Merge branch 'development' into feature/policy

Conflicts:
	toxcreate.rb

9 files changed, 436 insertions, 63 deletions

diff --git a/.gitignore b/.gitignore
index 023a583..03b0f63 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 .yardoc
-dump.rdb
+dump
+reference
 bak
diff --git a/Rakefile b/Rakefile
index 49b72f8..f183527 100644
--- a/Rakefile
+++ b/Rakefile
@@ -21,11 +21,13 @@ end
 task :setup do
   @@subjectid = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW) 
   @@classification_training_dataset = OpenTox::Dataset.create_from_csv_file("data/hamster_carcinogenicity.csv", @@subjectid)
+  @@multinomial_training_dataset = OpenTox::Dataset.create_from_csv_file("data/ISSCAN-multi.csv", @@subjectid)
   @@regression_training_dataset = OpenTox::Dataset.create_from_csv_file("data/EPAFHM.csv", @@subjectid)
 end
 
 task :teardown do
   @@classification_training_dataset.delete(@@subjectid)
+  @@multinomial_training_dataset.delete(@@subjectid)
   @@regression_training_dataset.delete(@@subjectid)
   OpenTox::Authorization.logout(@@subjectid)
 end
diff --git a/compound.rb b/compound.rb
index ef87845..048e012 100644
--- a/compound.rb
+++ b/compound.rb
@@ -4,26 +4,39 @@ require 'test/unit'
 
 class CompoundTest < Test::Unit::TestCase
 
-  def test_compound
-
+  def test_compound_from_smiles_0
     c = OpenTox::Compound.from_smiles "F[B-](F)(F)F.[Na+]"
     assert_equal "InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1", c.inchi
     #assert_equal "[Na+].F[B-](F)(F)F", c.smiles # still does not work on 64bit machines
+  end
+
+  def test_compound_from_smiles_1
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
     assert_equal "InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3", c.inchi
     assert_equal "CC(CC(=O)C)C#N", c.to_smiles
+  end
+
+  def test_compound_from_name
     c = OpenTox::Compound.from_name "Benzene"
     assert_equal "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H", c.inchi
     assert_equal "c1ccccc1", c.to_smiles
+  end
+
+  def test_compound_from_smiles_2  
     c = OpenTox::Compound.from_smiles "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F"
     assert_equal "InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1", c.inchi
     assert_equal "N#[N+]c1ccccc1.F[B-](F)(F)F", c.to_smiles
+  end
+
+  def test_compound_from_inchi
     c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
     assert_equal "c1ccccc1", c.to_smiles
+  end
+
+  def test_compound_ambit
     c = OpenTox::Compound.new "http://apps.ideaconsult.net:8080/ambit2/compound/144036"
     assert_equal "InChI=1S/C6H11NO2/c1-3-5-6(4-2)7(8)9/h5H,3-4H2,1-2H3", c.inchi
     assert_equal "CCC=C(CC)N(=O)=O", c.to_smiles
   end
 
-
 end
diff --git a/data/ISSCAN-multi.csv b/data/ISSCAN-multi.csv
new file mode 100644
index 0000000..b404683
--- /dev/null
+++ b/data/ISSCAN-multi.csv
@@ -0,0 +1,59 @@
+SMILES,ISSCAN
+CC(CCl)Cl,1
+C(Br)(Br)Br,1
+C=C(C)CCl,1
+O=Cc1ccco1,1
+COC34(C(COC(N)=O)C=1C(=O)C(N)=C(C)C(=O)C=1N4(CC2NC23)),1
+CC(N)Cc1ccccc1.CC(N)Cc1ccccc1,1
+Cc1cc(ccc1(N))C(=C2C=CC(=N)C=C2)c3ccc(N)cc3,1
+Oc1ccc(cc1)c2ccccc2,1
+CC(C)C=O,1
+N#CC(C#N)=Cc1ccccc1Cl,1
+Nc1ccc(cc1(N))[N+](=O)[O-],2
+NC(CCC(=O)NNc1ccc(CO)cc1)C(O)=O,2
+c1ccc2c(c1)nc(s2)SSc4nc3ccccc3s4,2
+C=CC=O,2
+CC(=O)Nc3cccc2Cc1ccccc1c23,2
+Cc1cccc2cccnc12,2
+Cc1ccc2ncccc2(c1),2
+CBr,2
+Nc1cc(ccc1(C(=O)O))[N+](=O)[O-],2
+C1N2CN3CN1CN(C2)C3,2
+O=[N+]([O-])c2cccc1ccccc12,2
+Oc1cccc2cccnc12,2
+O=CC(=C(C(=O)O)Cl)Cl,2
+CC1CN(N=O)C(=O)NC1(=O),2
+O1C2C1C3C4C2C5C3C6(C4(C(C5(C6(Cl)Cl)Cl)Cl)Cl)Cl,2
+OCCNc1ccc(cc1[N+](=O)[O-])N(CCO)CCO,2
+Cc1cc(N)ccc1(N).OS(=O)(=O)O,2
+CC(O)CCl,2
+O=[N+]([O-])C(Cl)(Cl)Cl,2
+Cc1ccc(cc1)S(=O)(=O)NC(=O)NN2CCCCCC2,2
+c1cc2ccc3cccc4ccc(c1)c2c34,2
+CC(=O)Nc1ccc(cc1)C(=O)CCl,2
+FC(F)Cl,2
+CN(N=O)c1ccc(cc1)[N+](=O)[O-],2
+C=CC,2
+Oc4c(cc1cc(ccc1c4(N=Nc2ccc(c3ccccc23)S(=O)(=O)[O-]))S(=O)(=O)[O-])S(=O)(=O)[O-],0
+CC=NN(C)C=O,0
+Nc2ccc(N=Nc1ccccc1)c(N)n2,0
+Cc3cc(C)c(N=Nc1cc(c2ccccc2(c1(O)))S(=O)(=O)[O-])c(c3)S(=O)(=O)[O-],0
+[O-]c1ccccc1c2ccccc2,0
+NNC(N)=O,0
+CNNCc1ccc(cc1)C(=O)NC(C)C,0
+c1cc(c(cc1c2ccc(c(c2Cl)Cl)Cl)Cl)Cl,0
+CCN(Cc1cccc(c1)S(=O)(=O)[O-])c2ccc(cc2)C(=C3C=CC(C=C3)=[N+](CC)Cc4cccc(c4)S(=O)(=O)[O-])c5ccc(cc5)S(=O)(=O)[O-],0
+COC(=O)C(c1ccccc1)C2CCCCN2,0
+CCCCC(CC)COS(=O)(=O)[O-],0
+Nc1ccccc1,0
+Cc1cccc(N)c1,0
+CN(C)CCN(Cc1cccs1)c2ccccn2,0
+CN(C)CCOC(C)(c1ccccc1)c2ccccn2,0
+Cc1cc(C)c(cc1(C))N=Nc3c(O)c(cc2cc(ccc23)S(=O)(=O)[O-])S(=O)(=O)[O-],0
+Cc1ccccc1(N),0
+CCC1(C(=O)N=C([O-])NC1(=O))c2ccccc2,0
+Nc5cc(cc6cc(c(N=Nc1ccc(cc1(O))c4ccc(N=Nc2c(O)c3c(N)cc(cc3(cc2S(=O)(=O)[O-]))S(=O)(=O)[O-])c(O)[c-]4)c(O)c56)S(=O)(=O)[O-])S(=O)(=O)[O-],0
+O=C1[N-]S(=O)(=O)c2ccccc12,0
+CN(C)c1ccc(cc1)C(c2ccc(cc2)N(C)C)=C3C=CC(C=C3)=[N+](C)C,0
+C13(C4(C2(C5(C(C1(C2(Cl)Cl)Cl)(C3(C(C45Cl)(Cl)Cl)Cl)Cl)Cl)Cl)Cl)Cl,0
+CCOCCc1c(nc(N)[n+]2[nH]cnc12)c3ccccc3,0
diff --git a/data/multicolumn.csv b/data/multicolumn.csv
index 551429e..2fa9a1c 100644
--- a/data/multicolumn.csv
+++ b/data/multicolumn.csv
@@ -1,5 +1,5 @@
 SMILES, Hamster Carcinogenicity, numeric feature, classification, mixed, string
-CC=O                                         , 1, 1, true , true , "test"
+c1ccccc1NN                                   , 1, 1, true , true , "test"
 C12C3=C(C=CC=C3)CC1=CC(=CC=2)NC(C)=O         , 1, 2, false, 7.5  , "test"
 O=C(N)\C(C2=CC=CO2)=C/C1=CC=C([N+]([O-])=O)O1, 1, 3, true , 5    , "test"
 C1(N=CNN=1)N                                 , 0, 4, false, false, "test"
diff --git a/fminer.rb b/fminer.rb
index 22fc945..25640fa 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -3,6 +3,12 @@ require 'opentox-ruby'
 require 'test/unit'
 require 'validate-owl.rb'
 
+class Float
+  def round_to(x)
+    (self * 10**x).round.to_f / 10**x
+  end
+end
+
 class FminerTest < Test::Unit::TestCase
 
   def setup
@@ -26,7 +32,35 @@ class FminerTest < Test::Unit::TestCase
     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
     dump 
-    assert_equal 52, @dataset.features.size
+    assert_equal 41, @dataset.features.size # 32 bit
+    #assert_equal 52, @dataset.features.size
+    # assert no hit counts present
+    count=0
+    @dataset.data_entries.each { |c,e|
+      if c.to_s.scan('InChI=1S/C10H13N3O2/c1-13(12-15)7-3-5-10(14)9-4-2-6-11-8-9/h2,4,6,8H,3,5,7H2,1H3').size > 0
+        e.each { |p,h|
+          if p.to_s.scan('bbrc/40').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('bbrc/29').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('bbrc/18').size>0
+            count += 1 if h[0] == true
+          end
+        }
+      end
+    }
+    assert_equal 3, count
+
+    # assert some values
+    @dataset.features.each { |c,e|
+      if c.to_s.scan('feature/bbrc/31').size > 0
+        assert_equal e['http://www.opentox.org/api/1.1#effect'], 2
+        assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.97
+        assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#6&a]-[#6&a]:[#6&a]:[#6&a]:[#6&a]-[#7&A]"
+      end
+    }
     cleanup
   end
 
@@ -34,38 +68,300 @@ class FminerTest < Test::Unit::TestCase
     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, :feature_type=>"paths"}).to_s
     dump
-    assert_equal 219, @dataset.features.size
+    assert_equal 131, @dataset.features.size # 32 bit
+    #assert_equal 219, @dataset.features.size
+    
+    # assert no hit counts present
+    count = 0
+    @dataset.data_entries.each { |c,e|
+      if c.to_s.scan('InChI=1S/C5H10N2O2S/c1-4(10-3)7-9-5(8)6-2/h1-3H3,(H,6,8)').size > 0
+        e.each { |p,h|
+          if p.to_s.scan('bbrc/86').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('bbrc/54').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('bbrc/32').size>0
+            count += 1 if h[0] == true
+          end
+        }
+      end
+    }
+    assert_equal 3, count
+
+    # assert some values
+    @dataset.features.each { |c,e|
+      if c.to_s.scan('feature/bbrc/188').size > 0
+        assert_equal e['http://www.opentox.org/api/1.1#effect'], "activating"
+        assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 1.0
+        assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#6&a]:[#6&a]:[#8&a]:[#6&a]:[#6&a]"
+      end
+    }
+
     cleanup
   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
     dump
-    assert_equal 23, @dataset.features.size
+    assert_in_delta 21, @dataset.features.size, 2 # 32 bit
+
+    # assert no hit counts present
+    count = 0
+    @dataset.data_entries.each { |c,e|
+      if c.to_s.scan('InChI=1S/C5H10N2O/c8-6-7-4-2-1-3-5-7/h1-5H2').size > 0
+        e.each { |p,h|
+          if p.to_s.scan('last/11').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('last/5').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('last/13').size>0
+            count += 1 if h[0] == true
+          end
+        }
+      end
+    }
+    #assert_equal 3, count
+
+    # assert some values
+    #@dataset.features.each { |c,e|
+    #  if c.to_s.scan('feature/last/3').size > 0
+    #    assert_equal e['http://www.opentox.org/api/1.1#effect'], 2
+    #    assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.99
+    #    assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#8&A]=[#6&A]-[#6&A]-[#6&A]"
+    #  end
+    #}
     cleanup
   end
 
-  def test_bbrc_rest_parameters
+
+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, 
+                                                          :min_frequency => 40,
+                                                          :subjectid => @@subjectid}).to_s
+  dump
+  assert_in_delta 16, @dataset.features.size, 2
+
+  
+  # assert no hit counts present
+  #count=0
+  #@dataset.data_entries.each { |c,e|
+  #  if c.to_s.scan('InChI=1S/C9H10O3/c1-2-12-9-5-7(6-10)3-4-8(9)11/h3-6,11H,2H2,1H3').size > 0
+  #    e.each { |p,h|
+  #      if p.to_s.scan('last/5').size>0
+  #        count += 1 if h[0] == true
+  #      end
+  #      if p.to_s.scan('last/11').size>0
+  #        count += 1 if h[0] == true
+  #      end
+  #      if p.to_s.scan('last/13').size>0
+  #        count += 1 if h[0] == true
+  #      end
+  #    }
+  #  end
+  #}
+  #assert_in_delta 3, count, 2
+
+  # assert some values
+  #@dataset.features.each { |c,e|
+  #  if c.to_s.scan('feature/last/3').size > 0
+  #    assert_equal e['http://www.opentox.org/api/1.1#effect'], "activating"
+  #    assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 1.0
+  #    assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#8&A]=[#6&A]-[#8&A]-[#6&A]"
+  #  end
+  #}
+  cleanup
+end
+
+
+
+  def test_bbrc_rest_parameters_nr_hits
     feature = @@classification_training_dataset.features.keys.first
     @dataset_uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-algorithm"],"fminer","bbrc"),{
       "dataset_uri" => @@classification_training_dataset.uri,
       "prediction_feature" => feature,
-      "backbone" => true,
-      "min_frequency" => 2,
+      "nr_hits" => true,
        :subjectid => @@subjectid })
     dump
-    assert_equal 52, @dataset.features.size
+    assert_equal 41, @dataset.features.size # 32 bit
+    #assert_equal 52, @dataset.features.size
+
+    # assert hit counts present
+    @dataset.data_entries.each { |c,e|
+      if c.to_s.scan('InChI=1S/C14H19N3S.ClH/c1-16(2)9-10-17(12-13-6-5-11-18-13)14-7-3-4-8-15-14;/h3-8,11H,9-10,12H2,1-2H3;1H').size > 0
+        e.each { |p,h|
+          if p.to_s.scan('bbrc/39').size>0
+            assert_equal 6, h[0]
+          end
+          if p.to_s.scan('bbrc/18').size>0
+            assert_equal 5, h[0]
+          end
+          if p.to_s.scan('bbrc/38').size>0
+            assert_equal 14, h[0]
+          end
+        }
+      end
+    }
+
+    # assert some values
+    @dataset.features.each { |c,e|
+      if c.to_s.scan('feature/bbrc/31').size > 0
+        assert_equal e['http://www.opentox.org/api/1.1#effect'], 2
+        assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.97
+        assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#6&a]-[#6&a]:[#6&a]:[#6&a]:[#6&a]-[#7&A]"
+      end
+    }
+
     cleanup
   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
-#    dump
-#    assert_equal 4, d.features.size
-#    cleanup
-#  end
+  def test_bbrc_rest_parameters_bb_false
+    feature = @@classification_training_dataset.features.keys.first
+    @dataset_uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-algorithm"],"fminer","bbrc"),{
+      "dataset_uri" => @@classification_training_dataset.uri,
+      "prediction_feature" => feature,
+      "backbone" => false,
+       :subjectid => @@subjectid })
+    dump
+    assert_equal 139, @dataset.features.size # 32 bit
+    #assert_equal 52, @dataset.features.size
+
+    # assert no hit counts present
+    count=0
+    @dataset.data_entries.each { |c,e|
+      if c.to_s.scan('InChI=1S/C10H13N3O2/c1-13(12-15)7-3-5-10(14)9-4-2-6-11-8-9/h2,4,6,8H,3,5,7H2,1H3').size > 0
+        e.each { |p,h|
+          if p.to_s.scan('bbrc/113').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('bbrc/99').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('bbrc/77').size>0
+            count += 1 if h[0] == true
+          end
+        }
+      end
+    }
+    assert_equal 3, count
+
+
+    # assert some values
+    @dataset.features.each { |c,e|
+      if c.to_s.scan('feature/bbrc/31').size > 0
+        assert_equal e['http://www.opentox.org/api/1.1#effect'], 2
+        assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.99
+        assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#8&A]-[#6&A]-[#7&A]-[#7&A]=[#8&A]"
+      end
+    }
+
+    cleanup
+  end
+
+  def test_bbrc_multinomial
+    feature = @@multinomial_training_dataset.features.keys.first
+    @dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@multinomial_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s
+    dump 
+    assert_equal 152, @dataset.features.size # 32 bit
+
+    #assert no hit counts present
+    count=0
+    @dataset.data_entries.each { |c,e|
+      if c.to_s.scan('InChI=1S/C10H7NO2/c12-11(13)10-7-3-5-8-4-1-2-6-9(8)10/h1-7H').size > 0
+        e.each { |p,h|
+          if p.to_s.scan('bbrc/37').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('bbrc/38').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('bbrc/39').size>0
+            count += 1 if h[0] == true
+          end
+        }
+      end
+    }
+    assert_equal 3, count
+
+    # assert some values
+    @dataset.features.each { |c,e|
+      if c.to_s.scan('feature/bbrc/0').size > 0
+        assert_equal e['http://www.opentox.org/api/1.1#effect'], 2
+        assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 1.00
+        assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#6&A]-[#6&A](=[#6&A])(-[#6&A])"
+      end
+    }
+    @dataset.features.each { |c,e|
+      if c.to_s.scan('feature/bbrc/92').size > 0
+        assert_equal e['http://www.opentox.org/api/1.1#effect'], 1
+        assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.99
+        assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#7&A]-[#6&a](:[#6&a]:[#6&a]:[#6&a])(:[#6&a]:[#6&a]-[#16&A])"
+      end
+    }
+    @dataset.features.each { |c,e|
+      if c.to_s.scan('feature/bbrc/42').size > 0
+        assert_equal e['http://www.opentox.org/api/1.1#effect'], 3
+        assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.99
+        assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#7&a]:[#6&a]"
+      end
+    }
+    cleanup
+  end
+
+  def test_last_multinomial
+    feature = @@multinomial_training_dataset.features.keys.first
+    @dataset_uri = OpenTox::Algorithm::Fminer::LAST.new.run({:dataset_uri => @@multinomial_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s
+    dump 
+    assert_in_delta 138, @dataset.features.size, 2 # 32 bit
+
+    #assert no hit counts present
+    count=0
+    @dataset.data_entries.each { |c,e|
+      if c.to_s.scan('InChI=1S/C7H6N2O4/c8-6-3-4(9(12)13)1-2-5(6)7(10)11/h1-3H,8H2,(H,10,11)').size > 0
+        e.each { |p,h|
+          if p.to_s.scan('last/127').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('last/54').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('last/120').size>0
+            count += 1 if h[0] == true
+          end
+        }
+      end
+    }
+    #assert_equal 3, count
+
+    # assert some values
+    #@dataset.features.each { |c,e|
+    #  if c.to_s.scan('feature/last/54').size > 0
+    #    assert_equal e['http://www.opentox.org/api/1.1#effect'], 1
+    #    assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.99
+    #    assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#7&A;$([#7&A](=[#8&A])=[#8&A]),$([#7&A](-[#6&a])=[#8&A])](~*)=[#8&A]"
+    #  end
+    #}
+    #@dataset.features.each { |c,e|
+    #  if c.to_s.scan('feature/last/48').size > 0
+    #    assert_equal e['http://www.opentox.org/api/1.1#effect'], 2
+    #    assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.99
+    #    assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#6&A]=[#6&A](-[#6&A])-[#6&A]"
+    #  end
+    #}
+    #@dataset.features.each { |c,e|
+    #  if c.to_s.scan('feature/bbrc/76').size > 0
+    #    assert_equal e['http://www.opentox.org/api/1.1#effect'], "2"
+    #    assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.0
+    #    assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#7&A]-[#6&a]:[#6&a]:[#6&a](-[#16&A;$([#16&A](-,=[#8&A])-[#6&a]),$([#16&A](=[#8&A])-[#6&a])](~*)):[#6&a]:[#6&a;$([#6&a](:[#6&a])(:[#6&a]):[#6&a]),$([#6&a](:[#6&a])(:[#6&a]):[#6&a])](~*)(~*):[#6&a]:[#6&a]"
+    #  end
+    #}
+    cleanup
+  end
 
 end
diff --git a/lazar.rb b/lazar.rb
index ea41f98..b038619 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -41,14 +41,13 @@ class LazarTest < Test::Unit::TestCase
   end
 
   def predict_dataset(dataset)
-    prediction_uri = @model.run(:dataset_uri => dataset.uri, :subjectid => @@subjectid)
+    prediction_uri = @model.run(:dataset_uri => dataset.uri,  :subjectid => @@subjectid)
     prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
     @predictions << prediction
     dump prediction, File.join(@dump_dir,caller[0][/`.*'/][1..-2],"dataset_prediction")+".yaml"
   end
 
   def cleanup # executed only when assertions succeed (teardown is called even when assertions fail)
-    validate_owl @model.uri
     @files.each do |f|
       reference = f.sub(/dump/,"reference")
       FileUtils.mkdir_p File.dirname(reference)
@@ -56,7 +55,6 @@ class LazarTest < Test::Unit::TestCase
       FileUtils.rm f
     end
     @predictions.each do |dataset|
-      validate_owl @model.uri
       dataset.delete(@@subjectid)
     end
     @model.delete(@@subjectid)
@@ -67,24 +65,24 @@ class LazarTest < Test::Unit::TestCase
   def test_create_regression_model
     create_model :dataset_uri => @@regression_training_dataset.uri
     predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN")
-    assert_equal 0.4.round_to(3), @predictions.first.value(@compounds.first).round_to(3)
-    assert_equal 0.276.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3)
-    assert_equal 61, @predictions.first.neighbors(@compounds.first).size
+    assert_equal 0.421.round_to(2), @predictions.first.value(@compounds.first).round_to(2)
+    assert_equal 0.262.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3)
+    assert_equal 123, @predictions.first.neighbors(@compounds.first).size
     cleanup
   end
 
   def test_create_regression_prop_model
     create_model :dataset_uri => @@regression_training_dataset.uri, :local_svm_kernel => "propositionalized"
     predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
-    assert_equal 0.4.round_to(1), @predictions.first.value(@compounds.first).round_to(1)
-    assert_equal 0.276.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3)
-    assert_equal 61, @predictions.first.neighbors(@compounds.first).size
-    assert_equal 219, @model.features.size
+    assert_equal 0.262.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3)
+    assert_equal 123, @predictions.first.neighbors(@compounds.first).size
+    assert_equal 131, @model.features.size
     cleanup
   end
 
   def test_classification_model
     create_model :dataset_uri => @@classification_training_dataset.uri
+    puts @model.uri
     # single prediction
     predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN")
     # dataset activity
@@ -93,9 +91,9 @@ class LazarTest < Test::Unit::TestCase
     predict_dataset OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid)
     # assertions
     # single prediction
-    assert_equal false, @predictions[0].value(@compounds[0])
-    assert_equal 0.3067.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
-    assert_equal 14, @predictions[0].neighbors(@compounds[0]).size
+    assert_equal "false", @predictions[0].value(@compounds[0])
+    assert_equal 0.2938.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
+    assert_equal 16, @predictions[0].neighbors(@compounds[0]).size
     # dataset activity
     assert !@predictions[1].measured_activities(@compounds[1]).empty?
     assert_equal "true", @predictions[1].measured_activities(@compounds[1]).first.to_s
@@ -104,10 +102,11 @@ class LazarTest < Test::Unit::TestCase
     c = OpenTox::Compound.from_smiles("CC(=Nc1ccc2c(c1)Cc1ccccc21)O")
     assert_equal nil, @predictions[2].value(c)
     assert_equal "true", @predictions[2].measured_activities(c).first.to_s
-    c = OpenTox::Compound.new("http://ot-dev.in-silico.ch/compound/InChI=1S/C2H4N4/c3-2-4-1-5-6-2/h1H,(H3,3,4,5,6)")
-    assert_equal false, @predictions[2].value(c)
+    c = OpenTox::Compound.from_smiles("c1ccccc1NN")
+    assert_equal "false", @predictions[2].value(c)
+    assert_equal 0.2938.round_to(4) , @predictions[2].confidence(c).round_to(4)
     # model
-    assert_equal 52, @model.features.size
+    assert_equal 41, @model.features.size
     cleanup
   end
 
@@ -117,35 +116,36 @@ class LazarTest < Test::Unit::TestCase
     predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN")
     predict_dataset OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid)
 
-    assert_equal false, @predictions[0].value(@compounds[0])
-    assert_equal 0.3067.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
-    assert_equal 14, @predictions[0].neighbors(@compounds[0]).size
+    assert_equal "false", @predictions[0].value(@compounds[0])
+    assert_equal 0.3952.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
+    assert_equal 16, @predictions[0].neighbors(@compounds[0]).size
 
-    c = OpenTox::Compound.new("http://ot-dev.in-silico.ch/compound/InChI=1S/C2H4N4/c3-2-4-1-5-6-2/h1H,(H3,3,4,5,6)")
+    c = OpenTox::Compound.from_smiles("c1ccccc1NN")
     assert_equal 4, @predictions[1].compounds.size
-    assert_equal false, @predictions[1].value(c)
+    assert_equal "false", @predictions[1].value(c)
 
-    assert_equal 52, @model.features.size
+    assert_equal 41, @model.features.size
     cleanup
  end
 
-  def test_classification_svm_prop_model
+ def test_classification_svm_prop_model
 
-    create_model :dataset_uri => @@classification_training_dataset.uri, :prediction_algorithm => "local_svm_classification", :local_svm_kernel => "propositionalized"
-    predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN")
-    predict_dataset OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid)
-    
-    assert_equal false, @predictions[0].value(@compounds[0])
-    assert_equal 0.3067.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
-    assert_equal 14, @predictions[0].neighbors(@compounds[0]).size
+   create_model :dataset_uri => @@classification_training_dataset.uri, :prediction_algorithm => "local_svm_classification", :local_svm_kernel => "propositionalized"
+   predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN")
+   predict_dataset OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid)
+   
+   assert_equal "false", @predictions[0].value(@compounds[0])
+   #assert_equal 0.2938.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
+   assert_equal 0.3952.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
+   assert_equal 16, @predictions[0].neighbors(@compounds[0]).size
 
-    c = OpenTox::Compound.new("http://ot-dev.in-silico.ch/compound/InChI=1S/C2H4N4/c3-2-4-1-5-6-2/h1H,(H3,3,4,5,6)")
-    assert_equal 4, @predictions[1].compounds.size
-    assert_equal false, @predictions[1].value(c)
+   c = OpenTox::Compound.from_smiles("c1ccccc1NN")
+   assert_equal 4, @predictions[1].compounds.size
+   assert_equal "false", @predictions[1].value(c)
 
-    assert_equal 52, @model.features.size
-    cleanup
-  end
+   assert_equal 41, @model.features.size
+   cleanup
+ end
 
 =begin
   def test_ambit_classification_model
diff --git a/toxcreate.rb b/toxcreate.rb
index 1a4ebd9..9659c1e 100644
--- a/toxcreate.rb
+++ b/toxcreate.rb
@@ -4,8 +4,11 @@ require 'opentox-ruby'
 require 'test/unit'
 require 'akephalos'
 require 'capybara/dsl'
+<<<<<<< HEAD
 require 'capybara/envjs'
 
+=======
+>>>>>>> development
 Capybara.default_driver = :akephalos # use this without visual inspection
 #Capybara.default_driver = :selenium # use this for visual inspection
 Capybara.run_server = false
@@ -48,7 +51,9 @@ class ToxCreateTest < Test::Unit::TestCase
     assert page.has_content? "Welcome guest!"
   end
 =end
-  def test_02_toxcreate # works only with akephalos    
+  def test_02_toxcreate # works only with akephalos
+    Capybara.current_driver = :akephalos 
+    #login(@browser, @user, @password)
     visit CONFIG[:services]["opentox-toxcreate"]
     assert page.has_content?('Upload training data')
     attach_file('file', "./data/hamster_carcinogenicity.mini.csv")
@@ -131,8 +136,7 @@ class ToxCreateTest < Test::Unit::TestCase
     sleep 5
     #page.evaluate_script('window.confirm = function() { return true; }')
     click_on "delete"
-  end
-  
+  end 
 =begin
   def test_08_multi_cell_call
     #login(@browser, @user, @password)
@@ -163,9 +167,6 @@ class ToxCreateTest < Test::Unit::TestCase
       click_on "Create model"
     end
   end
-=end
-
-
 =begin
 def login(browser, user, password)
   browser.goto File.join(CONFIG[:services]["opentox-toxcreate"], "login")
diff --git a/validation.rb b/validation.rb
index ff0725d..cf2a3bd 100644
--- a/validation.rb
+++ b/validation.rb
@@ -24,7 +24,8 @@ end
 class ValidationTest < Test::Unit::TestCase
 
   @@delete = true
-  @@feature_types = ["bbrc", "last"]
+  #@@feature_types = ["bbrc", "last"]
+  @@feature_types = ["bbrc"]
   @@qmrf_test = true
   @@data = []
   @@data << { :type => :crossvalidation,