Dpl936 json api - 2

Gemfile

@@ -62,7 +62,7 @@ group :default do
   # https://github.com/JamesGlover/sequencescape/tree/depfu/update/jsonapi-resources-0.9.5
   # but not only is there a failing test, but performance was tanking in a few places
   # due to not correctly eager loading dependencies on nested resources.
-  gem 'jsonapi-resources', '0.9.0'
+  gem 'jsonapi-resources' #, '0.9.0'
 
   # Wraps bunny with connection pooling ad consumer process handling
   gem 'sanger_warren'

Gemfile.lock

@@ -227,7 +227,7 @@ GEM
       mini_magick (>= 4.9.5, < 5)
       ruby-vips (>= 2.0.17, < 3)
     json (2.6.3)
-    jsonapi-resources (0.9.0)
+    jsonapi-resources (0.10.7)
       activerecord (>= 4.1)
       concurrent-ruby
       railties (>= 4.1)
@@ -241,7 +241,7 @@ GEM
     listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    loofah (2.21.4)
+    loofah (2.22.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     mail (2.8.1)
@@ -257,7 +257,7 @@ GEM
     mime-types-data (3.2023.0808)
     mini_magick (4.12.0)
     mini_mime (1.1.5)
-    mini_portile2 (2.8.4)
+    mini_portile2 (2.8.5)
     minitest (5.20.0)
     minitest-profiler (0.0.2)
       activesupport (>= 4.1.0)
@@ -353,7 +353,7 @@ GEM
       rake (>= 0.8.7)
       thor (>= 0.20.3, < 2.0)
     rainbow (3.1.1)
-    rake (13.0.6)
+    rake (13.1.0)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
@@ -482,7 +482,7 @@ GEM
     sys-uname (1.2.3)
       ffi (~> 1.1)
     test-prof (1.3.0)
-    thor (1.2.2)
+    thor (1.3.0)
     thread_safe (0.3.6)
     tilt (2.3.0)
     timecop (0.9.8)
@@ -555,7 +555,7 @@ DEPENDENCIES
   flipper-ui (~> 0.25.0)
   formtastic
   json
-  jsonapi-resources (= 0.9.0)
+  jsonapi-resources
   jsonapi-resources-matchers
   knapsack_pro
   launchy

app/controllers/api/v2/ancestors_controller.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Api
+  module V2
+    # Provides a JSON API controller for Assets
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
+    class AncestorsController < JSONAPI::ResourceController
+      # By default JSONAPI::ResourceController provides most the standard
+      # behaviour, and in many cases this file may be left empty.
+    end
+  end
+end

app/controllers/api/v2/children_controller.rb

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    class ChildrenController < JSONAPI::ResourceController
+    end
+  end
+end

app/controllers/api/v2/downstream_assets_controller.rb

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    class DownstreamAssetsController < JSONAPI::ResourceController
+    end
+  end
+end

app/controllers/api/v2/parents_controller.rb

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    class ParentsController < JSONAPI::ResourceController
+    end
+  end
+end

app/controllers/api/v2/qc_assays_controller.rb

@@ -8,11 +8,8 @@ def create
         @qc_result_factory = QcResultFactory.new(qc_assay_params)
         if @qc_result_factory.valid?
           @qc_result_factory.save
-          render json:
-                   JSONAPI::ResourceSerializer
-                     .new(QcAssayResource)
-                     .serialize_to_hash(QcAssayResource.new(@qc_result_factory.qc_assay, nil)),
-                 status: :created
+
+          render json: serialize_resource(QcAssayResource.new(@qc_result_factory.qc_assay, nil)), status: :created
         else
           render json: { errors: @qc_result_factory.errors }, status: :unprocessable_entity
         end

app/controllers/api/v2/qc_results_controller.rb

@@ -10,8 +10,8 @@ def create
         if @qc_result_factory.valid?
           @qc_result_factory.save
           @qc_result_resources = @qc_result_factory.qc_results.map { |qc_result| QcResultResource.new(qc_result, nil) }
-          render json: JSONAPI::ResourceSerializer.new(QcResultResource).serialize_to_hash(@qc_result_resources),
-                 status: :created
+
+          render json: serialize_array(@qc_result_resources), status: :created
         else
           render json: @qc_result_factory.errors, status: :unprocessable_entity
         end

app/controllers/api/v2/source_receptacles_controller.rb

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    class SourceReceptaclesController < JSONAPI::ResourceController
+    end
+  end
+end

app/controllers/api/v2/upstream_assets_controller.rb

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    class UpstreamAssetsController < JSONAPI::ResourceController
+    end
+  end
+end

app/resources/api/v2/aliquot_resource.rb

@@ -16,7 +16,7 @@ class AliquotResource < BaseResource
       has_one :request
       has_one :receptacle
       has_one :tag
-      has_one :tag2
+      has_one :tag2, class_name: 'Tag'
 
       # Attributes
       attribute :tag_oligo, readonly: true

app/resources/api/v2/ancestor_resource.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    # Provides a JSON API representation of Ancestor
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
+    class AncestorResource < LabwareResource
+      filter :purpose_name
+    end
+  end
+end

app/resources/api/v2/base_resource.rb

@@ -40,13 +40,13 @@ def self.inclusions
       end
 
       # Extends the default behaviour to add our default inclusions if provided
-      def self.apply_includes(records, options = {})
-        if @default_includes.present?
-          super(records.preload(*inclusions), options)
-        else
-          super
-        end
-      end
+      #def self.apply_includes(records, options = {})
+      #  if @default_includes.present?
+      #    super(records.preload(*inclusions), options)
+      #  else
+      #    super
+      #  end
+      #end
 
       # The majority of this is lifted from JSONAPI::Resource
       # We've had to modify the when Symbol chunk to handle nested includes

app/resources/api/v2/child_resource.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    # Provides a JSON API representation of Child
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
+    class ChildResource < JSONAPI::Resource
+    end
+  end
+end

app/resources/api/v2/comment_resource.rb

@@ -16,8 +16,8 @@ class CommentResource < BaseResource
       has_one :commentable, polymorphic: true
 
       # Attributes
-      attribute :title, readonly: true
-      attribute :description, readonly: true
+      attribute :title
+      attribute :description
       attribute :created_at, readonly: true
       attribute :updated_at, readonly: true
 

app/resources/api/v2/descendant_resource.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    # Provides a JSON API representation of Descendant
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
+    class DescendantResource < JSONAPI::Resource
+    end
+  end
+end

app/resources/api/v2/downstream_asset_resource.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    # Provides a JSON API representation of DownstreamAsset
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
+    class DownstreamAssetResource < JSONAPI::Resource
+    end
+  end
+end

app/resources/api/v2/parent_resource.rb

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+class ParentResource < JSONAPI::Resource
+  def self.records(options = {})
+    class_name = options[:_relation_helper_options][:join_manager].resource_klass
+    class_name.to_s.demodulize.sub(/Resource$/, '').constantize.all
+  end
+end

app/resources/api/v2/plate_resource.rb

@@ -18,7 +18,7 @@ class PlateResource < BaseResource
       default_includes :uuid_object, :barcodes, :plate_purpose, :transfer_requests
 
       # Associations:
-      has_many :wells, readonly: true
+      has_many :wells
 
       # Attributes
       attribute :number_of_rows, readonly: true, delegate: :height

app/resources/api/v2/project_resource.rb

@@ -2,6 +2,8 @@
 
 module Api
   module V2
+    # Provides a JSON API representation of Project
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
     class ProjectResource < BaseResource
       immutable # comment to make the resource mutable
 

app/resources/api/v2/sample_resource.rb

@@ -13,7 +13,7 @@ class SampleResource < BaseResource
       has_one :sample_manifest
 
       has_many :studies
-      has_many :component_samples
+      has_many :component_samples, class_name: 'Sample'
 
       attribute :name
       attribute :sanger_sample_id

app/resources/api/v2/shared_behaviour/labware.rb

@@ -12,7 +12,7 @@ module Api::V2::SharedBehaviour::Labware
 
   included do
     # Associations:
-    has_one :purpose, readonly: true, foreign_key: :plate_purpose_id, class_name: 'Purpose'
+    has_one :purpose, foreign_key: :plate_purpose_id, class_name: 'Purpose'
     has_one :custom_metadatum_collection, foreign_key_on: :related
 
     has_many :samples, readonly: true
@@ -24,13 +24,15 @@ module Api::V2::SharedBehaviour::Labware
     # expect a mix of plates and tubes. If we want to eager load their
     # contents we use the generic 'receptacles' association.
     has_many :receptacles, readonly: true, polymorphic: true
-    has_many :ancestors, readonly: true, polymorphic: true
-    has_many :descendants, readonly: true, polymorphic: true
-    has_many :parents, readonly: true, polymorphic: true
-    has_many :children, readonly: true, polymorphic: true
-    has_many :child_plates, readonly: true
-    has_many :child_tubes, readonly: true
-    has_many :direct_submissions, readonly: true
+    has_many :ancestors, readonly: true, class_name: 'Labware' #, polymorphic: true
+    has_many :descendants, readonly: true, class_name: 'Labware' #polymorphic: true
+
+    has_many :parents, readonly: true, class_name: 'Labware'
+    has_many :children, readonly: true, class_name: 'Labware'
+
+    has_many :child_plates, readonly: true, class_name: 'Plate'
+    has_many :child_tubes, readonly: true, class_name: 'Tube'
+    has_many :direct_submissions, readonly: true, class_name: 'Submission'
     has_many :state_changes, readonly: true
 
     # Attributes

app/resources/api/v2/shared_behaviour/receptacle.rb

@@ -17,23 +17,23 @@ module Api::V2::SharedBehaviour::Receptacle
     has_many :studies, readonly: true
     has_many :projects, readonly: true
 
-    has_many :requests_as_source, readonly: true
-    has_many :requests_as_target, readonly: true
+    has_many :requests_as_source, readonly: true, class_name: 'Request'
+    has_many :requests_as_target, readonly: true, class_name: 'Request'
     has_many :qc_results, readonly: true
     has_many :aliquots, readonly: true
 
     has_many :downstream_assets, readonly: true, polymorphic: true
-    has_many :downstream_wells, readonly: true
-    has_many :downstream_plates, readonly: true
-    has_many :downstream_tubes, readonly: true
+    has_many :downstream_wells, readonly: true, class_name: 'Well'
+    has_many :downstream_plates, readonly: true, class_name: 'Plate'
+    has_many :downstream_tubes, readonly: true, class_name: 'Tube'
 
     has_many :upstream_assets, readonly: true, polymorphic: true
-    has_many :upstream_wells, readonly: true
-    has_many :upstream_plates, readonly: true
-    has_many :upstream_tubes, readonly: true
+    has_many :upstream_wells, readonly: true, class_name: 'Well'
+    has_many :upstream_plates, readonly: true, class_name: 'Plate'
+    has_many :upstream_tubes, readonly: true, class_name: 'Tube'
 
-    has_many :transfer_requests_as_source, readonly: true
-    has_many :transfer_requests_as_target, readonly: true
+    has_many :transfer_requests_as_source, readonly: true, class_name: 'TransferRequest'
+    has_many :transfer_requests_as_target, readonly: true, class_name: 'TransferRequest'
 
     # Attributes
     attribute :uuid, readonly: true

app/resources/api/v2/source_receptacle_resource.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    # Provides a JSON API representation of SourceReceptacle
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
+    class SourceReceptacleResource < JSONAPI::Resource
+    end
+  end
+end

app/resources/api/v2/state_change_resource.rb

@@ -2,6 +2,8 @@
 
 module Api
   module V2
+    # Provides a JSON API representation of StateChange
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
     class StateChangeResource < BaseResource
       immutable # comment to make the resource mutable
 

app/resources/api/v2/study_resource.rb

@@ -2,6 +2,8 @@
 
 module Api
   module V2
+    # Provides a JSON API representation of Study
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
     class StudyResource < BaseResource
       immutable # comment to make the resource mutable
 

app/resources/api/v2/tag_layout_template_resource.rb

@@ -15,7 +15,7 @@ class TagLayoutTemplateResource < BaseResource
 
       # Associations:
       has_one :tag_group
-      has_one :tag2_group
+      has_one :tag2_group, class_name: 'TagGroup'
 
       # Attributes
       attribute :uuid, readonly: true

app/resources/api/v2/tag_resource.rb

@@ -12,7 +12,7 @@ class TagResource < BaseResource
       # model_name / model_hint if required
 
       # Associations:
-      has_one :tag_group
+      has_one :tag_group, class_name: 'TagGroup'
 
       # Attributes
       attribute :oligo, readonly: true

app/resources/api/v2/tube_rack_resource.rb

@@ -21,6 +21,7 @@ class TubeRackResource < BaseResource
 
       # Associations:
       has_many :racked_tubes
+      delegate :racked_tubes, to: :_model
       has_many :comments, readonly: true
       has_one :purpose, foreign_key: :plate_purpose_id
 

app/resources/api/v2/tube_resource.rb

@@ -15,7 +15,7 @@ class TubeResource < BaseResource
 
       # Associations:
       has_many :aliquots, readonly: true
-      has_many :transfer_requests_as_target, readonly: true
+      has_many :transfer_requests_as_target, readonly: true, class_name: 'TransferRequest'
       has_one :receptacle, readonly: true, foreign_key_on: :related
 
       # Attributes

app/resources/api/v2/upstream_asset_resource.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    # Provides a JSON API representation of UpstreamAsset
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
+    class UpstreamAssetResource < JSONAPI::Resource
+    end
+  end
+end