features/toxicities fixed

3 files changed, 27 insertions, 14 deletions

diff --git a/test/classification.rb b/test/classification.rb
index af23db6..7412714 100644
--- a/test/classification.rb
+++ b/test/classification.rb
@@ -30,14 +30,14 @@ class LazarClassificationTest < MiniTest::Test
 
     # make a dataset prediction
     compound_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini.csv")
-    prediction = model.predict compound_dataset
-    assert_equal compound_dataset.compounds, prediction.compounds
+    prediction_dataset = model.predict compound_dataset
+    assert_equal compound_dataset.compounds, prediction_dataset.compounds
 
-    cid = prediction.compounds[7].id.to_s
-    assert_equal "Could not find similar compounds with experimental data in the training dataset.", prediction.predictions[cid][:warning]
-    cid = prediction.compounds[9].id.to_s
-    assert_equal "1 compounds have been removed from neighbors, because they have the same structure as the query compound.", prediction.predictions[cid][:warning]
+    cid = prediction_dataset.compounds[7].id.to_s
+    assert_equal "Could not find similar compounds with experimental data in the training dataset.", prediction_dataset.predictions[cid][:warning]
+    cid = prediction_dataset.compounds[9].id.to_s
+    assert_equal "1 compounds have been removed from neighbors, because they have the same structure as the query compound.", prediction_dataset.predictions[cid][:warning]
     # cleanup
-    [training_dataset,model,compound_dataset].each{|o| o.delete}
+    [training_dataset,model,compound_dataset,prediction_dataset].each{|o| o.delete}
   end
 end
diff --git a/test/nanoparticles.rb b/test/nanoparticles.rb
index 6f241ec..46073a9 100644
--- a/test/nanoparticles.rb
+++ b/test/nanoparticles.rb
@@ -6,16 +6,29 @@ class NanoparticleTest  < MiniTest::Test
     dataset_ids = Import::Enanomapper.import
     assert_operator Nanoparticle.count , :>, 570, "Only #{Nanoparticle.count} nanoparticles imported"
     assert_operator dataset_ids.size, :>, 8, "Only #{dataset_ids.size} bundles imported"
-    p dataset_ids.collect{|d| Dataset.find(d).name}
     assert dataset_ids.collect{|d| Dataset.find(d).name}.include? ("NanoWiki")
     assert dataset_ids.collect{|d| Dataset.find(d).name}.include? ("Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles")
+    p dataset_ids.collect{|d| {d => Dataset.find(d).name}}
+    dataset_ids.collect do |d|
+      d = Dataset.find(d)
+      p d.name
+      puts d.to_csv
+    end
   end
 
-  def test_create_model
-    Model::NanoLazar.create_all.each do |model|
-      np = Nanoparticle.find(model.training_particle_ids.sample)
-      model.predict np
+  def test_export
+    Dataset.all.each do |d|
+      puts d.to_csv
     end
   end
 
+  def test_create_model
+    training_dataset = Dataset.find_or_create_by(:name => "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles")
+    model = Model::LazarRegression.create(training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression", :neighbor_algorithm => "nanoparticle_neighbors")
+    nanoparticle = training_dataset.nanoparticles[-34]
+    prediction = model.predict nanoparticle
+    p prediction
+    refute_nil prediction[:value]
+  end
+
 end
diff --git a/test/setup.rb b/test/setup.rb
index e7c32b4..6c97282 100644
--- a/test/setup.rb
+++ b/test/setup.rb
@@ -5,5 +5,5 @@ require_relative '../lib/lazar.rb'
 include OpenTox
 TEST_DIR ||= File.expand_path(File.dirname(__FILE__))
 DATA_DIR ||= File.join(TEST_DIR,"data")
-$mongo.database.drop
-$gridfs = $mongo.database.fs
+#$mongo.database.drop
+#$gridfs = $mongo.database.fs