Detailed Fminer tests

1 files changed, 290 insertions, 14 deletions

diff --git a/fminer.rb b/fminer.rb
index 2adf5e3..0a30962 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
@@ -28,6 +34,33 @@ class FminerTest < Test::Unit::TestCase
     dump 
     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'], "false"
+        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
 
@@ -37,55 +70,298 @@ class FminerTest < Test::Unit::TestCase
     dump
     assert_equal 207, @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/107').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('bbrc/57').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('bbrc/158').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_equal 21, @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/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'], "true"
+        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_equal 8, @dataset.features.size
+
+    
+    # assert no hit counts present
+    count=0
+    @dataset.data_entries.each { |c,e|
+      if c.to_s.scan('InChI=1S/C9H14O3/c1-7(2)9(10)12-6-8-4-3-5-11-8/h8H,1,3-6H2,2H3').size > 0
+        e.each { |p,h|
+          if p.to_s.scan('last/2').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('last/3').size>0
+            count += 1 if h[0] == true
+          end
+          if p.to_s.scan('last/7').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'], "deactivating"
+        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'], "[#8&A]-[#6&A](-[#6&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 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('39').size>0
+          if p.to_s.scan('bbrc/39').size>0
             assert_equal 6, h[0]
           end
-          if p.to_s.scan('18').size>0
+          if p.to_s.scan('bbrc/18').size>0
             assert_equal 5, h[0]
           end
-          if p.to_s.scan('38').size>0
+          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'], "false"
+        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
+
+  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'], "false"
+        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
 
-# 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_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'], "1"
+        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#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])"
+      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#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])"
+      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_equal 138, @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/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'], "0"
+        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#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