sequencescape-client-api 0.3.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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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@@ -0,0 +1,10 @@
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require 'sequencescape-api/resource'
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2
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3
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+
class Sequencescape::Asset < ::Sequencescape::Api::Resource
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4
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+
attribute_accessor :name
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5
|
+
attribute_accessor :qc_state
|
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6
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+
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7
|
+
# TODO: This is a hack for the warehouse that should be removed! The type is always known by the application
|
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8
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+
# that is using an asset (actually it comes from request JSON) so it's pointless this being here!
|
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9
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+
attribute_accessor :type
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10
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+
end
|
|
@@ -0,0 +1,14 @@
|
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1
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+
class BaitLibrary
|
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2
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+
include Sequencescape::Api::Composition::Target
|
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3
|
+
|
|
4
|
+
attribute_accessor :name
|
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5
|
+
attribute_accessor :created_at, :updated_at, :conversion => :to_time
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6
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+
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7
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+
attribute_group :supplier do
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8
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+
attribute_accessor :name, :identifier
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9
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+
end
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10
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+
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11
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+
attribute_group :target do
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12
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+
attribute_accessor :species
|
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13
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+
end
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|
14
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+
end
|
|
@@ -0,0 +1,9 @@
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1
|
+
require 'sequencescape-api/resource'
|
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2
|
+
|
|
3
|
+
class Sequencescape::BaitLibraryLayout < ::Sequencescape::Api::Resource
|
|
4
|
+
belongs_to :user
|
|
5
|
+
belongs_to :plate, :class_name => 'Plate'
|
|
6
|
+
attribute_reader :layout
|
|
7
|
+
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8
|
+
has_class_create_action(:preview!, :action => :preview)
|
|
9
|
+
end
|
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@@ -0,0 +1,13 @@
|
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1
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+
require 'sequencescape-api/resource'
|
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2
|
+
|
|
3
|
+
class Sequencescape::BarcodePrinter < Sequencescape::Api::Resource
|
|
4
|
+
attribute_reader :name, :active
|
|
5
|
+
|
|
6
|
+
attribute_group :service do
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|
7
|
+
attribute_reader :url
|
|
8
|
+
end
|
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9
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+
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10
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+
attribute_group :type do
|
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11
|
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attribute_reader :name, :layout
|
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12
|
+
end
|
|
13
|
+
end
|
|
@@ -0,0 +1,12 @@
|
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1
|
+
require 'sequencescape-api/resource'
|
|
2
|
+
require 'sequencescape/asset'
|
|
3
|
+
|
|
4
|
+
class Sequencescape::BarcodedAsset < ::Sequencescape::Asset
|
|
5
|
+
require 'sequencescape/behaviour/barcoded'
|
|
6
|
+
require 'sequencescape/behaviour/qced'
|
|
7
|
+
# Used in transfer to make barcodes easily retrieveable
|
|
8
|
+
include Sequencescape::Behaviour::Barcoded
|
|
9
|
+
include Sequencescape::Behaviour::Qced
|
|
10
|
+
|
|
11
|
+
belongs_to :stock_plate, :class_name => 'Plate'
|
|
12
|
+
end
|
|
@@ -0,0 +1,24 @@
|
|
|
1
|
+
require 'sequencescape-api/resource'
|
|
2
|
+
|
|
3
|
+
class Sequencescape::Batch < ::Sequencescape::Api::Resource
|
|
4
|
+
belongs_to :pipeline
|
|
5
|
+
has_many :requests, :disposition => :inline
|
|
6
|
+
composed_of :user
|
|
7
|
+
|
|
8
|
+
has_update_action :start!, :action => 'start'
|
|
9
|
+
has_update_action :complete!, :action => 'complete'
|
|
10
|
+
has_update_action :release!, :action => 'release'
|
|
11
|
+
|
|
12
|
+
attribute_accessor :state, :production_state, :qc_state, :barcode
|
|
13
|
+
|
|
14
|
+
def self.state_method(name)
|
|
15
|
+
class_eval(%Q{def #{name}? ; state == #{name.to_s.inspect} ; end})
|
|
16
|
+
end
|
|
17
|
+
|
|
18
|
+
state_method(:pending)
|
|
19
|
+
state_method(:started)
|
|
20
|
+
state_method(:completed)
|
|
21
|
+
state_method(:released)
|
|
22
|
+
|
|
23
|
+
validates_presence_of :requests, :allow_blank => false
|
|
24
|
+
end
|
|
@@ -0,0 +1,15 @@
|
|
|
1
|
+
# Anything that can have a barcode is considered to be barcoded!
|
|
2
|
+
module Sequencescape::Behaviour
|
|
3
|
+
module Barcoded
|
|
4
|
+
def self.included(base)
|
|
5
|
+
base.class_eval do
|
|
6
|
+
attribute_group :barcode do
|
|
7
|
+
attribute_accessor :prefix, :number # The pieces that make up a barcode
|
|
8
|
+
attribute_accessor :ean13 # The EAN13 barcode number
|
|
9
|
+
attribute_accessor :two_dimensional # The 2D barcode
|
|
10
|
+
attribute_accessor :type # The type of barcode (or rather barcode printer)
|
|
11
|
+
end
|
|
12
|
+
end
|
|
13
|
+
end
|
|
14
|
+
end
|
|
15
|
+
end
|
|
@@ -0,0 +1,14 @@
|
|
|
1
|
+
# Prefix depends on the submission template used and sumarises the order.
|
|
2
|
+
# Text at the moment is a bit redundant, being the purpose name. However
|
|
3
|
+
# it makes things much easier for cases where we are hashing our objects manually
|
|
4
|
+
module Sequencescape::Behaviour
|
|
5
|
+
module Labeled
|
|
6
|
+
def self.included(base)
|
|
7
|
+
base.class_eval do
|
|
8
|
+
attribute_group :label do
|
|
9
|
+
attribute_accessor :prefix, :text
|
|
10
|
+
end
|
|
11
|
+
end
|
|
12
|
+
end
|
|
13
|
+
end
|
|
14
|
+
end
|
|
@@ -0,0 +1,31 @@
|
|
|
1
|
+
module Sequencescape::Behaviour
|
|
2
|
+
module Qced
|
|
3
|
+
|
|
4
|
+
module QcFile
|
|
5
|
+
def create!(attributes = nil)
|
|
6
|
+
attributes ||= {}
|
|
7
|
+
|
|
8
|
+
new({}, false).tap do |qc_file|
|
|
9
|
+
api.create(actions.create, { 'qc_file' => attributes }, Sequencescape::Api::ModifyingHandler.new(qc_file))
|
|
10
|
+
end
|
|
11
|
+
end
|
|
12
|
+
|
|
13
|
+
def create_from_file!(file, filename)
|
|
14
|
+
attributes ||= {}
|
|
15
|
+
|
|
16
|
+
new({}, false).tap do |qc_file|
|
|
17
|
+
api.create_from_file(actions.create, file, filename, 'sequencescape/qc_file', Sequencescape::Api::ModifyingHandler.new(qc_file))
|
|
18
|
+
end
|
|
19
|
+
end
|
|
20
|
+
end
|
|
21
|
+
|
|
22
|
+
def self.included(base)
|
|
23
|
+
base.class_eval do
|
|
24
|
+
has_many :qc_files do
|
|
25
|
+
include Sequencescape::Behaviour::Qced::QcFile
|
|
26
|
+
end
|
|
27
|
+
end
|
|
28
|
+
end
|
|
29
|
+
|
|
30
|
+
end
|
|
31
|
+
end
|
|
@@ -0,0 +1,21 @@
|
|
|
1
|
+
require 'sequencescape/tag'
|
|
2
|
+
require 'sequencescape/bait_library'
|
|
3
|
+
|
|
4
|
+
module Sequencescape::Behaviour
|
|
5
|
+
module Receptacle
|
|
6
|
+
class Aliquot < Sequencescape::Api::Resource
|
|
7
|
+
belongs_to :sample, :disposition => :inline
|
|
8
|
+
composed_of :tag
|
|
9
|
+
composed_of :tag2, :class_name => 'Tag'
|
|
10
|
+
composed_of :bait_library
|
|
11
|
+
|
|
12
|
+
attribute_accessor :suboptimal
|
|
13
|
+
end
|
|
14
|
+
|
|
15
|
+
def self.included(base)
|
|
16
|
+
base.class_eval do
|
|
17
|
+
has_many :aliquots, :disposition => :inline, :class_name => 'Behaviours::Receptacle::Aliquot'
|
|
18
|
+
end
|
|
19
|
+
end
|
|
20
|
+
end
|
|
21
|
+
end
|
|
@@ -0,0 +1,19 @@
|
|
|
1
|
+
module Sequencescape::Behaviour
|
|
2
|
+
module StateDriven
|
|
3
|
+
def self.included(base)
|
|
4
|
+
base.class_eval do
|
|
5
|
+
attribute_reader :state
|
|
6
|
+
|
|
7
|
+
# Define a few default states
|
|
8
|
+
[ :pending, :started, :passed, :failed, :cancelled, :unknown, :qc_complete ].each do |state|
|
|
9
|
+
line = __LINE__ + 1
|
|
10
|
+
class_eval(%Q{
|
|
11
|
+
def #{state}?
|
|
12
|
+
state == #{state.to_s.inspect}
|
|
13
|
+
end
|
|
14
|
+
}, __FILE__, line)
|
|
15
|
+
end
|
|
16
|
+
end
|
|
17
|
+
end
|
|
18
|
+
end
|
|
19
|
+
end
|
|
@@ -0,0 +1,190 @@
|
|
|
1
|
+
en:
|
|
2
|
+
activemodel:
|
|
3
|
+
models:
|
|
4
|
+
sequencescape:
|
|
5
|
+
asset: "Asset"
|
|
6
|
+
asset_group: "Asset group"
|
|
7
|
+
batch: "Batch"
|
|
8
|
+
library_tube: "Library tube"
|
|
9
|
+
pipeline: "Pipeline"
|
|
10
|
+
plate: "Plate"
|
|
11
|
+
plate_purpose: "Plate purpose"
|
|
12
|
+
project: "Project"
|
|
13
|
+
sample: "Sample"
|
|
14
|
+
sample_tube: "Sample tube"
|
|
15
|
+
study: "Study"
|
|
16
|
+
submission: "Submission"
|
|
17
|
+
submission_template: "Submission template"
|
|
18
|
+
well: "Well"
|
|
19
|
+
|
|
20
|
+
attributes:
|
|
21
|
+
sequencescape:
|
|
22
|
+
asset: &asset
|
|
23
|
+
name: "Name"
|
|
24
|
+
qc_state: "QC state"
|
|
25
|
+
barcode_prefix: "Barcode prefix"
|
|
26
|
+
barcode: "Barcode"
|
|
27
|
+
two_dimensional_barcode: "2D Barcode"
|
|
28
|
+
|
|
29
|
+
request:
|
|
30
|
+
request_options: &request_options
|
|
31
|
+
read_length: "Read length"
|
|
32
|
+
library_type: "Library type"
|
|
33
|
+
fragment_size_required:
|
|
34
|
+
from: "Fragment size (from)"
|
|
35
|
+
to: "Fragment size (to)"
|
|
36
|
+
|
|
37
|
+
asset_group:
|
|
38
|
+
name: "Name"
|
|
39
|
+
study:
|
|
40
|
+
name: "Study name"
|
|
41
|
+
|
|
42
|
+
batch:
|
|
43
|
+
state: "State"
|
|
44
|
+
production_state: "Production state"
|
|
45
|
+
qc_state: "QC state"
|
|
46
|
+
barcode: "Barcode"
|
|
47
|
+
requests: "Requests"
|
|
48
|
+
user:
|
|
49
|
+
login: "User login"
|
|
50
|
+
|
|
51
|
+
library_tube:
|
|
52
|
+
<<: *asset
|
|
53
|
+
closed: "Closed"
|
|
54
|
+
concentration: "Concentration"
|
|
55
|
+
volume: "Volume"
|
|
56
|
+
scanned_in_date: "Date scanned into the lab"
|
|
57
|
+
|
|
58
|
+
sample:
|
|
59
|
+
name: "Sample name"
|
|
60
|
+
|
|
61
|
+
source_request:
|
|
62
|
+
<<: *request_options
|
|
63
|
+
|
|
64
|
+
tag:
|
|
65
|
+
uuid: "UUID"
|
|
66
|
+
expected_sequence: "Expected sequence"
|
|
67
|
+
|
|
68
|
+
group:
|
|
69
|
+
uuid: "UUID"
|
|
70
|
+
name: "Name"
|
|
71
|
+
|
|
72
|
+
pipeline:
|
|
73
|
+
name: "Name"
|
|
74
|
+
|
|
75
|
+
plate:
|
|
76
|
+
<<: *asset
|
|
77
|
+
size: "Size"
|
|
78
|
+
wells: "Wells"
|
|
79
|
+
|
|
80
|
+
plate_purpose:
|
|
81
|
+
name: "Plate purpose name"
|
|
82
|
+
|
|
83
|
+
plate_purpose:
|
|
84
|
+
name: "Name"
|
|
85
|
+
|
|
86
|
+
project:
|
|
87
|
+
name: "Name"
|
|
88
|
+
approved: "Approval status"
|
|
89
|
+
state: "State"
|
|
90
|
+
|
|
91
|
+
project_manager: "Project manager"
|
|
92
|
+
cost_code: "Cost code"
|
|
93
|
+
funding_comments: "Funding comments"
|
|
94
|
+
collaborators: "Collaborators"
|
|
95
|
+
external_funding_source: "External funding source"
|
|
96
|
+
budget_division: "Budget division"
|
|
97
|
+
budget_cost_centre: "Budget cost centre"
|
|
98
|
+
funding_model: "Funding model"
|
|
99
|
+
|
|
100
|
+
roles: "Roles"
|
|
101
|
+
|
|
102
|
+
sample:
|
|
103
|
+
name: "Name"
|
|
104
|
+
sanger_id: "Sanger sample identifier"
|
|
105
|
+
control: "Control sample"
|
|
106
|
+
|
|
107
|
+
organism: "Organism"
|
|
108
|
+
cohort: "Cohort"
|
|
109
|
+
country_of_origin: "Country of origin"
|
|
110
|
+
geographical_region: "Geographical region"
|
|
111
|
+
ethnicity: "Ethnicity"
|
|
112
|
+
volume: "Volume"
|
|
113
|
+
supplier_plate_id: "Supplier plate identifier"
|
|
114
|
+
mother: "Mother"
|
|
115
|
+
father: "Father"
|
|
116
|
+
replicate: "Replicate"
|
|
117
|
+
gc_content: "GC content level"
|
|
118
|
+
gender: "Gender"
|
|
119
|
+
dna_source: "DNA source"
|
|
120
|
+
public_name: "Public name"
|
|
121
|
+
common_name: "Common name"
|
|
122
|
+
strain_att: "Strain"
|
|
123
|
+
taxon_id: "Taxon identifier"
|
|
124
|
+
ebi_accession_number: "ENA accession number"
|
|
125
|
+
description: "Description"
|
|
126
|
+
sra_hold: "Sample visibility"
|
|
127
|
+
reference_genome: "Reference genome"
|
|
128
|
+
|
|
129
|
+
sample_tube:
|
|
130
|
+
<<: *asset
|
|
131
|
+
closed: "Closed"
|
|
132
|
+
concentration: "Concentration"
|
|
133
|
+
volume: "Volume"
|
|
134
|
+
scanned_in_date: "Date scanned into lab"
|
|
135
|
+
|
|
136
|
+
sample:
|
|
137
|
+
name: "Sample name"
|
|
138
|
+
|
|
139
|
+
study:
|
|
140
|
+
name: "Name"
|
|
141
|
+
ethically_approved: "Ethical approval status"
|
|
142
|
+
state: "State"
|
|
143
|
+
abbreviation: "Abbreviation"
|
|
144
|
+
|
|
145
|
+
type: "Type of study"
|
|
146
|
+
sac_sponsor: "Faculty sponsor"
|
|
147
|
+
reference_genome: "Reference genome"
|
|
148
|
+
accession_number: "ENA accession number"
|
|
149
|
+
description: "Description"
|
|
150
|
+
abstract: "Abstract"
|
|
151
|
+
|
|
152
|
+
contaminated_human_dna: "Contaminated with human DNA"
|
|
153
|
+
contains_human_dna: "Contains human DNA"
|
|
154
|
+
data_release_sort_of_study: "Type of study"
|
|
155
|
+
data_release_strategy: "Release strategy"
|
|
156
|
+
|
|
157
|
+
submission:
|
|
158
|
+
state: "State"
|
|
159
|
+
|
|
160
|
+
# TODO: Wonder how you can deal with nesting of 'name' in these
|
|
161
|
+
study: "Study"
|
|
162
|
+
project: "Project"
|
|
163
|
+
asset_group: "Asset group"
|
|
164
|
+
|
|
165
|
+
assets: "Asset UUIDs"
|
|
166
|
+
|
|
167
|
+
request_types: "Request types"
|
|
168
|
+
|
|
169
|
+
request_options:
|
|
170
|
+
<<: *request_options
|
|
171
|
+
number_of_lanes: "Number of lanes"
|
|
172
|
+
|
|
173
|
+
submission_template:
|
|
174
|
+
name: "Name"
|
|
175
|
+
|
|
176
|
+
well:
|
|
177
|
+
location: "Location on plate"
|
|
178
|
+
|
|
179
|
+
errors:
|
|
180
|
+
models:
|
|
181
|
+
sequencescape:
|
|
182
|
+
request:
|
|
183
|
+
attributes:
|
|
184
|
+
state:
|
|
185
|
+
inclusion: "is not a valid state"
|
|
186
|
+
|
|
187
|
+
study:
|
|
188
|
+
attributes:
|
|
189
|
+
name:
|
|
190
|
+
blank: "can't be blank"
|