rdf tools turned to dynamic

2 files changed, 9 insertions, 9 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 8d135a6..4351dc5 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -38,14 +38,14 @@ module OpenTox
       # AM: read ordered dataset from RDF
       if ordered
         @uri = s[0].uri.to_s if have_rdf # AM: must rewrite URI
-        @compounds = OpenTox::Dataset.find_compounds_rdf(@rdf)
-        @features = OpenTox::Dataset.find_features_rdf(@rdf)
+        @compounds = find_compounds_rdf
+        @features = find_features_rdf
         numeric_features = @features.collect{|f| 
           f.get
           f[RDF.type].include?(RDF::OT.NumericFeature) or f[RDF.type].include?(RDF::OT.Substructure)
         }
         if have_rdf
-          table = OpenTox::Dataset.find_data_entries_rdf(@rdf)
+          table = find_data_entries_rdf
         else
           values = OpenTox::Dataset.find_data_entries_sparql(@uri)
           table = values + Array.new(@compounds.size*@features.size-values.size, "")
diff --git a/lib/utils/rdf/dataset.rb b/lib/utils/rdf/dataset.rb
index ab720d7..e101b67 100644
--- a/lib/utils/rdf/dataset.rb
+++ b/lib/utils/rdf/dataset.rb
@@ -11,29 +11,29 @@ module OpenTox
     # Load features via RDF (slow)
     # @param [String] uri Dataset URI
     # @return [Array] features Features in order
-    def self.find_features_rdf(rdf)
+    def find_features_rdf
       query = RDF::Query.new do
         pattern [:uri, RDF.type, RDF::OT.Feature]
         pattern [:uri, RDF::OLO.index, :idx]
       end
-      query.execute(rdf).sort_by{|s| s.idx}.collect{|s| OpenTox::Feature.new(s.uri.to_s)}
+      query.execute(@rdf).sort_by{|s| s.idx}.collect{|s| OpenTox::Feature.new(s.uri.to_s)}
     end
 
     # Load compounds via RDF (slow)
     # @param [String] uri Dataset URI
     # @return [Array] compounds Compounds in order
-    def self.find_compounds_rdf(rdf)
+    def find_compounds_rdf
       query = RDF::Query.new do
         pattern [:uri, RDF.type, RDF::OT.Compound]
         pattern [:uri, RDF::OLO.index, :idx]
       end
-      query.execute(rdf).sort_by{|s| s.idx}.collect{|s| OpenTox::Compound.new(s.uri.to_s)}
+      query.execute(@rdf).sort_by{|s| s.idx}.collect{|s| OpenTox::Compound.new(s.uri.to_s)}
     end
 
     # Load data entries via RDF (slow)
     # @param [String] uri Dataset uri
     # @return [Array] entries Data entries, ordered primarily over cols and secondarily over rows
-    def self.find_data_entries_rdf(rdf)
+    def find_data_entries_rdf
       query = RDF::Query.new do
         pattern [:data_entry, RDF::OLO.index, :cidx] # compound index: now a free variable
         pattern [:data_entry, RDF::OT.values, :vals]
@@ -41,7 +41,7 @@ module OpenTox
         pattern [:f, RDF::OLO.index, :fidx]
         pattern [:vals, RDF::OT.value, :val]
       end
-      query.execute(rdf).order_by(:fidx, :cidx).collect { |s| s.val.to_s }
+      query.execute(@rdf).order_by(:fidx, :cidx).collect { |s| s.val.to_s }
     end
 
     # Query a dataset URI for ordered status