3 files changed, 125 insertions, 15 deletions

diff --git a/test/compound.rb b/test/compound.rb
index 06c19a2..6a3c696 100644
--- a/test/compound.rb
+++ b/test/compound.rb
@@ -97,4 +97,41 @@ print c.sdf
     c = Compound.from_inchi(inchi)
     assert_equal inchi, c.inchi
   end
+
+  def test_openbabel_fingerprint
+    [
+      "CC(=O)CC(C)C#N",
+      "CC(=O)CC(C)C",
+      "C(=O)CC(C)C#N",
+    ].each do |smi|
+      c = OpenTox::Compound.from_smiles smi
+      assert_equal c.openbabel_fingerprint("FP4").size, c.fp4.size
+    end
+  end
+
+  def test_fingerprint_neighbors
+    types = ["FP2", "FP3", "FP4", "MACCS"]
+    min_sim = 0.7
+    training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.csv")
+    [
+      "CC(=O)CC(C)C#N",
+      "CC(=O)CC(C)C",
+      "C(=O)CC(C)C#N",
+    ].each do |smi|
+      c = OpenTox::Compound.from_smiles smi
+      p c.smiles
+      types.each do |type|
+        p type
+        neighbors = c.fingerprint_neighbors({:type => type, :training_dataset_id => training_dataset.id, :min_sim => min_sim})
+        p neighbors.collect{|n| [Compound.find(n.first).smiles,n.last]}
+        if type == "FP4"
+          fp4_neighbors = c.neighbors
+          neighbors.each do |n|
+            p [Compound.find(n.first).smiles,n.last] unless fp4_neighbors.include?(n)
+            assert_includes fp4_neighbors, n
+          end
+        end
+      end
+    end
+  end
 end
diff --git a/test/experiment.rb b/test/experiment.rb
index c465d7b..4b54768 100644
--- a/test/experiment.rb
+++ b/test/experiment.rb
@@ -4,27 +4,88 @@ class ExperimentTest < MiniTest::Test
 
   def test_regression_experiment
     datasets = [
-      "EPAFHM.csv",
-      "FDA_v3b_Maximum_Recommended_Daily_Dose_mmol.csv",
+      "EPAFHM.medi.csv",
+      #"EPAFHM.csv",
+      #"FDA_v3b_Maximum_Recommended_Daily_Dose_mmol.csv",
       "LOAEL_mmol_corrected_smiles.csv"
+    ]
+    experiment = Experiment.create(
+      :name => "Default regression for datasets #{datasets}.",
+      :dataset_ids => datasets.collect{|d| Dataset.from_csv_file(File.join(DATA_DIR, d)).id},
+      :model_settings => [
+        {
+          :algorithm => "OpenTox::Model::LazarRegression",
+        }
       ]
-    model_algorithms = ["OpenTox::Model::LazarRegression"]
-    neighbor_algorithms = ["OpenTox::Algorithm::Neighbor.fingerprint_similarity"]
-    prediction_algorithms = ["OpenTox::Algorithm::Regression.weighted_average"]
-    neighbor_algorithm_parameters = [{:min_sim => 0.7}]
+    )
+    #experiment.run
+    puts experiment.report.to_yaml
+    assert_equal datasets.size, experiment.results.size
+    experiment.results.each do |dataset_id, result|
+      assert_equal 1, result.size
+      result.each do |r|
+        assert_kind_of BSON::ObjectId, r[:model_id]
+        assert_kind_of BSON::ObjectId, r[:repeated_crossvalidation_id]
+      end
+    end
+  end
+
+  def test_classification_experiment
+
+    datasets = [ "hamster_carcinogenicity.csv" ]
     experiment = Experiment.create(
-      :name => "Regression for datasets #{datasets}.",
+      :name => "Fminer vs fingerprint classification for datasets #{datasets}.",
       :dataset_ids => datasets.collect{|d| Dataset.from_csv_file(File.join(DATA_DIR, d)).id},
-      :model_algorithms => model_algorithms,
-      :neighbor_algorithms => neighbor_algorithms,
-      :neighbor_algorithm_parameters => neighbor_algorithm_parameters,
-      :prediction_algorithms => prediction_algorithms,
+      :model_settings => [
+        {
+          :algorithm => "OpenTox::Model::LazarClassification",
+        },{
+          :algorithm => "OpenTox::Model::LazarClassification",
+          :neighbor_algorithm_parameter => {:min_sim => 0.3}
+        },
+        #{
+          #:algorithm => "OpenTox::Model::LazarFminerClassification",
+        #}
+      ]
     )
-    experiment.run
+    #experiment.run
 =begin
-    p experiment
-    experiment.report
+    experiment = Experiment.find "55f944a22b72ed7de2000000"
 =end
-    refute_empty experiment.crossvalidation_ids
+    puts experiment.report.to_yaml
+    experiment.results.each do |dataset_id, result|
+      assert_equal 2, result.size
+      result.each do |r|
+        assert_kind_of BSON::ObjectId, r[:model_id]
+        assert_kind_of BSON::ObjectId, r[:repeated_crossvalidation_id]
+      end
+    end
+  end
+
+  def test_regression_fingerprints
+    datasets = [
+      "LOAEL_mmol_corrected_smiles.csv"
+    ]
+    min_sims = [0.3,0.7]
+    types = ["FP2","FP3","FP4","MACCS"]
+    experiment = Experiment.create(
+      :name => "Fminer vs fingerprint classification for datasets #{datasets}.",
+      :dataset_ids => datasets.collect{|d| Dataset.from_csv_file(File.join(DATA_DIR, d)).id},
+    )
+    types.each do |type|
+      min_sims.each do |min_sim|
+        experiment.model_settings << {
+          :algorithm => "OpenTox::Model::LazarRegression",
+          :neighbor_algorithm => "fingerprint_neighbors",
+          :neighbor_algorithm_parameter => {
+            :type => type,
+            :min_sim => min_sim,
+          }
+        }
+      end
+    end
+    experiment.run
+    p experiment.report
+
   end
 end
diff --git a/test/validation.rb b/test/validation.rb
index a4c3d80..dfa2c81 100644
--- a/test/validation.rb
+++ b/test/validation.rb
@@ -33,4 +33,16 @@ class ValidationTest < MiniTest::Test
     #assert cv.weighted_mae < cv.mae
   end
 
+  def test_repeated_crossvalidation
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
+    model = Model::LazarClassification.create dataset
+    repeated_cv = RepeatedCrossValidation.create model
+    p repeated_cv
+    repeated_cv.crossvalidations.each do |cv|
+      p cv
+      p cv.accuracy
+      assert cv.accuracy > 0.7
+    end
+  end
+
 end