sequencescape-client-api 0.3.5
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- checksums.yaml +7 -0
- data/.gitignore +7 -0
- data/.rspec +1 -0
- data/.rvmrc +52 -0
- data/.yardoc/checksums +96 -0
- data/.yardoc/complete +0 -0
- data/.yardoc/object_types +0 -0
- data/.yardoc/objects/root.dat +0 -0
- data/.yardoc/proxy_types +0 -0
- data/Gemfile +4 -0
- data/README.markdown +4 -0
- data/Rakefile +2 -0
- data/doc/Array.html +192 -0
- data/doc/BaitLibrary.html +139 -0
- data/doc/Hash.html +242 -0
- data/doc/NilClass.html +214 -0
- data/doc/Sequencescape/Api/Actions/ClassActionHelpers.html +213 -0
- data/doc/Sequencescape/Api/Actions/InstanceActionHelpers.html +282 -0
- data/doc/Sequencescape/Api/Actions.html +197 -0
- data/doc/Sequencescape/Api/Associations/Base/InstanceMethods.html +352 -0
- data/doc/Sequencescape/Api/Associations/Base.html +237 -0
- data/doc/Sequencescape/Api/Associations/BelongsTo/AssociationProxy.html +332 -0
- data/doc/Sequencescape/Api/Associations/BelongsTo/CommonBehaviour/LoadHandler.html +279 -0
- data/doc/Sequencescape/Api/Associations/BelongsTo/CommonBehaviour.html +432 -0
- data/doc/Sequencescape/Api/Associations/BelongsTo/InlineAssociationProxy.html +173 -0
- data/doc/Sequencescape/Api/Associations/BelongsTo.html +212 -0
- data/doc/Sequencescape/Api/Associations/HasMany/AssociationProxy.html +366 -0
- data/doc/Sequencescape/Api/Associations/HasMany/InlineAssociationProxy.html +529 -0
- data/doc/Sequencescape/Api/Associations/HasMany/Json.html +250 -0
- data/doc/Sequencescape/Api/Associations/HasMany/Validation/CompositeErrors.html +493 -0
- data/doc/Sequencescape/Api/Associations/HasMany/Validation.html +245 -0
- data/doc/Sequencescape/Api/Associations/HasMany.html +212 -0
- data/doc/Sequencescape/Api/Associations/InstanceMethods/CompositeErrors.html +379 -0
- data/doc/Sequencescape/Api/Associations/InstanceMethods.html +496 -0
- data/doc/Sequencescape/Api/Associations.html +201 -0
- data/doc/Sequencescape/Api/BasicErrorHandling.html +371 -0
- data/doc/Sequencescape/Api/Composition/Target.html +262 -0
- data/doc/Sequencescape/Api/Composition.html +215 -0
- data/doc/Sequencescape/Api/ConnectionFactory/Actions.html +611 -0
- data/doc/Sequencescape/Api/ConnectionFactory/Helpers.html +233 -0
- data/doc/Sequencescape/Api/ConnectionFactory.html +321 -0
- data/doc/Sequencescape/Api/ErrorHandling/TurnOffValidationOfUuidOnlyRecords.html +189 -0
- data/doc/Sequencescape/Api/ErrorHandling.html +201 -0
- data/doc/Sequencescape/Api/FinderMethods/AllHandler.html +279 -0
- data/doc/Sequencescape/Api/FinderMethods/Caching.html +183 -0
- data/doc/Sequencescape/Api/FinderMethods/Delegation.html +189 -0
- data/doc/Sequencescape/Api/FinderMethods/FindByUuidHandler.html +279 -0
- data/doc/Sequencescape/Api/FinderMethods.html +364 -0
- data/doc/Sequencescape/Api/GeneralError.html +176 -0
- data/doc/Sequencescape/Api/JsonError.html +205 -0
- data/doc/Sequencescape/Api/ModifyingHandler.html +359 -0
- data/doc/Sequencescape/Api/PageOfResults/UpdateHandler.html +279 -0
- data/doc/Sequencescape/Api/PageOfResults.html +611 -0
- data/doc/Sequencescape/Api/Rails/ApplicationController.html +207 -0
- data/doc/Sequencescape/Api/Rails/Resourced.html +269 -0
- data/doc/Sequencescape/Api/Rails.html +117 -0
- data/doc/Sequencescape/Api/Resource/ActiveModel.html +287 -0
- data/doc/Sequencescape/Api/Resource/Attributes/InstanceMethods.html +272 -0
- data/doc/Sequencescape/Api/Resource/Attributes.html +199 -0
- data/doc/Sequencescape/Api/Resource/Groups/InstanceMethods.html +378 -0
- data/doc/Sequencescape/Api/Resource/Groups/Json.html +112 -0
- data/doc/Sequencescape/Api/Resource/Groups/Proxy/InstanceMethods.html +256 -0
- data/doc/Sequencescape/Api/Resource/Groups/Proxy.html +177 -0
- data/doc/Sequencescape/Api/Resource/Groups.html +270 -0
- data/doc/Sequencescape/Api/Resource/InstanceMethods.html +344 -0
- data/doc/Sequencescape/Api/Resource/Json/ClassMethods.html +243 -0
- data/doc/Sequencescape/Api/Resource/Json/CoercionHandler.html +279 -0
- data/doc/Sequencescape/Api/Resource/Json.html +405 -0
- data/doc/Sequencescape/Api/Resource/Modifications.html +295 -0
- data/doc/Sequencescape/Api/Resource.html +436 -0
- data/doc/Sequencescape/Api/ResourceInvalid.html +289 -0
- data/doc/Sequencescape/Api/ResourceModelProxy.html +444 -0
- data/doc/Sequencescape/Api/Version1.html +218 -0
- data/doc/Sequencescape/Api/Version2.html +222 -0
- data/doc/Sequencescape/Api.html +704 -0
- data/doc/Sequencescape/Asset.html +262 -0
- data/doc/Sequencescape/AssetAudit.html +258 -0
- data/doc/Sequencescape/AssetGroup.html +258 -0
- data/doc/Sequencescape/BaitLibraryLayout.html +258 -0
- data/doc/Sequencescape/BarcodePrinter.html +258 -0
- data/doc/Sequencescape/BarcodedAsset.html +293 -0
- data/doc/Sequencescape/Batch.html +327 -0
- data/doc/Sequencescape/Behaviour/Barcoded.html +195 -0
- data/doc/Sequencescape/Behaviour/Labeled.html +189 -0
- data/doc/Sequencescape/Behaviour/Qced/QcFile.html +244 -0
- data/doc/Sequencescape/Behaviour/Qced.html +199 -0
- data/doc/Sequencescape/Behaviour/Receptacle/Aliquot.html +258 -0
- data/doc/Sequencescape/Behaviour/Receptacle.html +195 -0
- data/doc/Sequencescape/Behaviour/StateDriven.html +205 -0
- data/doc/Sequencescape/Behaviour.html +130 -0
- data/doc/Sequencescape/BulkTransfer.html +258 -0
- data/doc/Sequencescape/Comment.html +258 -0
- data/doc/Sequencescape/Lane.html +282 -0
- data/doc/Sequencescape/LibraryEvent.html +258 -0
- data/doc/Sequencescape/LibraryTube.html +322 -0
- data/doc/Sequencescape/Lot.html +258 -0
- data/doc/Sequencescape/LotType/LotCreator.html +182 -0
- data/doc/Sequencescape/LotType.html +268 -0
- data/doc/Sequencescape/MultiplexedLibraryTube.html +326 -0
- data/doc/Sequencescape/Order.html +338 -0
- data/doc/Sequencescape/OrderTemplate/OrderCreator.html +182 -0
- data/doc/Sequencescape/OrderTemplate.html +268 -0
- data/doc/Sequencescape/Pipeline.html +258 -0
- data/doc/Sequencescape/Plate/CommentsCreation.html +184 -0
- data/doc/Sequencescape/Plate/CurrentVolumeSubstraction.html +236 -0
- data/doc/Sequencescape/Plate/Pooling.html +249 -0
- data/doc/Sequencescape/Plate/WellStructure.html +313 -0
- data/doc/Sequencescape/Plate.html +446 -0
- data/doc/Sequencescape/PlateConversion.html +258 -0
- data/doc/Sequencescape/PlateCreation.html +258 -0
- data/doc/Sequencescape/PlatePurpose/PlateCreation.html +186 -0
- data/doc/Sequencescape/PlatePurpose.html +268 -0
- data/doc/Sequencescape/PlateTemplate.html +282 -0
- data/doc/Sequencescape/PooledPlateCreation.html +258 -0
- data/doc/Sequencescape/Project.html +258 -0
- data/doc/Sequencescape/QcDecision.html +258 -0
- data/doc/Sequencescape/QcFile.html +327 -0
- data/doc/Sequencescape/Qcable.html +258 -0
- data/doc/Sequencescape/QcableCreator.html +258 -0
- data/doc/Sequencescape/Request.html +258 -0
- data/doc/Sequencescape/Robot.html +258 -0
- data/doc/Sequencescape/Sample.html +258 -0
- data/doc/Sequencescape/SampleTube.html +318 -0
- data/doc/Sequencescape/Search/BaseHandler.html +234 -0
- data/doc/Sequencescape/Search/MultipleResultHandler.html +276 -0
- data/doc/Sequencescape/Search/SingleResultHandler.html +303 -0
- data/doc/Sequencescape/Search.html +431 -0
- data/doc/Sequencescape/SpecificTubeCreation.html +258 -0
- data/doc/Sequencescape/Stamp.html +258 -0
- data/doc/Sequencescape/StateChange.html +258 -0
- data/doc/Sequencescape/Study.html +258 -0
- data/doc/Sequencescape/Submission.html +258 -0
- data/doc/Sequencescape/SubmissionPool.html +258 -0
- data/doc/Sequencescape/Tag/Group.html +219 -0
- data/doc/Sequencescape/Tag.html +149 -0
- data/doc/Sequencescape/Tag2Layout.html +258 -0
- data/doc/Sequencescape/Tag2LayoutTemplate.html +258 -0
- data/doc/Sequencescape/TagGroup.html +258 -0
- data/doc/Sequencescape/TagLayout.html +258 -0
- data/doc/Sequencescape/TagLayoutTemplate.html +258 -0
- data/doc/Sequencescape/Template.html +258 -0
- data/doc/Sequencescape/Transfer.html +258 -0
- data/doc/Sequencescape/TransferTemplate.html +258 -0
- data/doc/Sequencescape/Tube.html +319 -0
- data/doc/Sequencescape/TubeCreation.html +258 -0
- data/doc/Sequencescape/TubeFromTubeCreation.html +258 -0
- data/doc/Sequencescape/TubePurpose/TubeCreation.html +186 -0
- data/doc/Sequencescape/TubePurpose.html +268 -0
- data/doc/Sequencescape/User.html +258 -0
- data/doc/Sequencescape/VolumeUpdate.html +258 -0
- data/doc/Sequencescape/Well.html +362 -0
- data/doc/Sequencescape.html +121 -0
- data/doc/_index.html +1248 -0
- data/doc/class_list.html +51 -0
- data/doc/css/common.css +1 -0
- data/doc/css/full_list.css +58 -0
- data/doc/css/style.css +481 -0
- data/doc/file.README.html +76 -0
- data/doc/file_list.html +56 -0
- data/doc/frames.html +17 -0
- data/doc/index.html +76 -0
- data/doc/js/app.js +243 -0
- data/doc/js/full_list.js +216 -0
- data/doc/js/jquery.js +4 -0
- data/doc/method_list.html +1411 -0
- data/doc/top-level-namespace.html +114 -0
- data/lib/sequencescape/asset.rb +10 -0
- data/lib/sequencescape/asset_audit.rb +7 -0
- data/lib/sequencescape/asset_group.rb +9 -0
- data/lib/sequencescape/bait_library.rb +14 -0
- data/lib/sequencescape/bait_library_layout.rb +9 -0
- data/lib/sequencescape/barcode_printer.rb +13 -0
- data/lib/sequencescape/barcoded_asset.rb +12 -0
- data/lib/sequencescape/batch.rb +24 -0
- data/lib/sequencescape/behaviour/barcoded.rb +15 -0
- data/lib/sequencescape/behaviour/labeled.rb +14 -0
- data/lib/sequencescape/behaviour/qced.rb +31 -0
- data/lib/sequencescape/behaviour/receptacle.rb +21 -0
- data/lib/sequencescape/behaviour/state_driven.rb +19 -0
- data/lib/sequencescape/bulk_transfer.rb +8 -0
- data/lib/sequencescape/comment.rb +7 -0
- data/lib/sequencescape/custom_metadatum_collection.rb +8 -0
- data/lib/sequencescape/lane.rb +8 -0
- data/lib/sequencescape/library_event.rb +5 -0
- data/lib/sequencescape/library_tube.rb +7 -0
- data/lib/sequencescape/locale/en.yml +190 -0
- data/lib/sequencescape/lot.rb +11 -0
- data/lib/sequencescape/lot_type.rb +20 -0
- data/lib/sequencescape/multiplexed_library_tube.rb +6 -0
- data/lib/sequencescape/order.rb +13 -0
- data/lib/sequencescape/order_template.rb +19 -0
- data/lib/sequencescape/pipeline.rb +10 -0
- data/lib/sequencescape/plate/pooling.rb +23 -0
- data/lib/sequencescape/plate/well_structure.rb +27 -0
- data/lib/sequencescape/plate.rb +71 -0
- data/lib/sequencescape/plate_conversion.rb +8 -0
- data/lib/sequencescape/plate_creation.rb +8 -0
- data/lib/sequencescape/plate_purpose.rb +24 -0
- data/lib/sequencescape/plate_template.rb +13 -0
- data/lib/sequencescape/pooled_plate_creation.rb +8 -0
- data/lib/sequencescape/project.rb +11 -0
- data/lib/sequencescape/qc_decision.rb +9 -0
- data/lib/sequencescape/qc_file.rb +14 -0
- data/lib/sequencescape/qcable.rb +17 -0
- data/lib/sequencescape/qcable_creator.rb +13 -0
- data/lib/sequencescape/request.rb +16 -0
- data/lib/sequencescape/robot.rb +5 -0
- data/lib/sequencescape/sample.rb +51 -0
- data/lib/sequencescape/sample_tube.rb +7 -0
- data/lib/sequencescape/search.rb +80 -0
- data/lib/sequencescape/specific_tube_creation.rb +8 -0
- data/lib/sequencescape/stamp.rb +9 -0
- data/lib/sequencescape/state_change.rb +11 -0
- data/lib/sequencescape/study.rb +14 -0
- data/lib/sequencescape/submission.rb +16 -0
- data/lib/sequencescape/submission_pool.rb +7 -0
- data/lib/sequencescape/tag.rb +14 -0
- data/lib/sequencescape/tag2_layout.rb +10 -0
- data/lib/sequencescape/tag2_layout_template.rb +9 -0
- data/lib/sequencescape/tag_group.rb +4 -0
- data/lib/sequencescape/tag_layout.rb +10 -0
- data/lib/sequencescape/tag_layout_template.rb +15 -0
- data/lib/sequencescape/template.rb +6 -0
- data/lib/sequencescape/transfer.rb +9 -0
- data/lib/sequencescape/transfer_request.rb +12 -0
- data/lib/sequencescape/transfer_request_collection.rb +8 -0
- data/lib/sequencescape/transfer_template.rb +9 -0
- data/lib/sequencescape/tube.rb +26 -0
- data/lib/sequencescape/tube_creation.rb +8 -0
- data/lib/sequencescape/tube_from_tube_creation.rb +8 -0
- data/lib/sequencescape/tube_purpose.rb +24 -0
- data/lib/sequencescape/user.rb +13 -0
- data/lib/sequencescape/volume_update.rb +6 -0
- data/lib/sequencescape/well.rb +19 -0
- data/lib/sequencescape/work_completion.rb +10 -0
- data/lib/sequencescape-api/actions.rb +69 -0
- data/lib/sequencescape-api/associations/base/instance_methods.rb +57 -0
- data/lib/sequencescape-api/associations/base.rb +15 -0
- data/lib/sequencescape-api/associations/belongs_to.rb +127 -0
- data/lib/sequencescape-api/associations/has_many/json.rb +10 -0
- data/lib/sequencescape-api/associations/has_many/validation.rb +37 -0
- data/lib/sequencescape-api/associations/has_many.rb +123 -0
- data/lib/sequencescape-api/associations.rb +112 -0
- data/lib/sequencescape-api/capabilities.rb +11 -0
- data/lib/sequencescape-api/composition.rb +37 -0
- data/lib/sequencescape-api/connection_factory/actions.rb +154 -0
- data/lib/sequencescape-api/connection_factory/helpers.rb +9 -0
- data/lib/sequencescape-api/connection_factory.rb +40 -0
- data/lib/sequencescape-api/core.rb +63 -0
- data/lib/sequencescape-api/core_ext/array.rb +7 -0
- data/lib/sequencescape-api/core_ext/hash.rb +18 -0
- data/lib/sequencescape-api/core_ext.rb +2 -0
- data/lib/sequencescape-api/error_handling.rb +42 -0
- data/lib/sequencescape-api/errors.rb +38 -0
- data/lib/sequencescape-api/finder_methods.rb +184 -0
- data/lib/sequencescape-api/locale/en.yml +7 -0
- data/lib/sequencescape-api/rails.rb +88 -0
- data/lib/sequencescape-api/resource/active_model.rb +17 -0
- data/lib/sequencescape-api/resource/attribute_groups.rb +94 -0
- data/lib/sequencescape-api/resource/attributes.rb +87 -0
- data/lib/sequencescape-api/resource/instance_methods.rb +24 -0
- data/lib/sequencescape-api/resource/json.rb +114 -0
- data/lib/sequencescape-api/resource/modifications.rb +111 -0
- data/lib/sequencescape-api/resource.rb +47 -0
- data/lib/sequencescape-api/resource_model_proxy.rb +44 -0
- data/lib/sequencescape-api/version.rb +5 -0
- data/lib/sequencescape-api.rb +16 -0
- data/lib/sequencescape.rb +81 -0
- data/sequencescape-api.gemspec +32 -0
- data/spec/sequencescape-api/associations_spec.rb +95 -0
- data/spec/sequencescape-api/contracts/belongs-to-association.txt +14 -0
- data/spec/sequencescape-api/contracts/client-fails-authentication.txt +6 -0
- data/spec/sequencescape-api/contracts/create-invalid-resource.txt +10 -0
- data/spec/sequencescape-api/contracts/create-model-c-has-many-inline-nested.txt +10 -0
- data/spec/sequencescape-api/contracts/create-model-c-has-many-inline.txt +10 -0
- data/spec/sequencescape-api/contracts/create-model-c-has-many.txt +10 -0
- data/spec/sequencescape-api/contracts/create-model-c.txt +11 -0
- data/spec/sequencescape-api/contracts/create-via-has-many.txt +9 -0
- data/spec/sequencescape-api/contracts/model-a-instance.txt +21 -0
- data/spec/sequencescape-api/contracts/model-b-instance.txt +38 -0
- data/spec/sequencescape-api/contracts/model-c-instance-created.txt +17 -0
- data/spec/sequencescape-api/contracts/model-c-instance-updated.txt +17 -0
- data/spec/sequencescape-api/contracts/model-c-instance.txt +28 -0
- data/spec/sequencescape-api/contracts/model-c-invalid-attribute.txt +8 -0
- data/spec/sequencescape-api/contracts/resource-not-found.txt +6 -0
- data/spec/sequencescape-api/contracts/results-page-1.txt +17 -0
- data/spec/sequencescape-api/contracts/results-page-2.txt +18 -0
- data/spec/sequencescape-api/contracts/results-page-3.txt +17 -0
- data/spec/sequencescape-api/contracts/retrieve-belongs-to-association.txt +3 -0
- data/spec/sequencescape-api/contracts/retrieve-model.txt +4 -0
- data/spec/sequencescape-api/contracts/retrieve-results-page-1.txt +3 -0
- data/spec/sequencescape-api/contracts/retrieve-results-page-2.txt +3 -0
- data/spec/sequencescape-api/contracts/retrieve-results-page-3.txt +3 -0
- data/spec/sequencescape-api/contracts/retrieve-root-with-an-authorised-client.txt +5 -0
- data/spec/sequencescape-api/contracts/retrieve-root-with-an-unauthorised-client.txt +4 -0
- data/spec/sequencescape-api/contracts/retrieve-unauthorised-model-a-list.txt +4 -0
- data/spec/sequencescape-api/contracts/retrieve-unauthorised-model-b-list.txt +4 -0
- data/spec/sequencescape-api/contracts/retrieve-unauthorised-model-c-list.txt +4 -0
- data/spec/sequencescape-api/contracts/root-response-for-authorised-client.txt +20 -0
- data/spec/sequencescape-api/contracts/root-response-for-unauthorised-client.txt +28 -0
- data/spec/sequencescape-api/contracts/unauthorised-model-a-list.txt +15 -0
- data/spec/sequencescape-api/contracts/unauthorised-model-b-list.txt +14 -0
- data/spec/sequencescape-api/contracts/unauthorised-model-c-list.txt +15 -0
- data/spec/sequencescape-api/contracts/update-invalid-resource.txt +10 -0
- data/spec/sequencescape-api/contracts/update-model-c.txt +11 -0
- data/spec/sequencescape-api/finding_methods_spec.rb +34 -0
- data/spec/sequencescape-api/modifications_spec.rb +169 -0
- data/spec/sequencescape-api/root_spec.rb +58 -0
- data/spec/spec_helper.rb +13 -0
- data/spec/support/contract_helper.rb +112 -0
- data/spec/support/namespaces.rb +67 -0
- data/spec/support/shared_examples.rb +12 -0
- metadata +540 -0
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require 'spec_helper'
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describe 'Handling authentication issues' do
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stub_request_from('retrieve-root-with-an-unauthorised-client') { response('client-fails-authentication') }
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subject { Sequencescape::Api.new(:url => 'http://localhost:3000/', :cookie => 'single-sign-on-cookie') }
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it 'raises an exception' do
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lambda { subject }.should raise_error(Sequencescape::Api::UnauthenticatedError)
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end
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end
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describe 'Retrieving the root URL' do
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context 'with an unauthorised client' do
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is_working_as_an_unauthorised_client
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context 'with no namespace' do
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subject { Sequencescape::Api.new(:url => 'http://localhost:3000/', :cookie => 'single-sign-on-cookie') }
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Unauthorised::MODELS_THROUGH_API.each do |model|
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it "provides the #{model} through the API instance" do
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subject.should respond_to(model.to_sym)
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end
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it "errors because Sequencescape::#{model.to_s.classify} is not defined" do
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# Note: Using a regex as > Ruby 2.3 'DidYouMean' changes the error message slightly.
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lambda { subject.send(model.to_sym) }.should raise_error(NameError, /uninitialized constant Sequencescape::#{model.to_s.classify}/)
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end
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end
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end
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context "with a specified namespace" do
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Unauthorised::MODELS_THROUGH_API.each do |model|
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context do
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stub_request_and_response("unauthorised-#{model.to_s.dasherize}-list")
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subject { api.send(model) }
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it "makes the correct request for Unauthorised::#{model.to_s.classify}" do
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subject.all
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end
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end
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end
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end
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end
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context 'with an authorised client' do
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is_working_as_an_authorised_client
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subject { api }
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[ :model_c, :model_d ].each do |model|
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it "provides the #{model} through the API instance" do
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+
subject.should respond_to(model.to_sym)
|
55
|
+
end
|
56
|
+
end
|
57
|
+
end
|
58
|
+
end
|
data/spec/spec_helper.rb
ADDED
@@ -0,0 +1,13 @@
|
|
1
|
+
require 'sequencescape-api'
|
2
|
+
require 'sequencescape'
|
3
|
+
|
4
|
+
# Make sure our support files can be loaded when required
|
5
|
+
$:.push(File.expand_path(File.join(File.dirname(__FILE__), 'support')))
|
6
|
+
require 'contract_helper'
|
7
|
+
require 'namespaces'
|
8
|
+
require 'shared_examples'
|
9
|
+
|
10
|
+
# Ensure that RSpec mocking is used
|
11
|
+
RSpec.configure do |config|
|
12
|
+
config.mock_framework = :rspec
|
13
|
+
end
|
@@ -0,0 +1,112 @@
|
|
1
|
+
# Fake the web connections so we don't trash anything
|
2
|
+
require 'webmock/rspec'
|
3
|
+
|
4
|
+
module ContractHelper
|
5
|
+
class StubRequestBuilder
|
6
|
+
include WebMock::API
|
7
|
+
include WebMock::Matchers
|
8
|
+
|
9
|
+
def initialize(root_directory)
|
10
|
+
@root = File.split(File.expand_path(root_directory))
|
11
|
+
end
|
12
|
+
|
13
|
+
REQUEST_REGEXP = %r{
|
14
|
+
(?<eol> \r\n|\r|\n){0}
|
15
|
+
(?<verb> GET|PUT|POST|DELETE){0}
|
16
|
+
(?<path> /[^\s]*){0}
|
17
|
+
(?<body> .+){0}
|
18
|
+
(?<header> [^:\r\n]+:[^\r\n]+){0}
|
19
|
+
(?<headers> \g<header>(\g<eol>\g<header>)*){0}
|
20
|
+
|
21
|
+
\g<verb>\s+\g<path>\s+HTTP/1.1\g<eol>
|
22
|
+
\g<headers>\g<eol>
|
23
|
+
(\g<eol>\g<body>?)?
|
24
|
+
}mx
|
25
|
+
|
26
|
+
def request(contract_name)
|
27
|
+
contract(contract_name) do |file|
|
28
|
+
match = REQUEST_REGEXP.match(file.read) or raise StandardError, "Invalidly formatted request in #{contract_name.inspect}"
|
29
|
+
|
30
|
+
@http_verb, @url = match[:verb].downcase.to_sym, "http://localhost:3000#{match[:path]}"
|
31
|
+
@conditions = {}
|
32
|
+
@conditions[:headers] = Hash[*match[:headers].split(/\r?\n/).map { |l| l.split(':') }.flatten.map(&:strip)]
|
33
|
+
@conditions[:body] = Yajl::Encoder.encode(Yajl::Parser.parse(match[:body])) unless match[:body].blank?
|
34
|
+
end
|
35
|
+
end
|
36
|
+
|
37
|
+
def response(contract_name)
|
38
|
+
contract(contract_name) do |file|
|
39
|
+
@content = file.read
|
40
|
+
end
|
41
|
+
end
|
42
|
+
|
43
|
+
def contract(contract_name, &block)
|
44
|
+
path = @root.dup
|
45
|
+
until path.empty?
|
46
|
+
filename = File.join(path, 'contracts', "#{contract_name}.txt")
|
47
|
+
return File.open(filename, 'r') { |file| yield(file) } if File.file?(filename)
|
48
|
+
path.pop
|
49
|
+
end
|
50
|
+
raise StandardError, "Cannot find contract #{filename.inspect} anywhere within #{@root.inspect}"
|
51
|
+
end
|
52
|
+
private :contract
|
53
|
+
|
54
|
+
def setup_request_and_response_mock
|
55
|
+
stub_request(@http_verb, @url).with(@conditions).to_return(@content)
|
56
|
+
end
|
57
|
+
private :setup_request_and_response_mock
|
58
|
+
|
59
|
+
def validate_request_and_response_called
|
60
|
+
a_request(@http_verb, @url).with(@conditions).should have_been_made
|
61
|
+
end
|
62
|
+
private :validate_request_and_response_called
|
63
|
+
|
64
|
+
def inject_into(spec)
|
65
|
+
builder = self
|
66
|
+
spec.before(:each) { builder.send(:setup_request_and_response_mock) }
|
67
|
+
spec.after(:each) { builder.send(:validate_request_and_response_called) }
|
68
|
+
end
|
69
|
+
end
|
70
|
+
|
71
|
+
def self.included(base)
|
72
|
+
base.extend(ClassMethods)
|
73
|
+
end
|
74
|
+
|
75
|
+
module ClassMethods
|
76
|
+
def stub_request_from(request_filename, &block)
|
77
|
+
stubbed_request = StubRequestBuilder.new(File.join(File.dirname(__FILE__), %w{.. sequencescape-api contracts}))
|
78
|
+
stubbed_request.request(request_filename)
|
79
|
+
stubbed_request.instance_eval(&block)
|
80
|
+
stubbed_request.inject_into(self)
|
81
|
+
end
|
82
|
+
|
83
|
+
def stub_request_and_response(contract_name)
|
84
|
+
stub_request_from("retrieve-#{contract_name}") { response(contract_name) }
|
85
|
+
end
|
86
|
+
|
87
|
+
def is_working_as_an_unauthorised_client
|
88
|
+
stub_request_from('retrieve-root-with-an-unauthorised-client') { response('root-response-for-unauthorised-client') }
|
89
|
+
let(:api) do
|
90
|
+
Sequencescape::Api.new(
|
91
|
+
:url => 'http://localhost:3000/', :cookie => 'single-sign-on-cookie',
|
92
|
+
:namespace => Unauthorised
|
93
|
+
)
|
94
|
+
end
|
95
|
+
end
|
96
|
+
|
97
|
+
def is_working_as_an_authorised_client
|
98
|
+
stub_request_from('retrieve-root-with-an-authorised-client') { response('root-response-for-authorised-client') }
|
99
|
+
|
100
|
+
let(:api) do
|
101
|
+
Sequencescape::Api.new(
|
102
|
+
:url => 'http://localhost:3000/', :cookie => 'single-sign-on-cookie',
|
103
|
+
:authorisation => 'authorised!', :namespace => Authenticated
|
104
|
+
)
|
105
|
+
end
|
106
|
+
end
|
107
|
+
end
|
108
|
+
end
|
109
|
+
|
110
|
+
RSpec.configure do |config|
|
111
|
+
config.include ContractHelper
|
112
|
+
end
|
@@ -0,0 +1,67 @@
|
|
1
|
+
module Unauthorised
|
2
|
+
MODELS_THROUGH_API = [ :model_a, :model_b, :model_c ]
|
3
|
+
|
4
|
+
class ModelA < Sequencescape::Api::Resource
|
5
|
+
module LotCreator
|
6
|
+
def create!(attributes=nil)
|
7
|
+
attributes ||= {}
|
8
|
+
new({}, false).tap do |lot|
|
9
|
+
api.create(actions.create, { 'model_b' => attributes }, Sequencescape::Api::ModifyingHandler.new(lot))
|
10
|
+
end
|
11
|
+
end
|
12
|
+
end
|
13
|
+
|
14
|
+
has_many :model_bs do
|
15
|
+
include ModelA::LotCreator
|
16
|
+
# has_create_action
|
17
|
+
end
|
18
|
+
|
19
|
+
attribute_accessor :name, :data
|
20
|
+
attribute_group :group do
|
21
|
+
attribute_accessor :data
|
22
|
+
end
|
23
|
+
end
|
24
|
+
|
25
|
+
class ModelB < Sequencescape::Api::Resource
|
26
|
+
belongs_to :model_a
|
27
|
+
belongs_to :model_by_simple_name, :class_name => 'ModelA'
|
28
|
+
belongs_to :model_by_full_name, :class_name => 'Nested::Model'
|
29
|
+
belongs_to :model_with_early_data, :class_name => 'ModelA'
|
30
|
+
attribute_accessor :test_attribute
|
31
|
+
end
|
32
|
+
|
33
|
+
class ModelC < Sequencescape::Api::Resource
|
34
|
+
has_many :model_bs, :disposition => :inline
|
35
|
+
has_many :model_as
|
36
|
+
|
37
|
+
attribute_accessor :attribute_validated_at_client, :attribute_validated_at_server
|
38
|
+
validates_each(:attribute_validated_at_client) do |record, attribute, value|
|
39
|
+
record.errors.add(attribute, 'cannot be set') unless value.blank?
|
40
|
+
end
|
41
|
+
|
42
|
+
attribute_accessor :changes_during_update, :remains_same_during_update
|
43
|
+
|
44
|
+
attribute_reader :read_only
|
45
|
+
attribute_writer :write_only
|
46
|
+
end
|
47
|
+
|
48
|
+
class Page < Sequencescape::Api::Resource
|
49
|
+
end
|
50
|
+
|
51
|
+
module Nested
|
52
|
+
class Model < Sequencescape::Api::Resource
|
53
|
+
attribute_accessor :name
|
54
|
+
end
|
55
|
+
end
|
56
|
+
end
|
57
|
+
|
58
|
+
module Authenticated
|
59
|
+
MODELS_THROUGH_API = [ :model_c, :model_d ]
|
60
|
+
|
61
|
+
class ModelC < Sequencescape::Api::Resource
|
62
|
+
|
63
|
+
end
|
64
|
+
class ModelD < Sequencescape::Api::Resource
|
65
|
+
|
66
|
+
end
|
67
|
+
end
|
@@ -0,0 +1,12 @@
|
|
1
|
+
shared_examples_for 'a paged result' do
|
2
|
+
it 'physically contains 3 items' do
|
3
|
+
subject.map(&:inspect).size.should == 3
|
4
|
+
end
|
5
|
+
|
6
|
+
it 'can be walked in pages' do
|
7
|
+
check = double('check that page gets called at least once')
|
8
|
+
check.should_receive(:called).at_least(1).at_most(3)
|
9
|
+
|
10
|
+
subject.each_page(&check.method(:called))
|
11
|
+
end
|
12
|
+
end
|
metadata
ADDED
@@ -0,0 +1,540 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: sequencescape-client-api
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.3.5
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Matthew Denner
|
8
|
+
- James Glover
|
9
|
+
- Eduardo Martin Rojo
|
10
|
+
autorequire:
|
11
|
+
bindir: bin
|
12
|
+
cert_chain: []
|
13
|
+
date: 2018-11-05 00:00:00.000000000 Z
|
14
|
+
dependencies:
|
15
|
+
- !ruby/object:Gem::Dependency
|
16
|
+
name: activesupport
|
17
|
+
requirement: !ruby/object:Gem::Requirement
|
18
|
+
requirements:
|
19
|
+
- - ">="
|
20
|
+
- !ruby/object:Gem::Version
|
21
|
+
version: 4.0.0
|
22
|
+
- - "<"
|
23
|
+
- !ruby/object:Gem::Version
|
24
|
+
version: '5.2'
|
25
|
+
type: :runtime
|
26
|
+
prerelease: false
|
27
|
+
version_requirements: !ruby/object:Gem::Requirement
|
28
|
+
requirements:
|
29
|
+
- - ">="
|
30
|
+
- !ruby/object:Gem::Version
|
31
|
+
version: 4.0.0
|
32
|
+
- - "<"
|
33
|
+
- !ruby/object:Gem::Version
|
34
|
+
version: '5.2'
|
35
|
+
- !ruby/object:Gem::Dependency
|
36
|
+
name: activemodel
|
37
|
+
requirement: !ruby/object:Gem::Requirement
|
38
|
+
requirements:
|
39
|
+
- - ">="
|
40
|
+
- !ruby/object:Gem::Version
|
41
|
+
version: 4.0.0
|
42
|
+
- - "<"
|
43
|
+
- !ruby/object:Gem::Version
|
44
|
+
version: '5.2'
|
45
|
+
type: :runtime
|
46
|
+
prerelease: false
|
47
|
+
version_requirements: !ruby/object:Gem::Requirement
|
48
|
+
requirements:
|
49
|
+
- - ">="
|
50
|
+
- !ruby/object:Gem::Version
|
51
|
+
version: 4.0.0
|
52
|
+
- - "<"
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '5.2'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: i18n
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - ">="
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: '0'
|
62
|
+
type: :runtime
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - ">="
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: '0'
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: yajl-ruby
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - ">="
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: 1.3.1
|
76
|
+
type: :runtime
|
77
|
+
prerelease: false
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - ">="
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: 1.3.1
|
83
|
+
- !ruby/object:Gem::Dependency
|
84
|
+
name: rspec
|
85
|
+
requirement: !ruby/object:Gem::Requirement
|
86
|
+
requirements:
|
87
|
+
- - "~>"
|
88
|
+
- !ruby/object:Gem::Version
|
89
|
+
version: 2.11.0
|
90
|
+
type: :development
|
91
|
+
prerelease: false
|
92
|
+
version_requirements: !ruby/object:Gem::Requirement
|
93
|
+
requirements:
|
94
|
+
- - "~>"
|
95
|
+
- !ruby/object:Gem::Version
|
96
|
+
version: 2.11.0
|
97
|
+
- !ruby/object:Gem::Dependency
|
98
|
+
name: pry
|
99
|
+
requirement: !ruby/object:Gem::Requirement
|
100
|
+
requirements:
|
101
|
+
- - ">="
|
102
|
+
- !ruby/object:Gem::Version
|
103
|
+
version: '0'
|
104
|
+
type: :development
|
105
|
+
prerelease: false
|
106
|
+
version_requirements: !ruby/object:Gem::Requirement
|
107
|
+
requirements:
|
108
|
+
- - ">="
|
109
|
+
- !ruby/object:Gem::Version
|
110
|
+
version: '0'
|
111
|
+
- !ruby/object:Gem::Dependency
|
112
|
+
name: webmock
|
113
|
+
requirement: !ruby/object:Gem::Requirement
|
114
|
+
requirements:
|
115
|
+
- - ">="
|
116
|
+
- !ruby/object:Gem::Version
|
117
|
+
version: '0'
|
118
|
+
type: :development
|
119
|
+
prerelease: false
|
120
|
+
version_requirements: !ruby/object:Gem::Requirement
|
121
|
+
requirements:
|
122
|
+
- - ">="
|
123
|
+
- !ruby/object:Gem::Version
|
124
|
+
version: '0'
|
125
|
+
- !ruby/object:Gem::Dependency
|
126
|
+
name: yard
|
127
|
+
requirement: !ruby/object:Gem::Requirement
|
128
|
+
requirements:
|
129
|
+
- - ">="
|
130
|
+
- !ruby/object:Gem::Version
|
131
|
+
version: '0'
|
132
|
+
type: :development
|
133
|
+
prerelease: false
|
134
|
+
version_requirements: !ruby/object:Gem::Requirement
|
135
|
+
requirements:
|
136
|
+
- - ">="
|
137
|
+
- !ruby/object:Gem::Version
|
138
|
+
version: '0'
|
139
|
+
- !ruby/object:Gem::Dependency
|
140
|
+
name: redcarpet
|
141
|
+
requirement: !ruby/object:Gem::Requirement
|
142
|
+
requirements:
|
143
|
+
- - ">="
|
144
|
+
- !ruby/object:Gem::Version
|
145
|
+
version: '0'
|
146
|
+
type: :development
|
147
|
+
prerelease: false
|
148
|
+
version_requirements: !ruby/object:Gem::Requirement
|
149
|
+
requirements:
|
150
|
+
- - ">="
|
151
|
+
- !ruby/object:Gem::Version
|
152
|
+
version: '0'
|
153
|
+
description: Provides all of the necessary code for interacting with the Sequencescape
|
154
|
+
API
|
155
|
+
email:
|
156
|
+
- md12@sanger.ac.uk
|
157
|
+
- james.glover@sanger.ac.uk
|
158
|
+
- emr@sanger.ac.uk
|
159
|
+
executables: []
|
160
|
+
extensions: []
|
161
|
+
extra_rdoc_files: []
|
162
|
+
files:
|
163
|
+
- ".gitignore"
|
164
|
+
- ".rspec"
|
165
|
+
- ".rvmrc"
|
166
|
+
- ".yardoc/checksums"
|
167
|
+
- ".yardoc/complete"
|
168
|
+
- ".yardoc/object_types"
|
169
|
+
- ".yardoc/objects/root.dat"
|
170
|
+
- ".yardoc/proxy_types"
|
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+
- spec/sequencescape-api/contracts/root-response-for-authorised-client.txt
|
461
|
+
- spec/sequencescape-api/contracts/root-response-for-unauthorised-client.txt
|
462
|
+
- spec/sequencescape-api/contracts/unauthorised-model-a-list.txt
|
463
|
+
- spec/sequencescape-api/contracts/unauthorised-model-b-list.txt
|
464
|
+
- spec/sequencescape-api/contracts/unauthorised-model-c-list.txt
|
465
|
+
- spec/sequencescape-api/contracts/update-invalid-resource.txt
|
466
|
+
- spec/sequencescape-api/contracts/update-model-c.txt
|
467
|
+
- spec/sequencescape-api/finding_methods_spec.rb
|
468
|
+
- spec/sequencescape-api/modifications_spec.rb
|
469
|
+
- spec/sequencescape-api/root_spec.rb
|
470
|
+
- spec/spec_helper.rb
|
471
|
+
- spec/support/contract_helper.rb
|
472
|
+
- spec/support/namespaces.rb
|
473
|
+
- spec/support/shared_examples.rb
|
474
|
+
homepage: ''
|
475
|
+
licenses: []
|
476
|
+
metadata: {}
|
477
|
+
post_install_message:
|
478
|
+
rdoc_options: []
|
479
|
+
require_paths:
|
480
|
+
- lib
|
481
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
482
|
+
requirements:
|
483
|
+
- - ">="
|
484
|
+
- !ruby/object:Gem::Version
|
485
|
+
version: '0'
|
486
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
487
|
+
requirements:
|
488
|
+
- - ">="
|
489
|
+
- !ruby/object:Gem::Version
|
490
|
+
version: '0'
|
491
|
+
requirements: []
|
492
|
+
rubyforge_project: sequencescape-client-api
|
493
|
+
rubygems_version: 2.6.14
|
494
|
+
signing_key:
|
495
|
+
specification_version: 4
|
496
|
+
summary: Gem for the client side of the Sequencescape API
|
497
|
+
test_files:
|
498
|
+
- spec/sequencescape-api/associations_spec.rb
|
499
|
+
- spec/sequencescape-api/contracts/belongs-to-association.txt
|
500
|
+
- spec/sequencescape-api/contracts/client-fails-authentication.txt
|
501
|
+
- spec/sequencescape-api/contracts/create-invalid-resource.txt
|
502
|
+
- spec/sequencescape-api/contracts/create-model-c-has-many-inline-nested.txt
|
503
|
+
- spec/sequencescape-api/contracts/create-model-c-has-many-inline.txt
|
504
|
+
- spec/sequencescape-api/contracts/create-model-c-has-many.txt
|
505
|
+
- spec/sequencescape-api/contracts/create-model-c.txt
|
506
|
+
- spec/sequencescape-api/contracts/create-via-has-many.txt
|
507
|
+
- spec/sequencescape-api/contracts/model-a-instance.txt
|
508
|
+
- spec/sequencescape-api/contracts/model-b-instance.txt
|
509
|
+
- spec/sequencescape-api/contracts/model-c-instance-created.txt
|
510
|
+
- spec/sequencescape-api/contracts/model-c-instance-updated.txt
|
511
|
+
- spec/sequencescape-api/contracts/model-c-instance.txt
|
512
|
+
- spec/sequencescape-api/contracts/model-c-invalid-attribute.txt
|
513
|
+
- spec/sequencescape-api/contracts/resource-not-found.txt
|
514
|
+
- spec/sequencescape-api/contracts/results-page-1.txt
|
515
|
+
- spec/sequencescape-api/contracts/results-page-2.txt
|
516
|
+
- spec/sequencescape-api/contracts/results-page-3.txt
|
517
|
+
- spec/sequencescape-api/contracts/retrieve-belongs-to-association.txt
|
518
|
+
- spec/sequencescape-api/contracts/retrieve-model.txt
|
519
|
+
- spec/sequencescape-api/contracts/retrieve-results-page-1.txt
|
520
|
+
- spec/sequencescape-api/contracts/retrieve-results-page-2.txt
|
521
|
+
- spec/sequencescape-api/contracts/retrieve-results-page-3.txt
|
522
|
+
- spec/sequencescape-api/contracts/retrieve-root-with-an-authorised-client.txt
|
523
|
+
- spec/sequencescape-api/contracts/retrieve-root-with-an-unauthorised-client.txt
|
524
|
+
- spec/sequencescape-api/contracts/retrieve-unauthorised-model-a-list.txt
|
525
|
+
- spec/sequencescape-api/contracts/retrieve-unauthorised-model-b-list.txt
|
526
|
+
- spec/sequencescape-api/contracts/retrieve-unauthorised-model-c-list.txt
|
527
|
+
- spec/sequencescape-api/contracts/root-response-for-authorised-client.txt
|
528
|
+
- spec/sequencescape-api/contracts/root-response-for-unauthorised-client.txt
|
529
|
+
- spec/sequencescape-api/contracts/unauthorised-model-a-list.txt
|
530
|
+
- spec/sequencescape-api/contracts/unauthorised-model-b-list.txt
|
531
|
+
- spec/sequencescape-api/contracts/unauthorised-model-c-list.txt
|
532
|
+
- spec/sequencescape-api/contracts/update-invalid-resource.txt
|
533
|
+
- spec/sequencescape-api/contracts/update-model-c.txt
|
534
|
+
- spec/sequencescape-api/finding_methods_spec.rb
|
535
|
+
- spec/sequencescape-api/modifications_spec.rb
|
536
|
+
- spec/sequencescape-api/root_spec.rb
|
537
|
+
- spec/spec_helper.rb
|
538
|
+
- spec/support/contract_helper.rb
|
539
|
+
- spec/support/namespaces.rb
|
540
|
+
- spec/support/shared_examples.rb
|