diff options
Diffstat (limited to 'test/lazar-long.rb')
| -rw-r--r-- | test/lazar-long.rb | 58 |
1 files changed, 29 insertions, 29 deletions
diff --git a/test/lazar-long.rb b/test/lazar-long.rb index 68b300f..8f59ec3 100644 --- a/test/lazar-long.rb +++ b/test/lazar-long.rb @@ -3,25 +3,18 @@ require_relative "setup.rb" class LazarExtendedTest < MiniTest::Test def test_lazar_bbrc_ham_minfreq - dataset = OpenTox::Dataset.new + dataset = OpenTox::MeasuredDataset.new dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.csv") - assert_equal dataset.uri.uri?, true - model_uri = OpenTox::Model::Lazar.create :dataset_uri => dataset.uri, :feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"), :min_frequency => 5 - assert_equal model_uri.uri?, true - model = OpenTox::Model::Lazar.new model_uri - assert_equal model.uri.uri?, true - feature_dataset_uri = model[RDF::OT.featureDataset] - feature_dataset = OpenTox::Dataset.new feature_dataset_uri + model = OpenTox::Model::Lazar.create OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset, :min_frequency => 5) + feature_dataset = OpenTox::CalculatedDataset.find model.feature_dataset_id assert_equal dataset.compounds.size, feature_dataset.compounds.size assert_equal 41, feature_dataset.features.size - assert_equal '[#7&A]-[#6&A]=[#7&A]', OpenTox::Feature.new(feature_dataset.features.first.uri).title + assert_equal '[#7&A]-[#6&A]=[#7&A]', feature_dataset.features.first.title compound = OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H") - prediction_uri = model.run :compound_uri => compound.uri - prediction_dataset = OpenTox::Dataset.new prediction_uri - assert_equal prediction_dataset.uri.uri?, true - prediction = prediction_dataset.predictions.select{|p| p[:compound].uri == compound.uri}.first - assert_equal "false", prediction[:value] - assert_equal 0.12380952380952381, prediction[:confidence] + prediction_dataset = model.predict :compound => compound + prediction = prediction_dataset.data_entries.first + assert_equal "false", prediction.first + assert_equal 0.12380952380952381, prediction.last dataset.delete model.delete feature_dataset.delete @@ -29,24 +22,20 @@ class LazarExtendedTest < MiniTest::Test end def test_lazar_bbrc_large_ds - dataset = OpenTox::Dataset.new + # TODO fminer crashes with these settings + dataset = OpenTox::MeasuredDataset.new dataset.upload File.join(DATA_DIR,"multi_cell_call_no_dup.csv") - assert_equal dataset.uri.uri?, true - model_uri = OpenTox::Model::Lazar.create :dataset_uri => dataset.uri, :feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"), :min_frequency => 75 - assert_equal model_uri.uri?, true - model = OpenTox::Model::Lazar.new model_uri - assert_equal model.uri.uri?, true - feature_dataset_uri = model[RDF::OT.featureDataset] - feature_dataset = OpenTox::Dataset.new feature_dataset_uri + feature_dataset = OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset)#, :min_frequency => 15) + model = OpenTox::Model::Lazar.create 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]', OpenTox::Feature.new(feature_dataset.features.first.uri).title + 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_uri = model.run :compound_uri => compound.uri - prediction_dataset = OpenTox::Dataset.new prediction_uri - assert_equal prediction_dataset.uri.uri?, true - prediction = prediction_dataset.predictions.select{|p| p[:compound].uri == compound.uri}.first - assert_equal "0", prediction[:value] + prediction_dataset = model.predict :compound => 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: @@ -58,4 +47,15 @@ class LazarExtendedTest < MiniTest::Test prediction_dataset.delete end + def test_lazar_kazius + # TODO find a solution for feature datasets > 16M (size limit in mongodb) + dataset = OpenTox::MeasuredDataset.from_csv_file File.join(DATA_DIR,"kazius.csv") + feature_dataset = OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset, :min_frequency => 100) + assert_equal feature_dataset.compounds.size, dataset.compounds.size + model = OpenTox::Model::Lazar.create feature_dataset + p model.id + dataset.delete + #feature_dataset.delete + end + end |