From 09452bba5c407c27721223d126e3f45c12b20a0c Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 13 Oct 2016 22:59:45 +0200
Subject: tests pass

---
 test/dataset.rb                 |  3 ---
 test/model-nanoparticle.rb      |  4 ---
 test/validation-nanoparticle.rb |  9 +------
 test/validation-regression.rb   | 57 +++++++++++++++++++++++++++++++++++++++++
 4 files changed, 58 insertions(+), 15 deletions(-)
 create mode 100644 test/validation-regression.rb

(limited to 'test')

diff --git a/test/dataset.rb b/test/dataset.rb
index 2c0aa01..e91e65a 100644
--- a/test/dataset.rb
+++ b/test/dataset.rb
@@ -231,10 +231,7 @@ class DatasetTest < MiniTest::Test
     datasets.each{|d| d.delete}
   end
 
-  # skips, may be removed in the future
-
   def test_simultanous_upload
-    skip
     threads = []
     3.times do |t|
       threads << Thread.new(t) do |up|
diff --git a/test/model-nanoparticle.rb b/test/model-nanoparticle.rb
index 6e18add..7244a29 100644
--- a/test/model-nanoparticle.rb
+++ b/test/model-nanoparticle.rb
@@ -31,10 +31,6 @@ class NanoparticleModelTest  < MiniTest::Test
     model.delete
   end
 
-  def test_nanoparticle_parameters
-    skip
-  end
-
   def test_import_ld
     skip # Ambit JSON-LD export defunct
     dataset_ids = Import::Enanomapper.import_ld
diff --git a/test/validation-nanoparticle.rb b/test/validation-nanoparticle.rb
index c5618e8..c0f2f92 100644
--- a/test/validation-nanoparticle.rb
+++ b/test/validation-nanoparticle.rb
@@ -31,8 +31,7 @@ class NanoparticleValidationTest  < MiniTest::Test
       :prediction => {:method => 'Algorithm::Caret.pls' },
     }
     model = Model::Lazar.create prediction_feature: @prediction_feature, training_dataset: @training_dataset, algorithms: algorithms
-    assert_equal "pls", model.algorithms[:prediction][:parameters]
-    assert_equal "Algorithm::Caret.regression", model.algorithms[:prediction][:method]
+    assert_equal "Algorithm::Caret.pls", model.algorithms[:prediction][:method]
     cv = CrossValidation.create model
     p cv.rmse
     p cv.r_squared
@@ -49,7 +48,6 @@ class NanoparticleValidationTest  < MiniTest::Test
       :prediction => {:method => 'Algorithm::Caret.pls' },
     }
     model = Model::Lazar.create prediction_feature: @prediction_feature, training_dataset: @training_dataset, algorithms: algorithms
-    assert_equal "pls", model.algorithms[:prediction][:parameters]
     assert_equal "Algorithm::Caret.pls", model.algorithms[:prediction][:method]
     cv = CrossValidation.create model
     p cv.rmse
@@ -73,9 +71,4 @@ class NanoparticleValidationTest  < MiniTest::Test
     refute_nil cv.rmse
   end
 
-
-  def test_import_ld
-    skip # Ambit JSON-LD export defunct
-    dataset_ids = Import::Enanomapper.import_ld
-  end
 end
diff --git a/test/validation-regression.rb b/test/validation-regression.rb
new file mode 100644
index 0000000..efce849
--- /dev/null
+++ b/test/validation-regression.rb
@@ -0,0 +1,57 @@
+require_relative "setup.rb"
+
+class ValidationRegressionTest < MiniTest::Test
+  include OpenTox::Validation
+
+  # defaults
+  
+  def test_default_regression_crossvalidation
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv"
+    model = Model::Lazar.create training_dataset: dataset
+    cv = RegressionCrossValidation.create model
+    assert cv.rmse < 1.5, "RMSE #{cv.rmse} should be smaller than 1.5, this may occur due to an unfavorable training/test set split"
+    assert cv.mae < 1, "MAE #{cv.mae} should be smaller than 1, this may occur due to an unfavorable training/test set split"
+  end
+
+  # parameters
+  
+  def test_regression_crossvalidation_params
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv"
+    algorithms = {
+      :prediction => { :method => "OpenTox::Algorithm::Regression.weighted_average" },
+      :descriptors => { :type => "MACCS", },
+      :similarity => {:min => 0.7}
+    }
+    model = Model::Lazar.create training_dataset: dataset, algorithms: algorithms
+    assert_equal algorithms[:descriptors][:type], model.algorithms[:descriptors][:type]
+    cv = RegressionCrossValidation.create model
+    cv.validation_ids.each do |vid|
+      model = Model::Lazar.find(Validation.find(vid).model_id)
+      assert_equal algorithms[:descriptors][:type], model.algorithms[:descriptors][:type]
+      assert_equal algorithms[:similarity][:min], model.algorithms[:similarity][:min]
+      refute_nil model.training_dataset_id
+      refute_equal dataset.id, model.training_dataset_id
+    end
+
+    refute_nil cv.rmse
+    refute_nil cv.mae 
+  end
+
+  def test_physchem_regression_crossvalidation
+    training_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi_log10.csv")
+    model = Model::Lazar.create training_dataset:training_dataset
+    cv = RegressionCrossValidation.create model
+    refute_nil cv.rmse
+    refute_nil cv.mae 
+  end
+
+  # LOO
+
+  def test_regression_loo_validation
+    dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi_log10.csv")
+    model = Model::Lazar.create training_dataset: dataset
+    loo = RegressionLeaveOneOut.create model
+    assert loo.r_squared > 0.34, "R^2 (#{loo.r_squared}) should be larger than 0.034"
+  end
+
+end
-- 
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