From d7504cc422bbaeee3546589d87e7baeb4e977c0b Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 12 Jan 2017 17:57:03 +0100
Subject: source uris for core and coating

---
 lib/import.rb                         | 2 ++
 test/feature.rb                       | 4 ++--
 test/model-nanoparticle.rb            | 7 +++++++
 test/nanomaterial-model-validation.rb | 5 ++---
 test/validation-regression.rb         | 5 ++---
 5 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/lib/import.rb b/lib/import.rb
index fd00fbe..96e7ad1 100644
--- a/lib/import.rb
+++ b/lib/import.rb
@@ -22,6 +22,7 @@ module OpenTox
               uri = c["component"]["compound"]["URI"]
               uri = CGI.escape File.join(uri,"&media=application/json")
               data = JSON.parse(RestClientWrapper.get "https://data.enanomapper.net/query/compound/url/all?media=application/json&search=#{uri}")
+              source = data["dataEntry"][0]["compound"]["URI"]
               smiles = data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23SMILESDefault"]
               names = []
               names << data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault"]
@@ -33,6 +34,7 @@ module OpenTox
               else
                 compound = Compound.find_or_create_by(:name => names.first,:names => names.compact)
               end
+              compound.source = source
               compound.save
               if c["relation"] == "HAS_CORE"
                 core_id = compound.id.to_s
diff --git a/test/feature.rb b/test/feature.rb
index 533ac0f..40edb9f 100644
--- a/test/feature.rb
+++ b/test/feature.rb
@@ -55,7 +55,7 @@ class FeatureTest < MiniTest::Test
   end
 
   def test_physchem_description
-    assert_equal 355, PhysChem.descriptors.size
+    assert_equal 346, PhysChem.descriptors.size
     assert_equal 15, PhysChem.openbabel_descriptors.size
     assert_equal 295, PhysChem.cdk_descriptors.size
     assert_equal 45, PhysChem.joelib_descriptors.size
@@ -63,7 +63,7 @@ class FeatureTest < MiniTest::Test
   end
 
   def test_physchem
-    assert_equal 355, PhysChem.descriptors.size
+    assert_equal 346, PhysChem.descriptors.size
     c = Compound.from_smiles "CC(=O)CC(C)C"
     logP = PhysChem.find_or_create_by :name => "Openbabel.logP"
     assert_equal 1.6215, logP.calculate(c)
diff --git a/test/model-nanoparticle.rb b/test/model-nanoparticle.rb
index 8dc6830..67bbfdd 100644
--- a/test/model-nanoparticle.rb
+++ b/test/model-nanoparticle.rb
@@ -8,6 +8,13 @@ class NanoparticleModelTest  < MiniTest::Test
     @prediction_feature = @training_dataset.features.select{|f| f["name"] == 'log2(Net cell association)'}.first
   end
 
+  def test_core_coating_source_uris
+    @training_dataset.nanoparticles.each do |np|
+      refute_nil np.core.source
+      np.coating.each{|c| refute_nil c.source}
+    end
+  end
+
   def test_nanoparticle_model
     assert true, @prediction_feature.measured
     model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature
diff --git a/test/nanomaterial-model-validation.rb b/test/nanomaterial-model-validation.rb
index b91c389..9eaa17d 100644
--- a/test/nanomaterial-model-validation.rb
+++ b/test/nanomaterial-model-validation.rb
@@ -8,7 +8,7 @@ class NanomaterialValidationModelTest < MiniTest::Test
   end
 
   def test_default_nanomaterial_validation_model
-    validation_model = Model::NanoValidation.create
+    validation_model = Model::Validation.from_enanomapper
     [:endpoint,:species,:source].each do |p|
       refute_empty validation_model[p]
     end
@@ -39,7 +39,7 @@ class NanomaterialValidationModelTest < MiniTest::Test
       :prediction => { :method => "OpenTox::Algorithm::Regression.weighted_average" },
       :feature_selection => nil
     }
-    validation_model = Model::NanoValidation.create algorithms: algorithms
+    validation_model = Model::Validation.from_enanomapper algorithms: algorithms
     assert validation_model.regression?
     refute validation_model.classification?
     validation_model.crossvalidations.each do |cv|
@@ -50,6 +50,5 @@ class NanomaterialValidationModelTest < MiniTest::Test
     assert_includes nanoparticle.dataset_ids, @training_dataset.id
     prediction = validation_model.predict nanoparticle
     refute_nil prediction[:value]
-    assert_includes prediction[:prediction_interval][0]..prediction[:prediction_interval][1], prediction[:measurements].median, "This assertion assures that measured values are within the prediction interval. It may fail in 5% of the predictions."
   end
 end
diff --git a/test/validation-regression.rb b/test/validation-regression.rb
index 7630521..01ed644 100644
--- a/test/validation-regression.rb
+++ b/test/validation-regression.rb
@@ -83,10 +83,9 @@ class ValidationRegressionTest < MiniTest::Test
     model = Model::Lazar.create training_dataset: dataset
     repeated_cv = RepeatedCrossValidation.create model
     repeated_cv.crossvalidations.each do |cv|
-      #assert cv.r_squared > 0.34, "R^2 (#{cv.r_squared}) should be larger than 0.034"
-      #assert_operator cv.accuracy, :>, 0.7, "model accuracy < 0.7, this may happen by chance due to an unfavorable training/test set split"
+      assert cv.r_squared > 0.34, "R^2 (#{cv.r_squared}) should be larger than 0.034"
+      assert_operator cv.accuracy, :>, 0.7, "model accuracy < 0.7, this may happen by chance due to an unfavorable training/test set split"
     end
-    File.open("tmp.png","w+"){|f| f.puts repeated_cv.correlation_plot}
   end
 
 end
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