Merge branch 'release/v2.1.0' into development

3 files changed, 28 insertions, 25 deletions

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/fminer.rb b/fminer.rb
index 4927af2..c8cece6 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -56,7 +56,7 @@ class FminerTest < Test::Unit::TestCase
     # 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'], "false"
+        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
@@ -132,7 +132,7 @@ class FminerTest < Test::Unit::TestCase
     # 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'], "true"
+        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
@@ -213,7 +213,7 @@ 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'], "false"
+        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
@@ -256,7 +256,7 @@ 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'], "false"
+        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
@@ -293,23 +293,23 @@ end
     # 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'], "1"
+        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'], "2"
+        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'], "[#6&a]:[#6&a](:[#6&a])(:[#6&a]:[#6&a]:[#6&a]:[#6&a]-[#16&A])"
+        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'], "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](:[#7&a]:[#6&a])(:[#6&a]:[#6&a])"
+        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
@@ -343,14 +343,14 @@ end
     # 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'], "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'], "1"
+        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
diff --git a/lazar.rb b/lazar.rb
index 62a512b..b038619 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -65,7 +65,7 @@ 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 0.421.round_to(3), @predictions.first.value(@compounds.first).round_to(3)
+    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
@@ -80,16 +80,6 @@ class LazarTest < Test::Unit::TestCase
     cleanup
   end
 
-  def test_create_regression_prop_mlr_model
-    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop"
-    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
-    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
-    assert_equal 0.374.round_to(3), @predictions.first.value(@compounds.first).round_to(3)
-    cleanup
-  end
-
   def test_classification_model
     create_model :dataset_uri => @@classification_training_dataset.uri
     puts @model.uri