Merge pull request #4426 from sanger/Y24-190-fix-api-v2-transfers

Y24-190: Fix API v2 transfers

.rubocop_todo.yml

@@ -294,7 +294,7 @@ Lint/UselessAssignment:
 # Configuration parameters: AllowedMethods, AllowedPatterns, CountRepeatedAttributes, Max.
 Metrics/AbcSize:
   Exclude:
-    - 'app/controllers/api/v2/transfers/transfers_controller.rb'
+    - 'app/controllers/api/v2/transfers_controller.rb'
     - 'app/jobs/export_pool_xp_to_traction_job.rb'
     - 'app/sample_manifest_excel/sample_manifest_excel/manifest_type_list.rb'
 
@@ -717,7 +717,7 @@ RSpec/ExampleLength:
     - 'spec/requests/api/v2/shared_examples/api_key_authenticatable.rb'
     - 'spec/requests/api/v2/tag_layout_templates_spec.rb'
     - 'spec/requests/api/v2/tag_layouts_spec.rb'
-    - 'spec/requests/api/v2/transfers/transfers_spec.rb'
+    - 'spec/requests/api/v2/transfers_spec.rb'
     - 'spec/requests/api/v2/tube_purposes_spec.rb'
     - 'spec/requests/api/v2/users_spec.rb'
     - 'spec/requests/api/v2/volume_update_spec.rb'
@@ -736,7 +736,6 @@ RSpec/ExampleLength:
     - 'spec/resources/api/v2/sample_metadata_resource_spec.rb'
     - 'spec/resources/api/v2/submission_resource_spec.rb'
     - 'spec/resources/api/v2/tag_group_resource_spec.rb'
-    - 'spec/resources/api/v2/transfers/transfer_resource_spec.rb'
     - 'spec/resources/api/v2/tube_rack_resource_spec.rb'
     - 'spec/resources/api/v2/tube_resource_spec.rb'
     - 'spec/sample_manifest_excel/configuration_spec.rb'
@@ -1085,7 +1084,7 @@ RSpec/MultipleExpectations:
     - 'spec/requests/api/v2/transfer_request_collections_spec.rb'
     - 'spec/requests/api/v2/transfer_requests_spec.rb'
     - 'spec/requests/api/v2/transfer_templates_spec.rb'
-    - 'spec/requests/api/v2/transfers/transfers_spec.rb'
+    - 'spec/requests/api/v2/transfers_spec.rb'
     - 'spec/requests/api/v2/tube_purposes_spec.rb'
     - 'spec/requests/api/v2/tube_racks_spec.rb'
     - 'spec/requests/api/v2/tubes_spec.rb'
@@ -1271,7 +1270,7 @@ RSpec/MultipleMemoizedHelpers:
     - 'spec/requests/api/v2/state_changes_spec.rb'
     - 'spec/requests/api/v2/tag_layouts_spec.rb'
     - 'spec/requests/api/v2/transfer_request_collections_spec.rb'
-    - 'spec/requests/api/v2/transfers/transfers_spec.rb'
+    - 'spec/requests/api/v2/transfers_spec.rb'
     - 'spec/requests/api/v2/tube_from_tube_creations_spec.rb'
     - 'spec/requests/api/v2/wells_spec.rb'
     - 'spec/requests/plate_picks_request_spec.rb'
@@ -1434,7 +1433,7 @@ RSpec/NestedGroups:
     - 'spec/requests/api/v2/state_changes_spec.rb'
     - 'spec/requests/api/v2/tag_layouts_spec.rb'
     - 'spec/requests/api/v2/transfer_request_collections_spec.rb'
-    - 'spec/requests/api/v2/transfers/transfers_spec.rb'
+    - 'spec/requests/api/v2/transfers_spec.rb'
     - 'spec/requests/api/v2/tube_from_tube_creations_spec.rb'
     - 'spec/requests/api/v2/users_spec.rb'
     - 'spec/sample_manifest_excel/upload/processor_spec.rb'
@@ -2424,7 +2423,7 @@ Style/StringConcatenation:
 Style/SuperArguments:
   Exclude:
     - 'app/api/model_extensions/order.rb'
-    - 'app/controllers/api/v2/transfers/transfers_controller.rb'
+    - 'app/controllers/api/v2/transfers_controller.rb'
     - 'app/models/broadcast_event/plate_cherrypicked.rb'
     - 'app/models/pipeline.rb'
     - 'app/models/plate_purpose/additional_input.rb'

app/controllers/api/v2/transfers_controller.rb

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+module Api
+  module V2
+    # Provides a JSON API controller for Transfers.
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation.
+    class TransfersController < JSONAPI::ResourceController
+      # By default JSONAPI::ResourceController provides most of the standard behaviour.
+      # However in this case we want to redirect create and update operations to the correct polymorphic type.
+
+      def process_operations(operations)
+        # We need to determine the polymorphic type of the transfer to create based on any template provided.
+        operations.each do |operation|
+          # Neither data nor attributes are guaranteed among the operation options.
+          attributes = operation.options.fetch(:data, {}).fetch(:attributes, {})
+
+          # Skip the operation if it does not contain a transfer template.
+          next unless attributes.key?(:transfer_template_uuid)
+
+          # Get the transfer template and use it to update the context and attributes.
+          template = TransferTemplate.with_uuid(attributes[:transfer_template_uuid]).first
+          operation.options[:context][:polymorphic_type] = template.transfer_class_name
+          attributes[:transfers] = template.transfers if template.transfers.present?
+
+          # Remove the UUID of the transfer template from the attributes.
+          attributes.delete(:transfer_template_uuid)
+        end
+
+        super(operations)
+      end
+    end
+  end
+end

app/models/transfer.rb

@@ -65,3 +65,15 @@ def should_well_not_be_transferred?(well)
     well.nil? or well.aliquots.empty? or well.failed? or well.cancelled?
   end
 end
+
+# Required for the descendants method to work when eager loading is off in test
+require_dependency 'transfer/between_plate_and_tubes'
+require_dependency 'transfer/between_plates_by_submission'
+require_dependency 'transfer/between_plates'
+require_dependency 'transfer/between_specific_tubes'
+require_dependency 'transfer/between_tubes_by_submission'
+require_dependency 'transfer/from_plate_to_specific_tubes_by_pool'
+require_dependency 'transfer/from_plate_to_specific_tubes'
+require_dependency 'transfer/from_plate_to_tube_by_multiplex'
+require_dependency 'transfer/from_plate_to_tube_by_submission'
+require_dependency 'transfer/from_plate_to_tube'

app/resources/api/v2/aliquot_resource.rb

@@ -27,13 +27,13 @@ class AliquotResource < BaseResource
       has_one :library
 
       # Attributes
-      attribute :tag_oligo, readonly: true
-      attribute :tag_index, readonly: true
-      attribute :tag2_oligo, readonly: true
-      attribute :tag2_index, readonly: true
-      attribute :suboptimal, readonly: true
-      attribute :library_type, readonly: true
-      attribute :insert_size_to, readonly: true
+      attribute :tag_oligo, write_once: true
+      attribute :tag_index, write_once: true
+      attribute :tag2_oligo, write_once: true
+      attribute :tag2_index, write_once: true
+      attribute :suboptimal, write_once: true
+      attribute :library_type, write_once: true
+      attribute :insert_size_to, write_once: true
 
       # Filters
 

app/resources/api/v2/bait_library_layout_resource.rb

@@ -22,7 +22,7 @@ class BaitLibraryLayoutResource < BaseResource
       #   @param value [String] The UUID of the plate for this bait library layout.
       #   @return [Void]
       #   @see #plate
-      attribute :plate_uuid
+      attribute :plate_uuid, writeonly: true
 
       def plate_uuid=(value)
         @model.plate = Plate.with_uuid(value).first
@@ -35,7 +35,7 @@ def plate_uuid=(value)
       #   @param value [String] The UUID of the user who created this bait library layout.
       #   @return [Void]
       #   @see #user
-      attribute :user_uuid
+      attribute :user_uuid, writeonly: true
 
       def user_uuid=(value)
         @model.user = User.with_uuid(value).first
@@ -64,17 +64,6 @@ def user_uuid=(value)
       #   @return [PlateResource] The plate for this bait library layout.
       #   @note This relationship is required.
       has_one :plate
-
-      def self.creatable_fields(context)
-        # The layout is generated by the system.
-        # The UUID is set by the system.
-        super - %i[layout uuid]
-      end
-
-      def fetchable_fields
-        # UUIDs for relationships are not fetchable. They should be accessed via the relationship itself.
-        super - %i[plate_uuid user_uuid]
-      end
     end
   end
 end

app/resources/api/v2/barcode_printer_resource.rb

@@ -25,7 +25,7 @@ class BarcodePrinterResource < BaseResource
 
       # @!attribute [r] name
       #   @return [String] the name of the barcode printer.
-      attribute :name
+      attribute :name, readonly: true
 
       # @!attribute [r] uuid
       #   @return [String] the UUID of the barcode printer.

app/resources/api/v2/base_resource.rb

@@ -21,18 +21,27 @@ class BaseResource < JSONAPI::Resource
       Plate.descendants.each { |subclass| model_hint model: subclass, resource: :plate }
       Tube.descendants.each { |subclass| model_hint model: subclass, resource: :tube }
       Request.descendants.each { |subclass| model_hint model: subclass, resource: :request }
+      Transfer.descendants.each { |subclass| model_hint model: subclass, resource: :transfer }
 
-      # This extension allows the readonly property to be used on attributes/relationships
-      # prior to the 0.10 upgrade. This avoids the need to override updatable_fields on
-      # every resource. Readonly does not work on attributes in 0.9 by default
+      # These extensions allow the use of readonly, write_once and writeonly properties.
+      #   readonly - The attribute/relationship can be read but not written to.
+      #   write_once - The attribute/relationship can be written to once on creation but not updated.
+      #   writeonly - The attribute/relationship can be written to but not read.
+      # This avoids the need to override self.creatable_fields, self.updatable_fields and fetchable_fields on every
+      # resource.
+      # readonly does not work on attributes in JSONAPI:Resources 0.9 by default.
       # This can be removed as soon as we update to 0.10, which is currently only in alpha
-      def self.updatable_fields(context)
+
+      def self.creatable_fields(context)
         super - _attributes.select { |_attr, options| options[:readonly] }.keys -
           _relationships.select { |_rel_key, rel| rel.options[:readonly] }.keys
       end
 
-      # This extension allows the writeonly property to be used on attributes/relationships.
-      # This avoids the need to override fetchable_fields on every resource.
+      def self.updatable_fields(context)
+        super - _attributes.select { |_attr, options| options[:readonly] || options[:write_once] }.keys -
+          _relationships.select { |_rel_key, rel| rel.options[:readonly] || rel.options[:write_once] }.keys
+      end
+
       def fetchable_fields
         super - self.class._attributes.select { |_attr, options| options[:writeonly] }.keys -
           self.class._relationships.select { |_rel_key, rel| rel.options[:writeonly] }.keys

app/resources/api/v2/comment_resource.rb

@@ -23,8 +23,8 @@ class CommentResource < BaseResource
       has_one :commentable, polymorphic: true
 
       # Attributes
-      attribute :title, readonly: true
-      attribute :description, readonly: true
+      attribute :title, write_once: true
+      attribute :description, write_once: true
       attribute :created_at, readonly: true
       attribute :updated_at, readonly: true
 

app/resources/api/v2/custom_metadatum_collection_resource.rb

@@ -22,33 +22,19 @@ class CustomMetadatumCollectionResource < BaseResource
 
       # @!attribute [r] uuid
       #   @return [String] The UUID of the collection.
-      attribute :uuid
+      attribute :uuid, readonly: true
 
       # @!attribute [rw] user_id
       #   @return [Int] The ID of the user who created this collection. Can only and must be set on creation.
-      attribute :user_id
+      attribute :user_id, write_once: true
 
       # @!attribute [rw] asset_id
       #   @return [Int] The ID of the labware the metadata corresponds to. Can only and must be set on creation.
-      attribute :asset_id
+      attribute :asset_id, write_once: true
 
       # @!attribute [rw] metadata
       #   @return [Hash] All metadata in this collection.
       attribute :metadata
-
-      ###
-      # Allowable fields (defining read/write permissions for POST and PATCH)
-      ###
-
-      # @return [Array<Symbol>] Fields that can be created in a POST request.
-      def self.creatable_fields(context)
-        super - %i[uuid]
-      end
-
-      # @return [Array<Symbol>] Fields that can be updated in a PATCH request.
-      def self.updatable_fields(context)
-        super - %i[uuid user_id asset_id] # PATCH should only update metadata
-      end
     end
   end
 end

app/resources/api/v2/lot_resource.rb

@@ -28,7 +28,7 @@ class LotResource < BaseResource
 
       # Attributes
       attribute :uuid, readonly: true
-      attribute :lot_number, readonly: true
+      attribute :lot_number, write_once: true
 
       # Filters
 

app/resources/api/v2/lot_type_resource.rb

@@ -24,12 +24,12 @@ class LotTypeResource < BaseResource
       default_includes :uuid_object
 
       # Associations:
-      has_one :target_purpose, readonly: true, class_name: 'Purpose'
+      has_one :target_purpose, write_once: true, class_name: 'Purpose'
 
       # Attributes
       attribute :uuid, readonly: true
-      attribute :name, readonly: true
-      attribute :template_type, readonly: true
+      attribute :name, write_once: true
+      attribute :template_type, write_once: true
 
       # Filters
 

app/resources/api/v2/order_resource.rb

@@ -24,7 +24,7 @@ class OrderResource < BaseResource
 
       # Attributes
       attribute :uuid, readonly: true
-      attribute :request_options, readonly: true
+      attribute :request_options, write_once: true
 
       # Filters
 

app/resources/api/v2/pick_list_resource.rb

@@ -25,8 +25,8 @@ class PickListResource < BaseResource
       # Attributes
       attribute :created_at, readonly: true
       attribute :updated_at, readonly: true
-      attribute :state, readonly: true
-      attribute :links, readonly: true
+      attribute :state, write_once: true
+      attribute :links, write_once: true
 
       attribute :pick_attributes
       attribute :labware_pick_attributes, writeonly: true