lazar model from ambit datasets

4 files changed, 97 insertions, 48 deletions

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/feature.rb b/feature.rb
index 7ed600c..523688f 100644
--- a/feature.rb
+++ b/feature.rb
@@ -25,7 +25,7 @@ class FeatureTest < Test::Unit::TestCase
 
   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..3e6dd0d 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -12,27 +12,29 @@ class FminerTest < Test::Unit::TestCase
     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
+    #puts dataset_uri
+    assert_equal 52, 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
+  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
     d =OpenTox::Dataset.new dataset_uri, @@subjectid
     d.load_features(@@subjectid)
-    assert_equal 35, d.features.size
-    #validate_owl
+    assert_equal 1354, 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
+=begin
+  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 225, d.features.size
+    assert_equal 35, d.features.size
+    #validate_owl
     d.delete(@@subjectid)
   end
 
@@ -44,7 +46,6 @@ class FminerTest < Test::Unit::TestCase
     assert_equal 16, d.features.size
     d.delete(@@subjectid)
   end
-=begin
 =end
 
 end
diff --git a/lazar.rb b/lazar.rb
index 1eb7645..512a614 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -8,62 +8,111 @@ 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 1354, 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), 0.17.round_to(4)
+    assert_equal prediction.confidence(compound).round_to(4), 0.5697.round_to(4)
+    assert_equal prediction.neighbors(compound).size, 77
   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
+
+end
 =begin
 =end
-end