Merge branch 'development' of github.com:helma/opentox-validation into development

Conflicts:
	application.rb
	example.rb
	report/report_persistance.rb

10 files changed, 56 insertions, 56 deletions

diff --git a/Rakefile b/Rakefile
index 3c39279..c344157 100644
--- a/Rakefile
+++ b/Rakefile
@@ -40,8 +40,8 @@ task :load_config do
   config_dir = File.join(basedir, "config")
   config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml")
   if File.exist?(config_file)
-    @@config = YAML.load_file(config_file)
-    raise "could not load config, config file: "+config_file.to_s unless @@config
+    CONFIG = YAML.load_file(config_file)
+    raise "could not load config, config file: "+config_file.to_s unless CONFIG
   end
   puts "config loaded"
 end
@@ -49,14 +49,14 @@ end
 # USER VERSION 0 instead
 #desc "Clear database"
 #task :clear_db => :load_config  do
-#  if  @@config[:database][:adapter]=="mysql"
+#  if  CONFIG[:database][:adapter]=="mysql"
 #    clear = nil
 #    IO.popen("locate clear_mysql.sh"){ |f| clear=f.gets.chomp("\n") }
 #    raise "clear_mysql.sh not found" unless clear
-#    cmd = clear+" "+@@config[:database][:username]+" "+@@config[:database][:password]+" "+@@config[:database][:database]
+#    cmd = clear+" "+CONFIG[:database][:username]+" "+CONFIG[:database][:password]+" "+CONFIG[:database][:database]
 #    IO.popen(cmd){ |f| puts f.gets }
 #  else
-#    raise "clear not implemented for database-type: "+@@config[:database][:adapter]
+#    raise "clear not implemented for database-type: "+CONFIG[:database][:adapter]
 #  end
 #end
 
@@ -64,11 +64,11 @@ desc "Migrate the database through scripts in db/migrate. Target specific versio
 task :migrate => :load_config do
   require 'active_record'
   ActiveRecord::Base.establish_connection(  
-       :adapter => @@config[:database][:adapter],
-       :host => @@config[:database][:host],
-       :database => @@config[:database][:database],
-       :username => @@config[:database][:username],
-       :password => @@config[:database][:password]
+       :adapter => CONFIG[:database][:adapter],
+       :host => CONFIG[:database][:host],
+       :database => CONFIG[:database][:database],
+       :username => CONFIG[:database][:username],
+       :password => CONFIG[:database][:password]
        )  
   ActiveRecord::Base.logger = Logger.new($stdout)
   ActiveRecord::Migrator.migrate('db/migrate', ENV["VERSION"] ? ENV["VERSION"].to_i : 2 )
diff --git a/application.rb b/application.rb
index a8ae5a8..f7208a4 100644
--- a/application.rb
+++ b/application.rb
@@ -1,6 +1,6 @@
 require 'rubygems'
 gem 'opentox-ruby-api-wrapper', '= 1.6.0'
-[ 'sinatra', 'sinatra/url_for', 'opentox-ruby-api-wrapper' ].each do |lib|
+[ 'sinatra', 'sinatra/url_for', 'opentox-ruby-api-wrapper', 'logger' ].each do |lib|
   require lib
 end
 
diff --git a/db/migrate/002_init_reports.rb b/db/migrate/002_init_reports.rb
index 8029223..dcf44a1 100644
--- a/db/migrate/002_init_reports.rb
+++ b/db/migrate/002_init_reports.rb
@@ -22,9 +22,9 @@ class InitReports < ActiveRecord::Migration
 
   def self.down
     drop_table :report_datum if table_exists? :report_datum
-    if @@config[:reports] and @@config[:reports][:report_dir]
+    if CONFIG[:reports] and CONFIG[:reports][:report_dir]
       ["validation", "crossvalidation", "algorithm_comparison"].each do |t|
-        dir = File.join(@@config[:reports][:report_dir],t)
+        dir = File.join(CONFIG[:reports][:report_dir],t)
         if File.exist?(dir)
           puts "deleting dir "+dir.to_s
           FileUtils.rm_rf(dir)
diff --git a/example.rb b/example.rb
index ceb1329..d71cc30 100644
--- a/example.rb
+++ b/example.rb
@@ -5,7 +5,7 @@ class Example
   
   @@file=File.new("data/hamster_carcinogenicity.yaml","r")
   @@file_type="text/x-yaml"
-  @@model=File.join @@config[:services]["opentox-model"],"1"
+  @@model=File.join CONFIG[:services]["opentox-model"],"1"
   @@feature= URI.encode("http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)")
   @@predicted_feature= URI.encode("http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)_lazar_classification")
   @@alg = File.join @@config[:services]["opentox-algorithm"],"lazar"
@@ -28,7 +28,7 @@ class Example
     end
     file.close
     
-    sub = { "validation_service" => @@config[:services]["opentox-validation"].chomp("/"), 
+    sub = { "validation_service" => CONFIG[:services]["opentox-validation"].chomp("/"), 
             "validation_id" => "1",
             "model_uri" => @@model,
             "dataset_uri" => @@data,
@@ -61,17 +61,17 @@ class Example
     ActiveRecord::Migrator.migrate('db/migrate', 1 )
     ActiveRecord::Migrator.migrate('db/migrate', 2 )
     
-    #delete_all(@@config[:services]["opentox-dataset"])
-    log OpenTox::RestClientWrapper.delete @@config[:services]["opentox-dataset"]
+    #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")
+    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"]
+    #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], 
@@ -87,7 +87,7 @@ class Example
     cv.perform_cv( @@alg_params )
     
     log "create validation report"
-    rep = Reports::ReportService.new(File.join(@@config[:services]["opentox-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)
     
diff --git a/lib/validation_db.rb b/lib/validation_db.rb
index 1152abf..7afab90 100644
--- a/lib/validation_db.rb
+++ b/lib/validation_db.rb
@@ -6,11 +6,11 @@ require "lib/merge.rb"
 
 unless ActiveRecord::Base.connected?
   ActiveRecord::Base.establish_connection(  
-     :adapter => @@config[:database][:adapter],
-     :host => @@config[:database][:host],
-     :database => @@config[:database][:database],
-     :username => @@config[:database][:username],
-     :password => @@config[:database][:password]
+     :adapter => CONFIG[:database][:adapter],
+     :host => CONFIG[:database][:host],
+     :database => CONFIG[:database][:database],
+     :username => CONFIG[:database][:username],
+     :password => CONFIG[:database][:password]
   )
   ActiveRecord::Base.logger = Logger.new("/dev/null")
 end
diff --git a/nightly/nightly.rb b/nightly/nightly.rb
index f402691..f68691e 100644
--- a/nightly/nightly.rb
+++ b/nightly/nightly.rb
@@ -98,7 +98,7 @@ class Nightly
       end
       
       #benchmarks.collect{|b| b.uris}.join(",")
-      File.join(@@config[:services]["opentox-validation"],"nightly")
+      File.join(CONFIG[:services]["opentox-validation"],"nightly")
     end
     if defined?(halt)
       halt 202,task_uri
@@ -219,4 +219,4 @@ class Nightly
     end
   end
   
-end
\ No newline at end of file
+end
diff --git a/report/environment.rb b/report/environment.rb
index 714cebe..04221de 100644
--- a/report/environment.rb
+++ b/report/environment.rb
@@ -8,11 +8,11 @@ gem 'ruby-plot', '= 0.0.2'
 
 unless ActiveRecord::Base.connected?
   ActiveRecord::Base.establish_connection(  
-     :adapter => @@config[:database][:adapter],
-     :host => @@config[:database][:host],
-     :database => @@config[:database][:database],
-     :username => @@config[:database][:username],
-     :password => @@config[:database][:password]
+     :adapter => CONFIG[:database][:adapter],
+     :host => CONFIG[:database][:host],
+     :database => CONFIG[:database][:database],
+     :username => CONFIG[:database][:username],
+     :password => CONFIG[:database][:password]
   )
   ActiveRecord::Base.logger = Logger.new("/dev/null")
 end
diff --git a/report/report_test.rb b/report/report_test.rb
index 1c838bf..2920fd3 100644
--- a/report/report_test.rb
+++ b/report/report_test.rb
@@ -119,12 +119,12 @@ end
 #class Reports::ReportServiceTest < Test::Unit::TestCase
 #  include Lib::TestUtil
 #
-#  WS_VAL = @@config[:services]["opentox-validation"]
-#  WS_DATA=@@config[:services]["opentox-dataset"]
+#  WS_VAL = CONFIG[:services]["opentox-validation"]
+#  WS_DATA=CONFIG[:services]["opentox-dataset"]
 #  FILE=File.new("data/hamster_carcinogenicity.owl","r")
 #  
-#  WS_CLASS_ALG=File.join(@@config[:services]["opentox-algorithm"],"lazar")
-#  WS_FEATURE_ALG=File.join(@@config[:services]["opentox-algorithm"],"fminer")
+#  WS_CLASS_ALG=File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+#  WS_FEATURE_ALG=File.join(CONFIG[:services]["opentox-algorithm"],"fminer")
 #  
 #  #WS_CLASS_ALG_2="localhost:4008/algorithm"
 #  #WS_FEATURE_ALG_2=nil
@@ -334,4 +334,4 @@ end
 #    
 #  end
 #  
-#end
\ No newline at end of file
+#end
diff --git a/test/test_examples.rb b/test/test_examples.rb
index bbe6ddd..34a9f67 100644
--- a/test/test_examples.rb
+++ b/test/test_examples.rb
@@ -67,15 +67,15 @@ module ValidationExamples
   
   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")
       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
@@ -93,15 +93,15 @@ module ValidationExamples
   
   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")
       super
     end
   end
@@ -118,15 +118,15 @@ module ValidationExamples
   
   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")
       super
     end
   end
@@ -142,15 +142,15 @@ 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
@@ -240,7 +240,7 @@ 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
@@ -301,4 +301,4 @@ module ValidationExamples
 end
 
 #puts ValidationExamples.list
-#puts ValidationExamples.select("1,2a").inspect
\ No newline at end of file
+#puts ValidationExamples.select("1,2a").inspect
diff --git a/test/test_examples_util.rb b/test/test_examples_util.rb
index 09f7d6c..7eb69ff 100644
--- a/test/test_examples_util.rb
+++ b/test/test_examples_util.rb
@@ -5,7 +5,7 @@ module ValidationExamples
 
     @@dataset_uris = {}
 
-    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)
@@ -40,7 +40,7 @@ module ValidationExamples
         $test_case.post uri,params 
         return wait($test_case.last_response.body)
       else
-        return OpenTox::RestClientWrapper.post(File.join(@@config[:services]["opentox-validation"],uri),params)
+        return OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],uri),params)
       end
     end
     
@@ -50,7 +50,7 @@ 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
     
@@ -295,4 +295,4 @@ module ValidationExamples
       "crossvalidation"
     end
   end
-end
\ No newline at end of file
+end