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require_relative "setup.rb"
class FminerTest < MiniTest::Test
def test_fminer_bbrc
dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv")
refute_nil dataset.id
feature_dataset = OpenTox::Algorithm::Fminer.bbrc dataset
feature_dataset = Dataset.find feature_dataset.id
assert_equal dataset.compounds.size, feature_dataset.compounds.size
# TODO: fminer calculates 62 instead of 54 features
# it is unclear which commit changed the numbers (occurs with old libraries/mongodb branch too
# modification of Compound to use smiles instead of inchis seems to have no effect
#assert_equal 54, feature_dataset.features.size
#assert_equal "C-C-C=C", feature_dataset.features.first.smarts
compounds = feature_dataset.compounds
smarts = feature_dataset.features
smarts.each do |smart|
assert smart.p_value.round(2) >= 0.95
end
match = OpenTox::Algorithm::Descriptor.smarts_match compounds, smarts
feature_dataset.data_entries.each_with_index do |fingerprint,i|
assert_equal match[i], fingerprint
end
dataset.delete
feature_dataset.delete
end
def test_fminer_last
skip "last features have to be activated"
dataset = OpenTox::Dataset.new
dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.csv")
feature_dataset = OpenTox::Algorithm::Fminer.last :dataset => dataset
assert_equal dataset.compounds.size, feature_dataset.compounds.size
assert_equal 21, feature_dataset.features.size
assert_equal '[#6&A]-[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#6&a]', feature_dataset.features.first.smarts
compounds = feature_dataset.compounds
smarts = feature_dataset.features.collect{|f| f.smarts}
match = OpenTox::Algorithm::Descriptor.smarts_match compounds, smarts
compounds.each_with_index do |c,i|
smarts.each_with_index do |s,j|
assert_equal match[i][j], feature_dataset.data_entries[i][j].to_i
end
end
dataset.delete
feature_dataset.delete
end
end
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