remaining merge conflicts removed

8 files changed, 9 insertions, 170 deletions

diff --git a/application.rb b/application.rb
index f543167..ad9653a 100755
--- a/application.rb
+++ b/application.rb
@@ -3,6 +3,14 @@ gem "opentox-ruby", "~> 0"
 [ 'sinatra', 'sinatra/url_for', 'opentox-ruby' ].each do |lib|
   require lib
 end
+['dm-core', 'dm-serializer', 'dm-timestamps', 'dm-types', 'dm-migrations', 'dm-validations' ].each{|lib| require lib }
+DataMapper.setup(:default, { 
+    :adapter  => CONFIG[:database][:adapter],
+    :database => CONFIG[:database][:database],
+    :username => CONFIG[:database][:username],
+    :password => CONFIG[:database][:password],
+    :host     => CONFIG[:database][:host]})
+set :lock, true
 
 #unless(defined? LOGGER)
   #LOGGER = Logger.new(STDOUT)
diff --git a/db/migrate/000_drop_validations.rb b/db/migrate/000_drop_validations.rb
deleted file mode 100755
index fb70967..0000000
--- a/db/migrate/000_drop_validations.rb
+++ /dev/null
@@ -1,13 +0,0 @@
-
-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
deleted file mode 100755
index 2189568..0000000
--- a/db/migrate/001_init_validation.rb
+++ /dev/null
@@ -1,65 +0,0 @@
-
-class InitValidation < ActiveRecord::Migration
-  def self.up
-
-    create_table :crossvalidations do |t|
-      
-      [: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, :finished ].each do |p|
-        t.column p, :boolean, :null => false
-      end
-    end
-    
-    create_table :validations do |t|
-      
-      [:validation_type,
-       :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
-      
-      [ :finished ].each do |p|
-        t.column p, :boolean, :null => false
-      end      
-    end
-  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/002_init_reports.rb b/db/migrate/002_init_reports.rb
deleted file mode 100755
index dcf44a1..0000000
--- a/db/migrate/002_init_reports.rb
+++ /dev/null
@@ -1,36 +0,0 @@
-
-class InitReports < ActiveRecord::Migration
-  def self.up
-
-    create_table :report_datum do |t|
-      
-      [:report_uri,
-       :report_type
-       ].each do |p|
-        t.column p, :string, :limit => 255
-      end
-      
-      [:created_at ].each do |p|
-        t.column p, :datetime 
-      end
-      
-      [:validation_uris, :crossvalidation_uris, :model_uris, :algorithm_uris].each do |p|
-        t.column(p, :text, :limit => 16320)
-      end
-    end
-  end
-
-  def self.down
-    drop_table :report_datum if table_exists? :report_datum
-    if CONFIG[:reports] and CONFIG[:reports][:report_dir]
-      ["validation", "crossvalidation", "algorithm_comparison"].each do |t|
-        dir = File.join(CONFIG[:reports][:report_dir],t)
-        if File.exist?(dir)
-          puts "deleting dir "+dir.to_s
-          FileUtils.rm_rf(dir)
-        end
-      end
-    end
-  end
-end
-
diff --git a/example.rb b/example.rb
index c691375..07151a8 100755
--- a/example.rb
+++ b/example.rb
@@ -58,44 +58,6 @@ class Example
     #TODO
     subjectid = nil
     
-<<<<<<< HEAD
-    #delete_all(CONFIG[:services]["opentox-dataset"])
-    log OpenTox::RestClientWrapper.delete CONFIG[:services]["opentox-dataset"]
-    
-    log "upload dataset"
-    halt 400,"File not found: "+@@file.path.to_s unless File.exist?(@@file.path)
-    data = File.read(@@file.path)
-    data_uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:content_type => @@file_type},data).chomp("\n")
-    
-    log "train-test-validation"
-    #delete_all(CONFIG[:services]["opentox-model"])
-    OpenTox::RestClientWrapper.delete CONFIG[:services]["opentox-model"]
-    
-    split_params = Validation::Util.train_test_dataset_split(data_uri, URI.decode(@@feature), 0.9, 1)
-    v = Validation::Validation.new :training_dataset_uri => split_params[:training_dataset_uri], 
-                   :test_dataset_uri => split_params[:test_dataset_uri],
-                   :test_target_dataset_uri => data_uri,
-                   :prediction_feature => URI.decode(@@feature),
-                   :algorithm_uri => @@alg
-    v.validate_algorithm( @@alg_params ) 
-    
-    log "crossvalidation"
-    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 )
-    
-    log "create validation report"
-    rep = Reports::ReportService.new(File.join(CONFIG[:services]["opentox-validation"],"report"))
-    rep.delete_all_reports("validation")
-    rep.create_report("validation",v.validation_uri)
-    
-    log "create crossvalidation report"
-    rep.delete_all_reports("crossvalidation")
-    rep.create_report("crossvalidation",cv.crossvalidation_uri)
-    
-    log "done"
-    @@summary
-=======
     task = OpenTox::Task.create("prepare examples", "n/a") do |task|
       @@summary = ""
       #delete validations
@@ -163,7 +125,6 @@ class Example
       @@summary
     end
     return_task(task)
->>>>>>> mguetlein/test
   end
   
   # performs all curl calls listed in examples after ">>>", next line is added if line ends with "\"
diff --git a/report/report_test.rb b/report/report_test.rb
index 57e867b..571d6d8 100755
--- a/report/report_test.rb
+++ b/report/report_test.rb
@@ -344,4 +344,4 @@ end
 #    
 #  end
 #  
-#end
+#end
\ No newline at end of file
diff --git a/test/test_examples.rb b/test/test_examples.rb
index 9476ed7..3c6f00e 100755
--- a/test/test_examples.rb
+++ b/test/test_examples.rb
@@ -188,11 +188,7 @@ module ValidationExamples
   class LazarHamsterTrainingTest < HamsterTrainingTest
     def initialize
       @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
-<<<<<<< HEAD
-      @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer")
-=======
       @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
->>>>>>> mguetlein/test
       super
     end
   end
@@ -220,11 +216,7 @@ module ValidationExamples
   class LazarHamsterCrossvalidation < HamsterCrossvalidation
     def initialize
       @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
-<<<<<<< HEAD
-      @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer")
-=======
       @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
->>>>>>> mguetlein/test
       super
     end
   end
diff --git a/test/test_examples_util.rb b/test/test_examples_util.rb
index 56bee6b..a5f2867 100755
--- a/test/test_examples_util.rb
+++ b/test/test_examples_util.rb
@@ -66,11 +66,7 @@ module ValidationExamples
         $test_case.post uri,params
         return wait($test_case.last_response.body)
       else
-<<<<<<< HEAD
-        return OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],uri),params)
-=======
         return OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],uri),params,nil,waiting_task).to_s
->>>>>>> mguetlein/test
       end
     end
     
@@ -93,11 +89,7 @@ module ValidationExamples
         $test_case.delete uri,{:subjectid => SUBJECTID},'HTTP_ACCEPT' => accept_header 
         return wait($test_case.last_response.body)
       else
-<<<<<<< HEAD
-        return OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],uri),{:accept => accept_header})
-=======
         return OpenTox::RestClientWrapper.delete(File.join(CONFIG[:services]["opentox-validation"],uri),{:accept => accept_header,:subjectid => SUBJECTID})
->>>>>>> mguetlein/test
       end
     end