added report examples and example tests, new module Validation

1 files changed, 75 insertions, 10 deletions

diff --git a/example.rb b/example.rb
index e58e5f6..eb424b1 100644
--- a/example.rb
+++ b/example.rb
@@ -10,6 +10,8 @@ class Example
   @@train_data=File.join @@config[:services]["opentox-dataset"],"2"
   @@test_data=File.join @@config[:services]["opentox-dataset"],"3"
   
+  @@summary=""
+  
   def self.transform_example
   
     file = File.new("EXAMPLES", "r")
@@ -28,7 +30,10 @@ class Example
             "prediction_feature" => @@feature,
             "algorithm_uri" => @@alg,
             "algorithm_params" => @@alg_params,
-            "crossvalidation_id" => "1",}
+            "crossvalidation_id" => "1",
+            "validation_report_id" => "1",
+            "crossvalidation_report_id" => "1",
+            }
     
     sub.each do |k,v|
       res.gsub!(/<#{k}>/,v)
@@ -37,37 +42,97 @@ class Example
   end
   
   def self.delete_all(uri_list_service)
-    uri_list = RestClient.get(uri_list_service)
+    uri_list = OpenTox::RestClientWrapper.get(uri_list_service)
     uri_list.split("\n").each do |uri|
-      RestClient.delete(uri)
+      OpenTox::RestClientWrapper.delete(uri)
     end
   end
   
+  def self.log(log_string)
+    LOGGER.debug log_string
+    @@summary += log_string+"\n"
+  end
+  
   def self.prepare_example_resources
     
+    @@summary = ""
     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
+    data_uri = OpenTox::RestClientWrapper.post @@config[:services]["opentox-dataset"], data, :content_type => "application/rdf+xml"
+    log "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"],'/training_test_split'), { :dataset_uri => data_uri,
+    vali_uri = OpenTox::RestClientWrapper.post File.join(@@config[:services]["opentox-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
+    log "created validation via training test split "+vali_uri
     raise "failed to prepare demo" unless vali_uri==File.join(@@config[:services]["opentox-validation"],'/1')
     
     Lib::Crossvalidation.auto_migrate!
-    cv_uri = RestClient.post File.join(@@config[:services]["opentox-validation"],'/crossvalidation'), { :dataset_uri => data_uri,
+    cv_uri = OpenTox::RestClientWrapper.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
+    log "created crossvalidation "+cv_uri
     raise "failed to prepare demo" unless cv_uri==File.join(@@config[:services]["opentox-validation"],'/crossvalidation/1')
     
+    delete_all(File.join(@@config[:services]["opentox-validation"],"/report/validation"))
+    val_report_uri = OpenTox::RestClientWrapper.post File.join(@@config[:services]["opentox-validation"],'/report/validation'), { :validation_uris => vali_uri }
+    log "created validation report: "+val_report_uri
+    raise "failed to prepare demo" unless val_report_uri==File.join(@@config[:services]["opentox-validation"],'/report/validation/1')
+    
+    delete_all(File.join(@@config[:services]["opentox-validation"],"/report/crossvalidation"))
+    cv_report_uri = OpenTox::RestClientWrapper.post File.join(@@config[:services]["opentox-validation"],'/report/crossvalidation'), { :validation_uris => cv_uri }
+    log "created crossvalidation report: "+cv_report_uri
+    raise "failed to prepare demo" unless cv_report_uri==File.join(@@config[:services]["opentox-validation"],'/report/crossvalidation/1')
+    log "done"
+
+    @@summary
+  end
+  
+  
+  def self.test_examples
+    lines = transform_example.split("\n")
+    curl_call = false
+    curl_calls = []
+    
+    lines.each do |line|
+      if line =~ /^\s*>>>\s*.*/
+        line.gsub!(/^\s*>>>\s*/,"")
+        if line =~ /.*\s*\\s*$/
+          curl_call = true
+          line.gsub!(/\s*\\s*$/," ")
+        else
+          curl_call = false
+        end
+        curl_calls.push( line )
+      elsif curl_call
+        if line =~ /.*\s*\\s*$/
+          curl_call = true
+          line.gsub!(/\s*\\s*$/," ")
+        else
+          curl_call = false
+        end
+        curl_calls[-1] = curl_calls[-1]+line
+      end
+    end
+    
+    @@summary = ""
+    curl_calls.each do |cmd|
+      log "testing: "+cmd
+      IO.popen(cmd.to_s+" 2> /dev/null") do |f| 
+        while line = f.gets
+          #response += indent.to_s+line
+        end
+      end
+      log ($?==0)?"ok":"failed"
+    end
+    @@summary  
   end
-end
\ No newline at end of file
+  
+end