Model::Prediction with tests, initial indexesv0.0.8

4 files changed, 30 insertions, 3 deletions

diff --git a/test/compound.rb b/test/compound.rb
index 7265ef5..06c19a2 100644
--- a/test/compound.rb
+++ b/test/compound.rb
@@ -54,7 +54,6 @@ print c.sdf
 
   def test_inchikey
     c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
-    p c
     assert_equal "UHOVQNZJYSORNB-UHFFFAOYSA-N", c.inchikey
   end
 
@@ -88,7 +87,8 @@ print c.sdf
       refute_nil c.fp4
     end
     c = d.compounds[371]
-    assert c.neighbors.size >= 19
+    n = c.neighbors
+    assert n.size >= 18, "Neighbors size (#{n.size}) should be larger than 17"
   end
 
   def test_openbabel_segfault
diff --git a/test/data/hamster_carcinogenicity.json b/test/data/hamster_carcinogenicity.json
new file mode 100644
index 0000000..8c17d9d
--- /dev/null
+++ b/test/data/hamster_carcinogenicity.json
@@ -0,0 +1,3 @@
+{ "species": "Hamster",
+"endpoint": "Carcinogenicity",
+"source": "http://www.epa.gov/ncct/dsstox/sdf_cpdbas.html" }
diff --git a/test/prediction_models.rb b/test/prediction_models.rb
new file mode 100644
index 0000000..b4ad415
--- /dev/null
+++ b/test/prediction_models.rb
@@ -0,0 +1,23 @@
+require_relative "setup.rb"
+
+class PredictionModelTest < MiniTest::Test
+
+  def test_prediction_model
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
+    model = Model::LazarFminerClassification.create dataset
+    cv = ClassificationCrossValidation.create model
+    metadata = JSON.parse(File.read("#{DATA_DIR}/hamster_carcinogenicity.json"))
+
+    metadata[:model_id] = model.id
+    metadata[:crossvalidation_id] = cv.id
+    pm = Model::Prediction.new(metadata)
+    pm.save
+    [:endpoint,:species,:source].each do |p|
+      refute_empty pm[p]
+    end
+    assert pm.crossvalidation.accuracy > 0.8
+    prediction = pm.predict Compound.from_smiles("CCCC(NN)C")
+    assert_equal "true", prediction[:value]
+    pm.delete
+  end
+end
diff --git a/test/setup.rb b/test/setup.rb
index 379fa53..538853d 100644
--- a/test/setup.rb
+++ b/test/setup.rb
@@ -3,4 +3,5 @@ require_relative '../lib/lazar.rb'
 include OpenTox
 TEST_DIR ||= File.expand_path(File.dirname(__FILE__))
 DATA_DIR ||= File.join(TEST_DIR,"data")
-#$mongo.database.drop
+$mongo.database.drop
+$gridfs = $mongo.database.fs # recreate GridFS indexes