bio-basespace-sdk 0.1.2
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- data/.document +5 -0
- data/.rspec +1 -0
- data/.travis.yml +11 -0
- data/Gemfile +16 -0
- data/License.txt +275 -0
- data/README.md +671 -0
- data/Rakefile +54 -0
- data/VERSION +1 -0
- data/examples/0_app_triggering.rb +135 -0
- data/examples/1_authentication.rb +156 -0
- data/examples/2_browsing.rb +84 -0
- data/examples/3_accessing_files.rb +129 -0
- data/examples/4_app_result_upload.rb +102 -0
- data/examples/5_purchasing.rb +119 -0
- data/lib/basespace.rb +126 -0
- data/lib/basespace/api/api_client.rb +313 -0
- data/lib/basespace/api/base_api.rb +242 -0
- data/lib/basespace/api/basespace_api.rb +789 -0
- data/lib/basespace/api/basespace_error.rb +80 -0
- data/lib/basespace/api/billing_api.rb +115 -0
- data/lib/basespace/model.rb +78 -0
- data/lib/basespace/model/app_result.rb +158 -0
- data/lib/basespace/model/app_result_response.rb +40 -0
- data/lib/basespace/model/app_session.rb +99 -0
- data/lib/basespace/model/app_session_compact.rb +43 -0
- data/lib/basespace/model/app_session_launch_object.rb +58 -0
- data/lib/basespace/model/app_session_response.rb +41 -0
- data/lib/basespace/model/application.rb +47 -0
- data/lib/basespace/model/application_compact.rb +44 -0
- data/lib/basespace/model/basespace_model.rb +60 -0
- data/lib/basespace/model/coverage.rb +48 -0
- data/lib/basespace/model/coverage_meta_response.rb +40 -0
- data/lib/basespace/model/coverage_metadata.rb +43 -0
- data/lib/basespace/model/coverage_response.rb +40 -0
- data/lib/basespace/model/file.rb +172 -0
- data/lib/basespace/model/file_response.rb +40 -0
- data/lib/basespace/model/genome_response.rb +40 -0
- data/lib/basespace/model/genome_v1.rb +56 -0
- data/lib/basespace/model/list_response.rb +53 -0
- data/lib/basespace/model/multipart_upload.rb +288 -0
- data/lib/basespace/model/product.rb +50 -0
- data/lib/basespace/model/project.rb +103 -0
- data/lib/basespace/model/project_response.rb +40 -0
- data/lib/basespace/model/purchase.rb +89 -0
- data/lib/basespace/model/purchase_response.rb +39 -0
- data/lib/basespace/model/purchased_product.rb +56 -0
- data/lib/basespace/model/query_parameters.rb +86 -0
- data/lib/basespace/model/query_parameters_purchased_product.rb +67 -0
- data/lib/basespace/model/refund_purchase_response.rb +40 -0
- data/lib/basespace/model/resource_list.rb +48 -0
- data/lib/basespace/model/response_status.rb +42 -0
- data/lib/basespace/model/run_compact.rb +55 -0
- data/lib/basespace/model/sample.rb +127 -0
- data/lib/basespace/model/sample_response.rb +40 -0
- data/lib/basespace/model/user.rb +80 -0
- data/lib/basespace/model/user_compact.rb +45 -0
- data/lib/basespace/model/user_response.rb +40 -0
- data/lib/basespace/model/variant.rb +57 -0
- data/lib/basespace/model/variant_header.rb +44 -0
- data/lib/basespace/model/variant_info.rb +48 -0
- data/lib/basespace/model/variants_header_response.rb +40 -0
- data/spec/basespaceapi_spec.rb +26 -0
- data/spec/basespaceerror_spec.rb +87 -0
- data/spec/basespacemodel_spec.rb +57 -0
- metadata +239 -0
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# Copyright 2013 Toshiaki Katayama, Joachim Baran
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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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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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require 'basespace/api/basespace_error'
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require 'basespace/model'
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module Bio
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module BaseSpace
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# Represents a BaseSpace Purchase object.
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class Purchase < Model
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# Create a new Purchase instance.
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def initialize
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@swagger_types = {
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'Id' => 'str',
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'Status' => 'str', # PENDING, CANCELLED, ERRORED, COMPLETED
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'RefundStatus' => 'str', # NOTREFUNDED, REFUNDED
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'DateCreated' => 'datetime',
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'DateUpdated' => 'datetime',
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'InvoiceNumber' => 'str',
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'Amount' => 'str',
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'AmountOfTax' => 'str',
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'AmountTotal' => 'str',
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'Products' => 'list<Product>',
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'PurchaseType' => 'str',
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'AppSession' => 'AppSessionCompact',
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'User' => 'UserCompact',
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'Application' => 'ApplicationCompact',
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'HrefPurchaseDialog' => 'str', # new purchases only
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'RefundSecret' => 'str', # new purchases only
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'ExceptionMessage' => 'str', # errors only
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'ExceptionStackTrace' => 'str', # errors only
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'DateRefunded' => 'datetime', # refunds only
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'UserRefundedBy' => 'str', # refunds only
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'RefundComment' => 'str', # refunds only
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}
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@attributes = {
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'Id' => nil,
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'Status' => nil,
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'RefundStatus' => nil,
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'DateCreated' => nil,
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'DateUpdated' => nil,
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'InvoiceNumber' => nil,
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'Amount' => nil,
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'AmountOfTax' => nil,
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'AmountTotal' => nil,
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'Products' => nil,
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'PurchaseType' => nil,
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'AppSession' => nil,
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'User' => nil,
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'Application' => nil,
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'HrefPurchaseDialog' => nil,
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'RefundSecret' => nil,
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'ExceptionMessage' => nil,
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'ExceptionStackTrace' => nil,
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'DateRefunded' => nil,
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'UserRefundedBy' => nil,
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'RefundComment' => nil,
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}
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end
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# Return the purchase ID.
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def to_s
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return @id.to_s
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end
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# Test if the Purchase instance has been initialized.
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#
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# Throws ModelNotInitializedError, if the object has not been populated yet.
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def is_init
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raise ModelNotInitializedError.new('The project model has not been initialized yet') unless get_attr('Id')
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end
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end
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end # module BaseSpace
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end # module Bio
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# Copyright 2013 Toshiaki Katayama, Joachim Baran
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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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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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require 'basespace/model'
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module Bio
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module BaseSpace
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# A Purchase response.
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class PurchaseResponse < Model
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# Create a new PurchaseResponse instance.
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def initialize
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@swagger_types = {
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'ResponseStatus' => 'ResponseStatus',
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'Response' => 'Purchase',
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'Notifications' => 'list<Str>',
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}
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@attributes = {
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'ResponseStatus' => nil, # ResponseStatus
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'Response' => nil, # Purchase
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'Notifications' => nil, # list<Str>
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}
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end
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end
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end # module BaseSpace
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end # module Bio
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# Copyright 2013 Toshiaki Katayama, Joachim Baran
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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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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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require 'basespace/model'
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module Bio
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module BaseSpace
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# Purchased product model.
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class PurchasedProduct < Model
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# Create a new PurchasedProduct instance.
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def initialize
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@swagger_types = {
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'PurchaseId' => 'str',
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'DatePurchased' => 'datetime',
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'Id' => 'str',
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'Name' => 'str',
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'Price' => 'str',
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'Quantity' => 'str',
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'PersistenceStatus' => 'str',
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'Tags' => 'list<str>', # only if provided as a query parameter
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'ProductIds' => 'list<str>', # only if provided as a query parameter
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}
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@attributes = {
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'PurchaseId' => nil,
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'DatePurchased' => nil,
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'Id' => nil,
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'Name' => nil,
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'Price' => nil,
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'Quantity' => nil,
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'PersistenceStatus' => nil,
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'Tags' => nil,
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'ProductIds' => nil,
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}
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end
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# Return the name of the purchased product.
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def to_s
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return get_attr('Name').to_s
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end
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end
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end # module BaseSpace
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end # module Bio
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# Copyright 2013 Toshiaki Katayama, Joachim Baran
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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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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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require 'basespace/api/basespace_error'
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module Bio
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module BaseSpace
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# The QueryParameters class can be passed as an optional arguments for
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# a specific sorting of list-responses (such as lists of Sample, AppResult,
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# or Variant).
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class QueryParameters
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attr_accessor :passed, :required
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# not very strict parameters testing
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LEGAL = {
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'Statuses' => [],
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'SortBy' => ['Id', 'Name', 'DateCreated', 'Path', 'Position'],
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'Format' => ['txt'],
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'Extensions' => [],
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'Offset' => [],
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'Limit' => [],
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'SortDir' => ['Asc', 'Desc'],
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'Name' => [],
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}
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# Create a new QueryParameters instance.
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#
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# +pars+:: Query parameters.
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# +required+:: List of required query parameters.
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def initialize(pars = {}, required = ['SortBy', 'Offset', 'Limit', 'SortDir'])
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@passed = {
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'SortBy' => 'Id',
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'Offset' => '0', # [TODO] .to_i?
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'Limit' => '100', # [TODO] .to_i?
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'SortDir' => 'Asc',
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}
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pars.each do |k, v|
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@passed[k] = v
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end
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@required = required
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end
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# Returns a string representation of all query parameters contained in the object.
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def to_s
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return @passed.to_s
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end
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# Returns a debugging string representation of the object.
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def to_str
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return self.inspect
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end
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# Returns all query parameters.
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def get_parameter_dict
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return @passed
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end
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# Check the validity of all query parameters.
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#
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# Throws UndefinedParameterError if a required parameters is not present.
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def validate
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@required.each do |p|
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raise UndefinedParameterError.new(p) unless @passed[p]
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end
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@passed.each do |p, v|
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raise UnknownParameterError.new(p) unless LEGAL[p]
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raise IllegalParameterError.new(p, LEGAL[p]) if (LEGAL[p].length > 0 and ! LEGAL[p].include?(@passed[p]))
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end
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end
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end
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end # module BaseSpace
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end # module Bio
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# Copyright 2013 Toshiaki Katayama, Joachim Baran
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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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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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require 'basespace/api/basespace_error'
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module Bio
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module BaseSpace
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# This class can be passed as an optional argument for a filtering getUserProducts list response.
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class QueryParametersPurchasedProduct
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attr_accessor :passed
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LEGAL = {
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'Tags' => [],
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'ProductIds' => [],
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}
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# Create a new QueryParametersPurchasedProduct instance.
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#
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# +pars+:: Query parameters used for list filtering.
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def initialize(pars = {})
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@passed = {}
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pars.each do |k, v|
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@passed[k] = v
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end
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validate
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end
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# Return a string representation of all query parameters.
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def to_s
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return @passed.to_s
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end
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# Return debugging information of the object.
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def to_str
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return self.inspect
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end
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# Return the query parameters.
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def get_parameter_dict
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return @passed
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end
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# Check if the query parameters are valid.
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#
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# Throws UnknownParameterError for illegal parameters.
|
57
|
+
def validate
|
58
|
+
@passed.each do |k, v|
|
59
|
+
raise UnknownParameterError.new(k) unless LEGAL.has_key?(k)
|
60
|
+
end
|
61
|
+
end
|
62
|
+
|
63
|
+
end
|
64
|
+
|
65
|
+
end # module BaseSpace
|
66
|
+
end # module Bio
|
67
|
+
|
@@ -0,0 +1,40 @@
|
|
1
|
+
# Copyright 2013 Toshiaki Katayama, Joachim Baran
|
2
|
+
#
|
3
|
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4
|
+
# you may not use this file except in compliance with the License.
|
5
|
+
# You may obtain a copy of the License at
|
6
|
+
# http://www.apache.org/licenses/LICENSE-2.0
|
7
|
+
#
|
8
|
+
# Unless required by applicable law or agreed to in writing, software
|
9
|
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
10
|
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
11
|
+
# See the License for the specific language governing permissions and
|
12
|
+
# limitations under the License.
|
13
|
+
|
14
|
+
require 'basespace/model'
|
15
|
+
|
16
|
+
module Bio
|
17
|
+
module BaseSpace
|
18
|
+
|
19
|
+
# Response of a refund purchase.
|
20
|
+
class RefundPurchaseResponse < Model
|
21
|
+
|
22
|
+
# Create a new RefundPurchaseResponse instance.
|
23
|
+
def initialize
|
24
|
+
@swagger_types = {
|
25
|
+
'ResponseStatus' => 'ResponseStatus',
|
26
|
+
'Response' => 'Purchase',
|
27
|
+
'Notifications' => 'list<Str>',
|
28
|
+
}
|
29
|
+
@attributes = {
|
30
|
+
'ResponseStatus' => nil, # ResponseStatus
|
31
|
+
'Response' => nil, # Purchase
|
32
|
+
'Notifications' => nil, # list<Str>
|
33
|
+
}
|
34
|
+
end
|
35
|
+
|
36
|
+
end
|
37
|
+
|
38
|
+
end # module BaseSpace
|
39
|
+
end # module Bio
|
40
|
+
|
@@ -0,0 +1,48 @@
|
|
1
|
+
# Copyright 2013 Toshiaki Katayama, Joachim Baran
|
2
|
+
#
|
3
|
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4
|
+
# you may not use this file except in compliance with the License.
|
5
|
+
# You may obtain a copy of the License at
|
6
|
+
# http://www.apache.org/licenses/LICENSE-2.0
|
7
|
+
#
|
8
|
+
# Unless required by applicable law or agreed to in writing, software
|
9
|
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
10
|
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
11
|
+
# See the License for the specific language governing permissions and
|
12
|
+
# limitations under the License.
|
13
|
+
|
14
|
+
require 'basespace/model'
|
15
|
+
|
16
|
+
module Bio
|
17
|
+
module BaseSpace
|
18
|
+
|
19
|
+
# Resource list model.
|
20
|
+
class ResourceList < Model
|
21
|
+
|
22
|
+
# Create a new ResourceList instance.
|
23
|
+
def initialize
|
24
|
+
@swagger_types = {
|
25
|
+
'Items' => 'list<Str>',
|
26
|
+
'DisplayedCount' => 'int',
|
27
|
+
'SortDir' => 'str',
|
28
|
+
'TotalCount' => 'int',
|
29
|
+
'Offset' => 'int',
|
30
|
+
'SortBy' => 'str',
|
31
|
+
'Limit' => 'int',
|
32
|
+
}
|
33
|
+
@attributes = {
|
34
|
+
'Items' => nil, # list<Str>
|
35
|
+
'DisplayedCount' => nil, # int
|
36
|
+
'SortDir' => nil, # str
|
37
|
+
'TotalCount' => nil, # int
|
38
|
+
'Offset' => nil, # int
|
39
|
+
'SortBy' => nil, # str
|
40
|
+
'Limit' => nil, # int
|
41
|
+
}
|
42
|
+
end
|
43
|
+
|
44
|
+
end
|
45
|
+
|
46
|
+
end # module BaseSpace
|
47
|
+
end # module Bio
|
48
|
+
|
@@ -0,0 +1,42 @@
|
|
1
|
+
# Copyright 2013 Toshiaki Katayama, Joachim Baran
|
2
|
+
#
|
3
|
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4
|
+
# you may not use this file except in compliance with the License.
|
5
|
+
# You may obtain a copy of the License at
|
6
|
+
# http://www.apache.org/licenses/LICENSE-2.0
|
7
|
+
#
|
8
|
+
# Unless required by applicable law or agreed to in writing, software
|
9
|
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
10
|
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
11
|
+
# See the License for the specific language governing permissions and
|
12
|
+
# limitations under the License.
|
13
|
+
|
14
|
+
require 'basespace/model'
|
15
|
+
|
16
|
+
module Bio
|
17
|
+
module BaseSpace
|
18
|
+
|
19
|
+
# Response status model.
|
20
|
+
class ResponseStatus < Model
|
21
|
+
|
22
|
+
# Create a new ResponseStatus instance.
|
23
|
+
def initialize
|
24
|
+
@swagger_types = {
|
25
|
+
'Message' => 'str',
|
26
|
+
'Errors' => 'list<Str>',
|
27
|
+
'ErrorCode' => 'str',
|
28
|
+
'StackTrace' => 'str',
|
29
|
+
}
|
30
|
+
@attributes = {
|
31
|
+
'Message' => nil, # str
|
32
|
+
'Errors' => nil, # list<Str>
|
33
|
+
'ErrorCode' => nil, # str
|
34
|
+
'StackTrace' => nil, # str
|
35
|
+
}
|
36
|
+
end
|
37
|
+
|
38
|
+
end
|
39
|
+
|
40
|
+
end # module BaseSpace
|
41
|
+
end # module Bio
|
42
|
+
|