Update workflow context to point to bioschemas and add dct namespace

lib/seek/bio_schema/resource_decorators/base_decorator.rb

@@ -8,10 +8,11 @@ class BaseDecorator
         include ActionView::Helpers::SanitizeHelper
         include Seek::Util.routes
 
-        attr_reader :resource
+        attr_reader :resource, :additional_context
 
         def initialize(resource)
           @resource = resource
+          @additional_context = {}
         end
 
         def mappings
@@ -26,7 +27,10 @@ def attributes
 
         # The @context to be used for the JSON-LD
         def context
-          Seek::BioSchema::Serializer::SCHEMA_ORG
+          {
+            '@vocab' => Seek::BioSchema::Serializer::SCHEMA_ORG,
+            dct: Seek::BioSchema::Serializer::DCT
+          }
         end
 
         # The schema.org @type .
@@ -78,10 +82,14 @@ def resource_url(resource, opts = {})
           #   associated_items member: :people
           #   create a method 'member' that returns a collection of Hash objects containing the
           #   minimal definition for each item resulting from calling 'people' on the resource
+          # Also adds to the additional_context the context for each item in the associated resources
           def associated_items(**pairs)
             pairs.each do |method, collection|
               define_method(method) do
-                mini_definitions(send(collection)) if respond_to?(collection)
+                return unless respond_to?(collection)
+
+                @additional_context.merge!(additional_contexts(send(collection)))
+                mini_definitions(send(collection))
               end
             end
           end
@@ -116,6 +124,19 @@ def mini_definitions(collection)
           mini_col
         end
 
+        def additional_contexts(collection)
+          return {} if collection.empty?
+
+          ctx = {}
+          collection.each do |item|
+            next if item.respond_to?(:public?) && !item.public?
+
+            decorator = Seek::BioSchema::ResourceDecorators::Factory.instance.get(item)
+            ctx.merge!(decorator.context)
+          end
+          ctx
+        end
+
         def respond_to_missing?(name, include_private = false)
           resource.respond_to?(name,
                                include_private) || resource.is_a_version? && resource.parent.respond_to?(name,

lib/seek/bio_schema/resource_decorators/event.rb

@@ -4,6 +4,9 @@ module ResourceDecorators
       # Decorator that provides extensions for a Event
       class Event < Thing
         EVENT_PROFILE = 'https://bioschemas.org/profiles/Event/0.3-DRAFT'.freeze
+        HOST_INSTITUTION_PROPERTY = 'https://bioschemas.org/terms/hostInstitution'.freeze
+        CONTACT_PROPERTY = 'https://bioschemas.org/terms/contact'.freeze
+        EVENT_TYPE_PROPERTY = 'https://bioschemas.org/terms/eventType'.freeze
 
         associated_items contact: :contributors,
                          host_institution: :projects,
@@ -19,6 +22,14 @@ class Event < Thing
                         created_at: :dateCreated,
                         updated_at: :dateModified
 
+        def context
+          super.merge(
+            contact: CONTACT_PROPERTY,
+            eventType: EVENT_TYPE_PROPERTY,
+            hostInstitution: HOST_INSTITUTION_PROPERTY
+          )
+        end
+
         def conformance
           EVENT_PROFILE
         end

lib/seek/bio_schema/resource_decorators/person.rb

@@ -12,7 +12,7 @@ class Person < Thing
                         last_name: :familyName,
                         image: :image,
                         member_of: :memberOf,
-                        orcid: :orcid,
+                        orcid: :identifier,
                         works_for: :worksFor
 
         def conformance

lib/seek/bio_schema/resource_decorators/sample.rb

@@ -6,6 +6,11 @@ class Sample < Thing
         schema_mappings properties: :additionalProperty
 
         SAMPLE_PROFILE = 'https://bioschemas.org/profiles/Sample/0.2-RELEASE-2018_11_10/'.freeze
+        SAMPLE_TYPE = 'https://bioschemas.org/types/Sample/0.2-DRAFT-2018_11_09'.freeze
+
+        def context
+          super.merge(Sample: SAMPLE_TYPE)
+        end
 
         def schema_type
           'Sample'
@@ -31,7 +36,7 @@ def describe_attribute(attribute)
             'value' => value.to_s
           }
           if attribute.pid
-            data['propertyId'] = attribute.pid
+            data['propertyID'] = attribute.pid
           end
           resolved = attribute.resolve(value)
           data['identifier'] = resolved if resolved

lib/seek/bio_schema/resource_decorators/sop.rb

@@ -3,10 +3,19 @@ module BioSchema
     module ResourceDecorators
       # Decorator that provides extensions for a Sop
       class Sop < CreativeWork
+        LAB_PROTOCOL_TYPE = 'https://bioschemas.org/types/LabProtocol/0.5-DRAFT'.freeze
+        COMPUTATIONAL_TOOL_PROPERTY = 'https://bioschemas.org/terms/computationalTool'.freeze
 
         associated_items computational_tool: :workflows
         schema_mappings computational_tool: :computationalTool
 
+        def context
+          super.merge(
+            LabProtocol: LAB_PROTOCOL_TYPE,
+            computationalTool: COMPUTATIONAL_TOOL_PROPERTY
+          )
+        end
+
         def schema_type
           'LabProtocol'
         end

lib/seek/bio_schema/resource_decorators/workflow.rb

@@ -4,14 +4,26 @@ module ResourceDecorators
       # Decorator that provides extensions for a Workflow
       class Workflow < CreativeWork
         WORKFLOW_PROFILE = 'https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/'.freeze
-
+        WORKFLOW_TYPE = 'https://bioschemas.org/terms/ComputationalWorkflow'.freeze
         FORMALPARAMETER_PROFILE = 'https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/'.freeze
+        FORMALPARAMETER_TYPE = 'https://bioschemas.org/terms/FormalParameter'.freeze
+        INPUT_PROPERTY = 'https://bioschemas.org/terms/input'.freeze
+        OUTPUT_PROPERTY = 'https://bioschemas.org/terms/output'.freeze
 
         schema_mappings programming_language: :programmingLanguage,
                         inputs: :input,
                         outputs: :output,
                         sd_publisher: :sdPublisher
 
+        def context
+          super.merge(
+            input: INPUT_PROPERTY,
+            output: OUTPUT_PROPERTY,
+            ComputationalWorkflow: WORKFLOW_TYPE,
+            FormalParameter: FORMALPARAMETER_TYPE
+          )
+        end
+
         def contributors
           [contributor]
         end

lib/seek/bio_schema/serializer.rb

@@ -7,7 +7,8 @@ class Serializer
       include ActionView::Helpers::SanitizeHelper
       attr_reader :resource
 
-      SCHEMA_ORG = 'https://schema.org'
+      SCHEMA_ORG = 'https://schema.org/'.freeze
+      DCT = 'http://purl.org/dc/terms/'.freeze
 
       # initialise with a resource
       def initialize(resource)
@@ -23,6 +24,8 @@ def json_representation
           representation['dct:conformsTo'] = { '@id' => resource_decorator.conformance }
         end
         representation = representation.merge(attributes_json)
+        # After attributes_json has been generated, additional context will be populated
+        representation['@context'].merge!(resource_decorator.additional_context)
         representation.deep_stringify_keys
       end
 

test/unit/bio_schema/data_dump_test.rb

@@ -97,7 +97,7 @@ class DataDumpTest < ActiveSupport::TestCase
 
     assert_equal 'workflows-bioschemas-dump.jsonld', dump.file_name
     assert dump.exists?
-    assert_in_delta 3800, dump.size, 500
+    assert_in_delta 5000, dump.size, 500
     assert_in_delta Time.now, dump.date_modified, 60
   end
 

test/unit/bio_schema/decorator_test.rb

@@ -8,9 +8,13 @@ class DecoratorTest < ActiveSupport::TestCase
 
     decorator = Seek::BioSchema::ResourceDecorators::Thing.new(data_file)
     identifier = "http://localhost:3000/data_files/#{data_file.id}"
+    context = {
+      '@vocab' => Seek::BioSchema::Serializer::SCHEMA_ORG,
+      :dct => Seek::BioSchema::Serializer::DCT
+    }
     assert_equal identifier, decorator.identifier
     assert_equal identifier, decorator.url
-    assert_equal Seek::BioSchema::Serializer::SCHEMA_ORG, decorator.context
+    assert_equal context, decorator.context
     assert_equal %w[blue green red], decorator.keywords.split(',').collect(&:strip).sort
 
     properties = decorator.attributes.collect(&:property).collect(&:to_s).sort