From 79238bddb59607aa9f759caa9e3c8db176709703 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 28 Apr 2016 12:19:48 +0200
Subject: compound validations fixed

---
 lib/model.rb        | 1 -
 lib/nanoparticle.rb | 2 +-
 lib/regression.rb   | 2 +-
 test/regression.rb  | 9 ++++-----
 test/setup.rb       | 4 ++--
 5 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/lib/model.rb b/lib/model.rb
index 80b4685..f61368e 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -50,7 +50,6 @@ module OpenTox
       end
 
       def predict_compound compound
-        #p compound
         neighbors = compound.send(neighbor_algorithm, neighbor_algorithm_parameters)
         # remove neighbors without prediction_feature
         # check for database activities (neighbors may include query compound)
diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb
index b5de5b9..83b97a9 100644
--- a/lib/nanoparticle.rb
+++ b/lib/nanoparticle.rb
@@ -8,7 +8,7 @@ module OpenTox
     field :bundles, type: Array, default: []
 
     def nanoparticle_neighbors params
-      Dataset.find(params[:training_dataset_id]).nanoparticles
+      Dataset.find(params[:training_dataset_id]).nanoparticles.collect{|np| {"_id" => np.id, "tanimoto" => 1}}
     end
 
     def add_feature feature, value
diff --git a/lib/regression.rb b/lib/regression.rb
index 3a59c14..694a2dc 100644
--- a/lib/regression.rb
+++ b/lib/regression.rb
@@ -85,7 +85,7 @@ module OpenTox
 
         activities = []
         weights = []
-        pc_ids = neighbors.collect{|n| n.physchem_descriptors.keys}.flatten.uniq
+        pc_ids = neighbors.collect{|n| Substance.find(n["_id"]).physchem_descriptors.keys}.flatten.uniq
         data_frame = []
         data_frame[0] = []
         
diff --git a/test/regression.rb b/test/regression.rb
index ad460b5..6d461ed 100644
--- a/test/regression.rb
+++ b/test/regression.rb
@@ -4,7 +4,7 @@ class LazarRegressionTest < MiniTest::Test
 
   def test_weighted_average
     training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
-    model = Model::LazarRegression.create training_dataset, {:neighbor_algorithm_parameters => {:min_sim => 0}, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_weighted_average"}
+    model = Model::LazarRegression.create training_dataset.features.first, training_dataset, {:neighbor_algorithm_parameters => {:min_sim => 0}, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_weighted_average"}
     compound = Compound.from_smiles "CC(C)(C)CN"
     prediction = model.predict compound
     assert_equal 7.2, prediction[:value].round(1)
@@ -13,7 +13,7 @@ class LazarRegressionTest < MiniTest::Test
 
   def test_mpd_fingerprints
     training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
-    model = Model::LazarRegression.create training_dataset
+    model = Model::LazarRegression.create training_dataset.features.first, training_dataset
     model.neighbor_algorithm_parameters[:type] = "MP2D"
     compound = Compound.from_smiles "CCCSCCSCC"
     prediction = model.predict compound
@@ -23,10 +23,9 @@ class LazarRegressionTest < MiniTest::Test
 
   def test_local_fingerprint_regression
     training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
-    model = Model::LazarRegression.create(training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_fingerprint_regression")
+    model = Model::LazarRegression.create(training_dataset.features.first, training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_fingerprint_regression")
     compound = Compound.from_smiles "NC(=O)OCCC"
     prediction = model.predict compound
-    p prediction
     refute_nil prediction[:value]
     refute_nil prediction[:prediction_interval]
     refute_empty prediction[:neighbors]
@@ -34,7 +33,7 @@ class LazarRegressionTest < MiniTest::Test
 
   def test_local_physchem_regression
     training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
-    model = Model::LazarRegression.create(training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression")
+    model = Model::LazarRegression.create(training_dataset.features.first, training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression")
     compound = Compound.from_smiles "NC(=O)OCCC"
     prediction = model.predict compound
     refute_nil prediction[:value]
diff --git a/test/setup.rb b/test/setup.rb
index 6c97282..e7c32b4 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
-- 
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