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/concerns/default_includes_parser.rb

@@ -0,0 +1,16 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    module Concerns
+      module DefaultIncludesParser
+        def parse_include_directives(resource_klass, raw_include)
+          if resource_klass.respond_to?(:format_default_includes)
+            default_includes = resource_klass.format_default_includes
+            raw_include = [raw_include.presence, default_includes.presence].compact.join(',')
+          end
+          super(resource_klass, raw_include)
+        end
+      end
+    end
+  end
+end

app/controllers/api/v2/concerns/include_optional_linkage.rb

@@ -0,0 +1,34 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    module Concerns
+      module IncludeOptionalLinkage
+        def relationship_object(source, relationship, rid, include_data)
+          hash = include_directives.include_directives
+          include_data ||= relationship_exists?(relationship.name.to_sym, hash)
+          include_data ||= relationship.always_include_optional_linkage_data
+          if relationship.is_a?(JSONAPI::Relationship::ToOne)
+            relationship_object_to_one(source, relationship, rid, include_data)
+          elsif relationship.is_a?(JSONAPI::Relationship::ToMany)
+            relationship_object_to_many(source, relationship, rid, include_data)
+          end
+        end
+
+        # https://jsonapi.org/format/#document-resource-object-linkage
+        def relationship_exists?(name, hash)
+          return false unless hash
+          hash.each do |key, value|
+            if key == :include_related && value.is_a?(Hash) && value.key?(name)
+              return true
+            end
+            if value.is_a?(Hash)
+              result = relationship_exists?(name, value)
+              return true if result
+            end
+          end
+          false
+        end
+      end
+    end
+  end
+end

app/controllers/api/v2/concerns/nested_include_expander.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+module Api
+  module V2
+    module Concerns
+      module NestedIncludeExpander
+        def parse_include_directives(resource_klass, raw_include)
+          raw_include ||= ''
+          raw_include = expand_include_parameters(raw_include)
+          super(resource_klass, raw_include)
+        end
+
+        def expand_include_parameters(raw_include)
+          raw_include.split(',').flat_map do |path|
+            path.split('.').each_with_index.map { |_, index| path.split('.')[0..index].join('.') }
+          end.uniq.join(',')
+        end
+      end
+    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

@@ -13,10 +13,10 @@ class AliquotResource < BaseResource
       has_one :study
       has_one :project
       has_one :sample
-      has_one :request
+      has_one :request, always_include_optional_linkage_data: true
       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

@@ -39,49 +39,59 @@ def self.inclusions
         @default_includes || [].freeze
       end
 
-      # Extends the default behaviour to add our default inclusions if provided
-      def self.apply_includes(records, options = {})
+      # TODO: Explain preloading and why we used it here.
+
+      def self.records_for_populate(options = {})
         if @default_includes.present?
-          super(records.preload(*inclusions), options)
+          super(options).preload(*inclusions)
         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
-      # We disable the cops for the shared section to avoid accidental drift
-      # due to auto-correct.
-      # rubocop:disable all
-      def self.resolve_relationship_names_to_relations(resource_klass, model_includes, options = {})
-        case model_includes
-        when Array
-          return model_includes.map { |value| resolve_relationship_names_to_relations(resource_klass, value, options) }
+      def self.format_default_includes
+        @format_default_includes ||= format_inclusions
+      end
+
+      def self.format_inclusions
+        formatted = Array(inclusions).filter_map { |inclusion| format_single_inclusion(inclusion) }
+        formatted.join(',')
+      end
+
+      def self.format_single_inclusion(inclusion, parent = nil)
+        case inclusion
+        when Symbol
+          format_symbol_inclusion(inclusion, parent)
         when Hash
-          model_includes.keys.each do |key|
-            relationship = resource_klass._relationships[key]
-            value = model_includes[key]
-            model_includes.delete(key)
+          format_hash_inclusion(inclusion, parent)
+        when Array
+          format_array_inclusion(inclusion, parent)
+        end
+      end
+
+      def self.format_symbol_inclusion(inclusion, parent)
+        resource_klass_for(inclusion.to_s) # Test that the resource exists
+        [parent, inclusion].compact.join('.') unless _relationship(inclusion).nil?
+      rescue StandardError
+        nil
+      end
 
-            # MODIFICATION BEGINS
-            included_relationships =
-              resolve_relationship_names_to_relations(relationship.resource_klass, value, options)
-            model_includes[relationship.relation_name(options)] =
-              relationship.resource_klass.inclusions + included_relationships
-            # MODIFICATION ENDS
+      def self.format_hash_inclusion(inclusion, parent)
+        result =
+          inclusion.filter_map do |key, value|
+            new_parent = format_single_inclusion(key, parent)
+            next if new_parent.nil?
+            format_single_inclusion(value, new_parent)
           end
-          return model_includes
-        when Symbol
-          relationship = resource_klass._relationships[model_includes]
+        result.join(',') unless result.empty?
+      end
 
-          # MODIFICATION BEGINS
-          # return relationship.relation_name(options)
-          inclusions = relationship.resource_klass.inclusions
-          { relationship.relation_name(options) => inclusions }
-          # MODIFICATION ENDS
-        end
+      def self.format_array_inclusion(inclusion, parent)
+        result = inclusion.filter_map { |value| format_single_inclusion(value, parent) }
+        result.join(',') unless result.empty?
       end
-      # rubocop:enable all
     end
   end
 end
+
+# {k1: {k2: { k3: 'v3' }}} # => "k1.k2.k3.v3"

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/labware_resource.rb

@@ -9,7 +9,7 @@ class LabwareResource < BaseResource
       # is automatically available on plate and tube.
       include Api::V2::SharedBehaviour::Labware
 
-      default_includes :uuid_object, :barcodes
+      default_includes :uuid_object, :barcodes, :purpose
 
       # Custom methods
       # These shouldn't be used for business logic, and a more about

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