dataset serialization to all bel.rb translators

updated dependencies to support all bel.rb translators

refs #99

Author: Anthony Bargnesi

Diff for: .gemspec

@@ -34,7 +34,16 @@ Gem::Specification.new do |spec|
   # Dependencies
 
   ## bel.rb
-  spec.add_runtime_dependency 'bel',               '0.4.3'
+  spec.add_runtime_dependency 'bel',               '0.5.0'
+
+  ## bel.rb translator dependencies
+  spec.add_runtime_dependency 'json-ld',           '1.99.0'
+  spec.add_runtime_dependency 'rdf-json',          '1.99.0'
+  spec.add_runtime_dependency 'rdf-rdfa',          '1.99.0'
+  spec.add_runtime_dependency 'rdf-rdfxml',        '1.99.0'
+  spec.add_runtime_dependency 'rdf-trig',          '1.99.0.1'
+  spec.add_runtime_dependency 'rdf-trix',          '1.99.0'
+  spec.add_runtime_dependency 'rdf-turtle',        '1.99.0'
 
   ## bel.rb plugin - annotation/namespace search
   spec.add_runtime_dependency 'bel-search-sqlite', '0.4.2'

Diff for: app/openbel/api/helpers/translators.rb

@@ -0,0 +1,71 @@
+require 'bel'
+
+module OpenBEL
+  module Helpers
+
+    # Helpers for translator functionality based on user's requested media
+    # type.
+    module Translators
+
+      # Patch {::Sinatra::Helpers::Stream} to respect the +puts+ and +write+
+      # method. This is necessary because the RDF.rb writers will call theseon
+      # the IO object (in this case {::Sinatra::Helpers::Stream}).
+      class ::Sinatra::Helpers::Stream
+
+        def puts(*args)
+          self << (
+            args.map { |string| "#{string.encode(Encoding::UTF_8)}\n" }.join
+          )
+        end
+
+        def write(string)
+          self << string.encode(Encoding::UTF_8)
+        end
+
+        # flush is a no-op; flushing is handled by sinatra/rack server
+        def flush; end
+      end
+
+      # Find a bel.rb translator plugin by value. The value is commonly the
+      # id, file extension, or media type associated with the translator
+      # plugin.
+      #
+      # @param  [#to_s] value     used to look up translator plugin registered
+      #        with bel.rb
+      # @return [BEL::Translator] the translator instance; or +nil+ if one
+      #         cannot be found
+      def self.for(value)
+        BEL.translator(symbolize_value(value))
+      end
+
+      def self.plugin_for(value)
+        BEL::Translator::Plugins.for(symbolize_value(value))
+      end
+
+      def self.requested_translator_plugin(request, params)
+        if params && params[:format]
+          self.plugin_for(params[:format])
+        else
+          request.accept.map { |accept_entry|
+            self.plugin_for(accept_entry)
+          }.compact.first
+        end
+      end
+
+      def self.requested_translator(request, params)
+        if params && params[:format]
+          self.for(params[:format])
+        else
+          request.accept.map { |accept_entry|
+            self.for(accept_entry)
+          }.compact.first
+        end
+      end
+
+      def self.symbolize_value(value)
+        value.to_s.to_sym
+      end
+      private_class_method :symbolize_value
+    end
+  end
+end

Diff for: app/openbel/api/routes/base.rb

@@ -21,14 +21,14 @@ class Base < Sinatra::Application
       include OpenBEL::Resource::Namespaces
       include OpenBEL::Schemas
 
-      DEFAULT_CONTENT_TYPE   = 'application/hal+json'
-      SPOKEN_CONTENT_TYPES   = %w[application/hal+json application/json]
+      DEFAULT_CONTENT_TYPE    = 'application/hal+json'
+      DEFAULT_CONTENT_TYPE_ID = :hal
+      SPOKEN_CONTENT_TYPES    = %w[application/hal+json application/json]
       SPOKEN_CONTENT_TYPES.concat(
         BEL::Translator.plugins.values.flat_map { |p| p.media_types.map(&:to_s) }
       )
-
-      SCHEMA_BASE_URL        = 'http://next.belframework.org/schemas/'
-      RESOURCE_SERIALIZERS   = {
+      SCHEMA_BASE_URL         = 'http://next.belframework.org/schemas/'
+      RESOURCE_SERIALIZERS    = {
         :annotation                 => AnnotationResourceSerializer,
         :annotation_collection      => AnnotationCollectionSerializer,
         :annotation_value           => AnnotationValueResourceSerializer,
@@ -80,6 +80,16 @@ def schema_url(name)
           SCHEMA_BASE_URL + "#{name}.schema.json"
         end
 
+        def wants_default?
+          if params[:format]
+            return params[:format] == DEFAULT_CONTENT_TYPE
+          end
+
+          request.accept.any? { |accept_entry|
+            accept_entry.to_s == DEFAULT_CONTENT_TYPE
+          }
+        end
+
         def validate_media_type!(content_type, options = {})
           ctype = request.content_type
           valid = ctype.start_with? content_type

Diff for: app/openbel/api/routes/datasets.rb

@@ -6,6 +6,7 @@
 require 'openbel/api/evidence/facet_filter'
 require_relative '../resources/evidence_transform'
 require_relative '../helpers/pager'
+require_relative '../helpers/translators'
 
 module OpenBEL
   module Routes
@@ -37,9 +38,6 @@ def initialize(app)
           :tdb_directory => OpenBEL::Settings[:resource_rdf][:jena][:tdb_directory]
         )
 
-        # Load RDF monkeypatches.
-        BEL::Translator.plugins[:rdf].create_translator
-
         # Annotations using RdfRepository
         annotations = BEL::Resource::Annotations.new(@rr)
         @annotation_transform = AnnotationTransform.new(annotations)
@@ -365,18 +363,12 @@ def keys_to_symbols(obj)
         filtered_total    = @api.count_evidence(filters)
         page_results      = @api.find_dataset_evidence(dataset, filters, start, size, faceted, max_values_per_facet)
 
-        accept_type = request.accept.find { |accept_entry|
-          ACCEPTED_TYPES.values.include?(accept_entry.to_s)
-        }
-        accept_type ||= DEFAULT_TYPE
+        translator        = Translators.requested_translator(request, params)
+        translator_plugin = Translators.requested_translator_plugin(request, params)
 
-        if params[:format]
-          translator  = BEL::Translator.plugins[params[:format].to_sym]
-          halt 501 if !translator || translator.id == :rdf
-          accept_type = [translator.media_types].flatten.first
-        end
-
-        if accept_type == DEFAULT_TYPE
+        # Serialize to HAL if they [Accept]ed it, specified it as ?format, or
+        # no translator was found to match request.
+        if wants_default? || !translator
           evidence          = page_results[:cursor].map { |item|
             item.delete('facets')
             item
@@ -410,24 +402,21 @@ def keys_to_symbols(obj)
 
           render_collection(evidence, :evidence, options)
         else
-          out_translator = BEL.translator(accept_type)
-          extension      = ACCEPTED_TYPES.key(accept_type.to_s)
+          extension = translator_plugin.file_extensions.first
 
-          response.headers['Content-Type'] = accept_type
+          response.headers['Content-Type'] = translator_plugin.media_types.first
           status 200
           attachment "#{dataset[:identifier].gsub(/[^\w]/, '_')}.#{extension}"
           stream :keep_open do |response|
             cursor             = page_results[:cursor]
-            json_evidence_enum = cursor.lazy.map { |evidence|
+            dataset_evidence = cursor.lazy.map { |evidence|
               evidence.delete('facets')
               evidence.delete('_id')
               evidence = keys_to_symbols(evidence)
               BEL::Model::Evidence.create(evidence)
             }
 
-            out_translator.write(json_evidence_enum) do |converted_evidence|
-              response << converted_evidence
-            end
+            translator.write(dataset_evidence, response)
           end
         end
       end