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|
require 'rubygems'
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
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
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::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
|