diff options
Diffstat (limited to 'test/lazar-fminer.rb')
| -rw-r--r-- | test/lazar-fminer.rb | 23 |
1 files changed, 12 insertions, 11 deletions
diff --git a/test/lazar-fminer.rb b/test/lazar-fminer.rb index 17a52b1..11fef72 100644 --- a/test/lazar-fminer.rb +++ b/test/lazar-fminer.rb @@ -3,16 +3,18 @@ require_relative "setup.rb" class LazarFminerTest < MiniTest::Test def test_lazar_fminer - dataset = OpenTox::MeasuredDataset.new - dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.csv") - model = OpenTox::Model::Lazar.create OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset) - feature_dataset = OpenTox::CalculatedDataset.find model.feature_dataset_id - assert_equal dataset.compounds.size, feature_dataset.compounds.size + training_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv") + feature_dataset = OpenTox::Algorithm::Fminer.bbrc(:dataset => training_dataset) + #p feature_dataset + model = OpenTox::Model::Lazar.create training_dataset, feature_dataset + #feature_dataset = OpenTox::Dataset.find model.feature_dataset_id + p model + assert_equal training_dataset.compounds.size, feature_dataset.compounds.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 '[#6&A]-[#6&A]-[#6&A]=[#6&A]', feature_dataset.features.first.title + #feature_dataset.data_entries.each do |e| + #assert_equal e.size, feature_dataset.features.size + #end + assert_equal '[#6&A]-[#6&A]-[#6&A]=[#6&A]', feature_dataset.features.first.smarts [ { :compound => OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"), @@ -32,8 +34,7 @@ class LazarFminerTest < MiniTest::Test end # make a dataset prediction - compound_dataset = OpenTox::MeasuredDataset.new - compound_dataset.upload File.join(DATA_DIR,"EPAFHM.mini.csv") + compound_dataset = OpenTox::Dataset.from_sdf File.join(DATA_DIR,"EPAFHM.mini.csv") #assert_equal compound_dataset.uri.uri?, true prediction = model.predict :dataset => compound_dataset assert_equal compound_dataset.compounds, prediction.compounds |