add validations to crossvalidation output

added param algorihtm_params to split and cv
added examples and example-preparation

1 files changed, 74 insertions, 18 deletions

diff --git a/application.rb b/application.rb
index fa444be..1c7106f 100644
--- a/application.rb
+++ b/application.rb
@@ -8,30 +8,86 @@ require "report/report_application.rb"
 end
 
 get '/examples/?' do
-  
-  transform_example
+  content_type "text/plain"
+  Demo.transform_example
+end
+
+get '/prepare_examples/?' do
+  Demo.prepare_example_resources
+  "done"
 end
 
 private
-def transform_example
 
-  file = File.new("EXAMPLES", "r")
-  res = ""
-  while (line = file.gets) 
-    res += line
-  end
-  file.close
+class Demo
   
-  sub = { "validation_service" => url_for("", :full), 
-          #"validation_id" => "??",
-          #"model_service" => "??",
-          #"model_id" => "??",
-          #"dataset_service" => "??",
-          "dataset_id" => "Hamster Carcenogenicity"}
+  @@file=File.new("data/hamster_carcinogenicity.owl","r")
+  @@model=File.join @@config[:services]["opentox-model"],"1"
+  @@feature="http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster"
+  @@alg = File.join @@config[:services]["opentox-algorithm"],"lazar"
+  @@alg_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+  @@data=File.join @@config[:services]["opentox-dataset"],"1"
+  @@train_data=File.join @@config[:services]["opentox-dataset"],"2"
+  @@test_data=File.join @@config[:services]["opentox-dataset"],"3"
   
-  sub.each do |k,v|
-    res.gsub!(/<#{k}>/,v)
+  def self.transform_example
+  
+    file = File.new("EXAMPLES", "r")
+    res = ""
+    while (line = file.gets) 
+      res += line
+    end
+    file.close
+    
+    sub = { "validation_service" => @@config[:services]["opentox-validation"], 
+            "validation_id" => "1",
+            "model_uri" => @@model,
+            "dataset_uri" => @@data,
+            "training_dataset_uri" => @@train_data,
+            "test_dataset_uri" => @@test_data,
+            "prediction_feature" => @@feature,
+            "algorithm_uri" => @@alg,
+            "algorithm_params" => @@alg_params,
+            "crossvalidation_id" => "1",}
+    
+    sub.each do |k,v|
+      res.gsub!(/<#{k}>/,v)
+    end
+    res
+  end
+  
+  def self.delete_all(uri_list_service)
+    uri_list = RestClient.get(uri_list_service)
+    uri_list.split("\n").each do |uri|
+      RestClient.delete(uri)
+    end
   end
   
-  res
+  def self.prepare_example_resources
+    
+    delete_all(@@config[:services]["opentox-dataset"])
+    data = File.read(@@file.path)
+    data_uri = RestClient.post @@config[:services]["opentox-dataset"], data, :content_type => "application/rdf+xml"
+    puts "uploaded dataset "+data_uri
+    raise "failed to prepare demo" unless data_uri==@@data
+    
+    Lib::Validation.auto_migrate!
+    delete_all(@@config[:services]["opentox-model"])
+    vali_uri = RestClient.post File.join(@@config[:services]["opentox-validation"],'/validation/training_test_split'), { :dataset_uri => data_uri,
+                                                         :algorithm_uri => @@alg,
+                                                         :prediction_feature => @@feature,
+                                                         :algorithm_params => @@alg_params }
+    puts "created validation via training test split "+vali_uri
+    raise "failed to prepare demo" unless vali_uri==File.join(@@config[:services]["opentox-validation"],'/validation/1')
+    
+    Lib::Crossvalidation.auto_migrate!
+    cv_uri = RestClient.post File.join(@@config[:services]["opentox-validation"],'/crossvalidation'), { :dataset_uri => data_uri,
+                                                         :algorithm_uri => @@alg,
+                                                         :prediction_feature => @@feature,
+                                                         :algorithm_params => @@alg_params,
+                                                         :num_folds => 5, :stratified => false }
+    puts "created crossvalidation "+cv_uri
+    raise "failed to prepare demo" unless cv_uri==File.join(@@config[:services]["opentox-validation"],'/crossvalidation/1')
+    
+  end
 end