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 'sequencescape-api/resource'
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class Sequencescape::Lot < ::Sequencescape::Api::Resource
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belongs_to :user
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belongs_to :lot_type
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belongs_to :template
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has_many :qcables
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attribute_accessor :lot_number, :received_at, :template_name, :lot_type_name
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end
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require 'sequencescape-api/resource'
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class Sequencescape::LotType < ::Sequencescape::Api::Resource
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module LotCreator
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def create!(attributes=nil)
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attributes ||= {}
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new({}, false).tap do |lot|
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api.create(actions.create, { 'lot' => attributes }, Sequencescape::Api::ModifyingHandler.new(lot))
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end
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end
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end
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has_many :lots do
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# has_create_action
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include Sequencescape::LotType::LotCreator
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end
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attribute_accessor :name, :template_class, :printer_type, :qcable_name
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end
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require 'sequencescape-api/resource'
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class Sequencescape::Order < ::Sequencescape::Api::Resource
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has_many :assets
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belongs_to :user
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belongs_to :study
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belongs_to :project
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# It does, but we don't care for now.
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# has_many :request_types
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attr_accessor :request_options
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end
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require 'sequencescape-api/resource'
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class Sequencescape::OrderTemplate < ::Sequencescape::Api::Resource
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module OrderCreator
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def create!(attributes=nil)
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attributes ||= {}
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new({}, false).tap do |order|
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api.create(actions.create, { 'order' => attributes }, Sequencescape::Api::ModifyingHandler.new(order))
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end
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end
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end
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|
14
|
+
has_many :orders do
|
15
|
+
include Sequencescape::OrderTemplate::OrderCreator
|
16
|
+
end
|
17
|
+
|
18
|
+
attribute_accessor :name
|
19
|
+
end
|
@@ -0,0 +1,23 @@
|
|
1
|
+
module Sequencescape::Plate::Pooling
|
2
|
+
def populate_wells_with_pool
|
3
|
+
wells.each do |well|
|
4
|
+
pool_id, pool = pools.detect { |_, pool| pool['wells'].include?(well.location) }
|
5
|
+
next if pool.nil?
|
6
|
+
well.pool = pool
|
7
|
+
end
|
8
|
+
end
|
9
|
+
|
10
|
+
def populate_wells_with_pre_cap_group
|
11
|
+
wells.each do |well|
|
12
|
+
pre_cap_group_id, pre_cap_group = pre_cap_groups.detect { |_, pre_cap_group| pre_cap_group['wells'].include?(well.location) }
|
13
|
+
next if pre_cap_group.nil?
|
14
|
+
well.pre_cap_group = pre_cap_group
|
15
|
+
end
|
16
|
+
end
|
17
|
+
|
18
|
+
def after_load
|
19
|
+
pools.each { |pool_id, pool| pool['id'] = pool_id } unless pools.nil?
|
20
|
+
pre_cap_groups.each { |pre_cap_group_id, pre_cap_group| pre_cap_group['id'] = pre_cap_group_id } unless pre_cap_groups.nil?
|
21
|
+
end
|
22
|
+
private :after_load
|
23
|
+
end
|
@@ -0,0 +1,27 @@
|
|
1
|
+
module Sequencescape::Plate::WellStructure
|
2
|
+
def rows
|
3
|
+
case self.size
|
4
|
+
when 96 then ('A'..'H')
|
5
|
+
when 384 then ('A'..'P')
|
6
|
+
else raise RuntimeError, "Unknown plate size #{self.size}"
|
7
|
+
end
|
8
|
+
end
|
9
|
+
|
10
|
+
def columns
|
11
|
+
case self.size
|
12
|
+
when 96 then (1..12)
|
13
|
+
when 384 then (1..24)
|
14
|
+
else raise RuntimeError, "Unknown plate size #{self.size}"
|
15
|
+
end
|
16
|
+
end
|
17
|
+
|
18
|
+
def locations_in_rows
|
19
|
+
[].tap do |locations|
|
20
|
+
self.rows.each do |row|
|
21
|
+
self.columns.each do |column|
|
22
|
+
locations << "#{row}#{column}"
|
23
|
+
end
|
24
|
+
end
|
25
|
+
end
|
26
|
+
end
|
27
|
+
end
|
@@ -0,0 +1,71 @@
|
|
1
|
+
require 'sequencescape/asset'
|
2
|
+
|
3
|
+
class Sequencescape::Plate < ::Sequencescape::Asset
|
4
|
+
require 'sequencescape/behaviour/barcoded'
|
5
|
+
require 'sequencescape/behaviour/state_driven'
|
6
|
+
require 'sequencescape/plate/well_structure'
|
7
|
+
require 'sequencescape/plate/pooling'
|
8
|
+
require 'sequencescape/behaviour/labeled'
|
9
|
+
require 'sequencescape/behaviour/qced'
|
10
|
+
|
11
|
+
include Sequencescape::Behaviour::Barcoded
|
12
|
+
include Sequencescape::Behaviour::StateDriven
|
13
|
+
include Sequencescape::Plate::WellStructure
|
14
|
+
include Sequencescape::Plate::Pooling
|
15
|
+
include Sequencescape::Behaviour::Labeled
|
16
|
+
include Sequencescape::Behaviour::Qced
|
17
|
+
|
18
|
+
has_many :wells
|
19
|
+
has_many :submission_pools
|
20
|
+
has_many :transfer_request_collections
|
21
|
+
|
22
|
+
belongs_to :plate_purpose
|
23
|
+
belongs_to :custom_metadatum_collection
|
24
|
+
composed_of :stock_plate, :class_name => 'Plate'
|
25
|
+
|
26
|
+
module CommentsCreation
|
27
|
+
def create!(attributes = nil)
|
28
|
+
attributes ||= {}
|
29
|
+
|
30
|
+
new({}, false).tap do |comment|
|
31
|
+
api.create(actions.create, { 'comment' => attributes }, Sequencescape::Api::ModifyingHandler.new(comment))
|
32
|
+
end
|
33
|
+
end
|
34
|
+
|
35
|
+
end
|
36
|
+
|
37
|
+
module CurrentVolumeSubstraction
|
38
|
+
def create!(attributes = nil)
|
39
|
+
attributes ||= {}
|
40
|
+
|
41
|
+
new({}, false).tap do |volume_update|
|
42
|
+
api.create(actions.create, { 'volume_update' => attributes }, Sequencescape::Api::ModifyingHandler.new(volume_update))
|
43
|
+
end
|
44
|
+
end
|
45
|
+
|
46
|
+
def substract_volume!(volume_change)
|
47
|
+
create!({ :volume_change => volume_change})
|
48
|
+
end
|
49
|
+
end
|
50
|
+
has_many :volume_updates do
|
51
|
+
include Sequencescape::Plate::CurrentVolumeSubstraction
|
52
|
+
end
|
53
|
+
|
54
|
+
has_many :comments do
|
55
|
+
include Sequencescape::Plate::CommentsCreation
|
56
|
+
end
|
57
|
+
|
58
|
+
has_many :source_transfers, :class_name => 'Transfer'
|
59
|
+
has_many :transfers_to_tubes, :class_name => 'Transfer'
|
60
|
+
has_many :creation_transfers, :class_name => 'Transfer'
|
61
|
+
|
62
|
+
attribute_accessor :size, :iteration, :pools, :pre_cap_groups, :location, :priority
|
63
|
+
|
64
|
+
# Provides backwards compatability
|
65
|
+
def creation_transfer
|
66
|
+
Rails.logger.warn "Creation transfer is deprecated, use creation_transfers instead"
|
67
|
+
return creation_transfers.first if creation_transfers.count == 1
|
68
|
+
raise Sequencescape::Api::Error, "Unexpected number of transfers found: #{creation_transfers.count} found, 1 expected."
|
69
|
+
end
|
70
|
+
|
71
|
+
end
|
@@ -0,0 +1,8 @@
|
|
1
|
+
require 'sequencescape-api/resource'
|
2
|
+
|
3
|
+
class Sequencescape::PlateConversion < ::Sequencescape::Api::Resource
|
4
|
+
belongs_to :user
|
5
|
+
belongs_to :target, :class_name => 'Plate'
|
6
|
+
belongs_to :parent, :class_name => 'Plate'
|
7
|
+
belongs_to :purpose, :class_name => 'PlatePurpose'
|
8
|
+
end
|
@@ -0,0 +1,8 @@
|
|
1
|
+
require 'sequencescape-api/resource'
|
2
|
+
|
3
|
+
class Sequencescape::PlateCreation < ::Sequencescape::Api::Resource
|
4
|
+
belongs_to :user
|
5
|
+
belongs_to :parent, :class_name => 'Plate'
|
6
|
+
belongs_to :child_purpose, :class_name => 'PlatePurpose'
|
7
|
+
belongs_to :child, :class_name => 'Plate'
|
8
|
+
end
|
@@ -0,0 +1,24 @@
|
|
1
|
+
require 'sequencescape-api/resource'
|
2
|
+
|
3
|
+
class Sequencescape::PlatePurpose < ::Sequencescape::Api::Resource
|
4
|
+
module PlateCreation
|
5
|
+
def create!(attributes = nil)
|
6
|
+
attributes ||= {}
|
7
|
+
attributes[:wells].delete_if { |_,v| v.blank? } if attributes.key?(:wells)
|
8
|
+
|
9
|
+
new({}, false).tap do |plate|
|
10
|
+
api.create(actions.create, { 'plate' => attributes }, Sequencescape::Api::ModifyingHandler.new(plate))
|
11
|
+
end
|
12
|
+
end
|
13
|
+
end
|
14
|
+
|
15
|
+
has_many :children, :class_name => 'PlatePurpose'
|
16
|
+
has_many :parents, :class_name => 'PlatePurpose'
|
17
|
+
|
18
|
+
has_many :plates do
|
19
|
+
include Sequencescape::PlatePurpose::PlateCreation
|
20
|
+
end
|
21
|
+
|
22
|
+
attribute_accessor :name, :lifespan, :cherrypickable_target, :stock_plate, :size
|
23
|
+
attribute_writer :input_plate
|
24
|
+
end
|
@@ -0,0 +1,13 @@
|
|
1
|
+
require 'sequencescape/asset'
|
2
|
+
|
3
|
+
class Sequencescape::PlateTemplate < ::Sequencescape::Asset
|
4
|
+
|
5
|
+
require 'sequencescape/plate/well_structure'
|
6
|
+
|
7
|
+
include Sequencescape::Plate::WellStructure
|
8
|
+
|
9
|
+
has_many :wells
|
10
|
+
|
11
|
+
attribute_accessor :size, :name
|
12
|
+
|
13
|
+
end
|
@@ -0,0 +1,8 @@
|
|
1
|
+
require 'sequencescape-api/resource'
|
2
|
+
|
3
|
+
class Sequencescape::PooledPlateCreation < ::Sequencescape::Api::Resource
|
4
|
+
belongs_to :user
|
5
|
+
has_many :parents, :class_name => 'Plate', :disposition => :inline
|
6
|
+
belongs_to :child_purpose, :class_name => 'PlatePurpose'
|
7
|
+
belongs_to :child, :class_name => 'Plate'
|
8
|
+
end
|
@@ -0,0 +1,11 @@
|
|
1
|
+
require 'sequencescape-api/resource'
|
2
|
+
|
3
|
+
class Sequencescape::Project < ::Sequencescape::Api::Resource
|
4
|
+
has_many :submissions
|
5
|
+
|
6
|
+
attribute_accessor :name
|
7
|
+
attribute_accessor :approved, :state
|
8
|
+
attribute_accessor :project_manager, :cost_code, :funding_comments, :external_funding_source, :budget_division, :budget_cost_centre, :funding_model
|
9
|
+
attribute_accessor :collaborators
|
10
|
+
attribute_accessor :roles
|
11
|
+
end
|
@@ -0,0 +1,14 @@
|
|
1
|
+
|
2
|
+
require 'sequencescape-api/resource'
|
3
|
+
|
4
|
+
class Sequencescape::QcFile < ::Sequencescape::Api::Resource
|
5
|
+
|
6
|
+
belongs_to :asset
|
7
|
+
|
8
|
+
attribute_accessor :filename, :size
|
9
|
+
|
10
|
+
def retrieve
|
11
|
+
api.retrieve(actions.read, Sequencescape::Api::ModifyingHandler.new(self), 'sequencescape/qc_file')
|
12
|
+
end
|
13
|
+
|
14
|
+
end
|
@@ -0,0 +1,17 @@
|
|
1
|
+
|
2
|
+
require 'sequencescape-api/resource'
|
3
|
+
|
4
|
+
class Sequencescape::Qcable < ::Sequencescape::Api::Resource
|
5
|
+
|
6
|
+
belongs_to :lot
|
7
|
+
belongs_to :qcable_creator
|
8
|
+
belongs_to :asset
|
9
|
+
|
10
|
+
attribute_accessor :state, :stamp_bed, :stamp_index
|
11
|
+
|
12
|
+
attribute_group :barcode do
|
13
|
+
attribute_accessor :prefix, :number # The pieces that make up a barcode
|
14
|
+
attribute_accessor :ean13 # The EAN13 barcode number
|
15
|
+
end
|
16
|
+
|
17
|
+
end
|
@@ -0,0 +1,16 @@
|
|
1
|
+
require 'sequencescape-api/resource'
|
2
|
+
|
3
|
+
class Sequencescape::Request < ::Sequencescape::Api::Resource
|
4
|
+
belongs_to :project
|
5
|
+
belongs_to :study
|
6
|
+
belongs_to :sample
|
7
|
+
belongs_to :submission
|
8
|
+
|
9
|
+
belongs_to :source_asset, :class_name => 'Asset'
|
10
|
+
belongs_to :target_asset, :class_name => 'Asset'
|
11
|
+
|
12
|
+
attribute_accessor :type, :state
|
13
|
+
validates_inclusion_of :state, :in => %w{pending started failed passed cancelled blocked hold}
|
14
|
+
|
15
|
+
attribute_accessor :read_length, :library_type, :fragment_size
|
16
|
+
end
|
@@ -0,0 +1,51 @@
|
|
1
|
+
require 'sequencescape-api/resource'
|
2
|
+
|
3
|
+
class Sequencescape::Sample < ::Sequencescape::Api::Resource
|
4
|
+
has_many :sample_tubes
|
5
|
+
|
6
|
+
attribute_group :sanger do
|
7
|
+
attribute_accessor :name, :sample_id, :resubmitted, :description
|
8
|
+
end
|
9
|
+
attribute_group :supplier do
|
10
|
+
attribute_accessor :sample_name, :storage_conditions
|
11
|
+
|
12
|
+
attribute_group :collection do
|
13
|
+
attribute_accessor :date
|
14
|
+
end
|
15
|
+
attribute_group :extraction do
|
16
|
+
attribute_accessor :date, :method
|
17
|
+
end
|
18
|
+
attribute_group :purification do
|
19
|
+
attribute_accessor :purified, :method
|
20
|
+
end
|
21
|
+
attribute_group :measurements do
|
22
|
+
attribute_accessor :volume, :concentration, :concentration_determined_by
|
23
|
+
attribute_accessor :gc_content, :gender
|
24
|
+
end
|
25
|
+
end
|
26
|
+
attribute_group :source do
|
27
|
+
attribute_accessor :dna_source, :cohort, :country, :region, :ethnicity, :control
|
28
|
+
end
|
29
|
+
attribute_group :family do
|
30
|
+
attribute_accessor :mother, :father, :replicate, :sibling
|
31
|
+
end
|
32
|
+
attribute_group :taxonomy do
|
33
|
+
attribute_accessor :id, :strain, :common_name, :organism
|
34
|
+
end
|
35
|
+
attribute_group :reference do
|
36
|
+
attribute_accessor :genome
|
37
|
+
end
|
38
|
+
attribute_group :data_release do
|
39
|
+
attribute_accessor :sample_type, :accession_number, :visibility, :public_name, :description
|
40
|
+
|
41
|
+
attribute_group :metagenomics do
|
42
|
+
attribute_accessor :genotype, :phenotype
|
43
|
+
attribute_accessor :age, :developmental_stage, :cell_type, :disease_state
|
44
|
+
attribute_accessor :compound, :dose, :immunoprecipitate, :growth_condition
|
45
|
+
attribute_accessor :rnai, :organism_part, :time_point, :treatment, :subject, :disease
|
46
|
+
end
|
47
|
+
attribute_group :managed do
|
48
|
+
attribute_accessor :treatment, :subject, :disease
|
49
|
+
end
|
50
|
+
end
|
51
|
+
end
|