google-api-client 0.9.pre1 → 0.9.pre2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (95) hide show
  1. checksums.yaml +4 -4
  2. data/CHANGELOG.md +5 -0
  3. data/README.md +4 -3
  4. data/api_names.yaml +42 -0
  5. data/api_names_out.yaml +977 -651
  6. data/generated/google/apis/adexchangebuyer_v1_3.rb +1 -1
  7. data/generated/google/apis/adexchangeseller_v2_0.rb +1 -1
  8. data/generated/google/apis/adsense_v1_4.rb +1 -1
  9. data/generated/google/apis/adsensehost_v4_1.rb +1 -1
  10. data/generated/google/apis/androidenterprise_v1/classes.rb +31 -24
  11. data/generated/google/apis/androidenterprise_v1/service.rb +11 -6
  12. data/generated/google/apis/androidenterprise_v1.rb +2 -1
  13. data/generated/google/apis/appstate_v1.rb +1 -1
  14. data/generated/google/apis/autoscaler_v1beta2.rb +1 -1
  15. data/generated/google/apis/bigquery_v2/classes.rb +34 -0
  16. data/generated/google/apis/bigquery_v2/representations.rb +14 -0
  17. data/generated/google/apis/bigquery_v2/service.rb +2 -2
  18. data/generated/google/apis/bigquery_v2.rb +1 -1
  19. data/generated/google/apis/calendar_v3/classes.rb +8 -0
  20. data/generated/google/apis/calendar_v3/representations.rb +1 -0
  21. data/generated/google/apis/calendar_v3.rb +1 -1
  22. data/generated/google/apis/civicinfo_v2/classes.rb +61 -0
  23. data/generated/google/apis/civicinfo_v2/representations.rb +8 -0
  24. data/generated/google/apis/civicinfo_v2.rb +1 -1
  25. data/generated/google/apis/classroom_v1beta1/classes.rb +447 -0
  26. data/generated/google/apis/classroom_v1beta1/representations.rb +190 -0
  27. data/generated/google/apis/classroom_v1beta1/service.rb +791 -0
  28. data/generated/google/apis/classroom_v1beta1.rb +49 -0
  29. data/generated/google/apis/cloudmonitoring_v2beta2.rb +4 -1
  30. data/generated/google/apis/cloudresourcemanager_v1beta1/classes.rb +20 -19
  31. data/generated/google/apis/cloudresourcemanager_v1beta1/service.rb +34 -34
  32. data/generated/google/apis/cloudresourcemanager_v1beta1.rb +2 -5
  33. data/generated/google/apis/compute_v1/classes.rb +2638 -1136
  34. data/generated/google/apis/compute_v1/representations.rb +580 -0
  35. data/generated/google/apis/compute_v1/service.rb +2448 -305
  36. data/generated/google/apis/compute_v1.rb +1 -1
  37. data/generated/google/apis/container_v1/classes.rb +438 -0
  38. data/generated/google/apis/container_v1/representations.rb +163 -0
  39. data/generated/google/apis/container_v1/service.rb +346 -0
  40. data/generated/google/apis/container_v1.rb +35 -0
  41. data/generated/google/apis/container_v1beta1.rb +1 -1
  42. data/generated/google/apis/content_v2/service.rb +48 -12
  43. data/generated/google/apis/content_v2.rb +1 -1
  44. data/generated/google/apis/deploymentmanager_v2beta2/classes.rb +13 -9
  45. data/generated/google/apis/deploymentmanager_v2beta2/service.rb +110 -15
  46. data/generated/google/apis/deploymentmanager_v2beta2.rb +1 -1
  47. data/generated/google/apis/discovery_v1/classes.rb +7 -0
  48. data/generated/google/apis/discovery_v1/representations.rb +1 -0
  49. data/generated/google/apis/dns_v1/service.rb +4 -1
  50. data/generated/google/apis/dns_v1.rb +1 -1
  51. data/generated/google/apis/doubleclicksearch_v2.rb +1 -1
  52. data/generated/google/apis/drive_v2.rb +1 -1
  53. data/generated/google/apis/fitness_v1/classes.rb +65 -2
  54. data/generated/google/apis/fitness_v1/representations.rb +27 -0
  55. data/generated/google/apis/fitness_v1.rb +1 -1
  56. data/generated/google/apis/games_configuration_v1configuration.rb +1 -1
  57. data/generated/google/apis/games_v1.rb +1 -1
  58. data/generated/google/apis/genomics_v1/classes.rb +2287 -0
  59. data/generated/google/apis/genomics_v1/representations.rb +796 -0
  60. data/generated/google/apis/genomics_v1/service.rb +1520 -0
  61. data/generated/google/apis/genomics_v1.rb +47 -0
  62. data/generated/google/apis/genomics_v1beta2/service.rb +36 -0
  63. data/generated/google/apis/genomics_v1beta2.rb +1 -1
  64. data/generated/google/apis/identitytoolkit_v3.rb +1 -1
  65. data/generated/google/apis/mapsengine_v1.rb +1 -1
  66. data/generated/google/apis/oauth2_v2.rb +1 -1
  67. data/generated/google/apis/plus_domains_v1.rb +1 -1
  68. data/generated/google/apis/plus_v1.rb +1 -1
  69. data/generated/google/apis/prediction_v1_6/classes.rb +1 -1
  70. data/generated/google/apis/pubsub_v1beta2/classes.rb +42 -42
  71. data/generated/google/apis/pubsub_v1beta2/service.rb +26 -22
  72. data/generated/google/apis/pubsub_v1beta2.rb +1 -1
  73. data/generated/google/apis/replicapool_v1beta2/classes.rb +10 -0
  74. data/generated/google/apis/replicapool_v1beta2/representations.rb +1 -0
  75. data/generated/google/apis/replicapool_v1beta2.rb +1 -1
  76. data/generated/google/apis/resourceviews_v1beta2.rb +1 -1
  77. data/generated/google/apis/storage_v1/classes.rb +4 -2
  78. data/generated/google/apis/storage_v1.rb +1 -1
  79. data/generated/google/apis/youtube_analytics_v1.rb +1 -1
  80. data/generated/google/apis/youtube_v3/classes.rb +3 -3
  81. data/generated/google/apis/youtube_v3/representations.rb +1 -1
  82. data/generated/google/apis/youtube_v3/service.rb +78 -0
  83. data/generated/google/apis/youtube_v3.rb +1 -1
  84. data/google-api-client.gemspec +0 -1
  85. data/lib/google/api_client/auth/installed_app.rb +6 -4
  86. data/lib/google/api_client/auth/key_utils.rb +93 -0
  87. data/lib/google/apis/core/api_command.rb +12 -5
  88. data/lib/google/apis/core/http_command.rb +17 -7
  89. data/lib/google/apis/core/json_representation.rb +6 -2
  90. data/lib/google/apis/errors.rb +9 -2
  91. data/lib/google/apis/version.rb +1 -1
  92. data/script/generate +4 -3
  93. data/spec/google/apis/core/http_command_spec.rb +20 -0
  94. data/spec/google/apis/core/json_representation_spec.rb +1 -1
  95. metadata +15 -16
@@ -0,0 +1,1520 @@
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+ # Copyright 2015 Google Inc.
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+ #
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+ # Licensed under the Apache License, Version 2.0 (the "License");
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+ # you may not use this file except in compliance with the License.
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+ # You may obtain a copy of the License at
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+ #
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+ # http://www.apache.org/licenses/LICENSE-2.0
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+ #
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+ # Unless required by applicable law or agreed to in writing, software
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+ # distributed under the License is distributed on an "AS IS" BASIS,
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+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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+ # See the License for the specific language governing permissions and
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+ # limitations under the License.
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+
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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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+
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+ module Google
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+ module Apis
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+ module GenomicsV1
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+ # Genomics API
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+ #
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+ # An API to store, process, explore, and share DNA sequence reads, reference-
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+ # based alignments, and variant calls.
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+ #
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+ # @example
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+ # require 'google/apis/genomics_v1'
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+ #
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+ # Genomics = Google::Apis::GenomicsV1 # Alias the module
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+ # service = Genomics::GenomicsService.new
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+ #
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+ # @see
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+ class GenomicsService < Google::Apis::Core::BaseService
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+ # @return [String]
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+ # API key. Your API key identifies your project and provides you with API access,
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+ # quota, and reports. Required unless you provide an OAuth 2.0 token.
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+ attr_accessor :key
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+
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+ # @return [String]
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+ # Available to use for quota purposes for server-side applications. Can be any
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+ # arbitrary string assigned to a user, but should not exceed 40 characters.
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+ attr_accessor :quota_user
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+
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+ def initialize
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+ super('https://genomics.googleapis.com/', '')
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+ end
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+
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+ # Lists datasets within a project.
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+ # @param [String] project_id
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+ # Required. The project to list datasets for.
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+ # @param [Fixnum] page_size
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+ # The maximum number of results returned by this request. If unspecified,
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+ # defaults to 50. The maximum value is 1024.
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+ # @param [String] page_token
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+ # The continuation token, which is used to page through large result sets. To
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+ # get the next page of results, set this parameter to the value of `
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+ # nextPageToken` from the previous response.
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+ # @param [String] fields
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+ # Selector specifying which fields to include in a partial response.
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+ # @param [String] quota_user
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+ # Available to use for quota purposes for server-side applications. Can be any
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+ # arbitrary string assigned to a user, but should not exceed 40 characters.
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+ # @param [Google::Apis::RequestOptions] options
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+ # Request-specific options
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+ #
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+ # @yield [result, err] Result & error if block supplied
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+ # @yieldparam result [Google::Apis::GenomicsV1::ListDatasetsResponse] parsed result object
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+ # @yieldparam err [StandardError] error object if request failed
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+ #
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+ # @return [Google::Apis::GenomicsV1::ListDatasetsResponse]
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+ #
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+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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+ # @raise [Google::Apis::AuthorizationError] Authorization is required
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+ def list_datasets(project_id: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block)
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+ path = 'v1/datasets'
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+ command = make_simple_command(:get, path, options)
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+ command.response_representation = Google::Apis::GenomicsV1::ListDatasetsResponse::Representation
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+ command.response_class = Google::Apis::GenomicsV1::ListDatasetsResponse
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+ command.query['projectId'] = project_id unless project_id.nil?
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+ command.query['pageSize'] = page_size unless page_size.nil?
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+ command.query['pageToken'] = page_token unless page_token.nil?
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+ command.query['fields'] = fields unless fields.nil?
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+ command.query['quotaUser'] = quota_user unless quota_user.nil?
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+ execute_or_queue_command(command, &block)
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+ end
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+
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+ # Creates a new dataset.
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+ # @param [Google::Apis::GenomicsV1::Dataset] dataset_object
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+ # @param [String] fields
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+ # Selector specifying which fields to include in a partial response.
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+ # @param [String] quota_user
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+ # Available to use for quota purposes for server-side applications. Can be any
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+ # arbitrary string assigned to a user, but should not exceed 40 characters.
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+ # @param [Google::Apis::RequestOptions] options
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+ # Request-specific options
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+ #
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+ # @yield [result, err] Result & error if block supplied
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+ # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
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+ # @yieldparam err [StandardError] error object if request failed
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+ #
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+ # @return [Google::Apis::GenomicsV1::Dataset]
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+ #
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+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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+ # @raise [Google::Apis::AuthorizationError] Authorization is required
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+ def create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil, &block)
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+ path = 'v1/datasets'
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+ command = make_simple_command(:post, path, options)
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+ command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation
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+ command.request_object = dataset_object
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+ command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
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+ command.response_class = Google::Apis::GenomicsV1::Dataset
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+ command.query['fields'] = fields unless fields.nil?
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+ command.query['quotaUser'] = quota_user unless quota_user.nil?
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+ execute_or_queue_command(command, &block)
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+ end
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+
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+ # Gets a dataset by ID.
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+ # @param [String] dataset_id
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+ # The ID of the dataset.
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+ # @param [String] fields
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+ # Selector specifying which fields to include in a partial response.
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+ # @param [String] quota_user
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+ # Available to use for quota purposes for server-side applications. Can be any
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+ # arbitrary string assigned to a user, but should not exceed 40 characters.
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+ # @param [Google::Apis::RequestOptions] options
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+ # Request-specific options
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+ #
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+ # @yield [result, err] Result & error if block supplied
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+ # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
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+ # @yieldparam err [StandardError] error object if request failed
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+ #
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+ # @return [Google::Apis::GenomicsV1::Dataset]
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+ #
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+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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+ # @raise [Google::Apis::AuthorizationError] Authorization is required
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+ def get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block)
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+ path = 'v1/datasets/{datasetId}'
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+ command = make_simple_command(:get, path, options)
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+ command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
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+ command.response_class = Google::Apis::GenomicsV1::Dataset
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+ command.params['datasetId'] = dataset_id unless dataset_id.nil?
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+ command.query['fields'] = fields unless fields.nil?
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+ command.query['quotaUser'] = quota_user unless quota_user.nil?
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+ execute_or_queue_command(command, &block)
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+ end
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+
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+ # Updates a dataset. This method supports patch semantics.
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+ # @param [String] dataset_id
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+ # The ID of the dataset to be updated.
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+ # @param [Google::Apis::GenomicsV1::Dataset] dataset_object
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+ # @param [String] update_mask
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+ # An optional mask specifying which fields to update. At this time, the only
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+ # mutable field is [name][google.genomics.v1.Dataset.name]. The only acceptable
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+ # value is "name". If unspecified, all mutable fields will be updated.
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+ # @param [String] fields
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+ # Selector specifying which fields to include in a partial response.
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+ # @param [String] quota_user
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+ # Available to use for quota purposes for server-side applications. Can be any
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+ # arbitrary string assigned to a user, but should not exceed 40 characters.
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+ # @param [Google::Apis::RequestOptions] options
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+ # Request-specific options
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+ #
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+ # @yield [result, err] Result & error if block supplied
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+ # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
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+ # @yieldparam err [StandardError] error object if request failed
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+ #
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+ # @return [Google::Apis::GenomicsV1::Dataset]
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+ #
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+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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+ # @raise [Google::Apis::AuthorizationError] Authorization is required
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+ def patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
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+ path = 'v1/datasets/{datasetId}'
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+ command = make_simple_command(:patch, path, options)
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+ command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation
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+ command.request_object = dataset_object
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+ command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
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+ command.response_class = Google::Apis::GenomicsV1::Dataset
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+ command.params['datasetId'] = dataset_id unless dataset_id.nil?
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+ command.query['updateMask'] = update_mask unless update_mask.nil?
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+ command.query['fields'] = fields unless fields.nil?
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+ command.query['quotaUser'] = quota_user unless quota_user.nil?
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+ execute_or_queue_command(command, &block)
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+ end
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+
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+ # Deletes a dataset.
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+ # @param [String] dataset_id
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+ # The ID of the dataset to be deleted.
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+ # @param [String] fields
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+ # Selector specifying which fields to include in a partial response.
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+ # @param [String] quota_user
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+ # Available to use for quota purposes for server-side applications. Can be any
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+ # arbitrary string assigned to a user, but should not exceed 40 characters.
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+ # @param [Google::Apis::RequestOptions] options
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+ # Request-specific options
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+ #
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+ # @yield [result, err] Result & error if block supplied
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+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
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+ # @yieldparam err [StandardError] error object if request failed
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+ #
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+ # @return [Google::Apis::GenomicsV1::Empty]
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+ #
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+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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+ # @raise [Google::Apis::AuthorizationError] Authorization is required
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+ def delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block)
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+ path = 'v1/datasets/{datasetId}'
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+ command = make_simple_command(:delete, path, options)
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+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
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+ command.response_class = Google::Apis::GenomicsV1::Empty
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+ command.params['datasetId'] = dataset_id unless dataset_id.nil?
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+ command.query['fields'] = fields unless fields.nil?
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+ command.query['quotaUser'] = quota_user unless quota_user.nil?
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+ execute_or_queue_command(command, &block)
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+ end
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+
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+ # Undeletes a dataset by restoring a dataset which was deleted via this API.
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+ # This operation is only possible for a week after the deletion occurred.
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+ # @param [String] dataset_id
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+ # The ID of the dataset to be undeleted.
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+ # @param [Google::Apis::GenomicsV1::UndeleteDatasetRequest] undelete_dataset_request_object
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+ # @param [String] fields
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+ # Selector specifying which fields to include in a partial response.
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+ # @param [String] quota_user
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+ # Available to use for quota purposes for server-side applications. Can be any
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+ # arbitrary string assigned to a user, but should not exceed 40 characters.
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+ # @param [Google::Apis::RequestOptions] options
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+ # Request-specific options
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+ #
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+ # @yield [result, err] Result & error if block supplied
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+ # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
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+ # @yieldparam err [StandardError] error object if request failed
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+ #
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+ # @return [Google::Apis::GenomicsV1::Dataset]
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+ #
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+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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+ # @raise [Google::Apis::AuthorizationError] Authorization is required
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+ def undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
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+ path = 'v1/datasets/{datasetId}:undelete'
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+ command = make_simple_command(:post, path, options)
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+ command.request_representation = Google::Apis::GenomicsV1::UndeleteDatasetRequest::Representation
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+ command.request_object = undelete_dataset_request_object
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+ command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
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+ command.response_class = Google::Apis::GenomicsV1::Dataset
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+ command.params['datasetId'] = dataset_id unless dataset_id.nil?
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+ command.query['fields'] = fields unless fields.nil?
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+ command.query['quotaUser'] = quota_user unless quota_user.nil?
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+ execute_or_queue_command(command, &block)
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+ end
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+
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+ # Gets the latest state of a long-running operation. Clients can use this method
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+ # to poll the operation result at intervals as recommended by the API service.
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+ # @param [String] name
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+ # The name of the operation resource.
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+ # @param [String] fields
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+ # Selector specifying which fields to include in a partial response.
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+ # @param [String] quota_user
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+ # Available to use for quota purposes for server-side applications. Can be any
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+ # arbitrary string assigned to a user, but should not exceed 40 characters.
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+ # @param [Google::Apis::RequestOptions] options
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+ # Request-specific options
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+ #
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+ # @yield [result, err] Result & error if block supplied
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+ # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
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+ # @yieldparam err [StandardError] error object if request failed
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+ #
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+ # @return [Google::Apis::GenomicsV1::Operation]
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+ #
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+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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+ # @raise [Google::Apis::AuthorizationError] Authorization is required
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+ def get_operation(name, fields: nil, quota_user: nil, options: nil, &block)
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+ path = 'v1/{+name}'
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+ command = make_simple_command(:get, path, options)
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+ command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
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+ command.response_class = Google::Apis::GenomicsV1::Operation
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+ command.params['name'] = name unless name.nil?
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+ command.query['fields'] = fields unless fields.nil?
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+ command.query['quotaUser'] = quota_user unless quota_user.nil?
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+ execute_or_queue_command(command, &block)
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+ end
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+
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+ # Lists operations that match the specified filter in the request.
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+ # @param [String] name
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+ # The name of the operation collection.
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+ # @param [String] filter
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+ # A string for filtering [Operations][google.longrunning.Operation]. The
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+ # following filter fields are supported: * projectId: Required. Corresponds to [
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+ # OperationMetadata.projectId][google.genomics.v1.OperationMetadata.project_id].
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+ # * createTime: The time this job was created, in seconds from the [epoch](http:/
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+ # /en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `= 1432140000` * `
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+ # projectId = my-project AND createTime >= 1432140000 AND createTime <=
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+ # 1432150000 AND status = RUNNING`
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+ # @param [Fixnum] page_size
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+ # The maximum number of results to return. If unspecified, defaults to 256. The
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+ # maximum value is 2048.
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+ # @param [String] page_token
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+ # The standard List page token.
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+ # @param [String] fields
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+ # Selector specifying which fields to include in a partial response.
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+ # @param [String] quota_user
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+ # Available to use for quota purposes for server-side applications. Can be any
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+ # arbitrary string assigned to a user, but should not exceed 40 characters.
310
+ # @param [Google::Apis::RequestOptions] options
311
+ # Request-specific options
312
+ #
313
+ # @yield [result, err] Result & error if block supplied
314
+ # @yieldparam result [Google::Apis::GenomicsV1::ListOperationsResponse] parsed result object
315
+ # @yieldparam err [StandardError] error object if request failed
316
+ #
317
+ # @return [Google::Apis::GenomicsV1::ListOperationsResponse]
318
+ #
319
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
320
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
321
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
322
+ def list_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block)
323
+ path = 'v1/{+name}'
324
+ command = make_simple_command(:get, path, options)
325
+ command.response_representation = Google::Apis::GenomicsV1::ListOperationsResponse::Representation
326
+ command.response_class = Google::Apis::GenomicsV1::ListOperationsResponse
327
+ command.params['name'] = name unless name.nil?
328
+ command.query['filter'] = filter unless filter.nil?
329
+ command.query['pageSize'] = page_size unless page_size.nil?
330
+ command.query['pageToken'] = page_token unless page_token.nil?
331
+ command.query['fields'] = fields unless fields.nil?
332
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
333
+ execute_or_queue_command(command, &block)
334
+ end
335
+
336
+ # Starts asynchronous cancellation on a long-running operation. The server makes
337
+ # a best effort to cancel the operation, but success is not guaranteed. Clients
338
+ # may use [Operations.GetOperation][google.longrunning.Operations.GetOperation]
339
+ # or [Operations.ListOperations][google.longrunning.Operations.ListOperations]
340
+ # to check whether the cancellation succeeded or the operation completed despite
341
+ # cancellation.
342
+ # @param [String] name
343
+ # The name of the operation resource to be cancelled.
344
+ # @param [Google::Apis::GenomicsV1::CancelOperationRequest] cancel_operation_request_object
345
+ # @param [String] fields
346
+ # Selector specifying which fields to include in a partial response.
347
+ # @param [String] quota_user
348
+ # Available to use for quota purposes for server-side applications. Can be any
349
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
350
+ # @param [Google::Apis::RequestOptions] options
351
+ # Request-specific options
352
+ #
353
+ # @yield [result, err] Result & error if block supplied
354
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
355
+ # @yieldparam err [StandardError] error object if request failed
356
+ #
357
+ # @return [Google::Apis::GenomicsV1::Empty]
358
+ #
359
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
360
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
361
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
362
+ def cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
363
+ path = 'v1/{+name}:cancel'
364
+ command = make_simple_command(:post, path, options)
365
+ command.request_representation = Google::Apis::GenomicsV1::CancelOperationRequest::Representation
366
+ command.request_object = cancel_operation_request_object
367
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
368
+ command.response_class = Google::Apis::GenomicsV1::Empty
369
+ command.params['name'] = name unless name.nil?
370
+ command.query['fields'] = fields unless fields.nil?
371
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
372
+ execute_or_queue_command(command, &block)
373
+ end
374
+
375
+ # This method is not implemented. To cancel an operation, please use [Operations.
376
+ # CancelOperation][google.longrunning.Operations.CancelOperation].
377
+ # @param [String] name
378
+ # The name of the operation resource to be deleted.
379
+ # @param [String] fields
380
+ # Selector specifying which fields to include in a partial response.
381
+ # @param [String] quota_user
382
+ # Available to use for quota purposes for server-side applications. Can be any
383
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
384
+ # @param [Google::Apis::RequestOptions] options
385
+ # Request-specific options
386
+ #
387
+ # @yield [result, err] Result & error if block supplied
388
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
389
+ # @yieldparam err [StandardError] error object if request failed
390
+ #
391
+ # @return [Google::Apis::GenomicsV1::Empty]
392
+ #
393
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
394
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
395
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
396
+ def delete_operation(name, fields: nil, quota_user: nil, options: nil, &block)
397
+ path = 'v1/{+name}'
398
+ command = make_simple_command(:delete, path, options)
399
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
400
+ command.response_class = Google::Apis::GenomicsV1::Empty
401
+ command.params['name'] = name unless name.nil?
402
+ command.query['fields'] = fields unless fields.nil?
403
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
404
+ execute_or_queue_command(command, &block)
405
+ end
406
+
407
+ # Creates read group sets by asynchronously importing the provided information.
408
+ # Note that currently comments in the input file header are **not** imported and
409
+ # some custom tags will be converted to strings, rather than preserving tag
410
+ # types. The caller must have WRITE permissions to the dataset.
411
+ # @param [Google::Apis::GenomicsV1::ImportReadGroupSetsRequest] import_read_group_sets_request_object
412
+ # @param [String] fields
413
+ # Selector specifying which fields to include in a partial response.
414
+ # @param [String] quota_user
415
+ # Available to use for quota purposes for server-side applications. Can be any
416
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
417
+ # @param [Google::Apis::RequestOptions] options
418
+ # Request-specific options
419
+ #
420
+ # @yield [result, err] Result & error if block supplied
421
+ # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
422
+ # @yieldparam err [StandardError] error object if request failed
423
+ #
424
+ # @return [Google::Apis::GenomicsV1::Operation]
425
+ #
426
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
427
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
428
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
429
+ def import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
430
+ path = 'v1/readgroupsets:import'
431
+ command = make_simple_command(:post, path, options)
432
+ command.request_representation = Google::Apis::GenomicsV1::ImportReadGroupSetsRequest::Representation
433
+ command.request_object = import_read_group_sets_request_object
434
+ command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
435
+ command.response_class = Google::Apis::GenomicsV1::Operation
436
+ command.query['fields'] = fields unless fields.nil?
437
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
438
+ execute_or_queue_command(command, &block)
439
+ end
440
+
441
+ # Exports a read group set to a BAM file in Google Cloud Storage. Note that
442
+ # currently there may be some differences between exported BAM files and the
443
+ # original BAM file at the time of import. In particular, comments in the input
444
+ # file header will not be preserved, some custom tags will be converted to
445
+ # strings, and original reference sequence order is not necessarily preserved.
446
+ # @param [String] read_group_set_id
447
+ # Required. The ID of the read group set to export.
448
+ # @param [Google::Apis::GenomicsV1::ExportReadGroupSetRequest] export_read_group_set_request_object
449
+ # @param [String] fields
450
+ # Selector specifying which fields to include in a partial response.
451
+ # @param [String] quota_user
452
+ # Available to use for quota purposes for server-side applications. Can be any
453
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
454
+ # @param [Google::Apis::RequestOptions] options
455
+ # Request-specific options
456
+ #
457
+ # @yield [result, err] Result & error if block supplied
458
+ # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
459
+ # @yieldparam err [StandardError] error object if request failed
460
+ #
461
+ # @return [Google::Apis::GenomicsV1::Operation]
462
+ #
463
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
464
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
465
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
466
+ def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
467
+ path = 'v1/readgroupsets/{readGroupSetId}:export'
468
+ command = make_simple_command(:post, path, options)
469
+ command.request_representation = Google::Apis::GenomicsV1::ExportReadGroupSetRequest::Representation
470
+ command.request_object = export_read_group_set_request_object
471
+ command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
472
+ command.response_class = Google::Apis::GenomicsV1::Operation
473
+ command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
474
+ command.query['fields'] = fields unless fields.nil?
475
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
476
+ execute_or_queue_command(command, &block)
477
+ end
478
+
479
+ # Searches for read group sets matching the criteria. Implements [
480
+ # GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/
481
+ # v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
482
+ # @param [Google::Apis::GenomicsV1::SearchReadGroupSetsRequest] search_read_group_sets_request_object
483
+ # @param [String] fields
484
+ # Selector specifying which fields to include in a partial response.
485
+ # @param [String] quota_user
486
+ # Available to use for quota purposes for server-side applications. Can be any
487
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
488
+ # @param [Google::Apis::RequestOptions] options
489
+ # Request-specific options
490
+ #
491
+ # @yield [result, err] Result & error if block supplied
492
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] parsed result object
493
+ # @yieldparam err [StandardError] error object if request failed
494
+ #
495
+ # @return [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse]
496
+ #
497
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
498
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
499
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
500
+ def search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
501
+ path = 'v1/readgroupsets/search'
502
+ command = make_simple_command(:post, path, options)
503
+ command.request_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsRequest::Representation
504
+ command.request_object = search_read_group_sets_request_object
505
+ command.response_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse::Representation
506
+ command.response_class = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse
507
+ command.query['fields'] = fields unless fields.nil?
508
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
509
+ execute_or_queue_command(command, &block)
510
+ end
511
+
512
+ # Updates a read group set. This method supports patch semantics.
513
+ # @param [String] read_group_set_id
514
+ # The ID of the read group set to be updated. The caller must have WRITE
515
+ # permissions to the dataset associated with this read group set.
516
+ # @param [Google::Apis::GenomicsV1::ReadGroupSet] read_group_set_object
517
+ # @param [String] update_mask
518
+ # An optional mask specifying which fields to update. At this time, mutable
519
+ # fields are [referenceSetId][google.genomics.v1.ReadGroupSet.reference_set_id]
520
+ # and [name][google.genomics.v1.ReadGroupSet.name]. Acceptable values are "
521
+ # referenceSetId" and "name". If unspecified, all mutable fields will be updated.
522
+ # @param [String] fields
523
+ # Selector specifying which fields to include in a partial response.
524
+ # @param [String] quota_user
525
+ # Available to use for quota purposes for server-side applications. Can be any
526
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
527
+ # @param [Google::Apis::RequestOptions] options
528
+ # Request-specific options
529
+ #
530
+ # @yield [result, err] Result & error if block supplied
531
+ # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
532
+ # @yieldparam err [StandardError] error object if request failed
533
+ #
534
+ # @return [Google::Apis::GenomicsV1::ReadGroupSet]
535
+ #
536
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
537
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
538
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
539
+ def patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
540
+ path = 'v1/readgroupsets/{readGroupSetId}'
541
+ command = make_simple_command(:patch, path, options)
542
+ command.request_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
543
+ command.request_object = read_group_set_object
544
+ command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
545
+ command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
546
+ command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
547
+ command.query['updateMask'] = update_mask unless update_mask.nil?
548
+ command.query['fields'] = fields unless fields.nil?
549
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
550
+ execute_or_queue_command(command, &block)
551
+ end
552
+
553
+ # Deletes a read group set.
554
+ # @param [String] read_group_set_id
555
+ # The ID of the read group set to be deleted. The caller must have WRITE
556
+ # permissions to the dataset associated with this read group set.
557
+ # @param [String] fields
558
+ # Selector specifying which fields to include in a partial response.
559
+ # @param [String] quota_user
560
+ # Available to use for quota purposes for server-side applications. Can be any
561
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
562
+ # @param [Google::Apis::RequestOptions] options
563
+ # Request-specific options
564
+ #
565
+ # @yield [result, err] Result & error if block supplied
566
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
567
+ # @yieldparam err [StandardError] error object if request failed
568
+ #
569
+ # @return [Google::Apis::GenomicsV1::Empty]
570
+ #
571
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
572
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
573
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
574
+ def delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block)
575
+ path = 'v1/readgroupsets/{readGroupSetId}'
576
+ command = make_simple_command(:delete, path, options)
577
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
578
+ command.response_class = Google::Apis::GenomicsV1::Empty
579
+ command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
580
+ command.query['fields'] = fields unless fields.nil?
581
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
582
+ execute_or_queue_command(command, &block)
583
+ end
584
+
585
+ # Gets a read group set by ID.
586
+ # @param [String] read_group_set_id
587
+ # The ID of the read group set.
588
+ # @param [String] fields
589
+ # Selector specifying which fields to include in a partial response.
590
+ # @param [String] quota_user
591
+ # Available to use for quota purposes for server-side applications. Can be any
592
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
593
+ # @param [Google::Apis::RequestOptions] options
594
+ # Request-specific options
595
+ #
596
+ # @yield [result, err] Result & error if block supplied
597
+ # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
598
+ # @yieldparam err [StandardError] error object if request failed
599
+ #
600
+ # @return [Google::Apis::GenomicsV1::ReadGroupSet]
601
+ #
602
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
603
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
604
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
605
+ def get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block)
606
+ path = 'v1/readgroupsets/{readGroupSetId}'
607
+ command = make_simple_command(:get, path, options)
608
+ command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
609
+ command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
610
+ command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
611
+ command.query['fields'] = fields unless fields.nil?
612
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
613
+ execute_or_queue_command(command, &block)
614
+ end
615
+
616
+ # Lists fixed width coverage buckets for a read group set, each of which
617
+ # correspond to a range of a reference sequence. Each bucket summarizes coverage
618
+ # information across its corresponding genomic range. Coverage is defined as the
619
+ # number of reads which are aligned to a given base in the reference sequence.
620
+ # Coverage buckets are available at several precomputed bucket widths, enabling
621
+ # retrieval of various coverage 'zoom levels'. The caller must have READ
622
+ # permissions for the target read group set.
623
+ # @param [String] read_group_set_id
624
+ # Required. The ID of the read group set over which coverage is requested.
625
+ # @param [String] reference_name
626
+ # The name of the reference to query, within the reference set associated with
627
+ # this query. Optional.
628
+ # @param [String] start
629
+ # The start position of the range on the reference, 0-based inclusive. If
630
+ # specified, `referenceName` must also be specified. Defaults to 0.
631
+ # @param [String] end_
632
+ # The end position of the range on the reference, 0-based exclusive. If
633
+ # specified, `referenceName` must also be specified. If unset or 0, defaults to
634
+ # the length of the reference.
635
+ # @param [String] target_bucket_width
636
+ # The desired width of each reported coverage bucket in base pairs. This will be
637
+ # rounded down to the nearest precomputed bucket width; the value of which is
638
+ # returned as `bucketWidth` in the response. Defaults to infinity (each bucket
639
+ # spans an entire reference sequence) or the length of the target range, if
640
+ # specified. The smallest precomputed `bucketWidth` is currently 2048 base pairs;
641
+ # this is subject to change.
642
+ # @param [String] page_token
643
+ # The continuation token, which is used to page through large result sets. To
644
+ # get the next page of results, set this parameter to the value of `
645
+ # nextPageToken` from the previous response.
646
+ # @param [Fixnum] page_size
647
+ # The maximum number of results to return in a single page. If unspecified,
648
+ # defaults to 1024. The maximum value is 2048.
649
+ # @param [String] fields
650
+ # Selector specifying which fields to include in a partial response.
651
+ # @param [String] quota_user
652
+ # Available to use for quota purposes for server-side applications. Can be any
653
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
654
+ # @param [Google::Apis::RequestOptions] options
655
+ # Request-specific options
656
+ #
657
+ # @yield [result, err] Result & error if block supplied
658
+ # @yieldparam result [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] parsed result object
659
+ # @yieldparam err [StandardError] error object if request failed
660
+ #
661
+ # @return [Google::Apis::GenomicsV1::ListCoverageBucketsResponse]
662
+ #
663
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
664
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
665
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
666
+ def list_coverage_buckets(read_group_set_id, reference_name: nil, start: nil, end_: nil, target_bucket_width: nil, page_token: nil, page_size: nil, fields: nil, quota_user: nil, options: nil, &block)
667
+ path = 'v1/readgroupsets/{readGroupSetId}/coveragebuckets'
668
+ command = make_simple_command(:get, path, options)
669
+ command.response_representation = Google::Apis::GenomicsV1::ListCoverageBucketsResponse::Representation
670
+ command.response_class = Google::Apis::GenomicsV1::ListCoverageBucketsResponse
671
+ command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
672
+ command.query['referenceName'] = reference_name unless reference_name.nil?
673
+ command.query['start'] = start unless start.nil?
674
+ command.query['end'] = end_ unless end_.nil?
675
+ command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil?
676
+ command.query['pageToken'] = page_token unless page_token.nil?
677
+ command.query['pageSize'] = page_size unless page_size.nil?
678
+ command.query['fields'] = fields unless fields.nil?
679
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
680
+ execute_or_queue_command(command, &block)
681
+ end
682
+
683
+ # Gets a list of reads for one or more read group sets. Reads search operates
684
+ # over a genomic coordinate space of reference sequence & position defined over
685
+ # the reference sequences to which the requested read group sets are aligned. If
686
+ # a target positional range is specified, search returns all reads whose
687
+ # alignment to the reference genome overlap the range. A query which specifies
688
+ # only read group set IDs yields all reads in those read group sets, including
689
+ # unmapped reads. All reads returned (including reads on subsequent pages) are
690
+ # ordered by genomic coordinate (reference sequence & position). Reads with
691
+ # equivalent genomic coordinates are returned in a deterministic order.
692
+ # Implements [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/
693
+ # blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).
694
+ # @param [Google::Apis::GenomicsV1::SearchReadsRequest] search_reads_request_object
695
+ # @param [String] fields
696
+ # Selector specifying which fields to include in a partial response.
697
+ # @param [String] quota_user
698
+ # Available to use for quota purposes for server-side applications. Can be any
699
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
700
+ # @param [Google::Apis::RequestOptions] options
701
+ # Request-specific options
702
+ #
703
+ # @yield [result, err] Result & error if block supplied
704
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchReadsResponse] parsed result object
705
+ # @yieldparam err [StandardError] error object if request failed
706
+ #
707
+ # @return [Google::Apis::GenomicsV1::SearchReadsResponse]
708
+ #
709
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
710
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
711
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
712
+ def search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
713
+ path = 'v1/reads/search'
714
+ command = make_simple_command(:post, path, options)
715
+ command.request_representation = Google::Apis::GenomicsV1::SearchReadsRequest::Representation
716
+ command.request_object = search_reads_request_object
717
+ command.response_representation = Google::Apis::GenomicsV1::SearchReadsResponse::Representation
718
+ command.response_class = Google::Apis::GenomicsV1::SearchReadsResponse
719
+ command.query['fields'] = fields unless fields.nil?
720
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
721
+ execute_or_queue_command(command, &block)
722
+ end
723
+
724
+ # Searches for reference sets which match the given criteria. Implements [
725
+ # GlobalAllianceApi.searchReferenceSets](http://ga4gh.org/documentation/api/v0.5.
726
+ # 1/ga4gh_api.html#/schema/org.ga4gh.searchReferenceSets).
727
+ # @param [Google::Apis::GenomicsV1::SearchReferenceSetsRequest] search_reference_sets_request_object
728
+ # @param [String] fields
729
+ # Selector specifying which fields to include in a partial response.
730
+ # @param [String] quota_user
731
+ # Available to use for quota purposes for server-side applications. Can be any
732
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
733
+ # @param [Google::Apis::RequestOptions] options
734
+ # Request-specific options
735
+ #
736
+ # @yield [result, err] Result & error if block supplied
737
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] parsed result object
738
+ # @yieldparam err [StandardError] error object if request failed
739
+ #
740
+ # @return [Google::Apis::GenomicsV1::SearchReferenceSetsResponse]
741
+ #
742
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
743
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
744
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
745
+ def search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
746
+ path = 'v1/referencesets/search'
747
+ command = make_simple_command(:post, path, options)
748
+ command.request_representation = Google::Apis::GenomicsV1::SearchReferenceSetsRequest::Representation
749
+ command.request_object = search_reference_sets_request_object
750
+ command.response_representation = Google::Apis::GenomicsV1::SearchReferenceSetsResponse::Representation
751
+ command.response_class = Google::Apis::GenomicsV1::SearchReferenceSetsResponse
752
+ command.query['fields'] = fields unless fields.nil?
753
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
754
+ execute_or_queue_command(command, &block)
755
+ end
756
+
757
+ # Gets a reference set. Implements [GlobalAllianceApi.getReferenceSet](https://
758
+ # github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.
759
+ # avdl#L83).
760
+ # @param [String] reference_set_id
761
+ # The ID of the reference set.
762
+ # @param [String] fields
763
+ # Selector specifying which fields to include in a partial response.
764
+ # @param [String] quota_user
765
+ # Available to use for quota purposes for server-side applications. Can be any
766
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
767
+ # @param [Google::Apis::RequestOptions] options
768
+ # Request-specific options
769
+ #
770
+ # @yield [result, err] Result & error if block supplied
771
+ # @yieldparam result [Google::Apis::GenomicsV1::ReferenceSet] parsed result object
772
+ # @yieldparam err [StandardError] error object if request failed
773
+ #
774
+ # @return [Google::Apis::GenomicsV1::ReferenceSet]
775
+ #
776
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
777
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
778
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
779
+ def get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil, &block)
780
+ path = 'v1/referencesets/{referenceSetId}'
781
+ command = make_simple_command(:get, path, options)
782
+ command.response_representation = Google::Apis::GenomicsV1::ReferenceSet::Representation
783
+ command.response_class = Google::Apis::GenomicsV1::ReferenceSet
784
+ command.params['referenceSetId'] = reference_set_id unless reference_set_id.nil?
785
+ command.query['fields'] = fields unless fields.nil?
786
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
787
+ execute_or_queue_command(command, &block)
788
+ end
789
+
790
+ # Searches for references which match the given criteria. Implements [
791
+ # GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.
792
+ # 1/src/main/resources/avro/referencemethods.avdl#L146).
793
+ # @param [Google::Apis::GenomicsV1::SearchReferencesRequest] search_references_request_object
794
+ # @param [String] fields
795
+ # Selector specifying which fields to include in a partial response.
796
+ # @param [String] quota_user
797
+ # Available to use for quota purposes for server-side applications. Can be any
798
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
799
+ # @param [Google::Apis::RequestOptions] options
800
+ # Request-specific options
801
+ #
802
+ # @yield [result, err] Result & error if block supplied
803
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchReferencesResponse] parsed result object
804
+ # @yieldparam err [StandardError] error object if request failed
805
+ #
806
+ # @return [Google::Apis::GenomicsV1::SearchReferencesResponse]
807
+ #
808
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
809
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
810
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
811
+ def search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
812
+ path = 'v1/references/search'
813
+ command = make_simple_command(:post, path, options)
814
+ command.request_representation = Google::Apis::GenomicsV1::SearchReferencesRequest::Representation
815
+ command.request_object = search_references_request_object
816
+ command.response_representation = Google::Apis::GenomicsV1::SearchReferencesResponse::Representation
817
+ command.response_class = Google::Apis::GenomicsV1::SearchReferencesResponse
818
+ command.query['fields'] = fields unless fields.nil?
819
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
820
+ execute_or_queue_command(command, &block)
821
+ end
822
+
823
+ # Gets a reference. Implements [GlobalAllianceApi.getReference](https://github.
824
+ # com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#
825
+ # L158).
826
+ # @param [String] reference_id
827
+ # The ID of the reference.
828
+ # @param [String] fields
829
+ # Selector specifying which fields to include in a partial response.
830
+ # @param [String] quota_user
831
+ # Available to use for quota purposes for server-side applications. Can be any
832
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
833
+ # @param [Google::Apis::RequestOptions] options
834
+ # Request-specific options
835
+ #
836
+ # @yield [result, err] Result & error if block supplied
837
+ # @yieldparam result [Google::Apis::GenomicsV1::Reference] parsed result object
838
+ # @yieldparam err [StandardError] error object if request failed
839
+ #
840
+ # @return [Google::Apis::GenomicsV1::Reference]
841
+ #
842
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
843
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
844
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
845
+ def get_reference(reference_id, fields: nil, quota_user: nil, options: nil, &block)
846
+ path = 'v1/references/{referenceId}'
847
+ command = make_simple_command(:get, path, options)
848
+ command.response_representation = Google::Apis::GenomicsV1::Reference::Representation
849
+ command.response_class = Google::Apis::GenomicsV1::Reference
850
+ command.params['referenceId'] = reference_id unless reference_id.nil?
851
+ command.query['fields'] = fields unless fields.nil?
852
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
853
+ execute_or_queue_command(command, &block)
854
+ end
855
+
856
+ # Lists the bases in a reference, optionally restricted to a range. Implements [
857
+ # GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.
858
+ # 5.1/src/main/resources/avro/referencemethods.avdl#L221).
859
+ # @param [String] reference_id
860
+ # The ID of the reference.
861
+ # @param [String] start_position
862
+ # The start position (0-based) of this query. Defaults to 0.
863
+ # @param [String] end_position
864
+ # The end position (0-based, exclusive) of this query. Defaults to the length of
865
+ # this reference.
866
+ # @param [String] page_token
867
+ # The continuation token, which is used to page through large result sets. To
868
+ # get the next page of results, set this parameter to the value of `
869
+ # nextPageToken` from the previous response.
870
+ # @param [Fixnum] page_size
871
+ # Specifies the maximum number of bases to return in a single page.
872
+ # @param [String] fields
873
+ # Selector specifying which fields to include in a partial response.
874
+ # @param [String] quota_user
875
+ # Available to use for quota purposes for server-side applications. Can be any
876
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
877
+ # @param [Google::Apis::RequestOptions] options
878
+ # Request-specific options
879
+ #
880
+ # @yield [result, err] Result & error if block supplied
881
+ # @yieldparam result [Google::Apis::GenomicsV1::ListBasesResponse] parsed result object
882
+ # @yieldparam err [StandardError] error object if request failed
883
+ #
884
+ # @return [Google::Apis::GenomicsV1::ListBasesResponse]
885
+ #
886
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
887
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
888
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
889
+ def list_reference_bases(reference_id, start_position: nil, end_position: nil, page_token: nil, page_size: nil, fields: nil, quota_user: nil, options: nil, &block)
890
+ path = 'v1/references/{referenceId}/bases'
891
+ command = make_simple_command(:get, path, options)
892
+ command.response_representation = Google::Apis::GenomicsV1::ListBasesResponse::Representation
893
+ command.response_class = Google::Apis::GenomicsV1::ListBasesResponse
894
+ command.params['referenceId'] = reference_id unless reference_id.nil?
895
+ command.query['start'] = start_position unless start_position.nil?
896
+ command.query['end'] = end_position unless end_position.nil?
897
+ command.query['pageToken'] = page_token unless page_token.nil?
898
+ command.query['pageSize'] = page_size unless page_size.nil?
899
+ command.query['fields'] = fields unless fields.nil?
900
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
901
+ execute_or_queue_command(command, &block)
902
+ end
903
+
904
+ # Creates variant data by asynchronously importing the provided information. The
905
+ # variants for import will be merged with any existing data and each other
906
+ # according to the behavior of mergeVariants. In particular, this means for
907
+ # merged VCF variants that have conflicting INFO fields, some data will be
908
+ # arbitrarily discarded. As a special case, for single-sample VCF files, QUAL
909
+ # and FILTER fields will be moved to the call level; these are sometimes
910
+ # interpreted in a call-specific context. Imported VCF headers are appended to
911
+ # the metadata already in a variant set.
912
+ # @param [Google::Apis::GenomicsV1::ImportVariantsRequest] import_variants_request_object
913
+ # @param [String] fields
914
+ # Selector specifying which fields to include in a partial response.
915
+ # @param [String] quota_user
916
+ # Available to use for quota purposes for server-side applications. Can be any
917
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
918
+ # @param [Google::Apis::RequestOptions] options
919
+ # Request-specific options
920
+ #
921
+ # @yield [result, err] Result & error if block supplied
922
+ # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
923
+ # @yieldparam err [StandardError] error object if request failed
924
+ #
925
+ # @return [Google::Apis::GenomicsV1::Operation]
926
+ #
927
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
928
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
929
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
930
+ def import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
931
+ path = 'v1/variants:import'
932
+ command = make_simple_command(:post, path, options)
933
+ command.request_representation = Google::Apis::GenomicsV1::ImportVariantsRequest::Representation
934
+ command.request_object = import_variants_request_object
935
+ command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
936
+ command.response_class = Google::Apis::GenomicsV1::Operation
937
+ command.query['fields'] = fields unless fields.nil?
938
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
939
+ execute_or_queue_command(command, &block)
940
+ end
941
+
942
+ # Gets a list of variants matching the criteria. Implements [GlobalAllianceApi.
943
+ # searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/
944
+ # resources/avro/variantmethods.avdl#L126).
945
+ # @param [Google::Apis::GenomicsV1::SearchVariantsRequest] search_variants_request_object
946
+ # @param [String] fields
947
+ # Selector specifying which fields to include in a partial response.
948
+ # @param [String] quota_user
949
+ # Available to use for quota purposes for server-side applications. Can be any
950
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
951
+ # @param [Google::Apis::RequestOptions] options
952
+ # Request-specific options
953
+ #
954
+ # @yield [result, err] Result & error if block supplied
955
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantsResponse] parsed result object
956
+ # @yieldparam err [StandardError] error object if request failed
957
+ #
958
+ # @return [Google::Apis::GenomicsV1::SearchVariantsResponse]
959
+ #
960
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
961
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
962
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
963
+ def search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
964
+ path = 'v1/variants/search'
965
+ command = make_simple_command(:post, path, options)
966
+ command.request_representation = Google::Apis::GenomicsV1::SearchVariantsRequest::Representation
967
+ command.request_object = search_variants_request_object
968
+ command.response_representation = Google::Apis::GenomicsV1::SearchVariantsResponse::Representation
969
+ command.response_class = Google::Apis::GenomicsV1::SearchVariantsResponse
970
+ command.query['fields'] = fields unless fields.nil?
971
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
972
+ execute_or_queue_command(command, &block)
973
+ end
974
+
975
+ # Creates a new variant.
976
+ # @param [Google::Apis::GenomicsV1::Variant] variant_object
977
+ # @param [String] fields
978
+ # Selector specifying which fields to include in a partial response.
979
+ # @param [String] quota_user
980
+ # Available to use for quota purposes for server-side applications. Can be any
981
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
982
+ # @param [Google::Apis::RequestOptions] options
983
+ # Request-specific options
984
+ #
985
+ # @yield [result, err] Result & error if block supplied
986
+ # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
987
+ # @yieldparam err [StandardError] error object if request failed
988
+ #
989
+ # @return [Google::Apis::GenomicsV1::Variant]
990
+ #
991
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
992
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
993
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
994
+ def create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil, &block)
995
+ path = 'v1/variants'
996
+ command = make_simple_command(:post, path, options)
997
+ command.request_representation = Google::Apis::GenomicsV1::Variant::Representation
998
+ command.request_object = variant_object
999
+ command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
1000
+ command.response_class = Google::Apis::GenomicsV1::Variant
1001
+ command.query['fields'] = fields unless fields.nil?
1002
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1003
+ execute_or_queue_command(command, &block)
1004
+ end
1005
+
1006
+ # Updates a variant. This method supports patch semantics. Returns the modified
1007
+ # variant without its calls.
1008
+ # @param [String] variant_id
1009
+ # The ID of the variant to be updated.
1010
+ # @param [Google::Apis::GenomicsV1::Variant] variant_object
1011
+ # @param [String] update_mask
1012
+ # An optional mask specifying which fields to update. At this time, mutable
1013
+ # fields are [names][google.genomics.v1.Variant.names] and [info][google.
1014
+ # genomics.v1.Variant.info]. Acceptable values are "names" and "info". If
1015
+ # unspecified, all mutable fields will be updated.
1016
+ # @param [String] fields
1017
+ # Selector specifying which fields to include in a partial response.
1018
+ # @param [String] quota_user
1019
+ # Available to use for quota purposes for server-side applications. Can be any
1020
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1021
+ # @param [Google::Apis::RequestOptions] options
1022
+ # Request-specific options
1023
+ #
1024
+ # @yield [result, err] Result & error if block supplied
1025
+ # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
1026
+ # @yieldparam err [StandardError] error object if request failed
1027
+ #
1028
+ # @return [Google::Apis::GenomicsV1::Variant]
1029
+ #
1030
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1031
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1032
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1033
+ def patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
1034
+ path = 'v1/variants/{variantId}'
1035
+ command = make_simple_command(:patch, path, options)
1036
+ command.request_representation = Google::Apis::GenomicsV1::Variant::Representation
1037
+ command.request_object = variant_object
1038
+ command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
1039
+ command.response_class = Google::Apis::GenomicsV1::Variant
1040
+ command.params['variantId'] = variant_id unless variant_id.nil?
1041
+ command.query['updateMask'] = update_mask unless update_mask.nil?
1042
+ command.query['fields'] = fields unless fields.nil?
1043
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1044
+ execute_or_queue_command(command, &block)
1045
+ end
1046
+
1047
+ # Deletes a variant.
1048
+ # @param [String] variant_id
1049
+ # The ID of the variant to be deleted.
1050
+ # @param [String] fields
1051
+ # Selector specifying which fields to include in a partial response.
1052
+ # @param [String] quota_user
1053
+ # Available to use for quota purposes for server-side applications. Can be any
1054
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1055
+ # @param [Google::Apis::RequestOptions] options
1056
+ # Request-specific options
1057
+ #
1058
+ # @yield [result, err] Result & error if block supplied
1059
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
1060
+ # @yieldparam err [StandardError] error object if request failed
1061
+ #
1062
+ # @return [Google::Apis::GenomicsV1::Empty]
1063
+ #
1064
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1065
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1066
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1067
+ def delete_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block)
1068
+ path = 'v1/variants/{variantId}'
1069
+ command = make_simple_command(:delete, path, options)
1070
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
1071
+ command.response_class = Google::Apis::GenomicsV1::Empty
1072
+ command.params['variantId'] = variant_id unless variant_id.nil?
1073
+ command.query['fields'] = fields unless fields.nil?
1074
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1075
+ execute_or_queue_command(command, &block)
1076
+ end
1077
+
1078
+ # Gets a variant by ID.
1079
+ # @param [String] variant_id
1080
+ # The ID of the variant.
1081
+ # @param [String] fields
1082
+ # Selector specifying which fields to include in a partial response.
1083
+ # @param [String] quota_user
1084
+ # Available to use for quota purposes for server-side applications. Can be any
1085
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1086
+ # @param [Google::Apis::RequestOptions] options
1087
+ # Request-specific options
1088
+ #
1089
+ # @yield [result, err] Result & error if block supplied
1090
+ # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
1091
+ # @yieldparam err [StandardError] error object if request failed
1092
+ #
1093
+ # @return [Google::Apis::GenomicsV1::Variant]
1094
+ #
1095
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1096
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1097
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1098
+ def get_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block)
1099
+ path = 'v1/variants/{variantId}'
1100
+ command = make_simple_command(:get, path, options)
1101
+ command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
1102
+ command.response_class = Google::Apis::GenomicsV1::Variant
1103
+ command.params['variantId'] = variant_id unless variant_id.nil?
1104
+ command.query['fields'] = fields unless fields.nil?
1105
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1106
+ execute_or_queue_command(command, &block)
1107
+ end
1108
+
1109
+ # Merges the given variants with existing variants. Each variant will be merged
1110
+ # with an existing variant that matches its reference sequence, start, end,
1111
+ # reference bases, and alternative bases. If no such variant exists, a new one
1112
+ # will be created. When variants are merged, the call information from the new
1113
+ # variant is added to the existing variant, and other fields (such as key/value
1114
+ # pairs) are discarded.
1115
+ # @param [Google::Apis::GenomicsV1::MergeVariantsRequest] merge_variants_request_object
1116
+ # @param [String] fields
1117
+ # Selector specifying which fields to include in a partial response.
1118
+ # @param [String] quota_user
1119
+ # Available to use for quota purposes for server-side applications. Can be any
1120
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1121
+ # @param [Google::Apis::RequestOptions] options
1122
+ # Request-specific options
1123
+ #
1124
+ # @yield [result, err] Result & error if block supplied
1125
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
1126
+ # @yieldparam err [StandardError] error object if request failed
1127
+ #
1128
+ # @return [Google::Apis::GenomicsV1::Empty]
1129
+ #
1130
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1131
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1132
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1133
+ def merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1134
+ path = 'v1/variants:merge'
1135
+ command = make_simple_command(:post, path, options)
1136
+ command.request_representation = Google::Apis::GenomicsV1::MergeVariantsRequest::Representation
1137
+ command.request_object = merge_variants_request_object
1138
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
1139
+ command.response_class = Google::Apis::GenomicsV1::Empty
1140
+ command.query['fields'] = fields unless fields.nil?
1141
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1142
+ execute_or_queue_command(command, &block)
1143
+ end
1144
+
1145
+ # Creates a new variant set.
1146
+ # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
1147
+ # @param [String] fields
1148
+ # Selector specifying which fields to include in a partial response.
1149
+ # @param [String] quota_user
1150
+ # Available to use for quota purposes for server-side applications. Can be any
1151
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1152
+ # @param [Google::Apis::RequestOptions] options
1153
+ # Request-specific options
1154
+ #
1155
+ # @yield [result, err] Result & error if block supplied
1156
+ # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
1157
+ # @yieldparam err [StandardError] error object if request failed
1158
+ #
1159
+ # @return [Google::Apis::GenomicsV1::VariantSet]
1160
+ #
1161
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1162
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1163
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1164
+ def create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1165
+ path = 'v1/variantsets'
1166
+ command = make_simple_command(:post, path, options)
1167
+ command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1168
+ command.request_object = variant_set_object
1169
+ command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1170
+ command.response_class = Google::Apis::GenomicsV1::VariantSet
1171
+ command.query['fields'] = fields unless fields.nil?
1172
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1173
+ execute_or_queue_command(command, &block)
1174
+ end
1175
+
1176
+ # Exports variant set data to an external destination.
1177
+ # @param [String] variant_set_id
1178
+ # Required. The ID of the variant set that contains variant data which should be
1179
+ # exported. The caller must have READ access to this variant set.
1180
+ # @param [Google::Apis::GenomicsV1::ExportVariantSetRequest] export_variant_set_request_object
1181
+ # @param [String] fields
1182
+ # Selector specifying which fields to include in a partial response.
1183
+ # @param [String] quota_user
1184
+ # Available to use for quota purposes for server-side applications. Can be any
1185
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1186
+ # @param [Google::Apis::RequestOptions] options
1187
+ # Request-specific options
1188
+ #
1189
+ # @yield [result, err] Result & error if block supplied
1190
+ # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
1191
+ # @yieldparam err [StandardError] error object if request failed
1192
+ #
1193
+ # @return [Google::Apis::GenomicsV1::Operation]
1194
+ #
1195
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1196
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1197
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1198
+ def export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1199
+ path = 'v1/variantsets/{variantSetId}:export'
1200
+ command = make_simple_command(:post, path, options)
1201
+ command.request_representation = Google::Apis::GenomicsV1::ExportVariantSetRequest::Representation
1202
+ command.request_object = export_variant_set_request_object
1203
+ command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
1204
+ command.response_class = Google::Apis::GenomicsV1::Operation
1205
+ command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
1206
+ command.query['fields'] = fields unless fields.nil?
1207
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1208
+ execute_or_queue_command(command, &block)
1209
+ end
1210
+
1211
+ # Gets a variant set by ID.
1212
+ # @param [String] variant_set_id
1213
+ # Required. The ID of the variant set.
1214
+ # @param [String] fields
1215
+ # Selector specifying which fields to include in a partial response.
1216
+ # @param [String] quota_user
1217
+ # Available to use for quota purposes for server-side applications. Can be any
1218
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1219
+ # @param [Google::Apis::RequestOptions] options
1220
+ # Request-specific options
1221
+ #
1222
+ # @yield [result, err] Result & error if block supplied
1223
+ # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
1224
+ # @yieldparam err [StandardError] error object if request failed
1225
+ #
1226
+ # @return [Google::Apis::GenomicsV1::VariantSet]
1227
+ #
1228
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1229
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1230
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1231
+ def get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block)
1232
+ path = 'v1/variantsets/{variantSetId}'
1233
+ command = make_simple_command(:get, path, options)
1234
+ command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1235
+ command.response_class = Google::Apis::GenomicsV1::VariantSet
1236
+ command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
1237
+ command.query['fields'] = fields unless fields.nil?
1238
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1239
+ execute_or_queue_command(command, &block)
1240
+ end
1241
+
1242
+ # Returns a list of all variant sets matching search criteria. Implements [
1243
+ # GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.
1244
+ # 5.1/src/main/resources/avro/variantmethods.avdl#L49).
1245
+ # @param [Google::Apis::GenomicsV1::SearchVariantSetsRequest] search_variant_sets_request_object
1246
+ # @param [String] fields
1247
+ # Selector specifying which fields to include in a partial response.
1248
+ # @param [String] quota_user
1249
+ # Available to use for quota purposes for server-side applications. Can be any
1250
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1251
+ # @param [Google::Apis::RequestOptions] options
1252
+ # Request-specific options
1253
+ #
1254
+ # @yield [result, err] Result & error if block supplied
1255
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantSetsResponse] parsed result object
1256
+ # @yieldparam err [StandardError] error object if request failed
1257
+ #
1258
+ # @return [Google::Apis::GenomicsV1::SearchVariantSetsResponse]
1259
+ #
1260
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1261
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1262
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1263
+ def search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1264
+ path = 'v1/variantsets/search'
1265
+ command = make_simple_command(:post, path, options)
1266
+ command.request_representation = Google::Apis::GenomicsV1::SearchVariantSetsRequest::Representation
1267
+ command.request_object = search_variant_sets_request_object
1268
+ command.response_representation = Google::Apis::GenomicsV1::SearchVariantSetsResponse::Representation
1269
+ command.response_class = Google::Apis::GenomicsV1::SearchVariantSetsResponse
1270
+ command.query['fields'] = fields unless fields.nil?
1271
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1272
+ execute_or_queue_command(command, &block)
1273
+ end
1274
+
1275
+ # Deletes the contents of a variant set. The variant set object is not deleted.
1276
+ # @param [String] variant_set_id
1277
+ # The ID of the variant set to be deleted.
1278
+ # @param [String] fields
1279
+ # Selector specifying which fields to include in a partial response.
1280
+ # @param [String] quota_user
1281
+ # Available to use for quota purposes for server-side applications. Can be any
1282
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1283
+ # @param [Google::Apis::RequestOptions] options
1284
+ # Request-specific options
1285
+ #
1286
+ # @yield [result, err] Result & error if block supplied
1287
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
1288
+ # @yieldparam err [StandardError] error object if request failed
1289
+ #
1290
+ # @return [Google::Apis::GenomicsV1::Empty]
1291
+ #
1292
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1293
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1294
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1295
+ def delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block)
1296
+ path = 'v1/variantsets/{variantSetId}'
1297
+ command = make_simple_command(:delete, path, options)
1298
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
1299
+ command.response_class = Google::Apis::GenomicsV1::Empty
1300
+ command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
1301
+ command.query['fields'] = fields unless fields.nil?
1302
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1303
+ execute_or_queue_command(command, &block)
1304
+ end
1305
+
1306
+ # Updates a variant set. This method supports patch semantics.
1307
+ # @param [String] variant_set_id
1308
+ # The ID of the variant to be updated (must already exist).
1309
+ # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
1310
+ # @param [String] update_mask
1311
+ # An optional mask specifying which fields to update. At this time, the only
1312
+ # mutable field is [metadata][google.genomics.v1.VariantSet.metadata]. The only
1313
+ # acceptable value is "metadata". If unspecified, all mutable fields will be
1314
+ # updated.
1315
+ # @param [String] fields
1316
+ # Selector specifying which fields to include in a partial response.
1317
+ # @param [String] quota_user
1318
+ # Available to use for quota purposes for server-side applications. Can be any
1319
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1320
+ # @param [Google::Apis::RequestOptions] options
1321
+ # Request-specific options
1322
+ #
1323
+ # @yield [result, err] Result & error if block supplied
1324
+ # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
1325
+ # @yieldparam err [StandardError] error object if request failed
1326
+ #
1327
+ # @return [Google::Apis::GenomicsV1::VariantSet]
1328
+ #
1329
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1330
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1331
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1332
+ def patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
1333
+ path = 'v1/variantsets/{variantSetId}'
1334
+ command = make_simple_command(:patch, path, options)
1335
+ command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1336
+ command.request_object = variant_set_object
1337
+ command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1338
+ command.response_class = Google::Apis::GenomicsV1::VariantSet
1339
+ command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
1340
+ command.query['updateMask'] = update_mask unless update_mask.nil?
1341
+ command.query['fields'] = fields unless fields.nil?
1342
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1343
+ execute_or_queue_command(command, &block)
1344
+ end
1345
+
1346
+ # Gets a list of call sets matching the criteria. Implements [GlobalAllianceApi.
1347
+ # searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/
1348
+ # resources/avro/variantmethods.avdl#L178).
1349
+ # @param [Google::Apis::GenomicsV1::SearchCallSetsRequest] search_call_sets_request_object
1350
+ # @param [String] fields
1351
+ # Selector specifying which fields to include in a partial response.
1352
+ # @param [String] quota_user
1353
+ # Available to use for quota purposes for server-side applications. Can be any
1354
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1355
+ # @param [Google::Apis::RequestOptions] options
1356
+ # Request-specific options
1357
+ #
1358
+ # @yield [result, err] Result & error if block supplied
1359
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchCallSetsResponse] parsed result object
1360
+ # @yieldparam err [StandardError] error object if request failed
1361
+ #
1362
+ # @return [Google::Apis::GenomicsV1::SearchCallSetsResponse]
1363
+ #
1364
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1365
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1366
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1367
+ def search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1368
+ path = 'v1/callsets/search'
1369
+ command = make_simple_command(:post, path, options)
1370
+ command.request_representation = Google::Apis::GenomicsV1::SearchCallSetsRequest::Representation
1371
+ command.request_object = search_call_sets_request_object
1372
+ command.response_representation = Google::Apis::GenomicsV1::SearchCallSetsResponse::Representation
1373
+ command.response_class = Google::Apis::GenomicsV1::SearchCallSetsResponse
1374
+ command.query['fields'] = fields unless fields.nil?
1375
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1376
+ execute_or_queue_command(command, &block)
1377
+ end
1378
+
1379
+ # Creates a new call set.
1380
+ # @param [Google::Apis::GenomicsV1::CallSet] call_set_object
1381
+ # @param [String] fields
1382
+ # Selector specifying which fields to include in a partial response.
1383
+ # @param [String] quota_user
1384
+ # Available to use for quota purposes for server-side applications. Can be any
1385
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1386
+ # @param [Google::Apis::RequestOptions] options
1387
+ # Request-specific options
1388
+ #
1389
+ # @yield [result, err] Result & error if block supplied
1390
+ # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
1391
+ # @yieldparam err [StandardError] error object if request failed
1392
+ #
1393
+ # @return [Google::Apis::GenomicsV1::CallSet]
1394
+ #
1395
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1396
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1397
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1398
+ def create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1399
+ path = 'v1/callsets'
1400
+ command = make_simple_command(:post, path, options)
1401
+ command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation
1402
+ command.request_object = call_set_object
1403
+ command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
1404
+ command.response_class = Google::Apis::GenomicsV1::CallSet
1405
+ command.query['fields'] = fields unless fields.nil?
1406
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1407
+ execute_or_queue_command(command, &block)
1408
+ end
1409
+
1410
+ # Updates a call set. This method supports patch semantics.
1411
+ # @param [String] call_set_id
1412
+ # The ID of the call set to be updated.
1413
+ # @param [Google::Apis::GenomicsV1::CallSet] call_set_object
1414
+ # @param [String] update_mask
1415
+ # An optional mask specifying which fields to update. At this time, the only
1416
+ # mutable field is [name][google.genomics.v1.CallSet.name]. The only acceptable
1417
+ # value is "name". If unspecified, all mutable fields will be updated.
1418
+ # @param [String] fields
1419
+ # Selector specifying which fields to include in a partial response.
1420
+ # @param [String] quota_user
1421
+ # Available to use for quota purposes for server-side applications. Can be any
1422
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1423
+ # @param [Google::Apis::RequestOptions] options
1424
+ # Request-specific options
1425
+ #
1426
+ # @yield [result, err] Result & error if block supplied
1427
+ # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
1428
+ # @yieldparam err [StandardError] error object if request failed
1429
+ #
1430
+ # @return [Google::Apis::GenomicsV1::CallSet]
1431
+ #
1432
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1433
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1434
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1435
+ def patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
1436
+ path = 'v1/callsets/{callSetId}'
1437
+ command = make_simple_command(:patch, path, options)
1438
+ command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation
1439
+ command.request_object = call_set_object
1440
+ command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
1441
+ command.response_class = Google::Apis::GenomicsV1::CallSet
1442
+ command.params['callSetId'] = call_set_id unless call_set_id.nil?
1443
+ command.query['updateMask'] = update_mask unless update_mask.nil?
1444
+ command.query['fields'] = fields unless fields.nil?
1445
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1446
+ execute_or_queue_command(command, &block)
1447
+ end
1448
+
1449
+ # Deletes a call set.
1450
+ # @param [String] call_set_id
1451
+ # The ID of the call set to be deleted.
1452
+ # @param [String] fields
1453
+ # Selector specifying which fields to include in a partial response.
1454
+ # @param [String] quota_user
1455
+ # Available to use for quota purposes for server-side applications. Can be any
1456
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1457
+ # @param [Google::Apis::RequestOptions] options
1458
+ # Request-specific options
1459
+ #
1460
+ # @yield [result, err] Result & error if block supplied
1461
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
1462
+ # @yieldparam err [StandardError] error object if request failed
1463
+ #
1464
+ # @return [Google::Apis::GenomicsV1::Empty]
1465
+ #
1466
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1467
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1468
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1469
+ def delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block)
1470
+ path = 'v1/callsets/{callSetId}'
1471
+ command = make_simple_command(:delete, path, options)
1472
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
1473
+ command.response_class = Google::Apis::GenomicsV1::Empty
1474
+ command.params['callSetId'] = call_set_id unless call_set_id.nil?
1475
+ command.query['fields'] = fields unless fields.nil?
1476
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1477
+ execute_or_queue_command(command, &block)
1478
+ end
1479
+
1480
+ # Gets a call set by ID.
1481
+ # @param [String] call_set_id
1482
+ # The ID of the call set.
1483
+ # @param [String] fields
1484
+ # Selector specifying which fields to include in a partial response.
1485
+ # @param [String] quota_user
1486
+ # Available to use for quota purposes for server-side applications. Can be any
1487
+ # arbitrary string assigned to a user, but should not exceed 40 characters.
1488
+ # @param [Google::Apis::RequestOptions] options
1489
+ # Request-specific options
1490
+ #
1491
+ # @yield [result, err] Result & error if block supplied
1492
+ # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
1493
+ # @yieldparam err [StandardError] error object if request failed
1494
+ #
1495
+ # @return [Google::Apis::GenomicsV1::CallSet]
1496
+ #
1497
+ # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1498
+ # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1499
+ # @raise [Google::Apis::AuthorizationError] Authorization is required
1500
+ def get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block)
1501
+ path = 'v1/callsets/{callSetId}'
1502
+ command = make_simple_command(:get, path, options)
1503
+ command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
1504
+ command.response_class = Google::Apis::GenomicsV1::CallSet
1505
+ command.params['callSetId'] = call_set_id unless call_set_id.nil?
1506
+ command.query['fields'] = fields unless fields.nil?
1507
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1508
+ execute_or_queue_command(command, &block)
1509
+ end
1510
+
1511
+ protected
1512
+
1513
+ def apply_command_defaults(command)
1514
+ command.query['key'] = key unless key.nil?
1515
+ command.query['quotaUser'] = quota_user unless quota_user.nil?
1516
+ end
1517
+ end
1518
+ end
1519
+ end
1520
+ end