Merge remote branch 'rautenberg/master'

8 files changed, 62 insertions, 48 deletions

diff --git a/algorithm.rb b/algorithm.rb
index 055f0a2..94f3b5c 100644
--- a/algorithm.rb
+++ b/algorithm.rb
@@ -6,6 +6,7 @@ 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"),
@@ -20,7 +21,7 @@ class AlgorithmTest < Test::Unit::TestCase
   def test_metadata
     @algorithms.each do |algorithm|
       puts algorithm
-      validate_owl(algorithm)
+      validate_owl(algorithm, @@subjectid)
     end
   end
 
diff --git a/authorization.rb b/authorization.rb
index 0d3508b..3772638 100644
--- a/authorization.rb
+++ b/authorization.rb
@@ -85,7 +85,16 @@ class TestOpenToxAuthorizationLDAP < Test::Unit::TestCase
     logout(tok_anonymous)
   end
 
-    
+  def test_03_check_different_uris
+    res = OpenTox::Authorization.send_policy(TEST_URI, @@subjectid)
+    assert OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid)
+    assert OpenTox::Authorization.authorize(TEST_URI, "GET", @@subjectid), "GET request"
+    policies = OpenTox::Authorization.list_uri_policies(TEST_URI, @@subjectid)
+    policies.each do |policy|
+      assert OpenTox::Authorization.delete_policy(policy, @@subjectid)
+    end
+ 
+  end  
 end
 
 
diff --git a/dataset.rb b/dataset.rb
index 812a060..d15baf7 100644
--- a/dataset.rb
+++ b/dataset.rb
@@ -29,7 +29,7 @@ class DatasetTest < Test::Unit::TestCase
 =begin
   def test_save_external
 
-    @dataset = OpenTox::Dataset.find "http://apps.ideaconsult.net:8080/ambit2/dataset/2698"
+    @dataset = OpenTox::Dataset.find "http://apps.ideaconsult.net:8080/ambit2/dataset/2698", @@subjectid
     #File.open("test.rdf","w+"){|f| f.puts @dataset.to_rdfxml}
     @dataset.uri = "http://apps.ideaconsult.net:8080/ambit2/dataset" 
     uri = @dataset.save(@@subjectid)
@@ -47,7 +47,7 @@ class DatasetTest < Test::Unit::TestCase
   end
 
   def test_all
-    datasets = OpenTox::Dataset.all
+    datasets = OpenTox::Dataset.all(CONFIG[:services]["opentox-dataset"], @@subjectid)
     assert_kind_of Array, datasets
   end
 
@@ -59,36 +59,36 @@ class DatasetTest < Test::Unit::TestCase
   end
 
   def test_from_yaml
-    @dataset = OpenTox::Dataset.new
+    @dataset = OpenTox::Dataset.new nil, @@subjectid
     @dataset.load_yaml(File.open("data/hamster_carcinogenicity.yaml").read)
     hamster_carc?
   end
 
   def test_rest_csv
     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
+    @dataset = OpenTox::Dataset.new uri, @@subjectid
+    @dataset.load_all(@@subjectid)
     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"), :subjectid => @@subjectid}).to_s.chomp
-    @dataset = OpenTox::Dataset.new uri
-    @dataset.load_all
+    @dataset = OpenTox::Dataset.new uri, @@subjectid
+    @dataset.load_all(@@subjectid)
     assert_equal 5, @dataset.features.size
     assert_equal 4, @dataset.compounds.size
     
   end
 
   def test_from_csv
-    @dataset = OpenTox::Dataset.new
+    @dataset = OpenTox::Dataset.new(nil, @@subjectid)
     @dataset.load_csv(File.open("data/hamster_carcinogenicity.csv").read, @@subjectid)
     hamster_carc?
     @dataset.delete(@@subjectid)
   end
 
   def test_from_excel
-    @dataset = OpenTox::Dataset.new
+    @dataset = OpenTox::Dataset.new(nil, @@subjectid)
     @dataset.load_spreadsheet(Excel.new("data/hamster_carcinogenicity.xls"), @@subjectid)
     hamster_carc?
     @dataset.delete(@@subjectid)
@@ -96,39 +96,39 @@ class DatasetTest < Test::Unit::TestCase
 
   def test_load_metadata
     @datasets.each do |uri,data|
-      @dataset = OpenTox::Dataset.find(uri)
+      @dataset = OpenTox::Dataset.find(uri, @@subjectid)
       assert @dataset.metadata.size != 0
     end
   end
 
   def test_load_compounds
     @datasets.each do |uri,data|
-      @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_compounds
+      @dataset = OpenTox::Dataset.new(uri, @@subjectid)
+      @dataset.load_compounds(@@subjectid)
       assert_equal @dataset.compounds.size,data[:nr_compounds]
     end
   end
 
   def test_load_features
     @datasets.each do |uri,data|
-      @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_features
+      @dataset = OpenTox::Dataset.new(uri, @@subjectid)
+      @dataset.load_features(@@subjectid)
       assert_equal @dataset.features.keys.size,data[:nr_dataset_features]
     end
   end
 
   def test_load_all
     @datasets.each do |uri,data|
-      @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_all
+      @dataset = OpenTox::Dataset.new(uri, @@subjectid)
+      @dataset.load_all(@@subjectid)
       validate data
     end
   end
 
   def test_yaml
     @datasets.each do |uri,data|
-      @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_all
+      @dataset = OpenTox::Dataset.new(uri, @@subjectid)
+      @dataset.load_all(@@subjectid)
       #@dataset = YAML.load @dataset.to_yaml
       validate data
     end
@@ -136,8 +136,8 @@ class DatasetTest < Test::Unit::TestCase
 
   def test_csv
     @datasets.each do |uri,data|
-      @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_all
+      @dataset = OpenTox::Dataset.new(uri, @@subjectid)
+      @dataset.load_all(@@subjectid)
       csv = @dataset.to_csv.split("\n")
       assert_equal csv.size, data[:nr_compounds]+1
       assert_equal csv.first.split(", ").size, data[:nr_dataset_features]+1
@@ -146,8 +146,8 @@ class DatasetTest < Test::Unit::TestCase
 
   def test_excel
     @datasets.each do |uri,data|
-      @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_all
+      @dataset = OpenTox::Dataset.new(uri, @@subjectid)
+      @dataset.load_all(@@subjectid)
       book =  @dataset.to_spreadsheet
       assert_kind_of Spreadsheet::Workbook, book
       #File.open("#{@dataset.id}.xls","w+"){|f| book.write f.path}
@@ -156,16 +156,16 @@ class DatasetTest < Test::Unit::TestCase
 
   def test_ntriples
     @datasets.each do |uri,data|
-      @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_all
+      @dataset = OpenTox::Dataset.new(uri, @@subjectid)
+      @dataset.load_all(@@subjectid)
       assert_kind_of String, @dataset.to_ntriples
     end
   end
 
   def test_owl
     @datasets.each do |uri,data|
-      @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_all
+      @dataset = OpenTox::Dataset.new(uri, @@subjectid)
+      @dataset.load_all(@@subjectid)
       assert_kind_of String, @dataset.to_rdfxml
     end
   end
diff --git a/feature.rb b/feature.rb
index 9a9d9ab..7ed600c 100644
--- a/feature.rb
+++ b/feature.rb
@@ -25,7 +25,7 @@ class FeatureTest < Test::Unit::TestCase
 
   def test_owl
     #@features.each do |uri|
-      validate_owl @features.first
+      validate_owl @features.first, @@subjectid
       # Ambit does not validate
     #end
   end
diff --git a/fminer.rb b/fminer.rb
index a8552d7..de447bf 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -10,8 +10,8 @@ class FminerTest < Test::Unit::TestCase
   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
-    d.load_features
+    d =OpenTox::Dataset.new dataset_uri, @@subjectid
+    d.load_features(@@subjectid)
     assert_equal 41, d.features.size
     #validate_owl
     d.delete(@@subjectid)
@@ -20,8 +20,8 @@ class FminerTest < Test::Unit::TestCase
   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
-    d =OpenTox::Dataset.new dataset_uri
-    d.load_features
+    d =OpenTox::Dataset.new dataset_uri, @@subjectid
+    d.load_features(@@subjectid)
     assert_equal 36, d.features.size
     #validate_owl
     d.delete(@@subjectid)
@@ -30,8 +30,8 @@ class FminerTest < Test::Unit::TestCase
   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}).to_s
-    d =OpenTox::Dataset.new dataset_uri
-    d.load_features
+    d =OpenTox::Dataset.new dataset_uri, @@subjectid
+    d.load_features(@@subjectid)
     assert_equal 222, d.features.size
     d.delete(@@subjectid)
   end
@@ -39,8 +39,8 @@ class FminerTest < Test::Unit::TestCase
   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
-    d.load_features
+    d =OpenTox::Dataset.new dataset_uri, @@subjectid
+    d.load_features(@@subjectid)
     assert_equal 16, d.features.size
     d.delete(@@subjectid)
   end
diff --git a/lazar.rb b/lazar.rb
index 0ee7a43..280f917 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -14,11 +14,11 @@ class LazarTest < Test::Unit::TestCase
 =end
   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
+    lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
     assert_equal lazar.features.size, 222
     compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
     prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
-    prediction = OpenTox::LazarPrediction.find(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.neighbors(compound).size, 81
@@ -29,12 +29,12 @@ class LazarTest < Test::Unit::TestCase
   def test_default_classification_model
     # create model
     model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@classification_training_dataset.uri, :subjectid => @@subjectid}).to_s
-    lazar = OpenTox::Model::Lazar.find model_uri
+    lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
     assert_equal lazar.features.size, 41
     # single prediction
     compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
     prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
-    prediction = OpenTox::LazarPrediction.find(prediction_uri)
+    prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
     assert_equal prediction.value(compound), false
     assert_equal prediction.confidence(compound).round_to(4), 0.25857114104619.round_to(4)
     assert_equal prediction.neighbors(compound).size, 15
@@ -42,7 +42,7 @@ class LazarTest < Test::Unit::TestCase
     # dataset activity
     compound = OpenTox::Compound.from_smiles("CNN")
     prediction_uri  = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
-    prediction = OpenTox::LazarPrediction.find prediction_uri 
+    prediction = OpenTox::LazarPrediction.find prediction_uri, @@subjectid
     assert !prediction.measured_activities(compound).empty?
     puts prediction.measured_activities(compound).first.inspect
     assert_equal prediction.measured_activities(compound).first, true
@@ -50,9 +50,13 @@ class LazarTest < Test::Unit::TestCase
     prediction.delete(@@subjectid)
     # dataset prediction
     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)
+    prediction = OpenTox::LazarPrediction.find lazar.run(:dataset_uri => test_dataset.uri, :subjectid => @@subjectid), @@subjectid
     assert_equal prediction.compounds.size, 4
     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)
diff --git a/parser.rb b/parser.rb
index 06f3709..7bae783 100644
--- a/parser.rb
+++ b/parser.rb
@@ -32,8 +32,8 @@ class ParserTest < Test::Unit::TestCase
 
   def test_dataset
     @datasets.each do |uri,properties|
-      parser = OpenTox::Parser::Owl::Dataset.new uri
-      @dataset = parser.load_uri
+      parser = OpenTox::Parser::Owl::Dataset.new uri, @@subjectid
+      @dataset = parser.load_uri(@@subjectid)
       validate properties
     end
   end
diff --git a/validate-owl.rb b/validate-owl.rb
index 569813f..736531b 100644
--- a/validate-owl.rb
+++ b/validate-owl.rb
@@ -1,9 +1,9 @@
 #require 'nokogiri'
 
-def validate_owl(uri)
+def validate_owl(uri, subjectid=nil)
   if validator_available?
-    owl = OpenTox::RestClientWrapper.get(uri,:accept => "application/rdf+xml")
-    html = OpenTox::RestClientWrapper.post("http://www.mygrid.org.uk/OWL/Validator",{:rdf => owl, :level => "DL"})
+    owl = OpenTox::RestClientWrapper.get(uri,{:accept => "application/rdf+xml",:subjectid => subjectid})
+    html = OpenTox::RestClientWrapper.post("http://www.mygrid.org.uk/OWL/Validator",{:rdf => owl, :level => "DL",:subjectid => subjectid})
     assert_match(/YES/,html)
   else
     puts "http://www.mygrid.org.uk/OWL/Validator offline"