diff options
Diffstat (limited to 'fminer.rb')
| -rw-r--r-- | fminer.rb | 375 |
1 files changed, 348 insertions, 27 deletions
@@ -3,44 +3,365 @@ require 'opentox-ruby' require 'test/unit' require 'validate-owl.rb' +class Float + def round_to(x) + (self * 10**x).round.to_f / 10**x + end +end + class FminerTest < Test::Unit::TestCase + def setup + @dump_dir = FileUtils.mkdir_p File.join(File.dirname(__FILE__),"dump",File.basename(__FILE__,".rb")) + FileUtils.mkdir_p File.join(File.dirname(__FILE__),"reference",File.basename(__FILE__,".rb")) + end + + def cleanup # executed only when assertions succeed (teardown is called even when assertions fail) + FileUtils.cp @dumpfile, @dumpfile.sub(/dump/,"reference") + FileUtils.rm @dumpfile + @dataset.delete(@@subjectid) + end + + def dump + @dataset = OpenTox::Dataset.find @dataset_uri, @@subjectid + @dumpfile = File.join(@dump_dir,caller[0][/`.*'/][1..-2])+".yaml" + File.open(@dumpfile,"w+"){|f| f.puts @dataset.to_yaml} + end + def test_bbrc feature = @@classification_training_dataset.features.keys.first - dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@classification_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s - d =OpenTox::Dataset.new dataset_uri, @@subjectid - d.load_features(@@subjectid) - assert_equal 52, d.features.size - d.delete(@@subjectid) + @dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@classification_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s + dump + assert_equal 41, @dataset.features.size # 32 bit + #assert_equal 52, @dataset.features.size + # assert no hit counts present + count=0 + @dataset.data_entries.each { |c,e| + if c.to_s.scan('InChI=1S/C10H13N3O2/c1-13(12-15)7-3-5-10(14)9-4-2-6-11-8-9/h2,4,6,8H,3,5,7H2,1H3').size > 0 + e.each { |p,h| + if p.to_s.scan('bbrc/40').size>0 + count += 1 if h[0] == 1 + end + if p.to_s.scan('bbrc/29').size>0 + count += 1 if h[0] == 1 + end + if p.to_s.scan('bbrc/18').size>0 + count += 1 if h[0] == 1 + end + } + end + } + assert_equal 3, count + + # assert some values + @dataset.features.each { |c,e| + if c.to_s.scan('feature/bbrc/31').size > 0 + assert_equal e['http://www.opentox.org/api/1.1#effect'], 2 + assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.97 + assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#6&a]-[#6&a]:[#6&a]:[#6&a]:[#6&a]-[#7&A]" + end + } + cleanup end def test_regression_bbrc feature = File.join @@regression_training_dataset.uri,"feature/LC50_mmol" - dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@regression_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid, :feature_type=>"paths"}).to_s - d =OpenTox::Dataset.new dataset_uri, @@subjectid - d.load_features(@@subjectid) - #assert_equal 185, d.features.size - assert_equal 219, d.features.size - d.delete(@@subjectid) + @dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@regression_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid, :feature_type=>"paths"}).to_s + dump + assert_equal 131, @dataset.features.size # 32 bit + #assert_equal 219, @dataset.features.size + + # assert no hit counts present + count = 0 + @dataset.data_entries.each { |c,e| + if c.to_s.scan('InChI=1S/C5H10N2O2S/c1-4(10-3)7-9-5(8)6-2/h1-3H3,(H,6,8)').size > 0 + e.each { |p,h| + if p.to_s.scan('bbrc/86').size>0 + count += 1 if h[0] == 1 + end + if p.to_s.scan('bbrc/54').size>0 + count += 1 if h[0] == 1 + end + if p.to_s.scan('bbrc/32').size>0 + count += 1 if h[0] == 1 + end + } + end + } + assert_equal 3, count + + # assert some values + @dataset.features.each { |c,e| + if c.to_s.scan('feature/bbrc/188').size > 0 + assert_equal e['http://www.opentox.org/api/1.1#effect'], "activating" + assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 1.0 + assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#6&a]:[#6&a]:[#8&a]:[#6&a]:[#6&a]" + end + } + + cleanup end def test_last + + feature = @@classification_training_dataset.features.keys.first + @dataset_uri = OpenTox::Algorithm::Fminer::LAST.new.run({:dataset_uri => @@classification_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s + dump + assert_in_delta 21, @dataset.features.size, 2 # 32 bit + + # assert no hit counts present + count = 0 + @dataset.data_entries.each { |c,e| + if c.to_s.scan('InChI=1S/C5H10N2O/c8-6-7-4-2-1-3-5-7/h1-5H2').size > 0 + e.each { |p,h| + if p.to_s.scan('last/11').size>0 + count += 1 if h[0] == true + end + if p.to_s.scan('last/5').size>0 + count += 1 if h[0] == true + end + if p.to_s.scan('last/13').size>0 + count += 1 if h[0] == true + end + } + end + } + #assert_equal 3, count + + # assert some values + #@dataset.features.each { |c,e| + # if c.to_s.scan('feature/last/3').size > 0 + # assert_equal e['http://www.opentox.org/api/1.1#effect'], 2 + # assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.99 + # assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#8&A]=[#6&A]-[#6&A]-[#6&A]" + # end + #} + cleanup + end + + +def test_regression_last + feature = File.join @@regression_training_dataset.uri,"feature/LC50_mmol" + @dataset_uri = OpenTox::Algorithm::Fminer::LAST.new.run({:dataset_uri => @@regression_training_dataset.uri, :prediction_feature => feature, + :min_frequency => 40, + :subjectid => @@subjectid}).to_s + dump + assert_in_delta 16, @dataset.features.size, 8 + + + # assert no hit counts present + #count=0 + #@dataset.data_entries.each { |c,e| + # if c.to_s.scan('InChI=1S/C9H10O3/c1-2-12-9-5-7(6-10)3-4-8(9)11/h3-6,11H,2H2,1H3').size > 0 + # e.each { |p,h| + # if p.to_s.scan('last/5').size>0 + # count += 1 if h[0] == true + # end + # if p.to_s.scan('last/11').size>0 + # count += 1 if h[0] == true + # end + # if p.to_s.scan('last/13').size>0 + # count += 1 if h[0] == true + # end + # } + # end + #} + #assert_in_delta 3, count, 2 + + # assert some values + #@dataset.features.each { |c,e| + # if c.to_s.scan('feature/last/3').size > 0 + # assert_equal e['http://www.opentox.org/api/1.1#effect'], "activating" + # assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 1.0 + # assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#8&A]=[#6&A]-[#8&A]-[#6&A]" + # end + #} + cleanup +end + + + + def test_bbrc_rest_parameters_nr_hits feature = @@classification_training_dataset.features.keys.first - dataset_uri = OpenTox::Algorithm::Fminer::LAST.new.run({:dataset_uri => @@classification_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s - d =OpenTox::Dataset.new dataset_uri, @@subjectid - d.load_features(@@subjectid) - assert_equal 23, d.features.size - d.delete(@@subjectid) - end - -# Deactivated by AM because of efficiency problems (does not return) -# def test_regression_last -# feature = File.join @@regression_training_dataset.uri,"feature/LC50_mmol" -# dataset_uri = OpenTox::Algorithm::Fminer::LAST.new.run({:dataset_uri => @@regression_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s -# d =OpenTox::Dataset.new dataset_uri, @@subjectid -# d.load_features(@@subjectid) -# assert_equal 4, d.features.size -# d.delete(@@subjectid) -# end + @dataset_uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-algorithm"],"fminer","bbrc"),{ + "dataset_uri" => @@classification_training_dataset.uri, + "prediction_feature" => feature, + "nr_hits" => true, + :subjectid => @@subjectid }) + dump + assert_equal 41, @dataset.features.size # 32 bit + #assert_equal 52, @dataset.features.size + + # assert hit counts present + @dataset.data_entries.each { |c,e| + if c.to_s.scan('InChI=1S/C14H19N3S.ClH/c1-16(2)9-10-17(12-13-6-5-11-18-13)14-7-3-4-8-15-14;/h3-8,11H,9-10,12H2,1-2H3;1H').size > 0 + e.each { |p,h| + if p.to_s.scan('bbrc/39').size>0 + assert_equal 6, h[0] + end + if p.to_s.scan('bbrc/18').size>0 + assert_equal 5, h[0] + end + if p.to_s.scan('bbrc/38').size>0 + assert_equal 14, h[0] + end + } + end + } + + # assert some values + @dataset.features.each { |c,e| + if c.to_s.scan('feature/bbrc/31').size > 0 + assert_equal e['http://www.opentox.org/api/1.1#effect'], 2 + assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.97 + assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#6&a]-[#6&a]:[#6&a]:[#6&a]:[#6&a]-[#7&A]" + end + } + + cleanup + end + + def test_bbrc_rest_parameters_bb_false + feature = @@classification_training_dataset.features.keys.first + @dataset_uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-algorithm"],"fminer","bbrc"),{ + "dataset_uri" => @@classification_training_dataset.uri, + "prediction_feature" => feature, + "backbone" => false, + :subjectid => @@subjectid }) + dump + assert_equal 139, @dataset.features.size # 32 bit + #assert_equal 52, @dataset.features.size + + # assert no hit counts present + count=0 + @dataset.data_entries.each { |c,e| + if c.to_s.scan('InChI=1S/C10H13N3O2/c1-13(12-15)7-3-5-10(14)9-4-2-6-11-8-9/h2,4,6,8H,3,5,7H2,1H3').size > 0 + e.each { |p,h| + if p.to_s.scan('bbrc/113').size>0 + count += 1 if h[0] == 1 + end + if p.to_s.scan('bbrc/99').size>0 + count += 1 if h[0] == 1 + end + if p.to_s.scan('bbrc/77').size>0 + count += 1 if h[0] == 1 + end + } + end + } + assert_equal 3, count + + + # assert some values + @dataset.features.each { |c,e| + if c.to_s.scan('feature/bbrc/31').size > 0 + assert_equal e['http://www.opentox.org/api/1.1#effect'], 2 + assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.99 + assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#8&A]-[#6&A]-[#7&A]-[#7&A]=[#8&A]" + end + } + + cleanup + end + + def test_bbrc_multinomial + feature = @@multinomial_training_dataset.features.keys.first + @dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@multinomial_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s + dump + assert_equal 152, @dataset.features.size # 32 bit + + #assert no hit counts present + count=0 + @dataset.data_entries.each { |c,e| + if c.to_s.scan('InChI=1S/C10H7NO2/c12-11(13)10-7-3-5-8-4-1-2-6-9(8)10/h1-7H').size > 0 + e.each { |p,h| + if p.to_s.scan('bbrc/37').size>0 + count += 1 if h[0] == 1 + end + if p.to_s.scan('bbrc/38').size>0 + count += 1 if h[0] == 1 + end + if p.to_s.scan('bbrc/39').size>0 + count += 1 if h[0] == 1 + end + } + end + } + assert_equal 3, count + + # assert some values + @dataset.features.each { |c,e| + if c.to_s.scan('feature/bbrc/0').size > 0 + assert_equal e['http://www.opentox.org/api/1.1#effect'], 2 + assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 1.00 + assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#6&A]-[#6&A](=[#6&A])(-[#6&A])" + end + } + @dataset.features.each { |c,e| + if c.to_s.scan('feature/bbrc/92').size > 0 + assert_equal e['http://www.opentox.org/api/1.1#effect'], 1 + assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.99 + assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#7&A]-[#6&a](:[#6&a]:[#6&a]:[#6&a])(:[#6&a]:[#6&a]-[#16&A])" + end + } + @dataset.features.each { |c,e| + if c.to_s.scan('feature/bbrc/42').size > 0 + assert_equal e['http://www.opentox.org/api/1.1#effect'], 3 + assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.99 + assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#7&a]:[#6&a]" + end + } + cleanup + end + + def test_last_multinomial + feature = @@multinomial_training_dataset.features.keys.first + @dataset_uri = OpenTox::Algorithm::Fminer::LAST.new.run({:dataset_uri => @@multinomial_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s + dump + assert_in_delta 138, @dataset.features.size, 2 # 32 bit + + #assert no hit counts present + count=0 + @dataset.data_entries.each { |c,e| + if c.to_s.scan('InChI=1S/C7H6N2O4/c8-6-3-4(9(12)13)1-2-5(6)7(10)11/h1-3H,8H2,(H,10,11)').size > 0 + e.each { |p,h| + if p.to_s.scan('last/127').size>0 + count += 1 if h[0] == true + end + if p.to_s.scan('last/54').size>0 + count += 1 if h[0] == true + end + if p.to_s.scan('last/120').size>0 + count += 1 if h[0] == true + end + } + end + } + #assert_equal 3, count + + # assert some values + #@dataset.features.each { |c,e| + # if c.to_s.scan('feature/last/54').size > 0 + # assert_equal e['http://www.opentox.org/api/1.1#effect'], 1 + # assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.99 + # assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#7&A;$([#7&A](=[#8&A])=[#8&A]),$([#7&A](-[#6&a])=[#8&A])](~*)=[#8&A]" + # end + #} + #@dataset.features.each { |c,e| + # if c.to_s.scan('feature/last/48').size > 0 + # assert_equal e['http://www.opentox.org/api/1.1#effect'], 2 + # assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.99 + # assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#6&A]=[#6&A](-[#6&A])-[#6&A]" + # end + #} + #@dataset.features.each { |c,e| + # if c.to_s.scan('feature/bbrc/76').size > 0 + # assert_equal e['http://www.opentox.org/api/1.1#effect'], "2" + # assert_equal e['http://www.opentox.org/api/1.1#pValue'].to_f.round_to(2), 0.0 + # assert_equal e['http://www.opentox.org/api/1.1#smarts'], "[#7&A]-[#6&a]:[#6&a]:[#6&a](-[#16&A;$([#16&A](-,=[#8&A])-[#6&a]),$([#16&A](=[#8&A])-[#6&a])](~*)):[#6&a]:[#6&a;$([#6&a](:[#6&a])(:[#6&a]):[#6&a]),$([#6&a](:[#6&a])(:[#6&a]):[#6&a])](~*)(~*):[#6&a]:[#6&a]" + # end + #} + cleanup + end end |