test/nightly rewrite

1 files changed, 214 insertions, 0 deletions

diff --git a/test/test_examples.rb b/test/test_examples.rb
new file mode 100644
index 0000000..d08e358
--- /dev/null
+++ b/test/test_examples.rb
@@ -0,0 +1,214 @@
+
+require 'test/test_examples_util.rb'
+
+class Class
+  def humanize
+    self.to_s.gsub(/.*::/, "").gsub(/([^^A-Z_])([A-Z])/, '\1-\2').gsub(/_/,"-")
+  end
+end
+
+module ValidationExamples
+  
+  ########################################################################################################
+  
+  class ABSTRACTHamsterSplit < 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
+    def initialize
+      @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+      super
+    end
+  end
+  
+  class MajorityHamsterSplit < ABSTRACTHamsterSplit
+    def initialize
+      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+      super
+    end
+  end
+  
+  ########################################################################################################
+
+  class ABSTRACTHamsterTrainingTest < 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")
+      @test_dataset_file = File.new("data/hamster_carcinogenicity.test.yaml","r")
+      @prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+    end
+  end
+  
+  class MajorityHamsterTrainingTest < ABSTRACTHamsterTrainingTest
+    def initialize
+      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+      super
+    end
+  end
+  
+  class LazarHamsterTrainingTest < ABSTRACTHamsterTrainingTest
+    def initialize
+      @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+      super
+    end
+  end
+  
+  ########################################################################################################  
+
+  class ABSTRACTHamsterCrossvalidation < CrossValidation
+    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 MajorityHamsterCrossvalidation < ABSTRACTHamsterCrossvalidation
+    def initialize
+      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+      super
+    end
+  end
+
+  class LazarHamsterCrossvalidation < ABSTRACTHamsterCrossvalidation
+    def initialize
+      @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+      super
+    end
+  end
+  
+  ########################################################################################################  
+
+  class ABSTRACT_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
+    def initialize
+      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+      super
+    end
+  end
+  
+  class LazarISTHamsterCrossvalidation < ABSTRACT_ISTHamsterCrossvalidationInsilico
+    def initialize
+      @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+      super
+    end
+  end
+  
+  class ISTLazarISTHamsterCrossvalidation < ABSTRACT_ISTHamsterCrossvalidationInsilico
+    def initialize
+      @algorithm_uri = "http://webservices.in-silico.ch/algorithm/lazar"
+      @algorithm_params = "feature_generation_uri=http://webservices.in-silico.ch/algorithm/fminer"
+      super
+    end
+  end
+
+  
+  ########################################################################################################
+  
+  class LR_AmbitCacoModel < ModelValidation
+    def initialize
+      @model_uri = "http://apps.ideaconsult.net:8080/ambit2/model/33"
+      @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R545"
+      #@prediction_feature=http://apps.ideaconsult.net:8080/ambit2/feature/22200
+    end
+  end
+  
+  ########################################################################################################
+
+  class ABSTRACTCacoTrainingTest < 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"
+      @prediction_feature = "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/255510"
+    end
+  end
+  
+  class LR_AmbitCacoTrainingTest < ABSTRACTCacoTrainingTest
+    def initialize
+      @algorithm_uri = "http://ambit.uni-plovdiv.bg:8080/ambit2/algorithm/LR"
+      super
+    end
+  end
+  
+  class MLR_NTUA_CacoTrainingTest < ABSTRACTCacoTrainingTest
+    def initialize
+      @algorithm_uri = "http://opentox.ntua.gr:3003/algorithm/mlr"
+      super
+    end
+  end
+  
+  class MLR_NTUA2_CacoTrainingTest < ABSTRACTCacoTrainingTest
+    def initialize
+      @algorithm_uri = "http://opentox.ntua.gr:3004/algorithm/mlr"
+      super
+    end
+  end
+  
+  class MajorityCacoTrainingTest < ABSTRACTCacoTrainingTest
+    def initialize
+      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/regr/algorithm")
+      super
+    end
+  end
+  
+  ########################################################################################################
+    
+  @@list = {
+      "1" => [ LazarHamsterSplit, MajorityHamsterSplit ],
+      "1a" => [ LazarHamsterSplit ],
+      "1b" => [ MajorityHamsterSplit ],
+      
+      "2" => [ LazarHamsterTrainingTest, MajorityHamsterTrainingTest ],
+      "2a" => [ LazarHamsterTrainingTest ],
+      "2b" => [ MajorityHamsterTrainingTest ],
+      
+      "3" => [ LazarHamsterCrossvalidation, MajorityHamsterCrossvalidation ],
+      "3a" => [ LazarHamsterCrossvalidation ],
+      "3b" => [ MajorityHamsterCrossvalidation ],
+      
+      "4" => [ MajorityISTHamsterCrossvalidation, LazarISTHamsterCrossvalidation, ISTLazarISTHamsterCrossvalidation ],
+      "4a" => [ MajorityISTHamsterCrossvalidation ],
+      "4b" => [ LazarISTHamsterCrossvalidation ],
+      "4c" => [ ISTLazarISTHamsterCrossvalidation ],
+      
+      "5a" => [ LR_AmbitCacoModel ],
+      
+      "6" => [ LR_AmbitCacoTrainingTest, MLR_NTUA_CacoTrainingTest, MLR_NTUA2_CacoTrainingTest, MajorityCacoTrainingTest ],
+      "6a" => [ LR_AmbitCacoTrainingTest ],
+      "6b" => [ MLR_NTUA_CacoTrainingTest ],
+      "6c" => [ MLR_NTUA2_CacoTrainingTest ],
+      "6d" => [ MajorityCacoTrainingTest ],
+    }
+  
+  def self.list
+    @@list.sort.collect{|k,v| k+":\t"+v.collect{|vv| vv.humanize}.join("\n\t")+"\n"} #.join("\n")
+  end
+  
+  def self.select(csv_keys)
+    res = []
+    if csv_keys!=nil and csv_keys.size>0
+      csv_keys.split(",").each do |k|
+        raise "no key "+k.to_s unless @@list.has_key?(k)
+        res << @@list[k]
+      end
+    end
+    return res
+  end
+  
+end
+
+#puts ValidationExamples.list
+#puts ValidationExamples.select("1,2a").inspect
\ No newline at end of file