switch from datamapper/mysql to redis (sqlite for qmrf)

3 files changed, 73 insertions, 61 deletions

diff --git a/lib/merge.rb b/lib/merge.rb
index 527415e..ecbe133 100644
--- a/lib/merge.rb
+++ b/lib/merge.rb
@@ -20,8 +20,7 @@ module Lib
     def self.merge_array_objects( array )
       return nil if array.size == nil
       return array[0] if array.size==1
-        
-      m = self.merge_objects(array[0], array[1] )
+      m = self.merge_objects(array[0], array[1])
       (2..array.size-1).each do |i|
         m = self.merge_objects(m, array[i] )
       end
@@ -33,8 +32,7 @@ module Lib
     end
     
     def self.merge_objects( object1, object2 )
-      
-      raise "classes not equal" if object1.class != object2.class
+      raise "classes not equal : "+object1.class.to_s+" != "+object2.class.to_s if object1.class != object2.class
       object_class = object1.class
       raise "register which attributes to merge first, nothing found for class "+object_class.to_s unless merge_attributes_registered?(object_class)
       raise "not supported, successivly add unmerged object to a merge object" if merge_count(object2)>1
@@ -71,6 +69,11 @@ module Lib
       variance = nil
       
       if (avg=avg_attribute?(object_class, attribute)) || sum_attribute?(object_class, attribute)
+        # we string to numerics if wanted, value1 is no string anymore if weight>1
+        if value2.is_a?(String) and ((weight1==1 and value1.is_a?(String)) or (weight1>1 and value1.is_a?(Numeric)))
+          value1 = value1.to_f
+          value2 = value2.to_f
+        end
         if (value1==nil and value2==nil )
           #do nothing
         elsif value1.is_a?(Numeric) and value2.is_a?(Numeric)
@@ -104,7 +107,8 @@ module Lib
             end
           end        
         else
-          raise "invalid, cannot avg/sum non-numeric content for attribute: "+attribute.to_s+" contents: '"+value1.to_s+"', '"+value2.to_s+"'"
+          raise "invalid, cannot avg/sum non-numeric content for attribute: "+attribute.to_s+" contents: '"+value1.to_s+"' ("+
+            value1.class.to_s+"), '"+value2.to_s+"' ("+value2.class.to_s+")"
         end
       elsif non_numeric_attribute?(object_class, attribute)
         if (value1.is_a?(Hash) and value2.is_a?(Hash))
diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb
index f812854..5033425 100755
--- a/lib/ot_predictions.rb
+++ b/lib/ot_predictions.rb
@@ -184,9 +184,9 @@ module Lib
       res = {}
       case @feature_type
       when "classification"
-        (Lib::VAL_CLASS_PROPS).each{ |s| res[s] = send(s)}  
+        (Validation::VAL_CLASS_PROPS).each{ |s| res[s] = send(s)}  
       when "regression"
-        (Lib::VAL_REGR_PROPS).each{ |s| res[s] = send(s) }  
+        (Validation::VAL_REGR_PROPS).each{ |s| res[s] = send(s) }  
       end
       return res
     end
diff --git a/lib/validation_db.rb b/lib/validation_db.rb
index 0d5db21..0beb73d 100755
--- a/lib/validation_db.rb
+++ b/lib/validation_db.rb
@@ -4,7 +4,7 @@
 #end
 require "lib/merge.rb"
 
-module Lib
+module Validation
 
   VAL_PROPS_GENERAL = [ :validation_uri, :validation_type, :model_uri, :algorithm_uri, :training_dataset_uri, :prediction_feature,
                 :test_dataset_uri, :test_target_dataset_uri, :prediction_dataset_uri, :date ] 
@@ -48,42 +48,53 @@ module Lib
   VAL_MERGE_AVG = VAL_PROPS_AVG + VAL_CLASS_PROPS_SINGLE_AVG + VAL_CLASS_PROPS_PER_CLASS_AVG + VAL_REGR_PROPS
   
 
-#  class Validation < ActiveRecord::Base
-#    serialize :classification_statistics
-#    serialize :regression_statistics
-#    
-#    alias_attribute :date, :created_at
-    
-  class Validation 
-    include DataMapper::Resource
+  class Validation < Ohm::Model 
   
-    property :id, Serial
-    property :validation_type, String, :length => 512
-    property :model_uri, String, :length => 512
-    property :algorithm_uri, String, :length => 512
-    property :training_dataset_uri, String, :length => 512
-    property :test_target_dataset_uri, String, :length => 512
-    property :test_dataset_uri, String, :length => 512
-    property :prediction_dataset_uri, String, :length => 512
-    property :prediction_feature, String, :length => 512
-    property :created_at, DateTime
-    property :num_instances, Integer
-    property :num_without_class, Integer
-    property :num_unpredicted, Integer
-    property :crossvalidation_id, Integer
-    property :crossvalidation_fold, Integer
-    property :real_runtime, Float
-    property :percent_without_class, Float
-    property :percent_unpredicted, Float
-    property :classification_statistics, Object
-    property :regression_statistics, Object
-    property :finished, Boolean, :default => false
+    attribute :validation_type
+    attribute :model_uri
+    attribute :algorithm_uri
+    attribute :training_dataset_uri
+    attribute :test_target_dataset_uri
+    attribute :test_dataset_uri
+    attribute :prediction_dataset_uri
+    attribute :prediction_feature
+    attribute :created_at
+    attribute :num_instances
+    attribute :num_without_class
+    attribute :num_unpredicted
+    attribute :crossvalidation_id
+    attribute :crossvalidation_fold
+    attribute :real_runtime
+    attribute :percent_without_class
+    attribute :percent_unpredicted
+    attribute :classification_statistics_yaml
+    attribute :regression_statistics_yaml
+    attribute :finished    
+    
+    index :model_uri
+    index :validation_type
+    index :crossvalidation_id
     
     attr_accessor :subjectid
     
-    after :save, :check_policy
-    private
-    def check_policy
+    def classification_statistics
+      YAML.load(self.classification_statistics_yaml) if self.classification_statistics_yaml
+    end
+    
+    def classification_statistics=(cs)
+      self.classification_statistics_yaml = cs.to_yaml
+    end
+    
+    def regression_statistics
+      YAML.load(self.regression_statistics_yaml) if self.regression_statistics_yaml
+    end
+    
+    def regression_statistics=(rs)
+      self.regression_statistics_yaml = rs.to_yaml
+    end
+
+    def save
+      super
       OpenTox::Authorization.check_policy(validation_uri, subjectid)
     end
     
@@ -115,25 +126,27 @@ module Lib
     
   end
   
-#  class Crossvalidation < ActiveRecord::Base
-#    alias_attribute :date, :created_at
-  class Crossvalidation 
-    include DataMapper::Resource
+  class Crossvalidation < Ohm::Model
   
-    property :id, Serial
-    property :algorithm_uri, String, :length => 512
-    property :dataset_uri, String, :length => 512
-    property :created_at, DateTime
-    property :num_folds, Integer, :default => 10
-    property :random_seed, Integer, :default => 1
-    property :finished, Boolean, :default => false
-    property :stratified, Boolean, :default => false
+    attribute :algorithm_uri
+    attribute :dataset_uri
+    attribute :created_at
+    attribute :num_folds
+    attribute :random_seed
+    attribute :finished
+    attribute :stratified
     
     attr_accessor :subjectid
+    
+    index :algorithm_uri
+    index :dataset_uri
+    index :num_folds
+    index :random_seed
+    index :stratified
+    index :finished
         
-    after :save, :check_policy
-    private
-    def check_policy
+    def save
+      super
       OpenTox::Authorization.check_policy(crossvalidation_uri, subjectid)
     end
     
@@ -152,7 +165,7 @@ module Lib
     # further conditions can be specified in __conditions__
     def self.find_all_uniq(conditions={}, subjectid=nil )
       #cvs = Lib::Crossvalidation.find(:all, :conditions => conditions)
-      cvs = Lib::Crossvalidation.all(:conditions => conditions)
+      cvs = Crossvalidation.find( conditions )
       uniq = []
       cvs.each do |cv|
         next if AA_SERVER and !OpenTox::Authorization.authorized?(cv.crossvalidation_uri,"GET",subjectid)
@@ -171,8 +184,3 @@ module Lib
   end
 end
 
-
-Lib::Validation.auto_upgrade!
-Lib::Validation.raise_on_save_failure = true
-Lib::Crossvalidation.auto_upgrade!
-Lib::Crossvalidation.raise_on_save_failure = true