adjust to new wrapper, replace activerecord with datamapper (remove activerecord code), is_classification to feature_type

3 files changed, 167 insertions, 46 deletions

diff --git a/test/test_application.rb b/test/test_application.rb
index 48cced7..c6c7963 100644..100755
--- a/test/test_application.rb
+++ b/test/test_application.rb
@@ -2,7 +2,7 @@
 post '/test_validation/?' do
   validationExamples = ValidationExamples.select(params[:select])
   return "please \"select\" a single validation example:\n"+ValidationExamples.list if validationExamples.size!=1 or validationExamples[0].size!=1
-  OpenTox::Task.as_task("Test validation",url_for("/test_validation",:full), params) do
+  task = OpenTox::Task.create("Test validation",url_for("/test_validation",:full)) do #,params
     v = validationExamples[0][0]
     ex = v.new
     ex.upload_files
@@ -13,5 +13,6 @@ post '/test_validation/?' do
     raise ex.report_error if ex.report_error
     ex.validation_uri + (params[:report] ? ","+ex.report_uri : "")
   end
+  task.uri
 end
 
diff --git a/test/test_examples.rb b/test/test_examples.rb
index 8927fb1..63fb505 100644..100755
--- a/test/test_examples.rb
+++ b/test/test_examples.rb
@@ -19,15 +19,15 @@ module ValidationExamples
   
   class MajorityIrisCrossvalidation < IrisCrossvalidation
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/regr/algorithm")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/regr/algorithm")
       super
     end
   end
 
   class LazarIrisCrossvalidation < IrisCrossvalidation
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
-      @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer")
       super
     end
   end
@@ -43,15 +43,65 @@ module ValidationExamples
   
   class LazarIrisSplit < IrisSplit
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
-      @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+      @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 MajorityIrisSplit < IrisSplit
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/regr/algorithm")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/regr/algorithm")
+      super
+    end
+  end
+  
+  ########################################################################################################  
+  
+  class EPAFHMSplit < SplitTestValidation
+    def initialize
+      @dataset_file = File.new("data/EPAFHM.csv","r")
+      #@prediction_feature = "http://ot-dev.in-silico.ch/toxcreate/feature#IRIS%20unit%20risk"
+      @split_ratio = 0.95
+    end
+  end
+    
+  class LazarEPAFHMSplit < EPAFHMSplit
+    def initialize
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
+      super
+    end
+  end
+  
+  class MajorityEPAFHMSplit < EPAFHMSplit
+    def initialize
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/regr/algorithm")
+      super
+    end
+  end
+  
+    ########################################################################################################
+  
+    class EPAFHMCrossvalidation < CrossValidation
+    def initialize
+      @dataset_file = File.new("data/EPAFHM.csv","r")
+      #@prediction_feature = "http://ot-dev.in-silico.ch/toxcreate/feature#IRIS%20unit%20risk"
+      @num_folds = 10
+    end
+  end
+  
+  class MajorityEPAFHMCrossvalidation < EPAFHMCrossvalidation
+    def initialize
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/regr/algorithm")
+      super
+    end
+  end
+
+  class LazarEPAFHMCrossvalidation < EPAFHMCrossvalidation
+    def initialize
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
       super
     end
   end
@@ -61,21 +111,22 @@ module ValidationExamples
   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)"
+      #@prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+      @prediction_feature = "http://localhost/dataset/1/feature/hamster_carcinogenicity"
     end
   end
   
   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")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
       super
     end
   end
   
   class MajorityHamsterSplit < HamsterSplit
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
       super
     end
   end
@@ -85,21 +136,22 @@ module ValidationExamples
   class HamsterBootstrapping < BootstrappingValidation
     def initialize
       @dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
-      @prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+      #@prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+      @prediction_feature = "http://localhost/dataset/1/feature/hamster_carcinogenicity"
     end
   end
   
   class LazarHamsterBootstrapping < HamsterBootstrapping
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
-      @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
       super
     end
   end
   
   class MajorityHamsterBootstrapping < HamsterBootstrapping
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
       super
     end
   end  
@@ -111,21 +163,22 @@ module ValidationExamples
       @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)"
+      #@prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+      @prediction_feature = "http://localhost/dataset/1/feature/hamster_carcinogenicity"
     end
   end
   
   class MajorityHamsterTrainingTest < HamsterTrainingTest
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
       super
     end
   end
   
   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")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
       super
     end
   end
@@ -135,22 +188,23 @@ module ValidationExamples
   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)"
+      #@prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+      @prediction_feature = "http://localhost/dataset/1/feature/hamster_carcinogenicity"
       @num_folds = 10
     end
   end
   
   class MajorityHamsterCrossvalidation < HamsterCrossvalidation
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
       super
     end
   end
 
   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")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
       super
     end
   end
@@ -166,15 +220,15 @@ module ValidationExamples
   
   class MajorityISTHamsterCrossvalidation < ISTHamsterCrossvalidation
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
       super
     end
   end
   
   class LazarISTHamsterCrossvalidation < ISTHamsterCrossvalidation
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
-      @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer")
       super
     end
   end
@@ -215,7 +269,7 @@ module ValidationExamples
   
   class MajorityISTRatLiverCrossvalidation < ISTRatLiverCrossvalidation
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
       super
     end
   end
@@ -283,7 +337,7 @@ module ValidationExamples
   
   class MajorityCacoTrainingTest < CacoTrainingTest
     def initialize
-      @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/regr/algorithm")
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/regr/algorithm")
       super
     end
   end
@@ -331,6 +385,12 @@ module ValidationExamples
       "12" => [ LazarHamsterBootstrapping, MajorityHamsterBootstrapping ],
       "12a" => [ LazarHamsterBootstrapping ],
       "12b" => [ MajorityHamsterBootstrapping ],
+      
+      "13a" =>  [ LazarEPAFHMSplit ],
+      "13b" =>  [ MajorityEPAFHMSplit ],
+      
+      "14a" =>  [ LazarEPAFHMCrossvalidation ],
+      "14b" =>  [ MajorityEPAFHMCrossvalidation ],
     }
   
   def self.list
diff --git a/test/test_examples_util.rb b/test/test_examples_util.rb
index cc31fe5..b9a1c99 100644..100755
--- a/test/test_examples_util.rb
+++ b/test/test_examples_util.rb
@@ -4,20 +4,40 @@ module ValidationExamples
   class Util
 
     @@dataset_uris = {}
+    @@prediction_features = {}
 
-    def self.upload_dataset(file, dataset_service=@@config[:services]["opentox-dataset"], file_type="application/x-yaml")
+    def self.upload_dataset(file, dataset_service=CONFIG[:services]["opentox-dataset"]) #, file_type="application/x-yaml")
       raise "File not found: "+file.path.to_s unless File.exist?(file.path)
       if @@dataset_uris[file.path.to_s]==nil
-        data = File.read(file.path)
-        data_uri = OpenTox::RestClientWrapper.post(dataset_service,{:content_type => file_type},data).to_s.chomp
-        @@dataset_uris[file.path.to_s] = data_uri
-        LOGGER.debug "uploaded dataset: "+data_uri
+        LOGGER.debug "uploading file: "+file.path.to_s
+        if (file.path =~ /yaml$/)
+          data = File.read(file.path)
+          #data_uri = OpenTox::RestClientWrapper.post(dataset_service,{:content_type => file_type},data).to_s.chomp
+          #@@dataset_uris[file.path.to_s] = data_uri
+          #LOGGER.debug "uploaded dataset: "+data_uri
+          d = OpenTox::Dataset.create
+          d.load_yaml(data)
+          d.save
+          @@dataset_uris[file.path.to_s] = d.uri
+        elsif (file.path =~ /csv$/)
+          d = OpenTox::Dataset.create_from_csv_file(file.path)
+          raise "num features not 1 (="+d.features.keys.size.to_s+"), what to predict??" if d.features.keys.size != 1
+          @@prediction_features[file.path.to_s] = d.features.keys[0]
+          @@dataset_uris[file.path.to_s] = d.uri
+        else
+          raise "unknown file type: "+file.path.to_s
+        end
+        LOGGER.debug "uploaded dataset: "+d.uri
       else
         LOGGER.debug "file already uploaded: "+@@dataset_uris[file.path.to_s]
       end
       return @@dataset_uris[file.path.to_s]
     end
     
+    def self.prediction_feature_for_file(file)
+      @@prediction_features[file.path.to_s]
+    end
+    
     def self.build_compare_report(validation_examples)
       
       @comp = validation_examples[0].algorithm_uri==nil ? :model_uri : :algorithm_uri
@@ -35,12 +55,12 @@ module ValidationExamples
     end
     
     def self.validation_post(uri, params)
+      
       if $test_case
-        #puts "posting: "+uri+","+params.inspect
-        $test_case.post uri,params 
+        $test_case.post uri,params
         return wait($test_case.last_response.body)
       else
-        return OpenTox::RestClientWrapper.post(File.join(@@config[:services]["opentox-validation"],uri),params).to_s
+        return OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],uri),params).to_s
       end
     end
     
@@ -50,16 +70,27 @@ module ValidationExamples
         $test_case.get uri,nil,'HTTP_ACCEPT' => accept_header 
         return wait($test_case.last_response.body)
       else
-        return OpenTox::RestClientWrapper.get(File.join(@@config[:services]["opentox-validation"],uri),{:accept => accept_header})
+        return OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],uri),{:accept => accept_header})
+      end
+    end
+
+    def self.validation_delete(uri, accept_header='application/rdf+xml')
+      
+      if $test_case
+        $test_case.delete uri,nil,'HTTP_ACCEPT' => accept_header 
+        return wait($test_case.last_response.body)
+      else
+        return OpenTox::RestClientWrapper.delete(File.join(CONFIG[:services]["opentox-validation"],uri),{:accept => accept_header})
       end
     end
     
+    
     def self.wait(uri)
-      if OpenTox::Utils.task_uri?(uri)
-        task = OpenTox::Task.find(uri)
+      if uri.task_uri?
+        task = OpenTox::Task.find(uri.to_s.chomp)
         task.wait_for_completion
-        raise "task failed: "+uri.to_s+", error is:\n"+task.description if task.error?
-        uri = task.resultURI
+        raise "task failed: "+uri.to_s+", error is:\n"+task.description.to_s if task.error?
+        uri = task.result_uri
       end
       uri
     end
@@ -214,6 +245,10 @@ module ValidationExamples
             send("#{uri.to_s}=".to_sym, Util.upload_dataset(send(file)))
          end
       end
+     
+      if (params.include?(:prediction_feature) and @prediction_feature==nil and @dataset_uri and @dataset_file)
+        @prediction_feature = Util.prediction_feature_for_file(@dataset_file)
+      end
     end
       
     def check_requirements
@@ -222,21 +257,42 @@ module ValidationExamples
       end
     end
     
+    def delete
+      begin
+        if @validation_uri =~ /crossvalidation/
+          cv = "crossvalidation/"
+        else
+          cv = ""
+        end
+        Util.validation_delete '/'+cv+@validation_uri.split('/')[-1] if @validation_uri
+      rescue => ex
+        puts "Could not delete validation: "+ex.message
+      end
+      begin
+        Util.validation_delete '/report/'+report_type+'/'+@report_uri.split('/')[-1] if @report_uri
+      rescue => ex
+        puts "Could not delete report:' "+@report_uri+" "+ex.message
+      end
+    end
+    
     def report
       begin
         @report_uri = Util.validation_post '/report/'+report_type,{:validation_uris => @validation_uri}
       rescue => ex
+        puts "could not create report: "+ex.message
+        raise ex
         @report_error = ex.message
       end
     end
     
     def validate
-      #begin
+      begin
         @validation_uri = Util.validation_post '/'+validation_type, get_params
-      #rescue => ex
-      #  @validation_error = ex.message
-      #  LOGGER.error ex.message
-      #end
+      rescue => ex
+        puts "could not validate: "+ex.message
+        @validation_error = ex.message
+        LOGGER.error ex.message
+      end
     end
     
     def compare_yaml_vs_rdf
@@ -308,6 +364,10 @@ module ValidationExamples
     def opt_params
       [ :algorithm_params, :test_target_dataset_uri ]
     end
+    
+    def validation_type
+      "training_test_validation"
+    end
   end
   
   class SplitTestValidation < ValidationExample