diff options
Diffstat (limited to 'test/lazar-long.rb')
| -rw-r--r-- | test/lazar-long.rb | 41 |
1 files changed, 18 insertions, 23 deletions
diff --git a/test/lazar-long.rb b/test/lazar-long.rb index 487a015..b69adfa 100644 --- a/test/lazar-long.rb +++ b/test/lazar-long.rb @@ -3,30 +3,27 @@ require_relative "setup.rb" class LazarExtendedTest < MiniTest::Test def test_lazar_bbrc_ham_minfreq - dataset = OpenTox::MeasuredDataset.new - dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.csv") - model = OpenTox::Model::Lazar.create OpenTox::Algorithm::Fminer.bbrc(dataset, :min_frequency => 5) - feature_dataset = OpenTox::CalculatedDataset.find model.feature_dataset_id + 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 '[#7&A]-[#6&A]=[#7&A]', feature_dataset.features.first.title + 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_dataset = model.predict :compound => compound - prediction = prediction_dataset.data_entries.first - assert_equal "false", prediction.first - assert_equal 0.12380952380952381, prediction.last + prediction = model.predict compound + 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 # TODO fminer crashes with these settings - dataset = OpenTox::MeasuredDataset.new - dataset.upload File.join(DATA_DIR,"multi_cell_call_no_dup.csv") - feature_dataset = OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset)#, :min_frequency => 15) - model = OpenTox::Model::Lazar.create feature_dataset + 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 @@ -34,7 +31,7 @@ class LazarExtendedTest < MiniTest::Test 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 => compound + 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] @@ -56,15 +53,13 @@ class LazarExtendedTest < MiniTest::Test p model.id #prediction_times = [] 2.times do - compound = Compound.from_smiles("Clc1ccccc1NN") - prediction = model.predict :compound => compound - p prediction.data_entries - assert_equal "1", prediction.data_entries.first.first - assert_in_delta 0.019858401199860445, prediction.data_entries.first.last, 0.001 + 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 + dataset.delete + feature_dataset.delete end end |