Merge branch 'release/2.0.0'v2.0.0

14 files changed, 540 insertions, 104 deletions

diff --git a/Rakefile b/Rakefile
index 45affdc..49b72f8 100644
--- a/Rakefile
+++ b/Rakefile
@@ -31,7 +31,7 @@ task :teardown do
 end
 
 #[:all, :feature, :dataset, :fminer, :lazar, :authorization, :validation].each do |t|
-[:all, :feature, :dataset, :fminer, :lazar, :authorization].each do |t|
+[:all, :feature, :dataset, :fminer, :lazar, :authorization, :parser, :validation ].each do |t|
   task :teardown => t
   task t => :setup 
 end
diff --git a/algorithm.rb b/algorithm.rb
index 650a6df..772979b 100644
--- a/algorithm.rb
+++ b/algorithm.rb
@@ -20,8 +20,7 @@ class AlgorithmTest < Test::Unit::TestCase
 
   def test_metadata
     @algorithms.each do |algorithm|
-      #puts algorithm
-      validate_owl(algorithm, @@subjectid)
+      validate_owl(algorithm, @@subjectid) unless CONFIG[:services]["opentox-algorithm"].match(/localhost/)
     end
   end
 
diff --git a/authorization.rb b/authorization.rb
index 3772638..1d9b676 100644
--- a/authorization.rb
+++ b/authorization.rb
@@ -3,6 +3,10 @@ require "opentox-ruby"
 require "test/unit"
 
 TEST_URI  = "http://only_a_test/test/" + rand(1000000).to_s
+unless AA_SERVER #overwrite turned off A&A server for testing
+  AA_SERVER = "https://opensso.in-silico.ch"
+  @@subjectid = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW)
+end
 
 class TestOpenToxAuthorizationBasic < Test::Unit::TestCase
  
@@ -40,7 +44,7 @@ class TestOpenToxAuthorizationLDAP < Test::Unit::TestCase
   end  
 
   def test_02_list_user_groups
-    assert_kind_of Array, OpenTox::Authorization.list_groups(@@subjectid)
+    assert_kind_of Array, OpenTox::Authorization.list_user_groups(TEST_USER, @@subjectid)
   end
   
   def test_03_get_user
@@ -60,6 +64,7 @@ class TestOpenToxAuthorizationLDAP < Test::Unit::TestCase
     policies.each do |policy|
       assert OpenTox::Authorization.delete_policy(policy, @@subjectid)
     end
+    assert_equal false, OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid)
   end
 
   def test_02_check_policy_rules
@@ -104,4 +109,4 @@ end
 
 def login
   OpenTox::Authorization.authenticate(TEST_USER,TEST_PW)
-end 
\ No newline at end of file
+end 
diff --git a/data/EPAFHM.mini.csv b/data/EPAFHM.mini.csv
new file mode 100644
index 0000000..c86cd33
--- /dev/null
+++ b/data/EPAFHM.mini.csv
@@ -0,0 +1,21 @@
+"STRUCTURE_SMILES","LC50_mmol"
+"C1=CC(C=O)=CC(OC)=C1OCCCCCC",1.13E-02
+"C1(OC)=C([N+]([O-])=O)C(C=O)=CC(Br)=C1O",2.66E-01
+"CCCCCCCCOC(=O)C1=CC=CC(C(=O)OCCCCCCCC)=C1",
+"C1=CC(Cl)=CC=C1OC2=C([N+](=O)[O-])C=CC=C2",7.69E-03
+"CC1=C(NC=O)C=CC=C1Cl",2.75E-01
+"CCCCOC(=O)C1=CC=CC(C(=O)OCCCC)=C1",3.23E-03
+"C(C1=CC=CC=C1)(C2=CC=CC=C2)(O)C#C",5.33E-02
+"CCCSCCSCCC",4.22E-02
+"CCCCCCCCOC(=O)C1=CC=C(C(=O)OCCCCCCCC)C=C1",
+"OCCCCOC(=O)C1=CC=CC=C1C(=O)OCCCCOC(=O)C2=CC=CC=C2C(=O)OCCCCO",
+"CCCSCCCCSCCC",1.45E-02
+"C1([N+](=O)[O-])=CC=C(C)C=C1OP(=O)(OC2=C([N+](=O)[O-])C=CC(C)=C2)OC3=C([N+]([O-])=O)C=CC(C)=C3",
+"C1=C([N+]([O-])=O)C=CC=C1P(=O)(C2=CC([N+](=O)[O-])=CC=C2)C3=CC([N+](=O)[O-])=CC=C3",
+"ClCCOC(=O)NC1CCCCC1",1.70E-01
+"O=C1C(C2=CC=CC=C2)(C(=O)NC(=O)N1)CC",2.08E+00
+"OC1=C(C=C(C=C1)[N+](=O)[O-])[N+](=O)[O-]",5.92E-02
+"NC(=O)OCC",5.88E+01
+"[O-]C(C1=CC=CC=C1O)=O.[Na+]",1.25E+01
+"C1=CC=CC=C1C(=O)N",5.46E+00
+"CC[N+](CC)(CC)CC1(=CC=CC=C1).[Cl-]",7.07E-01
diff --git a/data/hamster_carcinogenicity.mini.csv b/data/hamster_carcinogenicity.mini.csv
new file mode 100644
index 0000000..4267235
--- /dev/null
+++ b/data/hamster_carcinogenicity.mini.csv
@@ -0,0 +1,11 @@
+SMILES, Hamster Carcinogenicity

+CC=O,1

+C12C3=C(C=CC=C3)CC1=CC(=CC=2)NC(C)=O,1

+O=C(N)\C(C2=CC=CO2)=C/C1=CC=C([N+]([O-])=O)O1,1

+C1(N=CNN=1)N,0

+Br(=O)(=O)[O-].[K+],1

+[Cl-].[Cd+2].[Cl-],0

+O=S(=O)([O-])[O-].[Cd+2],0

+ClC1=CC(=NC(=N1)SCC(=O)O)NC2=CC=CC(=C2C)C,0

+ClCOC,1

+C=C(Cl)C=C,0

diff --git a/dataset.rb b/dataset.rb
index 1e4134b..17d15f2 100644
--- a/dataset.rb
+++ b/dataset.rb
@@ -47,7 +47,7 @@ class DatasetTest < Test::Unit::TestCase
   end
 
   def test_all
-    datasets = OpenTox::Dataset.all
+    datasets = OpenTox::Dataset.all(CONFIG[:services]["opentox-dataset"], @@subjectid)
     assert_kind_of Array, datasets
   end
 
diff --git a/feature.rb b/feature.rb
index 7ed600c..c06f9f5 100644
--- a/feature.rb
+++ b/feature.rb
@@ -17,15 +17,15 @@ class FeatureTest < Test::Unit::TestCase
     @features.each do |uri|
       
       f = OpenTox::Feature.new(uri)
-      f.load_metadata
+      f.load_metadata(@@subjectid)
       assert_not_nil f.metadata[DC.title]
-      assert_not_nil f.metadata[OT.hasSource]
+      #assert_not_nil f.metadata[OT.hasSource]
     end
   end
 
   def test_owl
     #@features.each do |uri|
-      validate_owl @features.first, @@subjectid
+      validate_owl @features.first, @@subjectid unless CONFIG[:services]["opentox-dataset"].match(/localhost/)
       # Ambit does not validate
     #end
   end
diff --git a/fminer.rb b/fminer.rb
index 362bde9..1f99f77 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -5,46 +5,41 @@ require 'validate-owl.rb'
 
 class FminerTest < Test::Unit::TestCase
 
-=begin
-=end
   def test_bbrc
     feature = @@classification_training_dataset.features.keys.first
     dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@classification_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s
     d =OpenTox::Dataset.new dataset_uri, @@subjectid
     d.load_features(@@subjectid)
-    assert_equal 41, d.features.size
-    #validate_owl
-    d.delete(@@subjectid)
-  end
-
-  def test_last
-    feature = @@classification_training_dataset.features.keys.first
-    dataset_uri = OpenTox::Algorithm::Fminer::LAST.new.run({:dataset_uri => @@classification_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s
-    d =OpenTox::Dataset.new dataset_uri, @@subjectid
-    d.load_features(@@subjectid)
-    assert_equal 35, d.features.size
-    #validate_owl
+    assert_equal 52, d.features.size
     d.delete(@@subjectid)
   end
 
   def test_regression_bbrc
     feature = File.join @@regression_training_dataset.uri,"feature/LC50_mmol" 
-    dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@regression_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s
+    dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@regression_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid, :feature_type=>"paths"}).to_s
     d =OpenTox::Dataset.new dataset_uri, @@subjectid
     d.load_features(@@subjectid)
-    assert_equal 225, d.features.size
+    assert_equal 185, d.features.size
     d.delete(@@subjectid)
   end
 
-  def test_regression_last
-    feature = File.join @@regression_training_dataset.uri,"feature/LC50_mmol" 
-    dataset_uri = OpenTox::Algorithm::Fminer::LAST.new.run({:dataset_uri => @@regression_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s
+  def test_last
+    feature = @@classification_training_dataset.features.keys.first
+    dataset_uri = OpenTox::Algorithm::Fminer::LAST.new.run({:dataset_uri => @@classification_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s
     d =OpenTox::Dataset.new dataset_uri, @@subjectid
     d.load_features(@@subjectid)
-    assert_equal 16, d.features.size
+    assert_equal 23, d.features.size
     d.delete(@@subjectid)
   end
-=begin
-=end
+
+# Deactivated by AM because of efficiency problems (does not return)
+#  def test_regression_last
+#    feature = File.join @@regression_training_dataset.uri,"feature/LC50_mmol" 
+#    dataset_uri = OpenTox::Algorithm::Fminer::LAST.new.run({:dataset_uri => @@regression_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s
+#    d =OpenTox::Dataset.new dataset_uri, @@subjectid
+#    d.load_features(@@subjectid)
+#    assert_equal 4, d.features.size
+#    d.delete(@@subjectid)
+#  end
 
 end
diff --git a/lazar.rb b/lazar.rb
index 1eb7645..eb8b99e 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -8,62 +8,110 @@ class Float
   end
 end
 
-class LazarRegressionTest < Test::Unit::TestCase
+class LazarTest < Test::Unit::TestCase
+
+  def setup
+    @predictions = []
+    @models = []
+  end
+
+  def teardown
+    @predictions.each {|p| p.delete(@@subjectid)}
+    @models.each {|m| m.delete(@@subjectid)}
+  end
 
 =begin
 =end
   def test_create_regression_model
     model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@regression_training_dataset.uri, :subjectid => @@subjectid}).to_s
-    @lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
-    assert_equal 225, @lazar.features.size
+    lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
+    @models << lazar
+    assert_equal 185, lazar.features.size
     compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
-    prediction_uri = @lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid).to_s
-    @prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
-    assert_equal @prediction.value(compound).round_to(4), 0.1618.round_to(4)
-    assert_equal @prediction.confidence(compound).round_to(4), 0.6114.round_to(4)
-    assert_equal @prediction.neighbors(compound).size, 81
-    @prediction.delete(@@subjectid)
-    @lazar.delete(@@subjectid)
+    prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid).to_s
+    prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
+    @predictions << prediction
+    assert_equal prediction.value(compound).round_to(4), 0.3469.round_to(4)
+    assert_equal prediction.confidence(compound).round_to(4), 0.3223.round_to(4)
+    assert_equal prediction.neighbors(compound).size, 73
   end
-end
 
-class LazarClassificationTest < Test::Unit::TestCase
   def test_classification_model
 
     # create model
     model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@classification_training_dataset.uri, :subjectid => @@subjectid}).to_s
-    @lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
-    assert_equal @lazar.features.size, 41
+    lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
+    @models << lazar
+    assert_equal lazar.features.size, 52
 
     # single prediction
     compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
-    prediction_uri = @lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
-    @prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
-    assert_equal @prediction.value(compound), false
-    assert_equal @prediction.confidence(compound).round_to(4), 0.3005.round_to(4)
-    assert_equal @prediction.neighbors(compound).size, 15
-    @prediction.delete(@@subjectid)
+    prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
+    prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
+    @predictions << prediction
+    assert_equal prediction.value(compound), false
+    assert_equal prediction.confidence(compound).round_to(4), 0.3067.round_to(4)
+    assert_equal prediction.neighbors(compound).size, 14
 
     # dataset activity
     compound = OpenTox::Compound.from_smiles("CNN")
-    prediction_uri  = @lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
-    @prediction = OpenTox::LazarPrediction.find prediction_uri, @@subjectid
-    assert !@prediction.measured_activities(compound).empty?
-    assert_equal @prediction.measured_activities(compound).first, true
-    assert @prediction.value(compound).nil?
-    @prediction.delete(@@subjectid)
+    prediction_uri  = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
+    prediction = OpenTox::LazarPrediction.find prediction_uri, @@subjectid
+    @predictions << prediction
+    assert !prediction.measured_activities(compound).empty?
+    assert_equal prediction.measured_activities(compound).first, true
+    assert prediction.value(compound).nil?
 
     # dataset prediction
     test_dataset = OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid)
-    @prediction = OpenTox::LazarPrediction.find @lazar.run(:dataset_uri => test_dataset.uri, :subjectid => @@subjectid), @@subjectid
-    assert_equal @prediction.compounds.size, 4
-    compound = OpenTox::Compound.new "http://ot-dev.in-silico.ch/compound/InChI=1S/C15H13NO/c1-10(17)16-13-6-7-15-12(9-13)8-11-4-2-3-5-14(11)15/h2-7,9H,8H2,1H3,(H,16,17)" 
-    assert_equal @prediction.value(compound), nil
-    assert_equal @prediction.measured_activities(compound).first, true
-    @prediction.delete(@@subjectid)
-    @lazar.delete(@@subjectid)
+    prediction = OpenTox::LazarPrediction.find lazar.run(:dataset_uri => test_dataset.uri, :subjectid => @@subjectid), @@subjectid
+    @predictions << prediction
+    assert_equal prediction.compounds.size, 4
+    compound = OpenTox::Compound.from_smiles "CC(=Nc1ccc2c(c1)Cc1ccccc21)O"
+    assert_equal prediction.value(compound), nil
+    assert_equal prediction.measured_activities(compound).first, true
   end
 
+  def test_ambit_classification_model
+
+    # create model
+    dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/9"
+    feature_uri ="http://apps.ideaconsult.net:8080/ambit2/feature/21573"
+    #model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => dataset_uri, :prediction_feature => feature_uri}).to_s
+    #lazar = OpenTox::Model::Lazar.find model_uri
+    model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => dataset_uri, :prediction_feature => feature_uri, :subjectid => @@subjectid}).to_s
+    lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
+    assert_equal lazar.features.size, 6609
+    #puts "Model: #{lazar.uri}"
+    #puts lazar.features.size
+
+    # single prediction
+    compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
+    #prediction_uri = lazar.run(:compound_uri => compound.uri)
+    #prediction = OpenTox::LazarPrediction.find(prediction_uri)
+    prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
+    prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
+    #puts "Prediction: #{prediction.uri}"
+    #puts prediction.value(compound)
+    assert_equal prediction.value(compound), true
+    #puts @prediction.confidence(compound).round_to(4)
+    #assert_equal @prediction.confidence(compound).round_to(4), 0.3005.round_to(4)
+    #assert_equal @prediction.neighbors(compound).size, 15
+    #@prediction.delete(@@subjectid)
+
+    # dataset activity
+    #compound = OpenTox::Compound.from_smiles("CNN")
+    #prediction_uri  = @lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
+    #@prediction = OpenTox::LazarPrediction.find prediction_uri, @@subjectid
+    #assert !@prediction.measured_activities(compound).empty?
+    #assert_equal @prediction.measured_activities(compound).first, true
+    #assert @prediction.value(compound).nil?
+    #@prediction.delete(@@subjectid)
+
+    # dataset prediction
+    #@lazar.delete(@@subjectid)
+  end
 =begin
 =end
+
 end
diff --git a/task.rb b/task.rb
index 307d512..93aa8fb 100644
--- a/task.rb
+++ b/task.rb
@@ -20,7 +20,7 @@ class TaskTest < Test::Unit::TestCase
 
 
   def test_rdf
-    task = OpenTox::Task.new OpenTox::Task.all.last
+    task = OpenTox::Task.new OpenTox::Task.all.sort.last
     validate_owl(task.uri)
     #puts task.uri
   end
diff --git a/toxcreate.rb b/toxcreate.rb
index 368101b..5a995e2 100644
--- a/toxcreate.rb
+++ b/toxcreate.rb
@@ -10,17 +10,38 @@ class ToxCreateTest < Test::Unit::TestCase
     @user = "test_ch"
     @password = "test_ch"
   end
-
+  
 =begin
   def test_login
+    @browser.goto File.join(CONFIG[:services]["opentox-toxcreate"], "login")
+    @browser.button(:value, "Login").click
+    puts "Login without credentials"    
+    assert @browser.text.include? "Please enter username and password."
+    @browser.text_field(:id, "username").set(@user)
+    @browser.text_field(:id, "password").set(@password + "nonsense")
+    @browser.button(:value, "Login").click
+    puts "Login with wrong password"
+    assert @browser.text.include? "Login failed. Please try again." 
+    @browser.text_field(:id, "username").set(@user)
+    @browser.text_field(:id, "password").set(@password)
+    @browser.button(:value, "Login").click
+    puts "Login as user #{@user}"
+    assert @browser.text.include? "Welcome #{@user}!"
+    @browser.goto File.join(CONFIG[:services]["opentox-toxcreate"], "login")
+    @browser.button(:value, "Login as guest").click
+    puts "Login as user guest"    
+    assert @browser.text.include? "Welcome guest!"
+    @browser.close    
   end
 
+
   def teardown
     @browser.close
   end
 
-=end
+
   def test_toxcreate
+    login(@browser, @user, @password)
     @browser.goto CONFIG[:services]["opentox-toxcreate"]
     @browser.file_field(:id, "file").set(`pwd`.chomp+"/data/hamster_carcinogenicity.csv")
     @browser.button(:value, "Create model").click
@@ -28,9 +49,10 @@ class ToxCreateTest < Test::Unit::TestCase
     # check results (links, reports, results)
     puts @browser.url
   end
-
+=end
 =begin
   def test_multi_cell_call
+    login(@browser, @user, @password)
     @browser.goto CONFIG[:services]["opentox-toxcreate"]
     @browser.file_field(:id, "file").set(`pwd`.chomp+"/data/multi_cell_call.csv")
     @browser.button(:value, "Create model").click
@@ -40,6 +62,7 @@ class ToxCreateTest < Test::Unit::TestCase
   end
 
   def test_kazius
+    login(@browser, @user, @password)
     @browser.goto CONFIG[:services]["opentox-toxcreate"]
     @browser.file_field(:id, "file").set(`pwd`.chomp+"/data/kazius.csv")
     @browser.button(:value, "Create model").click
@@ -49,6 +72,7 @@ class ToxCreateTest < Test::Unit::TestCase
   end
 
   def test_parallel_models
+    login(@browser, @user, @password)
     10.times do
       @browser.goto CONFIG[:services]["opentox-toxcreate"]
       @browser.file_field(:id, "file").set(`pwd`.chomp+"/data/hamster_carcinogenicity.csv")
@@ -58,3 +82,10 @@ class ToxCreateTest < Test::Unit::TestCase
   end
 =end
 end
+
+def login(browser, user, password)
+  browser.goto File.join(CONFIG[:services]["opentox-toxcreate"], "login")
+  browser.text_field(:id, "username").set(user)
+  browser.text_field(:id, "password").set(password)
+  browser.button(:value, "Login").click
+end
\ No newline at end of file
diff --git a/validate-owl.rb b/validate-owl.rb
index 736531b..e219d58 100644
--- a/validate-owl.rb
+++ b/validate-owl.rb
@@ -1,8 +1,6 @@
-#require 'nokogiri'
-
 def validate_owl(uri, subjectid=nil)
   if validator_available?
-    owl = OpenTox::RestClientWrapper.get(uri,{:accept => "application/rdf+xml",:subjectid => subjectid})
+    owl = OpenTox::RestClientWrapper.get(uri,{:accept => "application/rdf+xml",:subjectid => subjectid}, nil, false)
     html = OpenTox::RestClientWrapper.post("http://www.mygrid.org.uk/OWL/Validator",{:rdf => owl, :level => "DL",:subjectid => subjectid})
     assert_match(/YES/,html)
   else
diff --git a/validation.rb b/validation.rb
index beb1c02..14ef5ee 100644
--- a/validation.rb
+++ b/validation.rb
@@ -1,45 +1,327 @@
-require 'rubygems'
-require 'opentox-ruby'
+ENV['RACK_ENV'] = 'production'
+
 require 'test/unit'
+require 'validation_util.rb'
+
+#TEST_USER = "guest"
+#TEST_PW = "guest"
+
+#LOGGER = OTLogger.new(STDOUT)
+#LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
+#LOGGER.formatter = Logger::Formatter.new
 
-class Float
-  def round_to(x)
-    (self * 10**x).round.to_f / 10**x
+module Sinatra
+  set :raise_errors, false
+  set :show_exceptions, false
+end
+
+class Exception
+  def message
+    errorCause ? errorCause.to_yaml : to_s
   end
 end
 
 class ValidationTest < Test::Unit::TestCase
+  
+  def global_setup
+    puts "login and upload datasets"
+    if AA_SERVER
+      @@subjectid = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW)
+      raise "could not log in" unless @@subjectid
+      puts "logged in: "+@@subjectid.to_s
+    else
+      puts "AA disabled"
+      @@subjectid = nil
+    end
+
+    @@data = []
+    files = { File.new("data/hamster_carcinogenicity.mini.csv") => :crossvalidation,  
+              File.new("data/EPAFHM.mini.csv") => :crossvalidation,
+              File.new("data/hamster_carcinogenicity.csv") => :validation,
+              File.new("data/EPAFHM.csv") => :validation,
+#              File.new("data/StJudes-HepG2-testset_Class.csv") => :crossvalidation
+               }
+    files.each do |file,type|
+      @@data << { :type => type,
+        :data => ValidationTestUtil.upload_dataset(file, @@subjectid),
+        :feat => ValidationTestUtil.prediction_feature_for_file(file),
+        :info => file.path, :delete => true} 
+    end
+#    @@data << { :type => :crossvalidation,
+#      :data => "http://apps.ideaconsult.net:8080/ambit2/dataset/9?max=50",
+#      :feat => "http://apps.ideaconsult.net:8080/ambit2/feature/21573",
+#      :info => "http://apps.ideaconsult.net:8080/ambit2/dataset/9?max=50" }
+#    @@data << { :type => :validation,
+#      :data => "http://apps.ideaconsult.net:8080/ambit2/dataset/272?max=50",
+#      :feat => "http://apps.ideaconsult.net:8080/ambit2/feature/26221",
+#      :info => "http://apps.ideaconsult.net:8080/ambit2/dataset/272?max=50" } 
+  end
+  
+  def global_teardown
+    puts "delete and logout"
+    @@data.each{|data| OpenTox::Dataset.find(data[:data],@@subjectid).delete(@@subjectid) if data[:delete]}
+    @@vs.each{|v| v.delete(@@subjectid)} if defined?@@vs
+    @@cvs.each{|cv| cv.delete(@@subjectid)} if defined?@@cvs
+    @@reports.each{|report| report.delete(@@subjectid)} if defined?@@reports
+    @@qmrfReports.each{|qmrfReport| qmrfReport.delete(@@subjectid)} if defined?@@qmrfReports
+    OpenTox::Authorization.logout(@@subjectid) if AA_SERVER
+  end
+  
+  def test_validation_list
+    puts "test_validation_list"
+    list = OpenTox::Validation.list
+    assert list.is_a?(Array)
+    list.each do |l|
+      assert l.uri?
+    end
+  end
+ 
+  def test_training_test_split
+    
+    @@vs = []
+    @@data.each do |data|
+      if data[:type]==:validation
+        puts "test_training_test_split "+data[:info].to_s
+        p = { 
+          :dataset_uri => data[:data],
+          :algorithm_uri => File.join(CONFIG[:services]["opentox-algorithm"],"lazar"),
+          :algorithm_params => "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc"),
+          :prediction_feature => data[:feat],
+          :split_ratio => 0.95,
+          :random_seed => 2}
+        t = OpenTox::SubTask.new(nil,0,1)
+        def t.progress(pct)
+          if !defined?@last_msg or @last_msg+3<Time.new
+            puts "waiting for training-test-split validation: "+pct.to_s
+            @last_msg=Time.new
+          end
+        end
+        def t.waiting_for(task_uri); end
+        v = OpenTox::Validation.create_training_test_split(p, @@subjectid, t)
+        assert v.uri.uri?
+        if @@subjectid
+          assert_rest_call_error OpenTox::NotAuthorizedError do
+            OpenTox::Validation.find(v.uri)
+          end
+        end
+        v = OpenTox::Validation.find(v.uri, @@subjectid)
+        assert_valid_date v
+        assert v.uri.uri?
+        model = v.metadata[OT.model]
+        assert model.uri?
+        v_list = OpenTox::Validation.list( {:model => model} )
+        assert v_list.size==1 and v_list.include?(v.uri)
+        @@vs << v
+      end
+    end
+  end
+  
+  def test_validation_report
+    #@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/48", @@subjectid)
+    
+    @@reports = [] unless defined?@@reports
+    @@vs.each do |v|
+      puts "test_validation_report"
+      assert defined?v,"no validation defined"
+      assert_kind_of OpenTox::Validation,v
+      if @@subjectid
+        assert_rest_call_error OpenTox::NotAuthorizedError do
+          OpenTox::ValidationReport.create(v.uri)
+        end
+      end
+      report = OpenTox::ValidationReport.find_for_validation(v.uri,@@subjectid)
+      assert report==nil,"report already exists for validation\nreport: "+(report ? report.uri.to_s : "")+"\nvalidation: "+v.uri.to_s
+      report = OpenTox::ValidationReport.create(v.uri,@@subjectid)
+      assert report.uri.uri?
+      if @@subjectid
+        assert_rest_call_error OpenTox::NotAuthorizedError do
+          OpenTox::ValidationReport.find(report.uri)
+        end
+      end
+      report = OpenTox::ValidationReport.find(report.uri,@@subjectid)
+      assert_valid_date report
+      assert report.uri.uri?
+      report2 = OpenTox::ValidationReport.find_for_validation(v.uri,@@subjectid)
+      assert_equal report.uri,report2.uri
+      report3_uri = v.find_or_create_report(@@subjectid)
+      assert_equal report.uri,report3_uri
+      @@reports << report2
+    end  
+  end
+
+  def test_crossvalidation_list
+    puts "test_crossvalidation_list"
+    list = OpenTox::Crossvalidation.list
+    assert list.is_a?(Array)
+    list.each do |l|
+      assert l.uri?
+    end
+  end
 
-=begin
-=end
   def test_crossvalidation
+    
+    #assert_rest_call_error OpenTox::NotFoundError do 
+    #  OpenTox::Crossvalidation.find(File.join(CONFIG[:services]["opentox-validation"],"crossvalidation/noexistingid"))
+    #end
+    @@cvs = []
+    @@data.each do |data|
+      if data[:type]==:crossvalidation
+        puts "test_crossvalidation "+data[:info].to_s
+        p = { 
+          :dataset_uri => data[:data],
+          :algorithm_uri => File.join(CONFIG[:services]["opentox-algorithm"],"lazar"),
+          :algorithm_params => "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc"),
+          :prediction_feature => data[:feat],
+          :num_folds => 2 }
+        t = OpenTox::SubTask.new(nil,0,1)
+        def t.progress(pct)
+          if !defined?@last_msg or @last_msg+3<Time.new
+            puts "waiting for crossvalidation: "+pct.to_s
+            @last_msg=Time.new
+          end
+        end
+        def t.waiting_for(task_uri); end
+        cv = OpenTox::Crossvalidation.create(p, @@subjectid, t)
+        assert cv.uri.uri?
+        if @@subjectid
+          assert_rest_call_error OpenTox::NotAuthorizedError do
+            OpenTox::Crossvalidation.find(cv.uri)
+          end
+        end
+        cv = OpenTox::Crossvalidation.find(cv.uri, @@subjectid)
+        assert_valid_date cv
+        assert cv.uri.uri?
+        if @@subjectid
+          assert_rest_call_error OpenTox::NotAuthorizedError do
+            cv.summary(cv)
+          end
+        end
+        summary = cv.summary(@@subjectid)
+        assert_kind_of Hash,summary
+        
+        algorithm = cv.metadata[OT.algorithm]
+        assert algorithm.uri?
+        cv_list = OpenTox::Crossvalidation.list( {:algorithm => algorithm} )
+        assert cv_list.include?(cv.uri)
+        cv_list.each do |cv_uri|
+          alg = OpenTox::Crossvalidation.find(cv_uri).metadata[OT.algorithm]
+          assert alg==algorithm,"wrong algorithm for filtered crossvalidation, should be: '"+algorithm.to_s+"', is: '"+alg.to_s+"'"
+        end
+        
+        @@cvs << cv
+      end
+    end
+  end
+    
+  def test_crossvalidation_report
+    #@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/48", @@subjectid)
+    
+    @@reports = [] unless defined?@@reports
+    @@cvs.each do |cv|
+      puts "test_crossvalidation_report"
+      assert defined?cv,"no crossvalidation defined"
+      assert_kind_of OpenTox::Crossvalidation,cv
+      #assert_rest_call_error OpenTox::NotFoundError do 
+      #  OpenTox::CrossvalidationReport.find_for_crossvalidation(cv.uri)
+      #end
+      if @@subjectid
+        assert_rest_call_error OpenTox::NotAuthorizedError do
+          OpenTox::CrossvalidationReport.create(cv.uri)
+        end
+      end
+      assert OpenTox::ValidationReport.find_for_validation(cv.uri,@@subjectid)==nil
+      report = OpenTox::CrossvalidationReport.create(cv.uri,@@subjectid)
+      assert report.uri.uri?
+      if @@subjectid
+        assert_rest_call_error OpenTox::NotAuthorizedError do
+          OpenTox::CrossvalidationReport.find(report.uri)
+        end
+      end
+      report = OpenTox::CrossvalidationReport.find(report.uri,@@subjectid)
+      assert_valid_date report
+      assert report.uri.uri?
+      report2 = OpenTox::CrossvalidationReport.find_for_crossvalidation(cv.uri,@@subjectid)
+      assert_equal report.uri,report2.uri
+      report3_uri = cv.find_or_create_report(@@subjectid)
+      assert_equal report.uri,report3_uri
+      @@reports << report2
+    end  
+  end
+  
+  def test_qmrf_report
+    #@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/13", @@subjectid)
+    
+    @@qmrfReports = []
+    @@cvs.each do |cv|
+      puts "test_qmrf_report"
+      assert defined?cv,"no crossvalidation defined"
+      validations = cv.metadata[OT.validation]
+      assert_kind_of Array,validations
+      assert validations.size==cv.metadata[OT.numFolds].to_i,validations.size.to_s+"!="+cv.metadata[OT.numFolds].to_s
+      val = OpenTox::Validation.find(validations[0], @@subjectid)
+      model_uri = val.metadata[OT.model]
+      
+      model = OpenTox::Model::Generic.find(model_uri, @@subjectid)
+      assert model!=nil
+      
+      #assert_rest_call_error OpenTox::NotFoundError do 
+      #  OpenTox::QMRFReport.find_for_model(model_uri, @@subjectid)
+      #end
+      
+      @@qmrfReports << OpenTox::QMRFReport.create(model_uri, @@subjectid)
+    end
+  end
+  
+  ################### utils and overrides ##########################
+  
+  def app
+    Sinatra::Application
+  end
+  
+  # checks RestCallError type
+  def assert_rest_call_error( ex )
+    if ex==OpenTox::NotAuthorizedError and @@subjectid==nil
+      puts "AA disabled: skipping test for not authorized"
+      return
+    end
+    begin
+      yield
+    rescue OpenTox::RestCallError => e
+      raise "error Report of RestCallError is no errorReport: "+e.errorCause.class.to_s+":\n"+e.errorCause.to_yaml  unless e.errorCause.is_a?(OpenTox::ErrorReport)
+      report = e.errorCause
+      while report.errorCause
+        report = report.errorCause
+      end
+      assert_equal report.errorType,ex.to_s
+    end
+  end
+  
+  # checks if opento_object has date defined in metadata, and time is less than max_time seconds ago
+  def assert_valid_date( opentox_object, max_time=600 )
+    
+    raise "no opentox object" unless opentox_object.class.to_s.split("::").first=="OpenTox"
+    assert opentox_object.metadata.is_a?(Hash)
+    assert opentox_object.metadata[DC.date].to_s.length>0,"date not set for "+opentox_object.uri.to_s+", is metadata loaded? (use find)"
 =begin
+    time = Time.parse(opentox_object.metadata[DC.date])
+    assert time<Time.new,"date of "+opentox_object.uri.to_s+" is in the future: "+time.to_s
+    assert time>Time.new-(10*60),opentox_object.uri.to_s+" took longer than 10 minutes "+time.to_s
 =end
-    puts "creating model ..."
-    model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@classification_training_dataset.uri, :subjectid => @@subjectid}).to_s
-    lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
-    puts @@classification_training_dataset.features.to_yaml
-    params = {
-      :algorithm_uri => File.join(CONFIG[:services]["opentox-algorithm"],"lazar"),
-      :dataset_uri => lazar.parameter("dataset_uri"),
-      #:dataset_uri => @@classification_training_dataset.uri,
-      :subjectid => @@subjectid,
-      #:prediction_feature => @@classification_training_dataset.features.keys.first,
-      #:algorithm_params => "feature_generation_uri=#{File.join(CONFIG[:services]["opentox-algorithm"],"bbrc")}"
-      :prediction_feature => lazar.parameter("prediction_feature"),
-      :algorithm_params => "feature_generation_uri=#{lazar.parameter("feature_generation_uri")}"
-    }
-    puts params.to_yaml
-    cv = OpenTox::Validation.create_crossvalidation(params)
-    puts cv.uri
-  #@@subjectid = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW) 
-    cv = OpenTox::Validation.new "http://opentox.informatik.uni-freiburg.de/validation/crossvalidation/6"
-    puts cv.uri
-    #puts cv.create_report(@@subjectid)
-    #puts cv.create_qmrf_report(@@subjectid)
-    #v = YAML.load OpenTox::RestClientWrapper.get(cv.uri,{:accept => "application/x-yaml", :subjectid => @@subjectid}).to_s
-    v = YAML.load OpenTox::RestClientWrapper.get(File.join(cv.uri, 'statistics'),{:accept => "application/x-yaml", :subjectid => @@subjectid}).to_s
-    puts v.to_yaml
-    #puts cv.summary("classification",@@subjectid)
   end
+  
+  # hack to have a global_setup and global_teardown 
+  def teardown
+    if((@@expected_test_count-=1) == 0)
+      global_teardown
+    end
+  end
+  def setup
+    unless defined?@@expected_test_count
+      @@expected_test_count = (self.class.instance_methods.reject{|method| method[0..3] != 'test'}).length
+      global_setup
+    end
+  end
+
 end
+
+  
diff --git a/validation_util.rb b/validation_util.rb
new file mode 100755
index 0000000..a5206b3
--- /dev/null
+++ b/validation_util.rb
@@ -0,0 +1,46 @@
+
+require 'test/unit'
+
+  class ValidationTestUtil    
+    
+    @@dataset_uris = {}
+    @@prediction_features = {}
+
+    def self.upload_dataset(file, subjectid=nil, 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
+        LOGGER.debug "uploading file: "+file.path.to_s
+        if (file.path =~ /yaml$/)
+          data = File.read(file.path)
+          #data_uri = OpenTox::RestClientWrapper.post(dataset_service,{:content_type => file_type},data).to_s.chomp
+          #@@dataset_uris[file.path.to_s] = data_uri
+          #LOGGER.debug "uploaded dataset: "+data_uri
+          d = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid)
+          d.load_yaml(data)
+          d.save( subjectid )
+          @@dataset_uris[file.path.to_s] = d.uri
+        elsif (file.path =~ /csv$/)
+          d = OpenTox::Dataset.create_from_csv_file(file.path, subjectid)
+          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
+        elsif (file.path =~ /rdf$/)
+          d = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid)
+          d.load_rdfxml_file(file, subjectid)
+          d.save(subjectid)
+          @@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
+
+  end