From d5bf97c2cb999539c56bf59aa1d7d3286745be84 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 23 Sep 2015 14:51:41 +0200 Subject: validations fixed (all models were executed with default parameters) --- test/lazar-physchem-short.rb | 34 ++++++++++++++++++---------------- 1 file changed, 18 insertions(+), 16 deletions(-) (limited to 'test/lazar-physchem-short.rb') diff --git a/test/lazar-physchem-short.rb b/test/lazar-physchem-short.rb index e74a4b9..59d8112 100644 --- a/test/lazar-physchem-short.rb +++ b/test/lazar-physchem-short.rb @@ -2,27 +2,29 @@ require_relative "setup.rb" class LazarPhyschemDescriptorTest < MiniTest::Test def test_epafhm - skip "Physchem Regression not yet implemented." - # check available descriptors - @descriptors = OpenTox::Algorithm::Descriptor::DESCRIPTORS.keys - assert_equal 111,@descriptors.size,"wrong number of physchem descriptors" - @descriptor_values = OpenTox::Algorithm::Descriptor::DESCRIPTOR_VALUES - # select descriptors for test - @num_features_offset = 0 - @descriptors.keep_if{|x| x=~/^Openbabel\./} - @descriptors.delete("Openbabel.L5") # TODO Openbabel.L5 does not work, investigate!!! - puts "Descriptors: #{@descriptors}" + @descriptors = OpenTox::Algorithm::Descriptor::OBDESCRIPTORS.keys + refute_empty @descriptors # UPLOAD DATA training_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi.csv") - puts "Dataset: "+training_dataset.id -# feature_dataset = Algorithm::Descriptor.physchem training_dataset, @descriptors - model = Model::LazarRegression.create training_dataset#, feature_dataset - #p model + feature_dataset = Algorithm::Descriptor.physchem training_dataset, @descriptors + scaled_feature_dataset = feature_dataset.scale + model = Model::LazarRegression.create training_dataset + model.neighbor_algorithm = "physchem_neighbors" + model.neighbor_algorithm_parameters = { + :feature_calculation_algorithm => "OpenTox::Algorithm::Descriptor.physchem", + :descriptors => @descriptors, + :feature_dataset_id => scaled_feature_dataset.id, + :min_sim => 0.3 + } + model.save compound = Compound.from_smiles "CC(C)(C)CN" prediction = model.predict compound - p prediction - + refute_nil prediction[:value] + refute_nil prediction[:confidence] + prediction[:neighbors].each do |line| + assert_operator line[1], :>, 0.3 + end end end -- cgit v1.2.3