Merge branch 'development' of github.com:opentox/opentox-ruby into development

2 files changed, 44 insertions, 22 deletions

diff --git a/lib/model.rb b/lib/model.rb
index 1ff9df1..f1a8dc9 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -50,38 +50,49 @@ module OpenTox
         @predicted_variable
       end
 
+      def predicted_variables( subjectid )
+        load_predicted_variables( subjectid, false ) unless @predicted_variables
+        @predicted_variables
+      end
+
       def predicted_confidence( subjectid )
         load_predicted_variables( subjectid ) unless @predicted_confidence
         @predicted_confidence
       end
   
       private
-      def load_predicted_variables( subjectid=nil )
+      def load_predicted_variables( subjectid=nil, use_confidence=true )
         load_metadata(subjectid) if @metadata==nil or @metadata.size==0 or (@metadata.size==1 && @metadata.values[0]==@uri)
         if @metadata[OT.predictedVariables]
           predictedVariables = @metadata[OT.predictedVariables]
           if predictedVariables.is_a?(Array)
             if (predictedVariables.size==1)
               @predicted_variable = predictedVariables[0]
-            elsif (predictedVariables.size==2)
+            elsif (predictedVariables.size>=2)
               # PENDING identify confidence
-              conf_index = -1
-              predictedVariables.size.times do |i|
-                f = OpenTox::Feature.find(predictedVariables[i])
-                conf_index = i if f.metadata[DC.title]=~/(?i)confidence/
+              if use_confidence
+                conf_index = -1
+                predictedVariables.size.times do |i|
+                  f = OpenTox::Feature.find(predictedVariables[i])
+                  conf_index = i if f.metadata[DC.title]=~/(?i)confidence/
+                end
+                raise "could not estimate predicted variable from model: '"+uri.to_s+
+                  "', number of predicted-variables==2, but no confidence found" if conf_index==-1
+              end
+              if (predictedVariables.size==2) && use_confidence
+                @predicted_variable = predictedVariables[1-conf_index]
+                @predicted_confidence = predictedVariables[conf_index]
+              else
+                @predicted_variables = predictedVariables
               end
-              raise "could not estimate predicted variable from model: '"+uri.to_s+
-                "', number of predicted-variables==2, but no confidence found" if conf_index==-1
-              @predicted_variable = predictedVariables[1-conf_index]
-              @predicted_confidence = predictedVariables[conf_index]
             else
-              raise "could not estimate predicted variable from model: '"+uri.to_s+"', number of predicted-variables > 2"  
+              raise "could not estimate predicted variable from model: '"+uri.to_s+"', number of predicted-variables == 0"  
             end
           else
             raise "could not estimate predicted variable from model: '"+uri.to_s+"', predicted-variables is no array"
           end        
         end
-        raise "could not estimate predicted variable from model: '"+uri.to_s+"'" unless @predicted_variable
+        raise "could not estimate predicted variable from model: '"+uri.to_s+"'" unless (@predicted_variable || @predicted_variables)
       end
     end
 
diff --git a/lib/parser.rb b/lib/parser.rb
index 8fa5847..4ee4a22 100644
--- a/lib/parser.rb
+++ b/lib/parser.rb
@@ -86,7 +86,11 @@ module OpenTox
       # @param [String] rdf
       # @param [String] type of the info (e.g. OT.Task, OT.ErrorReport) needed to get the subject-uri
       # @return [Owl] with uri and metadata set 
-      def self.from_rdf( rdf, type )
+      def self.from_rdf( rdf, type, allow_multiple = false )
+
+        uris = Array.new
+        owls = Array.new
+
         # write to file and read convert with rapper into tripples
         file = Tempfile.new("ot-rdfxml")
         file.puts rdf
@@ -99,20 +103,27 @@ module OpenTox
         triples.each_line do |line|
           triple = line.to_triple
           if triple[1] == RDF['type'] and triple[2]==type
-             raise "uri already set, two uris found with type: "+type.to_s if uri
+             if !allow_multiple
+               raise "uri already set, two uris found with type: "+type.to_s if uri
+             end
              uri = triple[0]
+             uris << uri
           end
         end
         File.delete(file.path)
+
         # load metadata
-        metadata = {}
-        triples.each_line do |line|
-          triple = line.to_triple
-          metadata[triple[1]] = triple[2].split('^^').first if triple[0] == uri and triple[1] != RDF['type']
-        end
-        owl = Owl::Generic.new(uri)
-        owl.metadata = metadata
-        owl
+        uris.each { |uri|
+          metadata = {}
+          triples.each_line do |line|
+            triple = line.to_triple
+            metadata[triple[1]] = triple[2].split('^^').first if triple[0] == uri and triple[1] != RDF['type']
+          end
+          owl = Owl::Generic.new(uri)
+          owl.metadata = metadata
+          owls << owl
+        }
+        allow_multiple ? owls : owls[0]
       end
       
       # Generic parser for all OpenTox classes