From d0850e2983a219da214a67190fe881c7650f532f Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 13 Aug 2015 18:57:11 +0200
Subject: majority of tests working

---
 test/lazar-long.rb | 72 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 test/lazar-long.rb

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

diff --git a/test/lazar-long.rb b/test/lazar-long.rb
new file mode 100644
index 0000000..c0deaa2
--- /dev/null
+++ b/test/lazar-long.rb
@@ -0,0 +1,72 @@
+require_relative "setup.rb"
+
+class LazarExtendedTest < MiniTest::Test
+
+  def test_lazar_bbrc_ham_minfreq
+    dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv")
+    model = OpenTox::Model::Lazar.create dataset, OpenTox::Algorithm::Fminer.bbrc(dataset, :min_frequency => 5)
+    feature_dataset = OpenTox::Dataset.find model.feature_dataset_id
+    assert_equal dataset.compounds.size, feature_dataset.compounds.size
+    assert_equal 41, feature_dataset.features.size
+    assert_equal 'N-C=N', feature_dataset.features.first.smarts
+    compound = OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H")
+    prediction = model.predict compound
+    assert_equal "false", prediction[:value]
+    assert_equal 0.12380952380952381, prediction[:confidence]
+    dataset.delete
+    model.delete
+    feature_dataset.delete
+  end
+
+  def test_lazar_bbrc_large_ds
+    # TODO fminer crashes with these settings
+    skip "it seems that fminer aborts without further notice"
+    dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"multi_cell_call_no_dup.csv")
+    feature_dataset = OpenTox::Algorithm::Fminer.bbrc dataset#, :min_frequency => 15)
+    model = OpenTox::Model::Lazar.create dataset, feature_dataset
+    model.save
+    p model.id
+    feature_dataset = OpenTox::CalculatedDataset.find model.feature_dataset_id
+    assert_equal dataset.compounds.size, feature_dataset.compounds.size
+    assert_equal 52, feature_dataset.features.size
+    assert_equal '[#17&A]-[#6&A]', feature_dataset.features.first.title
+    compound = OpenTox::Compound.from_inchi("InChI=1S/C10H9NO2S/c1-8-2-4-9(5-3-8)13-6-10(12)11-7-14/h2-5H,6H2,1H3")
+    prediction_dataset = model.predict compound
+    prediction = prediction_dataset.data_entries.first
+    assert_in_delta 0.025, prediction[:confidence], 0.001
+    #assert_equal 0.025885845574483608, prediction[:confidence]
+    # with compound change in training_dataset see:
+    # https://github.com/opentox/opentox-test/commit/0e78c9c59d087adbd4cc58bab60fb29cbe0c1da0
+    #assert_equal 0.02422364949075546, prediction[:confidence]
+    dataset.delete
+    model.delete
+    feature_dataset.delete
+    prediction_dataset.delete
+  end
+
+  def test_lazar_kazius
+    t = Time.now
+    dataset = Dataset.from_csv_file File.join(DATA_DIR,"kazius.csv")
+    p "Dataset upload: #{Time.now-t}"
+    t = Time.now
+    feature_dataset = Algorithm::Fminer.bbrc(dataset, :min_frequency => 100)
+    p "Feature mining: #{Time.now-t}"
+    t = Time.now
+    assert_equal feature_dataset.compounds.size, dataset.compounds.size
+    model = Model::Lazar.create dataset, feature_dataset
+=begin
+=end
+    #model = Model::Lazar.find('55bcf5bf7a7838381200017e')
+    #p model.id
+    #prediction_times = []
+    2.times do
+      compound = Compound.from_smiles("Clc1ccccc1NN")
+      prediction = model.predict compound
+      assert_equal "1", prediction[:value]
+      assert_in_delta 0.019858401199860445, prediction[:confidence], 0.001
+    end
+    #dataset.delete
+    #feature_dataset.delete
+  end
+
+end
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