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require 'rubygems'
require 'opentox-ruby'
require 'test/unit'
require "./validate-owl.rb"
class AlgorithmTest < Test::Unit::TestCase
def setup
@@subjectid = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW)
@algorithms = [
File.join(CONFIG[:services]["opentox-algorithm"],"fminer","bbrc"),
File.join(CONFIG[:services]["opentox-algorithm"],"fminer","last"),
File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
#"http://apps.ideaconsult.net:8080/ambit2/algorithm/J48",
]
end
def teardown
end
def test_metadata
@algorithms.each do |algorithm|
validate_owl(algorithm, @@subjectid) unless CONFIG[:services]["opentox-algorithm"].match(/localhost/)
end
end
def test_p_sum_support
params = {}
params[:compound_features_hits] = { "c:c" => 10, "c:c:c" => 5, "O:N" => 2}
params[:training_compound] = "http://localhost/compound/InChI=1S/CH2O/c1-2/h1H2"
params[:training_compound_features_hits] = {"c:c" => 6, "c:c:c" => 3, "O:O" => 2}
params[:weights] = { "c:c" => 0.95, "c:c:c" => 0.96, "O:N" => 0.97, "O:O" => 0.98}
params[:features] = (params[:compound_features_hits].keys + params[:training_compound_features_hits].keys).uniq
2.times{
params[:mode] = "min"
assert_in_delta OpenTox::Algorithm.p_sum_support(params), 12.8762796504849, 0.00001
params[:mode] = "max"
assert_in_delta OpenTox::Algorithm.p_sum_support(params), 18.8034091184372, 0.00001
}
end
def test_tanimoto
params = {}
params[:training_compound] = "http://localhost/compound/InChI=1S/CH2O/c1-2/h1H2"
weights = { "c:c" => 0.95, "c:c:c" => 0.96, "O:N" => 0.97, "O:O" => 0.98}
params[:compound_features_hits] = { "c:c" => 10, "c:c:c" => 5, "O:N" => 2}
features_a = params[:compound_features_hits].keys
params[:training_compound_features_hits] = {"c:c" => 6, "c:c:c" => 3, "O:O" => 2}
features_b = params[:training_compound_features_hits].keys
2.times{
params[:nr_hits] = false
#test without weights
assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_b, nil, params), 0.5, 0.000001
#test with weights
assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_b, weights, params), 0.498056105472291, 0.000001
#test with weights and nr_hits true
params[:nr_hits] = true
assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_b, weights, params), 0.472823526091916, 0.000001
}
params[:training_compound_features_hits] = {"c:c" => 2, "O:N" => 2}
features_c = params[:training_compound_features_hits].keys
2.times{
params[:nr_hits] = false
#test without weights
assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_c, nil, params), 0.666666666666667, 0.000001
#test with weights
assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_c, weights, params), 0.666545393630348, 0.000001
#test with weights and nr_hits true
params[:nr_hits] = true
assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_c, weights, params), 0.235749338271022, 0.000001
}
end
def test_mlr
n_prop = [ [ -2.0, -2.0 ],
[ -1.0, -1.0 ],
[ 0.0, 0.0 ],
[ 1.0, 1.0 ],
[ 2.0, 2.0 ] ]
q_prop = [ 1.0, 1.0 ]
#acts = [ -2.0,
# -1.0,
# 0.0,
# 1.0,
# 2.0 ]
acts = [ 0.0,
0.5,
1.0,
1.5,
2.0 ]
maxcols = 2
res1 = OpenTox::Algorithm::Neighbors::mlr(:n_prop => n_prop, :q_prop => q_prop, :acts => acts, :maxcols => maxcols)
maxcols = 1
res2 = OpenTox::Algorithm::Neighbors::mlr(:n_prop => n_prop, :q_prop => q_prop, :acts => acts, :maxcols => maxcols)
assert_in_delta res1, 1.4958008960423, 10E-06
assert_equal res1, res2
end
def test_pcr
n_prop = [ [ -2.0, -2.0 ],
[ -1.0, -1.0 ],
[ 0.0, 0.0 ],
[ 1.0, 1.0 ],
[ 2.0, 2.0 ] ]
q_prop = [ 1.0, 1.0 ]
#acts = [ -2.0,
# -1.0,
# 0.0,
# 1.0,
# 2.0 ]
acts = [ 0.0,
0.5,
1.0,
1.5,
2.0 ]
maxcols = 2
res1 = OpenTox::Algorithm::Neighbors::pcr(:n_prop => n_prop, :q_prop => q_prop, :acts => acts, :maxcols => maxcols)
maxcols = 1
res2 = OpenTox::Algorithm::Neighbors::pcr(:n_prop => n_prop, :q_prop => q_prop, :acts => acts, :maxcols => maxcols)
assert_in_delta res1, 1.4958008960423, 10E-06
assert_equal res1, res2
end
=begin
def test_clustering
# Parameters
dataset_uri = @@classification_training_dataset.uri
query_compound = OpenTox::Compound.from_smiles("O1COc2cc(ccc12)C")
c = OpenTox::Algorithm::Similarity::StructuralClustering.new dataset_uri
cluster_datasets = Array.new
if c.trained?
c.get_clusters query_compound.uri
cluster_datasets = c.target_clusters_array
end
assert_equal cluster_datasets.size, 2
end
=end
end
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