replace remaining occurences of dataset.add with add_data_entry, adjust parsing code respectively

3 files changed, 12 insertions, 6 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 27457c9..c075790 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -319,7 +319,7 @@ module OpenTox
     # @param [String] feature Compound URI
     # @param [Boolean,Float] value Feature value
     def add (compound,feature,value)
-      LOGGER.warn("dataset.add is deprecated and should not be used any longer")
+      raise("dataset.add is deprecated, use add_data_entry instead")
       self.add_compound(compound)
       self.add_data_entry(compound,feature,value)
     end
@@ -334,6 +334,8 @@ module OpenTox
         @data_entries[compound] = {} unless @data_entries[compound]
         @data_entries[compound][feature] = [] unless @data_entries[compound][feature]
         @data_entries[compound][feature] << value
+      else
+        raise "dataset.add_data_entry> add compound #{compound} first"
       end
     end
 
diff --git a/lib/parser.rb b/lib/parser.rb
index fb67882..1f15621 100644
--- a/lib/parser.rb
+++ b/lib/parser.rb
@@ -206,8 +206,9 @@ module OpenTox
           end
           File.delete(to_delete) if to_delete
           data.each do |id,entry|
-            if entry[:values].size==0
+            if entry[:values].size==0 and !@dataset.compounds.include?(entry[:compound])
               # no feature values add plain compounds
+              #RDF has no support for multiple occurences yet! 
               @dataset.add_compound(entry[:compound])
             else
               entry[:values].each do |value_id|
@@ -222,7 +223,9 @@ module OpenTox
                     value = split.first
                   end
                 end
-                @dataset.add entry[:compound],feature[value_id],value
+                #RDF has no support for multiple occurences yet!
+                @dataset.add_compound(entry[:compound]) unless @dataset.compounds.include?(entry[:compound])
+                @dataset.add_data_entry entry[:compound],feature[value_id],value
               end
             end
           end
@@ -591,6 +594,7 @@ module OpenTox
         end
 
         @data.each do |compound,row|
+          dataset.add_compound(compound)
           unless row.empty?
             row.each do |feature,value|
               if OpenTox::Algorithm::numeric?(value)
@@ -601,7 +605,7 @@ module OpenTox
                 value = value.to_s
               end
               feature_uri = File.join(dataset.uri,"feature",URI.encode(feature))
-              dataset.add(compound, feature_uri, value)
+              dataset.add_data_entry(compound, feature_uri, value)
               #dataset.features[feature_uri][RDF.type] = feature_types(feature)
               #dataset.features[feature_uri][OT.acceptValue] = feature_values(feature)
               if feature_types(feature).include? OT.NumericFeature
diff --git a/lib/serializer.rb b/lib/serializer.rb
index 8d41f05..019d9a2 100644
--- a/lib/serializer.rb
+++ b/lib/serializer.rb
@@ -466,7 +466,7 @@ module OpenTox
         features.sort!
 
         # prepare for subgraphs
-        have_substructures = features.collect{ |id| dataset.features[id][RDF.type].include? OT.Substructure}.compact.uniq
+        have_substructures = features.collect{ |id| (dataset.features[id][RDF.type] and dataset.features[id][RDF.type].include?(OT.Substructure))}.compact.uniq
         if have_substructures.size == 1 && have_substructures[0] 
           features_smarts = features.collect{ |id| "\"" + dataset.features[id][OT.smarts] + "\"" }
         end
@@ -501,7 +501,7 @@ module OpenTox
         feature_quoting = {}
         features.each_with_index { |f,idx|
           feature_quoting[f] = false
-          if dataset.features[f][RDF.type].size == 1 && dataset.features[f][RDF.type][0] == OT.NominalFeature
+          if dataset.features[f][RDF.type] && dataset.features[f][RDF.type].size == 1 && dataset.features[f][RDF.type][0] == OT.NominalFeature
             feature_quoting[f] = true
           end
         }