From 6ab86c253ba0eb79b9e6a20effa2d18626accf2b Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 13 Aug 2015 11:56:40 +0200
Subject: OpenBabel can (canonical smiles) instead of inchi as internal
 identifier to avoid OpenBabel InChi bug.

---
 test/lazar-fminer.rb | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 test/lazar-fminer.rb

(limited to 'test/lazar-fminer.rb')

diff --git a/test/lazar-fminer.rb b/test/lazar-fminer.rb
new file mode 100644
index 0000000..fbfa3d2
--- /dev/null
+++ b/test/lazar-fminer.rb
@@ -0,0 +1,51 @@
+require_relative "setup.rb"
+
+class LazarFminerTest < MiniTest::Test
+
+  def test_lazar_fminer
+    training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv")
+    model = Model::LazarFminerClassification.create training_dataset#, feature_dataset
+    feature_dataset = Dataset.find model.neighbor_algorithm_parameters[:feature_dataset_id]
+    assert_equal training_dataset.compounds.size, feature_dataset.compounds.size
+    p feature_dataset.features.size
+    #assert_equal 54, feature_dataset.features.size
+    feature_dataset.data_entries.each do |e|
+      assert_equal e.size, feature_dataset.features.size
+    end
+    #assert_equal 'C-C-C=C', feature_dataset.features.first.smarts
+
+    [ {
+      :compound => OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"),
+      :prediction => "false",
+      :confidence => 0.25281385281385277,
+      :nr_neighbors => 11
+    },{
+      :compound => OpenTox::Compound.from_smiles("c1ccccc1NN"),
+      :prediction => "false",
+      :confidence => 0.3639589577089577,
+      :nr_neighbors => 14
+    }, {
+      :compound => Compound.from_smiles('OCCCCCCCC\C=C/CCCCCCCC'),
+      :prediction => "false",
+      :confidence => 0.5555555555555556,
+      :nr_neighbors => 1
+    }].each do |example|
+      prediction = model.predict example[:compound]
+
+      p prediction
+      #assert_equal example[:prediction], prediction[:value]
+      #assert_equal example[:confidence], prediction[:confidence]
+      #assert_equal example[:nr_neighbors], prediction[:neighbors].size
+    end
+
+    # 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
+
+    assert_match /No neighbors/, prediction.data_entries[7][2]
+    assert_equal "measured", prediction.data_entries[14][1]
+    # cleanup
+    [training_dataset,model,feature_dataset,compound_dataset].each{|o| o.delete}
+  end
+end
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