replacing datamapper with activerecord for validation objects

13 files changed, 283 insertions, 177 deletions

diff --git a/Rakefile b/Rakefile
index 642cd30..185f948 100644
--- a/Rakefile
+++ b/Rakefile
@@ -18,3 +18,47 @@ task :test do
 	load 'test.rb'
 end
 
+desc "load config"
+task :load_config do
+  require 'yaml'
+  ENV['RACK_ENV'] = 'test' unless ENV['RACK_ENV']
+  basedir = File.join(ENV['HOME'], ".opentox")
+  config_dir = File.join(basedir, "config")
+  config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml")
+  if File.exist?(config_file)
+    @@config = YAML.load_file(config_file)
+    raise "could not load config, config file: "+config_file.to_s unless @@config
+  end
+  puts "config loaded"
+end
+
+# USER VERSION 0 instead
+#desc "Clear database"
+#task :clear_db => :load_config  do
+#  if  @@config[:database][:adapter]=="mysql"
+#    clear = nil
+#    IO.popen("locate clear_mysql.sh"){ |f| clear=f.gets.chomp("\n") }
+#    raise "clear_mysql.sh not found" unless clear
+#    cmd = clear+" "+@@config[:database][:username]+" "+@@config[:database][:password]+" "+@@config[:database][:database]
+#    IO.popen(cmd){ |f| puts f.gets }
+#  else
+#    raise "clear not implemented for database-type: "+@@config[:database][:adapter]
+#  end
+#end
+
+desc "Migrate the database through scripts in db/migrate. Target specific version with VERSION=x"
+task :migrate => :load_config do
+  require 'active_record'
+  ActiveRecord::Base.establish_connection(  
+       :adapter => @@config[:database][:adapter],
+       :host => @@config[:database][:host],
+       :database => @@config[:database][:database],
+       :username => @@config[:database][:username],
+       :password => @@config[:database][:password]
+       )  
+  ActiveRecord::Base.logger = Logger.new($stdout)
+  ActiveRecord::Migrator.migrate('db/migrate', ENV["VERSION"] ? ENV["VERSION"].to_i : nil )
+end
+
+
+
diff --git a/application.rb b/application.rb
index 236280c..3b0dc71 100644
--- a/application.rb
+++ b/application.rb
@@ -4,6 +4,15 @@ gem 'opentox-ruby-api-wrapper', '= 1.4.4.4'
   require lib
 end
 
+require 'active_record'
+ActiveRecord::Base.establish_connection(  
+   :adapter => @@config[:database][:adapter],
+   :host => @@config[:database][:host],
+   :database => @@config[:database][:database],
+   :username => @@config[:database][:username],
+   :password => @@config[:database][:password]
+) 
+       
 #unless(defined? LOGGER)
   #LOGGER = Logger.new(STDOUT)
   #LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
diff --git a/db/migrate/000_drop_validations.rb b/db/migrate/000_drop_validations.rb
new file mode 100644
index 0000000..4b0288d
--- /dev/null
+++ b/db/migrate/000_drop_validations.rb
@@ -0,0 +1,13 @@
+
+class DropValidations < ActiveRecord::Migration
+  def self.up
+    drop_table :validations if table_exists? :validations
+    drop_table :crossvalidations if table_exists? :crossvalidations
+  end
+
+  def self.down
+    drop_table :validations if table_exists? :validations
+    drop_table :crossvalidations if table_exists? :crossvalidations
+  end
+end
+
diff --git a/db/migrate/001_init_validation.rb b/db/migrate/001_init_validation.rb
new file mode 100644
index 0000000..d38afd7
--- /dev/null
+++ b/db/migrate/001_init_validation.rb
@@ -0,0 +1,64 @@
+
+class InitValidation < ActiveRecord::Migration
+  def self.up
+
+    create_table :crossvalidations do |t|
+      
+      [:crossvalidation_uri, #accesss to :uri somehow does not work, create uri-function in object
+       :algorithm_uri, 
+       :dataset_uri ].each do |p|
+        t.column p, :string, :limit => 255
+      end
+      
+      [:created_at ].each do |p|
+        t.column p, :datetime 
+      end
+      
+      [:num_folds, 
+       :random_seed ].each do |p|
+        t.column p, :integer, :null => false
+      end
+     
+      [ :stratified ].each do |p|
+        t.column p, :boolean, :null => false
+      end
+      
+    end
+    
+    create_table :validations do |t|
+      
+      [:validation_uri, #accesss to :uri somehow does not work, create uri-function in obejct
+       :model_uri,
+       :algorithm_uri, 
+       :training_dataset_uri, 
+       :test_target_dataset_uri, 
+       :test_dataset_uri, 
+       :prediction_dataset_uri, 
+       :prediction_feature ].each do |p|
+        t.column p, :string, :limit => 255
+      end
+      
+      [:created_at ].each do |p|
+        t.column p, :datetime 
+      end
+      
+      [:real_runtime, :num_instances, :num_without_class, :num_unpredicted, :crossvalidation_id, :crossvalidation_fold ].each do |p|
+        t.column p, :integer
+      end
+      
+      [:real_runtime, :percent_without_class, :percent_unpredicted ].each do |p|
+        t.column p, :float 
+      end
+      
+      [:classification_statistics, :regression_statistics].each do |p|
+        t.column(p, :text, :limit => 16320)
+      end
+    end
+  end
+
+  def self.down
+    drop_table :validations
+    drop_table :crossvalidations
+  end
+end
+
diff --git a/example.rb b/example.rb
index 5d81061..8775569 100644
--- a/example.rb
+++ b/example.rb
@@ -51,6 +51,12 @@ class Example
   def self.prepare_example_resources
     
     @@summary = ""
+    #delete validations
+    log "delete validations"
+    ActiveRecord::Base.logger = Logger.new("/dev/null")
+    ActiveRecord::Migrator.migrate('db/migrate', 0 )
+    ActiveRecord::Migrator.migrate('db/migrate', 1 )
+    
     #delete_all(@@config[:services]["opentox-dataset"])
     log OpenTox::RestClientWrapper.delete @@config[:services]["opentox-dataset"]
     
@@ -60,7 +66,6 @@ class Example
     data_uri = OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type => @@file_type},data).chomp("\n")
     
     log "train-test-validation"
-    Lib::Validation.auto_migrate!
     #delete_all(@@config[:services]["opentox-model"])
     OpenTox::RestClientWrapper.delete @@config[:services]["opentox-model"]
     
@@ -73,7 +78,6 @@ class Example
     v.validate_algorithm( @@alg_params ) 
     
     log "crossvalidation"
-    Lib::Crossvalidation.auto_migrate!
     cv = Validation::Crossvalidation.new({ :dataset_uri => data_uri, :algorithm_uri => @@alg, :num_folds => 5, :stratified => false })
     cv.create_cv_datasets(  URI.decode(@@feature) )
     cv.perform_cv( @@alg_params )
diff --git a/lib/validation_db.rb b/lib/validation_db.rb
index 9bca160..17e8f74 100644
--- a/lib/validation_db.rb
+++ b/lib/validation_db.rb
@@ -47,66 +47,15 @@ module Lib
   VAL_MERGE_SUM = VAL_PROPS_SUM + VAL_CLASS_PROPS_SINGLE_SUM + VAL_CLASS_PROPS_PER_CLASS_SUM
   VAL_MERGE_AVG = VAL_PROPS_AVG + VAL_CLASS_PROPS_SINGLE_AVG + VAL_CLASS_PROPS_PER_CLASS_AVG + VAL_REGR_PROPS
  
-  class Validation
-    include DataMapper::Resource 
-  
-    property :id, Serial
-    property :uri, String, :length => 255
-    property :model_uri, String, :length => 255
-    property :algorithm_uri, String, :length => 255
-    property :training_dataset_uri, String, :length => 255
-    property :test_target_dataset_uri, String, :length => 255
-    property :test_dataset_uri, String, :length => 255
-    property :prediction_dataset_uri, String, :length => 255
-    property :prediction_feature, String, :length => 255
-    property :created_at, DateTime
-    property :real_runtime, Float
-    
-    property :num_instances, Integer
-    property :num_without_class, Integer
-    property :percent_without_class, Float
-    property :num_unpredicted, Integer
-    property :percent_unpredicted, Float
-        
-    property :classification_statistics, Object #Hash
-    property :regression_statistics, Object
-    
-    property :crossvalidation_id, Integer
-    property :crossvalidation_fold, Integer
+  class Validation < ActiveRecord::Base
+    def uri
+      self.validation_uri
+    end
   end
   
-  class Crossvalidation
-    include DataMapper::Resource
-    property :id, Serial
-    property :uri, String, :length => 255
-    property :algorithm_uri, String, :length => 255
-    property :dataset_uri, String, :length => 255
-    property :num_folds, Integer, :default => 10
-    property :stratified, Boolean, :default => false
-    property :random_seed, Integer, :default => 1
+  class Crossvalidation < ActiveRecord::Base
+    def uri
+      self.crossvalidation_uri
+    end
   end
 end
-
-# sqlite is used for storing validations and crossvalidations
-#sqlite = "#{File.expand_path(File.dirname(__FILE__))}/#{Sinatra::Base.environment}.sqlite3"
-#DataMapper.setup(:default, "sqlite3:///#{sqlite}")
-#unless FileTest.exists?("#{sqlite}")
-#  [Lib::Validation, Lib::Crossvalidation].each do |model|
-#    model.auto_migrate!
-#  end
-#end
-
-#raise "':database:' configuration missing in config file" unless @@config.has_key?(:database)
-#[ "adapter","database","username","password","host" ].each do |field|
-  #raise "field '"+field+":' missing in database configuration" unless @@config[:database].has_key?(field)
-#end
-#DataMapper.setup(:default, { 
-    #:adapter  => @@config[:database]["adapter"],
-    #:database => @@config[:database]["database"],
-    #:username => @@config[:database]["username"],
-   # :password => @@config[:database]["password"],
-#    :host     => @@config[:database]["host"]
-  #})
-[Lib::Validation, Lib::Crossvalidation].each do |resource|
-    resource.auto_migrate! unless resource.storage_exists?
-end
diff --git a/nightly/nightly.rb b/nightly/nightly.rb
index 594d4ee..558a5ea 100644
--- a/nightly/nightly.rb
+++ b/nightly/nightly.rb
@@ -28,15 +28,18 @@ class Nightly
       
       running = []
       report = Reports::XMLReport.new("Nightly Validation", Time.now.strftime("Created at %m.%d.%Y - %H:%M"))
+      count = 1
       benchmarks.each do |b|
-        running << b.class.to_s.gsub(/Nightly::/, "")+b.object_id.to_s
+        id = "["+count.to_s+"]-"+b.title
+        count += 1
+        running << id
         Thread.new do
           begin
             b.build
           rescue => ex
             LOGGER.error "uncaught nightly build error: "+ex.message
           ensure
-            running.delete(b.class.to_s.gsub(/Nightly::/, "")+b.object_id.to_s)
+            running.delete id
           end
         end
       end
@@ -126,7 +129,11 @@ class Nightly
     end
     
     def title
-      @validation_examples.collect{|e| e.title}.join(" + ")
+      if @validation_examples.size==0
+        @validation_examples[0].class.humanize
+      else
+        @validation_examples[0].class.superclass.humanize  
+      end
     end
     
     def result_table
@@ -174,7 +181,7 @@ class Nightly
       
       @validation_examples.each do |v|
 
-        id = v.title+count.to_s
+        id = "["+count.to_s+"]-"+v.title
         count += 1
         running << id
         LOGGER.debug "Uploading datasets: "+v.title
@@ -200,7 +207,7 @@ class Nightly
 
       wait = 0
       while running.size>0
-        LOGGER.debug self.class.to_s.gsub(/Nightly::/, "")+" waiting for "+running.inspect if wait%20==0
+        LOGGER.debug self.title+" waiting for "+running.inspect if wait%20==0
         wait += 1
         sleep 1
       end
diff --git a/report/validation_access.rb b/report/validation_access.rb
index ac90b0f..f85698f 100644
--- a/report/validation_access.rb
+++ b/report/validation_access.rb
@@ -59,7 +59,7 @@ class Reports::ValidationDB < Reports::ValidationAccess
     validation_uris.each do |u|
       if u.to_s =~ /.*\/crossvalidation\/[0-9]+/
         cv_id = u.split("/")[-1].to_i
-        res += Lib::Validation.all(:crossvalidation_id => cv_id).collect{|v| v.uri.to_s}
+        res += Lib::Validation.find( :all, :conditions => { :crossvalidation_id => cv_id } ).collect{|v| v.uri.to_s}
       else
         res += [u.to_s]
       end
@@ -76,7 +76,7 @@ class Reports::ValidationDB < Reports::ValidationAccess
       (validation_id.to_i > 0 || validation_id.to_s=="0" )
     v = nil
     begin
-      v = Lib::Validation.get(validation_id)
+      v = Lib::Validation.find(validation_id)
     rescue => ex
       raise "could not access validation with id "+validation_id.to_s+", error-msg: "+ex.message
     end
@@ -88,14 +88,14 @@ class Reports::ValidationDB < Reports::ValidationAccess
     
     {:classification_statistics => Lib::VAL_CLASS_PROPS, 
      :regression_statistics => Lib::VAL_REGR_PROPS}.each do |subset_name,subset_props|
-      subset = v[subset_name]
+      subset = YAML.load(v[subset_name].to_s)
       subset_props.each{ |prop| validation.send("#{prop.to_s}=".to_sym, subset[prop]) } if subset
     end
   end
     
   def init_cv(validation)
     
-    cv = Lib::Crossvalidation.get(validation.crossvalidation_id)
+    cv = Lib::Crossvalidation.find(validation.crossvalidation_id)
     raise Reports::BadRequest.new "no crossvalidation found with id "+validation.crossvalidation_id.to_s unless cv
     
     Lib::CROSS_VAL_PROPS.each do |p|
diff --git a/test/test_examples.rb b/test/test_examples.rb
index 0b817fb..beeaa30 100644
--- a/test/test_examples.rb
+++ b/test/test_examples.rb
@@ -11,14 +11,14 @@ module ValidationExamples
   
   ########################################################################################################
   
-  class ABSTRACTHamsterSplit < SplitTestValidation
+  class HamsterSplit < SplitTestValidation
     def initialize
       @dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
       @prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
     end
   end
   
-  class LazarHamsterSplit < ABSTRACTHamsterSplit
+  class LazarHamsterSplit < HamsterSplit
     def initialize
       @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
       @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
@@ -26,7 +26,7 @@ module ValidationExamples
     end
   end
   
-  class MajorityHamsterSplit < ABSTRACTHamsterSplit
+  class MajorityHamsterSplit < HamsterSplit
     def initialize
       @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
       super
@@ -35,7 +35,7 @@ module ValidationExamples
   
   ########################################################################################################
 
-  class ABSTRACTHamsterTrainingTest < TrainingTestValidation
+  class HamsterTrainingTest < TrainingTestValidation
     def initialize
       @test_target_dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
       @training_dataset_file = File.new("data/hamster_carcinogenicity.train.yaml","r")
@@ -44,14 +44,14 @@ module ValidationExamples
     end
   end
   
-  class MajorityHamsterTrainingTest < ABSTRACTHamsterTrainingTest
+  class MajorityHamsterTrainingTest < HamsterTrainingTest
     def initialize
       @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
       super
     end
   end
   
-  class LazarHamsterTrainingTest < ABSTRACTHamsterTrainingTest
+  class LazarHamsterTrainingTest < HamsterTrainingTest
     def initialize
       @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
       @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
@@ -61,21 +61,22 @@ module ValidationExamples
   
   ########################################################################################################  
 
-  class ABSTRACTHamsterCrossvalidation < CrossValidation
+  class HamsterCrossvalidation < CrossValidation
     def initialize
       @dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
       @prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+      @num_folds = 10
     end
   end
   
-  class MajorityHamsterCrossvalidation < ABSTRACTHamsterCrossvalidation
+  class MajorityHamsterCrossvalidation < HamsterCrossvalidation
     def initialize
       @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
       super
     end
   end
 
-  class LazarHamsterCrossvalidation < ABSTRACTHamsterCrossvalidation
+  class LazarHamsterCrossvalidation < HamsterCrossvalidation
     def initialize
       @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
       @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
@@ -85,21 +86,21 @@ module ValidationExamples
   
   ########################################################################################################  
 
-  class ABSTRACT_ISTHamsterCrossvalidationInsilico < CrossValidation
+  class ISTHamsterCrossvalidationInsilico < CrossValidation
     def initialize
       @dataset_uri = "http://webservices.in-silico.ch/dataset/108"
       @prediction_feature = "http://toxcreate.org/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
     end
   end
   
-  class MajorityISTHamsterCrossvalidation < ABSTRACT_ISTHamsterCrossvalidationInsilico
+  class MajorityISTHamsterCrossvalidation < ISTHamsterCrossvalidationInsilico
     def initialize
       @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
       super
     end
   end
   
-  class LazarISTHamsterCrossvalidation < ABSTRACT_ISTHamsterCrossvalidationInsilico
+  class LazarISTHamsterCrossvalidation < ISTHamsterCrossvalidationInsilico
     def initialize
       @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
       @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
@@ -107,7 +108,7 @@ module ValidationExamples
     end
   end
   
-  class ISTLazarISTHamsterCrossvalidation < ABSTRACT_ISTHamsterCrossvalidationInsilico
+  class ISTLazarISTHamsterCrossvalidation < ISTHamsterCrossvalidationInsilico
     def initialize
       @algorithm_uri = "http://webservices.in-silico.ch/algorithm/lazar"
       @algorithm_params = "feature_generation_uri=http://webservices.in-silico.ch/algorithm/fminer"
@@ -128,7 +129,7 @@ module ValidationExamples
   
   ########################################################################################################
 
-  class ABSTRACTCacoTrainingTest < TrainingTestValidation
+  class CacoTrainingTest < TrainingTestValidation
     def initialize
       @training_dataset_uri = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R7798"
       @test_dataset_uri = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R8353"
@@ -136,28 +137,28 @@ module ValidationExamples
     end
   end
   
-  class LR_AmbitCacoTrainingTest < ABSTRACTCacoTrainingTest
+  class LR_AmbitCacoTrainingTest < CacoTrainingTest
     def initialize
       @algorithm_uri = "http://ambit.uni-plovdiv.bg:8080/ambit2/algorithm/LR"
       super
     end
   end
   
-  class MLR_NTUA_CacoTrainingTest < ABSTRACTCacoTrainingTest
+  class MLR_NTUA_CacoTrainingTest < CacoTrainingTest
     def initialize
       @algorithm_uri = "http://opentox.ntua.gr:3003/algorithm/mlr"
       super
     end
   end
   
-  class MLR_NTUA2_CacoTrainingTest < ABSTRACTCacoTrainingTest
+  class MLR_NTUA2_CacoTrainingTest < CacoTrainingTest
     def initialize
       @algorithm_uri = "http://opentox.ntua.gr:3004/algorithm/mlr"
       super
     end
   end
   
-  class MajorityCacoTrainingTest < ABSTRACTCacoTrainingTest
+  class MajorityCacoTrainingTest < CacoTrainingTest
     def initialize
       @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/regr/algorithm")
       super
diff --git a/validation/validation_application.rb b/validation/validation_application.rb
index f9e6f16..13dc26d 100644
--- a/validation/validation_application.rb
+++ b/validation/validation_application.rb
@@ -23,7 +23,7 @@ end
 
 get '/crossvalidation/:id' do
   LOGGER.info "get crossvalidation with id "+params[:id].to_s
-  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Validation::Crossvalidation.get(params[:id])
+  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Validation::Crossvalidation.find(params[:id])
   
   case request.env['HTTP_ACCEPT'].to_s
   when "application/rdf+xml"
@@ -41,13 +41,13 @@ end
 delete '/crossvalidation/:id/?' do
   LOGGER.info "delete crossvalidation with id "+params[:id].to_s
   content_type "text/plain"
-  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Validation::Crossvalidation.get(params[:id])
+  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Validation::Crossvalidation.find(params[:id])
   crossvalidation.delete
 end
 
 get '/crossvalidation/:id/validations' do
   LOGGER.info "get all validations for crossvalidation with id "+params[:id].to_s
-  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Validation::Crossvalidation.get(params[:id])
+  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Validation::Crossvalidation.find(params[:id])
   content_type "text/uri-list"
   Validation::Validation.all(:crossvalidation_id => params[:id]).collect{ |v| v.uri.to_s }.join("\n")+"\n"
 end
@@ -55,7 +55,7 @@ end
 
 get '/crossvalidation/:id/statistics' do
   LOGGER.info "get merged validation-result for crossvalidation with id "+params[:id].to_s
-  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Validation::Crossvalidation.get(params[:id])
+  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Validation::Crossvalidation.find(params[:id])
   
   Lib::MergeObjects.register_merge_attributes( Validation::Validation,
     Lib::VAL_MERGE_AVG,Lib::VAL_MERGE_SUM,Lib::VAL_MERGE_GENERAL) unless 
@@ -104,7 +104,7 @@ end
 
 get '/:id' do
   LOGGER.info "get validation with id "+params[:id].to_s+" '"+request.env['HTTP_ACCEPT'].to_s+"'"
-  halt 404, "Validation '#{params[:id]}' not found." unless validation = Validation::Validation.get(params[:id])
+  halt 404, "Validation '#{params[:id]}' not found." unless validation = Validation::Validation.find(params[:id])
   
   case request.env['HTTP_ACCEPT'].to_s
   when "application/rdf+xml"
@@ -143,7 +143,7 @@ post '/?' do
         "params given: "+params.inspect
     end
     content_type "text/uri-list"
-    v.uri
+    v.validation_uri
   end
   halt 202,task_uri
 end
@@ -198,7 +198,7 @@ end
 
 get '/:id/:attribute' do
   LOGGER.info "access validation attribute "+params.inspect
-  halt 404, "Validation #{params[:id]} not found." unless validation = Validation::Validation.get(params[:id])
+  halt 404, "Validation #{params[:id]} not found." unless validation = Validation::Validation.find(params[:id])
   begin
     raise unless validation.attribute_loaded?(params[:attribute])
   rescue
@@ -210,7 +210,7 @@ end
 
 delete '/:id' do
   LOGGER.info "delete validation with id "+params[:id].to_s
-  halt 404, "Validation #{params[:id]} not found." unless validation = Validation::Validation.get(params[:id])
+  halt 404, "Validation #{params[:id]} not found." unless validation = Validation::Validation.find(params[:id])
   content_type "text/plain"
   validation.delete
 end
\ No newline at end of file
diff --git a/validation/validation_format.rb b/validation/validation_format.rb
index f23d00e..357d96e 100644
--- a/validation/validation_format.rb
+++ b/validation/validation_format.rb
@@ -23,6 +23,8 @@ module Validation
     # the right properties, classes for to_rdf
     def get_content_as_hash
       
+      LOGGER.debug self.validation_uri
+      
       h = {}
       Lib::VAL_PROPS.each{|p| h[p] = self.send(p)}
       if crossvalidation_id!=nil
@@ -35,14 +37,15 @@ module Validation
         h[:crossvalidation_info] = cv
       end
       if classification_statistics 
+        class_stats = YAML.load(classification_statistics.to_s)
         clazz = {}
-        Lib::VAL_CLASS_PROPS_SINGLE.each{ |p| clazz[p] = classification_statistics[p] }
+        Lib::VAL_CLASS_PROPS_SINGLE.each{ |p| clazz[p] = class_stats[p] }
         
         # transpose results per class
         class_values = {}
         Lib::VAL_CLASS_PROPS_PER_CLASS.each do |p|
-          $sinatra.halt 500, "missing classification statitstics: "+p.to_s+" "+classification_statistics.inspect unless classification_statistics[p]
-          classification_statistics[p].each do |class_value, property_value|
+          $sinatra.halt 500, "missing classification statitstics: "+p.to_s+" "+class_stats.inspect unless class_stats[p]
+          class_stats[p].each do |class_value, property_value|
             class_values[class_value] = {:class_value => class_value} unless class_values.has_key?(class_value)
             map = class_values[class_value]
             map[p] = property_value
@@ -52,8 +55,8 @@ module Validation
         
         #converting confusion matrix
         cells = []
-        $sinatra.halt 500,"confusion matrix missing" unless classification_statistics[:confusion_matrix]!=nil
-        classification_statistics[:confusion_matrix].each do |k,v|
+        $sinatra.halt 500,"confusion matrix missing" unless class_stats[:confusion_matrix]!=nil
+        class_stats[:confusion_matrix].each do |k,v|
           cell = {}
           # key in confusion matrix is map with predicted and actual attribute 
           k.each{ |kk,vv| cell[kk] = vv }
@@ -153,7 +156,7 @@ module Validation
       Lib::CROSS_VAL_PROPS_REDUNDANT.each{|p| h[p] = self.send(p)}
       
       v = []
-      Validation.all(:crossvalidation_id => self.id).each do |val|
+      Validation.find( :all, :conditions => { :crossvalidation_id => self.id } ).each do |val|
         v.push( val.uri.to_s )
       end
       h[:validations] = v
diff --git a/validation/validation_service.rb b/validation/validation_service.rb
index 1b6678b..cdc0ac9 100644
--- a/validation/validation_service.rb
+++ b/validation/validation_service.rb
@@ -39,20 +39,21 @@ module Validation
       $sinatra.halt 500,"do not set id manually" if params[:id]
       $sinatra.halt 500,"do not set uri manually" if params[:uri]
       super params
-      # hack to overcome datamapper bug: save to set id
-      unless save
-        raise "error saving validation "+errors.inspect
-      end
-      reload
-      raise "internal error, validation-id not set "+to_yaml if @id==nil
-      update :uri => $sinatra.url_for("/"+@id.to_s, :full)
+      self.save
+      raise "internal error, validation-id not set "+to_yaml if self.id==nil
+      self.attributes = { :validation_uri => $sinatra.url_for("/"+self.id.to_s, :full).to_s }
+      self.save
+    end
+    
+    def uri
+      self.validation_uri
     end
     
     # deletes a validation
     # PENDING: model and referenced datasets are deleted as well, keep it that way?
     def delete
     
-      model = OpenTox::Model::PredictionModel.find(@model_uri) if @model_uri
+      model = OpenTox::Model::PredictionModel.find(self.model_uri) if self.model_uri
       model.destroy if model
       
       #[@test_dataset_uri, @training_dataset_uri, @prediction_dataset_uri].each do  |d|
@@ -60,19 +61,18 @@ module Validation
         #dataset.delete if dataset
       #end
       destroy
-      "Successfully deleted validation "+@id.to_s+"."
+      "Successfully deleted validation "+self.id.to_s+"."
     end
     
     # validates an algorithm by building a model and validating this model
     def validate_algorithm( algorithm_params=nil )
       
-      $sinatra.halt 404, "no algorithm uri: '"+algorithm_uri.to_s+"'" if @algorithm_uri==nil or @algorithm_uri.to_s.size<1
+      $sinatra.halt 404, "no algorithm uri: '"+self.algorithm_uri.to_s+"'" if self.algorithm_uri==nil or self.algorithm_uri.to_s.size<1
       
-      params = { :dataset_uri => @training_dataset_uri, :prediction_feature => @prediction_feature }
+      params = { :dataset_uri => self.training_dataset_uri, :prediction_feature => self.prediction_feature }
       if (algorithm_params!=nil)
         algorithm_params.split(";").each do |alg_params|
           alg_param = alg_params.split("=")
-          #puts "param "+alg_param.to_s
           $sinatra.halt 404, "invalid algorithm param: '"+alg_params.to_s+"'" unless alg_param.size==2 or alg_param[0].to_s.size<1 or alg_param[1].to_s.size<1
           LOGGER.warn "algorihtm param contains empty space, encode? "+alg_param[1].to_s if alg_param[1] =~ /\s/
           params[alg_param[0].to_sym] = alg_param[1]
@@ -82,10 +82,11 @@ module Validation
       
       model = OpenTox::Model::PredictionModel.build(algorithm_uri, params)
       $sinatra.halt 500,"model building failed" unless model
-      update :model_uri => model.uri
+      self.attributes = { :model_uri => model.uri }
+      self.save
       
       $sinatra.halt 500,"error after building model: model.dependent_variable != validation.prediciton_feature ("+
-        model.dependentVariables.to_s+" != "+@prediction_feature+")" if @prediction_feature!=model.dependentVariables
+        model.dependentVariables.to_s+" != "+self.prediction_feature+")" if self.prediction_feature!=model.dependentVariables
           
       validate_model
     end
@@ -94,59 +95,61 @@ module Validation
     # PENDING: a new dataset is created to store the predictions, this should be optional: delete predictions afterwards yes/no
     def validate_model
       
-      LOGGER.debug "validating model '"+@model_uri+"'"
+      LOGGER.debug "validating model '"+self.model_uri+"'"
       
-      #test_dataset = OpenTox::Dataset.find @test_dataset_uri
-      #$sinatra.halt 400, "test dataset no found: "+@test_dataset_uri.to_s unless test_dataset
+      model = OpenTox::Model::PredictionModel.find(self.model_uri)
+      $sinatra.halt 400, "model not found: "+self.model_uri.to_s unless model
       
-      model = OpenTox::Model::PredictionModel.find(@model_uri)
-      $sinatra.halt 400, "model not found: "+@model_uri.to_s unless model
-      
-      unless @algorithm_uri
-        update :algorithm_uri => model.algorithm
+      unless self.algorithm_uri
+        self.attributes = { :algorithm_uri => model.algorithm }
+        self.save
       end
       
-      if @prediction_feature
+      if self.prediction_feature
         $sinatra.halt 400, "error validating model: model.dependent_variable != validation.prediciton_feature ("+
-          model.dependentVariables+" != "+@prediction_feature+")" if @prediction_feature!=model.dependentVariables
+          model.dependentVariables+" != "+self.prediction_feature+")" if self.prediction_feature!=model.dependentVariables
       else
         $sinatra.halt 400, "model has no dependentVariables specified, please give prediction feature for model validation" unless model.dependentVariables
-        update :prediction_feature => model.dependentVariables
+        self.attributes = { :prediction_feature => model.dependentVariables }
+        self.save
       end
       
       prediction_dataset_uri = ""
       benchmark = Benchmark.measure do 
-        prediction_dataset_uri = model.predict_dataset(@test_dataset_uri)
+        prediction_dataset_uri = model.predict_dataset(self.test_dataset_uri)
       end
-      update :prediction_dataset_uri => prediction_dataset_uri,
-             :real_runtime => benchmark.real
+      self.attributes = { :prediction_dataset_uri => prediction_dataset_uri,
+             :real_runtime => benchmark.real }
+      self.save
       
       compute_validation_stats(model)
     end
     
     def compute_validation_stats(model = nil)
       
-      model = OpenTox::Model::PredictionModel.find(@model_uri) unless model
-      $sinatra.halt 400, "model not found: "+@model_uri.to_s unless model
+      model = OpenTox::Model::PredictionModel.find(self.model_uri) unless model
+      $sinatra.halt 400, "model not found: "+self.model_uri.to_s unless model
       
-      update :prediction_feature => model.dependentVariables unless @prediction_feature
-      update :algorithm_uri => model.algorithm unless @algorithm_uri
+      self.attributes = { :prediction_feature => model.dependentVariables } unless self.prediction_feature 
+      self.attributes = { :algorithm_uri => model.algorithm } unless self.algorithm_uri
+      self.save
       
       LOGGER.debug "computing prediction stats"
       prediction = Lib::OTPredictions.new( model.classification?, 
-        @test_dataset_uri, @test_target_dataset_uri, @prediction_feature, 
-        @prediction_dataset_uri, model.predictedVariables )
+        self.test_dataset_uri, self.test_target_dataset_uri, self.prediction_feature, 
+        self.prediction_dataset_uri, model.predictedVariables )
       if prediction.classification?
-        update :classification_statistics => prediction.compute_stats
+        self.attributes = { :classification_statistics => prediction.compute_stats.to_yaml }
       else
-        update :regression_statistics => prediction.compute_stats
+        self.attributes = { :regression_statistics => prediction.compute_stats.to_yaml }
       end
       
-      update :num_instances => prediction.num_instances,
+      self.attributes = { :num_instances => prediction.num_instances,
              :num_without_class => prediction.num_without_class,
              :percent_without_class => prediction.percent_without_class,
              :num_unpredicted => prediction.num_unpredicted,
-             :percent_unpredicted => prediction.percent_unpredicted
+             :percent_unpredicted => prediction.percent_unpredicted }
+      self.save
     end
   end
   
@@ -157,21 +160,26 @@ module Validation
       
       $sinatra.halt 500,"do not set id manually" if params[:id]
       $sinatra.halt 500,"do not set uri manually" if params[:uri]
-      super params
       
-      unless save
-        raise "error saving crossvalidation "+errors.inspect
-      end
-      reload
-      raise "internal error, crossvalidation-id not set" if @id==nil
-      update :uri => $sinatra.url_for("/crossvalidation/"+@id.to_s, :full)
+      params[:num_folds] = 10 if params[:num_folds]==nil
+      params[:random_seed] = 1 if params[:random_seed]==nil
+      params[:stratified] = false if params[:stratified]==nil
+      super params
+      self.save
+      raise "internal error, crossvalidation-id not set" if self.id==nil
+      self.attributes = { :crossvalidation_uri => $sinatra.url_for("/crossvalidation/"+self.id.to_s, :full) }
+      self.save
+    end
+    
+    def uri
+      self.crossvalidation_uri
     end
     
     # deletes a crossvalidation, all validations are deleted as well
     def delete
-        Validation.all(:crossvalidation_id => @id).each{ |v| v.delete }
+        Validation.all(:crossvalidation_id => self.id).each{ |v| v.delete }
         destroy
-        "Successfully deleted crossvalidation "+@id.to_s+"."
+        "Successfully deleted crossvalidation "+self.id.to_s+"."
     end
     
     # creates the cv folds
@@ -185,7 +193,7 @@ module Validation
     def perform_cv ( algorithm_params=nil )
       
       LOGGER.debug "perform cv validations"
-      Validation.all( :crossvalidation_id => id ).each do |v|
+      Validation.find( :all, :conditions => { :crossvalidation_id => id } ).each do |v|
         v.validate_algorithm( algorithm_params )
         #break
       end
@@ -196,26 +204,26 @@ module Validation
     # returns true if successfull, false otherwise
     def copy_cv_datasets( prediction_feature )
       
-      equal_cvs = Crossvalidation.all( { :dataset_uri => @dataset_uri, :num_folds => @num_folds, 
-                                          :stratified => @stratified, :random_seed => @random_seed } ).reject{ |cv| cv.id == @id }
+      equal_cvs = Crossvalidation.all( { :dataset_uri => self.dataset_uri, :num_folds => self.num_folds, 
+                                          :stratified => self.stratified, :random_seed => self.random_seed } ).reject{ |cv| cv.id == self.id }
       return false if equal_cvs.size == 0 
       cv = equal_cvs[0]
       Validation.all( :crossvalidation_id => cv.id ).each do |v|
         
-        if @stratified and v.prediction_feature != prediction_feature
+        if self.stratified and v.prediction_feature != prediction_feature
           return false;
         end
         unless (OpenTox::Dataset.find(v.training_dataset_uri) and 
               OpenTox::Dataset.find(v.test_dataset_uri))
           LOGGER.debug "dataset uris obsolete, aborting copy of datasets"
-          Validation.all( :crossvalidation_id => @id ).each{ |v| v.delete }
+          Validation.all( :crossvalidation_id => self.id ).each{ |v| v.delete }
           return false
         end
-        validation = Validation.new :crossvalidation_id => @id,
+        validation = Validation.new :crossvalidation_id => self.id,
                                     :crossvalidation_fold => v.crossvalidation_fold,
                                     :training_dataset_uri => v.training_dataset_uri, 
                                     :test_dataset_uri => v.test_dataset_uri,
-                                    :algorithm_uri => @algorithm_uri
+                                    :algorithm_uri => self.algorithm_uri
       end
       LOGGER.debug "copyied dataset uris from cv "+cv.uri.to_s
       return true
@@ -225,14 +233,15 @@ module Validation
     # stores uris in validation objects 
     def create_new_cv_datasets( prediction_feature )
       
+      $sinatra.halt(500,"random seed not set") unless self.random_seed
       LOGGER.debug "creating datasets for crossvalidation"
-      orig_dataset = OpenTox::Dataset.find(@dataset_uri)
-      $sinatra.halt 400, "Dataset not found: "+@dataset_uri.to_s unless orig_dataset
+      orig_dataset = OpenTox::Dataset.find(self.dataset_uri)
+      $sinatra.halt 400, "Dataset not found: "+self.dataset_uri.to_s unless orig_dataset
       
-      shuffled_compounds = orig_dataset.compounds.shuffle( @random_seed )
+      shuffled_compounds = orig_dataset.compounds.shuffle( self.random_seed )
       
-      unless @stratified        
-        split_compounds = shuffled_compounds.chunk( @num_folds )
+      unless self.stratified        
+        split_compounds = shuffled_compounds.chunk( self.num_folds )
       else
         class_compounds = {} # "inactive" => compounds[], "active" => compounds[] .. 
         shuffled_compounds.each do |c|
@@ -247,7 +256,7 @@ module Validation
       
         split_class_compounds = [] # inactive_compounds[fold_i][], active_compounds[fold_i][], ..
         class_compounds.values.each do |compounds|
-          split_class_compounds.push( compounds.chunk( @num_folds ) )
+          split_class_compounds.push( compounds.chunk( self.num_folds ) )
         end
         LOGGER.debug "stratified cv: splits for class values: "+split_class_compounds.collect{ |c| c.collect{ |cc| cc.size }.join("/") }.join(", ")
         
@@ -258,7 +267,7 @@ module Validation
           # step 1: sort current split in ascending order
           split_comp.sort!{|x,y| x.size <=> y.size }
           # step 2: add splits
-          (0..@num_folds-1).each do |i|
+          (0..self.num_folds-1).each do |i|
             unless split_compounds[i]
               split_compounds[i] = split_comp[i]
             else
@@ -273,19 +282,19 @@ module Validation
       
       test_features = orig_dataset.features.dclone - [prediction_feature]
       
-      (1..@num_folds).each do |n|
+      (1..self.num_folds).each do |n|
         
-        datasetname = 'cv'+@id.to_s +
+        datasetname = 'cv'+self.id.to_s +
                #'_d'+orig_dataset.name.to_s +
-               '_f'+n.to_s+'of'+@num_folds.to_s+
-               '_r'+@random_seed.to_s+
-               '_s'+@stratified.to_s 
+               '_f'+n.to_s+'of'+self.num_folds.to_s+
+               '_r'+self.random_seed.to_s+
+               '_s'+self.stratified.to_s 
         source = $sinatra.url_for('/crossvalidation',:full)
         
         test_compounds = []
         train_compounds = []
         
-        (1..@num_folds).each do |nn|
+        (1..self.num_folds).each do |nn|
           compounds = split_compounds.at(nn-1)
           
           if n == nn
@@ -295,7 +304,7 @@ module Validation
           end 
         end
         
-        $sinatra.halt 500,"internal error, num test compounds not correct" unless (shuffled_compounds.size/@num_folds - test_compounds.size).abs <= 1 
+        $sinatra.halt 500,"internal error, num test compounds not correct" unless (shuffled_compounds.size/self.num_folds - test_compounds.size).abs <= 1 
         $sinatra.halt 500,"internal error, num train compounds not correct" unless shuffled_compounds.size - test_compounds.size == train_compounds.size
         
         LOGGER.debug "training set: "+datasetname+"_train, compounds: "+train_compounds.size.to_s
@@ -306,10 +315,10 @@ module Validation
       
         validation = Validation.new :training_dataset_uri => train_dataset_uri, 
                                     :test_dataset_uri => test_dataset_uri,
-                                    :test_target_dataset_uri => @dataset_uri,
-                                    :crossvalidation_id => @id, :crossvalidation_fold => n,
+                                    :test_target_dataset_uri => self.dataset_uri,
+                                    :crossvalidation_id => self.id, :crossvalidation_fold => n,
                                     :prediction_feature => prediction_feature,
-                                    :algorithm_uri => @algorithm_uri
+                                    :algorithm_uri => self.algorithm_uri
       end
     end
   end
diff --git a/validation/validation_test.rb b/validation/validation_test.rb
index 0d59c42..1e3908a 100644
--- a/validation/validation_test.rb
+++ b/validation/validation_test.rb
@@ -15,16 +15,20 @@ class ValidationTest < Test::Unit::TestCase
   include Lib::TestUtil
   
   def test_it
+    $test_case = self
+
+    #get "/1"
+    #puts last_response.body
     
 #    post "/test_validation",:select=>"6d" #,:report=>"yes,please"
 #    puts last_response.body
     
-    #run_test("6a")
+    run_test("2b")
  
-    #puts Nightly.build_nightly("6")
+    #puts Nightly.build_nightly("1", false)
     
     #prepare_examples
-    do_test_examples # USES CURL, DO NOT FORGET TO RESTART VALIDATION SERVICE
+    #do_test_examples # USES CURL, DO NOT FORGET TO RESTART VALIDATION SERVICE
   end
 
   def app
@@ -32,7 +36,6 @@ class ValidationTest < Test::Unit::TestCase
   end
   
   def run_test(select)
-    $test_case = self
     validationExamples = ValidationExamples.select(select)
     validationExamples.each do |vv|
       vv.each do |v|