRITE
|
|
# permission for the associated dataset. This method supports patch semantics.
|
|
# @param [String] annotation_id
|
|
# The ID of the annotation set to be updated.
|
|
# @param [Google::Apis::GenomicsV1beta2::Annotation] annotation_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Annotation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Annotation]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def patch_annotation(annotation_id, annotation_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'annotations/{annotationId}'
|
|
command = make_simple_command(:patch, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
|
|
command.request_object = annotation_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Annotation
|
|
command.params['annotationId'] = annotation_id unless annotation_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Searches for annotations that match the given criteria. Results are returned
|
|
# ordered by start position. Annotations that have matching start positions are
|
|
# ordered deterministically. Caller must have READ permission for the queried
|
|
# annotation sets.
|
|
# @param [Google::Apis::GenomicsV1beta2::SearchAnnotationsRequest] search_annotations_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::SearchAnnotationsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::SearchAnnotationsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'annotations/search'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::SearchAnnotationsRequest::Representation
|
|
command.request_object = search_annotations_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::SearchAnnotationsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::SearchAnnotationsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates an annotation. The update must respect all mutability restrictions and
|
|
# other invariants described on the annotation resource. Caller must have WRITE
|
|
# permission for the associated dataset.
|
|
# @param [String] annotation_id
|
|
# The ID of the annotation set to be updated.
|
|
# @param [Google::Apis::GenomicsV1beta2::Annotation] annotation_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Annotation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Annotation]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def update_annotation(annotation_id, annotation_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'annotations/{annotationId}'
|
|
command = make_simple_command(:put, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
|
|
command.request_object = annotation_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Annotation
|
|
command.params['annotationId'] = annotation_id unless annotation_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Creates a new call set.
|
|
# @param [Google::Apis::GenomicsV1beta2::CallSet] call_set_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::CallSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::CallSet]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def create_call_set(call_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'callsets'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
|
|
command.request_object = call_set_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::CallSet
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Deletes a call set.
|
|
# @param [String] call_set_id
|
|
# The ID of the call set to be deleted.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [NilClass] No result returned for this method
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [void]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def delete_call_set(call_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'callsets/{callSetId}'
|
|
command = make_simple_command(:delete, path, options)
|
|
command.params['callSetId'] = call_set_id unless call_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a call set by ID.
|
|
# @param [String] call_set_id
|
|
# The ID of the call set.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::CallSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::CallSet]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def get_call_set(call_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'callsets/{callSetId}'
|
|
command = make_simple_command(:get, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::CallSet
|
|
command.params['callSetId'] = call_set_id unless call_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates a call set. This method supports patch semantics.
|
|
# @param [String] call_set_id
|
|
# The ID of the call set to be updated.
|
|
# @param [Google::Apis::GenomicsV1beta2::CallSet] call_set_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::CallSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::CallSet]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def patch_call_set(call_set_id, call_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'callsets/{callSetId}'
|
|
command = make_simple_command(:patch, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
|
|
command.request_object = call_set_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::CallSet
|
|
command.params['callSetId'] = call_set_id unless call_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a list of call sets matching the criteria.
|
|
# Implements GlobalAllianceApi.searchCallSets.
|
|
# @param [Google::Apis::GenomicsV1beta2::SearchCallSetsRequest] search_call_sets_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::SearchCallSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::SearchCallSetsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'callsets/search'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::SearchCallSetsRequest::Representation
|
|
command.request_object = search_call_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::SearchCallSetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::SearchCallSetsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates a call set.
|
|
# @param [String] call_set_id
|
|
# The ID of the call set to be updated.
|
|
# @param [Google::Apis::GenomicsV1beta2::CallSet] call_set_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::CallSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::CallSet]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def update_call_set(call_set_id, call_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'callsets/{callSetId}'
|
|
command = make_simple_command(:put, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
|
|
command.request_object = call_set_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::CallSet
|
|
command.params['callSetId'] = call_set_id unless call_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Creates a new dataset.
|
|
# @param [Google::Apis::GenomicsV1beta2::Dataset] dataset_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Dataset]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def create_dataset(dataset_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'datasets'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
|
|
command.request_object = dataset_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Dataset
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Deletes a dataset.
|
|
# @param [String] dataset_id
|
|
# The ID of the dataset to be deleted.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [NilClass] No result returned for this method
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [void]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def delete_dataset(dataset_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'datasets/{datasetId}'
|
|
command = make_simple_command(:delete, path, options)
|
|
command.params['datasetId'] = dataset_id unless dataset_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a dataset by ID.
|
|
# @param [String] dataset_id
|
|
# The ID of the dataset.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Dataset]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def get_dataset(dataset_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'datasets/{datasetId}'
|
|
command = make_simple_command(:get, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Dataset
|
|
command.params['datasetId'] = dataset_id unless dataset_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Lists datasets within a project.
|
|
# @param [Fixnum] page_size
|
|
# The maximum number of results returned by this request. If unspecified,
|
|
# defaults to 50.
|
|
# @param [String] page_token
|
|
# The continuation token, which is used to page through large result sets. To
|
|
# get the next page of results, set this parameter to the value of nextPageToken
|
|
# from the previous response.
|
|
# @param [String] project_number
|
|
# Required. The project to list datasets for.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::ListDatasetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::ListDatasetsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def list_datasets(page_size: nil, page_token: nil, project_number: nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'datasets'
|
|
command = make_simple_command(:get, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::ListDatasetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::ListDatasetsResponse
|
|
command.query['pageSize'] = page_size unless page_size.nil?
|
|
command.query['pageToken'] = page_token unless page_token.nil?
|
|
command.query['projectNumber'] = project_number unless project_number.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates a dataset. This method supports patch semantics.
|
|
# @param [String] dataset_id
|
|
# The ID of the dataset to be updated.
|
|
# @param [Google::Apis::GenomicsV1beta2::Dataset] dataset_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Dataset]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def patch_dataset(dataset_id, dataset_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'datasets/{datasetId}'
|
|
command = make_simple_command(:patch, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
|
|
command.request_object = dataset_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Dataset
|
|
command.params['datasetId'] = dataset_id unless dataset_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Undeletes a dataset by restoring a dataset which was deleted via this API.
|
|
# This operation is only possible for a week after the deletion occurred.
|
|
# @param [String] dataset_id
|
|
# The ID of the dataset to be undeleted.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Dataset]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def undelete_dataset(dataset_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'datasets/{datasetId}/undelete'
|
|
command = make_simple_command(:post, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Dataset
|
|
command.params['datasetId'] = dataset_id unless dataset_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates a dataset.
|
|
# @param [String] dataset_id
|
|
# The ID of the dataset to be updated.
|
|
# @param [Google::Apis::GenomicsV1beta2::Dataset] dataset_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Dataset]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def update_dataset(dataset_id, dataset_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'datasets/{datasetId}'
|
|
command = make_simple_command(:put, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
|
|
command.request_object = dataset_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Dataset
|
|
command.params['datasetId'] = dataset_id unless dataset_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Creates and asynchronously runs an ad-hoc job. This is an experimental call
|
|
# and may be removed or changed at any time.
|
|
# @param [Google::Apis::GenomicsV1beta2::ExperimentalCreateJobRequest] experimental_create_job_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::ExperimentalCreateJobResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::ExperimentalCreateJobResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def create_experimental_job(experimental_create_job_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'experimental/jobs/create'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::ExperimentalCreateJobRequest::Representation
|
|
command.request_object = experimental_create_job_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::ExperimentalCreateJobResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::ExperimentalCreateJobResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Cancels a job by ID. Note that it is possible for partial results to be
|
|
# generated and stored for cancelled jobs.
|
|
# @param [String] job_id
|
|
# Required. The ID of the job.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [NilClass] No result returned for this method
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [void]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def cancel_job(job_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'jobs/{jobId}/cancel'
|
|
command = make_simple_command(:post, path, options)
|
|
command.params['jobId'] = job_id unless job_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a job by ID.
|
|
# @param [String] job_id
|
|
# Required. The ID of the job.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Job] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Job]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def get_job(job_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'jobs/{jobId}'
|
|
command = make_simple_command(:get, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Job::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Job
|
|
command.params['jobId'] = job_id unless job_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a list of jobs matching the criteria.
|
|
# @param [Google::Apis::GenomicsV1beta2::SearchJobsRequest] search_jobs_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::SearchJobsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::SearchJobsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def search_jobs(search_jobs_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'jobs/search'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::SearchJobsRequest::Representation
|
|
command.request_object = search_jobs_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::SearchJobsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::SearchJobsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Aligns read data from existing read group sets or files from Google Cloud
|
|
# Storage. See the alignment and variant calling documentation for more details.
|
|
# @param [Google::Apis::GenomicsV1beta2::AlignReadGroupSetsRequest] align_read_group_sets_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::AlignReadGroupSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::AlignReadGroupSetsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def align_read_group_sets(align_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'readgroupsets/align'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::AlignReadGroupSetsRequest::Representation
|
|
command.request_object = align_read_group_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::AlignReadGroupSetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::AlignReadGroupSetsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Calls variants on read data from existing read group sets or files from Google
|
|
# Cloud Storage. See the alignment and variant calling documentation for more
|
|
# details.
|
|
# @param [Google::Apis::GenomicsV1beta2::CallReadGroupSetsRequest] call_read_group_sets_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::CallReadGroupSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::CallReadGroupSetsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def call_read_group_sets(call_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'readgroupsets/call'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::CallReadGroupSetsRequest::Representation
|
|
command.request_object = call_read_group_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::CallReadGroupSetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::CallReadGroupSetsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Deletes a read group set.
|
|
# @param [String] read_group_set_id
|
|
# The ID of the read group set to be deleted. The caller must have WRITE
|
|
# permissions to the dataset associated with this read group set.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [NilClass] No result returned for this method
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [void]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'readgroupsets/{readGroupSetId}'
|
|
command = make_simple_command(:delete, path, options)
|
|
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Exports read group sets to a BAM file in Google Cloud Storage.
|
|
# Note that currently there may be some differences between exported BAM files
|
|
# and the original BAM file at the time of import. In particular, comments in
|
|
# the input file header will not be preserved, some custom tags will be
|
|
# converted to strings, and original reference sequence order is not necessarily
|
|
# preserved.
|
|
# @param [Google::Apis::GenomicsV1beta2::ExportReadGroupSetsRequest] export_read_group_sets_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::ExportReadGroupSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::ExportReadGroupSetsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def export_read_group_sets(export_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'readgroupsets/export'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::ExportReadGroupSetsRequest::Representation
|
|
command.request_object = export_read_group_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::ExportReadGroupSetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::ExportReadGroupSetsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a read group set by ID.
|
|
# @param [String] read_group_set_id
|
|
# The ID of the read group set.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::ReadGroupSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::ReadGroupSet]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'readgroupsets/{readGroupSetId}'
|
|
command = make_simple_command(:get, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::ReadGroupSet
|
|
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Creates read group sets by asynchronously importing the provided information.
|
|
# Note that currently comments in the input file header are not imported and
|
|
# some custom tags will be converted to strings, rather than preserving tag
|
|
# types. The caller must have WRITE permissions to the dataset.
|
|
# @param [Google::Apis::GenomicsV1beta2::ImportReadGroupSetsRequest] import_read_group_sets_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::ImportReadGroupSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::ImportReadGroupSetsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'readgroupsets/import'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::ImportReadGroupSetsRequest::Representation
|
|
command.request_object = import_read_group_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::ImportReadGroupSetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::ImportReadGroupSetsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates a read group set. This method supports patch semantics.
|
|
# @param [String] read_group_set_id
|
|
# The ID of the read group set to be updated. The caller must have WRITE
|
|
# permissions to the dataset associated with this read group set.
|
|
# @param [Google::Apis::GenomicsV1beta2::ReadGroupSet] read_group_set_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::ReadGroupSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::ReadGroupSet]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def patch_read_group_set(read_group_set_id, read_group_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'readgroupsets/{readGroupSetId}'
|
|
command = make_simple_command(:patch, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation
|
|
command.request_object = read_group_set_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::ReadGroupSet
|
|
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Searches for read group sets matching the criteria.
|
|
# Implements GlobalAllianceApi.searchReadGroupSets.
|
|
# @param [Google::Apis::GenomicsV1beta2::SearchReadGroupSetsRequest] search_read_group_sets_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::SearchReadGroupSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::SearchReadGroupSetsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'readgroupsets/search'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::SearchReadGroupSetsRequest::Representation
|
|
command.request_object = search_read_group_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::SearchReadGroupSetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::SearchReadGroupSetsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates a read group set.
|
|
# @param [String] read_group_set_id
|
|
# The ID of the read group set to be updated. The caller must have WRITE
|
|
# permissions to the dataset associated with this read group set.
|
|
# @param [Google::Apis::GenomicsV1beta2::ReadGroupSet] read_group_set_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::ReadGroupSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::ReadGroupSet]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def update_read_group_set(read_group_set_id, read_group_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'readgroupsets/{readGroupSetId}'
|
|
command = make_simple_command(:put, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation
|
|
command.request_object = read_group_set_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::ReadGroupSet
|
|
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Lists fixed width coverage buckets for a read group set, each of which
|
|
# correspond to a range of a reference sequence. Each bucket summarizes coverage
|
|
# information across its corresponding genomic range.
|
|
# Coverage is defined as the number of reads which are aligned to a given base
|
|
# in the reference sequence. Coverage buckets are available at several
|
|
# precomputed bucket widths, enabling retrieval of various coverage 'zoom levels'
|
|
# . The caller must have READ permissions for the target read group set.
|
|
# @param [String] read_group_set_id
|
|
# Required. The ID of the read group set over which coverage is requested.
|
|
# @param [Fixnum] page_size
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
# defaults to 1024. The maximum value is 2048.
|
|
# @param [String] page_token
|
|
# The continuation token, which is used to page through large result sets. To
|
|
# get the next page of results, set this parameter to the value of nextPageToken
|
|
# from the previous response.
|
|
# @param [String] range_end
|
|
# The end position of the range on the reference, 0-based exclusive. If
|
|
# specified, referenceName must also be specified.
|
|
# @param [String] range_reference_name
|
|
# The reference sequence name, for example chr1, 1, or chrX.
|
|
# @param [String] range_start
|
|
# The start position of the range on the reference, 0-based inclusive. If
|
|
# specified, referenceName must also be specified.
|
|
# @param [String] target_bucket_width
|
|
# The desired width of each reported coverage bucket in base pairs. This will be
|
|
# rounded down to the nearest precomputed bucket width; the value of which is
|
|
# returned as bucketWidth in the response. Defaults to infinity (each bucket
|
|
# spans an entire reference sequence) or the length of the target range, if
|
|
# specified. The smallest precomputed bucketWidth is currently 2048 base pairs;
|
|
# this is subject to change.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::ListCoverageBucketsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::ListCoverageBucketsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def list_coverage_buckets(read_group_set_id, page_size: nil, page_token: nil, range_end: nil, range_reference_name: nil, range_start: nil, target_bucket_width: nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'readgroupsets/{readGroupSetId}/coveragebuckets'
|
|
command = make_simple_command(:get, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::ListCoverageBucketsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::ListCoverageBucketsResponse
|
|
command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
|
|
command.query['pageSize'] = page_size unless page_size.nil?
|
|
command.query['pageToken'] = page_token unless page_token.nil?
|
|
command.query['range.end'] = range_end unless range_end.nil?
|
|
command.query['range.referenceName'] = range_reference_name unless range_reference_name.nil?
|
|
command.query['range.start'] = range_start unless range_start.nil?
|
|
command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a list of reads for one or more read group sets. Reads search operates
|
|
# over a genomic coordinate space of reference sequence & position defined over
|
|
# the reference sequences to which the requested read group sets are aligned.
|
|
# If a target positional range is specified, search returns all reads whose
|
|
# alignment to the reference genome overlap the range. A query which specifies
|
|
# only read group set IDs yields all reads in those read group sets, including
|
|
# unmapped reads.
|
|
# All reads returned (including reads on subsequent pages) are ordered by
|
|
# genomic coordinate (reference sequence & position). Reads with equivalent
|
|
# genomic coordinates are returned in a deterministic order.
|
|
# Implements GlobalAllianceApi.searchReads.
|
|
# @param [Google::Apis::GenomicsV1beta2::SearchReadsRequest] search_reads_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::SearchReadsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::SearchReadsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'reads/search'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::SearchReadsRequest::Representation
|
|
command.request_object = search_reads_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::SearchReadsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::SearchReadsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a reference.
|
|
# Implements GlobalAllianceApi.getReference.
|
|
# @param [String] reference_id
|
|
# The ID of the reference.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Reference] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Reference]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def get_reference(reference_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'references/{referenceId}'
|
|
command = make_simple_command(:get, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Reference::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Reference
|
|
command.params['referenceId'] = reference_id unless reference_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Searches for references which match the given criteria.
|
|
# Implements GlobalAllianceApi.searchReferences.
|
|
# @param [Google::Apis::GenomicsV1beta2::SearchReferencesRequest] search_references_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::SearchReferencesResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::SearchReferencesResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def search_references(search_references_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'references/search'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::SearchReferencesRequest::Representation
|
|
command.request_object = search_references_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::SearchReferencesResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::SearchReferencesResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Lists the bases in a reference, optionally restricted to a range.
|
|
# Implements GlobalAllianceApi.getReferenceBases.
|
|
# @param [String] reference_id
|
|
# The ID of the reference.
|
|
# @param [String] end_position
|
|
# The end position (0-based, exclusive) of this query. Defaults to the length of
|
|
# this reference.
|
|
# @param [Fixnum] page_size
|
|
# Specifies the maximum number of bases to return in a single page.
|
|
# @param [String] page_token
|
|
# The continuation token, which is used to page through large result sets. To
|
|
# get the next page of results, set this parameter to the value of nextPageToken
|
|
# from the previous response.
|
|
# @param [String] start_position
|
|
# The start position (0-based) of this query. Defaults to 0.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::ListBasesResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::ListBasesResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def list_reference_bases(reference_id, end_position: nil, page_size: nil, page_token: nil, start_position: nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'references/{referenceId}/bases'
|
|
command = make_simple_command(:get, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::ListBasesResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::ListBasesResponse
|
|
command.params['referenceId'] = reference_id unless reference_id.nil?
|
|
command.query['end'] = end_position unless end_position.nil?
|
|
command.query['pageSize'] = page_size unless page_size.nil?
|
|
command.query['pageToken'] = page_token unless page_token.nil?
|
|
command.query['start'] = start_position unless start_position.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a reference set.
|
|
# Implements GlobalAllianceApi.getReferenceSet.
|
|
# @param [String] reference_set_id
|
|
# The ID of the reference set.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::ReferenceSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::ReferenceSet]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def get_reference_set(reference_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'referencesets/{referenceSetId}'
|
|
command = make_simple_command(:get, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::ReferenceSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::ReferenceSet
|
|
command.params['referenceSetId'] = reference_set_id unless reference_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Searches for reference sets which match the given criteria.
|
|
# Implements GlobalAllianceApi.searchReferenceSets.
|
|
# @param [Google::Apis::GenomicsV1beta2::SearchReferenceSetsRequest] search_reference_sets_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::SearchReferenceSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::SearchReferenceSetsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'referencesets/search'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::SearchReferenceSetsRequest::Representation
|
|
command.request_object = search_reference_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::SearchReferenceSetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::SearchReferenceSetsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Creates a new variant.
|
|
# @param [Google::Apis::GenomicsV1beta2::Variant] variant_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Variant] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Variant]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def create_variant(variant_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variants'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::Variant::Representation
|
|
command.request_object = variant_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Variant::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Variant
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Deletes a variant.
|
|
# @param [String] variant_id
|
|
# The ID of the variant to be deleted.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [NilClass] No result returned for this method
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [void]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def delete_variant(variant_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variants/{variantId}'
|
|
command = make_simple_command(:delete, path, options)
|
|
command.params['variantId'] = variant_id unless variant_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a variant by ID.
|
|
# @param [String] variant_id
|
|
# The ID of the variant.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Variant] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Variant]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def get_variant(variant_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variants/{variantId}'
|
|
command = make_simple_command(:get, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Variant::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Variant
|
|
command.params['variantId'] = variant_id unless variant_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a list of variants matching the criteria.
|
|
# Implements GlobalAllianceApi.searchVariants.
|
|
# @param [Google::Apis::GenomicsV1beta2::SearchVariantsRequest] search_variants_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::SearchVariantsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::SearchVariantsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variants/search'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::SearchVariantsRequest::Representation
|
|
command.request_object = search_variants_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::SearchVariantsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::SearchVariantsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates a variant's names and info fields. All other modifications are
|
|
# silently ignored. Returns the modified variant without its calls.
|
|
# @param [String] variant_id
|
|
# The ID of the variant to be updated.
|
|
# @param [Google::Apis::GenomicsV1beta2::Variant] variant_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::Variant] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::Variant]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def update_variant(variant_id, variant_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variants/{variantId}'
|
|
command = make_simple_command(:put, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::Variant::Representation
|
|
command.request_object = variant_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::Variant::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::Variant
|
|
command.params['variantId'] = variant_id unless variant_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Creates a new variant set (only necessary in v1).
|
|
# @param [Google::Apis::GenomicsV1beta2::VariantSet] variant_set_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::VariantSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::VariantSet]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variantsets'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
|
|
command.request_object = variant_set_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::VariantSet
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Deletes the contents of a variant set. The variant set object is not deleted.
|
|
# @param [String] variant_set_id
|
|
# The ID of the variant set to be deleted.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [NilClass] No result returned for this method
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [void]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def delete_variantset(variant_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variantsets/{variantSetId}'
|
|
command = make_simple_command(:delete, path, options)
|
|
command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Exports variant set data to an external destination.
|
|
# @param [String] variant_set_id
|
|
# Required. The ID of the variant set that contains variant data which should be
|
|
# exported. The caller must have READ access to this variant set.
|
|
# @param [Google::Apis::GenomicsV1beta2::ExportVariantSetRequest] export_variant_set_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::ExportVariantSetResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::ExportVariantSetResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variantsets/{variantSetId}/export'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::ExportVariantSetRequest::Representation
|
|
command.request_object = export_variant_set_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::ExportVariantSetResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::ExportVariantSetResponse
|
|
command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Gets a variant set by ID.
|
|
# @param [String] variant_set_id
|
|
# Required. The ID of the variant set.
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::VariantSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::VariantSet]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def get_variantset(variant_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variantsets/{variantSetId}'
|
|
command = make_simple_command(:get, path, options)
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::VariantSet
|
|
command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Creates variant data by asynchronously importing the provided information.
|
|
# The variants for import will be merged with any existing data and each other
|
|
# according to the behavior of mergeVariants. In particular, this means for
|
|
# merged VCF variants that have conflicting INFO fields, some data will be
|
|
# arbitrarily discarded. As a special case, for single-sample VCF files, QUAL
|
|
# and FILTER fields will be moved to the call level; these are sometimes
|
|
# interpreted in a call-specific context. Imported VCF headers are appended to
|
|
# the metadata already in a variant set.
|
|
# @param [String] variant_set_id
|
|
# Required. The variant set to which variant data should be imported.
|
|
# @param [Google::Apis::GenomicsV1beta2::ImportVariantsRequest] import_variants_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::ImportVariantsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::ImportVariantsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def import_variants(variant_set_id, import_variants_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variantsets/{variantSetId}/importVariants'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::ImportVariantsRequest::Representation
|
|
command.request_object = import_variants_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::ImportVariantsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::ImportVariantsResponse
|
|
command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Merges the given variants with existing variants. Each variant will be merged
|
|
# with an existing variant that matches its reference sequence, start, end,
|
|
# reference bases, and alternative bases. If no such variant exists, a new one
|
|
# will be created.
|
|
# When variants are merged, the call information from the new variant is added
|
|
# to the existing variant, and other fields (such as key/value pairs) are
|
|
# discarded.
|
|
# @param [String] variant_set_id
|
|
# The destination variant set.
|
|
# @param [Google::Apis::GenomicsV1beta2::MergeVariantsRequest] merge_variants_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [NilClass] No result returned for this method
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [void]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def merge_variants(variant_set_id, merge_variants_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variantsets/{variantSetId}/mergeVariants'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::MergeVariantsRequest::Representation
|
|
command.request_object = merge_variants_request_object
|
|
command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates a variant set's metadata. All other modifications are silently ignored.
|
|
# This method supports patch semantics.
|
|
# @param [String] variant_set_id
|
|
# The ID of the variant to be updated (must already exist).
|
|
# @param [Google::Apis::GenomicsV1beta2::VariantSet] variant_set_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::VariantSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::VariantSet]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def patch_variantset(variant_set_id, variant_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variantsets/{variantSetId}'
|
|
command = make_simple_command(:patch, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
|
|
command.request_object = variant_set_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::VariantSet
|
|
command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Returns a list of all variant sets matching search criteria.
|
|
# Implements GlobalAllianceApi.searchVariantSets.
|
|
# @param [Google::Apis::GenomicsV1beta2::SearchVariantSetsRequest] search_variant_sets_request_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::SearchVariantSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::SearchVariantSetsResponse]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variantsets/search'
|
|
command = make_simple_command(:post, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::SearchVariantSetsRequest::Representation
|
|
command.request_object = search_variant_sets_request_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::SearchVariantSetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::SearchVariantSetsResponse
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# Updates a variant set's metadata. All other modifications are silently ignored.
|
|
# @param [String] variant_set_id
|
|
# The ID of the variant to be updated (must already exist).
|
|
# @param [Google::Apis::GenomicsV1beta2::VariantSet] variant_set_object
|
|
# @param [String] fields
|
|
# Selector specifying which fields to include in a partial response.
|
|
# @param [String] quota_user
|
|
# Available to use for quota purposes for server-side applications. Can be any
|
|
# arbitrary string assigned to a user, but should not exceed 40 characters.
|
|
# Overrides userIp if both are provided.
|
|
# @param [String] user_ip
|
|
# IP address of the site where the request originates. Use this if you want to
|
|
# enforce per-user limits.
|
|
# @param [Google::Apis::RequestOptions] options
|
|
# Request-specific options
|
|
#
|
|
# @yield [result, err] Result & error if block supplied
|
|
# @yieldparam result [Google::Apis::GenomicsV1beta2::VariantSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @return [Google::Apis::GenomicsV1beta2::VariantSet]
|
|
#
|
|
# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
|
|
# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
|
|
# @raise [Google::Apis::AuthorizationError] Authorization is required
|
|
def update_variantset(variant_set_id, variant_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
|
|
path = 'variantsets/{variantSetId}'
|
|
command = make_simple_command(:put, path, options)
|
|
command.request_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
|
|
command.request_object = variant_set_object
|
|
command.response_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
|
|
command.response_class = Google::Apis::GenomicsV1beta2::VariantSet
|
|
command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
protected
|
|
|
|
def apply_command_defaults(command)
|
|
command.query['key'] = key unless key.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['userIp'] = user_ip unless user_ip.nil?
|
|
end
|
|
end
|
|
end
|
|
end
|
|
end
|