A&A for dataset and lazar

3 files changed, 34 insertions, 27 deletions

diff --git a/Rakefile b/Rakefile
index d8026a6..eb2d231 100644
--- a/Rakefile
+++ b/Rakefile
@@ -1,19 +1,24 @@
 require 'rubygems'
 require 'opentox-ruby'
 
+TEST_USER = "guest"
+TEST_PW   = "guest"
+
 task ARGV[0] do
   puts ARGV[0]+".rb"
   require "./"+ARGV[0]+".rb"
 end
 
 task :setup do
-  @@classification_training_dataset = OpenTox::Dataset.create_from_csv_file("data/hamster_carcinogenicity.csv")
-  @@regression_training_dataset = OpenTox::Dataset.create_from_csv_file("data/EPAFHM.csv")
+  @@subjectid = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW) 
+  @@classification_training_dataset = OpenTox::Dataset.create_from_csv_file("data/hamster_carcinogenicity.csv", @@subjectid)
+  @@regression_training_dataset = OpenTox::Dataset.create_from_csv_file("data/EPAFHM.csv", @@subjectid)
 end
 
 task :teardown do
-  @@classification_training_dataset.delete
-  @@regression_training_dataset.delete
+  @@classification_training_dataset.delete(@@subjectid)
+  @@regression_training_dataset.delete(@@subjectid)
+  OpenTox::Authorization.logout(@@subjectid)
 end
 
 [:all, :feature, :dataset, :fminer, :lazar].each do |t|
diff --git a/dataset.rb b/dataset.rb
index 9cf8e63..812a060 100644
--- a/dataset.rb
+++ b/dataset.rb
@@ -32,7 +32,7 @@ class DatasetTest < Test::Unit::TestCase
     @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
+    uri = @dataset.save(@@subjectid)
     puts uri
     #@dataset.load_csv(File.open("data/hamster_carcinogenicity.csv").read)
     #@dataset.save
@@ -40,10 +40,10 @@ class DatasetTest < Test::Unit::TestCase
 =end
 
   def test_create
-    dataset = OpenTox::Dataset.create
-    dataset.save
+    dataset = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"], @@subjectid)
+    dataset.save(@@subjectid)
     assert_kind_of URI::HTTP, URI.parse(dataset.uri)
-    dataset.delete
+    dataset.delete(@@subjectid)
   end
 
   def test_all
@@ -65,32 +65,33 @@ class DatasetTest < Test::Unit::TestCase
   end
 
   def test_rest_csv
-    uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:accept => "text/uri-list"}, {:file => File.new("data/hamster_carcinogenicity.csv")}).to_s.chomp
+    uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:accept => "text/uri-list"}, {:file => File.new("data/hamster_carcinogenicity.csv"), :subjectid => @@subjectid}).to_s.chomp
     @dataset = OpenTox::Dataset.new uri
     @dataset.load_all
     hamster_carc?
   end
 
   def test_multicolumn_csv
-    uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:accept => "text/uri-list"}, {:file => File.new("data/multicolumn.csv")}).to_s.chomp
+    uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:accept => "text/uri-list"}, {:file => File.new("data/multicolumn.csv"), :subjectid => @@subjectid}).to_s.chomp
     @dataset = OpenTox::Dataset.new uri
     @dataset.load_all
     assert_equal 5, @dataset.features.size
     assert_equal 4, @dataset.compounds.size
+    
   end
 
   def test_from_csv
     @dataset = OpenTox::Dataset.new
-    @dataset.load_csv(File.open("data/hamster_carcinogenicity.csv").read)
+    @dataset.load_csv(File.open("data/hamster_carcinogenicity.csv").read, @@subjectid)
     hamster_carc?
-    @dataset.delete
+    @dataset.delete(@@subjectid)
   end
 
   def test_from_excel
     @dataset = OpenTox::Dataset.new
-    @dataset.load_spreadsheet(Excel.new("data/hamster_carcinogenicity.xls"))
+    @dataset.load_spreadsheet(Excel.new("data/hamster_carcinogenicity.xls"), @@subjectid)
     hamster_carc?
-    @dataset.delete
+    @dataset.delete(@@subjectid)
   end
 
   def test_load_metadata
diff --git a/lazar.rb b/lazar.rb
index e3c6908..6324f3c 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -7,48 +7,49 @@ class LazarTest < Test::Unit::TestCase
 =begin
 =end
   def test_create_regression_model
-    model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@regression_training_dataset.uri}).to_s
+    model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@regression_training_dataset.uri, :subjectid => @@subjectid}).to_s
     lazar = OpenTox::Model::Lazar.find model_uri
     assert_equal lazar.features.size, 222
     compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
-    prediction_uri = lazar.run(:compound_uri => compound.uri)
+    prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
     prediction = OpenTox::LazarPrediction.find(prediction_uri)
     assert_equal prediction.value(compound), 0.149480050002539
     assert_equal prediction.confidence(compound), 0.615246530364447
     assert_equal prediction.neighbors(compound).size, 81
-    prediction.delete
-    lazar.delete
+    prediction.delete(@@subjectid)
+    lazar.delete(@@subjectid)
   end
 
   def test_default_classification_model
     # create model
-    model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@classification_training_dataset.uri}).to_s
+    model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@classification_training_dataset.uri, :subjectid => @@subjectid}).to_s
     lazar = OpenTox::Model::Lazar.find model_uri
     assert_equal lazar.features.size, 41
     # single prediction
     compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
-    prediction_uri = lazar.run(:compound_uri => compound.uri)
+    prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
     prediction = OpenTox::LazarPrediction.find(prediction_uri)
     assert_equal prediction.value(compound), false
     assert_equal prediction.confidence(compound), 0.25857114104619
     assert_equal prediction.neighbors(compound).size, 15
-    prediction.delete
+    prediction.delete(@@subjectid)
     # dataset activity
     compound = OpenTox::Compound.from_smiles("CNN")
-    prediction = OpenTox::LazarPrediction.find lazar.run(:compound_uri => compound.uri)
+    prediction_uri  = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
+    prediction = OpenTox::LazarPrediction.find prediction_uri 
     assert !prediction.measured_activities(compound).empty?
     puts prediction.measured_activities(compound).first.inspect
     assert_equal prediction.measured_activities(compound).first, true
     assert prediction.value(compound).nil?
-    prediction.delete
+    prediction.delete(@@subjectid)
     # dataset prediction
-    test_dataset = OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv")
-    prediction = OpenTox::LazarPrediction.find lazar.run(:dataset_uri => test_dataset.uri)
+    test_dataset = OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid)
+    prediction = OpenTox::LazarPrediction.find lazar.run(:dataset_uri => test_dataset.uri, :subjectid => @@subjectid)
     assert_equal prediction.compounds.size, 4
     compound = OpenTox::Compound.new prediction.compounds.first
     assert_equal prediction.value(compound), false
-    prediction.delete
-    lazar.delete
+    prediction.delete(@@subjectid)
+    lazar.delete(@@subjectid)
   end
 
 end