return annotation/namespace defs in BEL Script

removed normalization of experiment_context annotation keywords. The
normalized names were in inconsistent with references.annotations
definitions.

integrate next version of bel.rb (0.4.3) to get fixes for
annotation/namespace formats.

refs #95

Author: Anthony Bargnesi

.gemspec

@@ -34,7 +34,7 @@ Gem::Specification.new do |spec|
   # Dependencies
 
   ## bel.rb
-  spec.add_runtime_dependency 'bel',               '0.4.1'
+  spec.add_runtime_dependency 'bel',               '0.4.3'
 
   ## bel.rb plugin - annotation/namespace search
   spec.add_runtime_dependency 'bel-search-sqlite', '0.4.2'

app/openbel/api/resources/evidence_transform.rb

@@ -94,23 +94,11 @@ def structured_annotation(name, value, base_url)
 
         def free_annotation(name, value)
           {
-            :name  => normalize_annotation_name(name),
+            :name  => name,
             :value => value
           }
         end
 
-        def normalize_annotation_name(name, options = {})
-          name_s = name.to_s
-
-          if name_s.empty?
-            nil
-          else
-            name_s.
-              split(%r{[^a-zA-Z0-9]+}).
-              map! { |word| word.capitalize }.
-              join
-          end
-        end
       end
 
       class AnnotationGroupingTransform

app/openbel/api/routes/datasets.rb

@@ -177,6 +177,23 @@ def retrieve_dataset(uri)
 
           dataset
         end
+
+        def keys_to_symbols(obj)
+          case obj
+						when Array
+							obj.inject([]) {|new_array, v|
+                new_array << keys_to_symbols(v)
+                new_array
+              }
+						when Hash
+							obj.inject({}) {|new_hash, (k, v)|
+                new_hash[k.to_sym] = keys_to_symbols(v)
+                new_hash
+              }
+            else
+              obj
+          end
+        end
       end
 
       options '/api/datasets' do
@@ -404,9 +421,7 @@ def retrieve_dataset(uri)
             json_evidence_enum = cursor.lazy.map { |evidence|
               evidence.delete('facets')
               evidence.delete('_id')
-              evidence.keys.each do |key|
-                evidence[key.to_sym] = evidence.delete(key)
-              end
+              evidence = keys_to_symbols(evidence)
               BEL::Model::Evidence.create(evidence)
             }