additional lazar tests moved to lazar-extended

1 files changed, 59 insertions, 0 deletions

diff --git a/test/lazar-extended.rb b/test/lazar-extended.rb
new file mode 100644
index 0000000..3da770c
--- /dev/null
+++ b/test/lazar-extended.rb
@@ -0,0 +1,59 @@
+require_relative "setup.rb"
+
+class LazarExtendedTest < MiniTest::Test
+
+  def test_lazar_bbrc_ham_minfreq
+    dataset = OpenTox::Dataset.new nil, SUBJECTID
+    dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.csv")
+    assert_equal dataset.uri.uri?, true
+    lazar = OpenTox::Algorithm.new File.join($algorithm[:uri],"lazar"), SUBJECTID
+    model_uri = lazar.run :dataset_uri => dataset.uri, :feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"), :min_frequency => 5
+    assert_equal model_uri.uri?, true
+    model = OpenTox::Model.new model_uri, SUBJECTID
+    assert_equal model.uri.uri?, true
+    feature_dataset_uri = model[RDF::OT.featureDataset]
+    feature_dataset = OpenTox::Dataset.new feature_dataset_uri , SUBJECTID
+    assert_equal dataset.compounds.size, feature_dataset.compounds.size
+    assert_equal 41, feature_dataset.features.size
+    assert_equal '[#7&A]-[#6&A]=[#7&A]', OpenTox::Feature.new(feature_dataset.features.first.uri, SUBJECTID).title
+    compound = OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H")
+    prediction_uri = model.run :compound_uri => compound.uri
+    prediction_dataset = OpenTox::Dataset.new prediction_uri, SUBJECTID
+    assert_equal prediction_dataset.uri.uri?, true
+    prediction = prediction_dataset.predictions.select{|p| p[:compound].uri == compound.uri}.first
+    assert_equal "false", prediction[:value]
+    assert_equal 0.12380952380952381, prediction[:confidence]
+    dataset.delete
+    model.delete
+    feature_dataset.delete
+    prediction_dataset.delete
+  end
+
+  def test_lazar_bbrc_large_ds
+    dataset = OpenTox::Dataset.new nil, SUBJECTID
+    dataset.upload File.join(DATA_DIR,"multi_cell_call_no_dup.csv")
+    assert_equal dataset.uri.uri?, true
+    lazar = OpenTox::Algorithm.new File.join($algorithm[:uri],"lazar"), SUBJECTID
+    model_uri = lazar.run :dataset_uri => dataset.uri, :feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"), :min_frequency => 75
+    assert_equal model_uri.uri?, true
+    model = OpenTox::Model.new model_uri, SUBJECTID
+    assert_equal model.uri.uri?, true
+    feature_dataset_uri = model[RDF::OT.featureDataset]
+    feature_dataset = OpenTox::Dataset.new feature_dataset_uri , SUBJECTID
+    assert_equal dataset.compounds.size, feature_dataset.compounds.size
+    assert_equal 51, feature_dataset.features.size
+    assert_equal '[#17&A]-[#6&A]', OpenTox::Feature.new(feature_dataset.features.first.uri, SUBJECTID).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_uri = model.run :compound_uri => compound.uri
+    prediction_dataset = OpenTox::Dataset.new prediction_uri, SUBJECTID
+    assert_equal prediction_dataset.uri.uri?, true
+    prediction = prediction_dataset.predictions.select{|p| p[:compound].uri == compound.uri}.first
+    assert_equal "0", prediction[:value]
+    assert_equal 0.025885845574483608, prediction[:confidence]
+    dataset.delete
+    model.delete
+    feature_dataset.delete
+    prediction_dataset.delete
+  end
+
+end