find methods for algorithm and model, split method for dataset, feature_type method for model and feature, perform single predicitons in resuce block, add to-html.rb, fix handling of rest-client-wrapper

1 files changed, 74 insertions, 2 deletions

diff --git a/lib/model.rb b/lib/model.rb
index c645bdc..fb266e0 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -24,8 +24,76 @@ module OpenTox
     # Generic OpenTox model class for all API compliant services
     class Generic
       include Model
+      
+      # Find Generic Opentox Model via URI, and loads metadata
+      # @param [String] uri Model URI
+      # @return [OpenTox::Model::Generic] Model instance, nil if model was not found
+      def self.find(uri)
+        model = Generic.new(uri)
+        model.load_metadata
+        if model.metadata==nil or model.metadata.size==0
+          nil
+        else
+          model
+        end
+      end
+    
+       # provides feature type, possible types are "regression" or "classification"
+       # @return [String] feature type, "unknown" if type could not be estimated
+      def feature_type
+        # dynamically perform restcalls if necessary
+        load_metadata if @metadata==nil or @metadata.size==0 or (@metadata.size==1 && @metadata.values[0]==@uri)
+        @dependentVariable = OpenTox::Feature.find( @metadata[OT.dependentVariables] ) unless @dependentVariable
+        
+        [@dependentVariable.feature_type, @metadata[OT.isA], @metadata[DC.title], @uri].each do |type|
+          case type
+          when /(?i)classification/
+            return "classification"
+          when /(?i)regression/
+            return "regression"
+          end
+        end
+        raise "unknown model "+[@dependentVariable.feature_type, @metadata[OT.isA], @metadata[DC.title], @uri].inspect
+      end
+      
+#      def classification?
+#        # TODO test on various services / request to ontology service needed?
+#        # TODO replace bool (for classification/regression) with string value (more types are coming)
+#        #raise "classification?: type: "+@type.to_s+", title: "+@title.to_s+", uri: "+@uri.to_s+" "+((@uri =~ /class/) != nil).to_s
+#        
+#        load_metadata if @metadata==nil or @metadata.size==0 or (@metadata.size==1 && @metadata.values[0]==@uri)
+#        @dependentVariable = OpenTox::Feature.find( @metadata[OT.dependentVariables] ) unless @dependentVariable
+#        case @dependentVariable.feature_type
+#        when "classification"
+#          return true
+#        when "regression"
+#          return false
+#        end
+#        
+#        if @metadata[OT.isA] =~ /(?i)classification/
+#          return true
+#        end
+#        
+#        if @metadata[DC.title] =~ /(?i)classification/
+#          return true
+#        elsif @metadata[DC.title] =~ /(?i)regression/
+#          return false
+#        elsif @uri =~/ntua/ and @metadata[DC.title] =~ /mlr/
+#          return false
+#        elsif @uri =~/tu-muenchen/ and @metadata[DC.title] =~ /regression|M5P|GaussP/
+#          return false
+#        elsif @uri =~/ambit2/ and @metadata[DC.title] =~ /pKa/ || @metadata[DC.title] =~ /Regression|Caco/
+#          return false
+#        elsif @uri =~/majority/
+#          return (@uri =~ /class/) != nil
+#        else
+#          raise "unknown model, uri:'"+@uri.to_s+"' title:'"+@metadata[DC.title].to_s+"'"
+#        end
+#      end
+#    end
+
     end
-   
+    
     # Lazy Structure Activity Relationship class
     class Lazar
 
@@ -101,7 +169,11 @@ module OpenTox
         d = Dataset.new(dataset_uri)
         d.load_compounds
         d.compounds.each do |compound_uri|
-          predict(compound_uri,false,subjectid)
+          begin
+            predict(compound_uri,false,subjectid)
+          rescue => ex
+            LOGGER.warn "prediction for compound "+compound_uri.to_s+" failed: "+ex.message
+          end
         end
         @prediction_dataset.save(subjectid)
         @prediction_dataset