remove rdf_provider to use rewritten owl.rb in wrapper

4 files changed, 39 insertions, 192 deletions

diff --git a/lib/format_util.rb b/lib/format_util.rb
new file mode 100644
index 0000000..abd83d6
--- /dev/null
+++ b/lib/format_util.rb
@@ -0,0 +1,32 @@
+
+
+class String
+  
+  # :prediction_feature -> predictionFeature
+  # :test_dataset_uri -> testDataset
+  def to_rdf_format
+    s = gsub(/_uri(s|)$/,"")
+    s.gsub(/_./) do |m|
+      m.gsub!(/^_/,"")
+      m.upcase
+    end
+  end
+end
+
+class Hash
+  
+  # applies to_rdf_format to all keys
+  def keys_to_rdf_format
+    res = {}
+    keys.each do |k|
+      v = self[k]
+      if v.is_a?(Hash)
+        v = v.keys_to_rdf_format
+      elsif v.is_a?(Array)
+        v = v.collect{ |vv| vv.is_a?(Hash) ? vv.keys_to_rdf_format : vv }
+      end
+      res[k.to_s.to_rdf_format] = v
+    end
+    return res
+  end
+end
\ No newline at end of file
diff --git a/lib/predictions.rb b/lib/predictions.rb
index f6351f8..2873689 100644
--- a/lib/predictions.rb
+++ b/lib/predictions.rb
@@ -441,8 +441,8 @@ module Lib
     def sample_correlation_coefficient
       # formula see http://en.wikipedia.org/wiki/Correlation_and_dependence#Pearson.27s_product-moment_coefficient
       return ( @num_predicted * @sum_multiply - @sum_actual * @sum_predicted ) /
-             ( Math.sqrt( @num_predicted * @sum_squares_actual - @sum_actual**2 ) *
-               Math.sqrt( @num_predicted * @sum_squares_predicted - @sum_predicted**2 ) )
+             ( Math.sqrt( [0, @num_predicted * @sum_squares_actual - @sum_actual**2].max ) *
+               Math.sqrt( [0, @num_predicted * @sum_squares_predicted - @sum_predicted**2].max ) )
     end
     
     def total_sum_of_squares
diff --git a/lib/rdf_provider.rb b/lib/rdf_provider.rb
deleted file mode 100644
index 7fa3ecc..0000000
--- a/lib/rdf_provider.rb
+++ /dev/null
@@ -1,188 +0,0 @@
-
-class String
-  def convert_underscore
-    gsub(/_./) do |m|
-      m.gsub!(/^_/,"")
-      m.upcase
-    end
-  end
-end
-
-module Lib
-  module RDFProvider
-    
-    def to_rdf
-      HashToOwl.to_rdf(self)
-    end
-    
-    def uri
-      raise "not implemented"
-    end
-    
-    def rdf_title
-      raise "not implemented"
-    end
-    
-    # the rdf output is generated from the hash that is provided by this method
-    # the keys in the hash structure are used to defined type of the resource (literal, objectProperty, dataProperty)
-    # example: if the structure should contain a literal named "size" with value 5
-    # * add :property_xy => 5 to your hash
-    # * make sure literal?(:property_xy) returns true
-    # * literal_name(:property_xy) must return "size"
-    #
-    def get_content_as_hash
-      raise "not implemented"
-    end
-    
-    def to_yaml
-      get_content_as_hash.to_yaml
-    end
-    
-    def rdf_ignore?( prop )
-      self.class::IGNORE.index( prop ) != nil
-    end
-    
-    def literal?( prop )
-      self.class::LITERALS.index( prop ) != nil
-    end
-    
-    def literal_name( prop )
-      if self.class::LITERAL_NAMES.has_key?(prop)
-        self.class::LITERAL_NAMES[prop]
-      else
-        OT[prop.to_s.convert_underscore]
-      end
-    end
-    
-    def object_property?( prop )
-      self.class::OBJECT_PROPERTIES.has_key?( prop )
-    end
-    
-    def object_property_name( prop )
-      return self.class::OBJECT_PROPERTIES[ prop ]
-    end
-    
-    def object_type( prop )
-      return self.class::OBJECTS[ prop ]
-    end
-  
-    def class?(prop)
-      self.class::CLASSES.has_key?( prop )
-    end
-    
-    def class_name( prop )
-      return self.class::CLASSES[ prop ]
-    end
-    
-  end
-  
-  class HashToOwl
-    #include OpenTox::Owl
-    
-    def self.to_rdf( rdf_provider )
-      
-      owl = OpenTox::Owl.create(rdf_provider.rdf_title, rdf_provider.uri )
-      toOwl = HashToOwl.new(owl)
-      toOwl.add_content(rdf_provider)
-      toOwl.rdf
-    end
-  
-    def add_content( rdf_provider ) 
-      @rdf_provider = rdf_provider
-      recursiv_add_content( @rdf_provider.get_content_as_hash, @owl.root_node )
-    end
-    
-    def rdf
-      @owl.rdf
-    end
-    
-    private
-    def initialize(owl)
-      @owl = owl
-      @model = owl.model
-    end
-    
-    def recursiv_add_content( output, node )
-      output.each do |k,v|
-        if v==nil
-          LOGGER.warn "skipping nil value: "+k.to_s
-          next
-        end
-        if @rdf_provider.rdf_ignore?(k)
-          #do nothing
-        elsif v.is_a?(Hash)
-          new_node = add_class( k, node )
-          recursiv_add_content( v, new_node )
-        elsif v.is_a?(Array)
-          v.each do |value|
-            if @rdf_provider.class?(k)
-              new_node = add_class( k, node )
-              recursiv_add_content( value, new_node )
-            else
-              add_object_property( k, value, node)
-            end
-          end
-        elsif @rdf_provider.literal?(k)
-          set_literal( k, v, node)
-        elsif @rdf_provider.object_property?(k)
-          add_object_property( k, v, node)
-        else
-          raise "illegal value k:"+k.to_s+" v:"+v.to_s
-        end
-      end
-    end
-  
-    def add_class( property, node )
-      raise "no object prop: "+property.to_s unless @rdf_provider.object_property?(property)
-      raise "no class name: "+property.to_s unless @rdf_provider.class_name(property)
-      # to avoid anonymous nodes, make up uris for sub-objects
-      # use counter to make sure each uri is unique
-      # for example we will get ../confusion_matrix_cell/1, ../confusion_matrix_cell/2, ...
-      count = 1
-      while (true)
-        res = Redland::Resource.new( File.join(node.uri.to_s,property.to_s+"/"+count.to_s) )  
-        break if @model.subject(@rdf_provider.object_property_name(property), res).nil?
-        count += 1
-      end
-      clazz = Redland::Resource.new(@rdf_provider.class_name(property))
-      @model.add res, RDF['type'], clazz
-      @model.add res, DC['title'], clazz
-      @model.add clazz, RDF['type'], OWL['Class']
-      @model.add DC['title'], RDF['type'],OWL['AnnotationProperty']
-      
-      objectProp = Redland::Resource.new(@rdf_provider.object_property_name(property))
-      @model.add objectProp, RDF['type'], OWL['ObjectProperty']
-      @model.add node, objectProp, res
-      return res
-    end
-    
-    def set_literal(property, value, node )
-      raise "empty literal value "+property.to_s if value==nil || value.to_s.size==0
-      raise "no literal name "+propety.to_s unless @rdf_provider.literal_name(property)
-      begin
-        l = @model.object(subject, @rdf_provider.literal_name(property))
-        @model.delete node, @rdf_provider.literal_name(property), l
-      rescue
-      end
-      literalProp =  Redland::Resource.new(@rdf_provider.literal_name(property))
-      @model.add literalProp, RDF['type'],OWL['AnnotationProperty']
-      @model.add node, literalProp, Redland::Literal.create(value)
-    end
-    
-    def add_object_property(property, value, node )
-      raise "empty object property value "+property.to_s if value==nil || value.to_s.size==0
-      raise "no object property name "+propety.to_s unless @rdf_provider.object_property_name(property)
-      raise "no object type "+property.to_s unless @rdf_provider.object_type(property)
-      
-      objectProp = Redland::Resource.new(@rdf_provider.object_property_name(property))
-      @model.add objectProp, RDF['type'], OWL['ObjectProperty']
-      
-      val = Redland::Resource.new(value)
-      type = Redland::Resource.new(@rdf_provider.object_type(property))
-      @model.add node, objectProp, val
-      @model.add val, RDF['type'], type
-      @model.add type, RDF['type'], OWL['Class']
-    end
-    
-  end
-end
diff --git a/lib/validation_db.rb b/lib/validation_db.rb
index 1152abf..09316ca 100644
--- a/lib/validation_db.rb
+++ b/lib/validation_db.rb
@@ -18,7 +18,7 @@ end
 module Lib
 
   VAL_PROPS_GENERAL = [ :validation_uri, :model_uri, :algorithm_uri, :training_dataset_uri, :prediction_feature,
-                :test_dataset_uri, :test_target_dataset_uri, :prediction_dataset_uri, :created_at ] 
+                :test_dataset_uri, :test_target_dataset_uri, :prediction_dataset_uri, :date ] 
   VAL_PROPS_SUM = [ :num_instances, :num_without_class, :num_unpredicted ]
   VAL_PROPS_AVG = [:real_runtime, :percent_without_class, :percent_unpredicted ]
   VAL_PROPS = VAL_PROPS_GENERAL + VAL_PROPS_SUM + VAL_PROPS_AVG
@@ -50,7 +50,7 @@ module Lib
     :target_variance_actual, :target_variance_predicted, :sum_squared_error, :sample_correlation_coefficient ]
   
   CROSS_VAL_PROPS = [:dataset_uri, :num_folds, :stratified, :random_seed]
-  CROSS_VAL_PROPS_REDUNDANT = [:crossvalidation_uri, :algorithm_uri, :created_at] + CROSS_VAL_PROPS 
+  CROSS_VAL_PROPS_REDUNDANT = [:crossvalidation_uri, :algorithm_uri, :date] + CROSS_VAL_PROPS 
   
   ALL_PROPS = VAL_PROPS + VAL_CV_PROPS + VAL_CLASS_PROPS_EXTENDED + VAL_REGR_PROPS + CROSS_VAL_PROPS
 
@@ -61,8 +61,11 @@ module Lib
   class Validation < ActiveRecord::Base
     serialize :classification_statistics
     serialize :regression_statistics
+    
+    alias_attribute :date, :created_at
   end
   
   class Crossvalidation < ActiveRecord::Base
+    alias_attribute :date, :created_at
   end
 end