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-rw-r--r--Rakefile22
-rw-r--r--all.rb2
-rw-r--r--dataset.rb18
-rw-r--r--fminer.rb4
-rw-r--r--lazar.rb19
-rw-r--r--model.rb2
-rw-r--r--parser.rb2
7 files changed, 37 insertions, 32 deletions
diff --git a/Rakefile b/Rakefile
index 5e23751..45affdc 100644
--- a/Rakefile
+++ b/Rakefile
@@ -1,14 +1,17 @@
require 'rubygems'
require 'opentox-ruby'
-if File.exists? "auth.rb"
- require "auth"
-else
- #exit "Please create an authenticatio
- TEST_USER = "guest"
- TEST_PW = "guest"
+=begin
+=end
+class Exception
+ def message
+ errorCause ? errorCause.to_yaml : to_s
+ end
end
+TEST_USER = "guest"
+TEST_PW = "guest"
+
task ARGV[0] do
puts "Environment: #{ENV["RACK_ENV"]}"
puts "Test: "+ARGV[0]+".rb"
@@ -27,12 +30,7 @@ task :teardown do
OpenTox::Authorization.logout(@@subjectid)
end
-class Exception
- def message
- errorCause ? errorCause.to_yaml : to_s
- end
-end
-
+#[:all, :feature, :dataset, :fminer, :lazar, :authorization, :validation].each do |t|
[:all, :feature, :dataset, :fminer, :lazar, :authorization].each do |t|
task :teardown => t
task t => :setup
diff --git a/all.rb b/all.rb
index 8712794..8c5babd 100644
--- a/all.rb
+++ b/all.rb
@@ -1,6 +1,7 @@
require 'rubygems'
require 'test/unit'
require 'opentox-ruby'
+require './authorization.rb'
require './compound.rb'
require './feature.rb'
require './dataset.rb'
@@ -9,3 +10,4 @@ require './task.rb'
require './algorithm.rb'
require './fminer.rb'
require './lazar.rb'
+#require './validation.rb'
diff --git a/dataset.rb b/dataset.rb
index db87b2b..1e4134b 100644
--- a/dataset.rb
+++ b/dataset.rb
@@ -28,23 +28,22 @@ class DatasetTest < Test::Unit::TestCase
end
=begin
+=end
def test_save_external
@dataset = OpenTox::Dataset.find "http://apps.ideaconsult.net:8080/ambit2/dataset/2698"
#File.open("test.rdf","w+"){|f| f.puts @dataset.to_rdfxml}
@dataset.uri = "http://apps.ideaconsult.net:8080/ambit2/dataset"
uri = @dataset.save(@@subjectid)
- puts uri
#@dataset.load_csv(File.open("data/hamster_carcinogenicity.csv").read)
#@dataset.save
end
-=end
def test_create
dataset = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"], @@subjectid)
dataset.save(@@subjectid)
assert_kind_of URI::HTTP, URI.parse(dataset.uri)
- dataset.delete(@@subjectid)
+ #dataset.delete(@@subjectid)
end
def test_all
@@ -66,15 +65,17 @@ class DatasetTest < Test::Unit::TestCase
end
def test_rest_csv
- uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:file => File.new("data/hamster_carcinogenicity.csv"), :subjectid => @@subjectid}, {:accept => "text/uri-list"}).to_s.chomp
- @dataset = OpenTox::Dataset.new uri
+ uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"], {:file => File.new("data/hamster_carcinogenicity.csv")} ,{:accept => "text/uri-list", :subjectid => @@subjectid}).to_s.chomp
+ @dataset = OpenTox::Dataset.new uri, @@subjectid
+ #@dataset = OpenTox::Dataset.new uri
@dataset.load_all @@subjectid
hamster_carc?
end
def test_multicolumn_csv
- uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:file => File.new("data/multicolumn.csv"), :subjectid => @@subjectid}, {:accept => "text/uri-list"}).to_s.chomp
- @dataset = OpenTox::Dataset.new uri
+ uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"], {:file => File.new("data/multicolumn.csv")},{:accept => "text/uri-list", :subjectid => @@subjectid}).to_s.chomp
+ @dataset = OpenTox::Dataset.new uri, @@subjectid
+ #@dataset = OpenTox::Dataset.new uri
@dataset.load_all @@subjectid
assert_equal 5, @dataset.features.size
assert_equal 4, @dataset.compounds.size
@@ -84,6 +85,7 @@ class DatasetTest < Test::Unit::TestCase
def test_from_csv
@dataset = OpenTox::Dataset.new
@dataset.load_csv(File.open("data/hamster_carcinogenicity.csv").read, @@subjectid)
+ #puts @dataset.to_yaml
hamster_carc?
@dataset.delete(@@subjectid)
end
@@ -171,8 +173,6 @@ class DatasetTest < Test::Unit::TestCase
end
end
-#=end
-
def test_rdf_conversion
@datasets.each do |uri,data|
#puts "dataset "+uri.to_s
diff --git a/fminer.rb b/fminer.rb
index de447bf..362bde9 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -22,7 +22,7 @@ class FminerTest < Test::Unit::TestCase
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 36, d.features.size
+ assert_equal 35, d.features.size
#validate_owl
d.delete(@@subjectid)
end
@@ -32,7 +32,7 @@ class FminerTest < Test::Unit::TestCase
dataset_uri = OpenTox::Algorithm::Fminer::BBRC.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 222, d.features.size
+ assert_equal 225, d.features.size
d.delete(@@subjectid)
end
diff --git a/lazar.rb b/lazar.rb
index a1ab6db..d4cdc36 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -15,12 +15,17 @@ class LazarTest < Test::Unit::TestCase
def test_create_regression_model
model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@regression_training_dataset.uri, :subjectid => @@subjectid}).to_s
lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
- assert_equal lazar.features.size, 222
+ assert_equal 225, lazar.features.size
compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
+ #puts lazar.uri
+ #puts compound.inspect
+ #puts "prediction"
+ #puts prediction.value(compound).inspect
prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
+ #puts prediction_uri
prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
- assert_equal prediction.value(compound).round_to(4), 0.149518871336721.round_to(4)
- assert_equal prediction.confidence(compound).round_to(4), 0.615246530364447.round_to(4)
+ assert_equal prediction.value(compound).round_to(4), 0.1618.round_to(4)
+ assert_equal prediction.confidence(compound).round_to(4), 0.6114.round_to(4)
assert_equal prediction.neighbors(compound).size, 81
prediction.delete(@@subjectid)
lazar.delete(@@subjectid)
@@ -34,11 +39,12 @@ class LazarTest < Test::Unit::TestCase
# single prediction
compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
- #puts compound.uri
prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
+ #puts prediction_uri
prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
+ puts prediction.inspect
assert_equal prediction.value(compound), false
- assert_equal prediction.confidence(compound).round_to(4), 0.25857114104619.round_to(4)
+ assert_equal prediction.confidence(compound).round_to(4), 0.3005.round_to(4)
assert_equal prediction.neighbors(compound).size, 15
prediction.delete(@@subjectid)
# dataset activity
@@ -57,13 +63,12 @@ class LazarTest < Test::Unit::TestCase
compound = OpenTox::Compound.new prediction.compounds.first
#puts "compound"
#puts compound.inspect
- #puts "prediction"
#puts prediction.value(compound).inspect
assert_equal prediction.value(compound), false
prediction.delete(@@subjectid)
lazar.delete(@@subjectid)
+ end
=begin
=end
- end
end
diff --git a/model.rb b/model.rb
index 098ed5f..2b11be0 100644
--- a/model.rb
+++ b/model.rb
@@ -37,6 +37,6 @@ class ModelTest < Test::Unit::TestCase
end
end
-end
=end
+end
diff --git a/parser.rb b/parser.rb
index 7bae783..84ba5f7 100644
--- a/parser.rb
+++ b/parser.rb
@@ -20,7 +20,7 @@ class ParserTest < Test::Unit::TestCase
"http://apps.ideaconsult.net:8080/ambit2/dataset/2698" => {
:nr_compounds => 3,
:nr_features => 8,
- :nr_dataset_features => 37,
+ :nr_dataset_features => 36,
:nr_data_entries => 3
}
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-10 16:44:51 +0000